# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:55:03 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-(3-methylphenyl)-1H-benzimidazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)n2cnc3cc(N)ccc23
#
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
 II4  II4  1-(3-methylphenyl)-1H-benzimidazol-5-amine  ligand  30  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_II4
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
 II4  C2    C  CR6   0   0.293   3.7443   0.5368  -0.2027
 II4  C3    C  CR16  0  -0.410   3.3437  -0.7689   0.0608
 II4  C4    C  CR56  0   0.135   1.9829  -1.0322   0.2072
 II4  C5    C  CR56  0   0.291   1.0387  -0.0035   0.0931
 II4  C6    C  CR16  0  -0.287   1.4195   1.3027  -0.1876
 II4  N7    N  NR5   0  -0.615  -0.1870  -0.6217   0.2678
 II4  C8    C  CR15  0   0.094   0.0806  -1.9401   0.4747
 II4  N9    N  N     0  -0.471   1.3479  -2.2301   0.4490
 II4  N2    N  NH2   0  -0.864   5.0889   0.8666  -0.2960
 II4  C10   C  CR6   0   0.103  -3.7640  -0.0814  -0.4990
 II4  C11   C  CR16  0  -0.347  -2.4852  -0.6307  -0.4813
 II4  C30   C  CR16  0  -0.336   2.7704   1.5540  -0.3278
 II4  C13   C  CR16  0  -0.316  -1.7019   1.1423   0.9565
 II4  C80   C  CR6   0   0.351  -1.4663  -0.0293   0.2479
 II4  C14   C  CR16  0  -0.238  -2.9673   1.7071   0.9181
 II4  C15   C  CR16  0  -0.300  -3.9897   1.1014   0.2018
 II4  H3    H  HCR6  0   0.254   4.0705  -1.5680   0.1460
 II4  H21N  H  HNH2  0   0.374   5.6915   0.1016  -0.5569
 II4  H22N  H  HNH2  0   0.374   5.2833   1.6776  -0.8619
 II4  H30   H  HCR6  0   0.259   3.0958   2.5644  -0.5449
 II4  H6    H  HCR6  0   0.271   0.7010   2.1039  -0.2994
 II4  H91C  H  HCH3  0   0.253  -5.3957  -1.4686  -0.6057
 II4  H92C  H  HCH3  0   0.247  -5.6107  -0.0388  -1.6044
 II4  H93C  H  HCH3  0   0.246  -4.4978  -1.3130  -2.1083
 II4  H8    H  HCR5  0   0.294  -0.7158  -2.6464   0.6609
 II4  H11   H  HCR6  0   0.269  -2.2791  -1.5302  -1.0501
 II4  H15   H  HCR6  0   0.254  -4.9745   1.5524   0.1882
 II4  H13   H  HCR6  0   0.277  -0.9163   1.5998   1.5431
 II4  H14   H  HCR6  0   0.264  -3.1583   2.6229   1.4615
 II4  C9    C  CH3   0  -0.719  -4.8733  -0.7580  -1.2492

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
 II4  C2   C3    aromatic  1.391  0.020  1.391
 II4  C2   N2    single    1.388  0.020  1.388
 II4  C2   C30   aromatic  1.414  0.020  1.414
 II4  C3   C4    aromatic  1.394  0.020  1.394
 II4  C4   C5    aromatic  1.401  0.020  1.401
 II4  C4   N9    aromatic  1.377  0.020  1.377
 II4  C5   C6    aromatic  1.389  0.020  1.389
 II4  C5   N7    aromatic  1.384  0.020  1.384
 II4  C6   C30   aromatic  1.381  0.020  1.381
 II4  C9   C10   single    1.500  0.020  1.500
 II4  N7   C8    aromatic  1.361  0.020  1.361
 II4  N7   C80   single    1.410  0.020  1.410
 II4  C8   N9    aromatic  1.300  0.020  1.300
 II4  C10  C11   aromatic  1.392  0.020  1.392
 II4  C10  C15   aromatic  1.393  0.020  1.393
 II4  C11  C80   aromatic  1.390  0.020  1.390
 II4  C13  C80   aromatic  1.389  0.020  1.389
 II4  C13  C14   aromatic  1.386  0.020  1.386
 II4  C14  C15   aromatic  1.388  0.020  1.388
 II4  C3   H3    single    0.930  0.020  1.080
 II4  N2   H21N  single    0.890  0.020  1.040
 II4  N2   H22N  single    0.890  0.020  1.040
 II4  C30  H30   single    0.930  0.020  1.080
 II4  C6   H6    single    0.930  0.020  1.080
 II4  C9   H91C  single    0.970  0.020  1.090
 II4  C9   H92C  single    0.970  0.020  1.090
 II4  C9   H93C  single    0.970  0.020  1.090
 II4  C8   H8    single    0.930  0.020  1.080
 II4  C11  H11   single    0.930  0.020  1.080
 II4  C15  H15   single    0.930  0.020  1.080
 II4  C13  H13   single    0.930  0.020  1.080
 II4  C14  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
 II4  C30   C2   N2    119.38  3.000
 II4  C30   C2   C3    119.59  3.000
 II4  N2    C2   C3    120.99  3.000
 II4  H3    C3   C4    120.48  3.000
 II4  H3    C3   C2    120.94  3.000
 II4  C4    C3   C2    118.58  3.000
 II4  N9    C4   C5    110.02  3.000
 II4  N9    C4   C3    129.27  3.000
 II4  C5    C4   C3    120.71  3.000
 II4  N7    C5   C6    133.49  3.000
 II4  N7    C5   C4    104.99  3.000
 II4  C6    C5   C4    121.47  3.000
 II4  H6    C6   C30   120.28  3.000
 II4  H6    C6   C5    122.35  3.000
 II4  C30   C6   C5    117.37  3.000
 II4  C80   N7   C8    125.99  3.000
 II4  C80   N7   C5    127.89  3.000
 II4  C8    N7   C5    106.12  3.000
 II4  H8    C8   N9    125.16  3.000
 II4  H8    C8   N7    120.95  3.000
 II4  N9    C8   N7    113.87  3.000
 II4  C8    N9   C4    105.00  3.000
 II4  H22N  N2   H21N  110.49  3.000
 II4  H22N  N2   C2    114.57  3.000
 II4  H21N  N2   C2    114.60  3.000
 II4  C15   C10  C11   118.52  3.000
 II4  C15   C10  C9    120.96  3.000
 II4  C11   C10  C9    120.51  3.000
 II4  H11   C11  C80   119.66  3.000
 II4  H11   C11  C10   119.70  3.000
 II4  C80   C11  C10   120.63  3.000
 II4  H30   C30  C6    118.93  3.000
 II4  H30   C30  C2    118.80  3.000
 II4  C6    C30  C2    122.26  3.000
 II4  H13   C13  C14   120.37  3.000
 II4  H13   C13  C80   120.66  3.000
 II4  C14   C13  C80   118.96  3.000
 II4  C13   C80  C11   120.54  3.000
 II4  C13   C80  N7    120.06  3.000
 II4  C11   C80  N7    119.40  3.000
 II4  H14   C14  C15   119.92  3.000
 II4  H14   C14  C13   119.47  3.000
 II4  C15   C14  C13   120.60  3.000
 II4  H15   C15  C14   119.64  3.000
 II4  H15   C15  C10   119.63  3.000
 II4  C14   C15  C10   120.72  3.000
 II4  H93C  C9   H92C  108.21  3.000
 II4  H93C  C9   H91C  107.35  3.000
 II4  H92C  C9   H91C  107.33  3.000
 II4  H93C  C9   C10   111.66  3.000
 II4  H92C  C9   C10   111.46  3.000
 II4  H91C  C9   C10   110.64  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
 II4  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 II4  CONST_02  N9    C4   C3   C2   180.00   0.0  0
 II4  CONST_03  C5    C6   C30  C2     0.00   0.0  0
 II4  CONST_04  C6    C30  C2   C3     0.00   0.0  0
 II4  CONST_05  C6    C5   C4   C3     0.00   0.0  0
 II4  CONST_06  N7    C5   C4   C3   180.00   0.0  0
 II4  CONST_07  C8    N9   C4   C3   180.00   0.0  0
 II4  CONST_08  C30   C2   C3   C4     0.00   0.0  0
 II4  CONST_09  C30   C6   C5   C4     0.00   0.0  0
 II4  CONST_10  C8    N7   C5   C4     0.00   0.0  0
 II4  CONST_11  C80   N7   C5   C4   180.00   0.0  0
 II4  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 II4  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 II4  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 II4  CONST_17  N9    C4   C5   C6   180.00   0.0  0
 II4  CONST_18  C8    N7   C5   C6   180.00   0.0  0
 II4  CONST_19  C80   N7   C5   C6     0.00   0.0  0
 II4  CONST_20  N9    C4   C5   N7     0.00   0.0  0
 II4  CONST_21  C30   C6   C5   N7   180.00   0.0  0
 II4  CONST_22  C10   C11  C80  N7   180.00   0.0  0
 II4  CONST_23  C14   C13  C80  N7   180.00   0.0  0
 II4  CONST_26  C80   N7   C8   N9   180.00   0.0  0
 II4  CONST_27  C13   C80  C11  C10    0.00   0.0  0
 II4  CONST_28  C13   C14  C15  C10    0.00   0.0  0
 II4  CONST_29  C14   C15  C10  C11    0.00   0.0  0
 II4  CONST_30  C14   C13  C80  C11    0.00   0.0  0
 II4  CONST_31  C15   C10  C11  C80    0.00   0.0  0
 II4  CONST_32  C15   C14  C13  C80    0.00   0.0  0
 II4  CONST_33  N2    C2   C3   C4   180.00   0.0  0
 II4  CONST_34  N2    C2   C30  C6   180.00   0.0  0
 II4  CONST_35  C80   C11  C10  C9   180.00   0.0  0
 II4  CONST_36  C14   C15  C10  C9   180.00   0.0  0
 II4  CONST_37  H6    C6   C30  C2   180.00   0.0  0
 II4  CONST_38  H30   C30  C2   C3   180.00   0.0  0
 II4  CONST_39  H8    C8   N9   C4   180.00   0.0  0
 II4  CONST_40  H3    C3   C4   C5   180.00   0.0  0
 II4  CONST_41  H11   C11  C80  N7     0.00   0.0  0
 II4  CONST_42  H13   C13  C80  N7     0.00   0.0  0
 II4  CONST_43  H14   C14  C15  C10  180.00   0.0  0
 II4  CONST_44  H15   C15  C10  C11  180.00   0.0  0
 II4  Var_01    H91C  C9   C10  C11   89.73  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
 II4  plan-1  N7    0.020
 II4  plan-1  C10   0.020
 II4  plan-1  C11   0.020
 II4  plan-1  C13   0.020
 II4  plan-1  C80   0.020
 II4  plan-1  C14   0.020
 II4  plan-1  C15   0.020
 II4  plan-1  H11   0.020
 II4  plan-1  H15   0.020
 II4  plan-1  H13   0.020
 II4  plan-1  H14   0.020
 II4  plan-1  C9    0.020
 II4  plan-2  C2    0.020
 II4  plan-2  C3    0.020
 II4  plan-2  C4    0.020
 II4  plan-2  C5    0.020
 II4  plan-2  C6    0.020
 II4  plan-2  N7    0.020
 II4  plan-2  C8    0.020
 II4  plan-2  N9    0.020
 II4  plan-2  N2    0.020
 II4  plan-2  C30   0.020
 II4  plan-2  C80   0.020
 II4  plan-2  H3    0.020
 II4  plan-2  H30   0.020
 II4  plan-2  H6    0.020
 II4  plan-2  H8    0.020
 II4  plan-3  C2    0.020
 II4  plan-3  N2    0.020
 II4  plan-3  H21N  0.020
 II4  plan-3  H22N  0.020

