# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 19:24:51 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(5-methoxy-2-methyl-benzimidazol-1-yl)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2n(c(C)nc2c1)c3ccc(C=O)cc3
#
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
 V2K  V2K  4-(5-methoxy-2-methyl-benzimidazol-1-yl)benzaldehyde  ligand  34  20  .  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_V2K
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
 V2K  C10  C  CR16  0  -0.396  -16.1214  -23.9299  -2.0070
 V2K  C11  C  CR6   0   0.380  -15.0322  -23.5683  -2.8182
 V2K  C13  C  CH3   0  -0.434  -15.3304  -25.4713  -4.2141
 V2K  C14  C  CR16  0  -0.435  -14.3004  -22.4155  -2.5537
 V2K  C15  C  CR56  0   0.155  -14.6727  -21.6373  -1.4642
 V2K  C17  C  CR5   0   0.426  -14.8444  -20.1263   0.0397
 V2K  C18  C  CH3   0  -0.762  -14.6052  -18.9254   0.8788
 V2K  C03  C  CR6   0  -0.011  -18.6172  -20.9649   3.4321
 V2K  C04  C  CR16  0  -0.274  -18.5343  -19.8882   2.5549
 V2K  C05  C  CR16  0  -0.257  -17.6258  -19.9014   1.5096
 V2K  C06  C  CR6   0   0.300  -16.7807  -20.9927   1.3557
 V2K  C08  C  CR56  0   0.309  -15.7543  -22.0169  -0.6595
 V2K  C09  C  CR16  0  -0.279  -16.4959  -23.1544  -0.9188
 V2K  C19  C  CR16  0  -0.265  -16.8548  -22.0756   2.2308
 V2K  C20  C  CR16  0  -0.263  -17.7740  -22.0626   3.2608
 V2K  N07  N  NR5   0  -0.641  -15.8499  -21.0247   0.2994
 V2K  N16  N  N     0  -0.476  -14.1297  -20.4629  -0.9968
 V2K  O12  O  O2    0  -0.475  -14.6280  -24.2923  -3.8863
 V2K  H1   H  HCR6  0   0.278  -16.6946  -24.8221  -2.2162
 V2K  H2   H  HCH3  0   0.256  -14.8426  -25.8873  -5.0927
 V2K  H3   H  HCH3  0   0.224  -15.2918  -26.2122  -3.4105
 V2K  H4   H  HCH3  0   0.224  -16.3781  -25.2733  -4.4575
 V2K  H5   H  HCR6  0   0.257  -13.4660  -22.1330  -3.1837
 V2K  H6   H  HCH3  0   0.275  -13.6185  -18.5271   0.6566
 V2K  H7   H  HCH3  0   0.270  -15.3374  -18.1424   0.6773
 V2K  H8   H  HCH3  0   0.266  -14.6568  -19.1595   1.9421
 V2K  H9   H  H     0   0.201  -20.2142  -20.0032   4.5546
 V2K  H12  H  HCR6  0   0.278  -19.1933  -19.0372   2.6800
 V2K  H13  H  HCR6  0   0.287  -17.5863  -19.0754   0.8122
 V2K  H14  H  HCR6  0   0.273  -17.3406  -23.4481  -0.3096
 V2K  H15  H  HCR6  0   0.287  -16.1856  -22.9169   2.1070
 V2K  H16  H  HCR6  0   0.274  -17.8283  -22.9026   3.9408
 V2K  O1   O  O     0  -0.370  -19.7523  -21.7984   5.3435
 V2K  C02  C  C1    0   0.119  -19.6015  -20.9217   4.5266

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
 V2K  O12  C13  single    1.411  0.020  1.411
 V2K  O12  C11  single    1.352  0.020  1.352
 V2K  C11  C14  aromatic  1.391  0.020  1.391
 V2K  C11  C10  aromatic  1.405  0.020  1.405
 V2K  C14  C15  aromatic  1.390  0.020  1.390
 V2K  C10  C09  aromatic  1.388  0.020  1.388
 V2K  C15  N16  aromatic  1.376  0.020  1.376
 V2K  C15  C08  aromatic  1.401  0.020  1.401
 V2K  C09  C08  aromatic  1.383  0.020  1.383
 V2K  N16  C17  aromatic  1.303  0.020  1.303
 V2K  C08  N07  aromatic  1.383  0.020  1.383
 V2K  C17  N07  aromatic  1.373  0.020  1.373
 V2K  C17  C18  single    1.484  0.020  1.484
 V2K  N07  C06  single    1.408  0.020  1.408
 V2K  C06  C05  aromatic  1.389  0.020  1.389
 V2K  C06  C19  aromatic  1.394  0.020  1.394
 V2K  C05  C04  aromatic  1.385  0.020  1.385
 V2K  C19  C20  aromatic  1.381  0.020  1.381
 V2K  C04  C03  aromatic  1.391  0.020  1.391
 V2K  C20  C03  aromatic  1.395  0.020  1.395
 V2K  C03  C02  single    1.473  0.020  1.473
 V2K  C10  H1   single    0.930  0.020  1.080
 V2K  C13  H2   single    0.970  0.020  1.090
 V2K  C13  H3   single    0.970  0.020  1.090
 V2K  C13  H4   single    0.970  0.020  1.090
 V2K  C14  H5   single    0.930  0.020  1.080
 V2K  C18  H6   single    0.970  0.020  1.090
 V2K  C18  H7   single    0.970  0.020  1.090
 V2K  C18  H8   single    0.970  0.020  1.090
 V2K  C02  H9   single    0.930  0.020  1.080
 V2K  C04  H12  single    0.930  0.020  1.080
 V2K  C05  H13  single    0.930  0.020  1.080
 V2K  C09  H14  single    0.930  0.020  1.080
 V2K  C19  H15  single    0.930  0.020  1.080
 V2K  C20  H16  single    0.930  0.020  1.080
 V2K  C02  O1   double    1.208  0.020  1.208

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
 V2K  H1   C10  C09  118.03  3.000
 V2K  H1   C10  C11  120.77  3.000
 V2K  C09  C10  C11  121.20  3.000
 V2K  O12  C11  C14  115.89  3.000
 V2K  C14  C11  C10  120.75  3.000
 V2K  O12  C11  C10  123.36  3.000
 V2K  H4   C13  H3   108.67  3.000
 V2K  H4   C13  H2   108.61  3.000
 V2K  H3   C13  H2   108.58  3.000
 V2K  H4   C13  O12  112.16  3.000
 V2K  H3   C13  O12  112.19  3.000
 V2K  H2   C13  O12  106.49  3.000
 V2K  H5   C14  C15  121.09  3.000
 V2K  H5   C14  C11  120.73  3.000
 V2K  C15  C14  C11  118.18  3.000
 V2K  N16  C15  C08  109.93  3.000
 V2K  C08  C15  C14  120.38  3.000
 V2K  N16  C15  C14  129.69  3.000
 V2K  N16  C17  N07  112.52  3.000
 V2K  N07  C17  C18  122.71  3.000
 V2K  N16  C17  C18  124.76  3.000
 V2K  H8   C18  H7   107.61  3.000
 V2K  H8   C18  H6   108.73  3.000
 V2K  H7   C18  H6   107.97  3.000
 V2K  H8   C18  C17  111.72  3.000
 V2K  H7   C18  C17  111.60  3.000
 V2K  H6   C18  C17  109.10  3.000
 V2K  C20  C03  C04  119.71  3.000
 V2K  C20  C03  C02  121.23  3.000
 V2K  C04  C03  C02  119.06  3.000
 V2K  H12  C04  C05  119.58  3.000
 V2K  H12  C04  C03  119.92  3.000
 V2K  C05  C04  C03  120.50  3.000
 V2K  H13  C05  C06  120.42  3.000
 V2K  H13  C05  C04  120.21  3.000
 V2K  C06  C05  C04  119.36  3.000
 V2K  N07  C06  C19  119.23  3.000
 V2K  C19  C06  C05  120.55  3.000
 V2K  N07  C06  C05  120.21  3.000
 V2K  N07  C08  C09  133.10  3.000
 V2K  N07  C08  C15  104.91  3.000
 V2K  C09  C08  C15  121.97  3.000
 V2K  H14  C09  C08  122.44  3.000
 V2K  H14  C09  C10  120.03  3.000
 V2K  C08  C09  C10  117.52  3.000
 V2K  H15  C19  C20  120.29  3.000
 V2K  H15  C19  C06  119.94  3.000
 V2K  C20  C19  C06  119.76  3.000
 V2K  H16  C20  C19  119.67  3.000
 V2K  H16  C20  C03  120.22  3.000
 V2K  C19  C20  C03  120.10  3.000
 V2K  C08  N07  C06  125.59  3.000
 V2K  C06  N07  C17  127.66  3.000
 V2K  C08  N07  C17  106.72  3.000
 V2K  C17  N16  C15  105.92  3.000
 V2K  C13  O12  C11  118.82  3.000
 V2K  O1   C02  H9   121.15  3.000
 V2K  O1   C02  C03  124.39  3.000
 V2K  H9   C02  C03  114.46  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
 V2K  CONST_01  C15  C14  C11  C10     0.00   0.0  0
 V2K  CONST_02  C15  C08  C09  C10     0.00   0.0  0
 V2K  CONST_03  N07  C08  C09  C10   180.00   0.0  0
 V2K  CONST_04  N16  C15  C14  C11   180.00   0.0  0
 V2K  CONST_05  C08  C15  C14  C11     0.00   0.0  0
 V2K  CONST_06  C08  C09  C10  C11     0.00   0.0  0
 V2K  CONST_07  C09  C10  C11  C14     0.00   0.0  0
 V2K  CONST_08  C17  N16  C15  C14   180.00   0.0  0
 V2K  CONST_09  C09  C08  C15  C14     0.00   0.0  0
 V2K  CONST_10  N07  C08  C15  C14   180.00   0.0  0
 V2K  CONST_11  N07  C17  N16  C15     0.00   0.0  0
 V2K  CONST_12  C17  N07  C08  C15     0.00   0.0  0
 V2K  CONST_13  C06  N07  C08  C15   180.00   0.0  0
 V2K  CONST_14  C08  C15  N16  C17     0.00   0.0  0
 V2K  CONST_15  C09  C08  N07  C17   180.00   0.0  0
 V2K  CONST_18  C06  C05  C04  C03     0.00   0.0  0
 V2K  CONST_19  C06  C19  C20  C03     0.00   0.0  0
 V2K  CONST_20  N07  C06  C05  C04   180.00   0.0  0
 V2K  CONST_21  C19  C06  C05  C04     0.00   0.0  0
 V2K  CONST_22  C19  C20  C03  C04     0.00   0.0  0
 V2K  CONST_24  C20  C19  C06  C05     0.00   0.0  0
 V2K  CONST_25  C20  C03  C04  C05     0.00   0.0  0
 V2K  CONST_26  C09  C08  N07  C06     0.00   0.0  0
 V2K  CONST_27  N16  C17  N07  C06   180.00   0.0  0
 V2K  CONST_28  N16  C17  N07  C08     0.00   0.0  0
 V2K  CONST_30  N16  C15  C08  C09   180.00   0.0  0
 V2K  CONST_31  N07  C06  C19  C20   180.00   0.0  0
 V2K  CONST_32  N16  C15  C08  N07     0.00   0.0  0
 V2K  CONST_33  O12  C11  C14  C15   180.00   0.0  0
 V2K  CONST_34  C18  C17  N16  C15   180.00   0.0  0
 V2K  CONST_35  C08  N07  C17  C18   180.00   0.0  0
 V2K  CONST_36  C06  N07  C17  C18     0.00   0.0  0
 V2K  CONST_37  C05  C04  C03  C02   180.00   0.0  0
 V2K  CONST_38  C19  C20  C03  C02   180.00   0.0  0
 V2K  CONST_39  O12  C11  C10  C09   180.00   0.0  0
 V2K  CONST_40  H5   C14  C11  C10   180.00   0.0  0
 V2K  CONST_41  H14  C09  C10  C11   180.00   0.0  0
 V2K  CONST_42  H1   C10  C11  C14   180.00   0.0  0
 V2K  CONST_43  H13  C05  C04  C03   180.00   0.0  0
 V2K  CONST_44  H15  C19  C20  C03   180.00   0.0  0
 V2K  CONST_45  H16  C20  C03  C04   180.00   0.0  0
 V2K  CONST_46  H12  C04  C05  C06   180.00   0.0  0
 V2K  Var_01    C14  C11  O12  C13  -179.75  30.0  2
 V2K  Var_02    O1   C02  C03  C04  -179.76  30.0  2
 V2K  Var_03    H6   C18  C17  N07   164.53  30.0  2
 V2K  Var_04    H2   C13  O12  C11  -179.99  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
 V2K  plan-1  C03  0.020
 V2K  plan-1  C04  0.020
 V2K  plan-1  C05  0.020
 V2K  plan-1  C06  0.020
 V2K  plan-1  C19  0.020
 V2K  plan-1  C20  0.020
 V2K  plan-1  N07  0.020
 V2K  plan-1  H12  0.020
 V2K  plan-1  H13  0.020
 V2K  plan-1  H15  0.020
 V2K  plan-1  H16  0.020
 V2K  plan-1  C02  0.020
 V2K  plan-2  C10  0.020
 V2K  plan-2  C11  0.020
 V2K  plan-2  C14  0.020
 V2K  plan-2  C15  0.020
 V2K  plan-2  C17  0.020
 V2K  plan-2  C18  0.020
 V2K  plan-2  C06  0.020
 V2K  plan-2  C08  0.020
 V2K  plan-2  C09  0.020
 V2K  plan-2  N07  0.020
 V2K  plan-2  N16  0.020
 V2K  plan-2  O12  0.020
 V2K  plan-2  H1   0.020
 V2K  plan-2  H5   0.020
 V2K  plan-2  H14  0.020
 V2K  plan-3  C03  0.020
 V2K  plan-3  H9   0.020
 V2K  plan-3  O1   0.020
 V2K  plan-3  C02  0.020

