# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 03:31:30 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-[(4-tert-butylphenyl)amino]-1H-benzimidazole-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(Nc2[nH]c3cc(ccc3n2)C#N)cc1
#
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
 0VN  0VN  2-[(4-tert-butylphenyl)amino]-1H-benzimidazole-6-carbonitrile  ligand  40  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0VN
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
 0VN  C4   C  CR6   0  -0.031  -5.4604   0.1612   0.1468
 0VN  C5   C  CR16  0  -0.298  -4.6475  -0.9430  -0.1294
 0VN  C6   C  CR56  0   0.347  -3.2894  -0.7188  -0.1116
 0VN  C8   C  CR56  0   0.220  -2.7230   0.5431   0.1642
 0VN  C9   C  CR16  0  -0.334  -3.5523   1.6281   0.4369
 0VN  C10  C  CR16  0  -0.256  -4.9198   1.4272   0.4265
 0VN  N3   N  NR15  0  -0.748  -2.2131  -1.5414  -0.3243
 0VN  C11  C  CR5   0   0.719  -1.0930  -0.7788  -0.1756
 0VN  N4   N  N     0  -0.530  -1.3593   0.4741   0.1158
 0VN  N1   N  NH1   0  -0.806   0.1225  -1.3420  -0.3285
 0VN  C7   C  CSP   0   0.043  -6.8746  -0.0027   0.1470
 0VN  N2   N  NS    0  -0.266  -8.0209  -0.1332   0.1536
 0VN  C12  C  CR6   0   0.184   4.0326   0.2414  -0.0656
 0VN  C13  C  CR16  0  -0.330   2.9250   1.0644   0.1002
 0VN  C14  C  CR16  0  -0.295   1.6187   0.5904   0.0226
 0VN  C15  C  CR6   0   0.340   1.3851  -0.7572  -0.2305
 0VN  C16  C  CR16  0  -0.341   2.4859  -1.6012  -0.4047
 0VN  C17  C  CR16  0  -0.300   3.7724  -1.1077  -0.3232
 0VN  C1   C  CH3   0  -0.628   6.1731   0.0160   1.1906
 0VN  C2   C  CH3   0  -0.631   6.2074   0.4285  -1.2803
 0VN  C3   C  CH3   0  -0.665   5.5501   2.2413   0.2824
 0VN  H1   H  HCR6  0   0.288  -5.0709  -1.9148  -0.3444
 0VN  H2   H  HCR6  0   0.266  -3.1385   2.6035   0.6542
 0VN  H3   H  HCR6  0   0.274  -5.5864   2.2525   0.6365
 0VN  H4   H  HNR5  0   0.427  -2.2446  -2.5234  -0.5520
 0VN  H6   H  HNH1  0   0.421   0.1240  -2.3316  -0.5205
 0VN  H7   H  HCR6  0   0.251   3.0551   2.1192   0.3010
 0VN  H8   H  HCR6  0   0.283   0.7957   1.2738   0.1604
 0VN  H9   H  HCR6  0   0.266   2.3321  -2.6559  -0.6031
 0VN  H10  H  HCR6  0   0.248   4.5897  -1.8045  -0.4647
 0VN  H11  H  HCH3  0   0.226   6.1736  -1.0674   1.0626
 0VN  H12  H  HCH3  0   0.225   7.2146   0.3364   1.2652
 0VN  H13  H  HCH3  0   0.227   5.6856   0.2392   2.1414
 0VN  H14  H  HCH3  0   0.228   5.7354   0.9337  -2.1248
 0VN  H15  H  HCH3  0   0.226   7.2434   0.7685  -1.2204
 0VN  H16  H  HCH3  0   0.227   6.2250  -0.6400  -1.4993
 0VN  H17  H  HCH3  0   0.229   5.0698   2.5260   1.2203
 0VN  H18  H  HCH3  0   0.236   6.5952   2.5500   0.3439
 0VN  H19  H  HCH3  0   0.229   5.0884   2.8164  -0.5228
 0VN  C18  C  CT    0  -0.171   5.4711   0.7355   0.0306

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
 0VN  N2   C7   triple    1.154  0.020  1.154
 0VN  C7   C4   single    1.424  0.020  1.424
 0VN  C3   C18  single    1.529  0.020  1.529
 0VN  C5   C4   aromatic  1.399  0.020  1.399
 0VN  C5   C6   aromatic  1.377  0.020  1.377
 0VN  C1   C18  single    1.535  0.020  1.535
 0VN  C4   C10  aromatic  1.405  0.020  1.405
 0VN  C18  C12  single    1.524  0.020  1.524
 0VN  C18  C2   single    1.535  0.020  1.535
 0VN  C13  C12  aromatic  1.390  0.020  1.390
 0VN  C13  C14  aromatic  1.392  0.020  1.392
 0VN  C6   N3   aromatic  1.371  0.020  1.371
 0VN  C6   C8   aromatic  1.410  0.020  1.410
 0VN  N3   C11  aromatic  1.363  0.020  1.363
 0VN  C12  C17  aromatic  1.398  0.020  1.398
 0VN  C10  C9   aromatic  1.382  0.020  1.382
 0VN  C14  C15  aromatic  1.391  0.020  1.391
 0VN  C17  C16  aromatic  1.380  0.020  1.380
 0VN  C8   C9   aromatic  1.393  0.020  1.393
 0VN  C8   N4   aromatic  1.366  0.020  1.366
 0VN  C15  C16  aromatic  1.398  0.020  1.398
 0VN  C15  N1   single    1.395  0.020  1.395
 0VN  C11  N1   single    1.348  0.020  1.348
 0VN  C11  N4   aromatic  1.314  0.020  1.314
 0VN  C5   H1   single    0.930  0.020  1.080
 0VN  C9   H2   single    0.930  0.020  1.080
 0VN  C10  H3   single    0.930  0.020  1.080
 0VN  N3   H4   single    0.860  0.020  1.020
 0VN  N1   H6   single    0.860  0.020  1.020
 0VN  C13  H7   single    0.930  0.020  1.080
 0VN  C14  H8   single    0.930  0.020  1.080
 0VN  C16  H9   single    0.930  0.020  1.080
 0VN  C17  H10  single    0.930  0.020  1.080
 0VN  C1   H11  single    0.970  0.020  1.090
 0VN  C1   H12  single    0.970  0.020  1.090
 0VN  C1   H13  single    0.970  0.020  1.090
 0VN  C2   H14  single    0.970  0.020  1.090
 0VN  C2   H15  single    0.970  0.020  1.090
 0VN  C2   H16  single    0.970  0.020  1.090
 0VN  C3   H17  single    0.970  0.020  1.090
 0VN  C3   H18  single    0.970  0.020  1.090
 0VN  C3   H19  single    0.970  0.020  1.090

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
 0VN  C7   C4   C10  119.08  3.000
 0VN  C10  C4   C5   121.81  3.000
 0VN  C7   C4   C5   119.11  3.000
 0VN  H1   C5   C6   122.35  3.000
 0VN  H1   C5   C4   121.40  3.000
 0VN  C6   C5   C4   116.24  3.000
 0VN  N3   C6   C8   104.59  3.000
 0VN  C8   C6   C5   122.99  3.000
 0VN  N3   C6   C5   132.42  3.000
 0VN  N4   C8   C9   129.84  3.000
 0VN  N4   C8   C6   110.41  3.000
 0VN  C9   C8   C6   119.76  3.000
 0VN  H2   C9   C10  120.74  3.000
 0VN  H2   C9   C8   120.94  3.000
 0VN  C10  C9   C8   118.32  3.000
 0VN  H3   C10  C9   119.83  3.000
 0VN  H3   C10  C4   119.29  3.000
 0VN  C9   C10  C4   120.88  3.000
 0VN  H4   N3   C11  126.51  3.000
 0VN  H4   N3   C6   126.49  3.000
 0VN  C11  N3   C6   107.00  3.000
 0VN  N1   C11  N4   127.32  3.000
 0VN  N4   C11  N3   113.03  3.000
 0VN  N1   C11  N3   119.65  3.000
 0VN  C11  N4   C8   104.97  3.000
 0VN  H6   N1   C15  115.07  3.000
 0VN  H6   N1   C11  115.65  3.000
 0VN  C15  N1   C11  129.26  3.000
 0VN  N2   C7   C4   180.00  3.000
 0VN  C18  C12  C17  120.01  3.000
 0VN  C17  C12  C13  116.43  3.000
 0VN  C18  C12  C13  123.56  3.000
 0VN  H7   C13  C14  117.09  3.000
 0VN  H7   C13  C12  120.25  3.000
 0VN  C14  C13  C12  122.66  3.000
 0VN  H8   C14  C15  120.60  3.000
 0VN  H8   C14  C13  119.56  3.000
 0VN  C15  C14  C13  119.85  3.000
 0VN  C16  C15  C14  118.38  3.000
 0VN  C16  C15  N1   116.80  3.000
 0VN  C14  C15  N1   124.82  3.000
 0VN  H9   C16  C17  119.40  3.000
 0VN  H9   C16  C15  119.89  3.000
 0VN  C17  C16  C15  120.71  3.000
 0VN  H10  C17  C16  117.74  3.000
 0VN  H10  C17  C12  120.30  3.000
 0VN  C16  C17  C12  121.96  3.000
 0VN  H13  C1   H12  107.84  3.000
 0VN  H13  C1   H11  107.79  3.000
 0VN  H12  C1   H11  107.40  3.000
 0VN  H13  C1   C18  110.99  3.000
 0VN  H12  C1   C18  110.50  3.000
 0VN  H11  C1   C18  112.15  3.000
 0VN  H16  C2   H15  107.50  3.000
 0VN  H16  C2   H14  107.76  3.000
 0VN  H15  C2   H14  107.98  3.000
 0VN  H16  C2   C18  112.03  3.000
 0VN  H15  C2   C18  110.25  3.000
 0VN  H14  C2   C18  111.15  3.000
 0VN  H19  C3   H18  107.31  3.000
 0VN  H19  C3   H17  108.08  3.000
 0VN  H18  C3   H17  107.41  3.000
 0VN  H19  C3   C18  112.06  3.000
 0VN  H18  C3   C18  109.71  3.000
 0VN  H17  C3   C18  112.07  3.000
 0VN  C3   C18  C2   108.23  3.000
 0VN  C2   C18  C1   109.41  3.000
 0VN  C3   C18  C1   108.28  3.000
 0VN  C2   C18  C12  109.52  3.000
 0VN  C1   C18  C12  109.11  3.000
 0VN  C3   C18  C12  112.24  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
 0VN  CONST_01  N3   C6   C5   C4   180.00   0.0  0
 0VN  CONST_02  C8   C6   C5   C4     0.00   0.0  0
 0VN  CONST_03  C8   C9   C10  C4     0.00   0.0  0
 0VN  CONST_04  C9   C10  C4   C5     0.00   0.0  0
 0VN  CONST_05  C11  N3   C6   C5   180.00   0.0  0
 0VN  CONST_06  C9   C8   C6   C5     0.00   0.0  0
 0VN  CONST_07  N4   C8   C6   C5   180.00   0.0  0
 0VN  CONST_08  C10  C4   C5   C6     0.00   0.0  0
 0VN  CONST_09  N4   C11  N3   C6     0.00   0.0  0
 0VN  CONST_10  C10  C9   C8   C6     0.00   0.0  0
 0VN  CONST_11  C11  N4   C8   C6     0.00   0.0  0
 0VN  CONST_12  C11  N3   C6   C8     0.00   0.0  0
 0VN  CONST_13  N3   C11  N4   C8     0.00   0.0  0
 0VN  CONST_14  N3   C6   C8   C9   180.00   0.0  0
 0VN  CONST_15  C11  N4   C8   C9   180.00   0.0  0
 0VN  CONST_16  N4   C8   C9   C10  180.00   0.0  0
 0VN  CONST_17  N4   C8   C6   N3     0.00   0.0  0
 0VN  CONST_18  C15  C14  C13  C12    0.00   0.0  0
 0VN  CONST_19  C15  C16  C17  C12    0.00   0.0  0
 0VN  CONST_20  C16  C17  C12  C13    0.00   0.0  0
 0VN  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 0VN  CONST_22  C17  C12  C13  C14    0.00   0.0  0
 0VN  CONST_23  C17  C16  C15  C14    0.00   0.0  0
 0VN  CONST_24  C7   C4   C5   C6   180.00   0.0  0
 0VN  CONST_25  N1   C11  N3   C6   180.00   0.0  0
 0VN  CONST_26  N1   C11  N4   C8   180.00   0.0  0
 0VN  CONST_27  C7   C4   C10  C9   180.00   0.0  0
 0VN  CONST_28  C13  C14  C15  N1   180.00   0.0  0
 0VN  CONST_29  C17  C16  C15  N1   180.00   0.0  0
 0VN  CONST_30  C18  C12  C13  C14  180.00   0.0  0
 0VN  CONST_31  C18  C12  C17  C16  180.00   0.0  0
 0VN  CONST_32  H2   C9   C10  C4   180.00   0.0  0
 0VN  CONST_33  H3   C10  C4   C5   180.00   0.0  0
 0VN  CONST_34  H4   N3   C6   C5     0.00   0.0  0
 0VN  CONST_35  H1   C5   C6   C8   180.00   0.0  0
 0VN  CONST_36  H8   C14  C13  C12  180.00   0.0  0
 0VN  CONST_37  H9   C16  C17  C12  180.00   0.0  0
 0VN  CONST_38  H10  C17  C12  C13  180.00   0.0  0
 0VN  CONST_39  H7   C13  C14  C15  180.00   0.0  0
 0VN  Var_01    C15  N1   C11  N3   179.61  30.0  2
 0VN  Var_02    C14  C15  N1   C11   -1.82  30.0  2
 0VN  Var_03    C3   C18  C12  C13   -1.92  30.0  3
 0VN  Var_04    H17  C3   C18  C12   60.78  30.0  3
 0VN  Var_05    H11  C1   C18  C12   58.87  30.0  3
 0VN  Var_06    H14  C2   C18  C12   60.89  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
 0VN  plan-1  N1   0.020
 0VN  plan-1  C12  0.020
 0VN  plan-1  C13  0.020
 0VN  plan-1  C14  0.020
 0VN  plan-1  C15  0.020
 0VN  plan-1  C16  0.020
 0VN  plan-1  C17  0.020
 0VN  plan-1  H7   0.020
 0VN  plan-1  H8   0.020
 0VN  plan-1  H9   0.020
 0VN  plan-1  H10  0.020
 0VN  plan-1  C18  0.020
 0VN  plan-2  C4   0.020
 0VN  plan-2  C5   0.020
 0VN  plan-2  C6   0.020
 0VN  plan-2  C8   0.020
 0VN  plan-2  C9   0.020
 0VN  plan-2  C10  0.020
 0VN  plan-2  N3   0.020
 0VN  plan-2  C11  0.020
 0VN  plan-2  N4   0.020
 0VN  plan-2  N1   0.020
 0VN  plan-2  C7   0.020
 0VN  plan-2  N2   0.020
 0VN  plan-2  H1   0.020
 0VN  plan-2  H2   0.020
 0VN  plan-2  H3   0.020
 0VN  plan-2  H4   0.020

