# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 00:22:59 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 5,6-dimethyl-1~{H}-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2[nH]c(N)nc2cc1C
#
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
 6RQ  6RQ  5,6-dimethyl-1~{H}-benzimidazol-2-amine  ligand  23  12  .  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_6RQ
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
 6RQ  C4   C  CR56  0   0.157  -0.5535  -0.6891   0.0278
 6RQ  C5   C  CR56  0   0.344  -0.5220   0.7097  -0.0483
 6RQ  C6   C  CR16  0  -0.363   0.6622   1.4246  -0.0778
 6RQ  C7   C  CR6   0   0.042   1.8605   0.7168  -0.0302
 6RQ  C8   C  CH3   0  -0.736   3.1636   1.4632  -0.0714
 6RQ  C11  C  CR5   0   0.597  -2.5862  -0.0558  -0.0208
 6RQ  C2   C  CR6   0   0.059   1.8512  -0.6920   0.0507
 6RQ  C1   C  CH3   0  -0.736   3.1484  -1.4478   0.1154
 6RQ  C3   C  CR16  0  -0.400   0.6472  -1.3889   0.0776
 6RQ  N9   N  NR15  0  -0.723  -1.8466   1.0860  -0.0800
 6RQ  N10  N  N     0  -0.525  -1.8552  -1.1409   0.0459
 6RQ  N12  N  NH2   0  -0.849  -3.9418  -0.0289  -0.0927
 6RQ  H1   H  HCR6  0   0.251   0.6661   2.5065  -0.1365
 6RQ  H2   H  HCH3  0   0.237   3.7840   1.2549   0.8030
 6RQ  H3   H  HCH3  0   0.237   3.7582   1.1952  -0.9479
 6RQ  H4   H  HCH3  0   0.247   2.9988   2.5397  -0.1061
 6RQ  H5   H  HCH3  0   0.236   3.7841  -1.2487  -0.7501
 6RQ  H6   H  HCH3  0   0.237   3.7309  -1.1784   0.9996
 6RQ  H7   H  HCH3  0   0.246   2.9752  -2.5227   0.1533
 6RQ  H8   H  HCR6  0   0.236   0.6473  -2.4713   0.1375
 6RQ  H9   H  HNR5  0   0.414  -2.2037   2.0257  -0.1437
 6RQ  H11  H  HNH2  0   0.396  -4.4032   0.8029   0.2394
 6RQ  H12  H  HNH2  0   0.395  -4.3958  -0.8760   0.2086

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
 6RQ  C1   C2   single    1.503  0.020  1.503
 6RQ  C2   C3   aromatic  1.391  0.020  1.391
 6RQ  C2   C7   aromatic  1.411  0.020  1.411
 6RQ  C3   C4   aromatic  1.391  0.020  1.391
 6RQ  C8   C7   single    1.502  0.020  1.502
 6RQ  C7   C6   aromatic  1.393  0.020  1.393
 6RQ  C4   N10  aromatic  1.378  0.020  1.378
 6RQ  C4   C5   aromatic  1.401  0.020  1.401
 6RQ  C6   C5   aromatic  1.384  0.020  1.384
 6RQ  N10  C11  aromatic  1.310  0.020  1.310
 6RQ  C5   N9   aromatic  1.377  0.020  1.377
 6RQ  C11  N9   aromatic  1.362  0.020  1.362
 6RQ  C11  N12  single    1.358  0.020  1.358
 6RQ  C6   H1   single    0.930  0.020  1.080
 6RQ  C8   H2   single    0.970  0.020  1.090
 6RQ  C8   H3   single    0.970  0.020  1.090
 6RQ  C8   H4   single    0.970  0.020  1.090
 6RQ  C1   H5   single    0.970  0.020  1.090
 6RQ  C1   H6   single    0.970  0.020  1.090
 6RQ  C1   H7   single    0.970  0.020  1.090
 6RQ  C3   H8   single    0.930  0.020  1.080
 6RQ  N9   H9   single    0.860  0.020  1.020
 6RQ  N12  H11  single    0.890  0.020  1.040
 6RQ  N12  H12  single    0.890  0.020  1.040

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
 6RQ  N10  C4   C3   130.55  3.000
 6RQ  N10  C4   C5   110.44  3.000
 6RQ  C3   C4   C5   119.01  3.000
 6RQ  N9   C5   C6   132.96  3.000
 6RQ  N9   C5   C4   104.62  3.000
 6RQ  C6   C5   C4   122.43  3.000
 6RQ  H1   C6   C7   120.42  3.000
 6RQ  H1   C6   C5   121.34  3.000
 6RQ  C7   C6   C5   118.24  3.000
 6RQ  C2   C7   C8   120.22  3.000
 6RQ  C8   C7   C6   119.53  3.000
 6RQ  C2   C7   C6   120.24  3.000
 6RQ  H4   C8   H3   107.40  3.000
 6RQ  H4   C8   H2   107.45  3.000
 6RQ  H3   C8   H2   106.64  3.000
 6RQ  H4   C8   C7   111.14  3.000
 6RQ  H3   C8   C7   111.85  3.000
 6RQ  H2   C8   C7   112.08  3.000
 6RQ  N12  C11  N10  125.18  3.000
 6RQ  N12  C11  N9   121.56  3.000
 6RQ  N10  C11  N9   113.18  3.000
 6RQ  C3   C2   C1   119.62  3.000
 6RQ  C3   C2   C7   120.45  3.000
 6RQ  C1   C2   C7   119.92  3.000
 6RQ  H7   C1   H6   107.45  3.000
 6RQ  H7   C1   H5   107.45  3.000
 6RQ  H6   C1   H5   106.62  3.000
 6RQ  H7   C1   C2   111.13  3.000
 6RQ  H6   C1   C2   111.78  3.000
 6RQ  H5   C1   C2   112.13  3.000
 6RQ  H8   C3   C2   120.07  3.000
 6RQ  H8   C3   C4   120.30  3.000
 6RQ  C2   C3   C4   119.63  3.000
 6RQ  H9   N9   C11  126.33  3.000
 6RQ  H9   N9   C5   126.68  3.000
 6RQ  C11  N9   C5   106.99  3.000
 6RQ  C11  N10  C4   104.76  3.000
 6RQ  H12  N12  H11  112.91  3.000
 6RQ  H12  N12  C11  114.68  3.000
 6RQ  H11  N12  C11  117.14  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
 6RQ  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 6RQ  CONST_02  N9   C11  N10  C4     0.00   0.0  0
 6RQ  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 6RQ  CONST_04  C11  N9   C5   C4     0.00   0.0  0
 6RQ  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 6RQ  CONST_06  C11  N10  C4   C5     0.00   0.0  0
 6RQ  CONST_07  C2   C7   C6   C5     0.00   0.0  0
 6RQ  CONST_08  N10  C11  N9   C5     0.00   0.0  0
 6RQ  CONST_09  C3   C2   C7   C6     0.00   0.0  0
 6RQ  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 6RQ  CONST_11  N10  C4   C5   C6   180.00   0.0  0
 6RQ  CONST_12  C11  N9   C5   C6   180.00   0.0  0
 6RQ  CONST_13  N9   C5   C6   C7   180.00   0.0  0
 6RQ  CONST_14  C3   C4   N10  C11  180.00   0.0  0
 6RQ  CONST_15  N10  C4   C3   C2   180.00   0.0  0
 6RQ  CONST_16  N9   C5   C4   C3   180.00   0.0  0
 6RQ  CONST_17  N10  C4   C5   N9     0.00   0.0  0
 6RQ  CONST_18  C1   C2   C3   C4   180.00   0.0  0
 6RQ  CONST_19  N12  C11  N10  C4   180.00   0.0  0
 6RQ  CONST_20  C8   C7   C6   C5   180.00   0.0  0
 6RQ  CONST_21  N12  C11  N9   C5   180.00   0.0  0
 6RQ  CONST_22  C1   C2   C7   C6   180.00   0.0  0
 6RQ  CONST_23  C3   C2   C7   C8   180.00   0.0  0
 6RQ  CONST_24  H1   C6   C5   C4   180.00   0.0  0
 6RQ  CONST_25  H9   N9   C5   C4   180.00   0.0  0
 6RQ  CONST_26  H8   C3   C4   C5   180.00   0.0  0
 6RQ  Var_01    H2   C8   C7   C6   122.05  30.0  2
 6RQ  Var_02    H5   C1   C2   C7   -58.53  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
 6RQ  plan-1  C4   0.020
 6RQ  plan-1  C5   0.020
 6RQ  plan-1  C6   0.020
 6RQ  plan-1  C7   0.020
 6RQ  plan-1  C8   0.020
 6RQ  plan-1  C11  0.020
 6RQ  plan-1  C2   0.020
 6RQ  plan-1  C1   0.020
 6RQ  plan-1  C3   0.020
 6RQ  plan-1  N9   0.020
 6RQ  plan-1  N10  0.020
 6RQ  plan-1  N12  0.020
 6RQ  plan-1  H1   0.020
 6RQ  plan-1  H8   0.020
 6RQ  plan-1  H9   0.020
 6RQ  plan-2  C11  0.020
 6RQ  plan-2  N12  0.020
 6RQ  plan-2  H11  0.020
 6RQ  plan-2  H12  0.020

