# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:38:05 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: N-[(Z)-2-phenylethenyl]-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N(\C=C/c1ccccc1)c2[nH]c3ccccc3n2
#
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
 WNG  WNG  N-[(Z)-2-phenylethenyl]-1H-benzimidazol-2-amine  ligand  31  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WNG
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
 WNG  C10  C  CR5   0   0.712  -32.1787   -7.8357  -18.5059
 WNG  C13  C  CR16  0  -0.310  -34.0395   -5.9790  -16.0977
 WNG  C15  C  CR16  0  -0.272  -36.0257   -7.3623  -16.3084
 WNG  C17  C  CR56  0   0.168  -34.1161   -7.8855  -17.6358
 WNG  C01  C  C1    0   0.010  -31.0209   -9.1084  -20.1837
 WNG  C02  C  C1    0  -0.404  -29.9717   -9.4405  -20.9492
 WNG  C03  C  CR6   0   0.127  -28.6306   -8.8515  -20.9523
 WNG  C04  C  CR16  0  -0.347  -27.9846   -8.4097  -19.7921
 WNG  C05  C  CR16  0  -0.235  -26.7145   -7.8524  -19.8507
 WNG  C06  C  CR16  0  -0.273  -26.0540   -7.7336  -21.0657
 WNG  C07  C  CR16  0  -0.239  -26.6715   -8.1923  -22.2233
 WNG  C08  C  CR16  0  -0.305  -27.9398   -8.7476  -22.1651
 WNG  C12  C  CR56  0   0.332  -33.4500   -6.7955  -17.0481
 WNG  C14  C  CR16  0  -0.286  -35.3461   -6.2830  -15.7354
 WNG  C16  C  CR16  0  -0.346  -35.4244   -8.1738  -17.2608
 WNG  N09  N  NH1   0  -0.737  -31.0672   -8.1036  -19.2421
 WNG  N11  N  NR15  0  -0.747  -32.2046   -6.7940  -17.6333
 WNG  N18  N  N     0  -0.524  -33.2936   -8.5154  -18.5422
 WNG  H1   H  HCR6  0   0.263  -33.5118   -5.1433  -15.6569
 WNG  H2   H  HCR6  0   0.249  -37.0432   -7.5677  -16.0021
 WNG  H3   H  H     0   0.291  -31.9547   -9.6407  -20.3003
 WNG  H4   H  H     0   0.257  -30.1603  -10.2076  -21.6899
 WNG  H5   H  HCR6  0   0.258  -28.4530   -8.5336  -18.8232
 WNG  H6   H  HCR6  0   0.257  -26.2364   -7.5217  -18.9376
 WNG  H7   H  HCR6  0   0.256  -25.0648   -7.2967  -21.1103
 WNG  H8   H  HCR6  0   0.256  -26.1633   -8.1149  -23.1761
 WNG  H9   H  HCR6  0   0.252  -28.4112   -9.0987  -23.0752
 WNG  H10  H  HCR6  0   0.251  -35.8471   -5.6716  -14.9964
 WNG  H11  H  HCR6  0   0.249  -35.9567   -9.0069  -17.7021
 WNG  H12  H  HNH1  0   0.419  -30.2875   -7.4689  -19.1611
 WNG  H13  H  HNR5  0   0.421  -31.4509   -6.1535  -17.4409

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
 WNG  C08  C07  aromatic  1.386  0.020  1.386
 WNG  C08  C03  aromatic  1.400  0.020  1.400
 WNG  C02  C01  double    1.341  0.020  1.341
 WNG  C02  C03  single    1.465  0.020  1.465
 WNG  C01  N09  single    1.378  0.020  1.378
 WNG  C07  C06  aromatic  1.390  0.020  1.390
 WNG  C03  C04  aromatic  1.399  0.020  1.399
 WNG  N09  C10  single    1.360  0.020  1.360
 WNG  C06  C05  aromatic  1.388  0.020  1.388
 WNG  C04  C05  aromatic  1.388  0.020  1.388
 WNG  C10  N18  aromatic  1.306  0.020  1.306
 WNG  C10  N11  aromatic  1.359  0.020  1.359
 WNG  N18  C17  aromatic  1.376  0.020  1.376
 WNG  N11  C12  aromatic  1.376  0.020  1.376
 WNG  C17  C12  aromatic  1.406  0.020  1.406
 WNG  C17  C16  aromatic  1.391  0.020  1.391
 WNG  C12  C13  aromatic  1.385  0.020  1.385
 WNG  C16  C15  aromatic  1.388  0.020  1.388
 WNG  C13  C14  aromatic  1.390  0.020  1.390
 WNG  C15  C14  aromatic  1.398  0.020  1.398
 WNG  C13  H1   single    0.930  0.020  1.080
 WNG  C15  H2   single    0.930  0.020  1.080
 WNG  C01  H3   single    0.930  0.020  1.080
 WNG  C02  H4   single    0.930  0.020  1.080
 WNG  C04  H5   single    0.930  0.020  1.080
 WNG  C05  H6   single    0.930  0.020  1.080
 WNG  C06  H7   single    0.930  0.020  1.080
 WNG  C07  H8   single    0.930  0.020  1.080
 WNG  C08  H9   single    0.930  0.020  1.080
 WNG  C14  H10  single    0.930  0.020  1.080
 WNG  C16  H11  single    0.930  0.020  1.080
 WNG  N09  H12  single    0.860  0.020  1.020
 WNG  N11  H13  single    0.860  0.020  1.020

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
 WNG  N18  C10  N11  113.60  3.000
 WNG  N11  C10  N09  120.94  3.000
 WNG  N18  C10  N09  125.46  3.000
 WNG  H1   C13  C14  121.42  3.000
 WNG  H1   C13  C12  121.82  3.000
 WNG  C14  C13  C12  116.76  3.000
 WNG  H2   C15  C16  119.37  3.000
 WNG  H2   C15  C14  119.17  3.000
 WNG  C16  C15  C14  121.46  3.000
 WNG  N18  C17  C16  130.14  3.000
 WNG  C16  C17  C12  119.56  3.000
 WNG  N18  C17  C12  110.30  3.000
 WNG  H3   C01  N09  113.81  3.000
 WNG  H3   C01  C02  119.50  3.000
 WNG  N09  C01  C02  126.67  3.000
 WNG  H4   C02  C03  116.29  3.000
 WNG  H4   C02  C01  115.45  3.000
 WNG  C03  C02  C01  128.18  3.000
 WNG  C08  C03  C04  117.85  3.000
 WNG  C04  C03  C02  123.22  3.000
 WNG  C08  C03  C02  118.92  3.000
 WNG  H5   C04  C05  118.64  3.000
 WNG  H5   C04  C03  120.38  3.000
 WNG  C05  C04  C03  120.93  3.000
 WNG  H6   C05  C06  120.14  3.000
 WNG  H6   C05  C04  119.41  3.000
 WNG  C06  C05  C04  120.44  3.000
 WNG  H7   C06  C07  120.33  3.000
 WNG  H7   C06  C05  120.37  3.000
 WNG  C07  C06  C05  119.30  3.000
 WNG  H8   C07  C08  119.69  3.000
 WNG  H8   C07  C06  120.06  3.000
 WNG  C08  C07  C06  120.26  3.000
 WNG  H9   C08  C07  119.53  3.000
 WNG  H9   C08  C03  119.28  3.000
 WNG  C07  C08  C03  121.19  3.000
 WNG  N11  C12  C17  104.58  3.000
 WNG  C17  C12  C13  122.84  3.000
 WNG  N11  C12  C13  132.58  3.000
 WNG  H10  C14  C15  119.40  3.000
 WNG  H10  C14  C13  119.33  3.000
 WNG  C15  C14  C13  121.27  3.000
 WNG  H11  C16  C17  120.79  3.000
 WNG  H11  C16  C15  121.10  3.000
 WNG  C17  C16  C15  118.11  3.000
 WNG  H12  N09  C01  119.19  3.000
 WNG  H12  N09  C10  117.68  3.000
 WNG  C01  N09  C10  122.76  3.000
 WNG  H13  N11  C12  126.61  3.000
 WNG  H13  N11  C10  126.55  3.000
 WNG  C12  N11  C10  106.83  3.000
 WNG  C17  N18  C10  104.69  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
 WNG  CONST_01  C12  C17  N18  C10     0.00   0.0  0
 WNG  CONST_02  C16  C17  N18  C10   180.00   0.0  0
 WNG  CONST_03  C17  C12  N11  C10     0.00   0.0  0
 WNG  CONST_04  C13  C12  N11  C10   180.00   0.0  0
 WNG  CONST_05  N18  C17  C12  C13   180.00   0.0  0
 WNG  CONST_06  C16  C17  C12  C13     0.00   0.0  0
 WNG  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 WNG  CONST_08  N18  C17  C16  C15   180.00   0.0  0
 WNG  CONST_09  C12  C17  C16  C15     0.00   0.0  0
 WNG  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 WNG  CONST_11  N11  C10  N18  C17     0.00   0.0  0
 WNG  CONST_12  C14  C13  C12  C17     0.00   0.0  0
 WNG  CONST_13  C14  C15  C16  C17     0.00   0.0  0
 WNG  CONST_14  C06  C07  C08  C03     0.00   0.0  0
 WNG  CONST_15  C06  C05  C04  C03     0.00   0.0  0
 WNG  CONST_16  C07  C08  C03  C04     0.00   0.0  0
 WNG  CONST_17  C07  C06  C05  C04     0.00   0.0  0
 WNG  CONST_18  C08  C07  C06  C05     0.00   0.0  0
 WNG  CONST_19  C08  C03  C04  C05     0.00   0.0  0
 WNG  CONST_20  N18  C10  N11  C12     0.00   0.0  0
 WNG  CONST_21  N11  C12  C13  C14   180.00   0.0  0
 WNG  CONST_22  N11  C12  C17  C16   180.00   0.0  0
 WNG  CONST_23  N18  C17  C12  N11     0.00   0.0  0
 WNG  CONST_24  N09  C10  N18  C17   180.00   0.0  0
 WNG  CONST_25  C07  C08  C03  C02   180.00   0.0  0
 WNG  CONST_26  C05  C04  C03  C02   180.00   0.0  0
 WNG  CONST_27  N09  C10  N11  C12   180.00   0.0  0
 WNG  CONST_28  H13  N11  C12  C13     0.00   0.0  0
 WNG  CONST_29  H2   C15  C14  C13   180.00   0.0  0
 WNG  CONST_30  H1   C13  C14  C15   180.00   0.0  0
 WNG  CONST_31  H8   C07  C08  C03   180.00   0.0  0
 WNG  CONST_32  H6   C05  C04  C03   180.00   0.0  0
 WNG  CONST_33  H9   C08  C03  C04   180.00   0.0  0
 WNG  CONST_34  H7   C06  C05  C04   180.00   0.0  0
 WNG  CONST_35  H5   C04  C05  C06   180.00   0.0  0
 WNG  CONST_36  H11  C16  C17  C12   180.00   0.0  0
 WNG  CONST_37  H10  C14  C13  C12   180.00   0.0  0
 WNG  CONST_38  N18  C10  N09  C01     0.00   0.0  0
 WNG  CONST_39  N11  C10  N09  C01   180.00   0.0  0
 WNG  CONST_40  H12  N09  C10  N11     0.00   0.0  0
 WNG  CONST_41  C02  C01  N09  C10   180.00   0.0  0
 WNG  CONST_42  H3   C01  N09  C10     0.00   0.0  0
 WNG  Var_01    C08  C03  C02  C01  -145.03  30.0  2
 WNG  Var_02    N09  C01  C02  C03     1.61   0.0  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
 WNG  plan-1  C02  0.020
 WNG  plan-1  C03  0.020
 WNG  plan-1  C04  0.020
 WNG  plan-1  C05  0.020
 WNG  plan-1  C06  0.020
 WNG  plan-1  C07  0.020
 WNG  plan-1  C08  0.020
 WNG  plan-1  H5   0.020
 WNG  plan-1  H6   0.020
 WNG  plan-1  H7   0.020
 WNG  plan-1  H8   0.020
 WNG  plan-1  H9   0.020
 WNG  plan-2  C10  0.020
 WNG  plan-2  C13  0.020
 WNG  plan-2  C15  0.020
 WNG  plan-2  C17  0.020
 WNG  plan-2  C12  0.020
 WNG  plan-2  C14  0.020
 WNG  plan-2  C16  0.020
 WNG  plan-2  N09  0.020
 WNG  plan-2  N11  0.020
 WNG  plan-2  N18  0.020
 WNG  plan-2  H1   0.020
 WNG  plan-2  H2   0.020
 WNG  plan-2  H10  0.020
 WNG  plan-2  H11  0.020
 WNG  plan-2  H13  0.020
 WNG  plan-3  C10  0.020
 WNG  plan-3  C01  0.020
 WNG  plan-3  N09  0.020
 WNG  plan-3  H12  0.020
 WNG  plan-4  C01  0.020
 WNG  plan-4  C02  0.020
 WNG  plan-4  C03  0.020
 WNG  plan-4  N09  0.020
 WNG  plan-4  H3   0.020
 WNG  plan-4  H4   0.020

