# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:50:46 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[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)c3sc4CNCCc4c3
#
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
 8EC  8EC  6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[2,3-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_8EC
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
 8EC  C02  C  C     0   0.470   3.5360  -2.2516  -0.3832
 8EC  C04  C  CR6   0  -0.127   3.3994  -0.7749  -0.2014
 8EC  C05  C  CR16  0  -0.459   4.5164   0.0466  -0.1276
 8EC  C06  C  CR6   0   0.527   4.3709   1.4265  -0.0096
 8EC  C08  C  CR16  0  -0.467   3.1523   2.0645   0.0512
 8EC  C09  C  CR56  0   0.365   2.0474   1.2284  -0.0172
 8EC  C11  C  CR5   0   0.525   0.0612   0.2922  -0.0681
 8EC  C12  C  CR5   0  -0.297  -1.3763   0.1648  -0.0488
 8EC  C13  C  CR15  0  -0.256  -2.0889  -1.0020  -0.0461
 8EC  C14  C  CR5   0   0.212  -3.4913  -0.7951  -0.0205
 8EC  C15  C  CH2   0  -0.485  -4.5536  -1.8512   0.0079
 8EC  C16  C  CH2   0  -0.313  -5.8855  -1.2302   0.4136
 8EC  C18  C  CH2   0  -0.327  -5.2204   1.0510   0.0267
 8EC  C19  C  CR5   0  -0.260  -3.8196   0.5302  -0.0130
 8EC  C22  C  CR56  0   0.148   2.1379  -0.1700  -0.1527
 8EC  F07  F  F     0  -0.318   5.4875   2.1720   0.0435
 8EC  N01  N  NH2   0  -0.800   4.5354  -2.8200   0.3087
 8EC  N10  N  NR15  0  -0.738   0.7092   1.4882   0.0283
 8EC  N17  N  NH1   0  -0.602  -6.1153  -0.0228  -0.3638
 8EC  N21  N  N     0  -0.460   0.8853  -0.7182  -0.1779
 8EC  O03  O  O     0  -0.470   2.7928  -2.8731  -1.1260
 8EC  S20  S  S2    0   0.245  -2.4298   1.5349  -0.0310
 8EC  H1   H  HCR6  0   0.284   5.5156  -0.3667  -0.1863
 8EC  H2   H  HCR6  0   0.295   3.0718   3.1392   0.1453
 8EC  H3   H  HCR5  0   0.263  -1.6200  -1.9766  -0.0543
 8EC  H4   H  HCH2  0   0.247  -4.6405  -2.3169  -0.9779
 8EC  H5   H  HCH2  0   0.248  -4.2828  -2.6452   0.7071
 8EC  H6   H  HCH2  0   0.245  -6.6968  -1.9320   0.2193
 8EC  H7   H  HCH2  0   0.203  -5.8779  -1.0373   1.4979
 8EC  H8   H  HCH2  0   0.231  -5.4263   1.4405   1.0364
 8EC  H9   H  HCH2  0   0.258  -5.3416   1.8897  -0.6630
 8EC  H10  H  HNH2  0   0.406   4.6968  -3.8116   0.2359
 8EC  H11  H  HNH2  0   0.413   5.0489  -2.3203   1.0140
 8EC  H12  H  HNR5  0   0.427   0.2932   2.3992   0.1492
 8EC  H13  H  HNH1  0   0.364  -7.0696   0.2877  -0.2414

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
 8EC  N17  C18  single    1.451  0.020  1.451
 8EC  N17  C16  single    1.454  0.020  1.454
 8EC  C18  C19  single    1.495  0.020  1.495
 8EC  C19  S20  aromatic  1.715  0.020  1.715
 8EC  C19  C14  aromatic  1.365  0.020  1.365
 8EC  C16  C15  single    1.524  0.020  1.524
 8EC  S20  C12  aromatic  1.728  0.020  1.728
 8EC  C14  C15  single    1.498  0.020  1.498
 8EC  C14  C13  aromatic  1.418  0.020  1.418
 8EC  C12  C13  aromatic  1.367  0.020  1.367
 8EC  C12  C11  single    1.443  0.020  1.443
 8EC  N10  C11  aromatic  1.364  0.020  1.364
 8EC  N10  C09  aromatic  1.364  0.020  1.364
 8EC  C11  N21  aromatic  1.308  0.020  1.308
 8EC  C08  C09  aromatic  1.387  0.020  1.387
 8EC  C08  C06  aromatic  1.377  0.020  1.377
 8EC  C09  C22  aromatic  1.408  0.020  1.408
 8EC  N21  C22  aromatic  1.368  0.020  1.368
 8EC  C06  F07  single    1.344  0.020  1.344
 8EC  C06  C05  aromatic  1.393  0.020  1.393
 8EC  C22  C04  aromatic  1.400  0.020  1.400
 8EC  C05  C04  aromatic  1.388  0.020  1.388
 8EC  C04  C02  single    1.494  0.020  1.494
 8EC  N01  C02  single    1.342  0.020  1.342
 8EC  C02  O03  double    1.221  0.020  1.221
 8EC  C05  H1   single    0.930  0.020  1.080
 8EC  C08  H2   single    0.930  0.020  1.080
 8EC  C13  H3   single    0.930  0.020  1.080
 8EC  C15  H4   single    0.970  0.020  1.090
 8EC  C15  H5   single    0.970  0.020  1.090
 8EC  C16  H6   single    0.970  0.020  1.090
 8EC  C16  H7   single    0.970  0.020  1.090
 8EC  C18  H8   single    0.970  0.020  1.090
 8EC  C18  H9   single    0.970  0.020  1.090
 8EC  N01  H10  single    0.860  0.020  1.020
 8EC  N01  H11  single    0.860  0.020  1.020
 8EC  N10  H12  single    0.860  0.020  1.020
 8EC  N17  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
 8EC  O03  C02  N01  123.47  3.000
 8EC  O03  C02  C04  121.44  3.000
 8EC  N01  C02  C04  115.09  3.000
 8EC  C22  C04  C05  117.87  3.000
 8EC  C05  C04  C02  121.18  3.000
 8EC  C22  C04  C02  120.91  3.000
 8EC  H1   C05  C06  118.63  3.000
 8EC  H1   C05  C04  120.90  3.000
 8EC  C06  C05  C04  120.45  3.000
 8EC  F07  C06  C08  118.47  3.000
 8EC  F07  C06  C05  117.80  3.000
 8EC  C08  C06  C05  123.73  3.000
 8EC  H2   C08  C09  122.94  3.000
 8EC  H2   C08  C06  122.01  3.000
 8EC  C09  C08  C06  115.06  3.000
 8EC  N10  C09  C22  104.80  3.000
 8EC  C22  C09  C08  123.51  3.000
 8EC  N10  C09  C08  131.68  3.000
 8EC  N21  C11  N10  112.57  3.000
 8EC  N21  C11  C12  124.08  3.000
 8EC  N10  C11  C12  123.35  3.000
 8EC  S20  C12  C13  111.02  3.000
 8EC  C13  C12  C11  126.47  3.000
 8EC  S20  C12  C11  122.50  3.000
 8EC  H3   C13  C14  124.09  3.000
 8EC  H3   C13  C12  122.89  3.000
 8EC  C14  C13  C12  113.02  3.000
 8EC  C19  C14  C15  120.91  3.000
 8EC  C15  C14  C13  126.78  3.000
 8EC  C19  C14  C13  112.31  3.000
 8EC  H5   C15  H4   106.69  3.000
 8EC  H5   C15  C16  110.03  3.000
 8EC  H4   C15  C16  110.12  3.000
 8EC  H5   C15  C14  110.41  3.000
 8EC  H4   C15  C14  109.84  3.000
 8EC  C16  C15  C14  109.72  3.000
 8EC  H7   C16  H6   107.06  3.000
 8EC  H7   C16  N17  112.45  3.000
 8EC  H6   C16  N17  108.76  3.000
 8EC  H7   C16  C15  109.11  3.000
 8EC  H6   C16  C15  109.91  3.000
 8EC  N17  C16  C15  109.51  3.000
 8EC  H9   C18  H8   106.64  3.000
 8EC  H9   C18  N17  109.26  3.000
 8EC  H8   C18  N17  113.14  3.000
 8EC  H9   C18  C19  110.77  3.000
 8EC  H8   C18  C19  108.82  3.000
 8EC  N17  C18  C19  108.23  3.000
 8EC  S20  C19  C18  123.74  3.000
 8EC  S20  C19  C14  111.94  3.000
 8EC  C18  C19  C14  124.31  3.000
 8EC  N21  C22  C09  109.94  3.000
 8EC  N21  C22  C04  130.66  3.000
 8EC  C09  C22  C04  119.37  3.000
 8EC  H11  N01  H10  117.27  3.000
 8EC  H11  N01  C02  122.11  3.000
 8EC  H10  N01  C02  119.94  3.000
 8EC  H12  N10  C11  127.19  3.000
 8EC  H12  N10  C09  125.50  3.000
 8EC  C11  N10  C09  107.27  3.000
 8EC  H13  N17  C18  108.80  3.000
 8EC  H13  N17  C16  109.84  3.000
 8EC  C18  N17  C16  111.90  3.000
 8EC  C22  N21  C11  105.41  3.000
 8EC  C19  S20  C12   91.70  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
 8EC  CONST_01  N10  C09  C22  C04  180.00   0.0  0
 8EC  CONST_02  C08  C09  C22  C04    0.00   0.0  0
 8EC  CONST_03  C11  N21  C22  C04  180.00   0.0  0
 8EC  CONST_04  C08  C06  C05  C04    0.00   0.0  0
 8EC  CONST_05  C09  C08  C06  C05    0.00   0.0  0
 8EC  CONST_06  C09  C22  C04  C05    0.00   0.0  0
 8EC  CONST_07  N21  C22  C04  C05  180.00   0.0  0
 8EC  CONST_08  N10  C09  C08  C06  180.00   0.0  0
 8EC  CONST_09  C22  C09  C08  C06    0.00   0.0  0
 8EC  CONST_10  C22  C04  C05  C06    0.00   0.0  0
 8EC  CONST_11  C11  N10  C09  C08  180.00   0.0  0
 8EC  CONST_12  N21  C22  C09  C08  180.00   0.0  0
 8EC  CONST_13  C12  C11  N10  C09  180.00   0.0  0
 8EC  CONST_14  N21  C11  N10  C09    0.00   0.0  0
 8EC  CONST_15  C11  N21  C22  C09    0.00   0.0  0
 8EC  CONST_16  C19  S20  C12  C11  180.00   0.0  0
 8EC  CONST_17  C14  C13  C12  C11  180.00   0.0  0
 8EC  CONST_18  C22  C09  N10  C11    0.00   0.0  0
 8EC  CONST_19  C14  C19  S20  C12    0.00   0.0  0
 8EC  CONST_20  C19  C14  C13  C12    0.00   0.0  0
 8EC  CONST_21  C22  N21  C11  C12  180.00   0.0  0
 8EC  CONST_22  S20  C19  C14  C13    0.00   0.0  0
 8EC  CONST_23  C19  S20  C12  C13    0.00   0.0  0
 8EC  CONST_24  N10  C11  C12  C13  180.00   0.0  0
 8EC  CONST_25  N21  C11  C12  C13    0.00   0.0  0
 8EC  CONST_26  S20  C12  C13  C14    0.00   0.0  0
 8EC  CONST_27  N10  C11  N21  C22    0.00   0.0  0
 8EC  CONST_28  S20  C12  C11  N10    0.00   0.0  0
 8EC  CONST_29  N21  C22  C09  N10    0.00   0.0  0
 8EC  CONST_30  S20  C12  C11  N21  180.00   0.0  0
 8EC  CONST_31  C09  C22  C04  C02  180.00   0.0  0
 8EC  CONST_32  N21  C22  C04  C02    0.00   0.0  0
 8EC  CONST_33  C06  C05  C04  C02  180.00   0.0  0
 8EC  CONST_34  F07  C06  C05  C04  180.00   0.0  0
 8EC  CONST_35  F07  C06  C08  C09  180.00   0.0  0
 8EC  CONST_36  H2   C08  C06  C05  180.00   0.0  0
 8EC  CONST_37  H12  N10  C09  C08    0.00   0.0  0
 8EC  CONST_38  H1   C05  C06  C08  180.00   0.0  0
 8EC  CONST_39  H3   C13  C12  C11    0.00   0.0  0
 8EC  CONST_40  H10  N01  C02  C04  180.00   0.0  0
 8EC  CONST_41  H11  N01  C02  C04    0.00   0.0  0
 8EC  Var_01    C16  C15  C14  C13  164.46  30.0  1
 8EC  Var_02    N17  C18  C19  C14  -17.64  30.0  1
 8EC  Var_03    N17  C16  C15  C14   47.80  30.0  1
 8EC  Var_04    C18  N17  C16  C15  -70.61  30.0  1
 8EC  Var_05    C19  C18  N17  C16   52.22  30.0  1
 8EC  Var_06    N01  C02  C04  C05   39.78  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
 8EC  plan-1  C02  0.020
 8EC  plan-1  C04  0.020
 8EC  plan-1  C05  0.020
 8EC  plan-1  C06  0.020
 8EC  plan-1  C08  0.020
 8EC  plan-1  C09  0.020
 8EC  plan-1  C11  0.020
 8EC  plan-1  C12  0.020
 8EC  plan-1  C22  0.020
 8EC  plan-1  F07  0.020
 8EC  plan-1  N10  0.020
 8EC  plan-1  N21  0.020
 8EC  plan-1  H1   0.020
 8EC  plan-1  H2   0.020
 8EC  plan-1  H12  0.020
 8EC  plan-2  C11  0.020
 8EC  plan-2  C12  0.020
 8EC  plan-2  C13  0.020
 8EC  plan-2  C14  0.020
 8EC  plan-2  C15  0.020
 8EC  plan-2  C18  0.020
 8EC  plan-2  C19  0.020
 8EC  plan-2  S20  0.020
 8EC  plan-2  H3   0.020
 8EC  plan-3  C02  0.020
 8EC  plan-3  C04  0.020
 8EC  plan-3  N01  0.020
 8EC  plan-3  O03  0.020
 8EC  plan-3  H10  0.020
 8EC  plan-3  H11  0.020

