# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 20:39:16 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: ~{N}-phenyl-2-sulfanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Sc1ccccc1C(=O)Nc2ccccc2
#
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
 9JK  9JK  ~{N}-phenyl-2-sulfanyl-benzamide  ligand  27  16  .  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_9JK
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
 9JK  C11  C  CR6   0   0.376  -2.1684  -0.2468   0.0513
 9JK  C12  C  CR16  0  -0.314  -2.7797   0.9137  -0.4252
 9JK  C13  C  CR16  0  -0.244  -4.1657   1.0094  -0.4160
 9JK  C14  C  CR16  0  -0.270  -4.9583  -0.0243   0.0587
 9JK  C15  C  CR16  0  -0.244  -4.3462  -1.1777   0.5331
 9JK  C02  C  CR6   0  -0.166   2.6628   0.3917   0.3664
 9JK  C03  C  CR16  0  -0.236   3.9030  -0.2417   0.4031
 9JK  C04  C  CR16  0  -0.239   4.0755  -1.5035  -0.1447
 9JK  C05  C  CR16  0  -0.252   3.0084  -2.1524  -0.7460
 9JK  C06  C  CR16  0  -0.263   1.7684  -1.5345  -0.7762
 9JK  C07  C  CR6   0  -0.015   1.5747  -0.2734  -0.2150
 9JK  C08  C  C     0   0.486   0.2200   0.3535  -0.3173
 9JK  O09  O  O     0  -0.455   0.0630   1.4847  -0.7455
 9JK  N10  N  NH1   0  -0.732  -0.7845  -0.4580   0.0866
 9JK  C16  C  CR16  0  -0.348  -2.9670  -1.2890   0.5297
 9JK  H1   H  HCR6  0   0.282  -2.1971   1.7387  -0.7993
 9JK  H2   H  HCR6  0   0.260  -4.6252   1.9149  -0.7905
 9JK  H3   H  HCR6  0   0.257  -6.0363   0.0658   0.0596
 9JK  H4   H  HCR6  0   0.261  -4.9420  -1.9997   0.9078
 9JK  H5   H  HSH1  0   0.255   1.6516   2.5430   0.4421
 9JK  H6   H  HCR6  0   0.275   4.7466   0.2642   0.8553
 9JK  H7   H  HCR6  0   0.270   5.0514  -1.9694  -0.1114
 9JK  H8   H  HCR6  0   0.268   3.1383  -3.1287  -1.1924
 9JK  H9   H  HCR6  0   0.277   0.9383  -2.0382  -1.2560
 9JK  H10  H  HNH1  0   0.425  -0.5044  -1.3386   0.4927
 9JK  H11  H  HCR6  0   0.272  -2.5021  -2.1945   0.9018
 9JK  S01  S  S2    0  -0.186   2.5724   1.9482   1.2040

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
 9JK  C05  C04  aromatic  1.386  0.020  1.386
 9JK  C05  C06  aromatic  1.386  0.020  1.386
 9JK  C04  C03  aromatic  1.386  0.020  1.386
 9JK  C06  C07  aromatic  1.394  0.020  1.394
 9JK  C03  C02  aromatic  1.393  0.020  1.393
 9JK  C07  C02  aromatic  1.402  0.020  1.402
 9JK  C07  C08  single    1.496  0.020  1.496
 9JK  N10  C08  single    1.353  0.020  1.353
 9JK  N10  C11  single    1.400  0.020  1.400
 9JK  C02  S01  single    1.770  0.020  1.770
 9JK  C12  C11  aromatic  1.395  0.020  1.395
 9JK  C12  C13  aromatic  1.389  0.020  1.389
 9JK  C08  O09  double    1.220  0.020  1.220
 9JK  C11  C16  aromatic  1.397  0.020  1.397
 9JK  C13  C14  aromatic  1.386  0.020  1.386
 9JK  C16  C15  aromatic  1.384  0.020  1.384
 9JK  C14  C15  aromatic  1.389  0.020  1.389
 9JK  C12  H1   single    0.930  0.020  1.080
 9JK  C13  H2   single    0.930  0.020  1.080
 9JK  C14  H3   single    0.930  0.020  1.080
 9JK  C15  H4   single    0.930  0.020  1.080
 9JK  S01  H5   single    1.200  0.020  1.300
 9JK  C03  H6   single    0.930  0.020  1.080
 9JK  C04  H7   single    0.930  0.020  1.080
 9JK  C05  H8   single    0.930  0.020  1.080
 9JK  C06  H9   single    0.930  0.020  1.080
 9JK  N10  H10  single    0.860  0.020  1.020
 9JK  C16  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
 9JK  C16  C11  N10  116.33  3.000
 9JK  C16  C11  C12  119.13  3.000
 9JK  N10  C11  C12  124.53  3.000
 9JK  H1   C12  C13  119.28  3.000
 9JK  H1   C12  C11  121.25  3.000
 9JK  C13  C12  C11  119.47  3.000
 9JK  H2   C13  C14  119.97  3.000
 9JK  H2   C13  C12  118.62  3.000
 9JK  C14  C13  C12  121.41  3.000
 9JK  H3   C14  C15  120.53  3.000
 9JK  H3   C14  C13  120.52  3.000
 9JK  C15  C14  C13  118.95  3.000
 9JK  H4   C15  C16  119.24  3.000
 9JK  H4   C15  C14  120.42  3.000
 9JK  C16  C15  C14  120.34  3.000
 9JK  C07  C02  C03  119.10  3.000
 9JK  C07  C02  S01  125.03  3.000
 9JK  C03  C02  S01  115.65  3.000
 9JK  H6   C03  C04  119.56  3.000
 9JK  H6   C03  C02  119.49  3.000
 9JK  C04  C03  C02  120.94  3.000
 9JK  H7   C04  C05  120.41  3.000
 9JK  H7   C04  C03  119.47  3.000
 9JK  C05  C04  C03  120.11  3.000
 9JK  H8   C05  C06  120.07  3.000
 9JK  H8   C05  C04  120.62  3.000
 9JK  C06  C05  C04  119.31  3.000
 9JK  H9   C06  C07  119.52  3.000
 9JK  H9   C06  C05  119.21  3.000
 9JK  C07  C06  C05  121.27  3.000
 9JK  C08  C07  C06  118.52  3.000
 9JK  C08  C07  C02  122.17  3.000
 9JK  C06  C07  C02  119.24  3.000
 9JK  N10  C08  O09  124.44  3.000
 9JK  O09  C08  C07  121.95  3.000
 9JK  N10  C08  C07  113.61  3.000
 9JK  H10  N10  C08  115.93  3.000
 9JK  H10  N10  C11  114.58  3.000
 9JK  C08  N10  C11  129.47  3.000
 9JK  H11  C16  C15  119.60  3.000
 9JK  H11  C16  C11  119.71  3.000
 9JK  C15  C16  C11  120.69  3.000
 9JK  H5   S01  C02   99.03  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
 9JK  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 9JK  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 9JK  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 9JK  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 9JK  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 9JK  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 9JK  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 9JK  CONST_08  C05  C06  C07  C02     0.00   0.0  0
 9JK  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 9JK  CONST_10  C06  C07  C02  C03     0.00   0.0  0
 9JK  CONST_11  C07  C06  C05  C04     0.00   0.0  0
 9JK  CONST_12  C07  C02  C03  C04     0.00   0.0  0
 9JK  CONST_13  N10  C11  C12  C13   180.00   0.0  0
 9JK  CONST_14  N10  C11  C16  C15   180.00   0.0  0
 9JK  CONST_15  C04  C03  C02  S01   180.00   0.0  0
 9JK  CONST_16  C06  C07  C02  S01   180.00   0.0  0
 9JK  CONST_17  C08  C07  C02  C03   180.00   0.0  0
 9JK  CONST_18  C08  C07  C06  C05   180.00   0.0  0
 9JK  CONST_19  H2   C13  C12  C11   180.00   0.0  0
 9JK  CONST_20  H4   C15  C16  C11   180.00   0.0  0
 9JK  CONST_21  H11  C16  C11  C12   180.00   0.0  0
 9JK  CONST_22  H3   C14  C13  C12   180.00   0.0  0
 9JK  CONST_23  H1   C12  C13  C14   180.00   0.0  0
 9JK  CONST_24  H7   C04  C03  C02   180.00   0.0  0
 9JK  CONST_25  H9   C06  C07  C02   180.00   0.0  0
 9JK  CONST_26  H8   C05  C04  C03   180.00   0.0  0
 9JK  CONST_27  H6   C03  C04  C05   180.00   0.0  0
 9JK  CONST_28  C07  C08  N10  C11   180.00   0.0  0
 9JK  CONST_29  C08  N10  C11  C12     0.00   0.0  0
 9JK  CONST_30  C16  C11  N10  C08   180.00   0.0  0
 9JK  CONST_31  H10  N10  C11  C12   180.00   0.0  0
 9JK  CONST_32  O09  C08  N10  C11     0.00   0.0  0
 9JK  Var_01    N10  C08  C07  C02  -132.49  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
 9JK  plan-1  C11  0.020
 9JK  plan-1  C12  0.020
 9JK  plan-1  C13  0.020
 9JK  plan-1  C14  0.020
 9JK  plan-1  C15  0.020
 9JK  plan-1  N10  0.020
 9JK  plan-1  C16  0.020
 9JK  plan-1  H1   0.020
 9JK  plan-1  H2   0.020
 9JK  plan-1  H3   0.020
 9JK  plan-1  H4   0.020
 9JK  plan-1  H11  0.020
 9JK  plan-2  C02  0.020
 9JK  plan-2  C03  0.020
 9JK  plan-2  C04  0.020
 9JK  plan-2  C05  0.020
 9JK  plan-2  C06  0.020
 9JK  plan-2  C07  0.020
 9JK  plan-2  C08  0.020
 9JK  plan-2  H6   0.020
 9JK  plan-2  H7   0.020
 9JK  plan-2  H8   0.020
 9JK  plan-2  H9   0.020
 9JK  plan-2  S01  0.020
 9JK  plan-3  C11  0.020
 9JK  plan-3  C07  0.020
 9JK  plan-3  C08  0.020
 9JK  plan-3  O09  0.020
 9JK  plan-3  N10  0.020
 9JK  plan-3  H10  0.020

