# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:23:04 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-phenyl-2-(sulfanylmethyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1CS)c2ccccc2
#
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
 S5Z  S5Z  '4-phenyl-2-(sulfanylmethyl)benzoic acid'  ligand  28  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S5Z
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
 S5Z  C10  C  CR16   0  -0.240   4.4527   1.1737   0.7365
 S5Z  C13  C  CR16   0  -0.315   3.3526  -0.9058  -0.7261
 S5Z  C15  C  C      0   0.109  -1.2215   0.4468   0.3537
 S5Z  O01  O  O      0  -0.589  -3.8751  -0.6408   1.2243
 S5Z  O03  O  OC    -1  -0.592  -3.5946  -2.0827  -0.4517
 S5Z  C04  C  C      0  -0.095  -1.7205  -0.8592   0.2641
 S5Z  C05  C  C1     0  -0.265  -0.8077  -1.8993   0.0990
 S5Z  C06  C  C1     0  -0.320   0.5573  -1.6738   0.0513
 S5Z  C07  C  C      0   0.103   1.0637  -0.3770   0.1278
 S5Z  C08  C  CR6    0   0.091   2.5157  -0.1156   0.0651
 S5Z  C09  C  CR16   0  -0.315   3.0890   0.9273   0.7963
 S5Z  C11  C  CR16   0  -0.268   5.2738   0.3788  -0.0527
 S5Z  C12  C  CR16   0  -0.239   4.7171  -0.6631  -0.7829
 S5Z  C14  C  C1     0  -0.352   0.1498   0.6663   0.2624
 S5Z  S17  S  S2     0  -0.250  -2.7424   2.0256  -1.2174
 S5Z  H1   H  HCR6   0   0.257   4.8756   1.9861   1.3135
 S5Z  H2   H  HCR6   0   0.253   2.9340  -1.7087  -1.3200
 S5Z  H4   H  H      0   0.247  -1.1736  -2.9154   0.0246
 S5Z  H5   H  H      0   0.248   1.2305  -2.5180  -0.0326
 S5Z  H6   H  HCR6   0   0.253   2.4665   1.5430   1.4336
 S5Z  H7   H  HCR6   0   0.257   6.3378   0.5707  -0.0993
 S5Z  H8   H  HCR6   0   0.257   5.3452  -1.2839  -1.4085
 S5Z  H9   H  H      0   0.246   0.5100   1.6891   0.2879
 S5Z  H10  H  HCH2   0   0.295  -2.9638   1.4401   1.1132
 S5Z  H11  H  HCH2   0   0.276  -1.5667   2.5022   0.8395
 S5Z  H12  H  HSH1   0   0.217  -3.5565   3.0362  -0.8882
 S5Z  C02  C  C      0   0.366  -3.2006  -1.2147   0.3483
 S5Z  C16  C  CH2    0  -0.635  -2.1206   1.6444   0.4619

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
 S5Z  S17  C16  single    1.831  0.020  1.831
 S5Z  C16  C15  single    1.501  0.020  1.501
 S5Z  C15  C14  aromatic  1.392  0.020  1.392
 S5Z  C15  C04  aromatic  1.401  0.020  1.401
 S5Z  C14  C07  aromatic  1.394  0.020  1.394
 S5Z  O01  C02  deloc     1.246  0.020  1.246
 S5Z  C02  O03  deloc     1.244  0.020  1.244
 S5Z  C02  C04  single    1.525  0.020  1.525
 S5Z  C04  C05  aromatic  1.394  0.020  1.394
 S5Z  C07  C08  single    1.477  0.020  1.477
 S5Z  C07  C06  aromatic  1.394  0.020  1.394
 S5Z  C09  C08  aromatic  1.397  0.020  1.397
 S5Z  C09  C10  aromatic  1.387  0.020  1.387
 S5Z  C08  C13  aromatic  1.397  0.020  1.397
 S5Z  C10  C11  aromatic  1.389  0.020  1.389
 S5Z  C13  C12  aromatic  1.387  0.020  1.387
 S5Z  C11  C12  aromatic  1.389  0.020  1.389
 S5Z  C05  C06  aromatic  1.384  0.020  1.384
 S5Z  C10  H1   single    0.930  0.020  1.080
 S5Z  C13  H2   single    0.930  0.020  1.080
 S5Z  C05  H4   single    0.930  0.020  1.080
 S5Z  C06  H5   single    0.930  0.020  1.080
 S5Z  C09  H6   single    0.930  0.020  1.080
 S5Z  C11  H7   single    0.930  0.020  1.080
 S5Z  C12  H8   single    0.930  0.020  1.080
 S5Z  C14  H9   single    0.930  0.020  1.080
 S5Z  C16  H10  single    0.970  0.020  1.090
 S5Z  C16  H11  single    0.970  0.020  1.090
 S5Z  S17  H12  single    1.200  0.020  1.300

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
 S5Z  H1   C10  C11  120.10  3.000
 S5Z  H1   C10  C09  119.63  3.000
 S5Z  C11  C10  C09  120.27  3.000
 S5Z  H2   C13  C12  119.18  3.000
 S5Z  H2   C13  C08  119.90  3.000
 S5Z  C12  C13  C08  120.91  3.000
 S5Z  C16  C15  C14  117.96  3.000
 S5Z  C14  C15  C04  119.59  3.000
 S5Z  C16  C15  C04  122.34  3.000
 S5Z  C05  C04  C02  117.93  3.000
 S5Z  C05  C04  C15  118.04  3.000
 S5Z  C02  C04  C15  124.03  3.000
 S5Z  H4   C05  C06  118.93  3.000
 S5Z  H4   C05  C04  119.17  3.000
 S5Z  C06  C05  C04  121.89  3.000
 S5Z  H5   C06  C07  120.23  3.000
 S5Z  H5   C06  C05  119.25  3.000
 S5Z  C07  C06  C05  120.51  3.000
 S5Z  C14  C07  C08  121.09  3.000
 S5Z  C08  C07  C06  121.30  3.000
 S5Z  C14  C07  C06  117.61  3.000
 S5Z  C09  C08  C07  120.90  3.000
 S5Z  C09  C08  C13  118.23  3.000
 S5Z  C07  C08  C13  120.87  3.000
 S5Z  H6   C09  C08  119.78  3.000
 S5Z  H6   C09  C10  119.31  3.000
 S5Z  C08  C09  C10  120.90  3.000
 S5Z  H7   C11  C12  120.30  3.000
 S5Z  H7   C11  C10  120.28  3.000
 S5Z  C12  C11  C10  119.42  3.000
 S5Z  H8   C12  C11  120.11  3.000
 S5Z  H8   C12  C13  119.62  3.000
 S5Z  C11  C12  C13  120.27  3.000
 S5Z  H9   C14  C07  119.37  3.000
 S5Z  H9   C14  C15  118.32  3.000
 S5Z  C07  C14  C15  122.31  3.000
 S5Z  H12  S17  C16   97.95  3.000
 S5Z  C04  C02  O03  115.76  3.000
 S5Z  C04  C02  O01  117.20  3.000
 S5Z  O03  C02  O01  127.01  3.000
 S5Z  H11  C16  H10  109.61  3.000
 S5Z  H11  C16  S17  109.08  3.000
 S5Z  H10  C16  S17  109.01  3.000
 S5Z  H11  C16  C15  110.42  3.000
 S5Z  H10  C16  C15  111.01  3.000
 S5Z  S17  C16  C15  107.66  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
 S5Z  CONST_01  C07  C08  C09  C10  180.00   0.0  0
 S5Z  CONST_02  C13  C08  C09  C10    0.00   0.0  0
 S5Z  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 S5Z  CONST_06  C08  C07  C14  C15  180.00   0.0  0
 S5Z  CONST_07  C06  C07  C14  C15    0.00   0.0  0
 S5Z  CONST_08  C06  C05  C04  C15    0.00   0.0  0
 S5Z  CONST_09  C07  C14  C15  C04    0.00   0.0  0
 S5Z  CONST_10  C07  C06  C05  C04    0.00   0.0  0
 S5Z  CONST_11  C14  C15  C04  C05    0.00   0.0  0
 S5Z  CONST_12  C14  C07  C06  C05    0.00   0.0  0
 S5Z  CONST_13  C08  C07  C06  C05  180.00   0.0  0
 S5Z  CONST_15  C12  C13  C08  C07  180.00   0.0  0
 S5Z  CONST_16  C11  C10  C09  C08    0.00   0.0  0
 S5Z  CONST_17  C11  C12  C13  C08    0.00   0.0  0
 S5Z  CONST_19  C12  C13  C08  C09    0.00   0.0  0
 S5Z  CONST_20  C12  C11  C10  C09    0.00   0.0  0
 S5Z  CONST_21  C14  C15  C04  C02  180.00   0.0  0
 S5Z  CONST_22  C06  C05  C04  C02  180.00   0.0  0
 S5Z  CONST_23  C16  C15  C04  C05  180.00   0.0  0
 S5Z  CONST_24  C16  C15  C14  C07  180.00   0.0  0
 S5Z  CONST_25  H8   C12  C11  C10  180.00   0.0  0
 S5Z  CONST_26  H6   C09  C08  C13  180.00   0.0  0
 S5Z  CONST_27  H7   C11  C12  C13  180.00   0.0  0
 S5Z  CONST_28  H4   C05  C04  C15  180.00   0.0  0
 S5Z  CONST_29  H9   C14  C15  C04  180.00   0.0  0
 S5Z  CONST_30  H5   C06  C05  C04  180.00   0.0  0
 S5Z  CONST_31  H2   C13  C08  C07    0.00   0.0  0
 S5Z  CONST_32  H1   C10  C09  C08  180.00   0.0  0
 S5Z  Var_01    O01  C02  C04  C15  -43.19  30.0  2
 S5Z  Var_02    S17  C16  C15  C04  -79.43  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
 S5Z  plan-1  C15  0.020
 S5Z  plan-1  C04  0.020
 S5Z  plan-1  C05  0.020
 S5Z  plan-1  C06  0.020
 S5Z  plan-1  C07  0.020
 S5Z  plan-1  C08  0.020
 S5Z  plan-1  C14  0.020
 S5Z  plan-1  H4   0.020
 S5Z  plan-1  H5   0.020
 S5Z  plan-1  H9   0.020
 S5Z  plan-1  C02  0.020
 S5Z  plan-1  C16  0.020
 S5Z  plan-2  C10  0.020
 S5Z  plan-2  C13  0.020
 S5Z  plan-2  C07  0.020
 S5Z  plan-2  C08  0.020
 S5Z  plan-2  C09  0.020
 S5Z  plan-2  C11  0.020
 S5Z  plan-2  C12  0.020
 S5Z  plan-2  H1   0.020
 S5Z  plan-2  H2   0.020
 S5Z  plan-2  H6   0.020
 S5Z  plan-2  H7   0.020
 S5Z  plan-2  H8   0.020
 S5Z  plan-3  O01  0.020
 S5Z  plan-3  O03  0.020
 S5Z  plan-3  C04  0.020
 S5Z  plan-3  C02  0.020

