# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 00:44:12 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-(methylamino)-1H-benzimidazole-5-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2ccc(cc2n1)C(=O)NN
#
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
 6H9  6H9  2-(methylamino)-1H-benzimidazole-5-carbohydrazide  ligand  26  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6H9
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
 6H9  C1   C  CR5   0   0.676  -2.9306   0.3955   0.0004
 6H9  C2   C  CR56  0   0.346  -1.1109  -0.8407  -0.1107
 6H9  C3   C  CR16  0  -0.300  -0.1370  -1.8184  -0.1863
 6H9  C4   C  CR16  0  -0.322   1.1852  -1.3937  -0.2117
 6H9  C5   C  CR6   0  -0.065   1.5172  -0.0322  -0.1709
 6H9  C6   C  C     0   0.511   2.9343   0.4383  -0.2269
 6H9  O    O  O     0  -0.482   3.2330   1.5157  -0.7182
 6H9  N2   N  NH1   0  -0.530   3.8329  -0.4083   0.3157
 6H9  N3   N  NH2   0  -0.638   5.1855  -0.1180   0.3013
 6H9  C7   C  CR16  0  -0.381   0.5188   0.9405  -0.1176
 6H9  C8   C  CR56  0   0.186  -0.8065   0.5344  -0.0734
 6H9  N1   N  NR15  0  -0.739  -2.4817  -0.8937  -0.0635
 6H9  N4   N  N     0  -0.538  -1.9571   1.2792  -0.0024
 6H9  N    N  NH1   0  -0.677  -4.2378   0.6875   0.0402
 6H9  C    C  CH3   0  -0.545  -5.2747  -0.3082   0.1559
 6H9  H1   H  HCR6  0   0.267  -0.3835  -2.8709  -0.2325
 6H9  H2   H  HCR6  0   0.254   1.9596  -2.1448  -0.2958
 6H9  H3   H  HNH1  0   0.404   3.5121  -1.2077   0.8414
 6H9  H4   H  HNH2  0   0.369   5.5063   0.0261   1.2504
 6H9  H5   H  HNH2  0   0.372   5.6845  -0.9159  -0.0695
 6H9  H6   H  HCR6  0   0.249   0.7712   1.9929  -0.1002
 6H9  H7   H  HNR5  0   0.425  -3.0449  -1.7292  -0.0558
 6H9  H9   H  HNH1  0   0.405  -4.4713   1.6519   0.2026
 6H9  H10  H  HCH3  0   0.244  -5.2659  -0.9950  -0.6923
 6H9  H11  H  HCH3  0   0.240  -5.2001  -0.8915   1.0773
 6H9  H12  H  HCH3  0   0.270  -6.2357   0.1974   0.1564

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
 6H9  C   N    single    1.442  0.020  1.442
 6H9  N   C1   single    1.340  0.020  1.340
 6H9  C1  N1   aromatic  1.367  0.020  1.367
 6H9  C1  N4   aromatic  1.315  0.020  1.315
 6H9  N1  C2   aromatic  1.373  0.020  1.373
 6H9  N4  C8   aromatic  1.373  0.020  1.373
 6H9  C2  C8   aromatic  1.409  0.020  1.409
 6H9  C2  C3   aromatic  1.382  0.020  1.382
 6H9  C8  C7   aromatic  1.387  0.020  1.387
 6H9  C3  C4   aromatic  1.389  0.020  1.389
 6H9  C7  C5   aromatic  1.395  0.020  1.395
 6H9  C4  C5   aromatic  1.402  0.020  1.402
 6H9  C5  C6   single    1.494  0.020  1.494
 6H9  C6  O    double    1.221  0.020  1.221
 6H9  C6  N2   single    1.349  0.020  1.349
 6H9  N2  N3   single    1.384  0.020  1.384
 6H9  C3  H1   single    0.930  0.020  1.080
 6H9  C4  H2   single    0.930  0.020  1.080
 6H9  N2  H3   single    0.860  0.020  1.020
 6H9  N3  H4   single    0.890  0.020  1.040
 6H9  N3  H5   single    0.890  0.020  1.040
 6H9  C7  H6   single    0.930  0.020  1.080
 6H9  N1  H7   single    0.860  0.020  1.020
 6H9  N   H9   single    0.860  0.020  1.020
 6H9  C   H10  single    0.970  0.020  1.090
 6H9  C   H11  single    0.970  0.020  1.090
 6H9  C   H12  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
 6H9  N    C1  N4   125.16  3.000
 6H9  N4   C1  N1   113.00  3.000
 6H9  N    C1  N1   121.83  3.000
 6H9  N1   C2  C8   104.63  3.000
 6H9  C8   C2  C3   122.66  3.000
 6H9  N1   C2  C3   132.71  3.000
 6H9  H1   C3  C4   120.89  3.000
 6H9  H1   C3  C2   122.01  3.000
 6H9  C4   C3  C2   117.10  3.000
 6H9  H2   C4  C5   120.46  3.000
 6H9  H2   C4  C3   118.06  3.000
 6H9  C5   C4  C3   121.45  3.000
 6H9  C7   C5  C6   117.43  3.000
 6H9  C6   C5  C4   121.95  3.000
 6H9  C7   C5  C4   120.58  3.000
 6H9  N2   C6  O    123.56  3.000
 6H9  N2   C6  C5   114.78  3.000
 6H9  O    C6  C5   121.65  3.000
 6H9  H3   N2  N3   118.85  3.000
 6H9  H3   N2  C6   119.68  3.000
 6H9  N3   N2  C6   121.03  3.000
 6H9  H5   N3  H4   107.44  3.000
 6H9  H5   N3  N2   108.70  3.000
 6H9  H4   N3  N2   109.26  3.000
 6H9  H6   C7  C8   120.47  3.000
 6H9  H6   C7  C5   120.78  3.000
 6H9  C8   C7  C5   118.75  3.000
 6H9  N4   C8  C7   130.08  3.000
 6H9  C7   C8  C2   119.43  3.000
 6H9  N4   C8  C2   110.48  3.000
 6H9  H7   N1  C2   126.20  3.000
 6H9  H7   N1  C1   126.74  3.000
 6H9  C2   N1  C1   107.05  3.000
 6H9  C8   N4  C1   104.84  3.000
 6H9  H9   N   C    118.84  3.000
 6H9  H9   N   C1   116.12  3.000
 6H9  C    N   C1   123.60  3.000
 6H9  H12  C   H11  107.96  3.000
 6H9  H12  C   H10  107.49  3.000
 6H9  H11  C   H10  108.58  3.000
 6H9  H12  C   N    108.35  3.000
 6H9  H11  C   N    112.77  3.000
 6H9  H10  C   N    111.49  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
 6H9  CONST_01  C8   C2  N1  C1    0.00   0.0  0
 6H9  CONST_02  C3   C2  N1  C1  180.00   0.0  0
 6H9  CONST_03  C2   C8  N4  C1    0.00   0.0  0
 6H9  CONST_04  C7   C8  N4  C1  180.00   0.0  0
 6H9  CONST_05  N4   C1  N1  C2    0.00   0.0  0
 6H9  CONST_06  C5   C7  C8  C2    0.00   0.0  0
 6H9  CONST_07  C5   C4  C3  C2    0.00   0.0  0
 6H9  CONST_08  N4   C8  C2  C3  180.00   0.0  0
 6H9  CONST_09  C7   C8  C2  C3    0.00   0.0  0
 6H9  CONST_10  C7   C5  C4  C3    0.00   0.0  0
 6H9  CONST_11  N1   C2  C3  C4  180.00   0.0  0
 6H9  CONST_12  C8   C2  C3  C4    0.00   0.0  0
 6H9  CONST_13  C8   C7  C5  C4    0.00   0.0  0
 6H9  CONST_14  N4   C8  C7  C5  180.00   0.0  0
 6H9  CONST_15  N1   C2  C8  C7  180.00   0.0  0
 6H9  CONST_16  N1   C1  N4  C8    0.00   0.0  0
 6H9  CONST_17  N4   C8  C2  N1    0.00   0.0  0
 6H9  CONST_18  N    C1  N1  C2  180.00   0.0  0
 6H9  CONST_19  C6   C5  C4  C3  180.00   0.0  0
 6H9  CONST_20  C8   C7  C5  C6  180.00   0.0  0
 6H9  CONST_21  N    C1  N4  C8  180.00   0.0  0
 6H9  CONST_22  H6   C7  C8  C2  180.00   0.0  0
 6H9  CONST_23  H2   C4  C3  C2  180.00   0.0  0
 6H9  CONST_24  H7   N1  C2  C3    0.00   0.0  0
 6H9  CONST_25  H1   C3  C4  C5  180.00   0.0  0
 6H9  CONST_26  C    N   C1  N1    0.00   0.0  0
 6H9  CONST_27  C    N   C1  N4  180.00   0.0  0
 6H9  CONST_28  H9   N   C1  N1  180.00   0.0  0
 6H9  CONST_29  N3   N2  C6  C5  180.00   0.0  0
 6H9  CONST_30  H3   N2  C6  C5    0.00   0.0  0
 6H9  CONST_31  N3   N2  C6  O     0.00   0.0  0
 6H9  Var_01    O    C6  C5  C4  149.96  30.0  2
 6H9  Var_02    H10  C   N   C1  -61.42  30.0  3
 6H9  Var_03    H4   N3  N2  C6  114.01  30.0  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
 6H9  plan-1  C1  0.020
 6H9  plan-1  C2  0.020
 6H9  plan-1  C3  0.020
 6H9  plan-1  C4  0.020
 6H9  plan-1  C5  0.020
 6H9  plan-1  C6  0.020
 6H9  plan-1  C7  0.020
 6H9  plan-1  C8  0.020
 6H9  plan-1  N1  0.020
 6H9  plan-1  N4  0.020
 6H9  plan-1  N   0.020
 6H9  plan-1  H1  0.020
 6H9  plan-1  H2  0.020
 6H9  plan-1  H6  0.020
 6H9  plan-1  H7  0.020
 6H9  plan-2  C5  0.020
 6H9  plan-2  C6  0.020
 6H9  plan-2  O   0.020
 6H9  plan-2  N2  0.020
 6H9  plan-2  N3  0.020
 6H9  plan-2  H3  0.020
 6H9  plan-3  C1  0.020
 6H9  plan-3  N   0.020
 6H9  plan-3  C   0.020
 6H9  plan-3  H9  0.020

