# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:37:57 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1sc2cccc(c3sc(cc3)C(=O)NCc4cccc(N)c4)c2c1
#
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
 OCJ  OCJ  4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide  ligand  45  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OCJ
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
 OCJ  N1   N  NH1   0  -0.660  -2.9838  -1.1854  -0.8864
 OCJ  C1   C  C     0   0.560  -2.3488  -2.3363  -1.1624
 OCJ  O1   O  O     0  -0.485  -2.9139  -3.3096  -1.6431
 OCJ  C2   C  CR5   0  -0.318  -0.9046  -2.3972  -0.8468
 OCJ  S1   S  S2    0   0.247  -0.0410  -1.1830   0.0177
 OCJ  C3   C  CR5   0  -0.247   1.4417  -2.0507  -0.1078
 OCJ  C4   C  CR15  0  -0.193   1.2558  -3.2333  -0.7717
 OCJ  C5   C  CR15  0  -0.170  -0.0776  -3.4292  -1.1919
 OCJ  C6   C  CR6   0   0.103   2.6725  -1.5653   0.5174
 OCJ  C7   C  CR16  0  -0.310   3.4145  -2.4284   1.3076
 OCJ  C8   C  CR16  0  -0.251   4.5954  -2.0166   1.9327
 OCJ  C9   C  CR16  0  -0.284   5.0630  -0.7267   1.7897
 OCJ  C10  C  CR56  0  -0.227   4.3292   0.1439   0.9893
 OCJ  C11  C  CR56  0   0.238   3.1434  -0.2468   0.3399
 OCJ  S2   S  S2    0   0.249   4.7305   1.7886   0.6449
 OCJ  C12  C  CR5   0  -0.298   3.3430   1.9514  -0.3877
 OCJ  C13  C  CR15  0  -0.271   2.6062   0.8149  -0.4513
 OCJ  C14  C  C     0   0.512   3.0074   3.1950  -1.1262
 OCJ  O2   O  O     0  -0.470   1.9338   3.2923  -1.7018
 OCJ  C15  C  CH2   0  -0.323  -4.3934  -0.9917  -1.1762
 OCJ  C16  C  CR6   0   0.061  -4.9059   0.2171  -0.4416
 OCJ  N2   N  NH2   0  -0.823   3.9272   4.1696  -1.1124
 OCJ  C17  C  CR16  0  -0.354  -5.1173   0.1461   0.9306
 OCJ  C18  C  CR6   0   0.319  -5.5712   1.2553   1.6505
 OCJ  C19  C  CR16  0  -0.332  -5.8007   2.4501   0.9537
 OCJ  C20  C  CR16  0  -0.236  -5.5870   2.5168  -0.4114
 OCJ  C21  C  CR16  0  -0.333  -5.1379   1.4081  -1.1199
 OCJ  N3   N  NH2   0  -0.861  -5.7426   1.1910   3.0167
 OCJ  H1   H  HNH1  0   0.405  -2.4608  -0.3636  -0.6267
 OCJ  H4   H  HCR5  0   0.274   2.0581  -3.9324  -0.9617
 OCJ  H6   H  HCR5  0   0.276  -0.4147  -4.2969  -1.7399
 OCJ  H8   H  HCR6  0   0.267   3.0602  -3.4387   1.4642
 OCJ  H9   H  HCR6  0   0.273   5.1409  -2.7184   2.5486
 OCJ  H10  H  HCR6  0   0.279   5.9718  -0.4049   2.2803
 OCJ  H11  H  HCR5  0   0.276   1.7217   0.7353  -1.0660
 OCJ  H12  H  HCH2  0   0.257  -4.5528  -0.8731  -2.2516
 OCJ  H13  H  HCH2  0   0.261  -4.9392  -1.8839  -0.8660
 OCJ  H14  H  HNH2  0   0.414   4.8499   4.0628  -0.7259
 OCJ  H15  H  HNH2  0   0.413   3.7510   5.0207  -1.6220
 OCJ  H16  H  HCR6  0   0.252  -4.9346  -0.7877   1.4525
 OCJ  H17  H  HCR6  0   0.256  -6.1531   3.3237   1.4894
 OCJ  H18  H  HCR6  0   0.253  -5.7769   3.4477  -0.9310
 OCJ  H19  H  HCR6  0   0.245  -4.9775   1.4676  -2.1892
 OCJ  H20  H  HNH2  0   0.379  -5.9049   0.2712   3.3940
 OCJ  H21  H  HNH2  0   0.379  -6.3747   1.8705   3.4086

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
 OCJ  S2   C10  aromatic  1.728  0.020  1.728
 OCJ  S2   C12  aromatic  1.737  0.020  1.737
 OCJ  C9   C10  aromatic  1.392  0.020  1.392
 OCJ  C9   C8   aromatic  1.379  0.020  1.379
 OCJ  O2   C14  double    1.222  0.020  1.222
 OCJ  C10  C11  aromatic  1.407  0.020  1.407
 OCJ  C8   C7   aromatic  1.398  0.020  1.398
 OCJ  C14  C12  single    1.485  0.020  1.485
 OCJ  C14  N2   single    1.340  0.020  1.340
 OCJ  C12  C13  aromatic  1.356  0.020  1.356
 OCJ  C11  C13  aromatic  1.429  0.020  1.429
 OCJ  C11  C6   aromatic  1.411  0.020  1.411
 OCJ  C7   C6   aromatic  1.386  0.020  1.386
 OCJ  C6   C3   single    1.463  0.020  1.463
 OCJ  C3   C4   aromatic  1.369  0.020  1.369
 OCJ  C3   S1   aromatic  1.722  0.020  1.722
 OCJ  C4   C5   aromatic  1.412  0.020  1.412
 OCJ  S1   C2   aromatic  1.723  0.020  1.723
 OCJ  C5   C2   aromatic  1.367  0.020  1.367
 OCJ  C2   C1   single    1.479  0.020  1.479
 OCJ  C1   O1   double    1.224  0.020  1.224
 OCJ  C1   N1   single    1.343  0.020  1.343
 OCJ  N1   C15  single    1.452  0.020  1.452
 OCJ  N3   C18  single    1.378  0.020  1.378
 OCJ  C17  C18  aromatic  1.398  0.020  1.398
 OCJ  C17  C16  aromatic  1.390  0.020  1.390
 OCJ  C15  C16  single    1.505  0.020  1.505
 OCJ  C18  C19  aromatic  1.402  0.020  1.402
 OCJ  C16  C21  aromatic  1.390  0.020  1.390
 OCJ  C19  C20  aromatic  1.383  0.020  1.383
 OCJ  C21  C20  aromatic  1.390  0.020  1.390
 OCJ  N1   H1   single    0.860  0.020  1.020
 OCJ  C4   H4   single    0.930  0.020  1.080
 OCJ  C5   H6   single    0.930  0.020  1.080
 OCJ  C7   H8   single    0.930  0.020  1.080
 OCJ  C8   H9   single    0.930  0.020  1.080
 OCJ  C9   H10  single    0.930  0.020  1.080
 OCJ  C13  H11  single    0.930  0.020  1.080
 OCJ  C15  H12  single    0.970  0.020  1.090
 OCJ  C15  H13  single    0.970  0.020  1.090
 OCJ  N2   H14  single    0.860  0.020  1.020
 OCJ  N2   H15  single    0.860  0.020  1.020
 OCJ  C17  H16  single    0.930  0.020  1.080
 OCJ  C19  H17  single    0.930  0.020  1.080
 OCJ  C20  H18  single    0.930  0.020  1.080
 OCJ  C21  H19  single    0.930  0.020  1.080
 OCJ  N3   H20  single    0.890  0.020  1.040
 OCJ  N3   H21  single    0.890  0.020  1.040

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
 OCJ  H1   N1   C15  116.51  3.000
 OCJ  H1   N1   C1   120.41  3.000
 OCJ  C15  N1   C1   122.16  3.000
 OCJ  C2   C1   O1   120.12  3.000
 OCJ  O1   C1   N1   122.95  3.000
 OCJ  C2   C1   N1   116.93  3.000
 OCJ  C5   C2   S1   110.83  3.000
 OCJ  C5   C2   C1   124.60  3.000
 OCJ  S1   C2   C1   124.57  3.000
 OCJ  C3   S1   C2    92.29  3.000
 OCJ  C6   C3   C4   127.44  3.000
 OCJ  C4   C3   S1   110.71  3.000
 OCJ  C6   C3   S1   121.72  3.000
 OCJ  H4   C4   C5   123.98  3.000
 OCJ  H4   C4   C3   122.90  3.000
 OCJ  C5   C4   C3   113.11  3.000
 OCJ  H6   C5   C4   123.86  3.000
 OCJ  H6   C5   C2   123.08  3.000
 OCJ  C4   C5   C2   113.05  3.000
 OCJ  C11  C6   C7   118.36  3.000
 OCJ  C7   C6   C3   119.17  3.000
 OCJ  C11  C6   C3   122.47  3.000
 OCJ  H8   C7   C8   119.13  3.000
 OCJ  H8   C7   C6   119.26  3.000
 OCJ  C8   C7   C6   121.59  3.000
 OCJ  H9   C8   C9   119.66  3.000
 OCJ  H9   C8   C7   119.31  3.000
 OCJ  C9   C8   C7   121.02  3.000
 OCJ  H10  C9   C10  121.17  3.000
 OCJ  H10  C9   C8   121.06  3.000
 OCJ  C10  C9   C8   117.76  3.000
 OCJ  S2   C10  C11  111.60  3.000
 OCJ  C11  C10  C9   122.41  3.000
 OCJ  S2   C10  C9   125.99  3.000
 OCJ  C13  C11  C10  111.47  3.000
 OCJ  C13  C11  C6   129.67  3.000
 OCJ  C10  C11  C6   118.85  3.000
 OCJ  C12  S2   C10   91.27  3.000
 OCJ  C14  C12  C13  123.77  3.000
 OCJ  C13  C12  S2   112.54  3.000
 OCJ  C14  C12  S2   123.68  3.000
 OCJ  H11  C13  C12  122.25  3.000
 OCJ  H11  C13  C11  124.62  3.000
 OCJ  C12  C13  C11  113.11  3.000
 OCJ  N2   C14  O2   123.37  3.000
 OCJ  N2   C14  C12  116.67  3.000
 OCJ  O2   C14  C12  119.96  3.000
 OCJ  H13  C15  H12  107.18  3.000
 OCJ  H13  C15  C16  110.35  3.000
 OCJ  H12  C15  C16  110.08  3.000
 OCJ  H13  C15  N1   108.66  3.000
 OCJ  H12  C15  N1   110.62  3.000
 OCJ  C16  C15  N1   109.90  3.000
 OCJ  C21  C16  C17  120.00  3.000
 OCJ  C21  C16  C15  120.46  3.000
 OCJ  C17  C16  C15  119.52  3.000
 OCJ  H15  N2   H14  116.38  3.000
 OCJ  H15  N2   C14  119.28  3.000
 OCJ  H14  N2   C14  123.79  3.000
 OCJ  H16  C17  C18  119.32  3.000
 OCJ  H16  C17  C16  119.54  3.000
 OCJ  C18  C17  C16  121.14  3.000
 OCJ  N3   C18  C19  120.79  3.000
 OCJ  C19  C18  C17  118.25  3.000
 OCJ  N3   C18  C17  120.91  3.000
 OCJ  H17  C19  C20  119.94  3.000
 OCJ  H17  C19  C18  119.64  3.000
 OCJ  C20  C19  C18  120.41  3.000
 OCJ  H18  C20  C21  119.84  3.000
 OCJ  H18  C20  C19  119.21  3.000
 OCJ  C21  C20  C19  120.95  3.000
 OCJ  H19  C21  C20  120.48  3.000
 OCJ  H19  C21  C16  120.28  3.000
 OCJ  C20  C21  C16  119.24  3.000
 OCJ  H21  N3   H20  111.66  3.000
 OCJ  H21  N3   C18  115.61  3.000
 OCJ  H20  N3   C18  115.71  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
 OCJ  CONST_01  C6   C3   S1   C2    180.00   0.0  0
 OCJ  CONST_02  C4   C3   S1   C2      0.00   0.0  0
 OCJ  CONST_03  C3   C4   C5   C2      0.00   0.0  0
 OCJ  CONST_06  C5   C4   C3   S1      0.00   0.0  0
 OCJ  CONST_07  C4   C5   C2   S1      0.00   0.0  0
 OCJ  CONST_08  C10  C11  C6   C3    180.00   0.0  0
 OCJ  CONST_09  C13  C11  C6   C3      0.00   0.0  0
 OCJ  CONST_10  C8   C7   C6   C3    180.00   0.0  0
 OCJ  CONST_11  C5   C2   S1   C3      0.00   0.0  0
 OCJ  CONST_14  C6   C3   C4   C5    180.00   0.0  0
 OCJ  CONST_15  S2   C10  C11  C6    180.00   0.0  0
 OCJ  CONST_16  C9   C10  C11  C6      0.00   0.0  0
 OCJ  CONST_17  C12  C13  C11  C6    180.00   0.0  0
 OCJ  CONST_18  C9   C8   C7   C6      0.00   0.0  0
 OCJ  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 OCJ  CONST_20  C10  C11  C6   C7      0.00   0.0  0
 OCJ  CONST_21  C13  C11  C6   C7    180.00   0.0  0
 OCJ  CONST_22  S2   C10  C9   C8    180.00   0.0  0
 OCJ  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 OCJ  CONST_24  C11  C6   C7   C8      0.00   0.0  0
 OCJ  CONST_25  C12  S2   C10  C9    180.00   0.0  0
 OCJ  CONST_26  C13  C11  C10  C9    180.00   0.0  0
 OCJ  CONST_27  C13  C12  S2   C10     0.00   0.0  0
 OCJ  CONST_28  C12  C13  C11  C10     0.00   0.0  0
 OCJ  CONST_29  C12  S2   C10  C11     0.00   0.0  0
 OCJ  CONST_30  S2   C12  C13  C11     0.00   0.0  0
 OCJ  CONST_31  C13  C11  C10  S2      0.00   0.0  0
 OCJ  CONST_32  C19  C18  C17  C16     0.00   0.0  0
 OCJ  CONST_33  C19  C20  C21  C16     0.00   0.0  0
 OCJ  CONST_34  C20  C19  C18  C17     0.00   0.0  0
 OCJ  CONST_35  C20  C21  C16  C17     0.00   0.0  0
 OCJ  CONST_36  C21  C16  C17  C18     0.00   0.0  0
 OCJ  CONST_37  C21  C20  C19  C18     0.00   0.0  0
 OCJ  CONST_38  C3   S1   C2   C1    180.00   0.0  0
 OCJ  CONST_39  C4   C5   C2   C1    180.00   0.0  0
 OCJ  CONST_40  C14  C12  S2   C10   180.00   0.0  0
 OCJ  CONST_41  C14  C12  C13  C11   180.00   0.0  0
 OCJ  CONST_42  C18  C17  C16  C15   180.00   0.0  0
 OCJ  CONST_43  C20  C21  C16  C15   180.00   0.0  0
 OCJ  CONST_44  N3   C18  C17  C16   180.00   0.0  0
 OCJ  CONST_45  N3   C18  C19  C20   180.00   0.0  0
 OCJ  CONST_46  H4   C4   C5   C2    180.00   0.0  0
 OCJ  CONST_47  H6   C5   C2   S1    180.00   0.0  0
 OCJ  CONST_48  H8   C7   C6   C3      0.00   0.0  0
 OCJ  CONST_49  H11  C13  C11  C6      0.00   0.0  0
 OCJ  CONST_50  H9   C8   C7   C6    180.00   0.0  0
 OCJ  CONST_51  H10  C9   C8   C7    180.00   0.0  0
 OCJ  CONST_52  H18  C20  C21  C16   180.00   0.0  0
 OCJ  CONST_53  H17  C19  C18  C17   180.00   0.0  0
 OCJ  CONST_54  H19  C21  C16  C17   180.00   0.0  0
 OCJ  CONST_55  H16  C17  C18  C19   180.00   0.0  0
 OCJ  CONST_58  C15  N1   C1   C2    180.00   0.0  0
 OCJ  CONST_59  H1   N1   C1   C2      0.00   0.0  0
 OCJ  CONST_60  H14  N2   C14  C12     0.00   0.0  0
 OCJ  CONST_61  H15  N2   C14  C12   180.00   0.0  0
 OCJ  CONST_62  C15  N1   C1   O1      0.00   0.0  0
 OCJ  Var_01    S1   C2   C1   N1      7.96  30.0  1
 OCJ  Var_02    C17  C16  C15  N1    -74.12  30.0  2
 OCJ  Var_03    O2   C14  C12  S2   -171.04  30.0  2
 OCJ  Var_04    C16  C15  N1   C1    164.94  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
 OCJ  plan-1  C1   0.020
 OCJ  plan-1  C2   0.020
 OCJ  plan-1  S1   0.020
 OCJ  plan-1  C3   0.020
 OCJ  plan-1  C4   0.020
 OCJ  plan-1  C5   0.020
 OCJ  plan-1  C6   0.020
 OCJ  plan-1  H4   0.020
 OCJ  plan-1  H6   0.020
 OCJ  plan-2  C15  0.020
 OCJ  plan-2  C16  0.020
 OCJ  plan-2  C17  0.020
 OCJ  plan-2  C18  0.020
 OCJ  plan-2  C19  0.020
 OCJ  plan-2  C20  0.020
 OCJ  plan-2  C21  0.020
 OCJ  plan-2  N3   0.020
 OCJ  plan-2  H16  0.020
 OCJ  plan-2  H17  0.020
 OCJ  plan-2  H18  0.020
 OCJ  plan-2  H19  0.020
 OCJ  plan-3  C3   0.020
 OCJ  plan-3  C6   0.020
 OCJ  plan-3  C7   0.020
 OCJ  plan-3  C8   0.020
 OCJ  plan-3  C9   0.020
 OCJ  plan-3  C10  0.020
 OCJ  plan-3  C11  0.020
 OCJ  plan-3  S2   0.020
 OCJ  plan-3  C12  0.020
 OCJ  plan-3  C13  0.020
 OCJ  plan-3  C14  0.020
 OCJ  plan-3  H8   0.020
 OCJ  plan-3  H9   0.020
 OCJ  plan-3  H10  0.020
 OCJ  plan-3  H11  0.020
 OCJ  plan-4  N1   0.020
 OCJ  plan-4  C1   0.020
 OCJ  plan-4  O1   0.020
 OCJ  plan-4  C2   0.020
 OCJ  plan-4  C15  0.020
 OCJ  plan-4  H1   0.020
 OCJ  plan-5  C12  0.020
 OCJ  plan-5  C14  0.020
 OCJ  plan-5  O2   0.020
 OCJ  plan-5  N2   0.020
 OCJ  plan-5  H14  0.020
 OCJ  plan-5  H15  0.020
 OCJ  plan-6  C18  0.020
 OCJ  plan-6  N3   0.020
 OCJ  plan-6  H20  0.020
 OCJ  plan-6  H21  0.020

