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