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1 ##############################################################################
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2 # #
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3 # Open Babel file: torlib.txt #
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4 # #
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5 # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #
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6 # Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison #
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7 # Part of the Open Babel package, under the GNU General Public License (GPL)#
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8 # #
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9 # First three lines represent: (used by rotor.cpp::OBRotorRules #
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10 # Hybridization pair (atom types around a rotatable bond) #
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11 # followed by a list of default bond rotation angles (in degrees) #
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12 # #
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13 # Later lines should specify: #
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14 # * A SMARTS pattern for the rotor rule #
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15 # * A set of 4 "reference atoms" (as integers, numbered from 1 #
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16 # in the specified SMARTS pattern #
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17 # * At least one torsion value (in degrees) #
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18 # * Optionally ending with "Delta" and a delta value #
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19 # (i.e., the resolution of a dihedral step #
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20 # #
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21 # SMARTS rules will be attempted first, then hybridization #
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22 # #
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23 ##############################################################################
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24
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25 SP3-SP3 60.0 -60.0 180.0
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26 SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0
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27 SP3-SP2 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0
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28
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29 # Many of these rules came from the Supporting Information
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30 # from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801
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31
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32 #polysaccaride bridges
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33 O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0
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34 O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0
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35
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36 #acids
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37 [OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0
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38 [a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0
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39 [OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0
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40
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41 #sulfonamides
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42 NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0
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43 c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0
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44 O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0
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45 O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0
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46 [c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0
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47 *=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0
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48 O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0
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49 [aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0
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50 [aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0
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51 [aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0
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52 [aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0
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53 [a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0
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54 aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0
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55 aaNS(=O)(=O) 1 2 3 4 90.0 -90.0
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56
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57 #sulfone
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58 O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0
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59
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60 #hydrazides
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61 [O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0
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62 [O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0
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63
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64 #cyclopropyl-ketones
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65 O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0
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66 O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0
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67 O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0
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68
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69 #epoxy-ketone
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70 O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0
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71
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72 #opposite end of tert amide
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73 O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0
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74 O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0
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75 O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0
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76
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77 #misc
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78 [CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0
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79 [cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0
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80 c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0
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81
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82 #carbonyls
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83 O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0
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84 C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0
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85 O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0
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86 O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0
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87 O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0
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88 O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0
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89 O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0
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90 O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0
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91 O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
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92 O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
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93 O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0
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94 O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0
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95 #O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0
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96
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97 #amidene and guanidine
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98 [aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
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99 [a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
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100 *[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
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101 [CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0
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102
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103 #ether
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104 aCO[CD2] 1 2 3 4 180.0 100.0 -100.0
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105
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106 #isoprene
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107 C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0
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108 C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0
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109
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110 #aryl secondary amines
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111 [aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0
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112 [aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0
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113 [aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0
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114 ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0
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115
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116 #aromatic subtituents
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117 [aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
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118 [aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0
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119 [aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0
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120 a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0
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121 an[CD2X4][CD1] 1 2 3 4 90.0 -90.0
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122 [aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0
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123 [aD3]c([aD2])O[CD2] 1 2 3 4 180.0
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124 a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0
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125 [ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0
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126 [aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0
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127 [a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0
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128 [a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0
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129 [a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
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130 [a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
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131
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132 #borderline low-res
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133 [CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0
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134
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135 #conjugated substituents
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136 a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0
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137 C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0
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138 cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0
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139 C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0
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140 c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0
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141 C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0
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142
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143 #ureas
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144 [ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0
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145 [ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0
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146
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147 #carbamates
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148 C[ND2]C(=O)O 1 2 3 4 0.0 180.0
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149 [ND2]C(=O)OC 3 2 4 5 0.0
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150 OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0
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151
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152 #piperidine amide
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153 O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0
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154
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155 #amides and esters
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156 [*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0
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157 [OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0
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158 [O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0
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159 [O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0
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160 [O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0
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161 [O,SD1]=C(C)cn 1 2 4 5 0.0 180.0
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162 [O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0
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163 [O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180
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164 O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0
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165 O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0
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166 O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0
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167 O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0
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168 O=C([CD1])O[CD1] 1 2 4 5 0.0
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169 [O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0
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170 O=CO[CD2][CD1] 2 3 4 5 180.0
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171 O=CO[CD2]* 2 3 4 5 180.0 60.0 -60.0 90.0 -90.0
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172 O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0
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173 O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0
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174 O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
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175 O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
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176 O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0
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177 O=C[ND3]* 1 2 3 4 0.0 180.0
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178 CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0
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179 [a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0
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180 [ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
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181 [CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0
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182
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183 #t-butyl
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184 C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0
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185 **C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0
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186
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187 #propyl
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188 [CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0
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189
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190 #highly substituted alkane
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191 #[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6
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192 *[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0
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193 c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0
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194 [CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0
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195 [*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0
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196 [*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0
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197 *[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0
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198 [CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0
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199
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200 #long unsubstituted alkanes
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201 [CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0
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202 [CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0
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203 [CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0
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204 [*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0
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205
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206 #nitro
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207 [aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0
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208 [a]cN(~[OD1])~[OD1] 1 2 3 4 0.0
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209
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210 #trifluoromethyl
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211 **C(F)(F)F 1 2 3 4 0.0
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212
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213 #trichloromethyl
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214 [a]cC(Cl)(Cl)Cl 1 2 3 4 0.0
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215
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216 #CSD SPECIFIC RULES
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217 a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0
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218 PPcc 1 2 3 4 60.0 -60.0
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219
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220 #phosphorus containing groups
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221 #[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0
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222 #[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0
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223 #S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0
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224 #[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0
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