# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 17:49:14 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: N-methyl-1H-benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[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
 1M2  1M2  N-methyl-1H-benzimidazol-2-amine  ligand  20  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1M2
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
 1M2  C01  C  CH3   0  -0.545  -3.6835   0.6528   0.0276
 1M2  N02  N  NH1   0  -0.674  -2.7836  -0.4596  -0.1622
 1M2  C03  C  CR5   0   0.666  -1.4454  -0.3296  -0.1024
 1M2  N04  N  NR15  0  -0.737  -0.8379   0.8909  -0.1071
 1M2  C05  C  CR56  0   0.335   0.5205   0.6663  -0.0748
 1M2  C06  C  CR16  0  -0.315   1.6093   1.5193  -0.0639
 1M2  C07  C  CR16  0  -0.291   2.8696   0.9314  -0.0251
 1M2  C08  C  CR16  0  -0.272   3.0178  -0.4574   0.0010
 1M2  C09  C  CR16  0  -0.353   1.9160  -1.3042  -0.0100
 1M2  C10  C  CR56  0   0.161   0.6464  -0.7352  -0.0477
 1M2  N11  N  N     0  -0.538  -0.5929  -1.3289  -0.0641
 1M2  H1   H  HCH3  0   0.243  -3.5279   1.4181  -0.7341
 1M2  H2   H  HCH3  0   0.267  -4.7022   0.2918  -0.0785
 1M2  H3   H  HCH3  0   0.237  -3.5887   1.1195   1.0123
 1M2  H4   H  HNH1  0   0.400  -3.1318  -1.3823   0.0368
 1M2  H5   H  HNR5  0   0.421  -1.2919   1.7898  -0.1316
 1M2  H6   H  HCR6  0   0.259   1.4911   2.5951  -0.0838
 1M2  H7   H  HCR6  0   0.247   3.7477   1.5637  -0.0143
 1M2  H8   H  HCR6  0   0.245   4.0133  -0.8821   0.0307
 1M2  H9   H  HCR6  0   0.244   2.0396  -2.3797   0.0097

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
 1M2  C01  N02  single    1.443  0.020  1.443
 1M2  N02  C03  single    1.346  0.020  1.346
 1M2  C03  N04  aromatic  1.363  0.020  1.363
 1M2  C03  N11  aromatic  1.314  0.020  1.314
 1M2  N04  C05  aromatic  1.377  0.020  1.377
 1M2  N11  C10  aromatic  1.374  0.020  1.374
 1M2  C05  C10  aromatic  1.407  0.020  1.407
 1M2  C05  C06  aromatic  1.383  0.020  1.383
 1M2  C10  C09  aromatic  1.392  0.020  1.392
 1M2  C06  C07  aromatic  1.391  0.020  1.391
 1M2  C09  C08  aromatic  1.390  0.020  1.390
 1M2  C07  C08  aromatic  1.397  0.020  1.397
 1M2  C01  H1   single    0.970  0.020  1.090
 1M2  C01  H2   single    0.970  0.020  1.090
 1M2  C01  H3   single    0.970  0.020  1.090
 1M2  N02  H4   single    0.890  0.020  1.040
 1M2  N04  H5   single    0.860  0.020  1.020
 1M2  C06  H6   single    0.930  0.020  1.080
 1M2  C07  H7   single    0.930  0.020  1.080
 1M2  C08  H8   single    0.930  0.020  1.080
 1M2  C09  H9   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
 1M2  H3   C01  H2   108.13  3.000
 1M2  H3   C01  H1   108.48  3.000
 1M2  H2   C01  H1   107.38  3.000
 1M2  H3   C01  N02  113.16  3.000
 1M2  H2   C01  N02  108.41  3.000
 1M2  H1   C01  N02  111.09  3.000
 1M2  H4   N02  C03  115.08  3.000
 1M2  H4   N02  C01  117.71  3.000
 1M2  C03  N02  C01  122.66  3.000
 1M2  N11  C03  N04  113.07  3.000
 1M2  N11  C03  N02  124.96  3.000
 1M2  N04  C03  N02  121.96  3.000
 1M2  H5   N04  C05  126.20  3.000
 1M2  H5   N04  C03  126.74  3.000
 1M2  C05  N04  C03  107.06  3.000
 1M2  C10  C05  C06  122.93  3.000
 1M2  C06  C05  N04  132.53  3.000
 1M2  C10  C05  N04  104.54  3.000
 1M2  H6   C06  C07  121.29  3.000
 1M2  H6   C06  C05  121.80  3.000
 1M2  C07  C06  C05  116.91  3.000
 1M2  H7   C07  C08  119.65  3.000
 1M2  H7   C07  C06  119.24  3.000
 1M2  C08  C07  C06  121.12  3.000
 1M2  H8   C08  C09  119.35  3.000
 1M2  H8   C08  C07  119.21  3.000
 1M2  C09  C08  C07  121.43  3.000
 1M2  H9   C09  C10  120.71  3.000
 1M2  H9   C09  C08  120.97  3.000
 1M2  C10  C09  C08  118.32  3.000
 1M2  N11  C10  C09  130.27  3.000
 1M2  C09  C10  C05  119.29  3.000
 1M2  N11  C10  C05  110.44  3.000
 1M2  C10  N11  C03  104.88  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
 1M2  CONST_01  C10  C05  N04  C03    0.00   0.0  0
 1M2  CONST_02  C06  C05  N04  C03  180.00   0.0  0
 1M2  CONST_03  C05  C10  N11  C03    0.00   0.0  0
 1M2  CONST_04  C09  C10  N11  C03  180.00   0.0  0
 1M2  CONST_05  C10  N11  C03  N04    0.00   0.0  0
 1M2  CONST_06  N11  C10  C05  N04    0.00   0.0  0
 1M2  CONST_07  C09  C10  C05  N04  180.00   0.0  0
 1M2  CONST_08  C07  C06  C05  N04  180.00   0.0  0
 1M2  CONST_09  N11  C03  N04  C05    0.00   0.0  0
 1M2  CONST_10  C08  C09  C10  C05    0.00   0.0  0
 1M2  CONST_11  C08  C07  C06  C05    0.00   0.0  0
 1M2  CONST_12  N11  C10  C05  C06  180.00   0.0  0
 1M2  CONST_13  C09  C10  C05  C06    0.00   0.0  0
 1M2  CONST_14  C09  C08  C07  C06    0.00   0.0  0
 1M2  CONST_15  C10  C05  C06  C07    0.00   0.0  0
 1M2  CONST_16  C10  C09  C08  C07    0.00   0.0  0
 1M2  CONST_17  N11  C10  C09  C08  180.00   0.0  0
 1M2  CONST_18  C05  N04  C03  N02  180.00   0.0  0
 1M2  CONST_19  C10  N11  C03  N02  180.00   0.0  0
 1M2  CONST_20  H6   C06  C05  N04    0.00   0.0  0
 1M2  CONST_21  H9   C09  C10  C05  180.00   0.0  0
 1M2  CONST_22  H7   C07  C06  C05  180.00   0.0  0
 1M2  CONST_23  H5   N04  C05  C06    0.00   0.0  0
 1M2  CONST_24  H8   C08  C07  C06  180.00   0.0  0
 1M2  CONST_25  N04  C03  N02  C01    0.00   0.0  0
 1M2  CONST_26  N11  C03  N02  C01  180.00   0.0  0
 1M2  CONST_27  H4   N02  C03  N04  180.00   0.0  0
 1M2  Var_01    H1   C01  N02  C03   61.67  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
 1M2  plan-1  N02  0.020
 1M2  plan-1  C03  0.020
 1M2  plan-1  N04  0.020
 1M2  plan-1  C05  0.020
 1M2  plan-1  C06  0.020
 1M2  plan-1  C07  0.020
 1M2  plan-1  C08  0.020
 1M2  plan-1  C09  0.020
 1M2  plan-1  C10  0.020
 1M2  plan-1  N11  0.020
 1M2  plan-1  H5   0.020
 1M2  plan-1  H6   0.020
 1M2  plan-1  H7   0.020
 1M2  plan-1  H8   0.020
 1M2  plan-1  H9   0.020
 1M2  plan-2  C01  0.020
 1M2  plan-2  N02  0.020
 1M2  plan-2  C03  0.020
 1M2  plan-2  H4   0.020

