# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:33:35 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (E)-3-(2-fluorophenyl)-2-methyl-N-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C\c1ccccc1F)/C(=O)NCc2ccc3NC(=O)Nc3c2
#
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
 FYC  FYC  (E)-3-(2-fluorophenyl)-2-methyl-N-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)methyl]prop-2-enamide  ligand  40  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FYC
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
 FYC  O1    O  O     0  -0.497  -7.4565  -1.9297  -0.3446
 FYC  C1    C  CR5   0   0.609  -6.4690  -1.2400  -0.1675
 FYC  N1    N  NR15  0  -0.736  -6.0999  -0.5912   0.9857
 FYC  C2    C  CR56  0   0.319  -4.9150   0.0874   0.8100
 FYC  C3    C  CR16  0  -0.298  -4.1551   0.8703   1.6576
 FYC  C4    C  CR16  0  -0.301  -2.9853   1.4220   1.1448
 FYC  C5    C  CR6   0   0.024  -2.5847   1.2034  -0.1737
 FYC  C6    C  CH2   0  -0.317  -1.2885   1.7791  -0.6715
 FYC  N2    N  NH1   0  -0.659  -0.1845   0.9296  -0.2604
 FYC  C7    C  C     0   0.554   1.0970   1.2736  -0.4628
 FYC  C8    C  C     0  -0.029   2.1172   0.2694  -0.0078
 FYC  C9    C  CH3   0  -0.786   1.6780  -0.8618   0.8730
 FYC  C10   C  C1    0  -0.259   3.3758   0.4818  -0.4115
 FYC  C11   C  CR6   0  -0.122   4.5306  -0.3856  -0.1611
 FYC  C12   C  CR16  0  -0.273   4.4942  -1.7717  -0.3322
 FYC  C13   C  CR16  0  -0.257   5.6180  -2.5550  -0.1175
 FYC  C14   C  CR16  0  -0.246   6.8127  -1.9633   0.2702
 FYC  C15   C  CR16  0  -0.403   6.8859  -0.5868   0.4348
 FYC  C16   C  CR6   0   0.515   5.7523   0.1666   0.2107
 FYC  F1    F  F     0  -0.305   5.8243   1.4983   0.3699
 FYC  O2    O  O     0  -0.503   1.4027   2.3375  -0.9903
 FYC  C17   C  CR16  0  -0.345  -3.3601   0.4115  -1.0211
 FYC  C18   C  CR56  0   0.344  -4.5218  -0.1355  -0.5137
 FYC  N3    N  NR15  0  -0.739  -5.4857  -0.9408  -1.0780
 FYC  H1    H  HNR5  0   0.420  -6.6282  -0.6500   1.8414
 FYC  H3    H  HNR5  0   0.420  -5.4886  -1.2861  -2.0245
 FYC  HA    H  HCR6  0   0.271  -4.4552   1.0514   2.6810
 FYC  H4    H  HCR6  0   0.256  -2.3728   2.0416   1.7881
 FYC  H61C  H  HCH2  0   0.254  -1.3099   1.8726  -1.7606
 FYC  H62C  H  HCH2  0   0.257  -1.1378   2.7831  -0.2698
 FYC  H17   H  HCR6  0   0.269  -3.0601   0.2356  -2.0467
 FYC  H2    H  HNH1  0   0.415  -0.4147   0.0148   0.0910
 FYC  H91C  H  HCH3  0   0.259   1.1141  -1.6195   0.3233
 FYC  H92C  H  HCH3  0   0.270   2.5260  -1.3622   1.3338
 FYC  H93C  H  HCH3  0   0.258   1.0384  -0.5027   1.6815
 FYC  H10   H  H     0   0.267   3.5703   1.3804  -0.9867
 FYC  H12   H  HCR6  0   0.276   3.5760  -2.2368  -0.6660
 FYC  H13   H  HCR6  0   0.265   5.5622  -3.6255  -0.2609
 FYC  H14   H  HCR6  0   0.271   7.6925  -2.5688   0.4420
 FYC  H15   H  HCR6  0   0.281   7.8079  -0.1059   0.7341

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
 FYC  O1   C1    double    1.217  0.020  1.217
 FYC  C1   N1    single    1.374  0.020  1.374
 FYC  C1   N3    single    1.373  0.020  1.373
 FYC  N1   C2    single    1.377  0.020  1.377
 FYC  C2   C3    aromatic  1.382  0.020  1.382
 FYC  C2   C18   aromatic  1.399  0.020  1.399
 FYC  C3   C4    aromatic  1.391  0.020  1.391
 FYC  C4   C5    aromatic  1.395  0.020  1.395
 FYC  C5   C6    single    1.503  0.020  1.503
 FYC  C5   C17   aromatic  1.395  0.020  1.395
 FYC  C6   N2    single    1.452  0.020  1.452
 FYC  N2   C7    single    1.342  0.020  1.342
 FYC  C7   C8    single    1.502  0.020  1.502
 FYC  C7   O2    double    1.226  0.020  1.226
 FYC  C8   C9    single    1.499  0.020  1.499
 FYC  C8   C10   double    1.339  0.020  1.339
 FYC  C10  C11   single    1.466  0.020  1.466
 FYC  C11  C12   aromatic  1.397  0.020  1.397
 FYC  C11  C16   aromatic  1.391  0.020  1.391
 FYC  C12  C13   aromatic  1.387  0.020  1.387
 FYC  C13  C14   aromatic  1.388  0.020  1.388
 FYC  C14  C15   aromatic  1.388  0.020  1.388
 FYC  C15  C16   aromatic  1.380  0.020  1.380
 FYC  C16  F1    single    1.343  0.020  1.343
 FYC  C17  C18   aromatic  1.381  0.020  1.381
 FYC  C18  N3    single    1.377  0.020  1.377
 FYC  N1   H1    single    0.860  0.020  1.020
 FYC  N3   H3    single    0.860  0.020  1.020
 FYC  C3   HA    single    0.930  0.020  1.080
 FYC  C4   H4    single    0.930  0.020  1.080
 FYC  C6   H61C  single    0.970  0.020  1.090
 FYC  C6   H62C  single    0.970  0.020  1.090
 FYC  C17  H17   single    0.930  0.020  1.080
 FYC  N2   H2    single    0.860  0.020  1.020
 FYC  C9   H91C  single    0.970  0.020  1.090
 FYC  C9   H92C  single    0.970  0.020  1.090
 FYC  C9   H93C  single    0.970  0.020  1.090
 FYC  C10  H10   single    0.930  0.020  1.080
 FYC  C12  H12   single    0.930  0.020  1.080
 FYC  C13  H13   single    0.930  0.020  1.080
 FYC  C14  H14   single    0.930  0.020  1.080
 FYC  C15  H15   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
 FYC  N3    C1   N1    105.15  3.000
 FYC  N3    C1   O1    127.44  3.000
 FYC  N1    C1   O1    127.42  3.000
 FYC  H1    N1   C2    126.05  3.000
 FYC  H1    N1   C1    123.00  3.000
 FYC  C2    N1   C1    110.91  3.000
 FYC  C18   C2   C3    121.08  3.000
 FYC  C18   C2   N1    106.51  3.000
 FYC  C3    C2   N1    132.41  3.000
 FYC  HA    C3   C4    121.03  3.000
 FYC  HA    C3   C2    121.51  3.000
 FYC  C4    C3   C2    117.46  3.000
 FYC  H4    C4   C5    119.25  3.000
 FYC  H4    C4   C3    118.91  3.000
 FYC  C5    C4   C3    121.84  3.000
 FYC  C17   C5   C6    119.71  3.000
 FYC  C17   C5   C4    120.22  3.000
 FYC  C6    C5   C4    120.03  3.000
 FYC  H62C  C6   H61C  106.88  3.000
 FYC  H62C  C6   N2    109.20  3.000
 FYC  H61C  C6   N2    110.30  3.000
 FYC  H62C  C6   C5    110.45  3.000
 FYC  H61C  C6   C5    110.23  3.000
 FYC  N2    C6   C5    109.74  3.000
 FYC  H2    N2   C7    120.26  3.000
 FYC  H2    N2   C6    117.16  3.000
 FYC  C7    N2   C6    122.22  3.000
 FYC  O2    C7   C8    122.76  3.000
 FYC  O2    C7   N2    121.69  3.000
 FYC  C8    C7   N2    115.56  3.000
 FYC  C10   C8   C9    124.91  3.000
 FYC  C10   C8   C7    116.17  3.000
 FYC  C9    C8   C7    118.91  3.000
 FYC  H93C  C9   H92C  107.13  3.000
 FYC  H93C  C9   H91C  107.36  3.000
 FYC  H92C  C9   H91C  107.25  3.000
 FYC  H93C  C9   C8    111.01  3.000
 FYC  H92C  C9   C8    111.57  3.000
 FYC  H91C  C9   C8    112.26  3.000
 FYC  H10   C10  C11   116.07  3.000
 FYC  H10   C10  C8    117.39  3.000
 FYC  C11   C10  C8    126.53  3.000
 FYC  C16   C11  C12   116.71  3.000
 FYC  C16   C11  C10   120.17  3.000
 FYC  C12   C11  C10   123.07  3.000
 FYC  H12   C12  C13   119.52  3.000
 FYC  H12   C12  C11   119.10  3.000
 FYC  C13   C12  C11   121.36  3.000
 FYC  H13   C13  C14   120.21  3.000
 FYC  H13   C13  C12   119.79  3.000
 FYC  C14   C13  C12   119.99  3.000
 FYC  H14   C14  C15   119.56  3.000
 FYC  H14   C14  C13   120.37  3.000
 FYC  C15   C14  C13   120.07  3.000
 FYC  H15   C15  C16   120.16  3.000
 FYC  H15   C15  C14   121.23  3.000
 FYC  C16   C15  C14   118.62  3.000
 FYC  F1    C16  C15   118.57  3.000
 FYC  F1    C16  C11   118.19  3.000
 FYC  C15   C16  C11   123.24  3.000
 FYC  H17   C17  C18   121.11  3.000
 FYC  H17   C17  C5    120.89  3.000
 FYC  C18   C17  C5    117.99  3.000
 FYC  N3    C18  C17   132.08  3.000
 FYC  N3    C18  C2    106.51  3.000
 FYC  C17   C18  C2    121.41  3.000
 FYC  H3    N3   C18   125.97  3.000
 FYC  H3    N3   C1    123.11  3.000
 FYC  C18   N3   C1    110.92  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
 FYC  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 FYC  CONST_02  C5    C17  C18  C2      0.00   0.0  0
 FYC  CONST_03  C17   C18  C2   C3      0.00   0.0  0
 FYC  CONST_04  C17   C5   C4   C3      0.00   0.0  0
 FYC  CONST_05  C18   C2   C3   C4      0.00   0.0  0
 FYC  CONST_06  C18   C17  C5   C4      0.00   0.0  0
 FYC  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 FYC  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 FYC  CONST_09  C15   C16  C11  C12     0.00   0.0  0
 FYC  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 FYC  CONST_11  C16   C11  C12  C13     0.00   0.0  0
 FYC  CONST_12  C16   C15  C14  C13     0.00   0.0  0
 FYC  CONST_13  C18   C2   N1   C1      0.00   0.0  0
 FYC  CONST_14  C2    C18  N3   C1      0.00   0.0  0
 FYC  CONST_15  C18   N3   C1   N1      0.00   0.0  0
 FYC  CONST_16  N3    C18  C2   N1      0.00   0.0  0
 FYC  CONST_17  N3    C1   N1   C2      0.00   0.0  0
 FYC  CONST_18  C6    C5   C4   C3    180.00   0.0  0
 FYC  CONST_19  C18   C17  C5   C6    180.00   0.0  0
 FYC  CONST_20  C13   C12  C11  C10   180.00   0.0  0
 FYC  CONST_21  C15   C16  C11  C10   180.00   0.0  0
 FYC  CONST_22  F1    C16  C11  C12   180.00   0.0  0
 FYC  CONST_23  F1    C16  C15  C14   180.00   0.0  0
 FYC  CONST_24  C2    N1   C1   O1    180.00   0.0  0
 FYC  CONST_25  C18   N3   C1   O1    180.00   0.0  0
 FYC  CONST_26  HA    C3   C2   N1      0.00   0.0  0
 FYC  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 FYC  CONST_28  H17   C17  C18  C2    180.00   0.0  0
 FYC  CONST_29  H13   C13  C12  C11   180.00   0.0  0
 FYC  CONST_30  H15   C15  C16  C11   180.00   0.0  0
 FYC  CONST_31  H14   C14  C13  C12   180.00   0.0  0
 FYC  CONST_32  H12   C12  C13  C14   180.00   0.0  0
 FYC  CONST_33  H3    N3   C1   N1    180.00   0.0  0
 FYC  CONST_34  H1    N1   C2   C18   180.00   0.0  0
 FYC  CONST_35  C8    C7   N2   C6    180.00   0.0  0
 FYC  CONST_36  O2    C7   N2   C6      0.00   0.0  0
 FYC  CONST_37  H2    N2   C7   C8      0.00   0.0  0
 FYC  Var_01    N2    C6   C5   C4     81.06  30.0  2
 FYC  Var_02    C12   C11  C10  C8     45.76  30.0  2
 FYC  Var_03    C11   C10  C8   C7   -176.58   0.0  2
 FYC  Var_04    C7    N2   C6   C5   -173.61  30.0  3
 FYC  Var_05    C9    C8   C7   N2    -12.80  30.0  2
 FYC  Var_06    H91C  C9   C8   C7     74.07  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
 FYC  plan-1  C10  0.020
 FYC  plan-1  C11  0.020
 FYC  plan-1  C12  0.020
 FYC  plan-1  C13  0.020
 FYC  plan-1  C14  0.020
 FYC  plan-1  C15  0.020
 FYC  plan-1  C16  0.020
 FYC  plan-1  F1   0.020
 FYC  plan-1  H12  0.020
 FYC  plan-1  H13  0.020
 FYC  plan-1  H14  0.020
 FYC  plan-1  H15  0.020
 FYC  plan-2  C7   0.020
 FYC  plan-2  C8   0.020
 FYC  plan-2  C9   0.020
 FYC  plan-2  C10  0.020
 FYC  plan-2  C11  0.020
 FYC  plan-2  H10  0.020
 FYC  plan-3  O1   0.020
 FYC  plan-3  C1   0.020
 FYC  plan-3  N1   0.020
 FYC  plan-3  C2   0.020
 FYC  plan-3  C3   0.020
 FYC  plan-3  C4   0.020
 FYC  plan-3  C5   0.020
 FYC  plan-3  C6   0.020
 FYC  plan-3  C17  0.020
 FYC  plan-3  C18  0.020
 FYC  plan-3  N3   0.020
 FYC  plan-3  H1   0.020
 FYC  plan-3  H3   0.020
 FYC  plan-3  HA   0.020
 FYC  plan-3  H4   0.020
 FYC  plan-3  H17  0.020
 FYC  plan-4  C6   0.020
 FYC  plan-4  N2   0.020
 FYC  plan-4  C7   0.020
 FYC  plan-4  C8   0.020
 FYC  plan-4  O2   0.020
 FYC  plan-4  H2   0.020

