# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:40:07 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: N-(propan-2-yl)-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Nc1[nH]c2ccccc2n1
#
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
 VWJ  VWJ  N-(propan-2-yl)-1H-benzimidazol-2-amine  ligand  26  13  .  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_VWJ
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
 VWJ  N1   N  NH1   0  -0.701  -10.0215  -0.9079  -75.9592
 VWJ  N3   N  NR15  0  -0.744   -9.2801   1.3151  -76.2278
 VWJ  C4   C  CR5   0   0.701   -9.0926  -0.0306  -76.3811
 VWJ  C5   C  CR56  0   0.167   -7.3324   0.8921  -77.1590
 VWJ  C6   C  CR16  0  -0.351   -6.0959   1.1867  -77.7233
 VWJ  C7   C  CR16  0  -0.274   -5.7240   2.5217  -77.8359
 VWJ  C8   C  CR16  0  -0.291   -6.5608   3.5495  -77.3964
 VWJ  C10  C  CR56  0   0.328   -8.1607   1.9431  -76.7220
 VWJ  C1   C  CH3   0  -0.660   -8.8372  -3.0403  -75.5519
 VWJ  C2   C  CH1   0  -0.089   -9.9948  -2.3373  -76.2505
 VWJ  C3   C  CH3   0  -0.663  -10.0328  -2.6377  -77.7463
 VWJ  N2   N  N     0  -0.528   -7.9380  -0.3217  -76.9355
 VWJ  C9   C  CR16  0  -0.316   -7.8015   3.2748  -76.8286
 VWJ  H1   H  HNH1  0   0.396  -10.9157  -0.5251  -75.7022
 VWJ  H2   H  HNR5  0   0.413  -10.0900   1.7613  -75.8289
 VWJ  H3   H  HCR6  0   0.243   -5.4422   0.3949  -78.0677
 VWJ  H4   H  HCR6  0   0.244   -4.7649   2.7710  -78.2717
 VWJ  H5   H  HCR6  0   0.246   -6.2410   4.5782  -77.4991
 VWJ  H6   H  HCH3  0   0.228   -8.8571  -2.8490  -74.4785
 VWJ  H7   H  HCH3  0   0.226   -8.9129  -4.1178  -75.7028
 VWJ  H8   H  HCH3  0   0.234   -7.8772  -2.7088  -75.9432
 VWJ  H9   H  HCH1  0   0.247  -10.9206  -2.7136  -75.8116
 VWJ  H10  H  HCH3  0   0.227  -10.1338  -3.7115  -77.9096
 VWJ  H11  H  HCH3  0   0.228  -10.8840  -2.1471  -78.2203
 VWJ  H12  H  HCH3  0   0.231   -9.1224  -2.3039  -78.2429
 VWJ  H14  H  HCR6  0   0.258   -8.4520   4.0709  -76.4894

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
 VWJ  C7   C8   aromatic  1.396  0.020  1.396
 VWJ  C7   C6   aromatic  1.390  0.020  1.390
 VWJ  C3   C2   single    1.526  0.020  1.526
 VWJ  C8   C9   aromatic  1.392  0.020  1.392
 VWJ  C6   C5   aromatic  1.391  0.020  1.391
 VWJ  C9   C10  aromatic  1.383  0.020  1.383
 VWJ  C5   C10  aromatic  1.408  0.020  1.408
 VWJ  C5   N2   aromatic  1.375  0.020  1.375
 VWJ  C10  N3   aromatic  1.375  0.020  1.375
 VWJ  N2   C4   aromatic  1.313  0.020  1.313
 VWJ  N3   C4   aromatic  1.367  0.020  1.367
 VWJ  C2   N1   single    1.459  0.020  1.459
 VWJ  C2   C1   single    1.524  0.020  1.524
 VWJ  C4   N1   single    1.346  0.020  1.346
 VWJ  N1   H1   single    0.890  0.020  1.040
 VWJ  N3   H2   single    0.860  0.020  1.020
 VWJ  C6   H3   single    0.930  0.020  1.080
 VWJ  C7   H4   single    0.930  0.020  1.080
 VWJ  C8   H5   single    0.930  0.020  1.080
 VWJ  C1   H6   single    0.970  0.020  1.090
 VWJ  C1   H7   single    0.970  0.020  1.090
 VWJ  C1   H8   single    0.970  0.020  1.090
 VWJ  C2   H9   single    0.970  0.020  1.090
 VWJ  C3   H10  single    0.970  0.020  1.090
 VWJ  C3   H11  single    0.970  0.020  1.090
 VWJ  C3   H12  single    0.970  0.020  1.090
 VWJ  C9   H14  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
 VWJ  H1   N1   C2   116.10  3.000
 VWJ  H1   N1   C4   116.47  3.000
 VWJ  C2   N1   C4   124.30  3.000
 VWJ  H2   N3   C10  126.48  3.000
 VWJ  H2   N3   C4   126.21  3.000
 VWJ  C10  N3   C4   107.31  3.000
 VWJ  N2   C4   N3   112.70  3.000
 VWJ  N3   C4   N1   120.78  3.000
 VWJ  N2   C4   N1   126.50  3.000
 VWJ  N2   C5   C10  110.46  3.000
 VWJ  N2   C5   C6   130.14  3.000
 VWJ  C10  C5   C6   119.40  3.000
 VWJ  H3   C6   C7   120.99  3.000
 VWJ  H3   C6   C5   120.71  3.000
 VWJ  C7   C6   C5   118.30  3.000
 VWJ  H4   C7   C8   119.22  3.000
 VWJ  H4   C7   C6   119.38  3.000
 VWJ  C8   C7   C6   121.40  3.000
 VWJ  H5   C8   C9   119.33  3.000
 VWJ  H5   C8   C7   119.52  3.000
 VWJ  C9   C8   C7   121.15  3.000
 VWJ  C9   C10  C5   122.82  3.000
 VWJ  C5   C10  N3   104.45  3.000
 VWJ  C9   C10  N3   132.73  3.000
 VWJ  H8   C1   H7   108.21  3.000
 VWJ  H8   C1   H6   108.46  3.000
 VWJ  H7   C1   H6   107.96  3.000
 VWJ  H8   C1   C2   111.38  3.000
 VWJ  H7   C1   C2   109.85  3.000
 VWJ  H6   C1   C2   110.88  3.000
 VWJ  H9   C2   C3   107.77  3.000
 VWJ  H9   C2   C1   107.52  3.000
 VWJ  C3   C2   C1   112.17  3.000
 VWJ  H9   C2   N1   104.00  3.000
 VWJ  C1   C2   N1   111.98  3.000
 VWJ  C3   C2   N1   112.84  3.000
 VWJ  H12  C3   H11  108.43  3.000
 VWJ  H12  C3   H10  108.10  3.000
 VWJ  H11  C3   H10  107.78  3.000
 VWJ  H12  C3   C2   111.45  3.000
 VWJ  H11  C3   C2   110.90  3.000
 VWJ  H10  C3   C2   110.05  3.000
 VWJ  C5   N2   C4   105.08  3.000
 VWJ  H14  C9   C10  121.85  3.000
 VWJ  H14  C9   C8   121.22  3.000
 VWJ  C10  C9   C8   116.93  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
 VWJ  CONST_01  C8   C9   C10  N3    180.00   0.0  0
 VWJ  CONST_02  C6   C5   C10  N3    180.00   0.0  0
 VWJ  CONST_03  N2   C5   C10  N3      0.00   0.0  0
 VWJ  CONST_04  C5   N2   C4   N3      0.00   0.0  0
 VWJ  CONST_05  C6   C5   N2   C4    180.00   0.0  0
 VWJ  CONST_06  C10  C5   N2   C4      0.00   0.0  0
 VWJ  CONST_07  C9   C10  N3   C4    180.00   0.0  0
 VWJ  CONST_08  C5   C10  N3   C4      0.00   0.0  0
 VWJ  CONST_09  C8   C7   C6   C5      0.00   0.0  0
 VWJ  CONST_10  C8   C9   C10  C5      0.00   0.0  0
 VWJ  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 VWJ  CONST_12  C9   C10  C5   C6      0.00   0.0  0
 VWJ  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 VWJ  CONST_14  C10  C5   C6   C7      0.00   0.0  0
 VWJ  CONST_15  N2   C5   C6   C7    180.00   0.0  0
 VWJ  CONST_16  N2   C4   N3   C10     0.00   0.0  0
 VWJ  CONST_17  C9   C10  C5   N2    180.00   0.0  0
 VWJ  CONST_18  C5   N2   C4   N1    180.00   0.0  0
 VWJ  CONST_19  C10  N3   C4   N1    180.00   0.0  0
 VWJ  CONST_20  H14  C9   C10  N3      0.00   0.0  0
 VWJ  CONST_21  H4   C7   C6   C5    180.00   0.0  0
 VWJ  CONST_22  H2   N3   C10  C5    180.00   0.0  0
 VWJ  CONST_23  H5   C8   C7   C6    180.00   0.0  0
 VWJ  CONST_24  H3   C6   C7   C8    180.00   0.0  0
 VWJ  CONST_25  C2   N1   C4   N3    180.00   0.0  0
 VWJ  CONST_26  N2   C4   N1   C2      0.00   0.0  0
 VWJ  CONST_27  H1   N1   C4   N3      0.00   0.0  0
 VWJ  Var_01    C3   C2   N1   C4    -60.01  30.0  2
 VWJ  Var_02    H10  C3   C2   N1   -173.13  30.0  3
 VWJ  Var_03    H6   C1   C2   N1     54.58  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
 VWJ  plan-1  N1   0.020
 VWJ  plan-1  N3   0.020
 VWJ  plan-1  C4   0.020
 VWJ  plan-1  C5   0.020
 VWJ  plan-1  C6   0.020
 VWJ  plan-1  C7   0.020
 VWJ  plan-1  C8   0.020
 VWJ  plan-1  C10  0.020
 VWJ  plan-1  N2   0.020
 VWJ  plan-1  C9   0.020
 VWJ  plan-1  H2   0.020
 VWJ  plan-1  H3   0.020
 VWJ  plan-1  H4   0.020
 VWJ  plan-1  H5   0.020
 VWJ  plan-1  H14  0.020
 VWJ  plan-2  N1   0.020
 VWJ  plan-2  C4   0.020
 VWJ  plan-2  C2   0.020
 VWJ  plan-2  H1   0.020

