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* \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////
* \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
* Alexander D. MacKerell Jr. and Nicolas Foloppe
* December, 2003
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
27 1
! model componds moved to toppar_all27_na_model.str
! NAD, ATP, PPI and related compounds moved to toppar_all27_na_nad_ppi.str
! base modification residues and patches moved to toppar_all27_na_base_modifications.str
!
!references
!
!NUCLEIC ACIDS
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data. 2000, 21: 86-104.
!
!and
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. 2000, 21: 105-120.
!
MASS 1 HT 1.008000 H ! TIPS3P WATER HYDROGEN
MASS 2 HN1 1.008000 H ! Nucleic acid amine proton
MASS 3 HN2 1.008000 H ! Nucleic acid ring nitrogen proton
MASS 4 HN3 1.008000 H ! Nucleic acid aromatic carbon proton
MASS 5 HN3B 1.008000 H ! NAD+ aromatic hydrogen
MASS 6 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene)
MASS 7 HNP 1.008000 H ! pure aromatic H
MASS 8 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 9 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton
MASS 10 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton
MASS 11 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA)
MASS 12 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds
MASS 13 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds
MASS 14 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 15 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 20 CN1 12.011000 C ! Nucleic acid carbonyl carbon
MASS 21 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon
MASS 22 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2)
MASS 23 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide
MASS 24 CN3 12.011000 C ! Nucleic acid aromatic carbon
MASS 25 CN3A 12.011000 C ! NAD+ aromatic carbon
MASS 26 CN3B 12.011000 C ! NAD+ aromatic carbon
MASS 27 CN3C 12.011000 C ! NADH aromatic carbon
MASS 28 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
MASS 29 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
MASS 30 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2
MASS 31 CN5 12.011000 C ! Nucleic acid purine C4 and C5
MASS 32 CN5G 12.011000 C ! Nucleic acid guanine C5
MASS 33 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
MASS 34 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'
MASS 35 CN7C 12.011000 C ! C2' in arabinose
MASS 36 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives
MASS 37 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 38 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 39 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
MASS 40 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 41 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 42 CNA 12.011000 C ! pure aromatic carbon
MASS 43 CNA2 12.011000 C ! pure aromatic carbon bound to F
MASS 44 CN6 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
MASS 45 CN7E 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
MASS 50 NN1 14.007000 N ! Nucleic acid amide nitrogen
MASS 51 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha)
MASS 52 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen
MASS 53 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE
MASS 54 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha)
MASS 55 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
MASS 56 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
MASS 57 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen
MASS 58 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
MASS 59 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3
MASS 60 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3
MASS 61 NN4 14.007000 N ! Nucleic acid purine N7
MASS 62 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen
MASS 63 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
MASS 70 OT 15.999400 O ! TIPS3P WATER OXYGEN
MASS 71 ON1 15.999400 O ! Nucleic acid carbonyl oxygen
MASS 72 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
MASS 73 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 74 ON3 15.999400 O ! Nucleic acid =O in phosphate
MASS 75 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 76 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen
MASS 77 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen
MASS 78 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen
MASS 79 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str)
MASS 80 FN1 18.998400 F ! Fluorine for sugar derivatives (NF)
MASS 81 FNA 18.998400 F ! Aromatic fluorine
MASS 82 P 30.974000 P ! phosphorus
MASS 83 P2 30.974000 P ! pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
MASS 84 P3 30.974000 P ! protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
MASS 90 SOD 22.989770 NA ! Sodium Ion
MASS 91 MG 24.305000 MG ! Magnesium Ion
MASS 92 POT 39.102000 K ! Potassium Ion! check masses
MASS 93 CES 132.900000 CS ! Cesium Ion
MASS 94 CAL 40.080000 CA ! Calcium Ion
MASS 95 CLA 35.450000 CL ! Chloride Ion
MASS 96 ZN 65.370000 ZN ! zinc (II) cation
MASS 99 DUM 0.001 H ! dummy atom
MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF)
MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF)
MASS 104 HR3 1.008000 H ! For imidazole model compound (NF)
MASS 105 HR1 1.008000 H ! For imidazole model compound (NF)
MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF)
MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF)
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS
RESI GUA -1.00 ! O6
ATOM P P 1.50 ! ||
ATOM O1P ON3 -0.78 ! C6
ATOM O2P ON3 -0.78 ! / \
ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\
ATOM C5' CN8B -0.08 ! | || C8-H8
ATOM H5' HN8 0.09 ! C2 C4--N9/
ATOM H5'' HN8 0.09 ! / \\ / \
GROUP ! H21-N2 N3 \
ATOM C4' CN7 0.16 ! | \
ATOM H4' HN7 0.09 ! H22 \
ATOM O4' ON6B -0.50 ! \
ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
ATOM H1' HN7 0.09 ! | | \ / \ \
GROUP ! -P-O5'-C5'---C4' C1'
ATOM N9 NN2B -0.02 ! | | \ / \
ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1'
ATOM N2 NN1 -0.68 ! / \ / \
ATOM H21 HN1 0.32 ! O3' H3' O2' H2''
ATOM H22 HN1 0.35 ! | |
ATOM N3 NN3G -0.74 ! H2'
ATOM C2 CN2 0.75
ATOM N1 NN2G -0.34
ATOM H1 HN2 0.26
ATOM C6 CN1 0.54
ATOM O6 ON1 -0.51
ATOM C5 CN5G 0.00
ATOM N7 NN4 -0.60
ATOM C8 CN4 0.25
ATOM H8 HN3 0.16
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 0.01
ATOM H3' HN7 0.09
ATOM O3' ON2 -0.57
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
BOND C2 N2 C2 N1 N2 H21
BOND N2 H22 N1 H1 N1 C6 C6 C5
BOND C5 N7 C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C8 H8
DOUBLE C2 N3 C4 C5 N7 C8 C6 O6
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 O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone in B-DNA like conformation
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI ADE -1.00 ! H61 H62!
ATOM P P 1.50 ! \ /
ATOM O1P ON3 -0.78 ! N6
ATOM O2P ON3 -0.78 ! |
ATOM O5' ON2 -0.57 ! C6
ATOM C5' CN8B -0.08 ! // \
ATOM H5' HN8 0.09 ! N1 C5--N7\\
ATOM H5'' HN8 0.09 ! | || C8-H8
GROUP ! C2 C4--N9/
ATOM C4' CN7 0.16 ! / \\ / \
ATOM H4' HN7 0.09 ! H2 N3 \
ATOM O4' ON6B -0.50 ! \
ATOM C1' CN7B 0.16 ! \
ATOM H1' HN7 0.09 ! \
GROUP ! O1P H5' H4' O4' \
ATOM N9 NN2 -0.05 ! | | \ / \ \
ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1'
ATOM N7 NN4 -0.71 ! | | \ / \
ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1'
ATOM H8 HN3 0.12 ! / \ / \
ATOM N1 NN3A -0.74 ! O3' H3' O2' H2''
ATOM C2 CN4 0.50 ! | |
ATOM H2 HN3 0.13 ! H2'
ATOM N3 NN3A -0.75
ATOM C4 CN5 0.43
ATOM C6 CN2 0.46
ATOM N6 NN1 -0.77
ATOM H61 HN1 0.38
ATOM H62 HN1 0.38
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 0.01
ATOM H3' HN7 0.09
ATOM O3' ON2 -0.57
BOND P O1P P O2P P O5'
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' O3' +P
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C8 H8 C2 H2
DOUBLE N1 C6 C2 N3 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 O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI CYT -1.00
ATOM P P 1.50 !
ATOM O1P ON3 -0.78 ! H42 H41
ATOM O2P ON3 -0.78 ! \ /
ATOM O5' ON2 -0.57 ! N4
ATOM C5' CN8B -0.08 ! |
ATOM H5' HN8 0.09 ! C4
ATOM H5'' HN8 0.09 ! / \\
GROUP ! H5-C5 N3
ATOM C4' CN7 0.16 ! || |
ATOM H4' HN7 0.09 ! H6-C6 C2
ATOM O4' ON6B -0.50 ! \ / \\
ATOM C1' CN7B 0.16 ! N1 O2
ATOM H1' HN7 0.09 ! \
GROUP ! \
ATOM N1 NN2 -0.13 ! \
ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \
ATOM H6 HN3 0.17 ! | | \ / \ \
ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1'
ATOM H5 HN3 0.07 ! | | \ / \
ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1'
ATOM O2 ON1C -0.49 ! / \ / \
ATOM N3 NN3 -0.66 ! O3' H3' O2' H2''
ATOM C4 CN2 0.65 ! | |
ATOM N4 NN1 -0.75 ! H2'
ATOM H41 HN1 0.37
ATOM H42 HN1 0.33
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 0.01
ATOM H3' HN7 0.09
ATOM O3' ON2 -0.57
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6
BOND C2 N3 C4 N4 N4 H41 N4 H42
BOND C4 C5 C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C5 H5 C6 H6
DOUBLE C2 O2 C5 C6 N3 C4
IMPR C2 N1 N3 O2 C4 N3 C5 N4
IMPR N4 C4 H41 H42
DONO H42 N4
DONO H2' O2'
DONO H41 N4
ACCE O2 C2
ACCE N3
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI THY -1.00 ! H51 O4
ATOM P P 1.50 ! | ||
ATOM O1P ON3 -0.78 ! H52-C5M C4 H3
ATOM O2P ON3 -0.78 ! | \ / \ /
ATOM O5' ON2 -0.57 ! H53 C5 N3
ATOM C5' CN8B -0.08 ! || |
ATOM H5' HN8 0.09 ! H6-C6 C2
ATOM H5'' HN8 0.09 ! \ / \\
GROUP ! N1 O2
ATOM C4' CN7 0.16 ! \
ATOM H4' HN7 0.09 ! \
ATOM O4' ON6B -0.50 ! \
ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
ATOM H1' HN7 0.09 ! | | \ / \ \
GROUP ! -P-O5'-C5'---C4' C1'
ATOM N1 NN2B -0.34 ! | | \ / \
ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1'
ATOM H6 HN3 0.17 ! / \ / \
ATOM C2 CN1T 0.51 ! O3' H3' O2' H2''
ATOM O2 ON1 -0.41 ! | |
ATOM N3 NN2U -0.46 ! H2'
ATOM H3 HN2 0.36 !
ATOM C4 CN1 0.50 !
ATOM O4 ON1 -0.45 !
ATOM C5 CN3T -0.15
ATOM C5M CN9 -0.11
ATOM H51 HN9 0.07
ATOM H52 HN9 0.07
ATOM H53 HN9 0.07
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 0.01
ATOM H3' HN7 0.09
ATOM O3' ON2 -0.57
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6
BOND C2 N3 N3 H3 N3 C4 C4 C5
BOND C5 C5M C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53
DOUBLE C2 O2 C4 O4 C5 C6
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 O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
RESI URA -1.00 ! O4
ATOM P P 1.50 ! ||
ATOM O1P ON3 -0.78 ! C4 H3
ATOM O2P ON3 -0.78 ! / \ /
ATOM O5' ON2 -0.57 ! H5-C5 N3
ATOM C5' CN8B -0.08 ! || |
ATOM H5' HN8 0.09 ! H6-C6 C2
ATOM H5'' HN8 0.09 ! \ / \\
GROUP ! N1 O2
ATOM C4' CN7 0.16 ! \
ATOM H4' HN7 0.09 ! \
ATOM O4' ON6B -0.50 ! \
ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
ATOM H1' HN7 0.09 ! | | \ / \ \
GROUP ! -P-O5'-C5'---C4' C1'
ATOM N1 NN2B -0.34 ! | | \ / \
ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1'
ATOM H6 HN3 0.14 ! / \ / \
ATOM C2 CN1T 0.55 ! O3' H3' O2' H2''
ATOM O2 ON1 -0.45 ! | |
ATOM N3 NN2U -0.46 ! H2'
ATOM H3 HN2 0.36 !
ATOM C4 CN1 0.53 !
ATOM O4 ON1 -0.48 !
ATOM C5 CN3 -0.15 !
ATOM H5 HN3 0.10 !
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 0.01
ATOM H3' HN7 0.09
ATOM O3' ON2 -0.57
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6
BOND C2 N3 N3 H3 N3 C4 C4 C5
BOND C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C5 H5 C6 H6
DOUBLE C2 O2 C4 O4 C5 C6
IMPR C2 N1 N3 O2 C4 N3 C5 O4
DONO H3 N3
DONO H2' O2'
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
! NOTE the option to regenerate all angles and dihedrals allows
! the explicit inclusion of the THET and DIHE terms to be omitted
! even if the PRES is used in a PATCH statement. It is important to
! inspect the patches prior to use to determine if they should be used
! in a GENErate or PATCh statement and/or if the AUTOgeneration of
! angles and dihedrals is required.
! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
! documentation
PRES DEO1 0.000 ! Patch to make DEOXYribose in PYRIMIDINES
DELETE ATOM O2' ! necessary due to auto-generate dihedrals
GROUP ! To correct O4' atom type in DNA (NF)
ATOM C4' CN7 0.16 !
ATOM H4' HN7 0.09 !
ATOM O4' ON6 -0.50 !
ATOM C1' CN7B 0.16 !
ATOM H1' HN7 0.09 !
GROUP
ATOM C2' CN8 -0.18
ATOM H2' HN8 0.09
ATOM H2'' HN8 0.09
BOND C2' H2'
THET C1' C2' H2' C3' C2' H2' H2' C2' H2''
DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1'
DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3'
BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
PRES DEO2 0.000 ! Patch to make DEOXYribose in PURINES
DELETE ATOM O2' ! necessary due to auto-generate dihedrals
GROUP ! To correct O4' atom type in DNA (NF)
ATOM C4' CN7 0.16 !
ATOM H4' HN7 0.09 !
ATOM O4' ON6 -0.50 !
ATOM C1' CN7B 0.16 !
ATOM H1' HN7 0.09 !
GROUP
ATOM C2' CN8 -0.18
ATOM H2' HN8 0.09
ATOM H2'' HN8 0.09
BOND C2' H2'
THET C1' C2' H2' C3' C2' H2' H2' C2' H2''
DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1'
DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3'
BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH
! use in generate statement
GROUP
ATOM H5T HN5 0.43
ATOM O5' ON5 -0.66
ATOM C5' CN8B 0.05
ATOM H5' HN8 0.09
ATOM H5'' HN8 0.09
!
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND H5T O5'
DONO H5T O5'
BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000
PRES 5MET 0.00 ! 5'-ribose METHYL patch
! use in generate statement
GROUP
ATOM C5' CN9 -0.27
ATOM H5' HN9 0.09
ATOM H5'' HN9 0.09
ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY
!
DELETE ATOM O5'
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND C5' H53'
IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000
IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000
IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000
PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch
! use in generate statement
GROUP
ATOM C5' CN8B -0.08
ATOM H5' HN8 0.09
ATOM H5'' HN8 0.09
ATOM P P 1.50
ATOM O1P ON3 -0.82
ATOM O2P ON3 -0.82
ATOM O5' ON2 -0.62
ATOM O5T ON4 -0.68
ATOM H5T HN4 0.34
BOND O5T P H5T O5T
DONO H5T O5T
! Built in B-DNA-like conformation (NF)
BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch
! use in generate statement
GROUP
ATOM C5' CN8B -0.08
ATOM H5' HN8 0.09
ATOM H5'' HN8 0.09
ATOM P P 1.50
ATOM O1P ON3 -0.78
ATOM O2P ON3 -0.78
ATOM O5' ON2 -0.57
ATOM O5T ON2 -0.57
ATOM C5T CN9 -0.17
ATOM H5T1 HN9 0.09
ATOM H5T2 HN9 0.09
ATOM H5T3 HN9 0.09
BOND O5T P O5T C5T C5T H5T1 C5T H5T2
BOND C5T H5T3
!DONO H5T O5T
! Built in B-DNA-like conformation (NF)
BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000
BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000
BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000
PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH
! use in generate statement
GROUP
ATOM C3' CN7 0.14
ATOM H3' HN7 0.09
ATOM O3' ON5 -0.66
ATOM H3T HN5 0.43
BOND O3' H3T
DONO H3T O3'
BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284
PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch
! use in generate statement
GROUP
ATOM C3' CN7 0.01
ATOM H3' HN7 0.09
ATOM P3 P 1.50
ATOM O1P3 ON3 -0.82
ATOM O2P3 ON3 -0.82
ATOM O3' ON2 -0.62
ATOM O3T ON4 -0.68
ATOM H3T HN4 0.34
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T
DONO H3T O3T
ACCE O3T
ACCE O1P2
ACCE O2P3
! Build in B-DNA-like conformation (NF)
BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000
BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch
! use in generate statement
! To build model compound with OPO3-CH3 at the 3' end (nicolas)
GROUP
ATOM C3' CN7 0.01
ATOM H3' HN7 0.09
ATOM P3 P 1.50
ATOM O1P3 ON3 -0.78
ATOM O2P3 ON3 -0.78
ATOM O3' ON2 -0.57
ATOM O3T ON2 -0.57
ATOM C3T CN9 -0.17
ATOM H3T1 HN9 0.09
ATOM H3T2 HN9 0.09
ATOM H3T3 HN9 0.09
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T
BOND C3T H3T1 C3T H3T2 C3T H3T3
ACCE O3'
ACCE O5'
ACCE O1P2
ACCE O1P3
BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000
BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000
BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000
BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000
PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch
! use in generate statement
! Added by Nicolas, to be consistent with model componds
GROUP
ATOM C3' CN7 -0.09
ATOM H3' HN7 0.09
ATOM P3 P 1.10
ATOM O3' ON2 -0.40
ATOM O1P3 ON3 -0.90
ATOM O2P3 ON3 -0.90
ATOM O3P3 ON3 -0.90
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3
ACCE O1P2
ACCE O1P3
BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000
BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000
BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000
BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000
PRES DELB 0.00 ! patch to delete all possible base atoms
! of Cyt,Gua,Ade,Thy and Ura
!
!note: error messages will be obtained due to atoms not present in
!residue being "deleted" by this patch
!cyt section
DELE ATOM N1
DELE ATOM C6
DELE ATOM H6
DELE ATOM C2
DELE ATOM O2
DELE ATOM N3
DELE ATOM C4
DELE ATOM N4
DELE ATOM H41
DELE ATOM H42
DELE ATOM C5
DELE ATOM H5
!gua section
DELE ATOM N9
DELE ATOM H1
DELE ATOM N2
DELE ATOM H21
DELE ATOM H22
DELE ATOM O6
DELE ATOM N7
DELE ATOM C8
DELE ATOM H8
!ade section
DELE ATOM H2
DELE ATOM N6
DELE ATOM H61
DELE ATOM H62
!thy/ura section
DELE ATOM H3
DELE ATOM O4
DELE ATOM C5M
DELE ATOM H51
DELE ATOM H52
DELE ATOM H53
PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide
! use AUTOGEN ANGLE DIHE after this patch
BOND O3' P ! but before water-generation
PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES)
! eg: patch sega 10 segb 1
! sega should have std 3' (gene sega ... last none)
! segb should have std 5' (gene segb ... first none)
! USE AUTOgen ANGL DIHE after this patch,
! but before water-generation
BOND 1O3' 2P
!following commented due to use of autogenerate
!THET 1C3' 1O3' 2P
!THET 1O3' 2P 2O5'
!THET 1O3' 2P 2O1P
!THET 1O3' 2P 2O2P
!DIHE 1O3' 2P 2O5' 2C5' 1O3' 2P 2O5' 2C5'
!DIHE 1C4' 1C3' 1O3' 2P
!DIHE 1C3' 1O3' 2P 2O5' 1C3' 1O3' 2P 2O5'
IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401
IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802
IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801
IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001
IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996
RESI TIP3 0.00 ! TIPS3P WATER MODEL
! GENERATE USING NOANGLE NODIHEDRAL
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE
ANGLE H1 OH2 H2 ! REQUIRED
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
GROUP
ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
! Ion parameters from Benoit Roux and Coworkers
! As of 8/98 no NBFIX terms required
!
RESI SOD 1.00 ! Sodium Ion
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE
RESI MG 2.00 ! Magnesium Ion
GROUP
ATOM MG MG 2.00
PATCHING FIRST NONE LAST NONE
RESI POT 1.00 ! Potassium Ion
GROUP
ATOM POT POT 1.00
PATCHING FIRST NONE LAST NONE
RESI CES 1.00 ! Cesium Ion
GROUP
ATOM CES CES 1.00
PATCHING FIRST NONE LAST NONE
RESI CAL 2.00 ! Calcium Ion
GROUP
ATOM CAL CAL 2.00
PATCHING FIRST NONE LAST NONE
RESI CLA -1.00 ! Chloride Ion
GROUP
ATOM CLA CLA -1.00
PATCHING FIRST NONE LAST NONE
RESI ZN2 2.00 ! Zinc ion, Roland Stote
GROUP
ATOM ZN ZN 2.00
PATCHING FIRST NONE LAST NONE
end
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