auto_namd_python/tests/0-forcefields/toppar_all36_na_nad_ppi.str

* CHARMM36 All-Hydrogen Nucleic Acid Force Toppar Stream File
* NAD+, NADH, ADP, ATP, PPI and related analogs
* A.D. MacKerell, Jr., July 2001
* stream following RTF and PARAM read of
*

!Update, 2015/1, nomenclature for NAD+ etc. consistent with PDB

!Parent files that have to be read prior to streaming this file
!top_all36_na.rtf
!par_all36_na.prm

!Testcase
!test_all36_na_nad_ppi.inp

!Reference
!Pavelites, J.J., Bash, P.A., Gao, J., and MacKerell, Jr.,
!A.D. A Molecular Mechanics Force Field for NAD+, NADH and the
!Pyrophosphate Groups of Nucleotides, Journal of Computational
!Chemistry, 1997, 18: 221-239.

read rtf card append
* NAD, PPI topology
*
31  1

MASS  -1  HN3B       1.00800 H ! NAD+ aromatic hydrogen
MASS  -1  CN1A      12.01100 C ! NAD+/NADH amide carbonyl carbon
MASS  -1  CN3A      12.01100 C ! NAD+ aromatic carbon
MASS  -1  CN3B      12.01100 C ! NAD+ aromatic carbon
MASS  -1  CN3C      12.01100 C ! NADH aromatic carbon
MASS  -1  P3        30.97400 P ! pyrophosphate phosphorus
MASS  -1  P4        30.97400 P ! protonated pyrophosphate phosphorus

RESI NIC         1.00  ! oxidized nicotinamide, jjp1/adm jr.
                       ! checked for consistency with new NA params, adm jr., 9/98
                       ! note that differences with respect to published results exist
                       ! due to new NA params
                       !
                       !       H15
GROUP                  !         \
ATOM H1   HN2     0.45 !     H16-N14     H8
ATOM N2   NN2    -0.52 !           \     |
ATOM C3   CN3B    0.16 !            C12  C7
ATOM H4   HN3B    0.19 !           // \ /  \\
ATOM C5   CN3    -0.10 !         O13   C9   C5-H6
ATOM H6   HN3B    0.16 !               ||   |
ATOM C7   CN3A   -0.05 !           H11-C10  C3-H4
ATOM H8   HN3B    0.16 !                \+ //
ATOM C9   CN3     0.05 !                 N2
ATOM C10  CN3B    0.18 !                 |
ATOM H11  HN3B    0.16 !                 H1
ATOM C12  CN1A    0.68 !
ATOM O13  ON1    -0.40 !
ATOM N14  NN1    -0.82 !
ATOM H15  HN1     0.34 ! trans to O13
ATOM H16  HN1     0.36 ! cis to O13
BOND N2  H1   C3  H4   C3  C5   C5  H6
BOND C7 H8   C7  C9   N2  C10
BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
DOUBLE C12 O13  C9 C10  C5 C7  N2 C3
! amide impropers
IMPR C12 N14 C9 O13   C12 C9  N14 O13
IMPR N14 C12 H16 H15  N14 C12 H15 H16
! ring hydrogen impropers
IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
IMPR C7   C5   C9   H8    C10  C9   N2   H11
! ic table for analysis
IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
patch first none last none

RESI NICH         0.00 ! reduced nicotinamide, jjp1/adm jr.
                       ! checked for consistency with new NA params, adm jr., 9/98
                       ! note that differences with respect to published results exist
                       ! due to new NA params
                       ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98
                       !
                       !       H15
GROUP                  !         \
ATOM H1   HN2     0.42 !     H16-N14   H8  H17
ATOM N2   NN2    -0.69 !           \    \  /
ATOM C3   CN3C   -0.06 !            C12  C7
ATOM H4   HN6     0.17 !           /  \ /  \
ATOM C5   CN3    -0.18 !         O13   C9   C5-H6
ATOM H6   HN6     0.14 !               ||   ||
ATOM C7   CN8    -0.28 !           H11-C10  C3-H4
ATOM H8   HN8     0.09 !                \  /
ATOM H17  HN8     0.09 !                 N2
ATOM C10  CN3C   -0.10 !                 |
ATOM H11  HN6     0.14 !                 H1
ATOM C9   CN3     0.36 !
ATOM C12  CN1A    0.55 !
ATOM O13  ON1    -0.51 !
ATOM N14  NN1    -0.72 !
ATOM H15  HN1     0.26 ! trans to O13
ATOM H16  HN1     0.32 ! cis to O13

BOND N2  H1   N2 C3   C3  H4   C5  H6
BOND C5  C7   C7 H8   C7  H17  C7  C9   N2  C10
BOND C10 H11  C9 C12  C12 N14  N14 H15  N14 H16
DOUBLE C12 O13   C9 C10   C3  C5
! amide impropers
IMPR C12 N14 C9 O13   C12 C9  N14 O13
IMPR N14 C12 H16 H15  N14 C12 H15 H16
! ring hydrogen impropers
IMPR N2   C10  C3   H1    C3   N2   C5   H4    C5   C3   C7   H6
IMPR C10  C9   N2   H11
! ic table for analysis
IC N2   C3   C5   C7    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   C9    0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C10   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C10  N2    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   C3    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   C5    0.0000  000.00  000.00  000.00  0.000
IC C9   C10  N2   H1    0.0000  000.00  000.00  000.00  0.000
IC C10  N2   C3   H4    0.0000  000.00  000.00  000.00  0.000
IC N2   C3   C5   H6    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H8    0.0000  000.00  000.00  000.00  0.000
IC C3   C5   C7   H17   0.0000  000.00  000.00  000.00  0.000
IC C5   C7   C9   C12   0.0000  000.00  000.00  000.00  0.000
IC N2   C10  C9   C12   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  O13   0.0000  000.00  000.00  000.00  0.000
IC C7   C9   C12  N14   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H15   0.0000  000.00  000.00  000.00  0.000
IC O13  C12  N14  H16   0.0000  000.00  000.00  000.00  0.000
patch first none last none

RESI PPI1        -3.00   ! Inorganic phosphate, jjp1/adm jr.
GROUP                    !
ATOM C1   CN9    -0.17   !
ATOM O11  ON2    -0.62   !
ATOM P1   P       1.50   !                 H11
ATOM O12  ON2    -0.74   !                  |
ATOM O13  ON3    -0.82   !            H13--C1--H12
ATOM O14  ON3    -0.82   !                  |
                         !                 O11
ATOM P2   P3      1.10   !                  |
ATOM O22  ON3    -0.90   !            O14==P1==O13  (-)
ATOM O23  ON3    -0.90   !                 |
ATOM O24  ON3    -0.90   !                 O12
                         !                 |
ATOM H11  HN9     0.09   !        (-) O24==P2==O23  (-)
ATOM H12  HN9     0.09   !                 ||
ATOM H13  HN9     0.09   !                 O22

BOND P1  O11   P1  O12   P1  O13   P1  O14   O11  C1
BOND C1  H11   C1  H12   C1  H13
BOND O12 P2    P2  O22   P2  O23   P2  O24
! IC Table
IC C1   O11  P1   O12  0.0000    000.00    180.0     000.00    0.0000
IC O11  P1   O12  P2   0.0000    000.00    180.0     000.00    0.0000
IC P1   O12  P2   O22  0.0000    000.00    180.0     000.00    0.0000
IC C1   O11  P1   O13  0.0000    000.00     60.0     000.00    0.0000
IC C1   O11  P1   O14  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O12  P2   O23  0.0000    000.00     60.0     000.00    0.0000
IC P1   O12  P2   O24  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O11  C1   H11  0.0000    000.00    180.0     000.00    0.0000
IC P1   O11  C1   H12  0.0000    000.00     60.0     000.00    0.0000
IC P1   O11  C1   H13  0.0000    000.00    -60.0     000.00    0.0000
PATC  FIRS NONE LAST NONE

RESI PPI2        -2.00   ! Inorganic phosphate, protonated, adm jr.
                         ! terminal P charges based on neutral  
GROUP                    ! methylphosphate
ATOM C1   CN9    -0.17   !
ATOM O11  ON2    -0.62   !
ATOM P1   P       1.46   !                 H11
ATOM O12  ON2    -0.63   !                  |
ATOM O13  ON3    -0.83   !            H13--C1--H12
ATOM O14  ON3    -0.83   !                  |
                         !                 O11
ATOM P2   P4      1.34   !                  |
ATOM O22  ON4    -0.72   !            O14==P1==O13  (-)
ATOM H22  HN4     0.45   !                 |
ATOM O23  ON3    -0.86   !                 |
ATOM O24  ON3    -0.86   !                 O12
                         !                 |
ATOM H11  HN9     0.09   !        (-) O24==P2==O23  (-)
ATOM H12  HN9     0.09   !                 | 
ATOM H13  HN9     0.09   !                 O22
                         !                   \
                         !                   H22

BOND P1  O11   P1  O12   P1  O13   P1  O14   O11  C1
BOND C1  H11   C1  H12   C1  H13
BOND O12 P2    P2  O22   P2  O23   P2  O24   O22  H22
! IC Table
IC C1   O11  P1   O12  0.0000    000.00    180.0     000.00    0.0000
IC O11  P1   O12  P2   0.0000    000.00    180.0     000.00    0.0000
IC P1   O12  P2   O22  0.0000    000.00    180.0     000.00    0.0000
IC C1   O11  P1   O13  0.0000    000.00     60.0     000.00    0.0000
IC C1   O11  P1   O14  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O12  P2   O23  0.0000    000.00     60.0     000.00    0.0000
IC P1   O12  P2   O24  0.0000    000.00    -60.0     000.00    0.0000
IC P1   O11  C1   H11  0.0000    000.00    180.0     000.00    0.0000
IC P1   O11  C1   H12  0.0000    000.00     60.0     000.00    0.0000
IC P1   O11  C1   H13  0.0000    000.00    -60.0     000.00    0.0000
IC O12  P2   O22  H22  0.0000    000.00    180.0     000.00    0.0000
PATC  FIRS NONE LAST NONE

!adenine nucleotides
RESI AMP         -2.00  ! adenosine monophosphate, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  !                  O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !                   |      |    \ /   \  \
ATOM C4   CN5     0.43  !              O3A=PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !                   |      |     \     / \
                        !                  O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7B    0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM PA   P       1.10
ATOM O1A  ON3    -0.90
ATOM O2A  ON3    -0.90
ATOM O3A  ON3    -0.90

BOND PA   O1A       PA   O2A       PA   O3A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6        
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

 IC    C5'     O5'     PA      O1A         1.4449  121.33   73.87  103.48   1.4828
 IC    C5'     O5'     PA      O2A         1.4449  121.33  -46.00  105.57   1.4776
 IC    O1A     O2A     *PA     O3A         1.4828  113.83 -132.36  114.06   1.4776
 IC    PA      O5'     C5'     C4'         1.5840  121.33 -147.38  113.85   1.5508
 IC    O5'     C5'     C4'     C3'         1.4449  113.85  128.15  110.17   1.5416
 IC    C5'     C4'     C3'     O3'         1.5508  110.17  151.98  114.50   1.4413
 IC    H3T     O3'     C3'     C4'         0.9638  105.27  160.52  114.50   1.5416
 IC    O4'     C3'     *C4'    C5'         1.4701  103.10 -121.12  110.17   1.5508
 IC    C2'     C4'     *C3'    O3'         1.5240  101.86 -123.48  114.50   1.4413
 IC    C4'     C3'     C2'     C1'         1.5416  101.86  -38.77  101.03   1.5059
 IC    C3'     C2'     C1'     N9          1.5240  101.03  155.09  111.78   1.4716
 IC    O4'     C1'     N9      C4          1.4137  114.18 -154.31  121.73   1.3703
 IC    C1'     C4      *N9     C8          1.4716  121.73  178.72  105.87   1.3855
 IC    C4      N9      C8      N7          1.3703  105.87    4.44  112.40   1.3266
 IC    C8      N9      C4      C5          1.3855  105.87   -3.48  106.32   1.3792
 IC    C8      N7      C5      C6          1.3266  104.45  179.66  132.25   1.4124
 IC    N7      C5      C6      N1          1.3786  132.25 -179.60  117.95   1.3597
 IC    C5      C6      N1      C2          1.4124  117.95   -0.70  118.00   1.3353
 IC    N9      C5      *C4     N3          1.3703  106.32 -179.31  126.63   1.3526
 IC    C5      N1      *C6     N6          1.4124  117.95 -179.56  118.80   1.3481
 IC    N1      C6      N6      H61         1.3597  118.80   -3.01  118.66   0.9923
 IC    H61     C6      *N6     H62         0.9923  118.66 -174.71  119.12   0.9995
 IC    C5      N1      *C6     N6          1.4124  117.95 -179.56  118.80   1.3481
 IC    N1      C6      N6      H61         1.3597  118.80   -3.01  118.66   0.9923
 IC    H61     C6      *N6     H62         0.9923  118.66 -174.71  119.12   0.9995
 IC    N9      N7      *C8     H8          1.3855  112.40 -179.62  125.31   1.0957
 IC    N1      N3      *C2     H2          1.3353  129.78  179.62  114.59   1.0943
 IC    C1'     C3'     *C2'    O2'         1.5059  101.03 -118.47  112.30   1.4247
 IC    H2'     O2'     C2'     C3'         0.9720  107.05  156.19  112.30   1.5240
 IC    O4'     C2'     *C1'    H1'         1.4137  108.71 -112.42  108.76   1.1146
 IC    C1'     C3'     *C2'    H2''        1.5059  101.03  117.01  109.50   1.1181
 IC    C2'     C4'     *C3'    H3'         1.5240  101.86  115.18  108.62   1.1109
 IC    C3'     O4'     *C4'    H4'         1.5416  103.10 -116.67  109.24   1.1099
 IC    C4'     O5'     *C5'    H5'         1.5508  113.85 -122.02  108.16   1.1124
 IC    C4'     O5'     *C5'    H5''        1.5508  113.85  122.40  110.00   1.1166
PATC  FIRS NONE LAST NONE


RESI ADP         -3.00  ! adenosine diphosphate, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  !           O3B    O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !           |       |      |    \ /   \  \
ATOM C4   CN5     0.43  !      O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !           |       |      |     \     / \
                        !           O2B    O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7B    0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6        
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B

 IC    C5'     O5'     PA      O1A         1.4410  122.32   87.94  100.49   1.4886
 IC    C5'     O5'     PA      O2A         1.4410  122.32  -34.46  103.58   1.4860
 IC    O1A     O2A     *PA     O3A         1.4886  117.99 -144.34  113.98   1.5239
 IC    O5'     PA      O3A     PB          1.5958   98.37 -161.33  117.20   1.6142
 IC    PA      O3A     PB      O1B         1.5239  117.20  -40.60  110.60   1.5279
 IC    O3A     PB      *O1B    O2B         2.5838   35.79 -113.37   34.28   2.5253
 IC    O3A     PB      *O1B    O3B         2.5838   35.79  119.13   32.99   2.5605
 IC    PA      O5'     C5'     C4'         1.5958  122.32  -51.67  114.79   1.5447
 IC    O5'     C5'     C4'     C3'         1.4410  114.79  -58.82  120.15   1.5575
 IC    C5'     C4'     C3'     O3'         1.5447  120.15   24.57  114.35   1.4341
 IC    H3T     O3'     C3'     C4'         0.9993  106.88   49.50  114.35   1.5575
 IC    O4'     C3'     *C4'    C5'         1.4692  104.72 -123.02  120.15   1.5447
 IC    C2'     C4'     *C3'    O3'         1.5185  103.84  123.29  114.35   1.4341
 IC    C4'     C3'     C2'     C1'         1.5575  103.84  -34.69  100.67   1.5216
 IC    C3'     C2'     C1'     N9          1.5185  100.67  159.08  113.67   1.4641
 IC    O4'     C1'     N9      C4          1.4113  111.63 -130.55  127.26   1.3686
 IC    C1'     C4      *N9     C8          1.4641  127.26  179.24  106.16   1.3741
 IC    C4      N9      C8      N7          1.3686  106.16    0.49  113.56   1.3167
 IC    C8      N9      C4      C5          1.3741  106.16   -0.36  105.63   1.3838
 IC    C8      N7      C5      C6          1.3167  103.56 -179.38  131.99   1.4088
 IC    N7      C5      C6      N1          1.3861  131.99  179.37  118.17   1.3553
 IC    C5      C6      N1      C2          1.4088  118.17    0.12  117.88   1.3365
 IC    N9      C5      *C4     N3          1.3686  105.63 -179.47  126.53   1.3462
 IC    C5      N1      *C6     N6          1.4088  118.17  179.95  118.70   1.3458
 IC    N1      C6      N6      H61         1.3553  118.70    0.02  117.62   0.9928
 IC    H61     C6      *N6     H62         0.9928  117.62 -177.97  120.15   0.9969
 IC    C5      N1      *C6     N6          1.4088  118.17  179.95  118.70   1.3458
 IC    N1      C6      N6      H61         1.3553  118.70    0.02  117.62   0.9928
 IC    H61     C6      *N6     H62         0.9928  117.62 -177.97  120.15   0.9969
 IC    N9      N7      *C8     H8          1.3741  113.56 -179.64  125.94   1.0936
 IC    N1      N3      *C2     H2          1.3365  129.74  179.76  115.01   1.0933
 IC    C1'     C3'     *C2'    O2'         1.5216  100.67  120.50  109.82   1.4183
 IC    H2'     O2'     C2'     C3'         0.9782  102.50   14.41  109.82   1.5185
 IC    O4'     C2'     *C1'    H1'         1.4113  108.03 -113.14  108.10   1.1140
 IC    C1'     C3'     *C2'    H2''        1.5216  100.67 -117.81  110.45   1.1106
 IC    C2'     C4'     *C3'    H3'         1.5185  103.84 -116.26  105.90   1.1117
 IC    C3'     O4'     *C4'    H4'         1.5575  104.72 -113.29  107.42   1.1138
 IC    C4'     O5'     *C5'    H5'         1.5447  114.79 -121.61  108.15   1.1098
 IC    C4'     O5'     *C5'    H5''        1.5447  114.79  121.78  108.81   1.1138
PATC  FIRS NONE LAST NONE

RESI ATP         -4.00  !adenosine triphosphate , jjp1/adm jr.
                        !atom names correspond to pdb nomenclature
                        !
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  ! (-)O3G   O2B     O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !    |      |       |      |    \ /   \  \
ATOM C4   CN5     0.43  !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !    |      |       |      |     \     / \
                        ! (-)O2G (-)O1B (-)O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7B    0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P3      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6       
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G

 IC    C5'     O5'     PA      O1A         1.4378  121.47   77.19  100.91   1.4899
 IC    C5'     O5'     PA      O2A         1.4378  121.47  -44.89  102.27   1.4823
 IC    O1A     O2A     *PA     O3A         1.4899  117.99 -149.47  116.28   1.5095
 IC    O5'     PA      O3A     PB          1.5970   94.16 -172.73  101.71   1.6154
 IC    PA      O3A     PB      O1B         1.5095  101.71   72.81  111.02   1.5359
 IC    O3A     PB      *O1B    O2B         2.5978   35.48 -133.09   31.39   2.6245
 IC    O3A     PB      *O1B    O3B         2.5978   35.48  104.92   37.93   2.6047
 IC    O3A     PB      O3B     PG          1.6154   96.78 -173.49  154.12   1.6853
 IC    PA      O3B     PG      O1G         3.7941  178.28 -151.96  107.36   1.5287
 IC    O3B     PG      *O1G    O2G         2.5914   38.37 -116.07   33.82   2.5436
 IC    O3B     PG      *O1G    O3G         2.5914   38.37  116.49   33.72   2.5459
 IC    PA      O5'     C5'     C4'         1.5970  121.47  -80.85  111.25   1.5321
 IC    O5'     C5'     C4'     C3'         1.4378  111.25  -31.77  117.04   1.5487
 IC    O5'     C5'     C4'     C3'         1.4378  111.25  -31.77  117.04   1.5487
 IC    C5'     C4'     C3'     O3'         1.5321  117.04  114.00  111.81   1.4379
 IC    H3T     O3'     C3'     C4'         1.0005  103.99  -64.58  111.81   1.5487
 IC    O4'     C3'     *C4'    C5'         1.4622  104.95 -122.79  117.04   1.5321
 IC    C2'     C4'     *C3'    O3'         1.5314  104.67 -124.46  111.81   1.4379
 IC    C4'     C3'     C2'     C1'         1.5487  104.67  -23.03  101.91   1.5055
 IC    C3'     C2'     C1'     N9          1.5314  101.91  158.43  111.95   1.4582
 IC    O4'     C1'     N9      C4          1.4051  110.48 -119.72  127.77   1.3720
 IC    C1'     C4      *N9     C8          1.4582  127.77 -179.09  106.11   1.3733
 IC    C4      N9      C8      N7          1.3720  106.11   -0.75  113.74   1.3140
 IC    C8      N9      C4      C5          1.3733  106.11    0.64  105.48   1.3837
 IC    C8      N7      C5      C6          1.3140  103.52  179.77  131.85   1.4097
 IC    N7      C5      C6      N1          1.3877  131.85 -179.91  118.18   1.3551
 IC    C5      C6      N1      C2          1.4097  118.18    0.04  117.81   1.3370
 IC    N9      C5      *C4     N3          1.3720  105.48 -179.86  126.34   1.3449
 IC    C5      N1      *C6     N6          1.4097  118.18  179.89  118.87   1.3458
 IC    N1      C6      N6      H61         1.3551  118.87   -0.85  117.73   0.9931
 IC    H61     C6      *N6     H62         0.9931  117.73 -179.14  119.98   0.9966
 IC    C5      N1      *C6     N6          1.4097  118.18  179.89  118.87   1.3458
 IC    N1      C6      N6      H61         1.3551  118.87   -0.85  117.73   0.9931
 IC    H61     C6      *N6     H62         0.9931  117.73 -179.14  119.98   0.9966
 IC    N9      N7      *C8     H8          1.3733  113.74 -179.49  125.37   1.0933
 IC    N1      N3      *C2     H2          1.3370  129.70 -179.80  114.84   1.0933
 IC    C1'     C3'     *C2'    O2'         1.5055  101.91 -119.05  111.28   1.4120
 IC    H2'     O2'     C2'     C3'         0.9769  102.12    8.83  111.28   1.5314
 IC    O4'     C2'     *C1'    H1'         1.4051  105.32 -114.88  110.01   1.1152
 IC    C1'     C3'     *C2'    H2''        1.5055  101.91  118.84  108.68   1.1120
 IC    C2'     C4'     *C3'    H3'         1.5314  104.67  115.81  108.72   1.1136
 IC    C3'     O4'     *C4'    H4'         1.5487  104.95 -114.27  108.43   1.1139
 IC    C4'     O5'     *C5'    H5'         1.5321  111.25 -119.46  107.24   1.1108
 IC    C4'     O5'     *C5'    H5''        1.5321  111.25  123.64  111.88   1.1145
PATC  FIRS NONE LAST NONE

!guanine nucleotides
RESI GMP         -2.00  ! guanine monophosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                      O6
ATOM H4'  HN7     0.09  !                      ||
ATOM O4'  ON6B   -0.50  !                      C6
ATOM C1'  CN7B    0.16  !                     /  \
ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
GROUP                   !                    |    ||     C8-H8
ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
ATOM C4   CN5     0.26  !                   / \\ /      \
ATOM N2   NN1    -0.68  !             H21-N2   N3        \
ATOM H21  HN1     0.32  !                 |               \
ATOM H22  HN1     0.35  !                H22               \
ATOM N3   NN3G   -0.74  !                                   \
ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN1     0.54  !        |       |      |     \     / \
ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
ATOM C5   CN5G    0.00  !                            / \   / \
ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
ATOM C8   CN4     0.25  !                          |       |
ATOM H8   HN3     0.16  !                         H3T     H2'
GROUP                 
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM PA   P       1.10
ATOM O1A  ON3    -0.90
ATOM O2A  ON3    -0.90
ATOM O3A  ON3    -0.90

BOND N9   C4        N9   C8        C4   N3        N3   C2
BOND C2   N1        N1   C6        C6   C5        C5   N7
BOND C4   C5        N7   C8        C6   O6        C8   H8
BOND C2   N2        N2   H21       N2   H22       N1   H1
BOND C1'  N9        C1'  C2'       
BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''     

IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22

DONO H21  N2            
DONO H22  N2   
DONO H1   N1   
DONO H2'  O2'
ACCE O6   C6         
ACCE N3
ACCE N7
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

 IC    C5'     O5'     PA      O1A         1.4449  117.42   52.17  105.04   1.4828
 IC    C5'     O5'     PA      O2A         1.4449  117.42  -67.15  104.81   1.4806
 IC    O1A     O2A     *PA     O3A         1.4828  113.00 -131.19  113.56   1.4790
 IC    PA      O5'     C5'     C4'         1.5977  117.42  162.15  110.69   1.5276
 IC    O5'     C5'     C4'     C3'         1.4449  110.69 -168.25  111.34   1.5446
 IC    C5'     C4'     C3'     O3'         1.5276  111.34  144.97  115.23   1.4384
 IC    H3T     O3'     C3'     C4'         0.9628  104.75  161.01  115.23   1.5446
 IC    O4'     C3'     *C4'    C5'         1.4655  104.84 -120.73  111.34   1.5276
 IC    C2'     C4'     *C3'    O3'         1.5224  102.02 -121.78  115.23   1.4384
 IC    C4'     C3'     C2'     C1'         1.5446  102.02  -39.49   99.95   1.5059
 IC    C3'     C2'     C1'     N9          1.5224   99.95  163.39  112.13   1.4653
 IC    O4'     C1'     N9      C4          1.4081  112.64 -161.94  125.06   1.3695
 IC    C1'     C4      *N9     C8          1.4653  125.06  179.61  106.74   1.3780
 IC    C4      N9      C8      N7          1.3695  106.74    1.12  112.45   1.3168
 IC    C8      N9      C4      C5          1.3780  106.74   -1.48  105.61   1.3806
 IC    N9      C5      *C4     N3          1.3695  105.61  179.30  128.48   1.3512
 IC    C5      C4      N3      C2          1.3806  128.48   -5.38  112.09   1.3200
 IC    C4      N3      C2      N1          1.3512  112.09    3.91  123.88   1.3723
 IC    N1      N3      *C2     N2          1.3723  123.88  179.31  119.43   1.3225
 IC    N3      C2      N2      H21         1.3200  119.43  175.82  123.65   0.9906
 IC    H21     C2      *N2     H22         0.9906  123.65 -173.52  114.75   0.9960
 IC    N3      C2      N1      C6          1.3200  123.88   -1.31  125.17   1.3919
 IC    C6      C2      *N1     H1          1.3919  125.17 -178.04  119.92   0.9977
 IC    C5      N1      *C6     O6          1.4225  111.56 -179.99  119.10   1.2332
 IC    N9      N7      *C8     H8          1.3780  112.45 -179.50  126.25   1.0962
 IC    C1'     C3'     *C2'    O2'         1.5059   99.95 -118.94  112.61   1.4256
 IC    H2'     O2'     C2'     C3'         0.9721  107.31  151.43  112.61   1.5224
 IC    O4'     C2'     *C1'    H1'         1.4081  106.93 -113.28  109.47   1.1132
 IC    C1'     C3'     *C2'    H2''        1.5059   99.95  116.92  109.70   1.1151
 IC    C2'     C4'     *C3'    H3'         1.5224  102.02  115.92  107.85   1.1103
 IC    C3'     O4'     *C4'    H4'         1.5446  104.84 -117.41  110.00   1.1117
 IC    C4'     O5'     *C5'    H5'         1.5276  110.69 -119.42  109.72   1.1174
 IC    C4'     O5'     *C5'    H5''        1.5276  110.69  122.86  109.05   1.1107
PATC  FIRS NONE LAST NONE

RESI GDP         -3.00  ! guanine diphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                      O6
ATOM H4'  HN7     0.09  !                      ||
ATOM O4'  ON6B   -0.50  !                      C6
ATOM C1'  CN7B    0.16  !                     /  \
ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
GROUP                   !                    |    ||     C8-H8
ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
ATOM C4   CN5     0.26  !                   / \\ /      \
ATOM N2   NN1    -0.68  !             H21-N2   N3        \
ATOM H21  HN1     0.32  !                 |               \
ATOM H22  HN1     0.35  !                H22               \
ATOM N3   NN3G   -0.74  !                                   \
ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN1     0.54  !        |       |      |     \     / \
ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
ATOM C5   CN5G    0.00  !                            / \   / \
ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
ATOM C8   CN4     0.25  !                          |       |
ATOM H8   HN3     0.16  !                         H3T     H2'
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND N9   C4        N9   C8        C4   N3        N3   C2
BOND C2   N1        N1   C6        C6   C5        C5   N7
BOND C4   C5        N7   C8        C6   O6        C8   H8
BOND C2   N2        N2   H21       N2   H22       N1   H1
BOND C1'  N9        C1'  C2'       
BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22

DONO H21  N2            
DONO H22  N2   
DONO H1   N1   
DONO H2'  O2'
ACCE O6   C6         
ACCE N3
ACCE N7
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B

 IC    C5'     O5'     PA      O1A         1.4413  122.93   91.71  100.28   1.4877
 IC    C5'     O5'     PA      O2A         1.4413  122.93  -30.68  103.81   1.4867
 IC    O1A     O2A     *PA     O3A         1.4877  117.98 -144.37  113.97   1.5234
 IC    O5'     PA      O3A     PB          1.5946   98.34 -162.17  116.89   1.6138
 IC    PA      O3A     PB      O1B         1.5234  116.89  -41.55  110.65   1.5281
 IC    O3A     PB      *O1B    O2B         2.5844   35.75 -113.28   34.27   2.5257
 IC    O3A     PB      *O1B    O3B         2.5844   35.75  119.32   33.00   2.5600
 IC    PA      O5'     C5'     C4'         1.5946  122.93  -50.51  114.80   1.5441
 IC    O5'     C5'     C4'     C3'         1.4413  114.80  -52.35  122.03   1.5606
 IC    C5'     C4'     C3'     O3'         1.5441  122.03    8.61  113.75   1.4344
 IC    H3T     O3'     C3'     C4'         0.9971  105.35   57.55  113.75   1.5606
 IC    O4'     C3'     *C4'    C5'         1.4660  105.23 -126.40  122.03   1.5441
 IC    C2'     C4'     *C3'    O3'         1.5255  104.77  124.76  113.75   1.4344
 IC    C4'     C3'     C2'     C1'         1.5606  104.77  -28.98  100.20   1.5185
 IC    C3'     C2'     C1'     N9          1.5255  100.20  165.88  114.82   1.4718
 IC    O4'     C1'     N9      C4          1.4065  112.89 -112.42  126.14   1.3705
 IC    C1'     C4      *N9     C8          1.4718  126.14 -179.09  106.47   1.3755
 IC    C4      N9      C8      N7          1.3705  106.47   -0.36  113.07   1.3168
 IC    C8      N9      C4      C5          1.3755  106.47    0.03  105.56   1.3833
 IC    N9      C5      *C4     N3          1.3705  105.56  179.81  128.27   1.3494
 IC    C5      C4      N3      C2          1.3833  128.27   -3.62  112.43   1.3156
 IC    C4      N3      C2      N1          1.3494  112.43    3.08  123.80   1.3729
 IC    N1      N3      *C2     N2          1.3729  123.80  179.83  119.72   1.3235
 IC    N3      C2      N2      H21         1.3156  119.72    3.65  114.36   0.9968
 IC    H21     C2      *N2     H22         0.9968  114.36  165.67  123.15   0.9891
 IC    N3      C2      N1      C6          1.3156  123.80   -1.16  125.17   1.3916
 IC    C6      C2      *N1     H1          1.3916  125.17 -180.00  119.89   0.9970
 IC    C5      N1      *C6     O6          1.4212  111.57 -179.85  119.32   1.2334
 IC    N9      N7      *C8     H8          1.3755  113.07  179.83  125.93   1.0925
 IC    C1'     C3'     *C2'    O2'         1.5185  100.20  120.66  109.78   1.4177
 IC    H2'     O2'     C2'     C3'         0.9775  101.98   11.65  109.78   1.5255
 IC    O4'     C2'     *C1'    H1'         1.4065  106.83 -111.81  107.72   1.1143
 IC    C1'     C3'     *C2'    H2''        1.5185  100.20 -117.60  110.39   1.1104
 IC    C2'     C4'     *C3'    H3'         1.5255  104.77 -116.17  105.28   1.1124
 IC    C3'     O4'     *C4'    H4'         1.5606  105.23 -111.13  105.99   1.1140
 IC    C4'     O5'     *C5'    H5'         1.5441  114.80 -121.03  108.08   1.1104
 IC    C4'     O5'     *C5'    H5''        1.5441  114.80  122.15  109.04   1.1132
PATC  FIRS NONE LAST NONE

RESI GTP         -4.00  !guanine triphosphate , adm jr.
                        !atom names correspond to pdb nomenclature
                        !
ATOM C4'  CN7     0.16  !                      O6
ATOM H4'  HN7     0.09  !                      ||
ATOM O4'  ON6B   -0.50  !                      C6
ATOM C1'  CN7B    0.16  !                     /  \
ATOM H1'  HN7     0.09  !                 H1-N1   C5--N7\\
GROUP                   !                    |    ||     C8-H8
ATOM N9   NN2B   -0.02  !                    C2   C4--N9/
ATOM C4   CN5     0.26  !                   / \\ /      \
ATOM N2   NN1    -0.68  !             H21-N2   N3        \
ATOM H21  HN1     0.32  !                 |               \
ATOM H22  HN1     0.35  !                H22               \
ATOM N3   NN3G   -0.74  !                                   \
ATOM C2   CN2     0.75  !        O3B    O1A    H5' H4'  O4'  \
ATOM N1   NN2G   -0.34  !        |       |      |    \ /   \  \
ATOM H1   HN2     0.26  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN1     0.54  !        |       |      |     \     / \
ATOM O6   ON1    -0.51  !        O2B    O2A    H5''   C3'--C2' H1'
ATOM C5   CN5G    0.00  !                            / \   / \
ATOM N7   NN4    -0.60  !                         O3' H3' O2' H2''
ATOM C8   CN4     0.25  !                          |       |
ATOM H8   HN3     0.16  !                         H3T     H2'
GROUP
ATOM C2'  CN7B    0.14
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P3      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND N9   C4        N9   C8        C4   N3        N3   C2
BOND C2   N1        N1   C6        C6   C5        C5   N7
BOND C4   C5        N7   C8        C6   O6        C8   H8
BOND C2   N2        N2   H21       N2   H22       N1   H1
BOND C1'  N9        C1'  C2'       
BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N3   N1   N2        C6   N1   C5   O6        N2   H21  C2   H22

DONO H21  N2            
DONO H22  N2   
DONO H1   N1   
DONO H2'  O2'
ACCE O6   C6         
ACCE N3
ACCE N7
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G

 IC    C5'     O5'     PA      O1A         1.4386  121.55   77.89  100.89   1.4893
 IC    C5'     O5'     PA      O2A         1.4386  121.55  -44.16  102.34   1.4826
 IC    O1A     O2A     *PA     O3A         1.4893  117.94 -149.15  116.36   1.5099
 IC    O5'     PA      O3A     PB          1.5972   94.38 -173.25  101.74   1.6158
 IC    PA      O3A     PB      O1B         1.5099  101.74   71.90  111.32   1.5358
 IC    O3A     PB      *O1B    O2B         2.6028   35.33 -132.99   31.41   2.6238
 IC    O3A     PB      *O1B    O3B         2.6028   35.33  105.17   37.87   2.6059
 IC    O3A     PB      O3B     PG          1.6158   96.85 -169.20  153.75   1.6849
 IC    PA      O3B     PG      O1G         3.7962  176.66 -118.03  107.34   1.5288
 IC    O3B     PG      *O1G    O2G         2.5907   38.37 -115.96   33.86   2.5425
 IC    O3B     PG      *O1G    O3G         2.5907   38.37  116.61   33.69   2.5467
 IC    PA      O5'     C5'     C4'         1.5972  121.55  -79.94  111.03   1.5309
 IC    O5'     C5'     C4'     C3'         1.4386  111.03  -34.44  116.91   1.5495
 IC    O5'     C5'     C4'     C3'         1.4386  111.03  -34.44  116.91   1.5495
 IC    C5'     C4'     C3'     O3'         1.5309  116.91  113.16  111.77   1.4390
 IC    H3T     O3'     C3'     C4'         1.0011  104.38  -62.53  111.77   1.5495
 IC    O4'     C3'     *C4'    C5'         1.4621  104.76 -123.13  116.91   1.5309
 IC    C2'     C4'     *C3'    O3'         1.5333  104.58 -124.03  111.77   1.4390
 IC    C4'     C3'     C2'     C1'         1.5495  104.58  -23.65  101.32   1.5036
 IC    C3'     C2'     C1'     N9          1.5333  101.32  162.27  112.43   1.4657
 IC    O4'     C1'     N9      C4          1.4076  111.90 -129.15  126.74   1.3696
 IC    C1'     C4      *N9     C8          1.4657  126.74  179.56  106.58   1.3750
 IC    C4      N9      C8      N7          1.3696  106.58   -0.26  113.09   1.3154
 IC    C8      N9      C4      C5          1.3750  106.58    0.48  105.46   1.3840
 IC    N9      C5      *C4     N3          1.3696  105.46 -179.39  128.28   1.3485
 IC    C5      C4      N3      C2          1.3840  128.28    2.26  112.50   1.3124
 IC    C4      N3      C2      N1          1.3485  112.50   -1.89  123.91   1.3730
 IC    N1      N3      *C2     N2          1.3730  123.91 -179.85  119.33   1.3219
 IC    N3      C2      N2      H21         1.3124  119.33 -174.37  124.20   0.9897
 IC    H21     C2      *N2     H22         0.9897  124.20  172.33  113.43   0.9968
 IC    N3      C2      N1      C6          1.3124  123.91    0.72  125.11   1.3919
 IC    C6      C2      *N1     H1          1.3919  125.11  179.82  119.77   0.9968
 IC    C5      N1      *C6     O6          1.4216  111.58  179.91  119.39   1.2342
 IC    N9      N7      *C8     H8          1.3750  113.09 -179.04  125.80   1.0922
 IC    C1'     C3'     *C2'    O2'         1.5036  101.32 -118.99  110.95   1.4134
 IC    H2'     O2'     C2'     C3'         0.9766  101.89    9.44  110.95   1.5333
 IC    O4'     C2'     *C1'    H1'         1.4076  104.92 -114.02  109.46   1.1150
 IC    C1'     C3'     *C2'    H2''        1.5036  101.32  118.43  109.28   1.1120
 IC    C2'     C4'     *C3'    H3'         1.5333  104.58  116.08  108.56   1.1134
 IC    C3'     O4'     *C4'    H4'         1.5495  104.76 -114.13  108.29   1.1140
 IC    C4'     O5'     *C5'    H5'         1.5309  111.03 -119.42  107.43   1.1107
 IC    C4'     O5'     *C5'    H5''        1.5309  111.03  123.45  111.83   1.1145
PATC  FIRS NONE LAST NONE

!cytosine nucleotides
RESI CMP         -2.00  ! cytosine monophosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP
ATOM C4'  CN7     0.16  !                              H42  H41
ATOM H4'  HN7     0.09  !                                \  /    
ATOM O4'  ON6B   -0.50  !                                 N4
ATOM C1'  CN7B    0.16  !                                 |
ATOM H1'  HN7     0.09  !                                 C4
GROUP                   !                                /  \\
ATOM N1   NN2    -0.13  !                            H5-C5   N3
ATOM C6   CN3     0.05  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C5   CN3    -0.13  !                                \  / \\
ATOM H5   HN3     0.07  !                                 N1   O2
ATOM C2   CN1     0.52  !                                  \
ATOM O2   ON1C   -0.49  !                                   \
ATOM N3   NN3    -0.66  !               O1A    H5' H4'  O4'  \
ATOM C4   CN2     0.65  !                |      |    \ /   \  \
ATOM N4   NN1    -0.75  !          O3A--PA-O5'-C5'---C4'    C1'
ATOM H41  HN1     0.37  !                |      |     \     / \  
ATOM H42  HN1     0.33  !               O2A    H5''   C3'--C2' H1'  
GROUP                   !                            / \   / \
ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
ATOM H2'' HN7     0.09  !                          |       |
ATOM O2'  ON5    -0.66  !                         H3T     H2'
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM PA   P       1.10
ATOM O1A  ON3    -0.90
ATOM O2A  ON3    -0.90
ATOM O3A  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C4   N4        N4   H41       N4   H42
BOND C2   O2        C5   H5        C6   H6
BOND C1'  N1        C1'  C2'       
BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''     

IMPR C2   N1   N3   O2        C4   N3   C5   N4
IMPR N4   C4   H41  H42      

DONO H2'  O2'
DONO H41  N4   
DONO H42  N4   
ACCE O2   C2
ACCE N3     
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

 IC    C5'     O5'     PA      O1A         1.4355  125.73   29.84  105.66   1.4793
 IC    C5'     O5'     PA      O2A         1.4355  125.73  -91.13  105.46   1.4775
 IC    O1A     O2A     *PA     O3A         1.4793  113.93 -131.58  113.82   1.4809
 IC    PA      O5'     C5'     C4'         1.5817  125.73 -106.56  114.58   1.5485
 IC    O5'     C5'     C4'     C3'         1.4355  114.58   82.54  114.21   1.5385
 IC    C5'     C4'     C3'     O3'         1.5485  114.21  139.15  113.65   1.4400
 IC    H3T     O3'     C3'     C4'         0.9657  102.79  157.45  113.65   1.5385
 IC    O4'     C3'     *C4'    C5'         1.4688  105.40 -125.30  114.21   1.5485
 IC    C2'     C4'     *C3'    O3'         1.5240  103.66 -122.40  113.65   1.4400
 IC    C4'     C3'     C2'     C1'         1.5385  103.66  -33.47  101.88   1.5143
 IC    C3'     C2'     C1'     N1          1.5240  101.88  154.47  110.60   1.4866
 IC    O4'     C1'     N1      C2          1.4277  113.60 -151.06  121.54   1.3966
 IC    C1'     C2      *N1     C6          1.4866  121.54  167.48  119.36   1.3726
 IC    C2      N1      C6      C5          1.3966  119.36    7.13  121.63   1.3363
 IC    C6      N1      C2      N3          1.3726  119.36  -10.00  119.51   1.3602
 IC    N1      N3      *C2     O2          1.3966  119.51 -178.93  121.39   1.2434
 IC    N1      C2      N3      C4          1.3966  119.51    8.49  119.33   1.3427
 IC    C5      N3      *C4     N4          1.4190  122.04  178.61  118.12   1.3332
 IC    N3      C4      N4      H41         1.3427  118.12   -6.92  114.61   0.9924
 IC    H41     C4      *N4     H42         0.9924  114.61 -157.30  119.69   0.9937
 IC    C6      C4      *C5     H5          1.3363  117.43  176.45  120.96   1.0882
 IC    N1      C5      *C6     H6          1.3726  121.63 -178.59  121.78   1.0892
 IC    C1'     C3'     *C2'    O2'         1.5143  101.88 -119.06  112.57   1.4272
 IC    H2'     O2'     C2'     C3'         0.9654  106.91  171.65  112.57   1.5240
 IC    O4'     C2'     *C1'    H1'         1.4277  108.35 -113.18  108.73   1.1143
 IC    C1'     C3'     *C2'    H2''        1.5143  101.88  117.56  108.68   1.1163
 IC    C2'     C4'     *C3'    H3'         1.5240  103.66  115.28  107.93   1.1146
 IC    C3'     O4'     *C4'    H4'         1.5385  105.40 -113.98  108.05   1.1106
 IC    C4'     O5'     *C5'    H5'         1.5485  114.58 -119.26  107.06   1.1096
 IC    C4'     O5'     *C5'    H5''        1.5485  114.58  124.53  111.01   1.1140
PATC  FIRS NONE LAST NONE

RESI CDP         -3.00  ! cytosine diphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature

ATOM C4'  CN7     0.16  !                              H42  H41
ATOM H4'  HN7     0.09  !                                \  /    
ATOM O4'  ON6B   -0.50  !                                 N4
ATOM C1'  CN7B    0.16  !                                 |
ATOM H1'  HN7     0.09  !                                 C4
GROUP                   !                                /  \\
ATOM N1   NN2    -0.13  !                            H5-C5   N3
ATOM C6   CN3     0.05  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C5   CN3    -0.13  !                                \  / \\
ATOM H5   HN3     0.07  !                                 N1   O2
ATOM C2   CN1     0.52  !                                  \
ATOM O2   ON1C   -0.49  !                                   \
ATOM N3   NN3    -0.66  !        O3B    O1A    H5' H4'  O4'  \
ATOM C4   CN2     0.65  !        |       |      |    \ /   \  \
ATOM N4   NN1    -0.75  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM H41  HN1     0.37  !        |       |      |     \     / \  
ATOM H42  HN1     0.33  !        O2B    O2A    H5''   C3'--C2' H1'  
GROUP                   !                            / \   / \
ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
ATOM H2'' HN7     0.09  !                          |       |
ATOM O2'  ON5    -0.66  !                         H3T     H2'
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C4   N4        N4   H41       N4   H42
BOND C2   O2        C5   H5        C6   H6
BOND C1'  N1        C1'  C2'       
BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   N4
IMPR N4   C4   H41  H42      

DONO H2'  O2'
DONO H41  N4   
DONO H42  N4   
ACCE O2   C2
ACCE N3     
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B

 IC    C5'     O5'     PA      O1A         1.4425  120.73 -171.23  102.18   1.4828
 IC    C5'     O5'     PA      O2A         1.4425  120.73   66.15  100.85   1.4861
 IC    O1A     O2A     *PA     O3A         1.4828  118.54 -146.08  114.13   1.5266
 IC    O5'     PA      O3A     PB          1.5949   97.60 -165.85  119.57   1.6105
 IC    PA      O3A     PB      O1B         1.5266  119.57  -43.22  109.89   1.5262
 IC    O3A     PB      *O1B    O2B         2.5681   36.14 -112.68   34.17   2.5275
 IC    O3A     PB      *O1B    O3B         2.5681   36.14  119.09   32.92   2.5612
 IC    PA      O5'     C5'     C4'         1.5949  120.73 -154.23  112.44   1.5457
 IC    O5'     C5'     C4'     C3'         1.4425  112.44   45.68  117.83   1.5501
 IC    C5'     C4'     C3'     O3'         1.5457  117.83  -32.52  117.14   1.4300
 IC    H3T     O3'     C3'     C4'         0.9882  105.85   24.62  117.14   1.5501
 IC    O4'     C3'     *C4'    C5'         1.4625  105.13 -124.89  117.83   1.5457
 IC    C2'     C4'     *C3'    O3'         1.5127  103.43  120.51  117.14   1.4300
 IC    C4'     C3'     C2'     C1'         1.5501  103.43   34.51  101.64   1.5272
 IC    C3'     C2'     C1'     N1          1.5127  101.64   94.90  112.49   1.4975
 IC    O4'     C1'     N1      C2          1.4246  112.69 -159.47  121.37   1.3985
 IC    C1'     C2      *N1     C6          1.4975  121.37  175.71  119.50   1.3804
 IC    C2      N1      C6      C5          1.3985  119.50    2.69  121.63   1.3352
 IC    C6      N1      C2      N3          1.3804  119.50   -3.85  119.51   1.3617
 IC    N1      N3      *C2     O2          1.3985  119.51  179.76  121.33   1.2430
 IC    N1      C2      N3      C4          1.3985  119.51    2.83  119.69   1.3444
 IC    C5      N3      *C4     N4          1.4196  121.99 -179.61  118.24   1.3337
 IC    N3      C4      N4      H41         1.3444  118.24   -2.06  116.78   0.9910
 IC    H41     C4      *N4     H42         0.9910  116.78 -175.36  120.63   0.9957
 IC    C6      C4      *C5     H5          1.3352  117.58  179.72  120.95   1.0898
 IC    N1      C5      *C6     H6          1.3804  121.63 -178.41  121.71   1.0928
 IC    C1'     C3'     *C2'    O2'         1.5272  101.64 -119.10  110.23   1.4207
 IC    H2'     O2'     C2'     C3'         0.9588  108.13  -87.19  110.23   1.5127
 IC    O4'     C2'     *C1'    H1'         1.4246  108.02 -113.99  108.53   1.1132
 IC    C1'     C3'     *C2'    H2''        1.5272  101.64  118.36  111.16   1.1128
 IC    C2'     C4'     *C3'    H3'         1.5127  103.43 -117.68  107.15   1.1105
 IC    C3'     O4'     *C4'    H4'         1.5501  105.13 -113.16  105.27   1.1104
 IC    C4'     O5'     *C5'    H5'         1.5457  112.44 -121.82  108.90   1.1132
 IC    C4'     O5'     *C5'    H5''        1.5457  112.44  120.84  110.82   1.1175
PATC  FIRS NONE LAST NONE

RESI CTP         -4.00  !cytosine triphosphate , adm jr.
                        !atom names correspond to pdb nomenclature
                        !
ATOM C4'  CN7     0.16  !                              H42  H41
ATOM H4'  HN7     0.09  !                                \  /    
ATOM O4'  ON6B   -0.50  !                                 N4
ATOM C1'  CN7B    0.16  !                                 |
ATOM H1'  HN7     0.09  !                                 C4
GROUP                   !                                /  \\
ATOM N1   NN2    -0.13  !                            H5-C5   N3
ATOM C6   CN3     0.05  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C5   CN3    -0.13  !                                \  / \\
ATOM H5   HN3     0.07  !                                 N1   O2
ATOM C2   CN1     0.52  !                                  \
ATOM O2   ON1C   -0.49  !                                   \
ATOM N3   NN3    -0.66  !        O3B    O1A    H5' H4'  O4'  \
ATOM C4   CN2     0.65  !        |       |      |    \ /   \  \
ATOM N4   NN1    -0.75  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM H41  HN1     0.37  !        |       |      |     \     / \  
ATOM H42  HN1     0.33  !        O2B    O2A    H5''   C3'--C2' H1'  
GROUP                   !                            / \   / \
ATOM C2'  CN7B    0.14  !                         O3' H3' O2' H2''
ATOM H2'' HN7     0.09  !                          |       |
ATOM O2'  ON5    -0.66  !                         H3T     H2'
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P3      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C4   N4        N4   H41       N4   H42
BOND C2   O2        C5   H5        C6   H6
BOND C1'  N1        C1'  C2'       
BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   N4
IMPR N4   C4   H41  H42      

DONO H2'  O2'
DONO H41  N4   
DONO H42  N4   
ACCE O2   C2
ACCE N3     
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G

 IC    C5'     O5'     PA      O1A         1.4374  124.19    9.59  104.00   1.4923
 IC    C5'     O5'     PA      O2A         1.4374  124.19 -114.42  104.65   1.4799
 IC    O1A     O2A     *PA     O3A         1.4923  117.63 -145.47  113.13   1.5080
 IC    O5'     PA      O3A     PB          1.5913   92.94 -156.20  107.64   1.5985
 IC    PA      O3A     PB      O1B         1.5080  107.64   80.47  107.43   1.5316
 IC    O3A     PB      *O1B    O2B         2.5234   37.18 -130.54   31.00   2.6293
 IC    O3A     PB      *O1B    O3B         2.5234   37.18  103.63   37.65   2.6119
 IC    O3A     PB      O3B     PG          1.5985   96.76 -173.66  156.81   1.6792
 IC    PA      O3B     PG      O1G         3.8251  173.26 -135.48  106.83   1.5253
 IC    O3B     PG      *O1G    O2G         2.5748   38.62 -119.21   33.03   2.5553
 IC    O3B     PG      *O1G    O3G         2.5748   38.62  112.99   35.25   2.4958
 IC    PA      O5'     C5'     C4'         1.5913  124.19  -89.15  114.76   1.5460
 IC    O5'     C5'     C4'     C3'         1.4374  114.76   53.17  118.79   1.5327
 IC    O5'     C5'     C4'     C3'         1.4374  114.76   53.17  118.79   1.5327
 IC    C5'     C4'     C3'     O3'         1.5460  118.79   69.96  109.76   1.4345
 IC    H3T     O3'     C3'     C4'         0.9919  101.28  -87.58  109.76   1.5327
 IC    O4'     C3'     *C4'    C5'         1.4600  103.99 -127.40  118.79   1.5460
 IC    C2'     C4'     *C3'    O3'         1.5077  100.80 -122.49  109.76   1.4345
 IC    C4'     C3'     C2'     C1'         1.5327  100.80   43.97   99.50   1.5247
 IC    C3'     C2'     C1'     N1          1.5077   99.50   89.23  109.95   1.4935
 IC    O4'     C1'     N1      C2          1.4364  113.05 -159.72  119.96   1.3986
 IC    C1'     C2      *N1     C6          1.4935  119.96  174.01  119.68   1.3780
 IC    C2      N1      C6      C5          1.3986  119.68    2.03  121.33   1.3337
 IC    C6      N1      C2      N3          1.3780  119.68   -1.80  119.80   1.3569
 IC    N1      N3      *C2     O2          1.3986  119.80 -179.96  121.55   1.2448
 IC    N1      C2      N3      C4          1.3986  119.80    4.60  119.43   1.3537
 IC    C5      N3      *C4     N4          1.4218  121.37  178.95  119.72   1.3264
 IC    N3      C4      N4      H41         1.3537  119.72  -51.72  111.09   0.9906
 IC    H41     C4      *N4     H42         0.9906  111.09 -118.26  112.11   1.0266
 IC    C6      C4      *C5     H5          1.3337  117.92  172.01  120.22   1.0891
 IC    N1      C5      *C6     H6          1.3780  121.33  179.06  120.93   1.0958
 IC    C1'     C3'     *C2'    O2'         1.5247   99.50 -119.79  110.03   1.4190
 IC    H2'     O2'     C2'     C3'         0.9679  101.70  -36.76  110.03   1.5077
 IC    O4'     C2'     *C1'    H1'         1.4364  107.34 -115.45  109.29   1.1119
 IC    C1'     C3'     *C2'    H2''        1.5247   99.50  117.77  110.99   1.1124
 IC    C2'     C4'     *C3'    H3'         1.5077  100.80  115.80  109.37   1.1105
 IC    C3'     O4'     *C4'    H4'         1.5327  103.99 -111.63  105.45   1.1095
 IC    C4'     O5'     *C5'    H5'         1.5460  114.76 -120.46  108.07   1.1105
 IC    C4'     O5'     *C5'    H5''        1.5460  114.76  122.97  110.78   1.1139
PATC  FIRS NONE LAST NONE

!thymine nucleotides
RESI TMP         -2.00  ! thymine monophosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                          H51    O4
ATOM C1'  CN7B    0.16  !                           |     ||
ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
GROUP                   !                           |  \ /  \  /
ATOM N1   NN2B   -0.34  !                          H53  C5   N3
ATOM C6   CN3     0.17  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C2   CN1T    0.51  !                                \  / \\
ATOM O2   ON1    -0.41  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.50  !               O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.45  !                |      |    \ /   \  \
ATOM C5   CN3T   -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
ATOM C5M  CN9    -0.11  !                |      |     \     / \  
ATOM H51  HN9     0.07  !               O2A    H5''   C3'--C2' H1'  
ATOM H52  HN9     0.07  !                            / \   / \
ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
GROUP                   !                          |       |
ATOM C2'  CN7B    0.14  !                         H3T     H2'
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM PA   P       1.10
ATOM O1A  ON3    -0.90
ATOM O2A  ON3    -0.90
ATOM O3A  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C2   O2        C4   O4        N3   H3        C6   H6        
BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
BOND C1'  N1        C1'  C2'       
BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''     

IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M

DONO H3   N3
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

 IC    C5'     O5'     PA      O1A         1.4400  125.37  137.83  103.50   1.4812
 IC    C5'     O5'     PA      O2A         1.4400  125.37   19.22  105.83   1.4793
 IC    O1A     O2A     *PA     O3A         1.4812  112.59 -131.81  114.29   1.4766
 IC    PA      O5'     C5'     C4'         1.5863  125.37 -107.59  114.23   1.5482
 IC    O5'     C5'     C4'     C3'         1.4400  114.23   68.41  114.41   1.5398
 IC    C5'     C4'     C3'     O3'         1.5482  114.41  143.93  114.36   1.4402
 IC    H3T     O3'     C3'     C4'         0.9640  103.41  159.98  114.36   1.5398
 IC    O4'     C3'     *C4'    C5'         1.4658  105.05 -123.89  114.41   1.5482
 IC    C2'     C4'     *C3'    O3'         1.5217  102.68 -122.25  114.36   1.4402
 IC    C4'     C3'     C2'     C1'         1.5398  102.68  -36.86  101.04   1.5223
 IC    C3'     C2'     C1'     N1          1.5217  101.04  154.90  113.33   1.4848
 IC    O4'     C1'     N1      C2          1.4189  110.62 -103.32  119.64   1.3741
 IC    C1'     C2      *N1     C6          1.4848  119.64 -175.07  121.11   1.3805
 IC    C2      N1      C6      C5          1.3741  121.11   -5.22  123.51   1.3386
 IC    C6      N1      C2      N3          1.3805  121.11    3.50  114.62   1.3735
 IC    N1      N3      *C2     O2          1.3741  114.62 -179.71  121.72   1.2273
 IC    N1      C2      N3      C4          1.3741  114.62   -2.55  127.21   1.3812
 IC    C5      N3      *C4     O4          1.4408  115.13  179.57  119.15   1.2323
 IC    C2      C4      *N3     H3          1.3735  127.21  175.47  117.05   0.9962
 IC    C4      C6      *C5     C5M         1.4408  118.17  171.46  120.65   1.4965
 IC    N1      C5      *C6     H6          1.3805  123.51 -176.23  120.19   1.0910
 IC    C6      C5      C5M     H51         1.3386  120.65   37.09  110.64   1.1161
 IC    C5      H51     *C5M    H52         1.4965  110.64  120.93  107.19   1.1127
 IC    H51     H52     *C5M    H53         1.1161  107.19 -116.03  108.61   1.1110
 IC    C1'     C3'     *C2'    O2'         1.5223  101.04 -120.82  113.11   1.4248
 IC    H2'     O2'     C2'     C3'         0.9628  105.68 -140.74  113.11   1.5217
 IC    O4'     C2'     *C1'    H1'         1.4189  107.84 -112.80  107.54   1.1154
 IC    C1'     C3'     *C2'    H2''        1.5223  101.04  117.63  108.19   1.1094
 IC    C2'     C4'     *C3'    H3'         1.5217  102.68  115.26  107.66   1.1144
 IC    C3'     O4'     *C4'    H4'         1.5398  105.05 -114.57  108.17   1.1101
 IC    C4'     O5'     *C5'    H5'         1.5482  114.23 -119.64  107.43   1.1103
 IC    C4'     O5'     *C5'    H5''        1.5482  114.23  123.75  111.18   1.1146
PATC  FIRS NONE LAST NONE

RESI TDP         -3.00  ! thymine diphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature

GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                          H51    O4
ATOM C1'  CN7B    0.16  !                           |     ||
ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
GROUP                   !                           |  \ /  \  /
ATOM N1   NN2B   -0.34  !                          H53  C5   N3
ATOM C6   CN3     0.17  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C2   CN1T    0.51  !                                \  / \\
ATOM O2   ON1    -0.41  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.50  !        O3B    O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.45  !        |       |      |    \ /   \  \
ATOM C5   CN3T   -0.15  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C5M  CN9    -0.11  !        |       |      |     \     / \
ATOM H51  HN9     0.07  !        O2B    O2A    H5''   C3'--C2' H1'
ATOM H52  HN9     0.07  !                            / \   / \
ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
GROUP                   !                          |       |
ATOM C2'  CN7B    0.14  !                         H3T     H2'
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C2   O2        C4   O4        N3   H3        C6   H6        
BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
BOND C1'  N1        C1'  C2'       
BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M

DONO H3   N3
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B

 IC    C5'     O5'     PA      O1A         1.4455  118.72  178.82  102.92   1.4827
 IC    C5'     O5'     PA      O2A         1.4455  118.72   55.43  102.27   1.4864
 IC    O1A     O2A     *PA     O3A         1.4827  118.46 -143.46  114.83   1.5249
 IC    O5'     PA      O3A     PB          1.6018   97.48 -176.70  126.12   1.6123
 IC    PA      O3A     PB      O1B         1.5249  126.12  -18.77  109.94   1.5251
 IC    O3A     PB      *O1B    O2B         2.5696   36.15 -114.07   33.74   2.5396
 IC    O3A     PB      *O1B    O3B         2.5696   36.15  116.77   33.21   2.5528
 IC    PA      O5'     C5'     C4'         1.6018  118.72  -94.65  112.53   1.5424
 IC    O5'     C5'     C4'     C3'         1.4455  112.53  -12.09  119.74   1.5559
 IC    C5'     C4'     C3'     O3'         1.5424  119.74  -30.51  116.31   1.4330
 IC    H3T     O3'     C3'     C4'         0.9848  103.20   51.10  116.31   1.5559
 IC    O4'     C3'     *C4'    C5'         1.4677  105.16 -123.76  119.74   1.5424
 IC    C2'     C4'     *C3'    O3'         1.5140  102.76  120.50  116.31   1.4330
 IC    C4'     C3'     C2'     C1'         1.5559  102.76   34.89  102.13   1.5267
 IC    C3'     C2'     C1'     N1          1.5140  102.13   91.37  112.87   1.4944
 IC    O4'     C1'     N1      C2          1.4165  111.23 -144.95  119.12   1.3725
 IC    C1'     C2      *N1     C6          1.4944  119.12  179.24  120.91   1.3836
 IC    C2      N1      C6      C5          1.3725  120.91   -0.93  123.77   1.3377
 IC    C6      N1      C2      N3          1.3836  120.91   -1.10  114.76   1.3735
 IC    N1      N3      *C2     O2          1.3725  114.76  179.57  121.97   1.2269
 IC    N1      C2      N3      C4          1.3725  114.76    0.33  127.20   1.3815
 IC    C5      N3      *C4     O4          1.4399  115.20 -179.93  119.31   1.2312
 IC    C2      C4      *N3     H3          1.3735  127.20  179.19  117.03   0.9968
 IC    C4      C6      *C5     C5M         1.4399  118.04  173.19  121.29   1.4971
 IC    N1      C5      *C6     H6          1.3836  123.77  178.29  120.97   1.0948
 IC    C6      C5      C5M     H51         1.3377  121.29   32.69  110.96   1.1155
 IC    C5      H51     *C5M    H52         1.4971  110.96  121.38  107.65   1.1125
 IC    H51     H52     *C5M    H53         1.1155  107.65 -115.95  108.29   1.1123
 IC    C1'     C3'     *C2'    O2'         1.5267  102.13 -117.96  110.34   1.4182
 IC    H2'     O2'     C2'     C3'         0.9640  107.13   43.83  110.34   1.5140
 IC    O4'     C2'     *C1'    H1'         1.4165  107.51 -113.71  108.81   1.1146
 IC    C1'     C3'     *C2'    H2''        1.5267  102.13  119.61  111.22   1.1110
 IC    C2'     C4'     *C3'    H3'         1.5140  102.76 -117.99  107.30   1.1139
 IC    C3'     O4'     *C4'    H4'         1.5559  105.16 -113.01  107.94   1.1119
 IC    C4'     O5'     *C5'    H5'         1.5424  112.53 -120.89  107.50   1.1103
 IC    C4'     O5'     *C5'    H5''        1.5424  112.53  123.23  112.75   1.1186
PATC  FIRS NONE LAST NONE

RESI TTP         -4.00  ! thymine triphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
                        !
GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                          H51    O4
ATOM C1'  CN7B    0.16  !                           |     ||
ATOM H1'  HN7     0.09  !                       H52-C5M   C4    H3
GROUP                   !                           |  \ /  \  /
ATOM N1   NN2B   -0.34  !                          H53  C5   N3
ATOM C6   CN3     0.17  !                               ||   |
ATOM H6   HN3     0.17  !                            H6-C6   C2
ATOM C2   CN1T    0.51  !                                \  / \\
ATOM O2   ON1    -0.41  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.50  !        O3B    O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.45  !        |       |      |    \ /   \  \
ATOM C5   CN3T   -0.15  !   O1B=PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C5M  CN9    -0.11  !        |       |      |     \     / \
ATOM H51  HN9     0.07  !        O2B    O2A    H5''   C3'--C2' H1'
ATOM H52  HN9     0.07  !                            / \   / \
ATOM H53  HN9     0.07  !                         O3' H3' O2' H2''
GROUP                   !                          |       |
ATOM C2'  CN7B    0.14  !                         H3T     H2'
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P3      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6
BOND C2   O2        C4   O4        N3   H3        C6   H6        
BOND C5   C5M       C5M  H51       C5M  H52       C5M  H53
BOND C1'  N1        C1'  C2'       
BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   O4        C5   C4   C6   C5M

DONO H3   N3
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G

 IC    C5'     O5'     PA      O1A         1.4401  123.09   16.55  102.93   1.4933
 IC    C5'     O5'     PA      O2A         1.4401  123.09 -107.14  103.98   1.4803
 IC    O1A     O2A     *PA     O3A         1.4933  118.07 -146.90  113.77   1.5140
 IC    O5'     PA      O3A     PB          1.5925   93.17 -158.62  104.64   1.6083
 IC    PA      O3A     PB      O1B         1.5140  104.64   79.95  107.61   1.5335
 IC    O3A     PB      *O1B    O2B         2.5359   37.19 -131.19   31.13   2.6313
 IC    O3A     PB      *O1B    O3B         2.5359   37.19  104.58   37.08   2.6197
 IC    O3A     PB      O3B     PG          1.6083   97.23 -147.19  153.72   1.6788
 IC    PA      O3B     PG      O1G         3.8073  169.46 -135.11  107.23   1.5280
 IC    O3B     PG      *O1G    O2G         2.5832   38.37 -115.26   33.76   2.5441
 IC    O3B     PG      *O1G    O3G         2.5832   38.37  116.43   33.28   2.5561
 IC    PA      O5'     C5'     C4'         1.5925  123.09  -95.33  113.20   1.5426
 IC    O5'     C5'     C4'     C3'         1.4401  113.20   41.03  118.58   1.5380
 IC    O5'     C5'     C4'     C3'         1.4401  113.20   41.03  118.58   1.5380
 IC    C5'     C4'     C3'     O3'         1.5426  118.58   78.12  109.57   1.4380
 IC    H3T     O3'     C3'     C4'         0.9928  102.84  -86.68  109.57   1.5380
 IC    O4'     C3'     *C4'    C5'         1.4580  104.71 -124.25  118.58   1.5426
 IC    C2'     C4'     *C3'    O3'         1.5167  102.03 -122.41  109.57   1.4380
 IC    C4'     C3'     C2'     C1'         1.5380  102.03   35.92  101.65   1.5275
 IC    C3'     C2'     C1'     N1          1.5167  101.65   97.44  112.77   1.4901
 IC    O4'     C1'     N1      C2          1.4164  110.59 -125.32  118.29   1.3771
 IC    C1'     C2      *N1     C6          1.4901  118.29  179.10  120.54   1.3963
 IC    C2      N1      C6      C5          1.3771  120.54    0.81  123.15   1.3377
 IC    C6      N1      C2      N3          1.3963  120.54   -2.65  114.92   1.3665
 IC    N1      N3      *C2     O2          1.3771  114.92  179.31  121.44   1.2292
 IC    N1      C2      N3      C4          1.3771  114.92   -2.57  127.52   1.3790
 IC    C5      N3      *C4     O4          1.4408  114.71 -177.54  118.30   1.2292
 IC    C2      C4      *N3     H3          1.3665  127.52  174.49  115.81   0.9947
 IC    C4      C6      *C5     C5M         1.4408  118.41  173.37  121.54   1.4945
 IC    N1      C5      *C6     H6          1.3963  123.15 -175.27  118.98   1.0993
 IC    C6      C5      C5M     H51         1.3377  121.54  -86.48  111.81   1.1122
 IC    C5      H51     *C5M    H52         1.4945  111.81  124.82  109.28   1.1162
 IC    H51     H52     *C5M    H53         1.1122  109.28 -114.95  105.93   1.1172
 IC    C1'     C3'     *C2'    O2'         1.5275  101.65 -119.10  110.11   1.4172
 IC    H2'     O2'     C2'     C3'         0.9713  101.08  -29.97  110.11   1.5167
 IC    O4'     C2'     *C1'    H1'         1.4164  108.58 -113.02  107.93   1.1147
 IC    C1'     C3'     *C2'    H2''        1.5275  101.65  118.88  110.18   1.1121
 IC    C2'     C4'     *C3'    H3'         1.5167  102.03  116.25  109.94   1.1106
 IC    C3'     O4'     *C4'    H4'         1.5380  104.71 -112.76  105.69   1.1100
 IC    C4'     O5'     *C5'    H5'         1.5426  113.20 -120.33  108.24   1.1112
 IC    C4'     O5'     *C5'    H5''        1.5426  113.20  122.84  111.42   1.1153
PATC  FIRS NONE LAST NONE

!uracil nucleotides
RESI UMP         -2.00  ! uracil monophosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                                 O4
ATOM C1'  CN7B    0.16  !                                 ||
ATOM H1'  HN7     0.09  !                                 C4    H3
GROUP                   !                                /  \  /
ATOM N1   NN2B   -0.34  !                            H5-C5   N3
ATOM C6   CN3     0.20  !                               ||   |
ATOM H6   HN3     0.14  !                            H6-C6   C2
ATOM C2   CN1T    0.55  !                                \  / \\
ATOM O2   ON1    -0.45  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
ATOM H5   HN3     0.10  !                |      |     \     / \  
GROUP                   !               O2A    H5''   C3'--C2' H1'  
ATOM C2'  CN7B    0.14  !                            / \   / \
ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
ATOM O2'  ON5    -0.66  !                          |       |
ATOM H2'  HN5     0.43  !                         H3T     H2'
GROUP                 
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.18
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
GROUP
ATOM O5'  ON2    -0.40
ATOM PA   P       1.10
ATOM O1A  ON3    -0.90
ATOM O2A  ON3    -0.90
ATOM O3A  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6        N3   H3
BOND C2   O2        C4   O4        C5   H5        C6   H6        
BOND C1'  N1        C1'  C2'       
BOND PA   O1A       PA   O2A       PA   O3A       PA   O5'       O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''     

IMPR C2   N1   N3   O2        C4   N3   C5   O4

DONO H3   N3   
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'

 IC    C5'     O5'     PA      O1A         1.4386  125.37   30.84  105.62   1.4796
 IC    C5'     O5'     PA      O2A         1.4386  125.37  -90.57  105.92   1.4765
 IC    O1A     O2A     *PA     O3A         1.4796  114.13 -131.09  114.21   1.4812
 IC    PA      O5'     C5'     C4'         1.5867  125.37 -107.44  114.55   1.5499
 IC    O5'     C5'     C4'     C3'         1.4386  114.55   73.74  113.74   1.5378
 IC    C5'     C4'     C3'     O3'         1.5499  113.74  143.96  114.47   1.4402
 IC    H3T     O3'     C3'     C4'         0.9641  103.40  157.99  114.47   1.5378
 IC    O4'     C3'     *C4'    C5'         1.4689  104.93 -124.30  113.74   1.5499
 IC    C2'     C4'     *C3'    O3'         1.5200  102.40 -122.09  114.47   1.4402
 IC    C4'     C3'     C2'     C1'         1.5378  102.40  -38.48  100.83   1.5198
 IC    C3'     C2'     C1'     N1          1.5200  100.83  156.79  112.75   1.4834
 IC    O4'     C1'     N1      C2          1.4213  110.92 -114.25  120.00   1.3727
 IC    C1'     C2      *N1     C6          1.4834  120.00 -178.72  121.10   1.3782
 IC    C2      N1      C6      C5          1.3727  121.10   -1.47  122.78   1.3422
 IC    C6      N1      C2      N3          1.3782  121.10    1.33  114.81   1.3720
 IC    N1      N3      *C2     O2          1.3727  114.81 -179.71  121.46   1.2270
 IC    N1      C2      N3      C4          1.3727  114.81   -0.62  127.53   1.3791
 IC    C5      N3      *C4     O4          1.4318  114.39 -179.77  119.32   1.2301
 IC    C2      C4      *N3     H3          1.3720  127.53  179.65  117.07   0.9957
 IC    C4      C6      *C5     H5          1.4318  119.38  179.73  120.76   1.0878
 IC    N1      C5      *C6     H6          1.3782  122.78 -178.04  121.26   1.0873
 IC    C1'     C3'     *C2'    O2'         1.5198  100.83 -121.43  112.64   1.4237
 IC    H2'     O2'     C2'     C3'         0.9640  105.10 -120.35  112.64   1.5200
 IC    O4'     C2'     *C1'    H1'         1.4213  107.25 -112.85  107.97   1.1150
 IC    C1'     C3'     *C2'    H2''        1.5198  100.83  116.88  108.80   1.1107
 IC    C2'     C4'     *C3'    H3'         1.5200  102.40  115.44  107.82   1.1136
 IC    C3'     O4'     *C4'    H4'         1.5378  104.93 -114.45  108.43   1.1100
 IC    C4'     O5'     *C5'    H5'         1.5499  114.55 -119.70  107.28   1.1099
 IC    C4'     O5'     *C5'    H5''        1.5499  114.55  123.87  110.91   1.1143
PATC  FIRS NONE LAST NONE

RESI UDP         -3.00  ! uracil diphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature

GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                                 O4
ATOM C1'  CN7B    0.16  !                                 ||
ATOM H1'  HN7     0.09  !                                 C4    H3
GROUP                   !                                /  \  /
ATOM N1   NN2B   -0.34  !                            H5-C5   N3
ATOM C6   CN3     0.20  !                               ||   |
ATOM H6   HN3     0.14  !                            H6-C6   C2
ATOM C2   CN1T    0.55  !                                \  / \\
ATOM O2   ON1    -0.45  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
ATOM H5   HN3     0.10  !                |      |     \     / \  
GROUP                   !               O2A    H5''   C3'--C2' H1'  
ATOM C2'  CN7B    0.14  !                            / \   / \
ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
ATOM O2'  ON5    -0.66  !                          |       |
ATOM H2'  HN5     0.43  !                         H3T     H2'
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.10
ATOM O1B  ON3    -0.90
ATOM O2B  ON3    -0.90
ATOM O3B  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6        N3   H3
BOND C2   O2        C4   O4        C5   H5        C6   H6        
BOND C1'  N1        C1'  C2'       
BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   O4

DONO H3   N3   
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B

 IC    C5'     O5'     PA      O1A         1.4452  119.36  179.48  102.79   1.4826
 IC    C5'     O5'     PA      O2A         1.4452  119.36   56.33  102.34   1.4877
 IC    O1A     O2A     *PA     O3A         1.4826  118.27 -143.92  114.07   1.5245
 IC    O5'     PA      O3A     PB          1.6044   97.44 -169.69  121.80   1.6100
 IC    PA      O3A     PB      O1B         1.5245  121.80  -34.02  110.11   1.5260
 IC    O3A     PB      *O1B    O2B         2.5710   36.02 -113.19   34.02   2.5317
 IC    O3A     PB      *O1B    O3B         2.5710   36.02  118.21   32.97   2.5592
 IC    PA      O5'     C5'     C4'         1.6044  119.36  -88.66  111.34   1.5371
 IC    O5'     C5'     C4'     C3'         1.4452  111.34  -23.34  117.61   1.5455
 IC    C5'     C4'     C3'     O3'         1.5371  117.61  -33.43  114.93   1.4337
 IC    H3T     O3'     C3'     C4'         0.9846  102.14   54.81  114.93   1.5455
 IC    O4'     C3'     *C4'    C5'         1.4644  104.98 -123.57  117.61   1.5371
 IC    C2'     C4'     *C3'    O3'         1.5125  102.66  121.49  114.93   1.4337
 IC    C4'     C3'     C2'     C1'         1.5455  102.66   34.63  102.26   1.5293
 IC    C3'     C2'     C1'     N1          1.5125  102.26   95.97  112.35   1.4894
 IC    O4'     C1'     N1      C2          1.4185  111.08 -145.64  119.10   1.3727
 IC    C1'     C2      *N1     C6          1.4894  119.10  177.16  120.97   1.3801
 IC    C2      N1      C6      C5          1.3727  120.97    1.27  122.77   1.3425
 IC    C6      N1      C2      N3          1.3801  120.97   -2.01  114.96   1.3711
 IC    N1      N3      *C2     O2          1.3727  114.96 -179.99  121.59   1.2266
 IC    N1      C2      N3      C4          1.3727  114.96    1.86  127.49   1.3787
 IC    C5      N3      *C4     O4          1.4327  114.41 -179.82  119.58   1.2291
 IC    C2      C4      *N3     H3          1.3711  127.49 -177.70  117.20   0.9968
 IC    C4      C6      *C5     H5          1.4327  119.37 -179.83  121.52   1.0872
 IC    N1      C5      *C6     H6          1.3801  122.77 -179.58  122.06   1.0949
 IC    C1'     C3'     *C2'    O2'         1.5293  102.26 -118.27  110.08   1.4181
 IC    H2'     O2'     C2'     C3'         0.9661  107.60   32.30  110.08   1.5125
 IC    O4'     C2'     *C1'    H1'         1.4185  108.13 -113.95  108.75   1.1149
 IC    C1'     C3'     *C2'    H2''        1.5293  102.26  119.74  111.10   1.1107
 IC    C2'     C4'     *C3'    H3'         1.5125  102.66 -117.67  107.54   1.1142
 IC    C3'     O4'     *C4'    H4'         1.5455  104.98 -113.44  108.49   1.1124
 IC    C4'     O5'     *C5'    H5'         1.5371  111.34 -120.03  107.51   1.1101
 IC    C4'     O5'     *C5'    H5''        1.5371  111.34  123.36  112.67   1.1172
PATC  FIRS NONE LAST NONE

RESI UTP         -4.00  ! uracil triphosphate, adm jr.
                        ! atom names correspond to pdb nomenclature
                        !
GROUP                   !
ATOM C4'  CN7     0.16  !                              
ATOM H4'  HN7     0.09  !                              
ATOM O4'  ON6B   -0.50  !                                 O4
ATOM C1'  CN7B    0.16  !                                 ||
ATOM H1'  HN7     0.09  !                                 C4    H3
GROUP                   !                                /  \  /
ATOM N1   NN2B   -0.34  !                            H5-C5   N3
ATOM C6   CN3     0.20  !                               ||   |
ATOM H6   HN3     0.14  !                            H6-C6   C2
ATOM C2   CN1T    0.55  !                                \  / \\
ATOM O2   ON1    -0.45  !                                 N1   O2
ATOM N3   NN2U   -0.46  !                                  \
ATOM H3   HN2     0.36  !                                   \
ATOM C4   CN1     0.53  !               O1A    H5' H4'  O4'  \
ATOM O4   ON1    -0.48  !                |      |    \ /   \  \
ATOM C5   CN3    -0.15  !          O3A--PA-O5'-C5'---C4'    C1'
ATOM H5   HN3     0.10  !                |      |     \     / \  
GROUP                   !               O2A    H5''   C3'--C2' H1'  
ATOM C2'  CN7B    0.14  !                            / \   / \
ATOM H2'' HN7     0.09  !                         O3' H3' O2' H2''
ATOM O2'  ON5    -0.66  !                          |       |
ATOM H2'  HN5     0.43  !                         H3T     H2'
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM PA   P       1.50
ATOM O1A  ON3    -0.82
ATOM O2A  ON3    -0.82
ATOM O3A  ON2    -0.74
ATOM PB   P3      1.50
ATOM O1B  ON3    -0.82
ATOM O2B  ON3    -0.82
ATOM O3B  ON2    -0.86 ! charge adjusted to yield total triP of -4.0
ATOM PG   P3      1.10
ATOM O1G  ON3    -0.90
ATOM O2G  ON3    -0.90
ATOM O3G  ON3    -0.90

BOND N1   C2        C2   N3        N3   C4        C4   C5
BOND C5   C6        N1   C6        N3   H3
BOND C2   O2        C4   O4        C5   H5        C6   H6        
BOND C1'  N1        C1'  C2'       
BOND O5'  C5'       O5'  PA        PA   O1A       PA   O2A       PA   O3A
BOND O3A  PB        PB   O1B       PB   O2B       PB   O3B       O3B  PG
BOND PG   O1G       PG   O2G       PG   O3G
BOND C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'       O3'  H3T
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''

IMPR C2   N1   N3   O2        C4   N3   C5   O4

DONO H3   N3   
DONO H2'  O2'
ACCE O2   C2
ACCE O4   C4
ACCE O1A  PA
ACCE O2A  PA
ACCE O3A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O2B
ACCE O1B
ACCE O3B
ACCE O3G
ACCE O2G
ACCE O2G

 IC    C5'     O5'     PA      O1A         1.4436  123.18   -4.19  104.07   1.4896
 IC    C5'     O5'     PA      O2A         1.4436  123.18 -128.27  105.09   1.4796
 IC    O1A     O2A     *PA     O3A         1.4896  117.48 -144.86  112.24   1.5060
 IC    O5'     PA      O3A     PB          1.5927   93.29 -154.64  107.67   1.5942
 IC    PA      O3A     PB      O1B         1.5060  107.67   68.87  110.34   1.5347
 IC    O3A     PB      *O1B    O2B         2.5686   35.59 -129.92   31.09   2.6307
 IC    O3A     PB      *O1B    O3B         2.5686   35.59  104.59   36.93   2.6213
 IC    O3A     PB      O3B     PG          1.5942   96.09 -119.52  151.10   1.6742
 IC    PA      O3B     PG      O1G         3.8152  152.27 -123.23  106.71   1.5270
 IC    O3B     PG      *O1G    O2G         2.5699   38.61 -114.53   33.79   2.5404
 IC    O3B     PG      *O1G    O3G         2.5699   38.61  116.98   33.14   2.5609
 IC    PA      O5'     C5'     C4'         1.5927  123.18  -89.06  115.64   1.5507
 IC    O5'     C5'     C4'     C3'         1.4436  115.64   49.18  119.96   1.5360
 IC    O5'     C5'     C4'     C3'         1.4436  115.64   49.18  119.96   1.5360
 IC    C5'     C4'     C3'     O3'         1.5507  119.96   74.41  110.78   1.4388
 IC    H3T     O3'     C3'     C4'         0.9867  102.53 -104.57  110.78   1.5360
 IC    O4'     C3'     *C4'    C5'         1.4601  104.58 -126.54  119.96   1.5507
 IC    C2'     C4'     *C3'    O3'         1.5122  101.75 -122.80  110.78   1.4388
 IC    C4'     C3'     C2'     C1'         1.5360  101.75   39.19  100.86   1.5243
 IC    C3'     C2'     C1'     N1          1.5122  100.86   92.81  111.95   1.4916
 IC    O4'     C1'     N1      C2          1.4265  111.16 -147.40  118.55   1.3742
 IC    C1'     C2      *N1     C6          1.4916  118.55  172.02  119.98   1.3897
 IC    C2      N1      C6      C5          1.3742  119.98   10.83  122.70   1.3455
 IC    C6      N1      C2      N3          1.3897  119.98  -10.49  115.19   1.3703
 IC    N1      N3      *C2     O2          1.3742  115.19  175.89  121.40   1.2306
 IC    N1      C2      N3      C4          1.3742  115.19    3.36  127.40   1.3788
 IC    C5      N3      *C4     O4          1.4296  114.47 -173.68  118.19   1.2356
 IC    C2      C4      *N3     H3          1.3703  127.40 -160.74  114.36   0.9907
 IC    C4      C6      *C5     H5          1.4296  119.28 -179.18  121.12   1.0872
 IC    N1      C5      *C6     H6          1.3897  122.70 -177.32  120.53   1.0892
 IC    C1'     C3'     *C2'    O2'         1.5243  100.86 -119.14  109.80   1.4201
 IC    H2'     O2'     C2'     C3'         0.9693  100.49  -35.37  109.80   1.5122
 IC    O4'     C2'     *C1'    H1'         1.4265  108.04 -114.27  108.39   1.1130
 IC    C1'     C3'     *C2'    H2''        1.5243  100.86  117.99  110.14   1.1147
 IC    C2'     C4'     *C3'    H3'         1.5122  101.75  114.23  109.76   1.1048
 IC    C3'     O4'     *C4'    H4'         1.5360  104.58 -111.39  105.32   1.1094
 IC    C4'     O5'     *C5'    H5'         1.5507  115.64 -120.26  107.77   1.1109
 IC    C4'     O5'     *C5'    H5''        1.5507  115.64  123.55  110.93   1.1137
PATC  FIRS NONE LAST NONE


PRES 5DP         -3.00  ! patch to create 5' diphosphate on nucleotides, jjp1/adm jr.
                        ! as in ADP, use in generate statement
GROUP
ATOM C5'  CN8    -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.62
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O13  ON2    -0.74
ATOM P2   P3      1.10
ATOM O21  ON3    -0.90
ATOM O22  ON3    -0.90
ATOM O23  ON3    -0.90

BOND P    O13       O13   P2       
BOND P2   O21       P2    O22      P2   O23
ACCE O13
ACCE O21
ACCE O22
ACCE O23
IC C5'  O5'  P    O13    0.0000  000.00  180.0   000.00   0.0000
IC O5'  P    O13  P2     0.0000  000.00  180.0   000.00   0.0000
IC P    O13  P2   O21    0.0000  000.00  180.0   000.00   0.0000
IC P    O13  P2   O22    0.0000  000.00   60.0   000.00   0.0000
IC P    O13  P2   O23    0.0000  000.00  -60.0   000.00   0.0000
PATC  FIRS NONE LAST NONE

!atom nomenclature consisent with PDB, 2015

RESI NAD         -1.00  ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
GROUP                   !
ATOM C4B  CN7     0.16  !                H61A  H62A
ATOM H4B  HN7     0.09  !                   \  /
ATOM O4B  ON6B   -0.50  !                   N6A
ATOM C1B  CN7B    0.16  !                    |
ATOM H1B  HN7     0.09  !                   C6A
GROUP                   !                  //  \
ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
ATOM H8A  HN3     0.12  !                 / \\ /     \
ATOM N9A  NN2    -0.05  !              H2A  N3A       \
                        !                              \
ATOM N1A  NN3A   -0.74  !                               \
ATOM C2A  CN4     0.50  !                                \
ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
ATOM N6A  NN1    -0.77  !   \                     / \   / \
ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
ATOM H62A HN1     0.38  !     \                 |       |
GROUP                   !      \              HO3A     HO2A
ATOM C2B  CN7B    0.14  !       \                        H71N
ATOM H2B  HN7     0.09  !        \                          \ 
ATOM O2B  ON5    -0.66  !         \                    H72N-N7N    N41N
ATOM HO2A HN5     0.43  !          \                          \     |
GROUP                   !           \                         C7N  C4N
ATOM C3B  CN7     0.14  !            \                        / \  /  \
ATOM H3B  HN7     0.09  !             \                    O7N  C3N  C5N-H5N
ATOM O3B  ON5    -0.66  !              \                          |    |
ATOM HO3A HN5     0.43  !               \ H51N H4D O4D       H2N-C2N C6N-HN6
GROUP                   !                \ |    \ /   \            \+ /   
ATOM C5B  CN8B   -0.08  !                 C5D --C4D    C1D ---------N1N
ATOM H51A HN8     0.09  !                  |     \     / \
ATOM H52A HN8     0.09  !                 H52N   C3D -C2D H1D 
ATOM PA   P       1.50  !                       / \   / \
ATOM O1A  ON3    -0.82  !                   O3D  H3D O2D H2D 
ATOM O2A  ON3    -0.82  !                    |       |
ATOM O5B  ON2    -0.62  !                   HO3N    HO2N
ATOM O3   ON2    -0.68
ATOM PN   P       1.50
ATOM O1N  ON3    -0.82
ATOM O2N  ON3    -0.82
ATOM O5D  ON2    -0.62
ATOM C5D  CN8B   -0.08
ATOM H51N HN8     0.09
ATOM H52N HN8     0.09 
GROUP                  
ATOM C2D  CN7B    0.14 
ATOM H2D  HN7     0.09 
ATOM O2D  ON5    -0.66
ATOM HO2N HN5     0.43
GROUP
ATOM C3D  CN7     0.14
ATOM H3D  HN7     0.09
ATOM O3D  ON5    -0.66
ATOM HO3N HN5     0.43
GROUP
ATOM C1D  CN7B    0.16
ATOM H1D  HN7     0.09
ATOM C4D  CN7     0.16
ATOM H4D  HN7     0.09
ATOM O4D  ON6B   -0.50
GROUP                  
ATOM N1N  NN2    -0.07
ATOM C6N  CN3B    0.16
ATOM HN6  HN3B    0.19
ATOM C5N  CN3    -0.10
ATOM H5N  HN3B    0.16
ATOM C4N  CN3A   -0.05
ATOM H41N HN3B    0.16 !H4N in official nomenclature
ATOM C3N  CN3     0.05 
ATOM C2N  CN3B    0.18
ATOM H2N  HN3B    0.16
ATOM C7N  CN1A    0.68 
ATOM O7N  ON1    -0.40 
ATOM N7N  NN1    -0.82
ATOM H71N HN1     0.34  ! trans to amide O
ATOM H72N HN1     0.36  ! cis to amide O

BOND N1A  C2A       N3A  C4A       C5A  C6A
BOND C6A  N6A       C5A  N7A       C8A  N9A
BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  HO2A      C2B  H2B 
BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
BOND C3N  C4N       C5N  C6N
BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
BOND N7N  H72N      C4N  H41N      C5N  H5N       C6N  HN6
DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
! adenine impropers
IMPR N6A  C6A  H61A H62A     C6A   N1A   C5A  N6A       
! amide impropers
IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N 
IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
! ring hydrogen impropers
IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
DONO H61A N6A
DONO H62A N6A
DONO HO2A O2B 
DONO HO3A O3B 
ACCE N1A
ACCE N3A
ACCE N7A
ACCE O4B 
ACCE O2B 
ACCE O3B 
ACCE O5B 
ACCE O1A  PA
ACCE O2A  PA
ACCE O3
ACCE O1N  PN
ACCE O2N  PN
ACCE O5D 
ACCE O4D 
ACCE O3D 
ACCE O2D 
ACCE O7N
DONO HO2N O2D 
DONO HO3N O3D 
DONO H71N N7N
DONO H72N N7N

IC O4B   C4B   C5B   O5B    1.4602  109.06  141.71  112.09   1.4439
IC O4B   C5B   *C4B  C3B    1.4602  109.06 -116.95  116.13   1.5393
IC C3B   C5B   *C4B  H4B    1.5393  116.13 -123.66  110.37   1.1118
IC C5B   C4B   O4B   C1B    1.5373  109.06 -136.33  109.65   1.4148
IC C4B   O4B   C1B   N9A    1.4602  109.65 -135.81  111.11   1.4598
IC N9A   O4B   *C1B  C2B    1.4598  111.11  122.68  107.19   1.5091
IC N9A   O4B   *C1B  H1B    1.4598  111.11 -120.43  106.09   1.1157
IC O4B   C1B   N9A   C4A    1.4148  111.11 -132.21  126.91   1.3718
IC C4A   C1B   *N9A  C8A    1.3718  126.91 -179.77  127.02   1.3735
IC C1B   N9A   C4A   C5A    1.4598  126.91 -179.47  105.60   1.3834
IC C5A   N9A   *C4A  N3A    1.3834  105.60 -179.98  127.70   1.3425
IC N9A   C4A   C5A   C6A    1.3718  105.60  179.90  116.93   1.4100
IC C6A   C4A   *C5A  N7A    1.4100  116.93 -179.96  110.88   1.3888
IC N7A   N9A   *C8A  H8A    1.3106  113.69  179.35  121.11   1.0928
IC C4A   C5A   C6A   N1A    1.3834  116.93   -0.07  117.90   1.3546
IC N1A   C5A   *C6A  N6A    1.3546  117.90  179.83  123.29   1.3450
IC C5A   C6A   N1A   C2A    1.4100  117.90    0.12  118.20   1.3359
IC N3A   N1A   *C2A  H2A    1.3354  129.50  179.91  115.36   1.0937
IC C5A   C6A   N6A   H61A   1.4100  123.29 -178.42  117.49   0.9946
IC H61A  C6A   *N6A  H62A   0.9946  117.49  176.18  120.81   0.9965
IC C3B   C1B   *C2B  O2B    1.5071  101.20  117.08  111.89   1.4144
IC C3B   C1B   *C2B  H2B    1.5071  101.20 -117.38  111.86   1.1141
IC C1B   C2B   O2B   HO2A   1.5091  111.89  178.91  108.27   0.9632
IC C2B   C4B   *C3B  O3B    1.5071  102.42  118.21  111.98   1.4364
IC C2B   C4B   *C3B  H3B    1.5071  102.42 -117.88  107.58   1.1121
IC C4B   C3B   O3B   HO3A   1.5393  111.98   53.77  108.82   0.9987
IC C3B   C4B   C5B   O5B    1.5393  116.13   24.76  112.09   1.4439
IC O5B   C4B   *C5B  H52A   1.4439  112.09 -118.16  109.00   1.1133
IC H52A  C4B   *C5B  H51A   1.1133  109.00 -114.98  109.51   1.1161
IC C4B   C5B   O5B   PA     1.5373  112.09   94.39  121.28   1.5826
IC C5B   O5B   PA    O3     1.4439  121.28  148.70   94.54   1.4969
IC O3    O5B   *PA   O1A    1.4969   94.54 -121.80  106.23   1.4772
IC O1A   O5B   *PA   O2A    1.4772  106.23 -125.48  100.49   1.4822
IC O5B   PA    O3    PN     1.5826   94.54 -171.26  103.25   1.5079
IC PA    O3    PN    O5D    1.4969  103.25 -156.08   92.59   1.5791
IC O5D   O3    *PN   O1N    1.5791   92.59 -108.10  112.08   1.4709
IC O1N   O3    *PN   O2N    1.4709  112.08 -147.35  119.96   1.4872
IC O3    PN    O5D   C5D    1.5079   92.59  169.85  121.25   1.4424
IC PN    O5D   C5D   C4D    1.5791  121.25 -120.85  113.63   1.5461
IC C4D   O5D   *C5D  H51N   1.5461  113.63 -118.98  107.36   1.1130
IC H51N  O5D   *C5D  H52N   1.1130  107.36 -116.76  113.02   1.1173
IC O5D   C5D   C4D   O4D    1.4424  113.63  -49.73  112.77   1.4709
IC O4D   C5D   *C4D  C3D    1.4709  112.77  124.54  119.31   1.5563
IC O4D   C5D   *C4D  H4D    1.4709  112.77 -115.70  107.56   1.1116
IC C5D   C4D   C3D   C2D    1.5461  119.31 -156.53   99.76   1.5184
IC C2D   C4D   *C3D  O3D    1.5184   99.76  119.65  119.67   1.4380
IC C2D   C4D   *C3D  H3D    1.5184   99.76 -115.32  107.95   1.1119
IC C4D   C3D   C2D   C1D    1.5563   99.76   43.53  100.45   1.5351
IC C1D   C3D   *C2D  O2D    1.5351  100.45  123.80  111.51   1.4145
IC C1D   C3D   *C2D  H2D    1.5351  100.45 -114.84  109.59   1.1136
IC C3D   C2D   O2D   HO2N   1.5184  111.51  -13.38  103.51   0.9747
IC C4D   C3D   O3D   HO3N   1.5563  119.67   42.59  111.67   0.9972
IC O4D   C2D   *C1D  N1N    1.4197  103.46  122.07  115.99   1.5110
IC O4D   C2D   *C1D  H1D    1.4197  103.46 -113.32  108.74   1.1122
IC C2D   C1D   N1N   C2N    1.5351  115.99   48.31  121.57   1.3422
IC C2N   C1D   *N1N  C6N    1.3422  121.57 -175.31  121.05   1.3474
IC C1D   N1N   C6N   C5N    1.5110  121.05  177.97  122.74   1.3691
IC C5N   N1N   *C6N  HN6    1.3691  122.74 -171.45  116.89   1.0961
IC N1N   C6N   C5N   C4N    1.3474  122.74   -3.94  119.48   1.3753
IC C4N   C6N   *C5N  H5N    1.3753  119.48 -170.98  120.63   1.0956
IC C6N   C5N   C4N   C3N    1.3691  119.48    1.56  118.55   1.3864
IC C3N   C5N   *C4N  H41N   1.3864  118.55 -175.37  120.26   1.0910
IC C3N   N1N   *C2N  H2N    1.3745  123.21  178.08  117.05   1.0911
IC C2N   C4N   *C3N  C7N    1.3745  118.63 -178.85  118.88   1.5091
IC C4N   C3N   C7N   N7N    1.3864  118.88   23.83  117.95   1.3519
IC N7N   C3N   *C7N  O7N    1.3519  117.95  175.54  118.43   1.2254
IC C3N   C7N   N7N   H71N   1.5091  117.95  160.64  114.22   0.9962
IC H71N  C7N   *N7N  H72N   0.9962  114.22 -140.75  118.52   1.0129
PATCH FIRST NONE LAST NONE   

RESI NAI         -2.00  ! reduced nicotinamide adenine dinucleotide, NADH, jjp1/adm jr.
                        ! some PDB files use NAD for NADH
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM C4B  CN7     0.16  !                H61A  H62A
ATOM H4B  HN7     0.09  !                   \  /
ATOM O4B  ON6B   -0.50  !                   N6A
ATOM C1B  CN7B    0.16  !                    |
ATOM H1B  HN7     0.09  !                   C6A
GROUP                   !                  //  \
ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
ATOM H8A  HN3     0.12  !                 / \\ /     \
ATOM N9A  NN2    -0.05  !              H2A  N3A       \
                        !                              \
ATOM N1A  NN3A   -0.74  !                               \
ATOM C2A  CN4     0.50  !                                \
ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
ATOM N6A  NN1    -0.77  !   \                     / \   / \
ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
ATOM H62A HN1     0.38  !     \                 |       |
GROUP                   !      \              HO3A     HO2A
ATOM C2B  CN7B    0.14  !       \                        H71N
ATOM H2B  HN7     0.09  !        \                          \
ATOM O2B  ON5    -0.66  !         \                    H72N-N7N  H41NH42N
ATOM HO2A HN5     0.43  !          \                          \    \ /
GROUP                   !           \                         C7N  C4N
ATOM C3B  CN7     0.14  !            \                        / \  /  \
ATOM H3B  HN7     0.09  !             \                    O7N  C3N  C5N-H5N
ATOM O3B  ON5    -0.66  !              \                          |    |
ATOM HO3A HN5     0.43  !               \ H51N H4D O4D       H2N-C2N C6N-HN6
GROUP                   !                \ |    \ /   \            \  /
ATOM C5B  CN8B   -0.08  !                 C5D --C4D    C1D ---------N1N
ATOM H51A HN8     0.09  !                  |     \     / \
ATOM H52A HN8     0.09  !                 H52N   C3D -C2D H1D 
ATOM PA   P       1.50  !                       / \   / \
ATOM O1A  ON3    -0.82  !                   O3D  H3D O2D H2D 
ATOM O2A  ON3    -0.82  !                    |       |
ATOM O5B  ON2    -0.62  !                   HO3N    HO2N
ATOM O3   ON2    -0.68
ATOM PN   P       1.50
ATOM O1N  ON3    -0.82
ATOM O2N  ON3    -0.82
ATOM O5D  ON2    -0.62
ATOM C5D  CN8B   -0.08
ATOM H51N HN8     0.09
ATOM H52N HN8     0.09
GROUP
ATOM C2D  CN7B    0.14
ATOM H2D  HN7     0.09
ATOM O2D  ON5    -0.66
ATOM HO2N HN5     0.43
GROUP
ATOM C3D  CN7     0.14
ATOM H3D  HN7     0.09
ATOM O3D  ON5    -0.66
ATOM HO3N HN5     0.43
GROUP
ATOM C1D  CN7B    0.16
ATOM H1D  HN7     0.09
ATOM C4D  CN7     0.16
ATOM H4D  HN7     0.09
ATOM O4D  ON6B   -0.50
GROUP
ATOM N1N  NN2    -0.27 !N2
ATOM C6N  CN3C   -0.06 !C3
ATOM HN6  HN6     0.17 !H4
ATOM C5N  CN3    -0.18 !C5
ATOM H5N  HN6     0.14 !H6
ATOM C4N  CN8    -0.28 !C7
ATOM H41N HN8     0.09 !H8
ATOM H42N HN8     0.09 !H17
ATOM C3N  CN3     0.36 !C9
ATOM C2N  CN3C   -0.10 !C10
ATOM H2N  HN6     0.14 !H11
ATOM C7N  CN1A    0.55 !C12
ATOM O7N  ON1    -0.51 !O13
ATOM N7N  NN1    -0.72 !N14
ATOM H71N HN1     0.26 !H15  ! trans to amide O
ATOM H72N HN1     0.32 !H16  ! cis to amide O

BOND N1A  C2A       N3A  C4A       C5A  C6A
BOND C6A  N6A       C5A  N7A       C8A  N9A
BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
DOUBLE  C6A  N1A      C2A  N3A      C4A  C5A      N7A  C8A
BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  HO2A      C2B  H2B 
BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
BOND C3N  C4N       C4N  C5N       C6N  N1N
BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
BOND N7N  H72N      C4N  H41N      C4N  H42N      C5N  H5N       C6N  HN6
DOUBLE  C2N  C3N      C5N  C6N
! adenine impropers
IMPR N6A  C6A  H61A H62A     C6A  N1A  C5A  N6A       
! amide impropers
IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N
IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
! ring hydrogen impropers
IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
DONO H61A N6A
DONO H62A N6A
DONO HO2A O2B 
DONO HO3A O3B 
ACCE N1A
ACCE N3A
ACCE N7A
ACCE O4B 
ACCE O2B 
ACCE O3B 
ACCE O5B 
ACCE O1A  PA
ACCE O2A  PA
ACCE O3
ACCE O1N  PN
ACCE O2N  PN
ACCE O5D 
ACCE O4D 
ACCE O3D 
ACCE O2D 
ACCE O7N
DONO HO2N O2D 
DONO HO3N O3D 
DONO H71N N7N
DONO H72N N7N

IC O4B   C4B   C5B   O5B    1.4592  109.88  127.15  112.06   1.4436
IC O4B   C5B   *C4B  C3B    1.4592  109.88 -119.04  118.31   1.5383
IC C3B   C5B   *C4B  H4B    1.5383  118.31 -123.09  109.39   1.1113
IC C5B   C4B   O4B   C1B    1.5404  109.88 -146.22  109.49   1.4139
IC C4B   O4B   C1B   N9A    1.4592  109.49 -127.93  110.13   1.4603
IC N9A   O4B   *C1B  C2B    1.4603  110.13  122.48  107.68   1.5154
IC N9A   O4B   *C1B  H1B    1.4603  110.13 -120.39  106.05   1.1153
IC O4B   C1B   N9A   C4A    1.4139  110.13 -117.96  127.68   1.3725
IC C4A   C1B   *N9A  C8A    1.3725  127.68  177.86  126.28   1.3734
IC C1B   N9A   C4A   C5A    1.4603  127.68  178.99  105.54   1.3840
IC C5A   N9A   *C4A  N3A    1.3840  105.54  179.70  127.97   1.3431
IC N9A   C4A   C5A   C6A    1.3725  105.54 -179.81  117.00   1.4096
IC C6A   C4A   *C5A  N7A    1.4096  117.00  179.47  111.00   1.3884
IC N7A   N9A   *C8A  H8A    1.3113  113.83  179.81  121.02   1.0926
IC C4A   C5A   C6A   N1A    1.3840  117.00   -0.40  118.02   1.3545
IC N1A   C5A   *C6A  N6A    1.3545  118.02  179.70  123.12   1.3454
IC C5A   C6A   N1A   C2A    1.4096  118.02    0.07  118.03   1.3365
IC N3A   N1A   *C2A  H2A    1.3345  129.58  179.79  115.39   1.0936
IC C5A   C6A   N6A   H61A   1.4096  123.12 -178.46  117.57   0.9939
IC H61A  C6A   *N6A  H62A   0.9939  117.57  176.57  120.42   0.9965
IC C3B   C1B   *C2B  O2B    1.5103  102.02  117.99  111.67   1.4134
IC C3B   C1B   *C2B  H2B    1.5103  102.02 -117.32  112.17   1.1132
IC C1B   C2B   O2B   HO2A   1.5154  111.67 -163.97  107.58   0.9678
IC C2B   C4B   *C3B  O3B    1.5103  101.80  116.77  110.83   1.4344
IC C2B   C4B   *C3B  H3B    1.5103  101.80 -119.13  108.74   1.1128
IC C4B   C3B   O3B   HO3A   1.5383  110.83   54.91  107.95   0.9983
IC C3B   C4B   C5B   O5B    1.5383  118.31    8.12  112.06   1.4436
IC O5B   C4B   *C5B  H52A   1.4436  112.06 -118.83  109.45   1.1125
IC H52A  C4B   *C5B  H51A   1.1125  109.45 -115.45  109.09   1.1167
IC C4B   C5B   O5B   PA     1.5404  112.06  103.36  120.31   1.5832
IC C5B   O5B   PA    O3     1.4436  120.31  176.42   94.39   1.5047
IC O3    O5B   *PA   O1A    1.5047   94.39 -120.03  104.05   1.4804
IC O1A   O5B   *PA   O2A    1.4804  104.05 -123.95  100.78   1.4839
IC O5B   PA    O3    PN     1.5832   94.39 -178.56  100.47   1.5104
IC PA    O3    PN    O5D    1.5047  100.47 -170.27   94.47   1.5770
IC O5D   O3    *PN   O1N    1.5770   94.47 -107.91  114.74   1.4790
IC O1N   O3    *PN   O2N    1.4790  114.74 -147.43  117.97   1.4863
IC O3    PN    O5D   C5D    1.5104   94.47 -177.92  120.58   1.4431
IC PN    O5D   C5D   C4D    1.5770  120.58 -122.07  113.80   1.5459
IC C4D   O5D   *C5D  H51N   1.5459  113.80 -119.75  107.60   1.1121
IC H51N  O5D   *C5D  H52N   1.1121  107.60 -117.14  112.75   1.1171
IC O5D   C5D   C4D   O4D    1.4431  113.80  -64.50  112.96   1.4660
IC O4D   C5D   *C4D  C3D    1.4660  112.96  127.07  120.95   1.5529
IC O4D   C5D   *C4D  H4D    1.4660  112.96 -113.76  106.56   1.1112
IC C5D   C4D   C3D   C2D    1.5459  120.95 -160.75   99.47   1.5206
IC C2D   C4D   *C3D  O3D    1.5206   99.47  121.69  119.59   1.4385
IC C2D   C4D   *C3D  H3D    1.5206   99.47 -114.49  107.55   1.1109
IC C4D   C3D   C2D   C1D    1.5529   99.47   42.83  101.15   1.5416
IC C1D   C3D   *C2D  O2D    1.5416  101.15  126.12  112.03   1.4127
IC C1D   C3D   *C2D  H2D    1.5416  101.15 -113.62  108.86   1.1129
IC C3D   C2D   O2D   HO2N   1.5206  112.03  -33.33  102.61   0.9714
IC C4D   C3D   O3D   HO3N   1.5529  119.59   46.10  109.78   0.9937
IC O4D   C2D   *C1D  N1N    1.4246  103.98  123.05  117.48   1.5125
IC O4D   C2D   *C1D  H1D    1.4246  103.98 -113.06  108.45   1.1101
IC C2D   C1D   N1N   C2N    1.5416  117.48   21.65  124.87   1.3754
IC C2N   C1D   *N1N  C6N    1.3754  124.87 -167.67  121.17   1.3759
IC C1D   N1N   C6N   C5N    1.5125  121.17  126.10  120.49   1.3282
IC C5N   N1N   *C6N  HN6    1.3282  120.49 -173.51  119.76   1.0882
IC N1N   C6N   C5N   C4N    1.3759  120.49   26.68  121.42   1.5170
IC C4N   C6N   *C5N  H5N    1.5170  121.42 -140.43  114.25   1.0930
IC C6N   C5N   C4N   C3N    1.3282  121.42   -4.55  109.89   1.5374
IC C3N   C5N   *C4N  H41N   1.5374  109.89  127.11  113.12   1.1052
IC C3N   C5N   *C4N  H42N   1.5374  109.89 -116.77  106.76   1.1126
IC C3N   N1N   *C2N  H2N    1.3514  121.98 -179.23  117.66   1.0902
IC C2N   C4N   *C3N  C7N    1.3514  119.70  156.64  121.99   1.5300
IC C4N   C3N   C7N   N7N    1.5374  121.99   23.57  115.90   1.3567
IC N7N   C3N   *C7N  O7N    1.3567  115.90  178.78  122.04   1.2305
IC C3N   C7N   N7N   H71N   1.5300  115.90  162.43  114.68   0.9962
IC H71N  C7N   *N7N  H72N   0.9962  114.68 -141.25  117.82   1.0104
PATCH FIRST NONE LAST NONE

RESI NAP         -2.00  ! oxidized nicotinamide adenine dinucleotide, NADP+, adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM C4B  CN7     0.16  !                H61A  H62A
ATOM H4B  HN7     0.09  !                   \  /
ATOM O4B  ON6B   -0.50  !                   N6A
ATOM C1B  CN7B    0.16  !                    |
ATOM H1B  HN7     0.09  !                   C6A
GROUP                   !                  //  \
ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
ATOM H8A  HN3     0.12  !                 / \\ /     \
ATOM N9A  NN2    -0.05  !              H2A  N3A       \
                        !                              \
ATOM N1A  NN3A   -0.74  !                               \
ATOM C2A  CN4     0.50  !                                \
ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM C4A  CN5     0.43  !O5D PN-O3--PA-O5B -C5B -C4B    C1B
ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ O2N     O2A    H51A C3B -C2B  H1B
ATOM N6A  NN1    -0.77  !   \                     / \   / \
ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B
ATOM H62A HN1     0.38  !     \                |        |
GROUP                   !      \             HO3A O1X =P2B==O2X  (-)
ATOM C2B  CN7B    0.01  !       \                       |    H71N
ATOM H2B  HN7     0.09  !        \                HO2A-O3X    /
ATOM O2B  ON2    -0.62  !         \                    H72N-N7N    H41N
ATOM P2B  P       1.50  !          \                          \     |
ATOM O1X  ON3    -0.82  !           \                         C7N  C4N
ATOM O2X  ON3    -0.82  !            \                        / \  /  \
ATOM O3X  ON4    -0.68  !             \                    O7N  C3N  C5N-H5N
ATOM HO2A HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM C3B  CN7     0.14  !                \ H51N H4D O4D       H2N-C2N C6N-HN6
ATOM H3B  HN7     0.09  !                 \ |    \ /   \           \   /
ATOM O3B  ON5    -0.66  !                  C5D --C4D    C1D --------N1N
ATOM HO3A HN5     0.43  !                   |     \     / \
GROUP                   !                 H52N   C3D--C2D H1D 
ATOM C5B  CN8B   -0.08  !                        / \   / \  
ATOM H51A HN8     0.09  !                    O3D  H3D O2D H2D   
ATOM H52A HN8     0.09  !                     |       |
ATOM PA   P       1.50  !                    HO3N    HO2N   
ATOM O1A  ON3    -0.82  !
ATOM O2A  ON3    -0.82  !
ATOM O5B  ON2    -0.62  !
ATOM O3   ON2    -0.68
ATOM PN   P       1.50
ATOM O1N  ON3    -0.82
ATOM O2N  ON3    -0.82
ATOM O5D  ON2    -0.62
ATOM C5D  CN8B   -0.08
ATOM H51N HN8     0.09
ATOM H52N HN8     0.09 
GROUP                  
ATOM C2D  CN7B    0.14 
ATOM H2D  HN7     0.09 
ATOM O2D  ON5    -0.66
ATOM HO2N HN5     0.43
GROUP
ATOM C3D  CN7     0.14
ATOM H3D  HN7     0.09
ATOM O3D  ON5    -0.66
ATOM HO3N HN5     0.43
GROUP
ATOM C1D  CN7B    0.16
ATOM H1D  HN7     0.09
ATOM C4D  CN7     0.16
ATOM H4D  HN7     0.09
ATOM O4D  ON6B   -0.50
GROUP                  
ATOM N1N  NN2    -0.07
ATOM C6N  CN3B    0.16
ATOM HN6  HN3B    0.19
ATOM C5N  CN3    -0.10
ATOM H5N  HN3B    0.16
ATOM C4N  CN3A   -0.05
ATOM H41N HN3B    0.16 !H4N in official nomenclature
ATOM C3N  CN3     0.05 
ATOM C2N  CN3B    0.18
ATOM H2N  HN3B    0.16
ATOM C7N  CN1A    0.68 
ATOM O7N  ON1    -0.40 
ATOM N7N  NN1    -0.82
ATOM H71N HN1     0.34  ! trans to amide O
ATOM H72N HN1     0.36  ! cis to amide O

BOND N1A  C2A       N3A  C4A       C5A  C6A
BOND C6A  N6A       C5A  N7A       C8A  N9A
BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  P2B      C2B  H2B 
BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O2N
BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
BOND C3N  C4N       C5N  C6N
BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
BOND N7N  H72N      C4N  H41N      C5N  H5N       C6N  HN6
BOND P2B  O1X       P2B  O2X       P2B  O3X       O3X  HO2A
DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
! adenine impropers
IMPR N6A  C6A  H61A H62A     C6A  N1A  C5A  N6A
! amide impropers
IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N 
IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
! ring hydrogen impropers
IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
DONO H61A N6A
DONO H62A N6A
DONO HO2A O2B 
DONO HO3A O3B 
ACCE N1A
ACCE N3A
ACCE N7A
ACCE O4B 
ACCE O2B 
ACCE O3B 
ACCE O5B 
ACCE O1A  PA
ACCE O2A  PA
ACCE O3
ACCE O1N  PN
ACCE O2N  PN
ACCE O5D 
ACCE O4D 
ACCE O3D 
ACCE O2D 
ACCE O7N
DONO HO2N O2D 
DONO HO3N O3D 
DONO H71N N7N
DONO H72N N7N
DONO HO2A O3X 
ACCE O3X 
ACCE O1X 
ACCE O2X 
ACCE O2B 

IC O4B   C4B   C5B   O5B    1.4585  109.71  159.30  112.46   1.4473
IC O4B   C5B   *C4B  C3B    1.4585  109.71 -116.16  111.85   1.5464
IC C3B   C5B   *C4B  H4B    1.5464  111.85 -123.40  110.92   1.1115
IC C5B   C4B   O4B   C1B    1.5376  109.71 -108.48  108.78   1.4075
IC C4B   O4B   C1B   N9A    1.4585  108.78 -152.38  111.04   1.4568
IC N9A   O4B   *C1B  C2B    1.4568  111.04  121.73  107.16   1.5067
IC N9A   O4B   *C1B  H1B    1.4568  111.04 -121.01  106.15   1.1159
IC O4B   C1B   N9A   C4A    1.4075  111.04 -116.40  127.62   1.3704
IC C4A   C1B   *N9A  C8A    1.3704  127.62 -179.20  126.23   1.3719
IC C1B   N9A   C4A   C5A    1.4568  127.62 -179.21  105.46   1.3840
IC C5A   N9A   *C4A  N3A    1.3840  105.46 -179.98  128.09   1.3448
IC N9A   C4A   C5A   C6A    1.3704  105.46  179.01  116.94   1.4094
IC C6A   C4A   *C5A  N7A    1.4094  116.94 -179.45  111.14   1.3881
IC N7A   N9A   *C8A  H8A    1.3133  113.83  179.37  120.83   1.0924
IC C4A   C5A   C6A   N1A    1.3840  116.94   -0.02  118.16   1.3545
IC N1A   C5A   *C6A  N6A    1.3545  118.16 -179.37  122.98   1.3453
IC C5A   C6A   N1A   C2A    1.4094  118.16   -0.02  117.86   1.3367
IC N3A   N1A   *C2A  H2A    1.3332  129.71  178.74  115.38   1.0931
IC C5A   C6A   N6A   H61A   1.4094  122.98  174.65  117.36   0.9937
IC H61A  C6A   *N6A  H62A   0.9937  117.36 -169.69  119.66   0.9963
IC C3B   C1B   *C2B  O2B    1.5188  101.16  119.53  108.66   1.4398
IC C3B   C1B   *C2B  H2B    1.5188  101.16 -116.17  111.47   1.1163
IC C1B   C2B   O2B   P2B    1.5067  108.66  164.95  121.64   1.5624
IC C2B   O2B   P2B   O3X    1.4398  121.64 -145.91  106.75   1.5575
IC O3X   O2B   *P2B  O1X    1.5575  106.75  112.52  112.63   1.4723
IC O1X   O2B   *P2B  O2X    1.4723  112.63  135.09  111.70   1.4730
IC O2B   P2B   O3X   HO2A   1.5624  106.75  179.79  107.64   0.9606
IC C1B   C2B   O2B   HO2A   1.5067  108.66  140.65  141.83   3.3318
IC C2B   C4B   *C3B  O3B    1.5188  105.43  121.35  109.34   1.4348
IC C2B   C4B   *C3B  H3B    1.5188  105.43 -117.32  108.06   1.1126
IC C4B   C3B   O3B   HO3A   1.5464  109.34   51.56  106.53   0.9936
IC C3B   C4B   C5B   O5B    1.5464  111.85   43.14  112.46   1.4473
IC O5B   C4B   *C5B  H52A   1.4473  112.46 -119.04  108.58   1.1125
IC H52A  C4B   *C5B  H51A   1.1125  108.58 -116.00  109.43   1.1155
IC C4B   C5B   O5B   PA     1.5376  112.46   78.42  120.97   1.5816
IC C5B   O5B   PA    O3     1.4473  120.97  163.89   94.51   1.5036
IC O3    O5B   *PA   O1A    1.5036   94.51 -121.21  105.58   1.4802
IC O1A   O5B   *PA   O2A    1.4802  105.58 -126.12  102.35   1.4824
IC O5B   PA    O3    PN     1.5816   94.51 -169.65  103.13   1.5074
IC PA    O3    PN    O5D    1.5036  103.13 -158.88   92.67   1.5783
IC O5D   O3    *PN   O1N    1.5783   92.67 -107.59  112.84   1.4735
IC O1N   O3    *PN   O2N    1.4735  112.84 -147.96  119.72   1.4863
IC O3    PN    O5D   C5D    1.5074   92.67  167.85  121.64   1.4408
IC PN    O5D   C5D   C4D    1.5783  121.64 -119.99  113.59   1.5457
IC C4D   O5D   *C5D  H51N   1.5457  113.59 -118.85  107.20   1.1125
IC H51N  O5D   *C5D  H52N   1.1125  107.20 -116.81  112.97   1.1169
IC O5D   C5D   C4D   O4D    1.4408  113.59  -47.57  113.01   1.4697
IC O4D   C5D   *C4D  C3D    1.4697  113.01  124.91  119.42   1.5538
IC O4D   C5D   *C4D  H4D    1.4697  113.01 -115.69  107.46   1.1114
IC C5D   C4D   C3D   C2D    1.5457  119.42 -158.23   99.73   1.5185
IC C2D   C4D   *C3D  O3D    1.5185   99.73  119.79  119.52   1.4371
IC C2D   C4D   *C3D  H3D    1.5185   99.73 -115.26  108.09   1.1115
IC C4D   C3D   C2D   C1D    1.5538   99.73   43.62  100.48   1.5339
IC C1D   C3D   *C2D  O2D    1.5339  100.48  123.65  111.48   1.4144
IC C1D   C3D   *C2D  H2D    1.5339  100.48 -114.85  109.66   1.1132
IC C3D   C2D   O2D   HO2N   1.5185  111.48  -19.41  103.55   0.9759
IC C4D   C3D   O3D   HO3N   1.5538  119.52   41.07  112.08   0.9969
IC O4D   C2D   *C1D  N1N    1.4209  103.89  122.79  115.51   1.5069
IC O4D   C2D   *C1D  H1D    1.4209  103.89 -113.36  108.85   1.1120
IC C2D   C1D   N1N   C2N    1.5339  115.51   54.88  121.01   1.3424
IC C2N   C1D   *N1N  C6N    1.3424  121.01 -177.68  121.58   1.3487
IC C1D   N1N   C6N   C5N    1.5069  121.58 -178.88  122.67   1.3689
IC C5N   N1N   *C6N  HN6    1.3689  122.67 -174.63  117.18   1.0940
IC N1N   C6N   C5N   C4N    1.3487  122.67   -2.95  119.09   1.3746
IC C4N   C6N   *C5N  H5N    1.3746  119.09 -173.56  121.44   1.0955
IC C6N   C5N   C4N   C3N    1.3689  119.09   -1.00  119.02   1.3830
IC C3N   C5N   *C4N  H41N   1.3830  119.02 -178.05  120.48   1.0937
IC C3N   N1N   *C2N  H2N    1.3696  123.10  177.36  117.15   1.0905
IC C2N   C4N   *C3N  C7N    1.3696  118.55 -179.48  116.96   1.5065
IC C4N   C3N   C7N   N7N    1.3830  116.96   49.86  116.48   1.3522
IC N7N   C3N   *C7N  O7N    1.3522  116.48  169.66  118.17   1.2276
IC C3N   C7N   N7N   H71N   1.5065  116.48 -148.55  113.04   1.0028
IC H71N  C7N   *N7N  H72N   1.0028  113.04  127.16  116.64   1.0104
PATCH FIRST NONE LAST NONE   

RESI NDP         -3.00  ! reduced nicotinamide adenine dinucleotide, NADPH, VARNAI/adm jr.
                        ! from NADH and 3PHO
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM C4B  CN7     0.16  !                H61A  H62A
ATOM H4B  HN7     0.09  !                   \  /
ATOM O4B  ON6B   -0.50  !                   N6A
ATOM C1B  CN7B    0.16  !                    |
ATOM H1B  HN7     0.09  !                   C6A
GROUP                   !                  //  \
ATOM C5A  CN5     0.28  !                 N1A  C5A--N7A\\
ATOM N7A  NN4    -0.71  !                  |    ||     C8A-H8A
ATOM C8A  CN4     0.34  !                 C2A  C4A--N9A/
ATOM H8A  HN3     0.12  !                 / \\ /     \
ATOM N9A  NN2    -0.05  !              H2A  N3A       \
                        !                              \
ATOM N1A  NN3A   -0.74  !                               \
ATOM C2A  CN4     0.50  !                                \
ATOM H2A  HN3     0.13  !    O1N     O1A    H52AH4B  O4B  \
ATOM N3A  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM C4A  CN5     0.43  ! O5D PN-O3--PA-O5B -C5B -C4B    C1B 
ATOM C6A  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ O2N     O2A    H51A C3B -C2B  H1B 
ATOM N6A  NN1    -0.77  !   \                     / \   / \
ATOM H61A HN1     0.38  !    \                O3B  H3B O2B H2B 
ATOM H62A HN1     0.38  !     \                |        |
GROUP                   !      \             HO3A O1X =P2B==O2X  (-)
ATOM C2B  CN7B    0.01  !       \                       |    H71N
ATOM H2B  HN7     0.09  !        \                HO2A-O3X    /
ATOM O2B  ON2    -0.62  !         \                    H72N-N7N  H41NH42N
ATOM P2B  P       1.50  !          \                          \    \ /
ATOM O1X  ON3    -0.82  !           \                         C7N  C4N
ATOM O2X  ON3    -0.82  !            \                        / \  /  \
ATOM O3X  ON4    -0.68  !             \                    O7N  C3N  C5N-H5N
ATOM HO2A HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM C3B  CN7     0.14  !                \ H51N H4D O4D       H2N-C2N C6N-HN6
ATOM H3B  HN7     0.09  !                 \ |    \ /   \           \   /
ATOM O3B  ON5    -0.66  !                  C5D --C4D    C1D --------N1N
ATOM HO3A HN5     0.43  !                   |     \     / \
GROUP                   !                 H52N   C3D -C2D  H1D 
ATOM C5B  CN8B   -0.08  !                        / \   / \  
ATOM H51A HN8     0.09  !                    O3D  H3D O2D H2D   
ATOM H52A HN8     0.09  !                     |       |
ATOM PA   P       1.50  !                    HO3N    HO2N   
ATOM O1A  ON3    -0.82  !                   
ATOM O2A  ON3    -0.82  !                    
ATOM O5B  ON2    -0.62  !                   
ATOM O3   ON2    -0.68
ATOM PN   P       1.50
ATOM O1N  ON3    -0.82
ATOM O2N  ON3    -0.82
ATOM O5D  ON2    -0.62
ATOM C5D  CN8B   -0.08
ATOM H51N HN8     0.09
ATOM H52N HN8     0.09
GROUP
ATOM C2D  CN7B    0.14
ATOM H2D  HN7     0.09
ATOM O2D  ON5    -0.66
ATOM HO2N HN5     0.43
GROUP
ATOM C3D  CN7     0.14
ATOM H3D  HN7     0.09
ATOM O3D  ON5    -0.66
ATOM HO3N HN5     0.43
GROUP
ATOM C1D  CN7B    0.16
ATOM H1D  HN7     0.09
ATOM C4D  CN7     0.16
ATOM H4D  HN7     0.09
ATOM O4D  ON6B   -0.50
GROUP
ATOM N1N  NN2    -0.27 !N2
ATOM C6N  CN3C   -0.06 !C3
ATOM HN6  HN6     0.17 !H4
ATOM C5N  CN3    -0.18 !C5
ATOM H5N  HN6     0.14 !H6
ATOM C4N  CN8    -0.28 !C7
ATOM H41N HN8     0.09 !H8
ATOM H42N HN8     0.09 !H17
ATOM C3N  CN3     0.36 !C9
ATOM C2N  CN3C   -0.10 !C10
ATOM H2N  HN6     0.14 !H11
ATOM C7N  CN1A    0.55 !C12
ATOM O7N  ON1    -0.51 !O13
ATOM N7N  NN1    -0.72 !N14
ATOM H71N HN1     0.26 !H15  ! trans to amide O
ATOM H72N HN1     0.32 !H16  ! cis to amide O
BOND N1A  C2A       N3A  C4A       C5A  C6A
BOND C6A  N6A       C5A  N7A       C8A  N9A
BOND N9A  C4A       C2A  H2A       N6A  H61A      N6A  H62A      C8A  H8A
DOUBLE C6A  N1A       C2A  N3A       C4A  C5A      N7A  C8A
BOND N9A  C1B       C1B  C2B       C2B  C3B       C3B  C4B       C4B  O4B 
BOND O4B  C1B       C1B  H1B       C2B  O2B       O2B  P2B       C2B  H2B 
BOND C3B  H3B       C3B  O3B       O3B  HO3A      C4B  H4B       C4B  C5B 
BOND C5B  H52A      C5B  H51A      C5B  O5B       O5B  PA        PA   O1A
BOND PA   O2A       PA   O3        O3   PN        PN   O1N       PN   O1N
BOND PN   O5D       O5D  C5D       C5D  H51N      C5D  H52N      C5D  C4D 
BOND C4D  O4D       O4D  C1D       C1D  C2D       C2D  C3D       C3D  C4D 
BOND C1D  H1D       C2D  H2D       C2D  O2D       O2D  HO2N      C3D  H3D 
BOND C3D  O3D       O3D  HO3N      C4D  H4D       C1D  N1N       N1N  C2N
BOND C3N  C4N       C5N  C6N       
BOND C2N  H2N       C3N  C7N       C7N  O7N       C7N  N7N       N7N  H71N
BOND N7N  H72N      C4N  H41N      C4N  H42N      C5N  H5N       C6N  HN6
BOND P2B  O1X       P2B  O2X       P2B  O3X       O3X  HO2A
DOUBLE C2N  C3N       C4N  C5N       C6N  N1N
! adenine impropers
IMPR N6A  C6A    H61A H62A   C6A   N1A   C5A   N6A
! amide impropers
IMPR C7N   N7N   C3N  O7N    C7N   C3N   N7N   O7N
IMPR N7N   C7N   H71N H72N   N7N   C7N   H72N  H71N
! ring hydrogen impropers
IMPR C6N   N1N   C5N  HN6    C5N   C6N   C4N   H5N
IMPR C4N   C5N   C3N  H41N   C2N   C3N   N1N   H2N
DONO H61A N6A
DONO H62A N6A
DONO HO3A O3B 
ACCE N1A
ACCE N3A
ACCE N7A
ACCE O4B 
ACCE O3B 
ACCE O5B 
ACCE O1A  PA
ACCE O2A  PA
ACCE O3
ACCE O1N  PN
ACCE O2N  PN
ACCE O5D 
ACCE O4D 
ACCE O3D 
ACCE O2D 
ACCE O7N
DONO HO2N O2D 
DONO HO3N O3D 
DONO H71N N7N
DONO H72N N7N
DONO HO2A O3X 
ACCE O3X 
ACCE O1X 
ACCE O2X 
ACCE O2B  

IC O4B   C4B   C5B   O5B    1.4582  108.69  147.29  113.38   1.4416
IC O4B   C5B   *C4B  C3B    1.4582  108.69 -118.37  116.42   1.5453
IC C3B   C5B   *C4B  H4B    1.5453  116.42 -123.26  110.26   1.1108
IC C5B   C4B   O4B   C1B    1.5423  108.69 -124.93  109.48   1.4122
IC C4B   O4B   C1B   N9A    1.4582  109.48 -147.01  110.04   1.4652
IC N9A   O4B   *C1B  C2B    1.4652  110.04  124.33  107.34   1.5182
IC N9A   O4B   *C1B  H1B    1.4652  110.04 -119.42  105.83   1.1152
IC O4B   C1B   N9A   C4A    1.4122  110.04  -86.61  125.65   1.3733
IC C4A   C1B   *N9A  C8A    1.3733  125.65  178.34  128.52   1.3773
IC C1B   N9A   C4A   C5A    1.4652  125.65  178.57  105.62   1.3829
IC C5A   N9A   *C4A  N3A    1.3829  105.62  179.51  128.22   1.3485
IC N9A   C4A   C5A   C6A    1.3733  105.62  178.87  117.03   1.4089
IC C6A   C4A   *C5A  N7A    1.4089  117.03 -179.61  111.33   1.3844
IC N7A   N9A   *C8A  H8A    1.3165  113.76 -178.62  121.49   1.0929
IC C4A   C5A   C6A   N1A    1.3829  117.03    0.17  118.37   1.3553
IC N1A   C5A   *C6A  N6A    1.3553  118.37 -179.13  122.76   1.3455
IC C5A   C6A   N1A   C2A    1.4089  118.37   -0.08  117.58   1.3367
IC N3A   N1A   *C2A  H2A    1.3316  129.88  179.50  115.45   1.0928
IC C5A   C6A   N6A   H61A   1.4089  122.76  172.71  117.17   0.9924
IC H61A  C6A   *N6A  H62A   0.9924  117.17 -165.83  118.92   0.9969
IC C3B   C1B   *C2B  O2B    1.5172  100.70  117.95  111.52   1.4469
IC C3B   C1B   *C2B  H2B    1.5172  100.70 -114.49  112.15   1.1158
IC C1B   C2B   O2B   P2B    1.5182  111.52   88.87  120.26   1.5695
IC C2B   O2B   P2B   O3X    1.4469  120.26  -89.09  105.16   1.5592
IC O3X   O2B   *P2B  O1X    1.5592  105.16  112.49  112.19   1.4735
IC O1X   O2B   *P2B  O2X    1.4735  112.19  138.98  113.24   1.4714
IC O2B   P2B   O3X   HO2A   1.5695  105.16 -143.03  105.24   0.9629
IC C1B   C2B   O2B   HO2A   1.5182  111.52   52.38  125.15   3.2167
IC C2B   C4B   *C3B  O3B    1.5172  104.21  119.99  110.36   1.4348
IC C2B   C4B   *C3B  H3B    1.5172  104.21 -117.77  107.81   1.1123
IC C4B   C3B   O3B   HO3A   1.5453  110.36   61.04  107.59   0.9899
IC C3B   C4B   C5B   O5B    1.5453  116.42   28.91  113.38   1.4416
IC O5B   C4B   *C5B  H52A   1.4416  113.38 -118.10  108.23   1.1129
IC H52A  C4B   *C5B  H51A   1.1129  108.23 -115.04  109.34   1.1144
IC C4B   C5B   O5B   PA     1.5423  113.38   90.70  124.02   1.5733
IC C5B   O5B   PA    O3     1.4416  124.02  151.99   89.67   1.5604
IC O3    O5B   *PA   O1A    1.5604   89.67 -118.40  102.31   1.4957
IC O1A   O5B   *PA   O2A    1.4957  102.31 -121.55   98.60   1.4978
IC O5B   PA    O3    PN     1.5733   89.67  175.92   82.07   1.5171
IC PA    O3    PN    O5D    1.5604   82.07 -130.29  100.52   1.5806
IC O5D   O3    *PN   O1N    1.5806  100.52 -112.12  108.73   1.4864
IC O1N   O3    *PN   O2N    1.4864  108.73  147.44  159.68   5.2397
IC O3    PN    O5D   C5D    1.5171  100.52 -156.02  122.16   1.4407
IC PN    O5D   C5D   C4D    1.5806  122.16 -155.55  113.98   1.5556
IC C4D   O5D   *C5D  H51N   1.5556  113.98 -119.58  108.24   1.1127
IC H51N  O5D   *C5D  H52N   1.1127  108.24 -117.86  112.23   1.1172
IC O5D   C5D   C4D   O4D    1.4407  113.98  -39.97  113.27   1.4728
IC O4D   C5D   *C4D  C3D    1.4728  113.27  123.24  116.41   1.5466
IC O4D   C5D   *C4D  H4D    1.4728  113.27 -117.97  108.11   1.1097
IC C5D   C4D   C3D   C2D    1.5556  116.41 -137.48  104.59   1.5300
IC C2D   C4D   *C3D  O3D    1.5300  104.59  128.04  115.55   1.4371
IC C2D   C4D   *C3D  H3D    1.5300  104.59 -114.00  106.10   1.1131
IC C4D   C3D   C2D   C1D    1.5466  104.59   26.25  103.50   1.5376
IC C1D   C3D   *C2D  O2D    1.5376  103.50  127.18  111.43   1.4128
IC C1D   C3D   *C2D  H2D    1.5376  103.50 -113.70  107.89   1.1128
IC C3D   C2D   O2D   HO2N   1.5300  111.43  -33.45  103.13   0.9733
IC C4D   C3D   O3D   HO3N   1.5466  115.55   84.57  105.43   0.9941
IC O4D   C2D   *C1D  N1N    1.4276  105.00  128.25  117.48   1.5144
IC O4D   C2D   *C1D  H1D    1.4276  105.00 -111.04  107.28   1.1120
IC C2D   C1D   N1N   C2N    1.5376  117.48   57.37  120.71   1.3843
IC C2N   C1D   *N1N  C6N    1.3843  120.71  160.76  120.55   1.3815
IC C1D   N1N   C6N   C5N    1.5144  120.55 -170.31  124.26   1.3287
IC C5N   N1N   *C6N  HN6    1.3287  124.26 -178.43  118.52   1.0918
IC N1N   C6N   C5N   C4N    1.3815  124.26    9.43  123.21   1.5077
IC C4N   C6N   *C5N  H5N    1.5077  123.21 -145.56  114.70   1.0925
IC C6N   C5N   C4N   C3N    1.3287  123.21   -9.51  109.08   1.5286
IC C3N   C5N   *C4N  H41N   1.5286  109.08  123.86  111.86   1.1053
IC C3N   C5N   *C4N  H42N   1.5286  109.08 -119.79  109.00   1.1069
IC C3N   N1N   *C2N  H2N    1.3470  124.38 -176.93  117.74   1.0900
IC C2N   C4N   *C3N  C7N    1.3470  121.40 -164.55  123.17   1.5301
IC C4N   C3N   C7N   N7N    1.5286  123.17   17.57  116.23   1.3547
IC N7N   C3N   *C7N  O7N    1.3547  116.23 -179.04  120.83   1.2310
IC C3N   C7N   N7N   H71N   1.5301  116.23  173.93  118.74   0.9953
IC H71N  C7N   *N7N  H72N   0.9953  118.74 -160.46  121.30   1.0065

PATCH FIRST NONE LAST NONE

!old NAD/NADP nomenclature for both residue and atom names.  maintained
!for back compatibility.  residue names differ from current nomenclature

!following was NAD in old nomenclature; change to NAD1 to avoid conflict with
!new nomenclature
!
RESI NAD1        -1.00  ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                 |       |
GROUP                   !      \              AH3T     AH2T
ATOM AC2' CN7B    0.14  !       \                        NH71
ATOM AH2' HN7     0.09  !        \                          \ 
ATOM AO2' ON5    -0.66  !         \                    NH72-NN7    NH4
ATOM AH2T HN5     0.43  !          \                          \     |
GROUP                   !           \                         NC7  NC4
ATOM AC3' CN7     0.14  !            \                        / \  /  \
ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
ATOM AO3' ON5    -0.66  !              \                          |    |
ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
GROUP                   !                \ |    \ /   \            \+ /   
ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
ATOM AH5' HN8     0.09  !                  |     \     / \
ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
ATOM AP   P       1.50  !                       / \   / \
ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
ATOM AO2  ON3    -0.82  !                    |       |
ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09 
GROUP                  
ATOM NC2' CN7B    0.14 
ATOM NH2' HN7     0.09 
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP                  
ATOM NN1  NN2    -0.07
ATOM NC6  CN3B    0.16
ATOM NH6  HN3B    0.19
ATOM NC5  CN3    -0.10
ATOM NH5  HN3B    0.16
ATOM NC4  CN3A   -0.05
ATOM NH4  HN3B    0.16
ATOM NC3  CN3     0.05 
ATOM NC2  CN3B    0.18
ATOM NH2  HN3B    0.16
ATOM NC7  CN1A    0.68 
ATOM NO7  ON1    -0.40 
ATOM NN7  NN1    -0.82
ATOM NH71 HN1     0.34  ! trans to amide O
ATOM NH72 HN1     0.36  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6   AN1   AC5  AN6       
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
PATCH FIRST NONE LAST NONE   

RESI NADH        -2.00  ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                 |       |
GROUP                   !      \              AH3T     AH2T
ATOM AC2' CN7B    0.14  !       \                        NH71
ATOM AH2' HN7     0.09  !        \                          \
ATOM AO2' ON5    -0.66  !         \                    NH72-NN7  NH4 NH42
ATOM AH2T HN5     0.43  !          \                          \    \ /
GROUP                   !           \                         NC7  NC4
ATOM AC3' CN7     0.14  !            \                        / \  /  \
ATOM AH3' HN7     0.09  !             \                    NO7  NC3  NC5-NH5
ATOM AO3' ON5    -0.66  !              \                          |    |
ATOM AH3T HN5     0.43  !               \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
GROUP                   !                \ |    \ /   \            \  /
ATOM AC5' CN8B   -0.08  !                 NC5'--NC4'   NC1'---------NN1
ATOM AH5' HN8     0.09  !                  |     \     / \
ATOM AH5s HN8     0.09  !                 NH5'   NC3'-NC2'NH1'
ATOM AP   P       1.50  !                       / \   / \
ATOM AO1  ON3    -0.82  !                   NO3' NH3'NO2'NH2'
ATOM AO2  ON3    -0.82  !                    |       |
ATOM AO5' ON2    -0.62  !                   NH3T    NH2T
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09
GROUP
ATOM NC2' CN7B    0.14
ATOM NH2' HN7     0.09
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP
ATOM NN1  NN2    -0.27 !N2
ATOM NC6  CN3C   -0.06 !C3
ATOM NH6  HN6     0.17 !H4
ATOM NC5  CN3    -0.18 !C5
ATOM NH5  HN6     0.14 !H6
ATOM NC4  CN8    -0.28 !C7
ATOM NH4  HN8     0.09 !H8
ATOM NH42 HN8     0.09 !H17
ATOM NC3  CN3     0.36 !C9
ATOM NC2  CN3C   -0.10 !C10
ATOM NH2  HN6     0.14 !H11
ATOM NC7  CN1A    0.55 !C12
ATOM NO7  ON1    -0.51 !O13
ATOM NN7  NN1    -0.72 !N14
ATOM NH71 HN1     0.26 !H15  ! trans to amide O
ATOM NH72 HN1     0.32 !H16  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE  AC6  AN1      AC2  AN3      AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AH2T      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC4  NC5       NC6  NN1
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
DOUBLE  NC2  NC3      NC5  NC6
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6       
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
IC AC1'   AC3'   *AC2   AO2'   4.3577   16.73   79.16   23.49   5.5426
IC AH2'   AO2'   AC2'   AC3'   2.0992   29.77  125.89  110.79   1.5171
IC AH2T   AO2'   AC2'   AC3'   0.9759  105.90    7.59  110.79   1.5171
IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
PATCH FIRST NONE LAST NONE

RESI NADP        -2.00  ! oxidized nicotinamide adenine dinucleotide,
                        ! NADP+, adm jr.
                        ! atom names correspond to pdb nomenclature
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                |        |
GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
ATOM AC2' CN7B    0.01  !       \                       |    NH71
ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
ATOM AP2  P       1.50  !          \                          \    \ /
ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
ATOM AO2P ON3    -0.82  !            \                        / \  /  \
ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
ATOM AH2T HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
ATOM AH3T HN5     0.43  !                   |     \     / \
GROUP                   !                 NH5'   NC3'-NC2'NH1'
ATOM AC5' CN8B   -0.08  !                        / \   / \  
ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
ATOM AH5s HN8     0.09  !                     |       |
ATOM AP   P       1.50  !                    NH3T    NH2T   
ATOM AO1  ON3    -0.82  !
ATOM AO2  ON3    -0.82  !
ATOM AO5' ON2    -0.62  !
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09 
GROUP                  
ATOM NC2' CN7B    0.14 
ATOM NH2' HN7     0.09 
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP                  
ATOM NN1  NN2    -0.07
ATOM NC6  CN3B    0.16
ATOM NH6  HN3B    0.19
ATOM NC5  CN3    -0.10
ATOM NH5  HN3B    0.16
ATOM NC4  CN3A   -0.05
ATOM NH4  HN3B    0.16
ATOM NC3  CN3     0.05 
ATOM NC2  CN3B    0.18
ATOM NH2  HN3B    0.16
ATOM NC7  CN1A    0.68 
ATOM NO7  ON1    -0.40 
ATOM NN7  NN1    -0.82
ATOM NH71 HN1     0.34  ! trans to amide O
ATOM NH72 HN1     0.36  ! cis to amide O

BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2      AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC5  NH5       NC6  NH6
BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6  AH61 AH62     AC6  AN1  AC5  AN6
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7 
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH2T AO2'
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO2'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2'
IC AP     O3     NP     NO5'   1.4863   65.28 -169.00   98.59   1.5977
IC AC5'   AO5'   AP     O3     1.4232  127.31 -165.10  103.27   1.4863
IC AC5'   AO5'   AP     AO2    1.4232  127.31   73.33  111.48   1.4836
IC AH5S   AC5'   AC4'   AC3'   0.9935  120.00  -58.20  111.58   1.6942
IC AP     O3     NP     NO1    1.4863   65.28   78.51  108.97   1.4756
IC AP     O3     NP     NO2    1.4863   65.28  -54.29  112.88   1.4636
IC AP     AO5'   AC5'   AC4'   1.5901  127.31  121.29  111.63   1.5491
IC AO1    AP     AO5'   AC5'   1.5901  127.31  121.29  127.31   1.4232
IC AO5'   AC5'   AC4'   AC3'   1.4232  111.63  -58.20  111.58   1.6942
IC AC5'   AC4'   AC3'   AO3'   1.5491  111.58  128.42  114.19   1.4337
IC AH3T   AO3'   AC3'   AC4'   0.9671   98.77  147.40  114.19   1.6942
IC AO4'   AC3'   *AC4   AC5'   1.8868  112.95 -118.10  111.58   1.5491
IC AC2'   AC4'   *AC3'  AO3'   1.5097   93.22 -117.72  114.19   1.4337
IC AC4'   AC3'   AC2'   AC1'   1.6942   93.22  -12.93  117.82   1.5415
IC AC3'   AC2'   AC1'   AN9    1.5097  117.82  135.56  115.01   1.4847
IC AO4'   AC1'   AN9    AC4    1.3646   95.44  -90.72  125.96   1.4013
IC AC1'   AC4    *AN9   AC8    1.4847  125.96 -176.52  105.34   1.3777
IC AC4    AN9    AC8    AN7    1.4013  105.34   -0.07  114.01   1.3282
IC AC8    AN9    AC4    AC5    1.3777  105.34    0.11  105.06   1.3782
IC AC8    AN7    AC5    AC6    1.3282  103.21 -179.92  130.78   1.4146
IC AN7    AC5    AC6    AN1    1.3814  130.78 -179.94  117.85   1.3482
IC AC5    AC6    AN1    AC2    1.4146  117.85   -0.14  118.87   1.3300
IC AN9    AC5    *AC4   AN3    1.4013  105.06 -179.67  126.14   1.3648
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AC5    AN1    *AC6   AN6    1.4146  117.85  179.89  119.69   1.3419
IC AN1    AC6    AN6    AH61   1.3482  119.69   -0.39  116.60   0.9912
IC AH61   AC6    *AN6   AH62   0.9912  116.60 -179.02  116.94   0.9978
IC AN9    AN7    *AC8   AH8    1.3777  114.01 -179.37  126.34   1.0962
IC AN1    AN3    *AC2   AH2    1.3300  129.42  179.97  114.82   1.0928
IC AC1'   AC3'   *AC2   AO2'   1.5415  117.82 -145.06  114.13   1.4294
IC AH2'   AO2'   AC2'   AC3'   2.0386   31.12  -93.63  114.13   1.5097
IC AH2T   AO2'   AC2'   AC3'   0.9953   99.36  -93.63  114.13   1.5097
IC AO4'   AC2'   *AC1'  AH1'   1.3646  120.77 -114.99  109.65   1.1105
IC AC1'   AC3'   *AC2   AH2'   1.5415  117.82  108.23   86.44   1.0999
IC AC2'   AC4'   *AC3'  AH3'   1.5097   93.22  117.28  111.94   1.1110
IC AC3'   AO4'   *AC4   AH4'   1.6942  112.95 -140.26   57.99   1.0000
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC AC4'   AO5'   *AC5   AH5'   1.5491  111.63 -123.75  111.23   1.1111
IC NC5'   NO5'   NP     NO2    1.4451  128.40  -49.72  108.83   1.4636
IC NH5S   NC5'   NO5'   NP     1.1110  109.50  115.00  128.40   1.5977
IC NH5'   NC5'   NO5'   NP     1.1110  109.50 -115.00  128.40   1.5977
IC NP     NO5'   NC5'   NC4'   1.5977  128.40    0.00  110.10   1.5160
IC NO5'   NC5'   NC4'   NC3'   1.4451  110.10    0.00  108.50   1.5160
IC NC5'   NC4'   NC3'   NC2'   1.5160  108.50    0.00  111.00   1.5160
IC NC4'   NC3'   NC2'   NC1'   1.5160  111.00    0.00  105.50   1.5270
IC NC3'   NC2'   NC1'   NO4'   1.5160  105.50    0.00  105.00   1.4100
IC NC2'   NC1'   NO4'   NC4'   1.5270  105.00    0.00  117.86   1.4712
IC NO2'   NC2'   NC1'   NO4'   1.4200  110.10  180.00  105.00   1.4100
IC NH2T   NO2'   NC2'   NC1'   0.9600  106.00  180.00  110.10   1.5270
IC NO4'   NC2'   *NC1'  NH1'   1.4100  105.00 -115.00  110.10   1.1110
IC NC1'   NC3'   *NC2   NH2'   1.5270  105.50  115.00  110.10   1.1110
IC NC2'   NC4'   *NC3   NH3'   1.5160  111.00  115.00  110.10   1.1110
IC NC3'   NO4'   *NC4   NH4'   1.5160  100.64 -115.00  107.24   1.1110
IC NC4'   NO5'   *NC5   NH5'   1.5160  110.10 -115.00  109.50   1.1110
IC NC4'   NO5'   *NC5   NH5S   1.5160  110.10  115.00  109.50   1.1110
IC NC3'   NC2'   NC1'   NN1    1.5160  105.50    0.00  113.70   1.4800
IC NO3'   NC3'   NC2'   NC1'   1.4200  110.10  180.00  105.50   1.5270
IC NH3T   NO3'   NC3'   NC2'   0.9600  106.00  180.00  110.10   1.5160
IC NC2'   NC1'   NN1    NC2    1.5270  113.70    0.00  121.70   1.3150
IC NC1'   NN1    NC2    NC3    1.4800  121.70    0.00  122.00   1.3500
IC NN1    NC2    NC3    NC4    1.3150  122.00    0.00  118.00   1.3600
IC NC2    NC3    NC4    NC5    1.3500  118.00    0.00  118.00   1.3600
IC NC3    NC4    NC5    NC6    1.3600  118.00    0.00  118.00   1.3500
IC NC4    NC5    NC6    NN1    1.3600  118.00    0.00  124.51   1.2199
IC NC5    NC6    NN1    NC2    1.3500  124.51    0.00  119.49   1.3150
IC NN1    NC2    NC3    NC7    1.3150  122.00    0.00  131.80   1.4800
IC NC2    NC3    NC7    NO7    1.3500  131.80    0.00  118.50   1.2300
IC NC2    NC3    NC7    NN7    1.3500  131.80    0.00  113.00   1.3600
IC NO7    NC7    NN7    NH71   1.2300    0.00  180.00  120.00   1.0000
IC NO7    NC7    NN7    NH72   1.2300    0.00    0.00  120.00   1.0000
IC NC2    NC3    NC4    NH4    1.3500  118.00    0.00  121.00   1.0900
IC NC3    NC4    NC5    NH5    1.3600  118.00    0.00  119.00   1.0900
IC NC4    NC5    NC6    NH6    1.3600  118.00    0.00  120.50   1.0900
IC NC6    NN1    NC2    NH2    1.2199  119.49    0.00  117.50   1.0900
IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
PATCH FIRST NONE LAST NONE   

RESI NDPH        -3.00  ! reduced nicotinamide adenine dinucleotide
                        ! NADPH, VARNAI/adm jr.
                        ! from NADH and 3PHO
                        ! checked for consistency with new NA params, adm jr., 9/98
                        ! note that differences with respect to published results exist
                        ! due to new NA params
                        !
GROUP                   !
ATOM AC4' CN7     0.16  !                AH61  AH62
ATOM AH4' HN7     0.09  !                   \  /
ATOM AO4' ON6B   -0.50  !                   AN6
ATOM AC1' CN7B    0.16  !                    |
ATOM AH1' HN7     0.09  !                   AC6
GROUP                   !                  //  \
ATOM AC5  CN5     0.28  !                 AN1  AC5--AN7\\
ATOM AN7  NN4    -0.71  !                  |    ||     AC8-AH8
ATOM AC8  CN4     0.34  !                 AC2  AC4--AN9/
ATOM AH8  HN3     0.12  !                 / \\ /     \
ATOM AN9  NN2    -0.05  !              AH2  AN3       \
                        !                              \
ATOM AN1  NN3A   -0.74  !                               \
ATOM AC2  CN4     0.50  !                                \
ATOM AH2  HN3     0.13  !    NO1     AO1    AH5sAH4' AO4' \
ATOM AN3  NN3A   -0.75  !     |       |      |    \ /   \  \
ATOM AC4  CN5     0.43  ! NO5'NP-O3--AP-AO5'-AC5'-AC4'   AC1'
ATOM AC6  CN2     0.46  ! \   |       |      |     \     / \
                        !  \ NO2     AO2    AH5' AC3'-AC2' AH1'
ATOM AN6  NN1    -0.77  !   \                     / \   / \
ATOM AH61 HN1     0.38  !    \                AO3' AH3'AO2'AH2'
ATOM AH62 HN1     0.38  !     \                |        |
GROUP                   !      \             AH3T AO1P=AP2==AO2P (-)
ATOM AC2' CN7B    0.01  !       \                       |    NH71
ATOM AH2' HN7     0.09  !        \                AH2T-AO2T   /
ATOM AO2' ON2    -0.62  !         \                    NH72-NN7  NH4 NH42
ATOM AP2  P       1.50  !          \                          \    \ /
ATOM AO1P ON3    -0.82  !           \                         NC7  NC4
ATOM AO2P ON3    -0.82  !            \                        / \  /  \
ATOM AO2T ON4    -0.68  !             \                    NO7  NC3  NC5-NH5
ATOM AH2T HN4     0.34  !              \                          |    |
GROUP                   !               \                         |    |
ATOM AC3' CN7     0.14  !                \ NH5s NH4'NO4'      NH2-NC2 NC6-NH6
ATOM AH3' HN7     0.09  !                 \ |    \ /   \           \   /
ATOM AO3' ON5    -0.66  !                  NC5'--NC4'   NC1'--------NN1
ATOM AH3T HN5     0.43  !                   |     \     / \
GROUP                   !                 NH5'   NC3'-NC2'NH1'
ATOM AC5' CN8B   -0.08  !                        / \   / \  
ATOM AH5' HN8     0.09  !                    NO3' NH3'NO2'NH2'  
ATOM AH5s HN8     0.09  !                     |       |
ATOM AP   P       1.50  !                    NH3T    NH2T   
ATOM AO1  ON3    -0.82  !                   
ATOM AO2  ON3    -0.82  !                    
ATOM AO5' ON2    -0.62  !                   
ATOM O3   ON2    -0.68
ATOM NP   P       1.50
ATOM NO1  ON3    -0.82
ATOM NO2  ON3    -0.82
ATOM NO5' ON2    -0.62
ATOM NC5' CN8B   -0.08
ATOM NH5s HN8     0.09
ATOM NH5' HN8     0.09
GROUP
ATOM NC2' CN7B    0.14
ATOM NH2' HN7     0.09
ATOM NO2' ON5    -0.66
ATOM NH2T HN5     0.43
GROUP
ATOM NC3' CN7     0.14
ATOM NH3' HN7     0.09
ATOM NO3' ON5    -0.66
ATOM NH3T HN5     0.43
GROUP
ATOM NC1' CN7B    0.16
ATOM NH1' HN7     0.09
ATOM NC4' CN7     0.16
ATOM NH4' HN7     0.09
ATOM NO4' ON6B   -0.50
GROUP
ATOM NN1  NN2    -0.27 !N2
ATOM NC6  CN3C   -0.06 !C3
ATOM NH6  HN6     0.17 !H4
ATOM NC5  CN3    -0.18 !C5
ATOM NH5  HN6     0.14 !H6
ATOM NC4  CN8    -0.28 !C7
ATOM NH4  HN8     0.09 !H8
ATOM NH42 HN8     0.09 !H17
ATOM NC3  CN3     0.36 !C9
ATOM NC2  CN3C   -0.10 !C10
ATOM NH2  HN6     0.14 !H11
ATOM NC7  CN1A    0.55 !C12
ATOM NO7  ON1    -0.51 !O13
ATOM NN7  NN1    -0.72 !N14
ATOM NH71 HN1     0.26 !H15  ! trans to amide O
ATOM NH72 HN1     0.32 !H16  ! cis to amide O
BOND AN1  AC2       AN3  AC4       AC5  AC6
BOND AC6  AN6       AC5  AN7       AC8  AN9
BOND AN9  AC4       AC2  AH2       AN6  AH61      AN6  AH62      AC8  AH8
DOUBLE AC6  AN1       AC2  AN3       AC4  AC5      AN7  AC8
BOND AN9  AC1'      AC1' AC2'      AC2' AC3'      AC3' AC4'      AC4' AO4'
BOND AO4' AC1'      AC1' AH1'      AC2' AO2'      AO2' AP2       AC2' AH2'
BOND AC3' AH3'      AC3' AO3'      AO3' AH3T      AC4' AH4'      AC4' AC5'
BOND AC5' AH5s      AC5' AH5'      AC5' AO5'      AO5' AP        AP   AO1
BOND AP   AO2       AP   O3        O3   NP        NP   NO1       NP   NO2
BOND NP   NO5'      NO5' NC5'      NC5' NH5s      NC5' NH5'      NC5' NC4'
BOND NC4' NO4'      NO4' NC1'      NC1' NC2'      NC2' NC3'      NC3' NC4'
BOND NC1' NH1'      NC2' NH2'      NC2' NO2'      NO2' NH2T      NC3' NH3'
BOND NC3' NO3'      NO3' NH3T      NC4' NH4'      NC1' NN1       NN1  NC2
BOND NC3  NC4       NC5  NC6       
BOND NC2  NH2       NC3  NC7       NC7  NO7       NC7  NN7       NN7  NH71
BOND NN7  NH72      NC4  NH4       NC4  NH42      NC5  NH5       NC6  NH6
BOND AP2  AO1P      AP2  AO2P      AP2  AO2T      AO2T AH2T
DOUBLE NC2  NC3       NC4  NC5       NC6  NN1
! adenine impropers
IMPR AN6  AC6    AH61 AH62   AC6   AN1   AC5   AN6
! amide impropers
IMPR NC7   NN7   NC3  NO7    NC7   NC3   NN7   NO7
IMPR NN7   NC7   NH71 NH72   NN7   NC7   NH72  NH71
! ring hydrogen impropers
IMPR NC6   NN1   NC5  NH6    NC5   NC6   NC4   NH5
IMPR NC4   NC5   NC3  NH4    NC2   NC3   NN1   NH2
DONO AH61 AN6
DONO AH62 AN6
DONO AH3T AO3'
ACCE AN1
ACCE AN3
ACCE AN7
ACCE AO4'
ACCE AO3'
ACCE AO5'
ACCE AO1  AP
ACCE AO2  AP
ACCE O3
ACCE NO1  NP
ACCE NO2  NP
ACCE NO5'
ACCE NO4'
ACCE NO3'
ACCE NO2'
ACCE NO7
DONO NH2T NO2'
DONO NH3T NO3'
DONO NH71 NN7
DONO NH72 NN7
DONO AH2T AO2T
ACCE AO2T
ACCE AO1P
ACCE AO2P
ACCE AO2' 
! the following ICs will not totally IC BUILD NADPH
IC AP     O3     NP     NO5'   1.5477  110.11  175.47   98.59   1.5945
IC AC5'   AO5'   AP     O3     1.4379  124.23 -120.69   96.29   1.5477
IC AC5'   AO5'   AP     AO2    1.4379  124.23   -4.20  104.25   1.4838
IC AH5S   AC5'   AC4'   AC3'   1.1127  107.45 -172.00  111.64   1.5309
IC AP     O3     NP     NO1    1.5477  110.11   63.14  114.14   1.4739
IC AP     O3     NP     NO2    1.5477  110.11  -73.96  111.08   1.4835
IC AP     AO5'   AC5'   AC4'   1.5968  124.23  104.17  111.45   1.5366
IC AO1    AP     AO5'   AC5'   1.4736  106.06  122.59  124.23   1.4379
IC AO5'   AC5'   AC4'   AC3'   1.4379  111.45  -54.02  111.64   1.5309
IC AC5'   AC4'   AC3'   AO3'   1.5366  111.64  117.91  108.23   1.4176
IC AH3T   AO3'   AC3'   AC4'   0.9780  101.86  -77.83  108.23   1.5309
IC AO4'   AC3'   *AC4   AC5'   3.7210   30.68   12.44   22.46   6.0953
IC AC2'   AC4'   *AC3'  AO3'   1.5171  107.22 -123.00  108.23   1.4176
IC AC4'   AC3'   AC2'   AC1'   1.5309  107.22  -27.93   98.01   1.5397
IC AC3'   AC2'   AC1'   AN9    1.5171   98.01  168.03  114.25   1.4756
IC AO4'   AC1'   AN9    AC4    1.4308  112.85 -160.05  123.87   1.3958
IC AC1'   AC4    *AN9   AC8    1.4756  123.87  160.62  105.30   1.3614
IC AC4    AN9    AC8    AN7    1.3958  105.30    2.73  114.72   1.3222
IC AC8    AN9    AC4    AC5    1.3614  105.30   -0.85  105.33   1.3777
IC AC8    AN7    AC5    AC6    1.3222  102.89 -175.73  131.43   1.4163
IC AN7    AC5    AC6    AN1    1.3877  131.43  177.76  117.35   1.3499
IC AC5    AC6    AN1    AC2    1.4163  117.35    0.19  119.36   1.3330
IC AN9    AC5    *AC4   AN3    1.3958  105.33 -177.76  126.56   1.3567
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AC5    AN1    *AC6   AN6    1.4163  117.35  178.91  119.82   1.3439
IC AN1    AC6    AN6    AH61   1.3499  119.82   -2.82  115.89   0.9932
IC AH61   AC6    *AN6   AH62   0.9932  115.89 -173.48  118.52   0.9961
IC AN9    AN7    *AC8   AH8    1.3614  114.72  173.63  127.58   1.0942
IC AN1    AN3    *AC2   AH2    1.3330  128.86  179.26  114.95   1.0940
IC AO4'   AC2'   *AC1'  AH1'   1.4308  104.32 -114.05  107.95   1.1153
IC AC1'   AC3'   *AC2   AH2'   4.3577   16.73  138.52   14.56   4.3331
IC AC2'   AC4'   *AC3'  AH3'   1.5171  107.22  118.77  114.33   1.1023
IC AC3'   AO4'   *AC4   AH4'   4.6236   30.68   55.38   18.92   5.2267
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC AC4'   AO5'   *AC5   AH5'   5.8410    8.40  125.34   12.50   6.6777
IC NC5'   NO5'   NP     NO2    1.4351  125.31   34.31  105.69   1.4835
IC NH5S   NC5'   NO5'   NP     1.1087  111.20   -6.79  125.31   1.5945
IC NH5'   NC5'   NO5'   NP     1.1115  107.95  108.24  125.31   1.5945
IC NP     NO5'   NC5'   NC4'   1.5945  125.31 -133.06  113.61   1.5644
IC NO5'   NC5'   NC4'   NC3'   1.4351  113.61   37.01  114.92   1.5111
IC NC5'   NC4'   NC3'   NC2'   1.5644  114.92   71.49   99.06   1.5369
IC NC4'   NC3'   NC2'   NC1'   1.5111   99.06   54.76   97.08   1.5500
IC NC3'   NC2'   NC1'   NO4'   1.5369   97.08  -39.12  103.14   1.4628
IC NC2'   NC1'   NO4'   NC4'   1.5500  103.14    9.47  109.09   1.4960
IC NO2'   NC2'   NC1'   NO4'   1.4207  114.02 -166.39  103.14   1.4628
IC NH2T   NO2'   NC2'   NC1'   0.9638  100.52  -89.37  114.02   1.5500
IC NO4'   NC2'   *NC1'  NH1'   1.4628  103.14 -111.22  105.40   1.1096
IC NC1'   NC3'   *NC2   NH2'   2.4663   46.96  -41.97   34.01   3.9460
IC NC2'   NC4'   *NC3   NH3'   3.9136   23.54 -115.76   16.12   3.6674
IC NC3'   NO4'   *NC4   NH4'   5.4003   24.61  -39.21   14.97   6.7904
IC NC4'   NO5'   *NC5   NH5'   5.9665   13.65  -41.47   15.17   7.7670
IC NC4'   NO5'   *NC5   NH5S   5.9665   13.65  -87.41   13.92   6.7251
IC NC3'   NC2'   NC1'   NN1    1.5369   97.08   88.64  116.58   1.5502
IC NO3'   NC3'   NC2'   NC1'   1.4176  119.76 -172.52   97.08   1.5500
IC NH3T   NO3'   NC3'   NC2'   0.9717  103.61   17.81  119.76   1.5369
IC NC2'   NC1'   NN1    NC2    1.5500  116.58  -19.65  116.34   1.3499
IC NC1'   NN1    NC2    NC3    1.5502  116.34  134.66  130.57   1.3607
IC NN1    NC2    NC3    NC4    1.3499  130.57    5.82  111.74   1.5356
IC NC2    NC3    NC4    NC5    1.3607  111.74   -1.05  119.26   1.5319
IC NC3    NC4    NC5    NC6    1.5356  119.26   -1.26  113.69   1.3745
IC NC4    NC5    NC6    NN1    1.5319  113.69   -0.29  128.15   1.3388
IC NC5    NC6    NN1    NC2    1.3745  128.15    4.14  116.26   1.3499
IC NN1    NC2    NC3    NC7    1.3499  130.57 -147.46  122.72   1.5282
IC NC2    NC3    NC7    NO7    1.3607  122.72 -140.47  119.41   1.2169
IC NC2    NC3    NC7    NN7    1.3607  122.72   46.61  116.68   1.3621
IC NO7    NC7    NN7    NH71   1.2169  123.49 -177.07  120.21   1.0093
IC NO7    NC7    NN7    NH72   1.2169  123.49   -4.94  119.16   1.0014
IC NC2    NC3    NC4    NH4    1.3607  111.74 -135.39  112.16   1.1099
IC NC2    NC3    NC4    NH42   1.3607  111.74  114.48  103.52   1.1129
IC NC3    NC4    NC5    NH5    1.5356  119.26 -171.18  122.65   1.0912
IC NC4    NC5    NC6    NH6    1.5319  113.69  179.92  118.00   1.0878
IC NC6    NN1    NC2    NH2    1.3388  116.26  162.03  117.47   1.0731
IC AC3'   AC2'   AO2'   AP2    0.0000  000.00  180.00  000.00   0.0000
IC AC2'   AO2'   AP2    AO2T   0.0000  000.00  -39.52  000.00   0.0000
IC AO2T   AO2'   *AP2   AO1P   0.0000  000.00 -115.82  000.00   0.0000
IC AO2T   AO2'   *AP2   AO2P   0.0000  000.00  115.90  000.00   0.0000
IC AH2T   AO2T   AP2    AO2'   0.0000  000.00  180.00  000.00   0.0000
PATCH FIRST NONE LAST NONE

end

read para card flex append
* NAD, PPI parameters
*

ATOMS
MASS  -1  HN3B       1.00800 ! NAD+ aromatic hydrogen
MASS  -1  CN1A      12.01100 ! NAD+/NADH amide carbonyl carbon
MASS  -1  CN3A      12.01100 ! NAD+ aromatic carbon
MASS  -1  CN3B      12.01100 ! NAD+ aromatic carbon
MASS  -1  CN3C      12.01100 ! NADH aromatic carbon
MASS  -1  P3        30.97400 ! pyrophosphate phosphorus
MASS  -1  P4        30.97400 ! protonated pyrophosphate phosphorus

BONDS
!
!atom types  Kb          b0
!
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
CN3C HN6    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
CN3  HN6    350.0       1.09    !nadh, adm jr., 8/98
!
CN1A CN3    302.0       1.480   !nad/ppi, jjp1/adm jr. 7/95
CN1A NN1    560.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
CN1A ON1    860.0       1.230   !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3    450.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3    420.0       1.350   !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3    420.0       1.320   !nadh/ppi, jjp1/adm jr. 7/95
CN3  CN8    222.5       1.490   !nadh/ppi, jjp1/adm jr. 7/95
CN3  HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3A HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3B HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3C HN3    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
CN3B NN2    420.0       1.315   !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2    420.0       1.355   !nadh/ppi, jjp1/adm jr. 7/95
ON2  P3     300.0       1.68    !nad/ppi, jjp1/adm jr. 7/95
ON3  P3     480.0       1.53    !nad/ppi, jjp1/adm jr. 7/95
ON2  P4     300.0       1.68    !PPI2, from nad/ppi, adm jr. 7/01
ON3  P4     480.0       1.53    !PPI2, from nad/ppi, adm jr. 7/01
ON4  P4     237.0       1.58    !PPI2, from MP_1, ADM Jr.

ANGLES
!
!atom types     Ktheta    Theta0   Kub     S0
!
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
CN3  CN1A NN1     85.0     113.0  80.0  2.46 !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A ON1     85.0     118.5  20.0  2.43 !nad/ppi, jjp1/adm jr. 7/95
NN1  CN1A ON1     85.0     128.5  20.0  2.17 !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3C HN6     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
HN6  CN3C CN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
HN6  CN3  CN8     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3  HN6     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3C     5.0     107.8  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN8    125.0     124.2  !nadh/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A    40.0     110.2  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A    10.0     131.8  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3     50.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN3B    40.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3  CN8     53.5     108.5  !nadh/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN8     53.5     108.5  !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3  CN8     43.5     128.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  HN3B    30.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  HN3B    30.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3C HN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3  HN3     42.0     116.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A HN3B    80.0     121.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3B HN3B    80.0     120.5  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3B NN2    120.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3C NN2     60.0     122.0  !nadh/ppi, jjp1/adm jr. 7/95
CN8  CN3  HN3     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
HN3B CN3B NN2     80.0     117.5  !nad/ppi, jjp1/adm jr. 7/95
HN3  CN3C NN2     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN8  CN3    125.0     108.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3  CN8  HN8     55.0     110.10 !nadh/ppi, jjp1/adm jr. 7/95
CN1A NN1  HN1     35.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN3B    30.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN3C    20.0     114.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  HN2     32.0     117.4  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  HN2     39.0     123.0  !nad/ppi, jjp1/adm jr. 7/95
CN9  ON2  P3      20.0     120.0  35.   2.33 !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
P4   ON2  P       45.0     140.0  40.0  3.15 !PPI2, from nad/ppi, adm jr., 7/01
P3   ON2  P3      15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
HN4  ON4  P4      30.0     120.0  40.0  2.35 !PPI2, from MP_1, adm jr., 7/01
CN7  CN7B ON2     115.0    109.7  !NF, 11/97, C4'C3'O3' for NADPH
ON2  P4   ON4     48.1     100.0  !PPI2, from MP_1, adm jr., 7/01
ON3  P4   ON4     98.9     108.23 !PPI2, from MP_1, adm jr., 7/01
ON2  P3   ON2     80.0     104.3  !nad/ppi, jjp1/adm jr. 7/95
ON2  P3   ON3     88.9     111.6  !nad/ppi, jjp1/adm jr. 7/95
ON2  P4   ON3     88.9     105.0  !PPI2, from nad/ppi, adm jr., 7/01
ON3  P3   ON3    104.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
ON3  P4   ON3    104.0     120.0  !PPI2, from nad/ppi, adm jr., 7/01

DIHEDRALS
!
!atom types             Kchi    n   delta
!
ON4  P    ON2  CN7B     0.95    2     0.0  !for NADPH
ON4  P    ON2  CN7B     0.50    3     0.0  !for NADPH
! nicotinamide adenine dinucleotide
CN3  NN2  CN3B HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN2  NN2  CN3B HN3B     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3  CN3A HN3B     2.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3B CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3A HN3B     5.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3  HN3      1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A NN1      0.35    1   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A NN1      0.35    1     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3  CN1A     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3  CN3B     6.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3B CN3  CN3A     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN3B CN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3A X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN8  X        1.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN1  CN1A X        2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN2  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
! nicotinamide adenine dinucleotide hydride, nadh
CN8  CN3  CN1A ON1      1.00    2   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A ON1      1.00    3     0.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A ON1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.50    2   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.35    3   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A ON1      0.30    1     0.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A ON1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A NN1      1.10    1   180.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A NN1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
HN2  NN2  CN3C HN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  NN2  CN3C HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3C CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN8  CN3  CN3C NN2      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3  CN8  CN3      4.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3C NN2      2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN2  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN3C CN3      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
! pyrophosphate (ppi)
P3   ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P3   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P3   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P3   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P3   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P3   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P3   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P3   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P3   ON2  P3   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
! protonated pyrophosphate (ppi2)
P    ON2  P4   ON2      0.03    2     0.0  !from P ON2 P2 ON2, adm jr. 7/01
P    ON2  P4   ON2      0.03    3     0.0  !from P ON2 P2 ON2, adm jr. 7/01
P4   ON2  P    ON2      0.03    2     0.0  !from P ON2 P2 ON2, adm jr. 7/01
P4   ON2  P    ON2      0.03    3     0.0  !from P ON2 P2 ON2, adm jr. 7/01
P    ON2  P4   ON3      0.10    2     0.0  !from P ON2 P2 ON3, adm jr. 7/01
P    ON2  P4   ON3      0.03    3     0.0  !from P ON2 P2 ON3, adm jr. 7/01
P4   ON2  P    ON3      0.10    2     0.0  !from P ON2 P2 ON3, adm jr. 7/01
P4   ON2  P    ON3      0.03    3     0.0  !from P ON2 P2 ON3, adm jr. 7/01
P    ON2  P4   ON4      0.10    2     0.0  !from P ON2 P2 ON4, adm jr. 7/01
P    ON2  P4   ON4      0.03    3     0.0  !from P ON2 P2 ON4, adm jr. 7/01
X    ON4  P4   X        0.30    3     0.0  !from MP_1, adm jr.
!for nadp/nadph (?), adm jr.
HN7  CN7  CN7  CN7       0.195   3         0.0
HN7  CN7B NN2  CN3B      0.195   3         0.0
HN7  CN7B NN2  CN3C      0.195   3         0.0
HN7  CN7  CN7B ON6       0.195   3         0.0
HN7  CN7  CN7B ON2       0.195   3         0.0
HN7  CN7  CN7B NN2       0.195   3         0.0
!
ON6  CN7B CN7  ON5       3.4     1       180.0 !gam
CN7  CN7B NN2  CN3B      0.0     3         0.0
CN8  CN7B NN2  CN3B      0.0     3         0.0 ! 25P1
CN7B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
ON6  CN7B NN2  CN3B      0.0     3         0.0 !
ON6B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
CN7  CN7B NN2  CN3C      0.0     3         0.0
CN7B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
ON6  CN7B NN2  CN3C      0.0     3         0.0 !
ON6B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
CN7  CN7  CN7B NN2       0.0     3         0.0
CN8  CN7  CN7B NN2       0.0     3         0.0 ! 25P1
CN7  CN7B NN2  CN5       0.3     3         0.0 ! NF
CN7  CN7B NN2  CN4       0.0     3       180.0 ! NF
ON2  CN7  CN7B NN2       0.0     3         0.0
ON5  CN7  CN7B NN2       0.0     3         0.0

IMPROPER
!
!atom types           Kpsi                   psi0
!
! nicotinamide adenine dinucleotide                                             
CN3  CN3C CN8  HN6     15.0     0     0.0  !nich, jjp1/adm jr.
HN3B X    X    CN3     15.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3B X    X    CN3A    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3B X    X    CN3B    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN2  CN3  CN3B NN2     50.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN1  HN1  CN1A NN1     -5.0     0     0.0  !nad/ppi, jjp1/adm jr.
ON1  X    X    CN1A    40.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3  X    X    CN3C    53.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN6  X    X    CN3C    53.0     0     0.0  !nich, adm jr.
HN8  CN3  CN3  CN8     18.0     0     0.0  !nad/ppi, jjp1/adm jr.

NONBONDED  NBXMOD 5  ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH -
     CUTNB 14.0  CTOFNB 12.0  CTONNB 10.0  EPS 1.0  E14FAC 1.0  WMIN 1.5
!
!atom  ignored    epsilon      Rmin/2   ignored   eps,1-4       Rmin/2,1-4
!
HN3B     0.0       -0.046     0.9000 !nad/ppi, jjp1/adm jr.
CN1A     0.0       -0.07      2.0000 ! nad/ppi, jjp1/adm jr. (protein CC)
CN3A     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
CN3B     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
CN3C     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
P3       0.0       -0.585     2.15  ! nad/ppi, jjp1/adm jr.
P4       0.0       -0.585     2.15  ! for PPI2, adm jr.

end