# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:40:50 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNC(=O)c1sc(cc1)c2cccc3sc(cc23)C(N)=O
#
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
 OD1  OD1  4-{5-[(3-aminopropyl)carbamoyl]thiophen-2-yl}-1-benzothiophene-2-carboxamide  ligand  41  24  .  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_OD1
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
 OD1  C4   C  CR16  0  -0.312  -2.5673   2.7195   0.7921
 OD1  C14  C  C     0   0.557   3.3564   1.4420  -0.8661
 OD1  C5   C  CR6   0   0.110  -1.8804   1.6562   0.2280
 OD1  C6   C  CR56  0   0.237  -2.5341   0.4079   0.1411
 OD1  C11  C  CR15  0  -0.194  -0.0700   2.9219  -1.0207
 OD1  C7   C  CR5   0  -0.300  -2.9986  -1.8166  -0.3488
 OD1  C8   C  CR15  0  -0.270  -2.0863  -0.8179  -0.4407
 OD1  C9   C  C     0   0.514  -2.7788  -3.1836  -0.8864
 OD1  C10  C  CR5   0  -0.250  -0.5208   1.8708  -0.2680
 OD1  C12  C  CR15  0  -0.169   1.3140   2.8569  -1.2912
 OD1  C13  C  CR5   0  -0.324   1.9174   1.7643  -0.7348
 OD1  N1   N  NH2   0  -0.823  -3.7201  -4.0966  -0.6125
 OD1  N2   N  NH1   0  -0.669   3.8342   0.4591  -0.0899
 OD1  C3   C  CR16  0  -0.251  -3.8687   2.5746   1.2820
 OD1  N3   N  NH2   0  -0.800   7.0734  -2.8013   1.5683
 OD1  C1   C  CR56  0  -0.228  -3.8387   0.2874   0.6543
 OD1  C2   C  CR16  0  -0.283  -4.5174   1.3584   1.2280
 OD1  S1   S  S2    0   0.247  -4.4623  -1.3096   0.4388
 OD1  O1   O  O     0  -0.470  -1.7777  -3.4256  -1.5446
 OD1  S2   S  S2    0   0.246   0.7733   0.8027   0.1226
 OD1  O2   O  O     0  -0.487   4.0541   2.0623  -1.6584
 OD1  C15  C  CH2   0  -0.240   5.2236   0.0470  -0.1302
 OD1  C16  C  CH2   0  -0.486   5.4418  -1.1734   0.7482
 OD1  C17  C  CH2   0  -0.272   6.8907  -1.6360   0.7166
 OD1  H1   H  HCR6  0   0.267  -2.0777   3.6810   0.8756
 OD1  H2   H  HCR5  0   0.274  -0.7197   3.7046  -1.3856
 OD1  H4   H  HCR5  0   0.275  -1.1305  -0.9555  -0.9234
 OD1  H6   H  HCR5  0   0.276   1.8482   3.5901  -1.8775
 OD1  H9   H  HNH2  0   0.414  -4.5126  -3.9234  -0.0178
 OD1  H10  H  HNH2  0   0.414  -3.6100  -5.0391  -0.9504
 OD1  H11  H  HNH1  0   0.405   3.2524   0.0459   0.6217
 OD1  H12  H  HCR6  0   0.273  -4.3669   3.4287   1.7204
 OD1  H13  H  HNH2  0   0.348   8.0267  -3.1311   1.4888
 OD1  H14  H  HNH2  0   0.339   6.9619  -2.5267   2.5369
 OD1  H16  H  HCR6  0   0.279  -5.5206   1.2420   1.6154
 OD1  H17  H  HCH2  0   0.238   5.5028  -0.1822  -1.1614
 OD1  H18  H  HCH2  0   0.235   5.8687   0.8671   0.1997
 OD1  H19  H  HCH2  0   0.232   5.1585  -0.9373   1.7798
 OD1  H20  H  HCH2  0   0.235   4.7959  -1.9916   0.4175
 OD1  H21  H  HCH2  0   0.194   7.5429  -0.7913   0.9815
 OD1  H22  H  HCH2  0   0.219   7.1520  -1.9152  -0.3074

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
 OD1  N3   C17  single    1.455  0.020  1.455
 OD1  C17  C16  single    1.521  0.020  1.521
 OD1  C16  C15  single    1.519  0.020  1.519
 OD1  C15  N2   single    1.450  0.020  1.450
 OD1  N2   C14  single    1.340  0.020  1.340
 OD1  O2   C14  double    1.224  0.020  1.224
 OD1  C14  C13  single    1.481  0.020  1.481
 OD1  C13  C12  aromatic  1.367  0.020  1.367
 OD1  C13  S2   aromatic  1.723  0.020  1.723
 OD1  C12  C11  aromatic  1.412  0.020  1.412
 OD1  S2   C10  aromatic  1.723  0.020  1.723
 OD1  C11  C10  aromatic  1.369  0.020  1.369
 OD1  C10  C5   single    1.463  0.020  1.463
 OD1  C5   C4   aromatic  1.386  0.020  1.386
 OD1  C5   C6   aromatic  1.412  0.020  1.412
 OD1  C4   C3   aromatic  1.398  0.020  1.398
 OD1  C8   C6   aromatic  1.429  0.020  1.429
 OD1  C8   C7   aromatic  1.356  0.020  1.356
 OD1  N1   C9   single    1.340  0.020  1.340
 OD1  C6   C1   aromatic  1.407  0.020  1.407
 OD1  C7   C9   single    1.485  0.020  1.485
 OD1  C7   S1   aromatic  1.738  0.020  1.738
 OD1  C3   C2   aromatic  1.379  0.020  1.379
 OD1  C9   O1   double    1.222  0.020  1.222
 OD1  C1   C2   aromatic  1.392  0.020  1.392
 OD1  C1   S1   aromatic  1.728  0.020  1.728
 OD1  C4   H1   single    0.930  0.020  1.080
 OD1  C11  H2   single    0.930  0.020  1.080
 OD1  C8   H4   single    0.930  0.020  1.080
 OD1  C12  H6   single    0.930  0.020  1.080
 OD1  N1   H9   single    0.860  0.020  1.020
 OD1  N1   H10  single    0.860  0.020  1.020
 OD1  N2   H11  single    0.860  0.020  1.020
 OD1  C3   H12  single    0.930  0.020  1.080
 OD1  N3   H13  single    0.890  0.020  1.040
 OD1  N3   H14  single    0.890  0.020  1.040
 OD1  C2   H16  single    0.930  0.020  1.080
 OD1  C15  H17  single    0.970  0.020  1.090
 OD1  C15  H18  single    0.970  0.020  1.090
 OD1  C16  H19  single    0.970  0.020  1.090
 OD1  C16  H20  single    0.970  0.020  1.090
 OD1  C17  H21  single    0.970  0.020  1.090
 OD1  C17  H22  single    0.970  0.020  1.090

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
 OD1  H1   C4   C3   119.09  3.000
 OD1  H1   C4   C5   119.27  3.000
 OD1  C3   C4   C5   121.63  3.000
 OD1  O2   C14  N2   122.90  3.000
 OD1  O2   C14  C13  120.05  3.000
 OD1  N2   C14  C13  117.05  3.000
 OD1  C10  C5   C6   122.63  3.000
 OD1  C6   C5   C4   118.29  3.000
 OD1  C10  C5   C4   119.08  3.000
 OD1  C1   C6   C8   111.44  3.000
 OD1  C1   C6   C5   118.86  3.000
 OD1  C8   C6   C5   129.68  3.000
 OD1  H2   C11  C12  123.92  3.000
 OD1  H2   C11  C10  122.94  3.000
 OD1  C12  C11  C10  113.12  3.000
 OD1  S1   C7   C9   123.86  3.000
 OD1  S1   C7   C8   112.49  3.000
 OD1  C9   C7   C8   123.63  3.000
 OD1  H4   C8   C7   122.15  3.000
 OD1  H4   C8   C6   124.67  3.000
 OD1  C7   C8   C6   113.17  3.000
 OD1  O1   C9   N1   123.41  3.000
 OD1  O1   C9   C7   119.90  3.000
 OD1  N1   C9   C7   116.69  3.000
 OD1  S2   C10  C11  110.69  3.000
 OD1  C11  C10  C5   127.22  3.000
 OD1  S2   C10  C5   122.02  3.000
 OD1  H6   C12  C13  123.04  3.000
 OD1  H6   C12  C11  123.89  3.000
 OD1  C13  C12  C11  113.06  3.000
 OD1  S2   C13  C12  110.83  3.000
 OD1  S2   C13  C14  124.61  3.000
 OD1  C12  C13  C14  124.56  3.000
 OD1  H10  N1   H9   116.45  3.000
 OD1  H10  N1   C9   119.49  3.000
 OD1  H9   N1   C9   123.86  3.000
 OD1  H11  N2   C15  117.16  3.000
 OD1  H11  N2   C14  120.25  3.000
 OD1  C15  N2   C14  122.27  3.000
 OD1  H12  C3   C2   119.70  3.000
 OD1  H12  C3   C4   119.27  3.000
 OD1  C2   C3   C4   121.03  3.000
 OD1  H14  N3   H13  105.50  3.000
 OD1  H14  N3   C17  109.20  3.000
 OD1  H13  N3   C17  109.47  3.000
 OD1  S1   C1   C2   125.92  3.000
 OD1  S1   C1   C6   111.61  3.000
 OD1  C2   C1   C6   122.45  3.000
 OD1  H16  C2   C1   121.13  3.000
 OD1  H16  C2   C3   121.14  3.000
 OD1  C1   C2   C3   117.73  3.000
 OD1  C1   S1   C7    91.27  3.000
 OD1  C13  S2   C10   92.29  3.000
 OD1  H18  C15  H17  106.92  3.000
 OD1  H18  C15  C16  110.06  3.000
 OD1  H17  C15  C16  109.90  3.000
 OD1  H18  C15  N2   110.09  3.000
 OD1  H17  C15  N2   109.32  3.000
 OD1  C16  C15  N2   110.48  3.000
 OD1  H20  C16  H19  107.05  3.000
 OD1  H20  C16  C17  109.19  3.000
 OD1  H19  C16  C17  109.36  3.000
 OD1  H20  C16  C15  109.95  3.000
 OD1  H19  C16  C15  109.52  3.000
 OD1  C17  C16  C15  111.65  3.000
 OD1  H22  C17  H21  106.27  3.000
 OD1  H22  C17  C16  108.96  3.000
 OD1  H21  C17  C16  109.05  3.000
 OD1  H22  C17  N3   108.29  3.000
 OD1  H21  C17  N3   113.56  3.000
 OD1  C16  C17  N3   110.55  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
 OD1  CONST_03  C8   C6   C5   C4    180.00   0.0  0
 OD1  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 OD1  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 OD1  CONST_06  C13  S2   C10  C5    180.00   0.0  0
 OD1  CONST_07  C12  C11  C10  C5    180.00   0.0  0
 OD1  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 OD1  CONST_09  C7   C8   C6   C5    180.00   0.0  0
 OD1  CONST_10  C2   C1   C6   C5      0.00   0.0  0
 OD1  CONST_11  S1   C1   C6   C5    180.00   0.0  0
 OD1  CONST_14  C3   C4   C5   C6      0.00   0.0  0
 OD1  CONST_15  S1   C7   C8   C6      0.00   0.0  0
 OD1  CONST_16  C3   C2   C1   C6      0.00   0.0  0
 OD1  CONST_17  C7   S1   C1   C6      0.00   0.0  0
 OD1  CONST_18  S2   C13  C12  C11     0.00   0.0  0
 OD1  CONST_19  C13  S2   C10  C11     0.00   0.0  0
 OD1  CONST_20  C1   C6   C8   C7      0.00   0.0  0
 OD1  CONST_21  C2   C1   S1   C7    180.00   0.0  0
 OD1  CONST_22  C10  C5   C6   C8      0.00   0.0  0
 OD1  CONST_23  C2   C1   C6   C8    180.00   0.0  0
 OD1  CONST_24  S1   C1   C6   C8      0.00   0.0  0
 OD1  CONST_25  C1   S1   C7   C8      0.00   0.0  0
 OD1  CONST_26  C12  C13  S2   C10     0.00   0.0  0
 OD1  CONST_27  C13  C12  C11  C10     0.00   0.0  0
 OD1  CONST_28  C3   C4   C5   C10   180.00   0.0  0
 OD1  CONST_29  C1   C6   C5   C10   180.00   0.0  0
 OD1  CONST_30  S2   C10  C11  C12     0.00   0.0  0
 OD1  CONST_31  S1   C1   C2   C3    180.00   0.0  0
 OD1  CONST_32  C11  C12  C13  C14   180.00   0.0  0
 OD1  CONST_33  C10  S2   C13  C14   180.00   0.0  0
 OD1  CONST_34  C9   C7   C8   C6    180.00   0.0  0
 OD1  CONST_35  C1   S1   C7   C9    180.00   0.0  0
 OD1  CONST_36  H16  C2   C3   C4    180.00   0.0  0
 OD1  CONST_37  H2   C11  C10  C5      0.00   0.0  0
 OD1  CONST_38  H12  C3   C4   C5    180.00   0.0  0
 OD1  CONST_39  H4   C8   C6   C5      0.00   0.0  0
 OD1  CONST_40  H1   C4   C5   C6    180.00   0.0  0
 OD1  CONST_41  H6   C12  C11  C10   180.00   0.0  0
 OD1  CONST_42  C15  N2   C14  C13   180.00   0.0  0
 OD1  CONST_43  H9   N1   C9   C7      0.00   0.0  0
 OD1  CONST_44  H10  N1   C9   C7    180.00   0.0  0
 OD1  CONST_45  H11  N2   C14  C13     0.00   0.0  0
 OD1  CONST_46  C15  N2   C14  O2      0.00   0.0  0
 OD1  Var_01    N1   C9   C7   C8    174.07  30.0  2
 OD1  Var_02    N2   C14  C13  C12   169.61  30.0  2
 OD1  Var_03    C16  C15  N2   C14  -174.24  30.0  1
 OD1  Var_04    C17  C16  C15  N2    179.54  30.0  1
 OD1  Var_05    C15  C16  C17  N3    179.80  30.0  3
 OD1  Var_06    H13  N3   C17  C16   176.36  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
 OD1  plan-1  C14  0.020
 OD1  plan-1  C5   0.020
 OD1  plan-1  C11  0.020
 OD1  plan-1  C10  0.020
 OD1  plan-1  C12  0.020
 OD1  plan-1  C13  0.020
 OD1  plan-1  S2   0.020
 OD1  plan-1  H2   0.020
 OD1  plan-1  H6   0.020
 OD1  plan-2  C4   0.020
 OD1  plan-2  C5   0.020
 OD1  plan-2  C6   0.020
 OD1  plan-2  C7   0.020
 OD1  plan-2  C8   0.020
 OD1  plan-2  C9   0.020
 OD1  plan-2  C10  0.020
 OD1  plan-2  C3   0.020
 OD1  plan-2  C1   0.020
 OD1  plan-2  C2   0.020
 OD1  plan-2  S1   0.020
 OD1  plan-2  H1   0.020
 OD1  plan-2  H4   0.020
 OD1  plan-2  H12  0.020
 OD1  plan-2  H16  0.020
 OD1  plan-3  C14  0.020
 OD1  plan-3  C13  0.020
 OD1  plan-3  N2   0.020
 OD1  plan-3  O2   0.020
 OD1  plan-3  C15  0.020
 OD1  plan-3  H11  0.020
 OD1  plan-4  C7   0.020
 OD1  plan-4  C9   0.020
 OD1  plan-4  N1   0.020
 OD1  plan-4  O1   0.020
 OD1  plan-4  H9   0.020
 OD1  plan-4  H10  0.020

