# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 06:31:03 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(CN)ccc12
#
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
 8W9  8W9  5-(aminomethyl)-1,3-dimethyl-benzimidazol-2-one  ligand  27  14  .  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_8W9
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
 8W9  C4   C  CR56  0   0.353  -0.0624  -0.3874   0.0425
 8W9  C5   C  CR56  0   0.318  -0.4638   0.9514   0.0776
 8W9  C6   C  CR16  0  -0.307   0.4639   1.9672   0.1779
 8W9  C11  C  CR6   0   0.069   2.2188   0.2706   0.2177
 8W9  C8   C  CR16  0  -0.354   1.2669  -0.7482   0.1097
 8W9  C12  C  CR16  0  -0.332   1.8090   1.6021   0.2441
 8W9  N2   N  NR5   0  -0.583  -1.2078  -1.1454  -0.0706
 8W9  N3   N  NR5   0  -0.580  -1.8394   0.9619  -0.0108
 8W9  C1   C  CR5   0   0.654  -2.3121  -0.3262  -0.0993
 8W9  O7   O  O     0  -0.506  -3.4774  -0.6734  -0.1870
 8W9  C15  C  CH2   0  -0.339   3.6830  -0.0750   0.3365
 8W9  N14  N  NH2   0  -0.793   4.0457  -1.1987  -0.5102
 8W9  H1   H  HCR6  0   0.268   0.1707   3.0088   0.1968
 8W9  H2   H  HCR6  0   0.261   1.5786  -1.7841   0.0708
 8W9  H3   H  HCH3  0   0.253  -0.9259  -3.0202   0.8217
 8W9  H4   H  HCH3  0   0.267  -2.2704  -2.9017  -0.3219
 8W9  H5   H  HCH3  0   0.254  -0.6101  -2.9549  -0.9212
 8W9  H6   H  HCH3  0   0.253  -2.4519   2.7639  -0.8825
 8W9  H7   H  HCH3  0   0.267  -3.7090   1.8425  -0.0508
 8W9  H8   H  HCH3  0   0.253  -2.5035   2.7281   0.8890
 8W9  H9   H  HCR6  0   0.247   2.5570   2.3824   0.3144
 8W9  H10  H  HCH2  0   0.214   4.2731   0.8321   0.1497
 8W9  H11  H  HCH2  0   0.237   3.8951  -0.3593   1.3715
 8W9  H12  H  HNH2  0   0.343   4.0279  -0.9110  -1.4806
 8W9  H13  H  HNH2  0   0.353   5.0005  -1.4710  -0.3159
 8W9  C9   C  CH3   0  -0.535  -1.2515  -2.5832  -0.1226
 8W9  C10  C  CH3   0  -0.534  -2.6653   2.1403  -0.0143

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
 8W9  C12  C6   aromatic  1.395  0.020  1.395
 8W9  C12  C11  aromatic  1.393  0.020  1.393
 8W9  C6   C5   aromatic  1.379  0.020  1.379
 8W9  C15  C11  single    1.509  0.020  1.509
 8W9  C15  N14  single    1.453  0.020  1.453
 8W9  C10  N3   single    1.439  0.020  1.439
 8W9  C11  C8   aromatic  1.398  0.020  1.398
 8W9  C5   N3   single    1.378  0.020  1.378
 8W9  C5   C4   aromatic  1.398  0.020  1.398
 8W9  N3   C1   single    1.375  0.020  1.375
 8W9  C8   C4   aromatic  1.379  0.020  1.379
 8W9  C4   N2   single    1.378  0.020  1.378
 8W9  C1   N2   single    1.375  0.020  1.375
 8W9  C1   O7   double    1.219  0.020  1.219
 8W9  N2   C9   single    1.439  0.020  1.439
 8W9  C6   H1   single    0.930  0.020  1.080
 8W9  C8   H2   single    0.930  0.020  1.080
 8W9  C9   H3   single    0.970  0.020  1.090
 8W9  C9   H4   single    0.970  0.020  1.090
 8W9  C9   H5   single    0.970  0.020  1.090
 8W9  C10  H6   single    0.970  0.020  1.090
 8W9  C10  H7   single    0.970  0.020  1.090
 8W9  C10  H8   single    0.970  0.020  1.090
 8W9  C12  H9   single    0.930  0.020  1.080
 8W9  C15  H10  single    0.970  0.020  1.090
 8W9  C15  H11  single    0.970  0.020  1.090
 8W9  N14  H12  single    0.890  0.020  1.040
 8W9  N14  H13  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
 8W9  N2   C4   C8   131.39  3.000
 8W9  N2   C4   C5   106.87  3.000
 8W9  C8   C4   C5   121.74  3.000
 8W9  N3   C5   C6   132.09  3.000
 8W9  N3   C5   C4   106.99  3.000
 8W9  C6   C5   C4   120.92  3.000
 8W9  H1   C6   C12  120.80  3.000
 8W9  H1   C6   C5   121.86  3.000
 8W9  C12  C6   C5   117.34  3.000
 8W9  C15  C11  C12  120.18  3.000
 8W9  C15  C11  C8   119.98  3.000
 8W9  C12  C11  C8   119.83  3.000
 8W9  H2   C8   C11  120.26  3.000
 8W9  H2   C8   C4   121.75  3.000
 8W9  C11  C8   C4   117.99  3.000
 8W9  H9   C12  C11  119.11  3.000
 8W9  H9   C12  C6   118.71  3.000
 8W9  C11  C12  C6   122.18  3.000
 8W9  C1   N2   C9   124.74  3.000
 8W9  C9   N2   C4   125.29  3.000
 8W9  C1   N2   C4   109.96  3.000
 8W9  C1   N3   C10  124.73  3.000
 8W9  C1   N3   C5   109.88  3.000
 8W9  C10  N3   C5   125.39  3.000
 8W9  O7   C1   N3   126.88  3.000
 8W9  O7   C1   N2   126.83  3.000
 8W9  N3   C1   N2   106.30  3.000
 8W9  H11  C15  H10  105.75  3.000
 8W9  H11  C15  N14  107.57  3.000
 8W9  H10  C15  N14  113.93  3.000
 8W9  H11  C15  C11  108.79  3.000
 8W9  H10  C15  C11  108.59  3.000
 8W9  N14  C15  C11  111.93  3.000
 8W9  H13  N14  H12  106.09  3.000
 8W9  H13  N14  C15  109.38  3.000
 8W9  H12  N14  C15  109.53  3.000
 8W9  H5   C9   H4   108.53  3.000
 8W9  H5   C9   H3   108.80  3.000
 8W9  H4   C9   H3   108.76  3.000
 8W9  H5   C9   N2   110.44  3.000
 8W9  H4   C9   N2   109.15  3.000
 8W9  H3   C9   N2   111.10  3.000
 8W9  H8   C10  H7   108.57  3.000
 8W9  H8   C10  H6   108.82  3.000
 8W9  H7   C10  H6   108.56  3.000
 8W9  H8   C10  N3   110.77  3.000
 8W9  H7   C10  N3   109.10  3.000
 8W9  H6   C10  N3   110.98  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
 8W9  CONST_01  C12  C6   C5   C4     0.00   0.0  0
 8W9  CONST_02  C12  C11  C8   C4     0.00   0.0  0
 8W9  CONST_03  C11  C12  C6   C5     0.00   0.0  0
 8W9  CONST_04  C11  C8   C4   C5     0.00   0.0  0
 8W9  CONST_05  C8   C11  C12  C6     0.00   0.0  0
 8W9  CONST_06  C8   C4   C5   C6     0.00   0.0  0
 8W9  CONST_07  C1   N3   C5   C4     0.00   0.0  0
 8W9  CONST_08  N3   C1   N2   C4     0.00   0.0  0
 8W9  CONST_09  N2   C1   N3   C5     0.00   0.0  0
 8W9  CONST_10  C1   N2   C4   C5     0.00   0.0  0
 8W9  CONST_11  N3   C5   C4   N2     0.00   0.0  0
 8W9  CONST_12  C15  C11  C8   C4   180.00   0.0  0
 8W9  CONST_13  C15  C11  C12  C6   180.00   0.0  0
 8W9  CONST_14  C10  N3   C5   C4   180.00   0.0  0
 8W9  CONST_15  O7   C1   N2   C4   180.00   0.0  0
 8W9  CONST_16  O7   C1   N3   C5   180.00   0.0  0
 8W9  CONST_17  C9   N2   C4   C5   180.00   0.0  0
 8W9  CONST_18  N3   C1   N2   C9   180.00   0.0  0
 8W9  CONST_19  N2   C1   N3   C10  180.00   0.0  0
 8W9  CONST_20  H1   C6   C5   C4   180.00   0.0  0
 8W9  CONST_21  H9   C12  C6   C5   180.00   0.0  0
 8W9  CONST_22  H2   C8   C4   C5   180.00   0.0  0
 8W9  CONST_23  O7   C1   N2   C9     0.00   0.0  0
 8W9  CONST_24  O7   C1   N3   C10    0.00   0.0  0
 8W9  Var_01    N14  C15  C11  C8    38.92  30.0  2
 8W9  Var_02    H3   C9   N2   C4    66.24  30.0  3
 8W9  Var_03    H6   C10  N3   C5    62.86  30.0  3
 8W9  Var_04    H12  N14  C15  C11   71.15  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
 8W9  plan-1  C4   0.020
 8W9  plan-1  C5   0.020
 8W9  plan-1  C6   0.020
 8W9  plan-1  C11  0.020
 8W9  plan-1  C8   0.020
 8W9  plan-1  C12  0.020
 8W9  plan-1  N2   0.020
 8W9  plan-1  N3   0.020
 8W9  plan-1  C1   0.020
 8W9  plan-1  O7   0.020
 8W9  plan-1  C15  0.020
 8W9  plan-1  H1   0.020
 8W9  plan-1  H2   0.020
 8W9  plan-1  H9   0.020
 8W9  plan-1  C9   0.020
 8W9  plan-1  C10  0.020

