1* \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File //// 2* \\\\\\\\\\\\\\\\\\ Developmental //////////////////////// 3* Alexander D. MacKerell Jr. and Nicolas Foloppe 4* December, 2003 5* All comments to ADM jr. via the CHARMM web site: www.charmm.org 6* parameter set discussion forum 7* 827 1 9 10! model componds moved to toppar_all27_na_model.str 11 12! NAD, ATP, PPI and related compounds moved to toppar_all27_na_nad_ppi.str 13 14! base modification residues and patches moved to toppar_all27_na_base_modifications.str 15 16! 17!references 18! 19!NUCLEIC ACIDS 20! 21!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for 22!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and 23!Condensed Phase Macromolecular Target Data. 2000, 21: 86-104. 24! 25!and 26! 27!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for 28!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA 29!and RNA in Solution. 2000, 21: 105-120. 30! 31 32MASS 1 HT 1.008000 H ! TIPS3P WATER HYDROGEN 33MASS 2 HN1 1.008000 H ! Nucleic acid amine proton 34MASS 3 HN2 1.008000 H ! Nucleic acid ring nitrogen proton 35MASS 4 HN3 1.008000 H ! Nucleic acid aromatic carbon proton 36MASS 5 HN3B 1.008000 H ! NAD+ aromatic hydrogen 37MASS 6 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene) 38MASS 7 HNP 1.008000 H ! pure aromatic H 39MASS 8 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton 40MASS 9 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton 41MASS 10 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton 42MASS 11 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) 43MASS 12 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds 44MASS 13 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds 45MASS 14 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha) 46MASS 15 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha) 47MASS 20 CN1 12.011000 C ! Nucleic acid carbonyl carbon 48MASS 21 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon 49MASS 22 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) 50MASS 23 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide 51MASS 24 CN3 12.011000 C ! Nucleic acid aromatic carbon 52MASS 25 CN3A 12.011000 C ! NAD+ aromatic carbon 53MASS 26 CN3B 12.011000 C ! NAD+ aromatic carbon 54MASS 27 CN3C 12.011000 C ! NADH aromatic carbon 55MASS 28 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC 56MASS 29 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 57MASS 30 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 58MASS 31 CN5 12.011000 C ! Nucleic acid purine C4 and C5 59MASS 32 CN5G 12.011000 C ! Nucleic acid guanine C5 60MASS 33 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) 61MASS 34 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1' 62MASS 35 CN7C 12.011000 C ! C2' in arabinose 63MASS 36 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives 64MASS 37 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) 65MASS 38 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) 66MASS 39 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) 67MASS 40 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha) 68MASS 41 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha) 69MASS 42 CNA 12.011000 C ! pure aromatic carbon 70MASS 43 CNA2 12.011000 C ! pure aromatic carbon bound to F 71MASS 44 CN6 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str) 72MASS 45 CN7E 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str) 73MASS 50 NN1 14.007000 N ! Nucleic acid amide nitrogen 74MASS 51 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) 75MASS 52 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen 76MASS 53 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE 77MASS 54 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) 78MASS 55 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 79MASS 56 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 80MASS 57 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen 81MASS 58 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 82MASS 59 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 83MASS 60 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 84MASS 61 NN4 14.007000 N ! Nucleic acid purine N7 85MASS 62 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen 86MASS 63 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) 87MASS 70 OT 15.999400 O ! TIPS3P WATER OXYGEN 88MASS 71 ON1 15.999400 O ! Nucleic acid carbonyl oxygen 89MASS 72 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 90MASS 73 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen 91MASS 74 ON3 15.999400 O ! Nucleic acid =O in phosphate 92MASS 75 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen 93MASS 76 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen 94MASS 77 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen 95MASS 78 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen 96MASS 79 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str) 97MASS 80 FN1 18.998400 F ! Fluorine for sugar derivatives (NF) 98MASS 81 FNA 18.998400 F ! Aromatic fluorine 99MASS 82 P 30.974000 P ! phosphorus 100MASS 83 P2 30.974000 P ! pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) 101MASS 84 P3 30.974000 P ! protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str) 102MASS 90 SOD 22.989770 NA ! Sodium Ion 103MASS 91 MG 24.305000 MG ! Magnesium Ion 104MASS 92 POT 39.102000 K ! Potassium Ion! check masses 105MASS 93 CES 132.900000 CS ! Cesium Ion 106MASS 94 CAL 40.080000 CA ! Calcium Ion 107MASS 95 CLA 35.450000 CL ! Chloride Ion 108MASS 96 ZN 65.370000 ZN ! zinc (II) cation 109MASS 99 DUM 0.001 H ! dummy atom 110MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF) 111MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF) 112MASS 104 HR3 1.008000 H ! For imidazole model compound (NF) 113MASS 105 HR1 1.008000 H ! For imidazole model compound (NF) 114MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF) 115MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF) 116 117DECL +P 118DECL +O1P 119DECL +O2P 120DECL +O5' 121DECL -O3' 122 123DEFA FIRS none LAST none 124AUTOGENERATE ANGLES DIHEDRALS 125 126RESI GUA -1.00 ! O6 127ATOM P P 1.50 ! || 128ATOM O1P ON3 -0.78 ! C6 129ATOM O2P ON3 -0.78 ! / \ 130ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\ 131ATOM C5' CN8B -0.08 ! | || C8-H8 132ATOM H5' HN8 0.09 ! C2 C4--N9/ 133ATOM H5'' HN8 0.09 ! / \\ / \ 134GROUP ! H21-N2 N3 \ 135ATOM C4' CN7 0.16 ! | \ 136ATOM H4' HN7 0.09 ! H22 \ 137ATOM O4' ON6B -0.50 ! \ 138ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 139ATOM H1' HN7 0.09 ! | | \ / \ \ 140GROUP ! -P-O5'-C5'---C4' C1' 141ATOM N9 NN2B -0.02 ! | | \ / \ 142ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' 143ATOM N2 NN1 -0.68 ! / \ / \ 144ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' 145ATOM H22 HN1 0.35 ! | | 146ATOM N3 NN3G -0.74 ! H2' 147ATOM C2 CN2 0.75 148ATOM N1 NN2G -0.34 149ATOM H1 HN2 0.26 150ATOM C6 CN1 0.54 151ATOM O6 ON1 -0.51 152ATOM C5 CN5G 0.00 153ATOM N7 NN4 -0.60 154ATOM C8 CN4 0.25 155ATOM H8 HN3 0.16 156GROUP 157ATOM C2' CN7B 0.14 158ATOM H2'' HN7 0.09 159ATOM O2' ON5 -0.66 160ATOM H2' HN5 0.43 161GROUP 162ATOM C3' CN7 0.01 163ATOM H3' HN7 0.09 164ATOM O3' ON2 -0.57 165BOND P O1P P O2P P O5' 166BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 167BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 168BOND C2 N2 C2 N1 N2 H21 169BOND N2 H22 N1 H1 N1 C6 C6 C5 170BOND C5 N7 C2' C3' C3' O3' O3' +P 171BOND C2' O2' O2' H2' 172BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 173BOND C5' H5'' C8 H8 174DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 175IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 176DONO H21 N2 177DONO H22 N2 178DONO H1 N1 179DONO H2' O2' 180ACCE O6 C6 181ACCE N3 182ACCE N7 183ACCE O1P P 184ACCE O2P P 185ACCE O2' 186ACCE O3' 187ACCE O4' 188ACCE O5' 189! Chi and sugar-phosphate backbone in B-DNA like conformation 190BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 191BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 192BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 193BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 194BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 195BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 196BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 197BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 198BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 199BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 200BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck 201BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 202BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi 203BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 204BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 205BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 206BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 207BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 208BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 209BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 210BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 211BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 212BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 213BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 214BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 215BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 216BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 217BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 218BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 219BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 220BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 221BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 222BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 223BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 224 225 226RESI ADE -1.00 ! H61 H62! 227ATOM P P 1.50 ! \ / 228ATOM O1P ON3 -0.78 ! N6 229ATOM O2P ON3 -0.78 ! | 230ATOM O5' ON2 -0.57 ! C6 231ATOM C5' CN8B -0.08 ! // \ 232ATOM H5' HN8 0.09 ! N1 C5--N7\\ 233ATOM H5'' HN8 0.09 ! | || C8-H8 234GROUP ! C2 C4--N9/ 235ATOM C4' CN7 0.16 ! / \\ / \ 236ATOM H4' HN7 0.09 ! H2 N3 \ 237ATOM O4' ON6B -0.50 ! \ 238ATOM C1' CN7B 0.16 ! \ 239ATOM H1' HN7 0.09 ! \ 240GROUP ! O1P H5' H4' O4' \ 241ATOM N9 NN2 -0.05 ! | | \ / \ \ 242ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1' 243ATOM N7 NN4 -0.71 ! | | \ / \ 244ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1' 245ATOM H8 HN3 0.12 ! / \ / \ 246ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' 247ATOM C2 CN4 0.50 ! | | 248ATOM H2 HN3 0.13 ! H2' 249ATOM N3 NN3A -0.75 250ATOM C4 CN5 0.43 251ATOM C6 CN2 0.46 252ATOM N6 NN1 -0.77 253ATOM H61 HN1 0.38 254ATOM H62 HN1 0.38 255GROUP 256ATOM C2' CN7B 0.14 257ATOM H2'' HN7 0.09 258ATOM O2' ON5 -0.66 259ATOM H2' HN5 0.43 260GROUP 261ATOM C3' CN7 0.01 262ATOM H3' HN7 0.09 263ATOM O3' ON2 -0.57 264BOND P O1P P O2P P O5' 265BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 266BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 267BOND C2 N1 C6 N6 268BOND N6 H61 N6 H62 C6 C5 C5 N7 269BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P 270BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 271BOND C5' H5'' C8 H8 C2 H2 272DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 273IMPR N6 C6 H61 H62 C6 N1 C5 N6 274DONO H61 N6 275DONO H62 N6 276DONO H2' O2' 277ACCE N3 278ACCE N7 279ACCE N1 280ACCE O1P P 281ACCE O2P P 282ACCE O2' 283ACCE O3' 284ACCE O4' 285ACCE O5' 286BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 287BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 288BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 289BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 290BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 291BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 292BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 293BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 294BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 295BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 296BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck 297BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 298BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi 299BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 300BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 301BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 302BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 303BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 304BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 305BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 306BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 307BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 308BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 309BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 310BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 311BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 312BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 313BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 314BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 315BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 316BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 317BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 318BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 319BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 320BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 321BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 322 323RESI CYT -1.00 324ATOM P P 1.50 ! 325ATOM O1P ON3 -0.78 ! H42 H41 326ATOM O2P ON3 -0.78 ! \ / 327ATOM O5' ON2 -0.57 ! N4 328ATOM C5' CN8B -0.08 ! | 329ATOM H5' HN8 0.09 ! C4 330ATOM H5'' HN8 0.09 ! / \\ 331GROUP ! H5-C5 N3 332ATOM C4' CN7 0.16 ! || | 333ATOM H4' HN7 0.09 ! H6-C6 C2 334ATOM O4' ON6B -0.50 ! \ / \\ 335ATOM C1' CN7B 0.16 ! N1 O2 336ATOM H1' HN7 0.09 ! \ 337GROUP ! \ 338ATOM N1 NN2 -0.13 ! \ 339ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ 340ATOM H6 HN3 0.17 ! | | \ / \ \ 341ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1' 342ATOM H5 HN3 0.07 ! | | \ / \ 343ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1' 344ATOM O2 ON1C -0.49 ! / \ / \ 345ATOM N3 NN3 -0.66 ! O3' H3' O2' H2'' 346ATOM C4 CN2 0.65 ! | | 347ATOM N4 NN1 -0.75 ! H2' 348ATOM H41 HN1 0.37 349ATOM H42 HN1 0.33 350GROUP 351ATOM C2' CN7B 0.14 352ATOM H2'' HN7 0.09 353ATOM O2' ON5 -0.66 354ATOM H2' HN5 0.43 355GROUP 356ATOM C3' CN7 0.01 357ATOM H3' HN7 0.09 358ATOM O3' ON2 -0.57 359BOND P O1P P O2P P O5' 360BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 361BOND C1' N1 C1' C2' N1 C2 N1 C6 362BOND C2 N3 C4 N4 N4 H41 N4 H42 363BOND C4 C5 C2' C3' C3' O3' O3' +P 364BOND C2' O2' O2' H2' 365BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 366BOND C5' H5'' C5 H5 C6 H6 367DOUBLE C2 O2 C5 C6 N3 C4 368IMPR C2 N1 N3 O2 C4 N3 C5 N4 369IMPR N4 C4 H41 H42 370DONO H42 N4 371DONO H2' O2' 372DONO H41 N4 373ACCE O2 C2 374ACCE N3 375ACCE O1P P 376ACCE O2P P 377ACCE O2' 378ACCE O3' 379ACCE O4' 380ACCE O5' 381 382BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 383BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 384BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 385BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 386BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 387BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 388BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 389BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 390BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 391BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 392BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 393BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 394BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi 395BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 396BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 397BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 398BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 399BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 400BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 401BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 402BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 403BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 404BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 405BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 406BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 407BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 408BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 409BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 410BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 411BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 412BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 413 414RESI THY -1.00 ! H51 O4 415ATOM P P 1.50 ! | || 416ATOM O1P ON3 -0.78 ! H52-C5M C4 H3 417ATOM O2P ON3 -0.78 ! | \ / \ / 418ATOM O5' ON2 -0.57 ! H53 C5 N3 419ATOM C5' CN8B -0.08 ! || | 420ATOM H5' HN8 0.09 ! H6-C6 C2 421ATOM H5'' HN8 0.09 ! \ / \\ 422GROUP ! N1 O2 423ATOM C4' CN7 0.16 ! \ 424ATOM H4' HN7 0.09 ! \ 425ATOM O4' ON6B -0.50 ! \ 426ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 427ATOM H1' HN7 0.09 ! | | \ / \ \ 428GROUP ! -P-O5'-C5'---C4' C1' 429ATOM N1 NN2B -0.34 ! | | \ / \ 430ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1' 431ATOM H6 HN3 0.17 ! / \ / \ 432ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' 433ATOM O2 ON1 -0.41 ! | | 434ATOM N3 NN2U -0.46 ! H2' 435ATOM H3 HN2 0.36 ! 436ATOM C4 CN1 0.50 ! 437ATOM O4 ON1 -0.45 ! 438ATOM C5 CN3T -0.15 439ATOM C5M CN9 -0.11 440ATOM H51 HN9 0.07 441ATOM H52 HN9 0.07 442ATOM H53 HN9 0.07 443GROUP 444ATOM C2' CN7B 0.14 445ATOM H2'' HN7 0.09 446ATOM O2' ON5 -0.66 447ATOM H2' HN5 0.43 448GROUP 449ATOM C3' CN7 0.01 450ATOM H3' HN7 0.09 451ATOM O3' ON2 -0.57 452BOND P O1P P O2P P O5' 453BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 454BOND C1' N1 C1' C2' N1 C2 N1 C6 455BOND C2 N3 N3 H3 N3 C4 C4 C5 456BOND C5 C5M C2' C3' C3' O3' O3' +P 457BOND C2' O2' O2' H2' 458BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 459BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 460DOUBLE C2 O2 C4 O4 C5 C6 461IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M 462DONO H3 N3 463DONO H2' O2' 464ACCE O2 C2 465ACCE O4 C4 466ACCE O1P P 467ACCE O2P P 468ACCE O2' 469ACCE O3' 470ACCE O4' 471ACCE O5' 472 473BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 474BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 475BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 476BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 477BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 478BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 479BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 480BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 481BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 482BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 483BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 484BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 485BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi 486BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 487BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 488BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 489BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 490BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 491BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 492BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 493BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 494BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 495BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 496BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 497BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 498BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 499BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 500BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 501BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 502BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 503BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 504BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 505BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 506 507RESI URA -1.00 ! O4 508ATOM P P 1.50 ! || 509ATOM O1P ON3 -0.78 ! C4 H3 510ATOM O2P ON3 -0.78 ! / \ / 511ATOM O5' ON2 -0.57 ! H5-C5 N3 512ATOM C5' CN8B -0.08 ! || | 513ATOM H5' HN8 0.09 ! H6-C6 C2 514ATOM H5'' HN8 0.09 ! \ / \\ 515GROUP ! N1 O2 516ATOM C4' CN7 0.16 ! \ 517ATOM H4' HN7 0.09 ! \ 518ATOM O4' ON6B -0.50 ! \ 519ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 520ATOM H1' HN7 0.09 ! | | \ / \ \ 521GROUP ! -P-O5'-C5'---C4' C1' 522ATOM N1 NN2B -0.34 ! | | \ / \ 523ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' 524ATOM H6 HN3 0.14 ! / \ / \ 525ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' 526ATOM O2 ON1 -0.45 ! | | 527ATOM N3 NN2U -0.46 ! H2' 528ATOM H3 HN2 0.36 ! 529ATOM C4 CN1 0.53 ! 530ATOM O4 ON1 -0.48 ! 531ATOM C5 CN3 -0.15 ! 532ATOM H5 HN3 0.10 ! 533GROUP 534ATOM C2' CN7B 0.14 535ATOM H2'' HN7 0.09 536ATOM O2' ON5 -0.66 537ATOM H2' HN5 0.43 538GROUP 539ATOM C3' CN7 0.01 540ATOM H3' HN7 0.09 541ATOM O3' ON2 -0.57 542BOND P O1P P O2P P O5' 543BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 544BOND C1' N1 C1' C2' N1 C2 N1 C6 545BOND C2 N3 N3 H3 N3 C4 C4 C5 546BOND C2' C3' C3' O3' O3' +P 547BOND C2' O2' O2' H2' 548BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 549BOND C5' H5'' C5 H5 C6 H6 550DOUBLE C2 O2 C4 O4 C5 C6 551IMPR C2 N1 N3 O2 C4 N3 C5 O4 552DONO H3 N3 553DONO H2' O2' 554ACCE O2 C2 555ACCE O4 C4 556ACCE O1P P 557ACCE O2P P 558ACCE O2' 559ACCE O3' 560ACCE O4' 561ACCE O5' 562BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 563BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 564BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 565BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 566BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 567BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 568BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 569BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 570BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 571BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 572BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 573BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 574BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 575BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 576BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 577BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 578BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 579BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 580BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 581BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 582BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 583BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 584BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 585BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 586BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 587BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 588BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 589BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 590BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 591BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 592 593! NOTE the option to regenerate all angles and dihedrals allows 594! the explicit inclusion of the THET and DIHE terms to be omitted 595! even if the PRES is used in a PATCH statement. It is important to 596! inspect the patches prior to use to determine if they should be used 597! in a GENErate or PATCh statement and/or if the AUTOgeneration of 598! angles and dihedrals is required. 599! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the 600! documentation 601 602PRES DEO1 0.000 ! Patch to make DEOXYribose in PYRIMIDINES 603DELETE ATOM O2' ! necessary due to auto-generate dihedrals 604 605GROUP ! To correct O4' atom type in DNA (NF) 606ATOM C4' CN7 0.16 ! 607ATOM H4' HN7 0.09 ! 608ATOM O4' ON6 -0.50 ! 609ATOM C1' CN7B 0.16 ! 610ATOM H1' HN7 0.09 ! 611GROUP 612ATOM C2' CN8 -0.18 613ATOM H2' HN8 0.09 614ATOM H2'' HN8 0.09 615 616BOND C2' H2' 617THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' 618DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' 619DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' 620BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 621 622PRES DEO2 0.000 ! Patch to make DEOXYribose in PURINES 623DELETE ATOM O2' ! necessary due to auto-generate dihedrals 624 625GROUP ! To correct O4' atom type in DNA (NF) 626ATOM C4' CN7 0.16 ! 627ATOM H4' HN7 0.09 ! 628ATOM O4' ON6 -0.50 ! 629ATOM C1' CN7B 0.16 ! 630ATOM H1' HN7 0.09 ! 631GROUP 632ATOM C2' CN8 -0.18 633ATOM H2' HN8 0.09 634ATOM H2'' HN8 0.09 635 636BOND C2' H2' 637THET C1' C2' H2' C3' C2' H2' H2' C2' H2'' 638DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' 639DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' 640BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 641 642PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH 643 ! use in generate statement 644GROUP 645ATOM H5T HN5 0.43 646ATOM O5' ON5 -0.66 647ATOM C5' CN8B 0.05 648ATOM H5' HN8 0.09 649ATOM H5'' HN8 0.09 650! 651DELETE ATOM P 652DELETE ATOM O1P 653DELETE ATOM O2P 654! 655BOND H5T O5' 656DONO H5T O5' 657BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 658 659PRES 5MET 0.00 ! 5'-ribose METHYL patch 660 ! use in generate statement 661GROUP 662ATOM C5' CN9 -0.27 663ATOM H5' HN9 0.09 664ATOM H5'' HN9 0.09 665ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY 666! 667DELETE ATOM O5' 668DELETE ATOM P 669DELETE ATOM O1P 670DELETE ATOM O2P 671! 672BOND C5' H53' 673IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000 674IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000 675IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000 676 677PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch 678 ! use in generate statement 679GROUP 680ATOM C5' CN8B -0.08 681ATOM H5' HN8 0.09 682ATOM H5'' HN8 0.09 683ATOM P P 1.50 684ATOM O1P ON3 -0.82 685ATOM O2P ON3 -0.82 686ATOM O5' ON2 -0.62 687ATOM O5T ON4 -0.68 688ATOM H5T HN4 0.34 689BOND O5T P H5T O5T 690DONO H5T O5T 691! Built in B-DNA-like conformation (NF) 692BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 693BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 694BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 695BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 696BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 697 698PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch 699 ! use in generate statement 700GROUP 701ATOM C5' CN8B -0.08 702ATOM H5' HN8 0.09 703ATOM H5'' HN8 0.09 704ATOM P P 1.50 705ATOM O1P ON3 -0.78 706ATOM O2P ON3 -0.78 707ATOM O5' ON2 -0.57 708ATOM O5T ON2 -0.57 709ATOM C5T CN9 -0.17 710ATOM H5T1 HN9 0.09 711ATOM H5T2 HN9 0.09 712ATOM H5T3 HN9 0.09 713 714BOND O5T P O5T C5T C5T H5T1 C5T H5T2 715BOND C5T H5T3 716!DONO H5T O5T 717! Built in B-DNA-like conformation (NF) 718BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 719BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 720BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 721BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 722BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 723BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000 724BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000 725BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000 726 727PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH 728 ! use in generate statement 729GROUP 730ATOM C3' CN7 0.14 731ATOM H3' HN7 0.09 732ATOM O3' ON5 -0.66 733ATOM H3T HN5 0.43 734BOND O3' H3T 735DONO H3T O3' 736BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 737 738PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch 739 ! use in generate statement 740GROUP 741ATOM C3' CN7 0.01 742ATOM H3' HN7 0.09 743ATOM P3 P 1.50 744ATOM O1P3 ON3 -0.82 745ATOM O2P3 ON3 -0.82 746ATOM O3' ON2 -0.62 747ATOM O3T ON4 -0.68 748ATOM H3T HN4 0.34 749BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T 750DONO H3T O3T 751ACCE O3T 752ACCE O1P2 753ACCE O2P3 754! Build in B-DNA-like conformation (NF) 755BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 756BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000 757BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 758BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 759BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 760 761PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch 762 ! use in generate statement 763! To build model compound with OPO3-CH3 at the 3' end (nicolas) 764GROUP 765ATOM C3' CN7 0.01 766ATOM H3' HN7 0.09 767ATOM P3 P 1.50 768ATOM O1P3 ON3 -0.78 769ATOM O2P3 ON3 -0.78 770ATOM O3' ON2 -0.57 771ATOM O3T ON2 -0.57 772ATOM C3T CN9 -0.17 773ATOM H3T1 HN9 0.09 774ATOM H3T2 HN9 0.09 775ATOM H3T3 HN9 0.09 776 777BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T 778BOND C3T H3T1 C3T H3T2 C3T H3T3 779ACCE O3' 780ACCE O5' 781ACCE O1P2 782ACCE O1P3 783BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 784BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000 785BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 786BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 787BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 788BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000 789BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000 790BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000 791 792PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch 793 ! use in generate statement 794 ! Added by Nicolas, to be consistent with model componds 795GROUP 796ATOM C3' CN7 -0.09 797ATOM H3' HN7 0.09 798ATOM P3 P 1.10 799ATOM O3' ON2 -0.40 800ATOM O1P3 ON3 -0.90 801ATOM O2P3 ON3 -0.90 802ATOM O3P3 ON3 -0.90 803BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3 804ACCE O1P2 805ACCE O1P3 806BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000 807BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000 808BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 809BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 810BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000 811BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000 812 813PRES DELB 0.00 ! patch to delete all possible base atoms 814 ! of Cyt,Gua,Ade,Thy and Ura 815 ! 816!note: error messages will be obtained due to atoms not present in 817!residue being "deleted" by this patch 818!cyt section 819DELE ATOM N1 820DELE ATOM C6 821DELE ATOM H6 822DELE ATOM C2 823DELE ATOM O2 824DELE ATOM N3 825DELE ATOM C4 826DELE ATOM N4 827DELE ATOM H41 828DELE ATOM H42 829DELE ATOM C5 830DELE ATOM H5 831!gua section 832DELE ATOM N9 833DELE ATOM H1 834DELE ATOM N2 835DELE ATOM H21 836DELE ATOM H22 837DELE ATOM O6 838DELE ATOM N7 839DELE ATOM C8 840DELE ATOM H8 841!ade section 842DELE ATOM H2 843DELE ATOM N6 844DELE ATOM H61 845DELE ATOM H62 846!thy/ura section 847DELE ATOM H3 848DELE ATOM O4 849DELE ATOM C5M 850DELE ATOM H51 851DELE ATOM H52 852DELE ATOM H53 853 854PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide 855 ! use AUTOGEN ANGLE DIHE after this patch 856BOND O3' P ! but before water-generation 857 858PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES) 859 ! eg: patch sega 10 segb 1 860 ! sega should have std 3' (gene sega ... last none) 861 ! segb should have std 5' (gene segb ... first none) 862 ! USE AUTOgen ANGL DIHE after this patch, 863 ! but before water-generation 864BOND 1O3' 2P 865!following commented due to use of autogenerate 866!THET 1C3' 1O3' 2P 867!THET 1O3' 2P 2O5' 868!THET 1O3' 2P 2O1P 869!THET 1O3' 2P 2O2P 870!DIHE 1O3' 2P 2O5' 2C5' 1O3' 2P 2O5' 2C5' 871!DIHE 1C4' 1C3' 1O3' 2P 872!DIHE 1C3' 1O3' 2P 2O5' 1C3' 1O3' 2P 2O5' 873IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401 874IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802 875IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801 876IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001 877IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996 878 879RESI TIP3 0.00 ! TIPS3P WATER MODEL 880 ! GENERATE USING NOANGLE NODIHEDRAL 881GROUP 882ATOM OH2 OT -0.834 883ATOM H1 HT 0.417 884ATOM H2 HT 0.417 885BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE 886ANGLE H1 OH2 H2 ! REQUIRED 887ACCEPTOR OH2 888PATCHING FIRS NONE LAST NONE 889 890RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p 891GROUP 892ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup 893ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup 894ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup 895BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p 896ANGLE H1 OH2 H2 ! required 897ACCEPTOR OH2 898PATCHING FIRS NONE LAST NONE 899 900! Ion parameters from Benoit Roux and Coworkers 901! As of 8/98 no NBFIX terms required 902! 903RESI SOD 1.00 ! Sodium Ion 904GROUP 905ATOM SOD SOD 1.00 906PATCHING FIRST NONE LAST NONE 907 908RESI MG 2.00 ! Magnesium Ion 909GROUP 910ATOM MG MG 2.00 911PATCHING FIRST NONE LAST NONE 912 913RESI POT 1.00 ! Potassium Ion 914GROUP 915ATOM POT POT 1.00 916PATCHING FIRST NONE LAST NONE 917 918RESI CES 1.00 ! Cesium Ion 919GROUP 920ATOM CES CES 1.00 921PATCHING FIRST NONE LAST NONE 922 923RESI CAL 2.00 ! Calcium Ion 924GROUP 925ATOM CAL CAL 2.00 926PATCHING FIRST NONE LAST NONE 927 928RESI CLA -1.00 ! Chloride Ion 929GROUP 930ATOM CLA CLA -1.00 931PATCHING FIRST NONE LAST NONE 932 933RESI ZN2 2.00 ! Zinc ion, Roland Stote 934GROUP 935ATOM ZN ZN 2.00 936PATCHING FIRST NONE LAST NONE 937 938end 939 940