# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 16:31:22 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2-methyl-1~{H}-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[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
 8P7  8P7  2-methyl-1~{H}-benzimidazole  ligand  18  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8P7
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
 8P7  N1  N  NR15  0  -0.686   1.1280  -1.0693  -0.0609
 8P7  C4  C  CR16  0  -0.309  -1.3747  -1.4318  -0.0729
 8P7  C5  C  CR16  0  -0.280  -2.5536  -0.7051  -0.0421
 8P7  C6  C  CR16  0  -0.273  -2.5488   0.6962   0.0162
 8P7  C7  C  CR16  0  -0.336  -1.3643   1.4122   0.0446
 8P7  C8  C  CR56  0   0.134  -0.1665   0.6995   0.0139
 8P7  C2  C  CR5   0   0.417   1.8719   0.0685  -0.0148
 8P7  C3  C  CR56  0   0.335  -0.1913  -0.7043  -0.0444
 8P7  N2  N  N     0  -0.479   1.1348   1.1460   0.0311
 8P7  H1  H  HNR5  0   0.418   1.4891  -2.0092  -0.1038
 8P7  H2  H  HCR6  0   0.264  -1.3804  -2.5131  -0.1167
 8P7  H3  H  HCR6  0   0.253  -3.4993  -1.2310  -0.0642
 8P7  H4  H  HCR6  0   0.250  -3.4923   1.2262   0.0390
 8P7  H5  H  HCR6  0   0.252  -1.3654   2.4939   0.0889
 8P7  H6  H  HCH3  0   0.264   3.7333  -0.4179  -0.9393
 8P7  H7  H  HCH3  0   0.263   3.7482   1.0461   0.0519
 8P7  H8  H  HCH3  0   0.263   3.7400  -0.5487   0.8152
 8P7  C1  C  CH3   0  -0.749   3.3557   0.0354  -0.0218

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
 8P7  C7  C8  aromatic  1.394  0.020  1.394
 8P7  C7  C6  aromatic  1.384  0.020  1.384
 8P7  N2  C8  aromatic  1.376  0.020  1.376
 8P7  N2  C2  aromatic  1.306  0.020  1.306
 8P7  C8  C3  aromatic  1.405  0.020  1.405
 8P7  C6  C5  aromatic  1.403  0.020  1.403
 8P7  C1  C2  single    1.484  0.020  1.484
 8P7  C2  N1  aromatic  1.360  0.020  1.360
 8P7  C3  N1  aromatic  1.369  0.020  1.369
 8P7  C3  C4  aromatic  1.389  0.020  1.389
 8P7  C5  C4  aromatic  1.385  0.020  1.385
 8P7  N1  H1  single    0.860  0.020  1.020
 8P7  C4  H2  single    0.930  0.020  1.080
 8P7  C5  H3  single    0.930  0.020  1.080
 8P7  C6  H4  single    0.930  0.020  1.080
 8P7  C7  H5  single    0.930  0.020  1.080
 8P7  C1  H6  single    0.970  0.020  1.090
 8P7  C1  H7  single    0.970  0.020  1.090
 8P7  C1  H8  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
 8P7  H1  N1  C3  126.48  3.000
 8P7  H1  N1  C2  125.85  3.000
 8P7  C3  N1  C2  107.67  3.000
 8P7  H2  C4  C3  121.90  3.000
 8P7  H2  C4  C5  121.37  3.000
 8P7  C3  C4  C5  116.73  3.000
 8P7  H3  C5  C6  119.30  3.000
 8P7  H3  C5  C4  119.23  3.000
 8P7  C6  C5  C4  121.48  3.000
 8P7  H4  C6  C7  119.48  3.000
 8P7  H4  C6  C5  119.15  3.000
 8P7  C7  C6  C5  121.37  3.000
 8P7  H5  C7  C8  120.84  3.000
 8P7  H5  C7  C6  121.12  3.000
 8P7  C8  C7  C6  118.05  3.000
 8P7  N2  C8  C3  109.96  3.000
 8P7  C3  C8  C7  119.77  3.000
 8P7  N2  C8  C7  130.27  3.000
 8P7  N2  C2  C1  125.64  3.000
 8P7  C1  C2  N1  121.87  3.000
 8P7  N2  C2  N1  112.50  3.000
 8P7  C8  C3  C4  122.61  3.000
 8P7  C4  C3  N1  132.92  3.000
 8P7  C8  C3  N1  104.47  3.000
 8P7  C2  N2  C8  105.40  3.000
 8P7  H8  C1  H7  108.59  3.000
 8P7  H8  C1  H6  107.52  3.000
 8P7  H7  C1  H6  108.57  3.000
 8P7  H8  C1  C2  111.14  3.000
 8P7  H7  C1  C2  109.88  3.000
 8P7  H6  C1  C2  111.06  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
 8P7  CONST_01  C8  N2  C2  N1    0.00   0.0  0
 8P7  CONST_02  C7  C8  C3  N1  180.00   0.0  0
 8P7  CONST_03  N2  C8  C3  N1    0.00   0.0  0
 8P7  CONST_04  C5  C4  C3  N1  180.00   0.0  0
 8P7  CONST_05  C7  C8  C3  C4    0.00   0.0  0
 8P7  CONST_06  N2  C8  C3  C4  180.00   0.0  0
 8P7  CONST_07  C2  N1  C3  C4  180.00   0.0  0
 8P7  CONST_08  C7  C6  C5  C4    0.00   0.0  0
 8P7  CONST_09  C8  C7  C6  C5    0.00   0.0  0
 8P7  CONST_10  C8  C3  C4  C5    0.00   0.0  0
 8P7  CONST_11  N2  C8  C7  C6  180.00   0.0  0
 8P7  CONST_12  C3  C8  C7  C6    0.00   0.0  0
 8P7  CONST_13  C3  C4  C5  C6    0.00   0.0  0
 8P7  CONST_14  C2  N2  C8  C7  180.00   0.0  0
 8P7  CONST_15  C2  N1  C3  C8    0.00   0.0  0
 8P7  CONST_16  C3  C8  N2  C2    0.00   0.0  0
 8P7  CONST_17  N2  C2  N1  C3    0.00   0.0  0
 8P7  CONST_18  C1  C2  N2  C8  180.00   0.0  0
 8P7  CONST_19  C3  N1  C2  C1  180.00   0.0  0
 8P7  CONST_20  H2  C4  C3  N1    0.00   0.0  0
 8P7  CONST_21  H1  N1  C3  C4    0.00   0.0  0
 8P7  CONST_22  H4  C6  C5  C4  180.00   0.0  0
 8P7  CONST_23  H5  C7  C6  C5  180.00   0.0  0
 8P7  CONST_24  H3  C5  C6  C7  180.00   0.0  0
 8P7  Var_01    H6  C1  C2  N1   61.64  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
 8P7  plan-1  N1  0.020
 8P7  plan-1  C4  0.020
 8P7  plan-1  C5  0.020
 8P7  plan-1  C6  0.020
 8P7  plan-1  C7  0.020
 8P7  plan-1  C8  0.020
 8P7  plan-1  C2  0.020
 8P7  plan-1  C3  0.020
 8P7  plan-1  N2  0.020
 8P7  plan-1  H1  0.020
 8P7  plan-1  H2  0.020
 8P7  plan-1  H3  0.020
 8P7  plan-1  H4  0.020
 8P7  plan-1  H5  0.020
 8P7  plan-1  C1  0.020

