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comparison tools/rdock/data/cnx.rtf @ 3:279ba0732f87 draft default tip

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date Mon, 29 Aug 2016 09:07:58 -0400
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2:7e52b8fb2df4 3:279ba0732f87
1 *>>>>>>>>> Combined Residue Topology File for Proteins <<<<<<<<<
2 *>>>>>>>>>>>>>>>>>>>> and Nucleic Acids <<<<<<<<<<<<<<<<<<<<<<<<
3 *>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<<
4 *>>>>>>>>>>>>>>>>>>>>> January 1996 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
5 *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
6 *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
7 * These files are a beta release; additional parameter development
8 * and testing may lead to alteration of the contents.
9 *
10 * $Id: //depot/dev/client3/rdock/2013.1/data/cnx.rtf#2 $
11 *
12 * 30 Apr 1999 (D Morley, RiboTargets)
13 * Modified for RiboDock:
14 * Added hybridisation state tags to comment field
15 * Removed all but the MASS records (added element name)
16 *
17 22 1
18 !MASS 1 H 1.00800 H ! polar H (RBT::SP3)
19 !MASS 2 HC 1.00800 H ! N-ter H (RBT::SP3)
20 !MASS 3 HA 1.00800 H ! nonpolar H (RBT::SP3)
21 MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN (RBT::SP3)
22 MASS 5 HP 1.00800 H ! aromatic H (RBT::SP3)
23 MASS 6 HB 1.00800 H ! backbone H (RBT::SP3)
24 MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 (RBT::SP3)
25 MASS 8 HR2 1.00800 H ! (+) his HE1 (RBT::SP3)
26 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 (RBT::SP3)
27 MASS 10 HS 1.00800 H ! thiol hydrogen (RBT::SP3)
28 MASS 11 HA1 1.00800 H ! for alkene; RHC=CR (RBT::SP3)
29 MASS 12 HA2 1.00800 H ! for alkene; H2C=CR (RBT::SP3)
30 !MASS 20 C 12.01100 C ! polar C (RBT::SP3)
31 MASS 21 CA 12.01100 C ! aromatic C (RBT::SP2)
32 MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH (RBT::SP3)
33 MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 (RBT::SP3)
34 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 (RBT::SP3)
35 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons (RBT::SP2)
36 MASS 26 CPH2 12.01100 C ! his CE1 carbon (RBT::SP2)
37 MASS 27 CPT 12.01100 C ! trp C between rings (RBT::SP2)
38 !MASS 28 CY 12.01100 C ! TRP C in pyrrole ring (RBT::SP2)
39 MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) (RBT::SP3)
40 MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) (RBT::SP3)
41 MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) (RBT::SP3)
42 MASS 32 CC 12.01100 C ! carbonyl C for sidechains asn,asp,gln,glu (RBT::SP2)
43 MASS 33 CD 12.01100 C ! carbonyl C for none amides, asp,glu,cter (RBT::SP2)
44 MASS 34 CPA 12.01100 C ! heme alpha-C
45 MASS 35 CPB 12.01100 C ! heme beta-C
46 MASS 36 CPM 12.01100 C ! heme meso-C
47 MASS 37 CM 12.01100 C ! heme CO carbon (RBT::SP2)
48 MASS 38 CS 12.01100 C ! thiolate carbon
49 MASS 39 CE1 12.01100 C ! for alkene; RHC=CR
50 MASS 40 CE2 12.01100 C ! for alkene; H2C=CR
51 !MASS 50 N 14.00700 N ! proline N (RBT::SP3)
52 MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen (RBT::TRI)
53 MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen (RBT::SP2)
54 MASS 53 NR3 14.00700 N ! charged his ring nitrogen (RBT::TRI)
55 !MASS 54 NH1 14.00700 N ! peptide nitrogen (RBT::TRI)
56 !MASS 55 NH2 14.00700 N ! amide nitrogen (RBT::TRI)
57 !MASS 56 NH3 14.00700 N ! ammonium nitrogen (RBT::SP3)
58 !MASS 57 NC2 14.00700 N ! guanidinium nitroogen (RBT::TRI)
59 MASS 58 NY 14.00700 N ! TRP N in pyrrole ring (RBT::TRI)
60 MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) (RBT::SP3)
61 MASS 60 NPH 14.00700 N ! heme pyrrole N (RBT::TRI)
62 !MASS 70 O 15.99900 O ! carbonyl oxygen (RBT::SP2)
63 MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid (RBT::SP2)
64 !MASS 72 OC 15.99900 O ! carboxylate oxygen (RBT::SP2)
65 !MASS 73 OH1 15.99900 O ! hydroxyl oxygen (RBT::SP3)
66 MASS 74 OS 15.99940 O ! ester oxygen (RBT::SP3)
67 MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN (RBT::SP3)
68 MASS 76 OM 15.99900 O ! heme CO/O2 oxygen (RBT::SP2)
69 MASS 81 S 32.06000 S ! sulphur (RBT::SP3)
70 !MASS 82 SM 32.06000 S ! sulfur C-S-S-C type (RBT::SP3)
71 MASS 83 SS 32.06000 S ! thiolate sulfur
72 !
73 ! nucleic acid section
74 !MASS 104 HT 1.008000 ! TIPS3P WATER HYDROGEN
75 MASS 106 HN1 1.008000 H ! Nucleic acid amine proton (RBT::SP3)
76 MASS 107 HN2 1.008000 H ! Nucleic acid ring nitrogen proton (RBT::SP3)
77 MASS 108 HN3 1.008000 H ! Nucleic acid aromatic carbon proton (RBT::SP3)
78 MASS 109 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton (RBT::SP3)
79 MASS 110 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton (RBT::SP3)
80 MASS 111 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton (RBT::SP3)
81 MASS 112 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) (RBT::SP3)
82 MASS 113 HN3B 1.008000 H ! NAD+ aromatic hydrogen (RBT::SP3)
83 MASS 128 CN1 12.011000 C ! Nucleic acid carbonyl carbon (RBT::SP2)
84 MASS 129 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide (RBT::SP2)
85 MASS 130 CN3 12.011000 C ! Nucleic acid aromatic carbon (RBT::SP2)
86 MASS 131 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 (RBT::SP2)
87 MASS 132 CN5 12.011000 C ! Nucleic acid purine C4 and C5 (RBT::SP2)
88 MASS 133 CN6 12.011000 C ! Nucleic acid sp3 ribose ring carbon (RBT::SP3)
89 MASS 134 CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1' (RBT::SP3)
90 MASS 135 CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2' (RBT::SP3)
91 MASS 136 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) (RBT::SP3)
92 MASS 137 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) (RBT::SP3)
93 MASS 138 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) (RBT::SP3)
94 MASS 139 CN3A 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
95 MASS 140 CN3B 12.011000 C ! NAD+ aromatic carbon (RBT::SP2)
96 MASS 141 CN3C 12.011000 C ! NADH aromatic carbon (RBT::SP2)
97 MASS 142 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC (RBT::SP2)
98 MASS 143 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon (RBT::SP2)
99 MASS 150 NN1 14.007000 N ! Nucleic acid amide nitrogen (RBT::TRI)
100 MASS 151 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen (RBT::TRI)
101 MASS 152 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 (RBT::TRI)
102 MASS 153 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 (RBT::TRI)
103 MASS 154 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen (RBT::SP2)
104 MASS 155 NN4 14.007000 N ! Nucleic acid purine N7 (RBT::SP2)
105 MASS 156 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen (RBT::TRI)
106 MASS 157 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 (RBT::SP2)
107 MASS 158 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 (RBT::SP2)
108 !MASS 164 OT 15.999400 ! TIPS3P WATER OXYGEN
109 MASS 165 ON1 15.999400 O ! Nucleic acid carbonyl oxygen (RBT::SP2)
110 MASS 166 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 (RBT::SP2)
111 MASS 167 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen (RBT::SP3)
112 MASS 168 ON3 15.999400 O ! Nucleic acid =O in phosphate (RBT::SP2)
113 MASS 169 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen (RBT::SP3)
114 MASS 170 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen (RBT::SP3)
115 MASS 171 ON6 15.999400 O ! Nucleic acid ribose ring oxygen (RBT::SP3)
116 MASS 172 ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate (RBT::SP3)
117 MASS 182 P 30.974000 P ! phosphorus (RBT::SP2)
118 MASS 183 P2 30.974000 P ! pyrophosphate phosphorus
119 MASS 192 SOD 22.989770 Na ! Sodium Ion
120 MASS 193 MG 24.305000 Mg ! Magnesium Ion
121
122 * 1 Nov 2002 (DM) Dummy atom type
123 MASS 666 DUM 0.00000 DU ! Dummy atom
124 !MASS 199 DUM 0.001 ! dummy atom
125
126 * 9 Dec 2002 (SJ) CNX atom types
127 * types with the same name but not necessarily with the same functionality
128 MASS 701 H 1.00800 H ! polar H (RBT::SP3)
129 MASS 702 HC 1.00800 H ! charged polar H ie in ARG,LYS (RBT::SP3)
130 MASS 703 HA 1.00800 H ! apolar H (RBT::SP3)
131 MASS 704 C 12.01100 C ! amide C (RBT::SP2)
132 MASS 705 CH1E 12.01100 C ! Alpha-carbons with one hydrogen (RBT::SP3)
133 MASS 706 CH2E 12.01100 C ! Carbon with two hydrogens (RBT::SP3)
134 MASS 707 CH3E 12.01100 C ! Carbon with three hydrogens (RBT::SP3)
135 MASS 708 CH2G 12.01100 C ! GLY alpha carbon (RBT::SP3)
136 MASS 709 CH2P 12.01100 C ! Gamma and delta carbons in prolin (RBT::SP3)
137 MASS 710 C5W 12.01100 C ! TRP gamma carbon in pyrrole ring (RBT::SP2)
138 MASS 711 CW 12.01100 C ! TRP CD2 and CE2 at the fuse of the rings (RBT::SP2)
139 MASS 712 CR1E 12.01100 C ! PHE aromatic deltas epss and zeta (RBT::SP2)
140 MASS 713 C5 12.01100 C ! HIS gamma carbon (RBT::SP2)
141 MASS 714 CRH 12.01100 C ! HIS doubly protonated CE1 (RBT::SP2)
142 MASS 715 CR1H 12.01100 C ! HIS delta CD2 (RBT::SP2)
143 MASS 716 CRHH 12.01100 C ! HIS epsilon CE1 (RBT::SP2)
144 MASS 717 CF 12.01100 C ! PHE gamma carbon (RBT::SP2)
145 MASS 718 CY 12.01100 C ! TYR CG (RBT::SP2)
146 MASS 719 CY2 12.01100 C ! TYR CZ (RBT::SP2)
147 MASS 720 N 14.00700 N ! PRO N (RBT::TRI)
148 MASS 721 NR 14.00700 N ! HIS non-protonated ND1 (RBT::SP2)
149 MASS 722 NH1 14.00700 N ! amide N (RBT::TRI)
150 MASS 723 NH2 14.00700 N ! ammonium N (RBT::SP3)
151 MASS 724 NH3 14.00700 N ! charged N (RBT::SP3)
152 MASS 725 NC2 14.00700 N ! guanidinium charged N (RBT::TRI)
153 MASS 726 O 15.99900 O ! carbonyl oxygen (RBT::SP2)
154 MASS 727 OC 15.99900 O ! carboxylate oxygen (RBT::SP2)
155 MASS 728 OH1 15.99900 O ! hydroxyl oxygen (RBT::SP3)
156 MASS 729 SH1E 32.06000 S ! CYS SG (RBT::SP3)
157 MASS 730 SM 32.06000 S ! MET SD (RBT::SP3)