# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:28:20 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-fluoranyl-2-(4,5,6,7-tetrahydrofuro[2,3-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)c3oc4CNCCc4c3
#
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
 8E3  8E3  6-fluoranyl-2-(4,5,6,7-tetrahydrofuro[2,3-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide  ligand  35  22  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8E3
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
 8E3  C02  C  C     0   0.469   3.4790  -2.1578   0.2370
 8E3  C04  C  CR6   0  -0.132   3.2370  -0.6865   0.1448
 8E3  C05  C  CR16  0  -0.460   4.2915   0.2169   0.1169
 8E3  C06  C  CR6   0   0.525   4.0454   1.5868   0.0790
 8E3  C08  C  CR16  0  -0.466   2.7833   2.1365   0.0546
 8E3  C09  C  CR56  0   0.367   1.7417   1.2204   0.0761
 8E3  C11  C  CR5   0   0.383  -0.1668   0.1427   0.0717
 8E3  C12  C  CR5   0   0.337  -1.5866  -0.0740   0.0429
 8E3  C13  C  CR15  0  -0.401  -2.3354  -1.2107   0.0518
 8E3  C14  C  CR5   0   0.033  -3.6929  -0.7860   0.0042
 8E3  C15  C  CR5   0   0.303  -3.6572   0.5696  -0.0371
 8E3  C17  C  CH2   0  -0.392  -4.8352   1.4792  -0.0762
 8E3  C19  C  CH2   0  -0.327  -6.1132  -0.5459   0.3585
 8E3  C20  C  CH2   0  -0.518  -4.9868  -1.5306   0.0138
 8E3  C22  C  CR56  0   0.147   1.9348  -0.1738   0.1329
 8E3  F07  F  F     0  -0.318   5.1042   2.4140   0.0697
 8E3  N01  N  NH2   0  -0.801   4.5146  -2.6109  -0.4846
 8E3  N10  N  NR15  0  -0.713   0.3887   1.3860   0.0432
 8E3  N18  N  NH1   0  -0.585  -6.0435   0.7201  -0.3599
 8E3  N21  N  N     0  -0.465   0.7254  -0.8130   0.1247
 8E3  O03  O  O     0  -0.473   2.7786  -2.8750   0.9348
 8E3  O16  O  O     0  -0.449  -2.3888   1.0171  -0.0095
 8E3  H1   H  HCR6  0   0.284   5.3184  -0.1252   0.1501
 8E3  H2   H  HCR6  0   0.295   2.6253   3.2062   0.0207
 8E3  H3   H  HCR5  0   0.264  -1.9586  -2.2205   0.0927
 8E3  H4   H  HCH2  0   0.253  -4.9416   2.0004   0.8820
 8E3  H5   H  HCH2  0   0.267  -4.7148   2.2531  -0.8377
 8E3  H6   H  HCH2  0   0.246  -7.0831  -1.0031   0.1576
 8E3  H7   H  HCH2  0   0.234  -6.0828  -0.3260   1.4296
 8E3  H8   H  HCH2  0   0.244  -5.1700  -1.9888  -0.9630
 8E3  H9   H  HCH2  0   0.248  -4.9664  -2.3460   0.7405
 8E3  H10  H  HNH2  0   0.406   4.7581  -3.5880  -0.4618
 8E3  H11  H  HNH2  0   0.414   5.0070  -2.0266  -1.1376
 8E3  H12  H  HNR5  0   0.427  -0.1031   2.2650  -0.0068
 8E3  H13  H  HNH1  0   0.352  -6.0928   0.5423  -1.3558

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
 8E3  C19  C20  single    1.535  0.020  1.535
 8E3  C19  N18  single    1.457  0.020  1.457
 8E3  C20  C14  single    1.493  0.020  1.493
 8E3  N18  C17  single    1.455  0.020  1.455
 8E3  C14  C13  aromatic  1.423  0.020  1.423
 8E3  C14  C15  aromatic  1.357  0.020  1.357
 8E3  C13  C12  aromatic  1.361  0.020  1.361
 8E3  C17  C15  single    1.489  0.020  1.489
 8E3  C15  O16  aromatic  1.345  0.020  1.345
 8E3  N01  C02  single    1.341  0.020  1.341
 8E3  C12  O16  aromatic  1.355  0.020  1.355
 8E3  C12  C11  single    1.436  0.020  1.436
 8E3  N21  C11  aromatic  1.309  0.020  1.309
 8E3  N21  C22  aromatic  1.368  0.020  1.368
 8E3  C11  N10  aromatic  1.362  0.020  1.362
 8E3  C02  O03  double    1.221  0.020  1.221
 8E3  C02  C04  single    1.494  0.020  1.494
 8E3  C22  C04  aromatic  1.400  0.020  1.400
 8E3  C22  C09  aromatic  1.409  0.020  1.409
 8E3  C04  C05  aromatic  1.389  0.020  1.389
 8E3  N10  C09  aromatic  1.364  0.020  1.364
 8E3  C09  C08  aromatic  1.387  0.020  1.387
 8E3  C05  C06  aromatic  1.392  0.020  1.392
 8E3  C08  C06  aromatic  1.377  0.020  1.377
 8E3  C06  F07  single    1.344  0.020  1.344
 8E3  C05  H1   single    0.930  0.020  1.080
 8E3  C08  H2   single    0.930  0.020  1.080
 8E3  C13  H3   single    0.930  0.020  1.080
 8E3  C17  H4   single    0.970  0.020  1.090
 8E3  C17  H5   single    0.970  0.020  1.090
 8E3  C19  H6   single    0.970  0.020  1.090
 8E3  C19  H7   single    0.970  0.020  1.090
 8E3  C20  H8   single    0.970  0.020  1.090
 8E3  C20  H9   single    0.970  0.020  1.090
 8E3  N01  H10  single    0.860  0.020  1.020
 8E3  N01  H11  single    0.860  0.020  1.020
 8E3  N10  H12  single    0.860  0.020  1.020
 8E3  N18  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
 8E3  O03  C02  N01  123.49  3.000
 8E3  O03  C02  C04  121.38  3.000
 8E3  N01  C02  C04  115.13  3.000
 8E3  C22  C04  C05  117.90  3.000
 8E3  C05  C04  C02  121.26  3.000
 8E3  C22  C04  C02  120.80  3.000
 8E3  H1   C05  C06  118.64  3.000
 8E3  H1   C05  C04  120.92  3.000
 8E3  C06  C05  C04  120.42  3.000
 8E3  F07  C06  C08  118.45  3.000
 8E3  F07  C06  C05  117.82  3.000
 8E3  C08  C06  C05  123.73  3.000
 8E3  H2   C08  C09  122.95  3.000
 8E3  H2   C08  C06  121.95  3.000
 8E3  C09  C08  C06  115.11  3.000
 8E3  N10  C09  C22  104.91  3.000
 8E3  N10  C09  C08  131.63  3.000
 8E3  C22  C09  C08  123.46  3.000
 8E3  N21  C11  N10  112.92  3.000
 8E3  N10  C11  C12  122.71  3.000
 8E3  N21  C11  C12  124.37  3.000
 8E3  O16  C12  C13  110.30  3.000
 8E3  O16  C12  C11  117.67  3.000
 8E3  C13  C12  C11  132.03  3.000
 8E3  H3   C13  C14  127.87  3.000
 8E3  H3   C13  C12  126.15  3.000
 8E3  C14  C13  C12  105.98  3.000
 8E3  C20  C14  C15  121.42  3.000
 8E3  C15  C14  C13  105.91  3.000
 8E3  C20  C14  C13  132.66  3.000
 8E3  O16  C15  C17  122.91  3.000
 8E3  O16  C15  C14  110.89  3.000
 8E3  C17  C15  C14  126.19  3.000
 8E3  H5   C17  H4   106.45  3.000
 8E3  H5   C17  N18  108.99  3.000
 8E3  H4   C17  N18  109.76  3.000
 8E3  H5   C17  C15  111.34  3.000
 8E3  H4   C17  C15  110.14  3.000
 8E3  N18  C17  C15  110.09  3.000
 8E3  H7   C19  H6   106.81  3.000
 8E3  H7   C19  N18  107.86  3.000
 8E3  H6   C19  N18  108.41  3.000
 8E3  H7   C19  C20  109.17  3.000
 8E3  H6   C19  C20  110.01  3.000
 8E3  N18  C19  C20  114.29  3.000
 8E3  H9   C20  H8   106.52  3.000
 8E3  H9   C20  C19  110.06  3.000
 8E3  H8   C20  C19  110.25  3.000
 8E3  H9   C20  C14  111.12  3.000
 8E3  H8   C20  C14  110.38  3.000
 8E3  C19  C20  C14  108.51  3.000
 8E3  N21  C22  C09  109.94  3.000
 8E3  C09  C22  C04  119.37  3.000
 8E3  N21  C22  C04  130.65  3.000
 8E3  H11  N01  H10  117.40  3.000
 8E3  H11  N01  C02  122.10  3.000
 8E3  H10  N01  C02  120.15  3.000
 8E3  H12  N10  C11  126.71  3.000
 8E3  H12  N10  C09  126.23  3.000
 8E3  C11  N10  C09  107.05  3.000
 8E3  H13  N18  C19  109.26  3.000
 8E3  H13  N18  C17  108.89  3.000
 8E3  C19  N18  C17  113.39  3.000
 8E3  C22  N21  C11  105.17  3.000
 8E3  C15  O16  C12  106.92  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
 8E3  CONST_01  C11  N21  C22  C04  180.00   0.0  0
 8E3  CONST_02  N10  C09  C22  C04  180.00   0.0  0
 8E3  CONST_03  C08  C09  C22  C04    0.00   0.0  0
 8E3  CONST_04  C08  C06  C05  C04    0.00   0.0  0
 8E3  CONST_05  N21  C22  C04  C05  180.00   0.0  0
 8E3  CONST_06  C09  C22  C04  C05    0.00   0.0  0
 8E3  CONST_07  C09  C08  C06  C05    0.00   0.0  0
 8E3  CONST_08  C22  C04  C05  C06    0.00   0.0  0
 8E3  CONST_09  C22  C09  C08  C06    0.00   0.0  0
 8E3  CONST_10  N10  C09  C08  C06  180.00   0.0  0
 8E3  CONST_11  N21  C22  C09  C08  180.00   0.0  0
 8E3  CONST_12  C11  N10  C09  C08  180.00   0.0  0
 8E3  CONST_13  C11  N21  C22  C09    0.00   0.0  0
 8E3  CONST_14  C12  C11  N10  C09  180.00   0.0  0
 8E3  CONST_15  N21  C11  N10  C09    0.00   0.0  0
 8E3  CONST_16  C14  C13  C12  C11  180.00   0.0  0
 8E3  CONST_17  C15  O16  C12  C11  180.00   0.0  0
 8E3  CONST_18  C22  C09  N10  C11    0.00   0.0  0
 8E3  CONST_19  C15  C14  C13  C12    0.00   0.0  0
 8E3  CONST_20  C14  C15  O16  C12    0.00   0.0  0
 8E3  CONST_21  C22  N21  C11  C12  180.00   0.0  0
 8E3  CONST_22  O16  C15  C14  C13    0.00   0.0  0
 8E3  CONST_23  C15  O16  C12  C13    0.00   0.0  0
 8E3  CONST_24  N21  C11  C12  C13    0.00   0.0  0
 8E3  CONST_25  N10  C11  C12  C13  180.00   0.0  0
 8E3  CONST_26  O16  C12  C13  C14    0.00   0.0  0
 8E3  CONST_27  N10  C11  N21  C22    0.00   0.0  0
 8E3  CONST_28  O16  C12  C11  N10    0.00   0.0  0
 8E3  CONST_29  N21  C22  C09  N10    0.00   0.0  0
 8E3  CONST_30  O16  C12  C11  N21  180.00   0.0  0
 8E3  CONST_31  N21  C22  C04  C02    0.00   0.0  0
 8E3  CONST_32  C09  C22  C04  C02  180.00   0.0  0
 8E3  CONST_33  C06  C05  C04  C02  180.00   0.0  0
 8E3  CONST_34  F07  C06  C05  C04  180.00   0.0  0
 8E3  CONST_35  F07  C06  C08  C09  180.00   0.0  0
 8E3  CONST_36  H2   C08  C06  C05  180.00   0.0  0
 8E3  CONST_37  H12  N10  C09  C08    0.00   0.0  0
 8E3  CONST_38  H1   C05  C06  C08  180.00   0.0  0
 8E3  CONST_39  H3   C13  C12  C11    0.00   0.0  0
 8E3  CONST_40  H10  N01  C02  C04  180.00   0.0  0
 8E3  CONST_41  H11  N01  C02  C04    0.00   0.0  0
 8E3  Var_01    C19  C20  C14  C13  163.48  30.0  1
 8E3  Var_02    N18  C19  C20  C14   45.25  30.0  1
 8E3  Var_03    N18  C17  C15  C14  -12.48  30.0  1
 8E3  Var_04    C19  N18  C17  C15   41.84  30.0  1
 8E3  Var_05    C20  C19  N18  C17  -61.89  30.0  1
 8E3  Var_06    N01  C02  C04  C05  -39.45  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
 8E3  plan-1  C02  0.020
 8E3  plan-1  C04  0.020
 8E3  plan-1  C05  0.020
 8E3  plan-1  C06  0.020
 8E3  plan-1  C08  0.020
 8E3  plan-1  C09  0.020
 8E3  plan-1  C11  0.020
 8E3  plan-1  C12  0.020
 8E3  plan-1  C22  0.020
 8E3  plan-1  F07  0.020
 8E3  plan-1  N10  0.020
 8E3  plan-1  N21  0.020
 8E3  plan-1  H1   0.020
 8E3  plan-1  H2   0.020
 8E3  plan-1  H12  0.020
 8E3  plan-2  C11  0.020
 8E3  plan-2  C12  0.020
 8E3  plan-2  C13  0.020
 8E3  plan-2  C14  0.020
 8E3  plan-2  C15  0.020
 8E3  plan-2  C17  0.020
 8E3  plan-2  C20  0.020
 8E3  plan-2  O16  0.020
 8E3  plan-2  H3   0.020
 8E3  plan-3  C02  0.020
 8E3  plan-3  C04  0.020
 8E3  plan-3  N01  0.020
 8E3  plan-3  O03  0.020
 8E3  plan-3  H10  0.020
 8E3  plan-3  H11  0.020

