# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 00:30:48 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-(methylamino)-1H-benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2ccc(cc2n1)C(N)=O
#
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
 6HD  6HD  2-(methylamino)-1H-benzimidazole-5-carboxamide  ligand  24  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6HD
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
 6HD  O    O  O     0  -0.491   3.6148  -1.5909  -0.0266
 6HD  C6   C  C     0   0.503   3.3502  -0.3934  -0.0086
 6HD  N2   N  NH2   0  -0.832   4.3186   0.5362   0.0156
 6HD  C5   C  CR6   0  -0.059   1.9321   0.0809  -0.0134
 6HD  C4   C  CR16  0  -0.317   1.5775   1.4380  -0.0245
 6HD  C3   C  CR16  0  -0.297   0.2505   1.8452  -0.0342
 6HD  C7   C  CR16  0  -0.384   0.9402  -0.9015  -0.0105
 6HD  C8   C  CR56  0   0.193  -0.3908  -0.5157  -0.0197
 6HD  C2   C  CR56  0   0.348  -0.7138   0.8547  -0.0326
 6HD  N1   N  NR15  0  -0.739  -2.0848   0.8885  -0.0423
 6HD  N3   N  N     0  -0.538  -1.5322  -1.2787  -0.0217
 6HD  C1   C  CR5   0   0.678  -2.5176  -0.4088  -0.0377
 6HD  N    N  NH1   0  -0.678  -3.8206  -0.7173  -0.0622
 6HD  C    C  CH3   0  -0.545  -4.8776   0.2611   0.0057
 6HD  H1   H  HNH2  0   0.402   5.2817   0.2436   0.0175
 6HD  H2   H  HNH2  0   0.412   4.1489   1.5246   0.0370
 6HD  H3   H  HCR6  0   0.241   2.3279   2.2163  -0.0293
 6HD  H4   H  HCR6  0   0.268  -0.0064   2.8961  -0.0442
 6HD  H5   H  HCR6  0   0.250   1.2055  -1.9501  -0.0024
 6HD  H6   H  HNR5  0   0.426  -2.6606   1.7154  -0.0466
 6HD  H8   H  HNH1  0   0.405  -4.0507  -1.6918   0.0281
 6HD  H9   H  HCH3  0   0.241  -4.8561   0.8387   0.9333
 6HD  H10  H  HCH3  0   0.243  -4.8399   0.9543  -0.8368
 6HD  H11  H  HCH3  0   0.270  -5.8291  -0.2599  -0.0408

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
 6HD  C   N    single    1.442  0.020  1.442
 6HD  N   C1   single    1.339  0.020  1.339
 6HD  C1  N1   aromatic  1.368  0.020  1.368
 6HD  C1  N3   aromatic  1.314  0.020  1.314
 6HD  N1  C2   aromatic  1.371  0.020  1.371
 6HD  N3  C8   aromatic  1.373  0.020  1.373
 6HD  C2  C8   aromatic  1.408  0.020  1.408
 6HD  C2  C3   aromatic  1.382  0.020  1.382
 6HD  C8  C7   aromatic  1.386  0.020  1.386
 6HD  C3  C4   aromatic  1.388  0.020  1.388
 6HD  C7  C5   aromatic  1.396  0.020  1.396
 6HD  C4  C5   aromatic  1.403  0.020  1.403
 6HD  C5  C6   single    1.495  0.020  1.495
 6HD  C6  O    double    1.226  0.020  1.226
 6HD  C6  N2   single    1.343  0.020  1.343
 6HD  N2  H1   single    0.860  0.020  1.020
 6HD  N2  H2   single    0.860  0.020  1.020
 6HD  C4  H3   single    0.930  0.020  1.080
 6HD  C3  H4   single    0.930  0.020  1.080
 6HD  C7  H5   single    0.930  0.020  1.080
 6HD  N1  H6   single    0.860  0.020  1.020
 6HD  N   H8   single    0.860  0.020  1.020
 6HD  C   H9   single    0.970  0.020  1.090
 6HD  C   H10  single    0.970  0.020  1.090
 6HD  C   H11  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
 6HD  C5   C6  N2   117.68  3.000
 6HD  N2   C6  O    121.37  3.000
 6HD  C5   C6  O    120.95  3.000
 6HD  H2   N2  H1   116.64  3.000
 6HD  H2   N2  C6   124.10  3.000
 6HD  H1   N2  C6   119.27  3.000
 6HD  C7   C5  C4   120.08  3.000
 6HD  C4   C5  C6   123.14  3.000
 6HD  C7   C5  C6   116.78  3.000
 6HD  H3   C4  C3   116.89  3.000
 6HD  H3   C4  C5   121.40  3.000
 6HD  C3   C4  C5   121.71  3.000
 6HD  H4   C3  C2   122.04  3.000
 6HD  H4   C3  C4   120.80  3.000
 6HD  C2   C3  C4   117.17  3.000
 6HD  H5   C7  C8   120.36  3.000
 6HD  H5   C7  C5   120.53  3.000
 6HD  C8   C7  C5   119.11  3.000
 6HD  N3   C8  C2   110.49  3.000
 6HD  C2   C8  C7   119.43  3.000
 6HD  N3   C8  C7   130.08  3.000
 6HD  N1   C2  C8   104.68  3.000
 6HD  C8   C2  C3   122.50  3.000
 6HD  N1   C2  C3   132.81  3.000
 6HD  H6   N1  C1   126.70  3.000
 6HD  H6   N1  C2   126.27  3.000
 6HD  C1   N1  C2   107.03  3.000
 6HD  C1   N3  C8   104.80  3.000
 6HD  N    C1  N3   125.25  3.000
 6HD  N3   C1  N1   112.99  3.000
 6HD  N    C1  N1   121.76  3.000
 6HD  H8   N   C    119.06  3.000
 6HD  H8   N   C1   116.38  3.000
 6HD  C    N   C1   123.78  3.000
 6HD  H11  C   H10  107.57  3.000
 6HD  H11  C   H9   107.89  3.000
 6HD  H10  C   H9   108.59  3.000
 6HD  H11  C   N    108.35  3.000
 6HD  H10  C   N    111.67  3.000
 6HD  H9   C   N    112.59  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
 6HD  CONST_01  N3  C8  C7  C5  180.00   0.0  0
 6HD  CONST_02  C2  C8  C7  C5    0.00   0.0  0
 6HD  CONST_03  C2  C3  C4  C5    0.00   0.0  0
 6HD  CONST_04  N1  C2  C3  C4  180.00   0.0  0
 6HD  CONST_05  C8  C2  C3  C4    0.00   0.0  0
 6HD  CONST_06  C8  C7  C5  C4    0.00   0.0  0
 6HD  CONST_07  C1  N1  C2  C3  180.00   0.0  0
 6HD  CONST_08  N3  C8  C2  C3  180.00   0.0  0
 6HD  CONST_09  C7  C8  C2  C3    0.00   0.0  0
 6HD  CONST_10  C7  C5  C4  C3    0.00   0.0  0
 6HD  CONST_11  C1  N3  C8  C7  180.00   0.0  0
 6HD  CONST_12  N1  C2  C8  C7  180.00   0.0  0
 6HD  CONST_13  N1  C1  N3  C8    0.00   0.0  0
 6HD  CONST_14  C1  N1  C2  C8    0.00   0.0  0
 6HD  CONST_15  N3  C1  N1  C2    0.00   0.0  0
 6HD  CONST_16  C1  N3  C8  C2    0.00   0.0  0
 6HD  CONST_17  N3  C8  C2  N1    0.00   0.0  0
 6HD  CONST_18  C8  C7  C5  C6  180.00   0.0  0
 6HD  CONST_19  C3  C4  C5  C6  180.00   0.0  0
 6HD  CONST_20  N   C1  N3  C8  180.00   0.0  0
 6HD  CONST_21  N   C1  N1  C2  180.00   0.0  0
 6HD  CONST_22  H4  C3  C4  C5  180.00   0.0  0
 6HD  CONST_23  H5  C7  C5  C4  180.00   0.0  0
 6HD  CONST_24  H6  N1  C2  C3    0.00   0.0  0
 6HD  CONST_25  H3  C4  C5  C7  180.00   0.0  0
 6HD  CONST_26  C   N   C1  N1    0.00   0.0  0
 6HD  CONST_27  C   N   C1  N3  180.00   0.0  0
 6HD  CONST_28  H8  N   C1  N1  180.00   0.0  0
 6HD  CONST_29  H1  N2  C6  C5  180.00   0.0  0
 6HD  CONST_30  H2  N2  C6  C5    0.00   0.0  0
 6HD  Var_01    C7  C5  C6  O     1.32  30.0  2
 6HD  Var_02    H9  C   N   C1  -61.18  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
 6HD  plan-1  C6  0.020
 6HD  plan-1  C5  0.020
 6HD  plan-1  C4  0.020
 6HD  plan-1  C3  0.020
 6HD  plan-1  C7  0.020
 6HD  plan-1  C8  0.020
 6HD  plan-1  C2  0.020
 6HD  plan-1  N1  0.020
 6HD  plan-1  N3  0.020
 6HD  plan-1  C1  0.020
 6HD  plan-1  N   0.020
 6HD  plan-1  H3  0.020
 6HD  plan-1  H4  0.020
 6HD  plan-1  H5  0.020
 6HD  plan-1  H6  0.020
 6HD  plan-2  O   0.020
 6HD  plan-2  C6  0.020
 6HD  plan-2  N2  0.020
 6HD  plan-2  C5  0.020
 6HD  plan-2  H1  0.020
 6HD  plan-2  H2  0.020
 6HD  plan-3  C1  0.020
 6HD  plan-3  N   0.020
 6HD  plan-3  C   0.020
 6HD  plan-3  H8  0.020

