# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:46:18 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[3,2-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(F)cc2[nH]c(nc12)c3sc4CCNCc4c3
#
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
 8E6  8E6  6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[3,2-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide  ligand  35  22  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8E6
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
 8E6  C02  C  C     0   0.469  -3.5033   2.2710   0.2060
 8E6  C04  C  CR6   0  -0.128  -3.3745   0.7836   0.1489
 8E6  C05  C  CR16  0  -0.457  -4.4970  -0.0333   0.1467
 8E6  C06  C  CR6   0   0.526  -4.3606  -1.4193   0.1453
 8E6  C08  C  CR16  0  -0.467  -3.1463  -2.0680   0.1316
 8E6  C09  C  CR56  0   0.365  -2.0358  -1.2364   0.1243
 8E6  C11  C  CR5   0   0.524  -0.0438  -0.3118   0.0874
 8E6  C12  C  CR5   0  -0.299   1.3945  -0.1987   0.0488
 8E6  C13  C  CR15  0  -0.250   2.1223   0.9546   0.1490
 8E6  C14  C  CR5   0   0.180   3.5194   0.7320   0.0765
 8E6  C15  C  CR5   0  -0.235   3.8358  -0.5858  -0.0883
 8E6  C17  C  CH2   0  -0.477   5.2268  -1.1098  -0.2165
 8E6  C18  C  CH2   0  -0.310   6.1529   0.0658  -0.5162
 8E6  C20  C  CH2   0  -0.331   4.5884   1.7797   0.1448
 8E6  C22  C  CR56  0   0.147  -2.1170   0.1690   0.1471
 8E6  F07  F  F     0  -0.318  -5.4820  -2.1592   0.1620
 8E6  N01  N  NH2   0  -0.799  -4.4840   2.7840  -0.5522
 8E6  N10  N  NR15  0  -0.737  -0.6998  -1.5073   0.0909
 8E6  N19  N  NH1   0  -0.605   5.8705   1.1513   0.4065
 8E6  N21  N  N     0  -0.460  -0.8609   0.7096   0.1182
 8E6  O03  O  O     0  -0.470  -2.7707   2.9473   0.9108
 8E6  S16  S  S2    0   0.241   2.4287  -1.5692  -0.1469
 8E6  H1   H  HCR6  0   0.284  -5.4933   0.3904   0.1716
 8E6  H2   H  HCR6  0   0.295  -3.0730  -3.1473   0.1249
 8E6  H3   H  HCR5  0   0.263   1.6675   1.9267   0.2826
 8E6  H4   H  HCH2  0   0.258   5.5331  -1.6008   0.7114
 8E6  H5   H  HCH2  0   0.257   5.2984  -1.8552  -1.0108
 8E6  H6   H  HCH2  0   0.247   7.1892  -0.2463  -0.3850
 8E6  H7   H  HCH2  0   0.205   6.0327   0.3589  -1.5705
 8E6  H8   H  HCH2  0   0.221   4.5735   2.3584  -0.7924
 8E6  H9   H  HCH2  0   0.251   4.3673   2.4873   0.9477
 8E6  H10  H  HNH2  0   0.406  -4.6466   3.7780  -0.5626
 8E6  H11  H  HNH2  0   0.413  -4.9905   2.2256  -1.2174
 8E6  H12  H  HNR5  0   0.427  -0.2887  -2.4287   0.0838
 8E6  H13  H  HNH1  0   0.363   6.5997   1.8484   0.3477

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
 8E6  N19  C20  single    1.452  0.020  1.452
 8E6  N19  C18  single    1.452  0.020  1.452
 8E6  C20  C14  single    1.498  0.020  1.498
 8E6  C18  C17  single    1.526  0.020  1.526
 8E6  C14  C13  aromatic  1.416  0.020  1.416
 8E6  C14  C15  aromatic  1.365  0.020  1.365
 8E6  C13  C12  aromatic  1.367  0.020  1.367
 8E6  C17  C15  single    1.492  0.020  1.492
 8E6  C15  S16  aromatic  1.718  0.020  1.718
 8E6  N10  C11  aromatic  1.364  0.020  1.364
 8E6  N10  C09  aromatic  1.364  0.020  1.364
 8E6  C12  C11  single    1.443  0.020  1.443
 8E6  C12  S16  aromatic  1.728  0.020  1.728
 8E6  C11  N21  aromatic  1.308  0.020  1.308
 8E6  C08  C09  aromatic  1.387  0.020  1.387
 8E6  C08  C06  aromatic  1.377  0.020  1.377
 8E6  C09  C22  aromatic  1.408  0.020  1.408
 8E6  F07  C06  single    1.344  0.020  1.344
 8E6  C06  C05  aromatic  1.393  0.020  1.393
 8E6  N21  C22  aromatic  1.368  0.020  1.368
 8E6  C22  C04  aromatic  1.400  0.020  1.400
 8E6  C05  C04  aromatic  1.388  0.020  1.388
 8E6  C04  C02  single    1.494  0.020  1.494
 8E6  C02  N01  single    1.342  0.020  1.342
 8E6  C02  O03  double    1.221  0.020  1.221
 8E6  C05  H1   single    0.930  0.020  1.080
 8E6  C08  H2   single    0.930  0.020  1.080
 8E6  C13  H3   single    0.930  0.020  1.080
 8E6  C17  H4   single    0.970  0.020  1.090
 8E6  C17  H5   single    0.970  0.020  1.090
 8E6  C18  H6   single    0.970  0.020  1.090
 8E6  C18  H7   single    0.970  0.020  1.090
 8E6  C20  H8   single    0.970  0.020  1.090
 8E6  C20  H9   single    0.970  0.020  1.090
 8E6  N01  H10  single    0.860  0.020  1.020
 8E6  N01  H11  single    0.860  0.020  1.020
 8E6  N10  H12  single    0.860  0.020  1.020
 8E6  N19  H13  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
 8E6  O03  C02  N01  123.58  3.000
 8E6  O03  C02  C04  121.45  3.000
 8E6  N01  C02  C04  114.96  3.000
 8E6  C22  C04  C05  117.91  3.000
 8E6  C05  C04  C02  121.08  3.000
 8E6  C22  C04  C02  120.97  3.000
 8E6  H1   C05  C06  118.66  3.000
 8E6  H1   C05  C04  120.90  3.000
 8E6  C06  C05  C04  120.42  3.000
 8E6  F07  C06  C08  118.47  3.000
 8E6  F07  C06  C05  117.79  3.000
 8E6  C08  C06  C05  123.74  3.000
 8E6  H2   C08  C09  122.94  3.000
 8E6  H2   C08  C06  122.00  3.000
 8E6  C09  C08  C06  115.06  3.000
 8E6  N10  C09  C22  104.78  3.000
 8E6  C22  C09  C08  123.51  3.000
 8E6  N10  C09  C08  131.71  3.000
 8E6  N21  C11  N10  112.58  3.000
 8E6  N21  C11  C12  124.18  3.000
 8E6  N10  C11  C12  123.24  3.000
 8E6  S16  C12  C13  111.02  3.000
 8E6  S16  C12  C11  122.50  3.000
 8E6  C13  C12  C11  126.48  3.000
 8E6  H3   C13  C14  124.22  3.000
 8E6  H3   C13  C12  122.90  3.000
 8E6  C14  C13  C12  112.87  3.000
 8E6  C20  C14  C15  121.00  3.000
 8E6  C15  C14  C13  112.73  3.000
 8E6  C20  C14  C13  126.26  3.000
 8E6  S16  C15  C17  124.04  3.000
 8E6  S16  C15  C14  111.53  3.000
 8E6  C17  C15  C14  124.43  3.000
 8E6  H5   C17  H4   107.00  3.000
 8E6  H5   C17  C18  110.08  3.000
 8E6  H4   C17  C18  110.03  3.000
 8E6  H5   C17  C15  111.31  3.000
 8E6  H4   C17  C15  110.24  3.000
 8E6  C18  C17  C15  108.18  3.000
 8E6  H7   C18  H6   107.17  3.000
 8E6  H7   C18  N19  112.85  3.000
 8E6  H6   C18  N19  108.80  3.000
 8E6  H7   C18  C17  109.08  3.000
 8E6  H6   C18  C17  109.43  3.000
 8E6  N19  C18  C17  109.45  3.000
 8E6  H9   C20  H8   106.39  3.000
 8E6  H9   C20  N19  109.06  3.000
 8E6  H8   C20  N19  113.12  3.000
 8E6  H9   C20  C14  110.00  3.000
 8E6  H8   C20  C14  108.59  3.000
 8E6  N19  C20  C14  109.62  3.000
 8E6  N21  C22  C09  109.95  3.000
 8E6  N21  C22  C04  130.66  3.000
 8E6  C09  C22  C04  119.35  3.000
 8E6  H11  N01  H10  117.39  3.000
 8E6  H11  N01  C02  121.99  3.000
 8E6  H10  N01  C02  120.08  3.000
 8E6  H12  N10  C11  127.20  3.000
 8E6  H12  N10  C09  125.50  3.000
 8E6  C11  N10  C09  107.29  3.000
 8E6  H13  N19  C20  109.17  3.000
 8E6  H13  N19  C18  109.77  3.000
 8E6  C20  N19  C18  112.38  3.000
 8E6  C22  N21  C11  105.39  3.000
 8E6  C15  S16  C12   91.85  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
 8E6  CONST_01  N10  C09  C22  C04  180.00   0.0  0
 8E6  CONST_02  C08  C09  C22  C04    0.00   0.0  0
 8E6  CONST_03  C11  N21  C22  C04  180.00   0.0  0
 8E6  CONST_04  C08  C06  C05  C04    0.00   0.0  0
 8E6  CONST_05  C09  C08  C06  C05    0.00   0.0  0
 8E6  CONST_06  C09  C22  C04  C05    0.00   0.0  0
 8E6  CONST_07  N21  C22  C04  C05  180.00   0.0  0
 8E6  CONST_08  N10  C09  C08  C06  180.00   0.0  0
 8E6  CONST_09  C22  C09  C08  C06    0.00   0.0  0
 8E6  CONST_10  C22  C04  C05  C06    0.00   0.0  0
 8E6  CONST_11  C11  N10  C09  C08  180.00   0.0  0
 8E6  CONST_12  N21  C22  C09  C08  180.00   0.0  0
 8E6  CONST_13  C12  C11  N10  C09  180.00   0.0  0
 8E6  CONST_14  N21  C11  N10  C09    0.00   0.0  0
 8E6  CONST_15  C11  N21  C22  C09    0.00   0.0  0
 8E6  CONST_16  C22  C09  N10  C11    0.00   0.0  0
 8E6  CONST_17  C14  C13  C12  C11  180.00   0.0  0
 8E6  CONST_18  C15  S16  C12  C11  180.00   0.0  0
 8E6  CONST_19  C15  C14  C13  C12    0.00   0.0  0
 8E6  CONST_20  C22  N21  C11  C12  180.00   0.0  0
 8E6  CONST_21  C14  C15  S16  C12    0.00   0.0  0
 8E6  CONST_22  S16  C15  C14  C13    0.00   0.0  0
 8E6  CONST_23  N10  C11  C12  C13  180.00   0.0  0
 8E6  CONST_24  N21  C11  C12  C13    0.00   0.0  0
 8E6  CONST_25  C15  S16  C12  C13    0.00   0.0  0
 8E6  CONST_26  S16  C12  C13  C14    0.00   0.0  0
 8E6  CONST_27  N10  C11  N21  C22    0.00   0.0  0
 8E6  CONST_28  S16  C12  C11  N10    0.00   0.0  0
 8E6  CONST_29  N21  C22  C09  N10    0.00   0.0  0
 8E6  CONST_30  S16  C12  C11  N21  180.00   0.0  0
 8E6  CONST_31  C09  C22  C04  C02  180.00   0.0  0
 8E6  CONST_32  N21  C22  C04  C02    0.00   0.0  0
 8E6  CONST_33  C06  C05  C04  C02  180.00   0.0  0
 8E6  CONST_34  F07  C06  C05  C04  180.00   0.0  0
 8E6  CONST_35  F07  C06  C08  C09  180.00   0.0  0
 8E6  CONST_36  H2   C08  C06  C05  180.00   0.0  0
 8E6  CONST_37  H12  N10  C09  C08    0.00   0.0  0
 8E6  CONST_38  H1   C05  C06  C08  180.00   0.0  0
 8E6  CONST_39  H3   C13  C12  C11    0.00   0.0  0
 8E6  CONST_40  H10  N01  C02  C04  180.00   0.0  0
 8E6  CONST_41  H11  N01  C02  C04    0.00   0.0  0
 8E6  Var_01    N19  C20  C14  C13  164.33  30.0  1
 8E6  Var_02    C18  N19  C20  C14   51.63  30.0  1
 8E6  Var_03    C18  C17  C15  C14  -15.35  30.0  1
 8E6  Var_04    N19  C18  C17  C15   47.76  30.0  1
 8E6  Var_05    C20  N19  C18  C17  -70.31  30.0  1
 8E6  Var_06    N01  C02  C04  C05  -41.13  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
 8E6  plan-1  C02  0.020
 8E6  plan-1  C04  0.020
 8E6  plan-1  C05  0.020
 8E6  plan-1  C06  0.020
 8E6  plan-1  C08  0.020
 8E6  plan-1  C09  0.020
 8E6  plan-1  C11  0.020
 8E6  plan-1  C12  0.020
 8E6  plan-1  C22  0.020
 8E6  plan-1  F07  0.020
 8E6  plan-1  N10  0.020
 8E6  plan-1  N21  0.020
 8E6  plan-1  H1   0.020
 8E6  plan-1  H2   0.020
 8E6  plan-1  H12  0.020
 8E6  plan-2  C11  0.020
 8E6  plan-2  C12  0.020
 8E6  plan-2  C13  0.020
 8E6  plan-2  C14  0.020
 8E6  plan-2  C15  0.020
 8E6  plan-2  C17  0.020
 8E6  plan-2  C20  0.020
 8E6  plan-2  S16  0.020
 8E6  plan-2  H3   0.020
 8E6  plan-3  C02  0.020
 8E6  plan-3  C04  0.020
 8E6  plan-3  N01  0.020
 8E6  plan-3  O03  0.020
 8E6  plan-3  H10  0.020
 8E6  plan-3  H11  0.020

