# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:06:25 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 1-chloro-2-(methylsulfanyl)benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccccc1Cl
#
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
 YGV  YGV  1-chloro-2-(methylsulfanyl)benzene  ligand  16  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YGV
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
 YGV  C01   C   CH3   0  -0.799  -35.5417  23.3364  -13.0811
 YGV  C03   C   CR6   0  -0.044  -37.3123  25.3828  -12.4151
 YGV  C04   C   CR16  0  -0.276  -36.4986  25.5688  -11.2980
 YGV  C05   C   CR16  0  -0.226  -36.7955  26.5445  -10.3574
 YGV  C06   C   CR16  0  -0.279  -37.9082  27.3574  -10.5121
 YGV  C07   C   CR16  0  -0.197  -38.7293  27.1887  -11.6173
 YGV  C08   C   CR6   0  -0.063  -38.4291  26.2116  -12.5497
 YGV  S02   S   S2    0   0.068  -37.0249  24.1773  -13.6621
 YGV  CL09  CL  CL    0  -0.119  -39.4693  26.0127  -13.9221
 YGV  H1    H   HCH3  0   0.297  -35.3370  22.5641  -13.8203
 YGV  H2    H   HCH3  0   0.277  -34.6853  24.0060  -13.0322
 YGV  H3    H   HCH3  0   0.277  -35.7013  22.8587  -12.1164
 YGV  H4    H   HCR6  0   0.273  -35.6236  24.9508  -11.1531
 YGV  H5    H   HCR6  0   0.265  -36.1463  26.6657   -9.5004
 YGV  H6    H   HCR6  0   0.266  -38.1409  28.1197   -9.7812
 YGV  H7    H   HCR6  0   0.280  -39.6012  27.8139  -11.7557

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
 YGV  CL09  C08  single    1.734  0.020  1.734
 YGV  C01   S02  single    1.801  0.020  1.801
 YGV  S02   C03  single    1.758  0.020  1.758
 YGV  C08   C03  aromatic  1.397  0.020  1.397
 YGV  C08   C07  aromatic  1.384  0.020  1.384
 YGV  C03   C04  aromatic  1.394  0.020  1.394
 YGV  C07   C06  aromatic  1.387  0.020  1.387
 YGV  C04   C05  aromatic  1.387  0.020  1.387
 YGV  C06   C05  aromatic  1.387  0.020  1.387
 YGV  C01   H1   single    0.970  0.020  1.090
 YGV  C01   H2   single    0.970  0.020  1.090
 YGV  C01   H3   single    0.970  0.020  1.090
 YGV  C04   H4   single    0.930  0.020  1.080
 YGV  C05   H5   single    0.930  0.020  1.080
 YGV  C06   H6   single    0.930  0.020  1.080
 YGV  C07   H7   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
 YGV  H3    C01  H2   110.22  3.000
 YGV  H3    C01  H1   108.55  3.000
 YGV  H2    C01  H1   108.61  3.000
 YGV  H3    C01  S02  111.72  3.000
 YGV  H2    C01  S02  112.05  3.000
 YGV  H1    C01  S02  105.49  3.000
 YGV  S02   C03  C08  117.98  3.000
 YGV  C08   C03  C04  117.68  3.000
 YGV  S02   C03  C04  124.35  3.000
 YGV  H4    C04  C05  118.97  3.000
 YGV  H4    C04  C03  120.23  3.000
 YGV  C05   C04  C03  120.80  3.000
 YGV  H5    C05  C06  120.28  3.000
 YGV  H5    C05  C04  119.17  3.000
 YGV  C06   C05  C04  120.55  3.000
 YGV  H6    C06  C07  119.79  3.000
 YGV  H6    C06  C05  120.70  3.000
 YGV  C07   C06  C05  119.51  3.000
 YGV  H7    C07  C08  119.79  3.000
 YGV  H7    C07  C06  120.59  3.000
 YGV  C08   C07  C06  119.62  3.000
 YGV  CL09  C08  C07  118.97  3.000
 YGV  C07   C08  C03  121.83  3.000
 YGV  CL09  C08  C03  119.20  3.000
 YGV  C03   S02  C01  103.06  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
 YGV  CONST_01  C06   C07  C08  C03     0.00   0.0  0
 YGV  CONST_02  C06   C05  C04  C03     0.00   0.0  0
 YGV  CONST_03  C07   C08  C03  C04     0.00   0.0  0
 YGV  CONST_04  C07   C06  C05  C04     0.00   0.0  0
 YGV  CONST_05  C08   C03  C04  C05     0.00   0.0  0
 YGV  CONST_06  C08   C07  C06  C05     0.00   0.0  0
 YGV  CONST_07  CL09  C08  C03  C04   180.00   0.0  0
 YGV  CONST_08  S02   C03  C04  C05   180.00   0.0  0
 YGV  CONST_09  CL09  C08  C07  C06   180.00   0.0  0
 YGV  CONST_10  S02   C03  C08  C07   180.00   0.0  0
 YGV  CONST_11  H7    C07  C08  C03   180.00   0.0  0
 YGV  CONST_12  H5    C05  C04  C03   180.00   0.0  0
 YGV  CONST_13  H6    C06  C05  C04   180.00   0.0  0
 YGV  CONST_14  H4    C04  C05  C06   180.00   0.0  0
 YGV  Var_01    C08   C03  S02  C01  -178.89  30.0  2
 YGV  Var_02    H1    C01  S02  C03   179.00  30.0  3

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
 YGV  plan-1  C03   0.020
 YGV  plan-1  C04   0.020
 YGV  plan-1  C05   0.020
 YGV  plan-1  C06   0.020
 YGV  plan-1  C07   0.020
 YGV  plan-1  C08   0.020
 YGV  plan-1  S02   0.020
 YGV  plan-1  CL09  0.020
 YGV  plan-1  H4    0.020
 YGV  plan-1  H5    0.020
 YGV  plan-1  H6    0.020
 YGV  plan-1  H7    0.020

