# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 20:20:08 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(6-methoxy-2-methyl-benzimidazol-1-yl)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc(C)n(c3ccc(C=O)cc3)c2c1
#
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
 V2N  V2N  4-(6-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_V2N
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
 V2N  C10  C  CR6   0   0.376  -13.5263  -19.2399  -0.0062
 V2N  C12  C  CH3   0  -0.437  -13.2747  -17.7762   1.8421
 V2N  C13  C  CR16  0  -0.353  -12.9938  -19.7025  -1.2273
 V2N  C14  C  CR16  0  -0.312  -13.6151  -20.6973  -1.9523
 V2N  C15  C  CR56  0   0.107  -14.7942  -21.2480  -1.4518
 V2N  C17  C  CR5   0   0.417  -16.5893  -22.3551  -1.1150
 V2N  C18  C  CH3   0  -0.762  -17.7121  -23.3177  -1.2413
 V2N  C03  C  CR6   0  -0.011  -18.9971  -21.1341   3.2633
 V2N  C04  C  CR16  0  -0.275  -19.4969  -20.9521   1.9775
 V2N  C05  C  CR16  0  -0.255  -18.6628  -21.0614   0.8773
 V2N  C06  C  CR6   0   0.298  -17.3241  -21.3794   1.0668
 V2N  C08  C  CR56  0   0.361  -15.3026  -20.7784  -0.2391
 V2N  C09  C  CR16  0  -0.446  -14.7012  -19.7714   0.5098
 V2N  C19  C  CR16  0  -0.265  -16.8149  -21.5682   2.3508
 V2N  C20  C  CR16  0  -0.263  -17.6481  -21.4387   3.4442
 V2N  N07  N  NR5   0  -0.645  -16.4611  -21.4977  -0.0408
 V2N  N16  N  N     0  -0.464  -15.6131  -22.2294  -1.9629
 V2N  O11  O  O2    0  -0.471  -12.8184  -18.2647   0.5991
 V2N  H1   H  HCH3  0   0.260  -12.5548  -17.0281   2.1653
 V2N  H2   H  HCH3  0   0.226  -14.2580  -17.3046   1.7610
 V2N  H3   H  HCH3  0   0.226  -13.3265  -18.5650   2.5980
 V2N  H4   H  HCR6  0   0.259  -12.0764  -19.2576  -1.5914
 V2N  H5   H  HCR6  0   0.256  -13.1952  -21.0389  -2.8896
 V2N  H6   H  HCH3  0   0.274  -17.4635  -24.0556  -2.0000
 V2N  H7   H  HCH3  0   0.264  -17.9080  -23.8360  -0.3028
 V2N  H8   H  HCH3  0   0.268  -18.6364  -22.8236  -1.5445
 V2N  H9   H  H     0   0.201  -20.9538  -20.7580   4.1376
 V2N  H12  H  HCR6  0   0.279  -20.5429  -20.7082   1.8335
 V2N  H13  H  HCR6  0   0.287  -19.0480  -20.8881  -0.1186
 V2N  H14  H  HCR6  0   0.290  -15.1370  -19.4317   1.4395
 V2N  H15  H  HCR6  0   0.288  -15.7722  -21.8243   2.4870
 V2N  H16  H  HCR6  0   0.275  -17.2526  -21.5856   4.4407
 V2N  O1   O  O     0  -0.370  -19.5827  -21.1299   5.5652
 V2N  C02  C  C1    0   0.119  -19.9106  -20.9977   4.4102

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
 V2N  N16  C15  aromatic  1.377  0.020  1.377
 V2N  N16  C17  aromatic  1.299  0.020  1.299
 V2N  C14  C15  aromatic  1.394  0.020  1.394
 V2N  C14  C13  aromatic  1.379  0.020  1.379
 V2N  C15  C08  aromatic  1.396  0.020  1.396
 V2N  C18  C17  single    1.484  0.020  1.484
 V2N  C17  N07  aromatic  1.380  0.020  1.380
 V2N  C13  C10  aromatic  1.410  0.020  1.410
 V2N  C08  N07  aromatic  1.378  0.020  1.378
 V2N  C08  C09  aromatic  1.392  0.020  1.392
 V2N  N07  C06  single    1.409  0.020  1.409
 V2N  C10  C09  aromatic  1.389  0.020  1.389
 V2N  C10  O11  single    1.349  0.020  1.349
 V2N  O11  C12  single    1.411  0.020  1.411
 V2N  C05  C06  aromatic  1.389  0.020  1.389
 V2N  C05  C04  aromatic  1.385  0.020  1.385
 V2N  C06  C19  aromatic  1.394  0.020  1.394
 V2N  C04  C03  aromatic  1.392  0.020  1.392
 V2N  C19  C20  aromatic  1.381  0.020  1.381
 V2N  C03  C20  aromatic  1.395  0.020  1.395
 V2N  C03  C02  single    1.473  0.020  1.473
 V2N  C12  H1   single    0.970  0.020  1.090
 V2N  C12  H2   single    0.970  0.020  1.090
 V2N  C12  H3   single    0.970  0.020  1.090
 V2N  C13  H4   single    0.930  0.020  1.080
 V2N  C14  H5   single    0.930  0.020  1.080
 V2N  C18  H6   single    0.970  0.020  1.090
 V2N  C18  H7   single    0.970  0.020  1.090
 V2N  C18  H8   single    0.970  0.020  1.090
 V2N  C02  H9   single    0.930  0.020  1.080
 V2N  C04  H12  single    0.930  0.020  1.080
 V2N  C05  H13  single    0.930  0.020  1.080
 V2N  C09  H14  single    0.930  0.020  1.080
 V2N  C19  H15  single    0.930  0.020  1.080
 V2N  C20  H16  single    0.930  0.020  1.080
 V2N  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
 V2N  O11  C10  C09  123.64  3.000
 V2N  O11  C10  C13  115.32  3.000
 V2N  C09  C10  C13  121.03  3.000
 V2N  H3   C12  H2   108.64  3.000
 V2N  H3   C12  H1   108.79  3.000
 V2N  H2   C12  H1   108.70  3.000
 V2N  H3   C12  O11  111.99  3.000
 V2N  H2   C12  O11  112.00  3.000
 V2N  H1   C12  O11  106.61  3.000
 V2N  H4   C13  C14  120.09  3.000
 V2N  H4   C13  C10  118.45  3.000
 V2N  C14  C13  C10  121.46  3.000
 V2N  H5   C14  C15  120.95  3.000
 V2N  H5   C14  C13  120.55  3.000
 V2N  C15  C14  C13  118.50  3.000
 V2N  N16  C15  C08  110.22  3.000
 V2N  C08  C15  C14  119.14  3.000
 V2N  N16  C15  C14  130.64  3.000
 V2N  N16  C17  N07  112.21  3.000
 V2N  N07  C17  C18  122.64  3.000
 V2N  N16  C17  C18  125.14  3.000
 V2N  H8   C18  H7   107.60  3.000
 V2N  H8   C18  H6   107.89  3.000
 V2N  H7   C18  H6   108.61  3.000
 V2N  H8   C18  C17  111.77  3.000
 V2N  H7   C18  C17  111.78  3.000
 V2N  H6   C18  C17  109.07  3.000
 V2N  C20  C03  C04  119.73  3.000
 V2N  C20  C03  C02  121.28  3.000
 V2N  C04  C03  C02  118.99  3.000
 V2N  H12  C04  C05  119.58  3.000
 V2N  H12  C04  C03  119.93  3.000
 V2N  C05  C04  C03  120.49  3.000
 V2N  H13  C05  C06  120.36  3.000
 V2N  H13  C05  C04  120.28  3.000
 V2N  C06  C05  C04  119.35  3.000
 V2N  N07  C06  C19  119.27  3.000
 V2N  C19  C06  C05  120.57  3.000
 V2N  N07  C06  C05  120.15  3.000
 V2N  N07  C08  C09  131.57  3.000
 V2N  C09  C08  C15  123.60  3.000
 V2N  N07  C08  C15  104.81  3.000
 V2N  H14  C09  C08  121.05  3.000
 V2N  H14  C09  C10  122.69  3.000
 V2N  C08  C09  C10  116.27  3.000
 V2N  H15  C19  C20  120.26  3.000
 V2N  H15  C19  C06  119.99  3.000
 V2N  C20  C19  C06  119.75  3.000
 V2N  H16  C20  C19  119.74  3.000
 V2N  H16  C20  C03  120.17  3.000
 V2N  C19  C20  C03  120.09  3.000
 V2N  C08  N07  C06  125.75  3.000
 V2N  C06  N07  C17  127.37  3.000
 V2N  C08  N07  C17  106.88  3.000
 V2N  C17  N16  C15  105.88  3.000
 V2N  C12  O11  C10  118.42  3.000
 V2N  O1   C02  H9   121.07  3.000
 V2N  O1   C02  C03  124.48  3.000
 V2N  H9   C02  C03  114.44  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
 V2N  CONST_01  C15  C14  C13  C10     0.00   0.0  0
 V2N  CONST_02  C15  C08  C09  C10     0.00   0.0  0
 V2N  CONST_03  N07  C08  C09  C10   180.00   0.0  0
 V2N  CONST_04  N16  C15  C14  C13   180.00   0.0  0
 V2N  CONST_05  C08  C15  C14  C13     0.00   0.0  0
 V2N  CONST_06  C08  C09  C10  C13     0.00   0.0  0
 V2N  CONST_07  C17  N16  C15  C14   180.00   0.0  0
 V2N  CONST_08  N07  C08  C15  C14   180.00   0.0  0
 V2N  CONST_09  C09  C08  C15  C14     0.00   0.0  0
 V2N  CONST_10  C09  C10  C13  C14     0.00   0.0  0
 V2N  CONST_11  N07  C17  N16  C15     0.00   0.0  0
 V2N  CONST_12  C17  N07  C08  C15     0.00   0.0  0
 V2N  CONST_13  C06  N07  C08  C15   180.00   0.0  0
 V2N  CONST_14  C08  C15  N16  C17     0.00   0.0  0
 V2N  CONST_15  C09  C08  N07  C17   180.00   0.0  0
 V2N  CONST_18  C06  C05  C04  C03     0.00   0.0  0
 V2N  CONST_19  C06  C19  C20  C03     0.00   0.0  0
 V2N  CONST_20  N07  C06  C05  C04   180.00   0.0  0
 V2N  CONST_21  C19  C06  C05  C04     0.00   0.0  0
 V2N  CONST_22  C19  C20  C03  C04     0.00   0.0  0
 V2N  CONST_24  C20  C19  C06  C05     0.00   0.0  0
 V2N  CONST_25  C20  C03  C04  C05     0.00   0.0  0
 V2N  CONST_26  N16  C17  N07  C06   180.00   0.0  0
 V2N  CONST_27  C09  C08  N07  C06     0.00   0.0  0
 V2N  CONST_28  N16  C17  N07  C08     0.00   0.0  0
 V2N  CONST_30  N16  C15  C08  C09   180.00   0.0  0
 V2N  CONST_31  N07  C06  C19  C20   180.00   0.0  0
 V2N  CONST_32  N16  C15  C08  N07     0.00   0.0  0
 V2N  CONST_33  O11  C10  C13  C14   180.00   0.0  0
 V2N  CONST_34  C18  C17  N16  C15   180.00   0.0  0
 V2N  CONST_35  C08  N07  C17  C18   180.00   0.0  0
 V2N  CONST_36  C06  N07  C17  C18     0.00   0.0  0
 V2N  CONST_37  C05  C04  C03  C02   180.00   0.0  0
 V2N  CONST_38  C19  C20  C03  C02   180.00   0.0  0
 V2N  CONST_39  O11  C10  C09  C08   180.00   0.0  0
 V2N  CONST_40  H5   C14  C13  C10   180.00   0.0  0
 V2N  CONST_41  H14  C09  C10  C13   180.00   0.0  0
 V2N  CONST_42  H4   C13  C14  C15   180.00   0.0  0
 V2N  CONST_43  H13  C05  C04  C03   180.00   0.0  0
 V2N  CONST_44  H15  C19  C20  C03   180.00   0.0  0
 V2N  CONST_45  H16  C20  C03  C04   180.00   0.0  0
 V2N  CONST_46  H12  C04  C05  C06   180.00   0.0  0
 V2N  Var_01    C13  C10  O11  C12  -178.46  30.0  1
 V2N  Var_02    O1   C02  C03  C04  -179.73  30.0  2
 V2N  Var_03    H6   C18  C17  N07  -164.57  30.0  2
 V2N  Var_04    H1   C12  O11  C10   178.34  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
 V2N  plan-1  C03  0.020
 V2N  plan-1  C04  0.020
 V2N  plan-1  C05  0.020
 V2N  plan-1  C06  0.020
 V2N  plan-1  C19  0.020
 V2N  plan-1  C20  0.020
 V2N  plan-1  N07  0.020
 V2N  plan-1  H12  0.020
 V2N  plan-1  H13  0.020
 V2N  plan-1  H15  0.020
 V2N  plan-1  H16  0.020
 V2N  plan-1  C02  0.020
 V2N  plan-2  C10  0.020
 V2N  plan-2  C13  0.020
 V2N  plan-2  C14  0.020
 V2N  plan-2  C15  0.020
 V2N  plan-2  C17  0.020
 V2N  plan-2  C18  0.020
 V2N  plan-2  C06  0.020
 V2N  plan-2  C08  0.020
 V2N  plan-2  C09  0.020
 V2N  plan-2  N07  0.020
 V2N  plan-2  N16  0.020
 V2N  plan-2  O11  0.020
 V2N  plan-2  H4   0.020
 V2N  plan-2  H5   0.020
 V2N  plan-2  H14  0.020
 V2N  plan-3  C03  0.020
 V2N  plan-3  H9   0.020
 V2N  plan-3  O1   0.020
 V2N  plan-3  C02  0.020

