Mercurial > repos > marcel > caddsuite_mac10_6
annotate CADDSuite-1.5/data/OpenBabel/gaff.prm @ 7:bfab27640f5e draft
CADDSuite version 1.5
author | Marcel Schumann <schumann.marcel@gmail.com> |
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date | Tue, 24 Jul 2012 11:13:59 -0400 |
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7
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1 // |
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2 // Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl> |
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3 // |
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4 // This is a SMARTS template-file for GAFF-atom types |
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5 // |
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6 // It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF" |
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7 // file included with the antechamber package of amber10. |
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8 // There is no 1-to-1 correspondence between the ATD format and SMARTS. |
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9 // Therefore the current definitions need to be tested and possibly changed |
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10 // |
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11 // |
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12 // |
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13 // GAFF atomtypes defined using SMARTS |
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14 // [SMARTS] [atomtype id number] [description] |
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15 // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE! |
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16 // |
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17 // Be careful lines do not exceed the maximum length of 80! |
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18 |
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19 atom [*] X |
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20 atom [#1X1] ha "other hydrogen e.g. on aromatic C" |
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21 atom [#1X1][CX4] hc "hydrogen on aliphatic C" |
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22 // "hydrogen on aliphatic C with 1 ewd" |
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23 atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1 |
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24 // "hydrogen on aliphatic C with 2 ewd" |
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25 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2 |
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26 // "hydrogen on aliphatic C with 3 ewd" |
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27 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3 |
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28 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3 |
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29 atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3 |
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30 // "hydrogen on sp2 C with 1 ewd" |
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31 atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4 |
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32 // "hydrogen on sp2 C with 2 ewd" |
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33 atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5 |
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34 atom [#1X1][#6](N)(N)(N)N hx "" |
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35 atom [#1X1]O ho "hydrogen on oxygen" |
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36 atom [#1X1][Oh1] hw "hydrogen on water" |
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37 atom [#1X1]N hn "nitrogen" |
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38 atom [#1X1]S hs "sulphur" |
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39 atom [#1X1]P hp "phosphor" |
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40 atom [#6X4] c3 "other sp3 C" |
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41 atom [#6X4r3] cx "3-membered ring atom" |
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42 atom [#6X4r4] cy "4-membered ring atom" |
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43 atom [#6X3] c2 "other sp2 C" |
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44 atom [#6X3](N)(N)N cz "guanidine carbon" |
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45 atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems" |
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46 atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems" |
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47 atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems" |
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48 atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated chain systems" |
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49 atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated chain systems" |
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50 atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated chain systems" |
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51 atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system" |
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52 atom [#6X3r3] cu "sp2 carbon in a 3-membered ring" |
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53 atom [#6X3r4] cv "sp2 carbon in a 4-membered ring" |
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54 atom [#6X3]=[O,S] c "C=O or C=S" |
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55 atom [c] ca "pure aromatic atom" |
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56 atom [#6X2] c1 "other sp C" |
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57 atom [#6X2](=*)-*=* cg "sp C of conjugated system" |
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58 atom [#6X2](#*)-*=* cg "sp C of conjugated system" |
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59 atom [#6X2](#*)-*#* cg "sp C of conjugated system" |
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60 atom [#6X1] c1 "other sp C" |
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61 |
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62 atom [F]* f (-*) "general fluorine" |
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63 atom [Cl]* cl (-*) "general chlorine" |
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64 atom [Br]* br (-*) "general bromine" |
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65 atom [I]* i (-*) "general iodine" |
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66 |
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67 atom [#15X1] p2 "other sp2 P" |
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68 atom [#15X2] p2 "other sp2 P" |
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69 atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems" |
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70 atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems" |
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71 atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems" |
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72 atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system" |
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73 atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system" |
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74 atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system" |
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75 atom [#15;a] pb "aromatic P" |
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76 atom [#15X3] p3 "other sp3 P" |
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77 atom [#15X3](=*)-*=* px "sp2 P of conjugated system" |
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78 atom [#15X3](=*)-*#* px "sp2 P of conjugated system" |
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79 atom [#15X3]=[O,S] p4 "hypervalent P" |
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80 atom [#15X4] p5 "hypervalent P" |
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81 atom [#15X4](=*)-*=* py "P of conjugated system" |
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82 atom [#15X4](=*)-*#* py "P of conjugated system" |
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83 atom [#15X5] p5 "hypervalent P" |
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84 atom [#15X6] p5 "hypervalent P" |
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85 |
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86 atom [#7X1] n1 "sp1 N" |
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87 |
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88 atom [#7X2] n2 "sp2 N" |
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89 atom [#7X2](=*)=* n1 "sp1 N" |
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90 atom [#7X2](-*)#* n1 "sp1 N" |
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91 atom [#7X2;R](=*)-*=* nc "inner sp2 N of conjugated ring systems" |
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92 atom [#7X2;R](=*)-*#* nc "inner sp2 N of conjugated ring systems" |
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93 atom [#7X2;R](#*)-*#* nc "inner sp2 N of conjugated ring systems" |
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94 atom [#7X2;!R](=*)-*=* ne "inner sp2 N of conjugated chain system" |
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95 atom [#7X2;!R](=*)-*#* ne "inner sp2 N of conjugated chain system" |
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96 atom [#7X2;!R](#*)-*#* ne "inner sp2 N of conjugated chain system" |
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97 atom [nX2] nb "aromatic N" |
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98 |
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99 atom [#7X3] n3 "sp3 N" |
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100 atom [#7X3]a nh "amine N connected to aromatic ring" |
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101 atom [#7X3]=[CX3] nh "" |
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102 atom [#7X3]=[N2] nh "" |
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103 atom [#7X3]=[P2] nh "" |
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104 atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides" |
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105 atom [#7X3](O)O no "N in nitro group" |
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106 atom [nX3] na "aromatic N" |
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107 |
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108 atom [#7X4] n4 "sp3 N" |
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109 |
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110 atom [OX1] o "sp2 O" |
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111 atom [OX2] os "sp3 O in esters and ethers" |
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112 atom [OX3] os "sp3 O in esters and ethers" |
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113 atom [OX2H] oh "sp3 O in hydroxyl group" |
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114 atom [OX3H] oh "sp3 O in hydroxyl group" |
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115 |
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116 atom [SX1] s "" |
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117 atom [SX2] ss "sp3 sulphur" |
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118 atom [SX2]=* s2 "sp2 sulphur" |
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119 atom [SX2]#* s2 "sp2 sulphur" |
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120 atom [SX2H] sh "sp3 S in thiol" |
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121 atom [SX3] s4 "hypervalent S" |
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122 atom [SX3](=*)-*=* sx "conjugated S" |
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123 atom [SX3](=*)-*#* sx "conjugated S" |
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124 atom [SX4] s6 "hypervalent S" |
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125 atom [SX4](=*)-*=* sy "conjugated S" |
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126 atom [SX4](=*)-*#* sy "conjugated S" |
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127 atom [SX5] s6 "hypervalent S" |
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128 atom [SX6] s6 "hypervalent S" |
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129 |
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130 atom [He] He "" |
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131 atom [Li] Li "" |
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132 atom [Be] Be "" |
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133 atom [B] B "" |
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134 atom [Ne] Ne "" |
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135 atom [Na] Na "" |
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136 atom [Mg] Mg "" |
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137 atom [Al] Al "" |
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138 atom [Si] Si "" |
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139 atom [Ar] Ar "" |
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140 atom [K] K "" |
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141 atom [Ca] Ca "" |
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142 atom [Sc] Sc "" |
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143 atom [Ti] Ti "" |
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144 atom [V] V "" |
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145 atom [Cr] Cr "" |
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146 atom [Mn] Mn "" |
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147 atom [Fe] Fe "" |
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148 atom [Co] Co "" |
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149 atom [Ni] Ni "" |
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150 atom [Cu] Cu "" |
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151 atom [Zn] Zn "" |
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152 atom [Ga] Ga "" |
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153 atom [Ge] Ge "" |
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154 atom [As] As "" |
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155 atom [Se] Se "" |
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156 atom [Kr] Kr "" |
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157 atom [Rb] Rb "" |
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158 atom [Sr] Sr "" |
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159 atom [Y] Y "" |
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160 atom [Zr] Zr "" |
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161 atom [Nb] Nb "" |
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162 atom [Mo] Mo "" |
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163 atom [Tc] Tc "" |
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164 atom [Ru] Ru "" |
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165 atom [Rh] Rh "" |
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166 atom [Pd] Pd "" |
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167 atom [Ag] Ag "" |
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168 atom [Cd] Cd "" |
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169 atom [In] In "" |
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170 atom [Sn] Sn "" |
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171 atom [Sb] Sb "" |
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172 atom [Te] Te "" |
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173 atom [Xe] Xe "" |
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174 atom [Cs] Cs "" |
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175 atom [Ba] Ba "" |
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176 atom [La] La "" |
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177 atom [Ce] Ce "" |
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178 atom [Pr] Pr "" |
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179 atom [Nd] Nd "" |
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180 atom [Pm] Pm "" |
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181 atom [Sm] Sm "" |
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182 atom [Eu] Eu "" |
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183 atom [Gd] Gd "" |
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184 atom [Tb] Tb "" |
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185 atom [Dy] Dy "" |
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186 atom [Ho] Ho "" |
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187 atom [Er] Er "" |
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188 atom [Tm] Tm "" |
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189 atom [Yb] Yb "" |
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190 atom [Lu] Lu "" |
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191 atom [Hf] Hf "" |
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192 atom [Ta] Ta "" |
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193 atom [W] W "" |
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194 atom [Re] Re "" |
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195 atom [Os] Os "" |
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196 atom [Ir] Ir "" |
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197 atom [Pt] Pt "" |
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198 atom [Au] Au "" |
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199 atom [Hg] Hg "" |
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200 atom [Tl] Tl "" |
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201 atom [Pb] Pb "" |
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202 atom [Bi] Bi "" |
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203 atom [Po] Po "" |
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204 atom [At] At "" |
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205 atom [Rn] Rn "" |
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206 atom [Fr] Fr "" |
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207 atom [Ra] Ra "" |
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208 atom [Ac] Ac "" |
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209 atom [Th] Th "" |
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210 atom [Pa] Pa "" |
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211 atom [U] U "" |
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212 atom [Np] Np "" |
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213 atom [Pu] Pu "" |
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214 atom [Am] Am "" |
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215 atom [Cm] Cm "" |
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216 atom [Bk] Bk "" |
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217 atom [Cf] Cf "" |
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218 atom [Es] Es "" |
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219 atom [Fm] Fm "" |
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220 atom [Md] Md "" |
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221 atom [No] No "" |
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222 atom [Lr] Lr "" |