# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:05:26 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-[(2-acetylphenyl)sulfanyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1ccccc1Sc2ccccc2C(O)=O
#
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
 8YM  8YM  '2-[(2-acetylphenyl)sulfanyl]benzoic acid'  ligand  30  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8YM
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
 8YM  C5   C  CR16   0  -0.244   1.2706  -2.7415  -0.0547
 8YM  C4   C  CR16   0  -0.255   2.6565  -2.6394  -0.0703
 8YM  C2   C  CR6    0  -0.037   2.4548  -0.2251   0.1037
 8YM  C6   C  CR16   0  -0.204   0.4811  -1.6108   0.0371
 8YM  C    C  CH3    0  -0.800   4.6257   1.1540   0.2113
 8YM  O    O  O      0  -0.403   2.4614   2.1148   0.1897
 8YM  C1   C  C      0   0.369   3.1213   1.0927   0.1701
 8YM  C10  C  CR16   0  -0.264  -3.3256  -0.3071   2.0094
 8YM  C11  C  CR16   0  -0.243  -4.1956  -0.4784   0.9406
 8YM  C12  C  CR16   0  -0.287  -3.7723  -0.1936  -0.3484
 8YM  C13  C  CR6    0   0.004  -2.4681   0.2245  -0.6133
 8YM  C14  C  C      0   0.361  -2.0621   0.4520  -2.0644
 8YM  C3   C  CR16   0  -0.292   3.2298  -1.3870   0.0074
 8YM  C7   C  CR6    0  -0.098   1.0477  -0.3378   0.1275
 8YM  C8   C  CR6    0  -0.232  -1.5996   0.3875   0.4696
 8YM  C9   C  CR16   0  -0.204  -2.0367   0.1423   1.7704
 8YM  O1   O  OC    -1  -0.598  -2.8984   1.0453  -2.7719
 8YM  O2   O  O      0  -0.571  -0.9592  -0.0007  -2.4094
 8YM  S    S  S2     0   0.105   0.0253   1.0903   0.2845
 8YM  H1   H  HCR6   0   0.264   0.7954  -3.7120  -0.1206
 8YM  H2   H  HCR6   0   0.262   3.2775  -3.5213  -0.1455
 8YM  H3   H  HCR6   0   0.266  -0.5922  -1.7249   0.0409
 8YM  H4   H  HCH3   0   0.267   5.0229   0.5900   1.0561
 8YM  H5   H  HCH3   0   0.269   5.0624   0.7296  -0.6943
 8YM  H6   H  HCH3   0   0.270   4.9483   2.1890   0.2985
 8YM  H7   H  HCR6   0   0.258  -3.6503  -0.5103   3.0214
 8YM  H8   H  HCR6   0   0.256  -5.2076  -0.8217   1.1140
 8YM  H9   H  HCR6   0   0.251  -4.4643  -0.3067  -1.1728
 8YM  H10  H  HCR6   0   0.267   4.3078  -1.3088  -0.0080
 8YM  H11  H  HCR6   0   0.263  -1.3575   0.3018   2.5984

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
 8YM  C    C1   single    1.506  0.020  1.506
 8YM  C1   O    double    1.217  0.020  1.217
 8YM  C1   C2   single    1.478  0.020  1.478
 8YM  C2   C3   aromatic  1.400  0.020  1.400
 8YM  C2   C7   aromatic  1.412  0.020  1.412
 8YM  C3   C4   aromatic  1.380  0.020  1.380
 8YM  S    C7   single    1.763  0.020  1.763
 8YM  S    C8   single    1.780  0.020  1.780
 8YM  C7   C6   aromatic  1.396  0.020  1.396
 8YM  C4   C5   aromatic  1.390  0.020  1.390
 8YM  C6   C5   aromatic  1.382  0.020  1.382
 8YM  C9   C8   aromatic  1.394  0.020  1.394
 8YM  C9   C10  aromatic  1.386  0.020  1.386
 8YM  C8   C13  aromatic  1.398  0.020  1.398
 8YM  O2   C14  deloc     1.241  0.020  1.241
 8YM  C10  C11  aromatic  1.389  0.020  1.389
 8YM  C13  C14  single    1.524  0.020  1.524
 8YM  C13  C12  aromatic  1.395  0.020  1.395
 8YM  C14  O1   deloc     1.246  0.020  1.246
 8YM  C11  C12  aromatic  1.386  0.020  1.386
 8YM  C5   H1   single    0.930  0.020  1.080
 8YM  C4   H2   single    0.930  0.020  1.080
 8YM  C6   H3   single    0.930  0.020  1.080
 8YM  C    H4   single    0.970  0.020  1.090
 8YM  C    H5   single    0.970  0.020  1.090
 8YM  C    H6   single    0.970  0.020  1.090
 8YM  C10  H7   single    0.930  0.020  1.080
 8YM  C11  H8   single    0.930  0.020  1.080
 8YM  C12  H9   single    0.930  0.020  1.080
 8YM  C3   H10  single    0.930  0.020  1.080
 8YM  C9   H11  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
 8YM  H1   C5   C6   119.12  3.000
 8YM  H1   C5   C4   120.19  3.000
 8YM  C6   C5   C4   120.68  3.000
 8YM  H2   C4   C3   120.37  3.000
 8YM  H2   C4   C5   120.91  3.000
 8YM  C3   C4   C5   118.72  3.000
 8YM  C7   C2   C3   119.12  3.000
 8YM  C7   C2   C1   121.32  3.000
 8YM  C3   C2   C1   119.56  3.000
 8YM  H3   C6   C7   119.98  3.000
 8YM  H3   C6   C5   118.80  3.000
 8YM  C7   C6   C5   121.22  3.000
 8YM  H6   C    H5   108.54  3.000
 8YM  H6   C    H4   108.78  3.000
 8YM  H5   C    H4   107.21  3.000
 8YM  H6   C    C1   109.71  3.000
 8YM  H5   C    C1   111.17  3.000
 8YM  H4   C    C1   111.34  3.000
 8YM  O    C1   C    120.47  3.000
 8YM  O    C1   C2   120.33  3.000
 8YM  C    C1   C2   119.20  3.000
 8YM  H7   C10  C9   120.08  3.000
 8YM  H7   C10  C11  120.57  3.000
 8YM  C9   C10  C11  119.34  3.000
 8YM  H8   C11  C12  119.96  3.000
 8YM  H8   C11  C10  120.10  3.000
 8YM  C12  C11  C10  119.93  3.000
 8YM  H9   C12  C13  118.98  3.000
 8YM  H9   C12  C11  119.44  3.000
 8YM  C13  C12  C11  121.57  3.000
 8YM  C8   C13  C14  123.70  3.000
 8YM  C14  C13  C12  118.33  3.000
 8YM  C8   C13  C12  117.95  3.000
 8YM  O2   C14  O1   127.76  3.000
 8YM  O1   C14  C13  115.66  3.000
 8YM  O2   C14  C13  116.55  3.000
 8YM  H10  C3   C2   119.54  3.000
 8YM  H10  C3   C4   118.64  3.000
 8YM  C2   C3   C4   121.82  3.000
 8YM  S    C7   C6   120.59  3.000
 8YM  C6   C7   C2   118.43  3.000
 8YM  S    C7   C2   120.98  3.000
 8YM  S    C8   C9   116.92  3.000
 8YM  C9   C8   C13  120.51  3.000
 8YM  S    C8   C13  122.19  3.000
 8YM  H11  C9   C8   119.41  3.000
 8YM  H11  C9   C10  119.96  3.000
 8YM  C8   C9   C10  120.64  3.000
 8YM  C8   S    C7   102.64  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
 8YM  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 8YM  CONST_02  C2   C7   C6   C5      0.00   0.0  0
 8YM  CONST_03  C7   C2   C3   C4      0.00   0.0  0
 8YM  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 8YM  CONST_05  C3   C2   C7   C6      0.00   0.0  0
 8YM  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 8YM  CONST_07  C13  C8   C9   C10     0.00   0.0  0
 8YM  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 8YM  CONST_09  C8   C9   C10  C11     0.00   0.0  0
 8YM  CONST_10  C8   C13  C12  C11     0.00   0.0  0
 8YM  CONST_11  C9   C8   C13  C12     0.00   0.0  0
 8YM  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 8YM  CONST_13  S    C7   C6   C5    180.00   0.0  0
 8YM  CONST_14  C1   C2   C3   C4    180.00   0.0  0
 8YM  CONST_15  C1   C2   C7   C6    180.00   0.0  0
 8YM  CONST_16  S    C8   C9   C10   180.00   0.0  0
 8YM  CONST_17  C14  C13  C12  C11   180.00   0.0  0
 8YM  CONST_18  S    C8   C13  C12   180.00   0.0  0
 8YM  CONST_19  C9   C8   C13  C14   180.00   0.0  0
 8YM  CONST_20  S    C7   C2   C3    180.00   0.0  0
 8YM  CONST_21  H10  C3   C4   C5    180.00   0.0  0
 8YM  CONST_22  H3   C6   C5   C4    180.00   0.0  0
 8YM  CONST_23  H2   C4   C3   C2    180.00   0.0  0
 8YM  CONST_24  H9   C12  C11  C10   180.00   0.0  0
 8YM  CONST_25  H11  C9   C10  C11   180.00   0.0  0
 8YM  CONST_26  H7   C10  C11  C12   180.00   0.0  0
 8YM  CONST_27  H8   C11  C12  C13   180.00   0.0  0
 8YM  CONST_28  H1   C5   C4   C3    180.00   0.0  0
 8YM  Var_01    C9   C8   S    C7     91.54  30.0  2
 8YM  Var_02    C3   C2   C1   C      -3.43  30.0  2
 8YM  Var_03    O2   C14  C13  C12  -135.56  30.0  2
 8YM  Var_04    H4   C    C1   C2    -57.28  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
 8YM  plan-1  C5   0.020
 8YM  plan-1  C4   0.020
 8YM  plan-1  C2   0.020
 8YM  plan-1  C6   0.020
 8YM  plan-1  C1   0.020
 8YM  plan-1  C3   0.020
 8YM  plan-1  C7   0.020
 8YM  plan-1  S    0.020
 8YM  plan-1  H1   0.020
 8YM  plan-1  H2   0.020
 8YM  plan-1  H3   0.020
 8YM  plan-1  H10  0.020
 8YM  plan-2  C10  0.020
 8YM  plan-2  C11  0.020
 8YM  plan-2  C12  0.020
 8YM  plan-2  C13  0.020
 8YM  plan-2  C14  0.020
 8YM  plan-2  C8   0.020
 8YM  plan-2  C9   0.020
 8YM  plan-2  S    0.020
 8YM  plan-2  H7   0.020
 8YM  plan-2  H8   0.020
 8YM  plan-2  H9   0.020
 8YM  plan-2  H11  0.020
 8YM  plan-3  C2   0.020
 8YM  plan-3  C    0.020
 8YM  plan-3  O    0.020
 8YM  plan-3  C1   0.020
 8YM  plan-4  C13  0.020
 8YM  plan-4  C14  0.020
 8YM  plan-4  O1   0.020
 8YM  plan-4  O2   0.020

