# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:42:09 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-(2-cyanophenyl)sulfanyl-~{N}-(2-sulfanylethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCNC(=O)c1ccccc1Sc2ccccc2C#N
#
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
 T4W  T4W  2-(2-cyanophenyl)sulfanyl-~{N}-(2-sulfanylethyl)benzamide  ligand  35  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T4W
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
 T4W  C1   C  CH2   0  -0.307  19.1316  17.0426   0.8992
 T4W  C2   C  C     0   0.487  18.7808  19.4609   1.0907
 T4W  C3   C  CR6   0   0.015  18.8860  20.6289   2.0260
 T4W  C4   C  CR16  0  -0.254  20.1278  20.9525   2.5641
 T4W  C5   C  CR16  0  -0.236  20.2772  22.0798   3.3586
 T4W  C6   C  CR16  0  -0.246  19.1811  22.8832   3.6387
 T4W  C7   C  CR16  0  -0.195  17.9345  22.5550   3.1276
 T4W  N    N  NH1   0  -0.611  19.0680  18.2764   1.6494
 T4W  C    C  CH2   0  -0.547  20.4110  16.8836   0.0913
 T4W  O    O  O     0  -0.461  18.4879  19.6099  -0.0841
 T4W  C10  C  CR16  0  -0.226  16.9567  22.6916  -0.2983
 T4W  C11  C  CR16  0  -0.223  16.6844  23.4921  -1.3967
 T4W  C12  C  CR16  0  -0.257  15.3866  23.6433  -1.8704
 T4W  C13  C  CR16  0  -0.236  14.3508  22.9897  -1.2307
 T4W  C14  C  CR6   0   0.026  14.6141  22.1934  -0.1155
 T4W  C15  C  CSP   0   0.021  13.5297  21.5428   0.5432
 T4W  C8   C  CR6   0  -0.214  17.7879  21.4389   2.3118
 T4W  C9   C  CR6   0  -0.091  15.9244  22.0356   0.3613
 T4W  N1   N  NS    0  -0.237  12.6494  21.0206   1.0734
 T4W  S    S  S2    0  -0.259  21.8524  17.0163   1.2026
 T4W  S1   S  S2    0   0.110  16.1657  20.9896   1.7572
 T4W  H1   H  HCH2  0   0.271  18.2805  16.9784   0.2195
 T4W  H2   H  HCH2  0   0.270  19.0357  16.2242   1.6115
 T4W  H3   H  HCR6  0   0.267  20.9851  20.3266   2.3477
 T4W  H4   H  HCR6  0   0.272  21.2502  22.3271   3.7619
 T4W  H5   H  HCR6  0   0.272  19.2917  23.7578   4.2658
 T4W  H6   H  HCR6  0   0.281  17.0714  23.1638   3.3633
 T4W  H7   H  HNH1  0   0.415  19.2686  18.2433   2.6360
 T4W  H8   H  HCH2  0   0.281  20.4061  15.9038  -0.3851
 T4W  H9   H  HCH2  0   0.274  20.4756  17.6431  -0.6864
 T4W  H10  H  HCR6  0   0.278  17.9762  22.5832   0.0433
 T4W  H11  H  HCR6  0   0.276  17.5021  23.9978  -1.8930
 T4W  H12  H  HCR6  0   0.274  15.1847  24.2671  -2.7298
 T4W  H13  H  HCR6  0   0.284  13.3324  23.0950  -1.5800
 T4W  H14  H  HSH1  0   0.226  22.7914  16.7211   0.2979

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
 T4W  C12  C13  aromatic  1.382  0.020  1.382
 T4W  C12  C11  aromatic  1.390  0.020  1.390
 T4W  C13  C14  aromatic  1.395  0.020  1.395
 T4W  C11  C10  aromatic  1.386  0.020  1.386
 T4W  C14  C15  single    1.426  0.020  1.426
 T4W  C14  C9   aromatic  1.403  0.020  1.403
 T4W  O    C2   double    1.220  0.020  1.220
 T4W  C    C1   single    1.521  0.020  1.521
 T4W  C    S    single    1.825  0.020  1.825
 T4W  C10  C9   aromatic  1.390  0.020  1.390
 T4W  C15  N1   triple    1.153  0.020  1.153
 T4W  C9   S1   single    1.761  0.020  1.761
 T4W  C1   N    single    1.445  0.020  1.445
 T4W  C2   N    single    1.341  0.020  1.341
 T4W  C2   C3   single    1.500  0.020  1.500
 T4W  S1   C8   single    1.772  0.020  1.772
 T4W  C3   C8   aromatic  1.394  0.020  1.394
 T4W  C3   C4   aromatic  1.392  0.020  1.392
 T4W  C8   C7   aromatic  1.390  0.020  1.390
 T4W  C4   C5   aromatic  1.387  0.020  1.387
 T4W  C7   C6   aromatic  1.387  0.020  1.387
 T4W  C5   C6   aromatic  1.388  0.020  1.388
 T4W  C1   H1   single    0.970  0.020  1.090
 T4W  C1   H2   single    0.970  0.020  1.090
 T4W  C4   H3   single    0.930  0.020  1.080
 T4W  C5   H4   single    0.930  0.020  1.080
 T4W  C6   H5   single    0.930  0.020  1.080
 T4W  C7   H6   single    0.930  0.020  1.080
 T4W  N    H7   single    0.860  0.020  1.020
 T4W  C    H8   single    0.970  0.020  1.090
 T4W  C    H9   single    0.970  0.020  1.090
 T4W  C10  H10  single    0.930  0.020  1.080
 T4W  C11  H11  single    0.930  0.020  1.080
 T4W  C12  H12  single    0.930  0.020  1.080
 T4W  C13  H13  single    0.930  0.020  1.080
 T4W  S    H14  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
 T4W  H2   C1   H1   107.12  3.000
 T4W  H2   C1   C    110.04  3.000
 T4W  H1   C1   C    108.60  3.000
 T4W  H2   C1   N    107.34  3.000
 T4W  H1   C1   N    109.83  3.000
 T4W  C    C1   N    113.69  3.000
 T4W  O    C2   N    124.10  3.000
 T4W  N    C2   C3   114.40  3.000
 T4W  O    C2   C3   121.48  3.000
 T4W  C8   C3   C4   119.24  3.000
 T4W  C4   C3   C2   119.00  3.000
 T4W  C8   C3   C2   121.67  3.000
 T4W  H3   C4   C5   119.91  3.000
 T4W  H3   C4   C3   119.64  3.000
 T4W  C5   C4   C3   120.44  3.000
 T4W  H4   C5   C6   120.19  3.000
 T4W  H4   C5   C4   119.74  3.000
 T4W  C6   C5   C4   120.07  3.000
 T4W  H5   C6   C7   119.79  3.000
 T4W  H5   C6   C5   120.29  3.000
 T4W  C7   C6   C5   119.91  3.000
 T4W  H6   C7   C8   119.70  3.000
 T4W  H6   C7   C6   120.23  3.000
 T4W  C8   C7   C6   120.07  3.000
 T4W  H7   N    C2   118.68  3.000
 T4W  H7   N    C1   118.13  3.000
 T4W  C2   N    C1   123.18  3.000
 T4W  H9   C    H8   108.37  3.000
 T4W  H9   C    S    109.71  3.000
 T4W  H8   C    S    109.59  3.000
 T4W  H9   C    C1   110.87  3.000
 T4W  H8   C    C1   108.81  3.000
 T4W  S    C    C1   109.46  3.000
 T4W  H10  C10  C9   120.22  3.000
 T4W  H10  C10  C11  119.59  3.000
 T4W  C9   C10  C11  120.19  3.000
 T4W  H11  C11  C12  119.90  3.000
 T4W  H11  C11  C10  119.00  3.000
 T4W  C12  C11  C10  121.09  3.000
 T4W  H12  C12  C13  120.07  3.000
 T4W  H12  C12  C11  120.54  3.000
 T4W  C13  C12  C11  119.39  3.000
 T4W  H13  C13  C14  119.42  3.000
 T4W  H13  C13  C12  120.68  3.000
 T4W  C14  C13  C12  119.90  3.000
 T4W  C9   C14  C15  120.12  3.000
 T4W  C9   C14  C13  120.79  3.000
 T4W  C15  C14  C13  119.08  3.000
 T4W  N1   C15  C14  180.00  3.000
 T4W  S1   C8   C7   118.93  3.000
 T4W  C7   C8   C3   120.25  3.000
 T4W  S1   C8   C3   120.63  3.000
 T4W  S1   C9   C14  117.65  3.000
 T4W  S1   C9   C10  123.71  3.000
 T4W  C14  C9   C10  118.64  3.000
 T4W  H14  S    C     97.27  3.000
 T4W  C9   S1   C8   102.88  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
 T4W  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 T4W  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 T4W  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 T4W  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 T4W  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 T4W  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 T4W  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 T4W  CONST_08  C13  C14  C9   C10     0.00   0.0  0
 T4W  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 T4W  CONST_10  C14  C9   C10  C11     0.00   0.0  0
 T4W  CONST_11  C9   C14  C13  C12     0.00   0.0  0
 T4W  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 T4W  CONST_13  C7   C8   C3   C2    180.00   0.0  0
 T4W  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 T4W  CONST_15  S1   C8   C3   C4    180.00   0.0  0
 T4W  CONST_16  S1   C8   C7   C6    180.00   0.0  0
 T4W  CONST_17  C15  C14  C9   C10   180.00   0.0  0
 T4W  CONST_18  S1   C9   C10  C11   180.00   0.0  0
 T4W  CONST_19  C15  C14  C13  C12   180.00   0.0  0
 T4W  CONST_20  S1   C9   C14  C13   180.00   0.0  0
 T4W  CONST_21  H6   C7   C8   C3    180.00   0.0  0
 T4W  CONST_22  H4   C5   C4   C3    180.00   0.0  0
 T4W  CONST_23  H5   C6   C5   C4    180.00   0.0  0
 T4W  CONST_24  H3   C4   C5   C6    180.00   0.0  0
 T4W  CONST_25  H12  C12  C11  C10   180.00   0.0  0
 T4W  CONST_26  H13  C13  C12  C11   180.00   0.0  0
 T4W  CONST_27  H10  C10  C11  C12   180.00   0.0  0
 T4W  CONST_28  H11  C11  C12  C13   180.00   0.0  0
 T4W  CONST_29  C3   C2   N    C1    180.00   0.0  0
 T4W  CONST_30  H7   N    C2   C3      0.00   0.0  0
 T4W  CONST_31  O    C2   N    C1      0.00   0.0  0
 T4W  Var_01    O    C2   C3   C4   -114.15  30.0  2
 T4W  Var_02    C    C1   N    C2     77.29  30.0  2
 T4W  Var_03    S    C    C1   N      56.44  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
 T4W  plan-1  C2   0.020
 T4W  plan-1  C3   0.020
 T4W  plan-1  C4   0.020
 T4W  plan-1  C5   0.020
 T4W  plan-1  C6   0.020
 T4W  plan-1  C7   0.020
 T4W  plan-1  C8   0.020
 T4W  plan-1  S1   0.020
 T4W  plan-1  H3   0.020
 T4W  plan-1  H4   0.020
 T4W  plan-1  H5   0.020
 T4W  plan-1  H6   0.020
 T4W  plan-2  C10  0.020
 T4W  plan-2  C11  0.020
 T4W  plan-2  C12  0.020
 T4W  plan-2  C13  0.020
 T4W  plan-2  C14  0.020
 T4W  plan-2  C15  0.020
 T4W  plan-2  C9   0.020
 T4W  plan-2  N1   0.020
 T4W  plan-2  S1   0.020
 T4W  plan-2  H10  0.020
 T4W  plan-2  H11  0.020
 T4W  plan-2  H12  0.020
 T4W  plan-2  H13  0.020
 T4W  plan-3  C1   0.020
 T4W  plan-3  C2   0.020
 T4W  plan-3  C3   0.020
 T4W  plan-3  N    0.020
 T4W  plan-3  O    0.020
 T4W  plan-3  H7   0.020

