# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:39:11 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  31  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  -0.239   1.3150  -2.7756   0.1276
 8YM  C4   C  CR16  0  -0.252   2.6959  -2.6630   0.0346
 8YM  C2   C  CR6   0  -0.031   2.4881  -0.2507   0.2201
 8YM  C6   C  CR16  0  -0.215   0.5237  -1.6494   0.2632
 8YM  C    C  CH3   0  -0.800   4.6366   1.1610   0.0917
 8YM  O    O  O     0  -0.402   2.4805   2.0773   0.4459
 8YM  C1   C  C     0   0.374   3.1447   1.0735   0.2670
 8YM  C10  C  CR16  0  -0.238  -3.4293  -0.3103   1.9387
 8YM  C11  C  CR16  0  -0.239  -4.2106  -0.4921   0.8086
 8YM  C12  C  CR16  0  -0.252  -3.6809  -0.2324  -0.4460
 8YM  C13  C  CR6   0   0.006  -2.3593   0.1860  -0.5902
 8YM  C14  C  C     0   0.492  -1.8081   0.3830  -1.9589
 8YM  C3   C  CR16  0  -0.291   3.2642  -1.4061   0.0803
 8YM  C7   C  CR6   0  -0.093   1.0865  -0.3743   0.3156
 8YM  C8   C  CR6   0  -0.213  -1.5671   0.3588   0.5529
 8YM  C9   C  CR16  0  -0.200  -2.1187   0.1254   1.8076
 8YM  O1   O  OH1   0  -0.590  -2.7256   0.8371  -2.8035
 8YM  O2   O  O     0  -0.415  -0.6718   0.1435  -2.2761
 8YM  S    S  S2    0   0.122   0.0693   1.0592   0.5099
 8YM  H1   H  HCR6  0   0.269   0.8434  -3.7492   0.0926
 8YM  H2   H  HCR6  0   0.265   3.3181  -3.5406  -0.0730
 8YM  H3   H  HCR6  0   0.267  -0.5466  -1.7769   0.3322
 8YM  H4   H  HCH3  0   0.271   5.1551   0.6446   0.9015
 8YM  H5   H  HCH3  0   0.269   4.9548   0.6976  -0.8427
 8YM  H6   H  HCH3  0   0.273   4.9471   2.2033   0.0916
 8YM  H7   H  HCR6  0   0.274  -3.8369  -0.5008   2.9225
 8YM  H8   H  HCR6  0   0.274  -5.2339  -0.8304   0.8994
 8YM  H9   H  HCR6  0   0.275  -4.3028  -0.3750  -1.3190
 8YM  H10  H  HCR6  0   0.271   4.3392  -1.3194   0.0072
 8YM  H11  H  HCR6  0   0.280  -1.5124   0.2845   2.6896
 8YM  H12  H  HOH1  0   0.488  -2.3518   0.8968  -3.6957

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    1.505  0.020  1.505
 8YM  C1   O    double    1.217  0.020  1.217
 8YM  C1   C2   single    1.479  0.020  1.479
 8YM  C2   C3   aromatic  1.399  0.020  1.399
 8YM  C2   C7   aromatic  1.410  0.020  1.410
 8YM  C3   C4   aromatic  1.380  0.020  1.380
 8YM  S    C7   single    1.768  0.020  1.768
 8YM  S    C8   single    1.781  0.020  1.781
 8YM  C7   C6   aromatic  1.395  0.020  1.395
 8YM  C4   C5   aromatic  1.389  0.020  1.389
 8YM  C6   C5   aromatic  1.383  0.020  1.383
 8YM  C9   C8   aromatic  1.390  0.020  1.390
 8YM  C9   C10  aromatic  1.387  0.020  1.387
 8YM  C8   C13  aromatic  1.401  0.020  1.401
 8YM  O2   C14  double    1.204  0.020  1.204
 8YM  C10  C11  aromatic  1.386  0.020  1.386
 8YM  C13  C14  single    1.489  0.020  1.489
 8YM  C13  C12  aromatic  1.394  0.020  1.394
 8YM  C14  O1   single    1.327  0.020  1.327
 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
 8YM  O1   H12  single    0.850  0.020  0.980

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   119.10  3.000
 8YM  H1   C5   C4   120.27  3.000
 8YM  C6   C5   C4   120.63  3.000
 8YM  H2   C4   C3   120.38  3.000
 8YM  H2   C4   C5   120.87  3.000
 8YM  C3   C4   C5   118.76  3.000
 8YM  C7   C2   C3   119.06  3.000
 8YM  C7   C2   C1   121.18  3.000
 8YM  C3   C2   C1   119.76  3.000
 8YM  H3   C6   C7   120.36  3.000
 8YM  H3   C6   C5   118.50  3.000
 8YM  C7   C6   C5   121.15  3.000
 8YM  H6   C    H5   108.90  3.000
 8YM  H6   C    H4   108.54  3.000
 8YM  H5   C    H4   107.22  3.000
 8YM  H6   C    C1   109.81  3.000
 8YM  H5   C    C1   111.37  3.000
 8YM  H4   C    C1   110.92  3.000
 8YM  O    C1   C    120.68  3.000
 8YM  O    C1   C2   120.06  3.000
 8YM  C    C1   C2   119.25  3.000
 8YM  H7   C10  C9   119.81  3.000
 8YM  H7   C10  C11  120.41  3.000
 8YM  C9   C10  C11  119.78  3.000
 8YM  H8   C11  C12  119.74  3.000
 8YM  H8   C11  C10  120.39  3.000
 8YM  C12  C11  C10  119.87  3.000
 8YM  H9   C12  C13  120.10  3.000
 8YM  H9   C12  C11  119.09  3.000
 8YM  C13  C12  C11  120.81  3.000
 8YM  C8   C13  C14  121.62  3.000
 8YM  C14  C13  C12  119.08  3.000
 8YM  C8   C13  C12  119.25  3.000
 8YM  O2   C14  O1   123.57  3.000
 8YM  O1   C14  C13  111.99  3.000
 8YM  O2   C14  C13  124.43  3.000
 8YM  H10  C3   C2   119.49  3.000
 8YM  H10  C3   C4   118.70  3.000
 8YM  C2   C3   C4   121.81  3.000
 8YM  S    C7   C6   120.87  3.000
 8YM  C6   C7   C2   118.60  3.000
 8YM  S    C7   C2   120.53  3.000
 8YM  S    C8   C9   116.90  3.000
 8YM  C9   C8   C13  119.41  3.000
 8YM  S    C8   C13  123.25  3.000
 8YM  H11  C9   C8   119.25  3.000
 8YM  H11  C9   C10  119.90  3.000
 8YM  C8   C9   C10  120.85  3.000
 8YM  H12  O1   C14  109.90  3.000
 8YM  C8   S    C7   102.26  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  CONST_29  H12  O1   C14  C13   180.00   0.0  0
 8YM  Var_01    C9   C8   S    C7     96.27  30.0  2
 8YM  Var_02    C3   C2   C1   C       3.14  30.0  2
 8YM  Var_03    O2   C14  C13  C12  -144.63  30.0  2
 8YM  Var_04    H4   C    C1   C2    -63.49  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
 8YM  plan-4  H12  0.020

