* 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