# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:28:56 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-(5-{[(2-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)NCc4ccccc4N)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
 OND  OND  4-(5-{[(2-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_OND
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
 OND  C1   C  C     0   0.514   2.8568  -3.3345   0.8627
 OND  C2   C  CR5   0  -0.299   3.2379  -2.0222   0.2813
 OND  O1   O  O     0  -0.470   1.7818  -3.4609   1.4305
 OND  C3   C  CR15  0  -0.272   2.4937  -0.8966   0.4148
 OND  C4   C  CR56  0   0.238   3.0815   0.2434  -0.2147
 OND  N1   N  NH2   0  -0.824   3.7384  -4.3341   0.7267
 OND  C5   C  CR6   0   0.106   2.6202   1.5758  -0.2769
 OND  N2   N  NH1   0  -0.647  -3.1793   1.3960   0.2035
 OND  C6   C  CR5   0  -0.250   1.3417   1.9945   0.2990
 OND  S1   S  S2    0   0.252  -0.1212   1.1432  -0.0216
 OND  C7   C  CR15  0  -0.194   1.1020   3.0947   1.0776
 OND  C8   C  CR15  0  -0.169  -0.2590   3.2424   1.4248
 OND  C9   C  CR5   0  -0.319  -1.0526   2.2649   0.8944
 OND  C10  C  C     0   0.550  -2.5163   2.1634   1.0840
 OND  O2   O  O     0  -0.483  -3.0624   2.7574   2.0037
 OND  C11  C  CH2   0  -0.362  -4.6149   1.1875   0.2592
 OND  C12  C  CR6   0   0.027  -4.9896  -0.1180  -0.3815
 OND  C13  C  CR16  0  -0.304  -5.6925  -0.1233  -1.5806
 OND  C14  C  CR16  0  -0.280  -6.0584  -1.3037  -2.2113
 OND  C15  C  CR16  0  -0.259  -5.7064  -2.5099  -1.6190
 OND  C16  C  CR16  0  -0.325  -5.0067  -2.5310  -0.4249
 OND  C17  C  CR6   0   0.274  -4.6316  -1.3424   0.2149
 OND  N3   N  NH2   0  -0.853  -3.8875  -1.3898   1.3709
 OND  C18  C  CR16  0  -0.310   3.4191   2.5195  -0.9026
 OND  C19  C  CR16  0  -0.251   4.6456   2.1754  -1.4789
 OND  C20  C  CR16  0  -0.284   5.1037   0.8746  -1.4521
 OND  C21  C  CR56  0  -0.227   4.3133  -0.0774  -0.8146
 OND  S2   S  S2    0   0.246   4.6962  -1.7511  -0.6235
 OND  H1   H  HCR5  0   0.275   1.5663  -0.8814   0.9684
 OND  H2   H  HNH2  0   0.415   4.6490  -4.2298   0.3117
 OND  H3   H  HNH2  0   0.413   3.5313  -5.2334   1.1311
 OND  H4   H  HNH1  0   0.404  -2.7119   1.0622  -0.6251
 OND  H6   H  HCR5  0   0.274   1.8857   3.7658   1.3997
 OND  H8   H  HCR5  0   0.276  -0.6420   4.0453   2.0380
 OND  H11  H  HCH2  0   0.261  -4.9269   1.2215   1.3058
 OND  H12  H  HCH2  0   0.271  -5.1391   2.0058  -0.2417
 OND  H13  H  HCR6  0   0.250  -5.9566   0.8282  -2.0280
 OND  H14  H  HCR6  0   0.245  -6.6072  -1.2819  -3.1432
 OND  H15  H  HCR6  0   0.252  -5.9782  -3.4473  -2.0879
 OND  H16  H  HCR6  0   0.255  -4.7436  -3.4799   0.0281
 OND  H17  H  HNH2  0   0.382  -3.9243  -0.5896   1.9801
 OND  H18  H  HNH2  0   0.382  -3.9367  -2.2538   1.8863
 OND  H19  H  HCR6  0   0.266   3.0756   3.5436  -0.9672
 OND  H20  H  HCR6  0   0.273   5.2363   2.9412  -1.9631
 OND  H21  H  HCR6  0   0.279   6.0478   0.6051  -1.9059

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
 OND  S2   C21  aromatic  1.728  0.020  1.728
 OND  S2   C2   aromatic  1.737  0.020  1.737
 OND  C20  C21  aromatic  1.392  0.020  1.392
 OND  C20  C19  aromatic  1.379  0.020  1.379
 OND  O1   C1   double    1.222  0.020  1.222
 OND  C21  C4   aromatic  1.407  0.020  1.407
 OND  C19  C18  aromatic  1.398  0.020  1.398
 OND  C2   C1   single    1.485  0.020  1.485
 OND  C2   C3   aromatic  1.356  0.020  1.356
 OND  C1   N1   single    1.340  0.020  1.340
 OND  C4   C3   aromatic  1.429  0.020  1.429
 OND  C4   C5   aromatic  1.411  0.020  1.411
 OND  C18  C5   aromatic  1.386  0.020  1.386
 OND  C5   C6   single    1.463  0.020  1.463
 OND  C6   C7   aromatic  1.369  0.020  1.369
 OND  C6   S1   aromatic  1.723  0.020  1.723
 OND  C7   C8   aromatic  1.412  0.020  1.412
 OND  S1   C9   aromatic  1.722  0.020  1.722
 OND  C8   C9   aromatic  1.366  0.020  1.366
 OND  C9   C10  single    1.479  0.020  1.479
 OND  C10  O2   double    1.223  0.020  1.223
 OND  C10  N2   single    1.343  0.020  1.343
 OND  N2   C11  single    1.452  0.020  1.452
 OND  C11  C12  single    1.502  0.020  1.502
 OND  C13  C12  aromatic  1.390  0.020  1.390
 OND  C13  C14  aromatic  1.388  0.020  1.388
 OND  C12  C17  aromatic  1.408  0.020  1.408
 OND  C14  C15  aromatic  1.389  0.020  1.389
 OND  C17  N3   single    1.376  0.020  1.376
 OND  C17  C16  aromatic  1.401  0.020  1.401
 OND  C15  C16  aromatic  1.384  0.020  1.384
 OND  C3   H1   single    0.930  0.020  1.080
 OND  N1   H2   single    0.860  0.020  1.020
 OND  N1   H3   single    0.860  0.020  1.020
 OND  N2   H4   single    0.860  0.020  1.020
 OND  C7   H6   single    0.930  0.020  1.080
 OND  C8   H8   single    0.930  0.020  1.080
 OND  C11  H11  single    0.970  0.020  1.090
 OND  C11  H12  single    0.970  0.020  1.090
 OND  C13  H13  single    0.930  0.020  1.080
 OND  C14  H14  single    0.930  0.020  1.080
 OND  C15  H15  single    0.930  0.020  1.080
 OND  C16  H16  single    0.930  0.020  1.080
 OND  N3   H17  single    0.890  0.020  1.040
 OND  N3   H18  single    0.890  0.020  1.040
 OND  C18  H19  single    0.930  0.020  1.080
 OND  C19  H20  single    0.930  0.020  1.080
 OND  C20  H21  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
 OND  N1   C1   O1   123.28  3.000
 OND  N1   C1   C2   116.79  3.000
 OND  O1   C1   C2   119.93  3.000
 OND  S2   C2   C3   112.49  3.000
 OND  C3   C2   C1   123.65  3.000
 OND  S2   C2   C1   123.85  3.000
 OND  H1   C3   C4   124.59  3.000
 OND  H1   C3   C2   122.24  3.000
 OND  C4   C3   C2   113.15  3.000
 OND  C21  C4   C5   118.85  3.000
 OND  C5   C4   C3   129.66  3.000
 OND  C21  C4   C3   111.47  3.000
 OND  H3   N1   H2   116.37  3.000
 OND  H3   N1   C1   119.34  3.000
 OND  H2   N1   C1   124.06  3.000
 OND  C18  C5   C6   119.11  3.000
 OND  C6   C5   C4   122.57  3.000
 OND  C18  C5   C4   118.32  3.000
 OND  H4   N2   C11  116.26  3.000
 OND  H4   N2   C10  119.94  3.000
 OND  C11  N2   C10  123.03  3.000
 OND  C7   C6   S1   110.75  3.000
 OND  S1   C6   C5   121.83  3.000
 OND  C7   C6   C5   127.35  3.000
 OND  C9   S1   C6    92.21  3.000
 OND  H6   C7   C8   124.09  3.000
 OND  H6   C7   C6   122.79  3.000
 OND  C8   C7   C6   113.11  3.000
 OND  H8   C8   C9   123.10  3.000
 OND  H8   C8   C7   123.98  3.000
 OND  C9   C8   C7   112.92  3.000
 OND  C10  C9   C8   125.03  3.000
 OND  C10  C9   S1   123.97  3.000
 OND  C8   C9   S1   111.00  3.000
 OND  O2   C10  C9   120.31  3.000
 OND  O2   C10  N2   123.36  3.000
 OND  C9   C10  N2   116.33  3.000
 OND  H12  C11  H11  106.18  3.000
 OND  H12  C11  C12  109.61  3.000
 OND  H11  C11  C12  111.37  3.000
 OND  H12  C11  N2   110.43  3.000
 OND  H11  C11  N2   108.34  3.000
 OND  C12  C11  N2   110.81  3.000
 OND  C17  C12  C13  119.38  3.000
 OND  C17  C12  C11  120.78  3.000
 OND  C13  C12  C11  119.84  3.000
 OND  H13  C13  C14  119.66  3.000
 OND  H13  C13  C12  118.42  3.000
 OND  C14  C13  C12  121.92  3.000
 OND  H14  C14  C15  120.89  3.000
 OND  H14  C14  C13  120.55  3.000
 OND  C15  C14  C13  118.56  3.000
 OND  H15  C15  C16  119.16  3.000
 OND  H15  C15  C14  120.23  3.000
 OND  C16  C15  C14  120.61  3.000
 OND  H16  C16  C17  119.14  3.000
 OND  H16  C16  C15  119.77  3.000
 OND  C17  C16  C15  121.09  3.000
 OND  N3   C17  C16  119.96  3.000
 OND  C16  C17  C12  118.44  3.000
 OND  N3   C17  C12  121.56  3.000
 OND  H18  N3   H17  111.75  3.000
 OND  H18  N3   C17  115.66  3.000
 OND  H17  N3   C17  117.49  3.000
 OND  H19  C18  C19  119.13  3.000
 OND  H19  C18  C5   119.24  3.000
 OND  C19  C18  C5   121.62  3.000
 OND  H20  C19  C20  119.67  3.000
 OND  H20  C19  C18  119.30  3.000
 OND  C20  C19  C18  121.02  3.000
 OND  H21  C20  C21  121.16  3.000
 OND  H21  C20  C19  121.11  3.000
 OND  C21  C20  C19  117.73  3.000
 OND  S2   C21  C20  125.98  3.000
 OND  C20  C21  C4   122.44  3.000
 OND  S2   C21  C4   111.57  3.000
 OND  C21  S2   C2    91.30  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
 OND  CONST_01  C20  C21  S2   C2    180.00   0.0  0
 OND  CONST_02  C4   C21  S2   C2      0.00   0.0  0
 OND  CONST_03  C21  C4   C3   C2      0.00   0.0  0
 OND  CONST_04  C5   C4   C3   C2    180.00   0.0  0
 OND  CONST_05  C21  S2   C2   C3      0.00   0.0  0
 OND  CONST_06  S2   C21  C4   C3      0.00   0.0  0
 OND  CONST_07  C20  C21  C4   C3    180.00   0.0  0
 OND  CONST_08  C18  C5   C4   C3    180.00   0.0  0
 OND  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 OND  CONST_10  C19  C20  C21  C4      0.00   0.0  0
 OND  CONST_11  S2   C2   C3   C4      0.00   0.0  0
 OND  CONST_12  C19  C18  C5   C4      0.00   0.0  0
 OND  CONST_15  S2   C21  C4   C5    180.00   0.0  0
 OND  CONST_16  C20  C21  C4   C5      0.00   0.0  0
 OND  CONST_17  C20  C19  C18  C5      0.00   0.0  0
 OND  CONST_18  C8   C7   C6   C5    180.00   0.0  0
 OND  CONST_19  C9   S1   C6   C5    180.00   0.0  0
 OND  CONST_20  C21  C4   C5   C6    180.00   0.0  0
 OND  CONST_21  C19  C18  C5   C6    180.00   0.0  0
 OND  CONST_22  C9   C8   C7   C6      0.00   0.0  0
 OND  CONST_23  C8   C9   S1   C6      0.00   0.0  0
 OND  CONST_25  C8   C7   C6   S1      0.00   0.0  0
 OND  CONST_26  C7   C8   C9   S1      0.00   0.0  0
 OND  CONST_28  C9   S1   C6   C7      0.00   0.0  0
 OND  CONST_29  C15  C14  C13  C12     0.00   0.0  0
 OND  CONST_30  C15  C16  C17  C12     0.00   0.0  0
 OND  CONST_31  C16  C17  C12  C13     0.00   0.0  0
 OND  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 OND  CONST_33  C17  C12  C13  C14     0.00   0.0  0
 OND  CONST_34  C17  C16  C15  C14     0.00   0.0  0
 OND  CONST_35  C21  C20  C19  C18     0.00   0.0  0
 OND  CONST_36  C21  C4   C5   C18     0.00   0.0  0
 OND  CONST_37  S2   C21  C20  C19   180.00   0.0  0
 OND  CONST_38  C21  S2   C2   C1    180.00   0.0  0
 OND  CONST_39  C4   C3   C2   C1    180.00   0.0  0
 OND  CONST_40  C10  C9   S1   C6    180.00   0.0  0
 OND  CONST_41  C10  C9   C8   C7    180.00   0.0  0
 OND  CONST_42  C14  C13  C12  C11   180.00   0.0  0
 OND  CONST_43  C16  C17  C12  C11   180.00   0.0  0
 OND  CONST_44  N3   C17  C12  C13   180.00   0.0  0
 OND  CONST_45  N3   C17  C16  C15   180.00   0.0  0
 OND  CONST_46  H21  C20  C21  C4    180.00   0.0  0
 OND  CONST_47  H19  C18  C5   C4    180.00   0.0  0
 OND  CONST_48  H1   C3   C4   C5      0.00   0.0  0
 OND  CONST_49  H20  C19  C18  C5    180.00   0.0  0
 OND  CONST_50  H6   C7   C6   C5      0.00   0.0  0
 OND  CONST_51  H8   C8   C7   C6    180.00   0.0  0
 OND  CONST_52  H14  C14  C13  C12   180.00   0.0  0
 OND  CONST_53  H16  C16  C17  C12   180.00   0.0  0
 OND  CONST_54  H15  C15  C14  C13   180.00   0.0  0
 OND  CONST_55  H13  C13  C14  C15   180.00   0.0  0
 OND  CONST_58  C11  N2   C10  C9    180.00   0.0  0
 OND  CONST_59  H2   N1   C1   C2      0.00   0.0  0
 OND  CONST_60  H3   N1   C1   C2    180.00   0.0  0
 OND  CONST_61  H4   N2   C10  C9      0.00   0.0  0
 OND  CONST_62  C11  N2   C10  O2      0.00   0.0  0
 OND  Var_01    S2   C2   C1   O1   -176.40  30.0  2
 OND  Var_02    S1   C9   C10  N2    -19.24  30.0  2
 OND  Var_03    C13  C12  C11  N2   -111.01  30.0  2
 OND  Var_04    C12  C11  N2   C10  -154.26  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
 OND  plan-1  C5   0.020
 OND  plan-1  C6   0.020
 OND  plan-1  S1   0.020
 OND  plan-1  C7   0.020
 OND  plan-1  C8   0.020
 OND  plan-1  C9   0.020
 OND  plan-1  C10  0.020
 OND  plan-1  H6   0.020
 OND  plan-1  H8   0.020
 OND  plan-2  C11  0.020
 OND  plan-2  C12  0.020
 OND  plan-2  C13  0.020
 OND  plan-2  C14  0.020
 OND  plan-2  C15  0.020
 OND  plan-2  C16  0.020
 OND  plan-2  C17  0.020
 OND  plan-2  N3   0.020
 OND  plan-2  H13  0.020
 OND  plan-2  H14  0.020
 OND  plan-2  H15  0.020
 OND  plan-2  H16  0.020
 OND  plan-3  C1   0.020
 OND  plan-3  C2   0.020
 OND  plan-3  C3   0.020
 OND  plan-3  C4   0.020
 OND  plan-3  C5   0.020
 OND  plan-3  C6   0.020
 OND  plan-3  C18  0.020
 OND  plan-3  C19  0.020
 OND  plan-3  C20  0.020
 OND  plan-3  C21  0.020
 OND  plan-3  S2   0.020
 OND  plan-3  H1   0.020
 OND  plan-3  H19  0.020
 OND  plan-3  H20  0.020
 OND  plan-3  H21  0.020
 OND  plan-4  C1   0.020
 OND  plan-4  C2   0.020
 OND  plan-4  O1   0.020
 OND  plan-4  N1   0.020
 OND  plan-4  H2   0.020
 OND  plan-4  H3   0.020
 OND  plan-5  N2   0.020
 OND  plan-5  C9   0.020
 OND  plan-5  C10  0.020
 OND  plan-5  O2   0.020
 OND  plan-5  C11  0.020
 OND  plan-5  H4   0.020
 OND  plan-6  C17  0.020
 OND  plan-6  N3   0.020
 OND  plan-6  H17  0.020
 OND  plan-6  H18  0.020

