# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 14:17:54 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2nc(N)n(Cc3ccc(F)c(Cl)c3)c2cc1C
#
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
 FVY  FVY  1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-1H-benzimidazol-2-amine  ligand  36  21  .  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_FVY
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
 FVY  C10   C   CR16  0  -0.358  -1.7096  -0.7797   0.7414
 FVY  N12   N   NR5   0  -0.559  -0.9234   1.6232   0.8227
 FVY  C13   C   CH2   0  -0.420   0.2852   1.4944   1.6007
 FVY  C15   C   CR16  0  -0.258   1.8124   1.2895  -0.3945
 FVY  C17   C   CR6   0   0.603   3.4345  -0.4532  -0.5414
 FVY  C21   C   CR16  0  -0.263   2.0015  -0.3219   1.3725
 FVY  N01   N   NH2   0  -0.857  -0.8315   3.9531   0.3188
 FVY  C02   C   CR5   0   0.612  -1.4434   2.7411   0.2278
 FVY  N03   N   N     0  -0.524  -2.5192   2.5017  -0.4761
 FVY  C04   C   CR56  0   0.148  -2.7265   1.1449  -0.3575
 FVY  C05   C   CR16  0  -0.393  -3.7219   0.3329  -0.8886
 FVY  C06   C   CR6   0   0.054  -3.7144  -1.0307  -0.6119
 FVY  C07   C   CH3   0  -0.737  -4.7810  -1.9142  -1.1949
 FVY  C08   C   CR6   0   0.047  -2.7068  -1.5892   0.2034
 FVY  C09   C   CH3   0  -0.736  -2.7006  -3.0632   0.4933
 FVY  C11   C   CR56  0   0.361  -1.7394   0.5727   0.4506
 FVY  C14   C   CR6   0   0.109   1.3892   0.8034   0.8398
 FVY  C16   C   CR16  0  -0.402   2.8340   0.6639  -1.0890
 FVY  C19   C   CR6   0  -0.215   3.0275  -0.9515   0.6829
 FVY  CL20  CL  CL    0  -0.090   3.7973  -2.3507   1.3276
 FVY  H1    H   HCR6  0   0.253  -0.9346  -1.2147   1.3609
 FVY  H2    H   HCH2  0   0.292   0.6160   2.4839   1.9150
 FVY  H3    H   HCH2  0   0.292   0.0574   0.9487   2.5182
 FVY  H4    H   HCR6  0   0.270   1.3488   2.1694  -0.8232
 FVY  H5    H   HCR6  0   0.290   1.6869  -0.7183   2.3300
 FVY  H6    H   HNH2  0   0.397  -0.3757   4.1773   1.1896
 FVY  H7    H   HNH2  0   0.397  -1.4042   4.7160  -0.0075
 FVY  H8    H   HCR6  0   0.238  -4.4993   0.7585  -1.5127
 FVY  H9    H   HCH3  0   0.238  -4.3578  -2.6787  -1.8508
 FVY  H10   H   HCH3  0   0.238  -5.3426  -2.4430  -0.4219
 FVY  H11   H   HCH3  0   0.248  -5.4947  -1.3362  -1.7805
 FVY  H12   H   HCH3  0   0.238  -3.6107  -3.3803   1.0079
 FVY  H13   H   HCH3  0   0.238  -2.6373  -3.6566  -0.4215
 FVY  H14   H   HCH3  0   0.247  -1.8552  -3.3384   1.1229
 FVY  H15   H   HCR6  0   0.294   3.1683   1.0383  -2.0475
 FVY  F18   F   F     0  -0.293   4.4231  -1.0637  -1.1970

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
 FVY  F18  C17   single    1.334  0.020  1.334
 FVY  C16  C17   aromatic  1.381  0.020  1.381
 FVY  C16  C15   aromatic  1.385  0.020  1.385
 FVY  C17  C19   aromatic  1.383  0.020  1.383
 FVY  C15  C14   aromatic  1.392  0.020  1.392
 FVY  N01  C02   single    1.361  0.020  1.361
 FVY  C19  CL20  single    1.722  0.020  1.722
 FVY  C19  C21   aromatic  1.387  0.020  1.387
 FVY  C14  C21   aromatic  1.387  0.020  1.387
 FVY  C14  C13   single    1.508  0.020  1.508
 FVY  C02  N12   aromatic  1.369  0.020  1.369
 FVY  C02  N03   aromatic  1.308  0.020  1.308
 FVY  C13  N12   single    1.443  0.020  1.443
 FVY  N12  C11   aromatic  1.381  0.020  1.381
 FVY  N03  C04   aromatic  1.378  0.020  1.378
 FVY  C11  C04   aromatic  1.398  0.020  1.398
 FVY  C11  C10   aromatic  1.384  0.020  1.384
 FVY  C04  C05   aromatic  1.390  0.020  1.390
 FVY  C10  C08   aromatic  1.393  0.020  1.393
 FVY  C05  C06   aromatic  1.391  0.020  1.391
 FVY  C08  C06   aromatic  1.411  0.020  1.411
 FVY  C08  C09   single    1.502  0.020  1.502
 FVY  C06  C07   single    1.503  0.020  1.503
 FVY  C10  H1    single    0.930  0.020  1.080
 FVY  C13  H2    single    0.970  0.020  1.090
 FVY  C13  H3    single    0.970  0.020  1.090
 FVY  C15  H4    single    0.930  0.020  1.080
 FVY  C21  H5    single    0.930  0.020  1.080
 FVY  N01  H6    single    0.890  0.020  1.040
 FVY  N01  H7    single    0.890  0.020  1.040
 FVY  C05  H8    single    0.930  0.020  1.080
 FVY  C07  H9    single    0.970  0.020  1.090
 FVY  C07  H10   single    0.970  0.020  1.090
 FVY  C07  H11   single    0.970  0.020  1.090
 FVY  C09  H12   single    0.970  0.020  1.090
 FVY  C09  H13   single    0.970  0.020  1.090
 FVY  C09  H14   single    0.970  0.020  1.090
 FVY  C16  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
 FVY  H1    C10  C11  121.88  3.000
 FVY  H1    C10  C08  119.99  3.000
 FVY  C11   C10  C08  118.14  3.000
 FVY  C11   N12  C02  106.23  3.000
 FVY  C11   N12  C13  124.90  3.000
 FVY  C02   N12  C13  128.71  3.000
 FVY  H3    C13  H2   105.96  3.000
 FVY  H3    C13  C14  110.35  3.000
 FVY  H2    C13  C14  109.84  3.000
 FVY  H3    C13  N12  108.84  3.000
 FVY  H2    C13  N12  109.19  3.000
 FVY  C14   C13  N12  112.45  3.000
 FVY  H4    C15  C16  118.97  3.000
 FVY  H4    C15  C14  120.29  3.000
 FVY  C16   C15  C14  120.74  3.000
 FVY  C19   C17  F18  119.23  3.000
 FVY  C19   C17  C16  120.95  3.000
 FVY  F18   C17  C16  119.83  3.000
 FVY  H5    C21  C19  119.22  3.000
 FVY  H5    C21  C14  120.54  3.000
 FVY  C19   C21  C14  120.24  3.000
 FVY  H7    N01  H6   111.60  3.000
 FVY  H7    N01  C02  113.39  3.000
 FVY  H6    N01  C02  117.33  3.000
 FVY  N03   C02  N01  124.67  3.000
 FVY  N03   C02  N12  113.39  3.000
 FVY  N01   C02  N12  121.83  3.000
 FVY  C04   N03  C02  104.93  3.000
 FVY  C11   C04  C05  119.16  3.000
 FVY  C05   C04  N03  130.55  3.000
 FVY  C11   C04  N03  110.28  3.000
 FVY  H8    C05  C06  120.21  3.000
 FVY  H8    C05  C04  120.28  3.000
 FVY  C06   C05  C04  119.51  3.000
 FVY  C08   C06  C07  119.88  3.000
 FVY  C07   C06  C05  119.68  3.000
 FVY  C08   C06  C05  120.43  3.000
 FVY  H11   C07  H10  107.49  3.000
 FVY  H11   C07  H9   107.60  3.000
 FVY  H10   C07  H9   106.57  3.000
 FVY  H11   C07  C06  111.20  3.000
 FVY  H10   C07  C06  112.03  3.000
 FVY  H9    C07  C06  111.68  3.000
 FVY  C09   C08  C06  120.18  3.000
 FVY  C09   C08  C10  119.53  3.000
 FVY  C06   C08  C10  120.29  3.000
 FVY  H14   C09  H13  107.57  3.000
 FVY  H14   C09  H12  107.51  3.000
 FVY  H13   C09  H12  106.56  3.000
 FVY  H14   C09  C08  111.26  3.000
 FVY  H13   C09  C08  111.82  3.000
 FVY  H12   C09  C08  111.86  3.000
 FVY  C04   C11  N12  105.16  3.000
 FVY  C04   C11  C10  122.46  3.000
 FVY  N12   C11  C10  132.38  3.000
 FVY  C21   C14  C15  119.30  3.000
 FVY  C21   C14  C13  120.06  3.000
 FVY  C15   C14  C13  120.64  3.000
 FVY  H15   C16  C17  119.78  3.000
 FVY  H15   C16  C15  121.06  3.000
 FVY  C17   C16  C15  119.16  3.000
 FVY  CL20  C19  C21  120.88  3.000
 FVY  C21   C19  C17  119.62  3.000
 FVY  CL20  C19  C17  119.50  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
 FVY  CONST_01  C02   N12  C11  C10   180.00   0.0  0
 FVY  CONST_02  N03   C04  C11  C10   180.00   0.0  0
 FVY  CONST_03  C05   C04  C11  C10     0.00   0.0  0
 FVY  CONST_04  C05   C06  C08  C10     0.00   0.0  0
 FVY  CONST_05  C04   N03  C02  N12     0.00   0.0  0
 FVY  CONST_06  N03   C04  C11  N12     0.00   0.0  0
 FVY  CONST_07  C05   C04  C11  N12   180.00   0.0  0
 FVY  CONST_08  C08   C10  C11  N12   180.00   0.0  0
 FVY  CONST_09  C19   C17  C16  C15     0.00   0.0  0
 FVY  CONST_10  C19   C21  C14  C15     0.00   0.0  0
 FVY  CONST_11  C14   C15  C16  C17     0.00   0.0  0
 FVY  CONST_12  C14   C21  C19  C17     0.00   0.0  0
 FVY  CONST_13  C16   C17  C19  C21     0.00   0.0  0
 FVY  CONST_14  C16   C15  C14  C21     0.00   0.0  0
 FVY  CONST_15  C04   C11  N12  C02     0.00   0.0  0
 FVY  CONST_16  C11   C04  N03  C02     0.00   0.0  0
 FVY  CONST_17  C05   C04  N03  C02   180.00   0.0  0
 FVY  CONST_18  C11   N12  C02  N03     0.00   0.0  0
 FVY  CONST_19  C06   C05  C04  N03   180.00   0.0  0
 FVY  CONST_20  C08   C10  C11  C04     0.00   0.0  0
 FVY  CONST_21  C08   C06  C05  C04     0.00   0.0  0
 FVY  CONST_22  C11   C04  C05  C06     0.00   0.0  0
 FVY  CONST_23  C11   C10  C08  C06     0.00   0.0  0
 FVY  CONST_24  C13   N12  C11  C10     0.00   0.0  0
 FVY  CONST_25  C07   C06  C08  C10   180.00   0.0  0
 FVY  CONST_26  C16   C15  C14  C13   180.00   0.0  0
 FVY  CONST_27  C19   C21  C14  C13   180.00   0.0  0
 FVY  CONST_28  N03   C02  N12  C13   180.00   0.0  0
 FVY  CONST_29  C04   C11  N12  C13   180.00   0.0  0
 FVY  CONST_30  F18   C17  C16  C15   180.00   0.0  0
 FVY  CONST_31  F18   C17  C19  C21   180.00   0.0  0
 FVY  CONST_32  C11   N12  C02  N01   180.00   0.0  0
 FVY  CONST_33  C04   N03  C02  N01   180.00   0.0  0
 FVY  CONST_34  C07   C06  C05  C04   180.00   0.0  0
 FVY  CONST_35  C09   C08  C06  C05   180.00   0.0  0
 FVY  CONST_36  C11   C10  C08  C09   180.00   0.0  0
 FVY  CONST_37  CL20  C19  C21  C14   180.00   0.0  0
 FVY  CONST_38  CL20  C19  C17  C16   180.00   0.0  0
 FVY  CONST_39  H1    C10  C11  N12     0.00   0.0  0
 FVY  CONST_40  H5    C21  C14  C15   180.00   0.0  0
 FVY  CONST_41  H4    C15  C16  C17   180.00   0.0  0
 FVY  CONST_42  H8    C05  C04  N03     0.00   0.0  0
 FVY  CONST_43  H15   C16  C15  C14   180.00   0.0  0
 FVY  CONST_45  H7    N01  C02  N12   180.00   0.0  0
 FVY  Var_01    C15   C14  C13  N12    55.61  30.0  2
 FVY  Var_02    C14   C13  N12  C02  -105.61  30.0  1
 FVY  Var_03    H12   C09  C08  C10   119.67  30.0  2
 FVY  Var_04    H9    C07  C06  C05   118.53  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
 FVY  plan-1  C13   0.020
 FVY  plan-1  C15   0.020
 FVY  plan-1  C17   0.020
 FVY  plan-1  C21   0.020
 FVY  plan-1  C14   0.020
 FVY  plan-1  C16   0.020
 FVY  plan-1  C19   0.020
 FVY  plan-1  CL20  0.020
 FVY  plan-1  H4    0.020
 FVY  plan-1  H5    0.020
 FVY  plan-1  H15   0.020
 FVY  plan-1  F18   0.020
 FVY  plan-2  C10   0.020
 FVY  plan-2  N12   0.020
 FVY  plan-2  C13   0.020
 FVY  plan-2  N01   0.020
 FVY  plan-2  C02   0.020
 FVY  plan-2  N03   0.020
 FVY  plan-2  C04   0.020
 FVY  plan-2  C05   0.020
 FVY  plan-2  C06   0.020
 FVY  plan-2  C07   0.020
 FVY  plan-2  C08   0.020
 FVY  plan-2  C09   0.020
 FVY  plan-2  C11   0.020
 FVY  plan-2  H1    0.020
 FVY  plan-2  H8    0.020
 FVY  plan-3  N01   0.020
 FVY  plan-3  C02   0.020
 FVY  plan-3  H6    0.020
 FVY  plan-3  H7    0.020

