# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:45:26 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[(S)-benzylsulfinyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1[S@@](=O)Cc2ccccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 3G1  3G1  '2-[(S)-benzylsulfinyl]benzoic acid'  ligand  30  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3G1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 3G1  C1   C  CR6   0  -0.214   1.6213   0.5722   0.1792
 3G1  C2   C  CR6   0  -0.040   2.4442  -0.5348  -0.0587
 3G1  C3   C  CR16  0  -0.255   3.7526  -0.3230  -0.4893
 3G1  C4   C  CR16  0  -0.237   4.2318   0.9624  -0.6840
 3G1  C6   C  CR16  0  -0.219   2.1090   1.8565   0.0072
 3G1  C8   C  CH2   0  -0.673  -0.8986   0.2238  -0.8113
 3G1  C10  C  CR16  0  -0.280  -2.9180  -1.1791  -0.3408
 3G1  C11  C  CR16  0  -0.241  -4.2735  -1.3150  -0.0790
 3G1  C12  C  CR16  0  -0.263  -5.0902  -0.1916  -0.0380
 3G1  C13  C  CR16  0  -0.243  -4.5447   1.0662  -0.2586
 3G1  C14  C  CR16  0  -0.282  -3.1876   1.2015  -0.5174
 3G1  O2   O  O     0  -0.436   0.7476  -2.1354   0.3412
 3G1  C7   C  C     0   0.535   1.9181  -1.9040   0.1414
 3G1  O3   O  OH1   0  -0.584   2.8476  -2.8398   0.0860
 3G1  C5   C  CR16  0  -0.229   3.4096   2.0507  -0.4360
 3G1  S1   S  S3    0   0.789  -0.0701   0.4400   0.8182
 3G1  O1   O  O     0  -0.751  -0.4547   1.8316   1.2475
 3G1  C9   C  CR6   0   0.107  -2.3647   0.0792  -0.5698
 3G1  H1   H  HCR6  0   0.279   4.4044  -1.1638  -0.6806
 3G1  H2   H  HCR6  0   0.276   5.2474   1.1118  -1.0239
 3G1  H3   H  HCR6  0   0.284   1.4754   2.7071   0.2194
 3G1  H4   H  HCH2  0   0.315  -0.6581   1.1199  -1.3853
 3G1  H5   H  HCH2  0   0.307  -0.4701  -0.6453  -1.3053
 3G1  H7   H  HCR6  0   0.258  -4.6929  -2.2978   0.0920
 3G1  H8   H  HCR6  0   0.259  -6.1488  -0.2970   0.1614
 3G1  H9   H  HCR6  0   0.258  -5.1773   1.9437  -0.2270
 3G1  H10  H  HCR6  0   0.253  -2.7687   2.1842  -0.6939
 3G1  H11  H  HOH1  0   0.494   2.4470  -3.7157   0.1942
 3G1  H12  H  HCR6  0   0.277   3.7796   3.0567  -0.5818
 3G1  H6   H  HCR6  0   0.256  -2.2835  -2.0569  -0.3736

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 3G1  C13  C12  aromatic  1.389  0.020  1.389
 3G1  C13  C14  aromatic  1.388  0.020  1.388
 3G1  C12  C11  aromatic  1.389  0.020  1.389
 3G1  C14  C9   aromatic  1.393  0.020  1.393
 3G1  C11  C10  aromatic  1.387  0.020  1.387
 3G1  C9   C10  aromatic  1.394  0.020  1.394
 3G1  C9   C8   single    1.493  0.020  1.493
 3G1  C8   S1   single    1.841  0.020  1.841
 3G1  O1   S1   double    1.506  0.020  1.506
 3G1  S1   C1   single    1.813  0.020  1.813
 3G1  C6   C1   aromatic  1.384  0.020  1.384
 3G1  C6   C5   aromatic  1.388  0.020  1.388
 3G1  C1   C2   aromatic  1.400  0.020  1.400
 3G1  C5   C4   aromatic  1.386  0.020  1.386
 3G1  O2   C7   double    1.210  0.020  1.210
 3G1  C2   C7   single    1.480  0.020  1.480
 3G1  C2   C3   aromatic  1.394  0.020  1.394
 3G1  C7   O3   single    1.320  0.020  1.320
 3G1  C4   C3   aromatic  1.386  0.020  1.386
 3G1  C3   H1   single    0.930  0.020  1.080
 3G1  C4   H2   single    0.930  0.020  1.080
 3G1  C6   H3   single    0.930  0.020  1.080
 3G1  C8   H4   single    0.970  0.020  1.090
 3G1  C8   H5   single    0.970  0.020  1.090
 3G1  C10  H6   single    0.930  0.020  1.080
 3G1  C11  H7   single    0.930  0.020  1.080
 3G1  C12  H8   single    0.930  0.020  1.080
 3G1  C13  H9   single    0.930  0.020  1.080
 3G1  C14  H10  single    0.930  0.020  1.080
 3G1  O3   H11  single    0.850  0.020  0.980
 3G1  C5   H12  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 3G1  S1   C1   C6   116.11  3.000
 3G1  C6   C1   C2   120.36  3.000
 3G1  S1   C1   C2   123.42  3.000
 3G1  C7   C2   C3   121.07  3.000
 3G1  C3   C2   C1   118.96  3.000
 3G1  C7   C2   C1   119.97  3.000
 3G1  H1   C3   C4   119.22  3.000
 3G1  H1   C3   C2   120.17  3.000
 3G1  C4   C3   C2   120.60  3.000
 3G1  H2   C4   C5   120.32  3.000
 3G1  H2   C4   C3   119.81  3.000
 3G1  C5   C4   C3   119.87  3.000
 3G1  H3   C6   C5   120.10  3.000
 3G1  H3   C6   C1   119.92  3.000
 3G1  C5   C6   C1   119.98  3.000
 3G1  H5   C8   H4   109.30  3.000
 3G1  H5   C8   C9   112.52  3.000
 3G1  H4   C8   C9   112.40  3.000
 3G1  H5   C8   S1   108.58  3.000
 3G1  H4   C8   S1   105.66  3.000
 3G1  C9   C8   S1   108.07  3.000
 3G1  H6   C10  C9   119.60  3.000
 3G1  H6   C10  C11  119.91  3.000
 3G1  C9   C10  C11  120.49  3.000
 3G1  H7   C11  C12  120.12  3.000
 3G1  H7   C11  C10  119.83  3.000
 3G1  C12  C11  C10  120.05  3.000
 3G1  H8   C12  C13  120.11  3.000
 3G1  H8   C12  C11  120.11  3.000
 3G1  C13  C12  C11  119.78  3.000
 3G1  H9   C13  C14  119.86  3.000
 3G1  H9   C13  C12  120.01  3.000
 3G1  C14  C13  C12  120.13  3.000
 3G1  H10  C14  C9   119.77  3.000
 3G1  H10  C14  C13  119.81  3.000
 3G1  C9   C14  C13  120.41  3.000
 3G1  O3   C7   O2   123.54  3.000
 3G1  O3   C7   C2   113.56  3.000
 3G1  O2   C7   C2   122.90  3.000
 3G1  H11  O3   C7   110.18  3.000
 3G1  H12  C5   C6   119.59  3.000
 3G1  H12  C5   C4   120.20  3.000
 3G1  C6   C5   C4   120.20  3.000
 3G1  O1   S1   C8   104.24  3.000
 3G1  O1   S1   C1   105.74  3.000
 3G1  C8   S1   C1    96.69  3.000
 3G1  C14  C9   C10  119.13  3.000
 3G1  C10  C9   C8   120.26  3.000
 3G1  C14  C9   C8   120.56  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 3G1  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 3G1  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 3G1  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 3G1  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 3G1  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 3G1  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 3G1  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 3G1  CONST_08  C13  C14  C9   C10    0.00   0.0  0
 3G1  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 3G1  CONST_10  C14  C9   C10  C11    0.00   0.0  0
 3G1  CONST_11  C9   C14  C13  C12    0.00   0.0  0
 3G1  CONST_12  C9   C10  C11  C12    0.00   0.0  0
 3G1  CONST_13  S1   C1   C2   C3   180.00   0.0  0
 3G1  CONST_14  C7   C2   C3   C4   180.00   0.0  0
 3G1  CONST_15  C7   C2   C1   C6   180.00   0.0  0
 3G1  CONST_16  C13  C14  C9   C8   180.00   0.0  0
 3G1  CONST_17  C11  C10  C9   C8   180.00   0.0  0
 3G1  CONST_18  S1   C1   C6   C5   180.00   0.0  0
 3G1  CONST_19  H12  C5   C6   C1   180.00   0.0  0
 3G1  CONST_20  H1   C3   C2   C1   180.00   0.0  0
 3G1  CONST_21  H3   C6   C1   C2   180.00   0.0  0
 3G1  CONST_22  H2   C4   C3   C2   180.00   0.0  0
 3G1  CONST_23  H8   C12  C11  C10  180.00   0.0  0
 3G1  CONST_24  H10  C14  C9   C10  180.00   0.0  0
 3G1  CONST_25  H9   C13  C12  C11  180.00   0.0  0
 3G1  CONST_26  H6   C10  C11  C12  180.00   0.0  0
 3G1  CONST_27  H7   C11  C12  C13  180.00   0.0  0
 3G1  CONST_28  H11  O3   C7   C2   180.00   0.0  0
 3G1  Var_01    C9   C8   S1   C1   179.78  30.0  1
 3G1  Var_02    O2   C7   C2   C1     9.73  30.0  2
 3G1  Var_03    C8   S1   C1   C2   -87.03  30.0  3
 3G1  Var_04    S1   C8   C9   C10  -88.82  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 3G1  plan-1  C1   0.020
 3G1  plan-1  C2   0.020
 3G1  plan-1  C3   0.020
 3G1  plan-1  C4   0.020
 3G1  plan-1  C6   0.020
 3G1  plan-1  C7   0.020
 3G1  plan-1  C5   0.020
 3G1  plan-1  S1   0.020
 3G1  plan-1  H1   0.020
 3G1  plan-1  H2   0.020
 3G1  plan-1  H3   0.020
 3G1  plan-1  H12  0.020
 3G1  plan-2  C8   0.020
 3G1  plan-2  C10  0.020
 3G1  plan-2  C11  0.020
 3G1  plan-2  C12  0.020
 3G1  plan-2  C13  0.020
 3G1  plan-2  C14  0.020
 3G1  plan-2  C9   0.020
 3G1  plan-2  H7   0.020
 3G1  plan-2  H8   0.020
 3G1  plan-2  H9   0.020
 3G1  plan-2  H10  0.020
 3G1  plan-2  H6   0.020
 3G1  plan-3  C2   0.020
 3G1  plan-3  O2   0.020
 3G1  plan-3  C7   0.020
 3G1  plan-3  O3   0.020
 3G1  plan-3  H11  0.020
 3G1  plan-4  C1   0.020
 3G1  plan-4  C8   0.020
 3G1  plan-4  S1   0.020
 3G1  plan-4  O1   0.020

