# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:49:08 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(ccc12)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
 V1T  V1T  1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide  ligand  26  15  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V1T
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
 V1T  C01   C  CH3   0  -0.535  -2.9154   2.1533  -0.0266
 V1T  N05   N  NR5   0  -0.582  -2.1185   0.9534  -0.0079
 V1T  C06   C  CR56  0   0.342  -0.7487   0.9087  -0.0141
 V1T  C07   C  CR16  0  -0.302   0.2061   1.9058  -0.0349
 V1T  C09   C  CR16  0  -0.304   1.5419   1.5167  -0.0356
 V1T  C11   C  CR6   0  -0.062   1.9189   0.1722  -0.0173
 V1T  C12   C  CR16  0  -0.348   0.9385  -0.8284   0.0006
 V1T  C14   C  CR56  0   0.364  -0.3807  -0.4412   0.0051
 V1T  N15   N  NR5   0  -0.585  -1.5459  -1.1738   0.0272
 V1T  C16   C  CH3   0  -0.535  -1.6243  -2.6121   0.0437
 V1T  C20   C  CR5   0   0.661  -2.6295  -0.3286   0.0147
 V1T  O21   O  O     0  -0.495  -3.8048  -0.6426   0.0232
 V1T  C22   C  C     0   0.508   3.3423  -0.2873  -0.0198
 V1T  N23   N  NH2   0  -0.830   4.2992   0.6519   0.0183
 V1T  O26   O  O     0  -0.487   3.6134  -1.4823  -0.0544
 V1T  H011  H  HCH3  0   0.258  -2.7064   2.7404  -0.9202
 V1T  H012  H  HCH3  0   0.270  -3.9665   1.8811  -0.0280
 V1T  H013  H  HCH3  0   0.258  -2.7153   2.7639   0.8533
 V1T  H07   H  HCR6  0   0.280  -0.0620   2.9536  -0.0506
 V1T  H09   H  HCR6  0   0.250   2.2795   2.3069  -0.0550
 V1T  H12   H  HCR6  0   0.276   1.2203  -1.8725   0.0100
 V1T  H161  H  HCH3  0   0.257  -1.0452  -3.0133   0.8746
 V1T  H162  H  HCH3  0   0.269  -2.6608  -2.9114   0.1673
 V1T  H163  H  HCH3  0   0.257  -1.2463  -3.0341  -0.8874
 V1T  H231  H  HNH2  0   0.414   4.1179   1.6376   0.0640
 V1T  H232  H  HNH2  0   0.404   5.2656   0.3703   0.0194

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
 V1T  C01  N05   single    1.441  0.020  1.441
 V1T  N05  C06   single    1.370  0.020  1.370
 V1T  N05  C20   single    1.380  0.020  1.380
 V1T  C06  C07   aromatic  1.381  0.020  1.381
 V1T  C06  C14   aromatic  1.399  0.020  1.399
 V1T  C07  C09   aromatic  1.391  0.020  1.391
 V1T  C09  C11   aromatic  1.397  0.020  1.397
 V1T  C11  C12   aromatic  1.401  0.020  1.401
 V1T  C11  C22   single    1.496  0.020  1.496
 V1T  C12  C14   aromatic  1.375  0.020  1.375
 V1T  C14  N15   single    1.377  0.020  1.377
 V1T  N15  C16   single    1.441  0.020  1.441
 V1T  N15  C20   single    1.374  0.020  1.374
 V1T  C20  O21   double    1.217  0.020  1.217
 V1T  C22  N23   single    1.341  0.020  1.341
 V1T  C22  O26   double    1.226  0.020  1.226
 V1T  C01  H011  single    0.970  0.020  1.090
 V1T  C01  H012  single    0.970  0.020  1.090
 V1T  C01  H013  single    0.970  0.020  1.090
 V1T  C07  H07   single    0.930  0.020  1.080
 V1T  C09  H09   single    0.930  0.020  1.080
 V1T  C12  H12   single    0.930  0.020  1.080
 V1T  C16  H161  single    0.970  0.020  1.090
 V1T  C16  H162  single    0.970  0.020  1.090
 V1T  C16  H163  single    0.970  0.020  1.090
 V1T  N23  H231  single    0.860  0.020  1.020
 V1T  N23  H232  single    0.860  0.020  1.020

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
 V1T  H013  C01  H012  108.62  3.000
 V1T  H013  C01  H011  108.98  3.000
 V1T  H012  C01  H011  108.65  3.000
 V1T  H013  C01  N05   110.78  3.000
 V1T  H012  C01  N05   109.07  3.000
 V1T  H011  C01  N05   110.70  3.000
 V1T  C20   N05  C06   109.86  3.000
 V1T  C20   N05  C01   124.68  3.000
 V1T  C06   N05  C01   125.45  3.000
 V1T  C14   C06  C07   121.00  3.000
 V1T  C14   C06  N05   107.11  3.000
 V1T  C07   C06  N05   131.89  3.000
 V1T  H07   C07  C09   120.59  3.000
 V1T  H07   C07  C06   121.89  3.000
 V1T  C09   C07  C06   117.52  3.000
 V1T  H09   C09  C11   121.32  3.000
 V1T  H09   C09  C07   116.79  3.000
 V1T  C11   C09  C07   121.89  3.000
 V1T  C22   C11  C12   116.52  3.000
 V1T  C22   C11  C09   123.55  3.000
 V1T  C12   C11  C09   119.93  3.000
 V1T  H12   C12  C14   121.45  3.000
 V1T  H12   C12  C11   120.49  3.000
 V1T  C14   C12  C11   118.06  3.000
 V1T  N15   C14  C12   131.48  3.000
 V1T  N15   C14  C06   106.92  3.000
 V1T  C12   C14  C06   121.60  3.000
 V1T  C20   N15  C16   124.84  3.000
 V1T  C20   N15  C14   109.87  3.000
 V1T  C16   N15  C14   125.28  3.000
 V1T  H163  C16  H162  108.75  3.000
 V1T  H163  C16  H161  108.95  3.000
 V1T  H162  C16  H161  108.61  3.000
 V1T  H163  C16  N15   110.97  3.000
 V1T  H162  C16  N15   109.17  3.000
 V1T  H161  C16  N15   110.34  3.000
 V1T  O21   C20  N15   127.08  3.000
 V1T  O21   C20  N05   126.69  3.000
 V1T  N15   C20  N05   106.23  3.000
 V1T  O26   C22  N23   121.71  3.000
 V1T  O26   C22  C11   120.66  3.000
 V1T  N23   C22  C11   117.63  3.000
 V1T  H232  N23  H231  116.63  3.000
 V1T  H232  N23  C22   119.28  3.000
 V1T  H231  N23  C22   124.08  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
 V1T  CONST_01  C11   C09  C07  C06    0.00   0.0  0
 V1T  CONST_02  C11   C12  C14  C06    0.00   0.0  0
 V1T  CONST_03  C12   C14  C06  C07    0.00   0.0  0
 V1T  CONST_04  C12   C11  C09  C07    0.00   0.0  0
 V1T  CONST_05  C14   C06  C07  C09    0.00   0.0  0
 V1T  CONST_06  C14   C12  C11  C09    0.00   0.0  0
 V1T  CONST_07  N15   C14  C06  N05    0.00   0.0  0
 V1T  CONST_08  C14   N15  C20  N05    0.00   0.0  0
 V1T  CONST_09  N15   C20  N05  C06    0.00   0.0  0
 V1T  CONST_10  C20   N15  C14  C06    0.00   0.0  0
 V1T  CONST_11  C20   N05  C06  C14    0.00   0.0  0
 V1T  CONST_12  C22   C11  C09  C07  180.00   0.0  0
 V1T  CONST_13  C22   C11  C12  C14  180.00   0.0  0
 V1T  CONST_14  C14   C06  N05  C01  180.00   0.0  0
 V1T  CONST_15  N15   C20  N05  C01  180.00   0.0  0
 V1T  CONST_16  C16   N15  C20  N05  180.00   0.0  0
 V1T  CONST_17  O21   C20  N05  C06  180.00   0.0  0
 V1T  CONST_18  C16   N15  C14  C06  180.00   0.0  0
 V1T  CONST_19  O21   C20  N15  C14  180.00   0.0  0
 V1T  CONST_20  H07   C07  C06  N05    0.00   0.0  0
 V1T  CONST_21  H09   C09  C07  C06  180.00   0.0  0
 V1T  CONST_22  H12   C12  C14  C06  180.00   0.0  0
 V1T  CONST_23  O21   C20  N05  C01    0.00   0.0  0
 V1T  CONST_24  O21   C20  N15  C16    0.00   0.0  0
 V1T  CONST_25  H231  N23  C22  C11    0.00   0.0  0
 V1T  CONST_26  H232  N23  C22  C11  180.00   0.0  0
 V1T  Var_01    N23   C22  C11  C09    2.85  30.0  2
 V1T  Var_02    H011  C01  N05  C06   59.84  30.0  3
 V1T  Var_03    H161  C16  N15  C14   54.69  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
 V1T  plan-1  C01   0.020
 V1T  plan-1  N05   0.020
 V1T  plan-1  C06   0.020
 V1T  plan-1  C07   0.020
 V1T  plan-1  C09   0.020
 V1T  plan-1  C11   0.020
 V1T  plan-1  C12   0.020
 V1T  plan-1  C14   0.020
 V1T  plan-1  N15   0.020
 V1T  plan-1  C16   0.020
 V1T  plan-1  C20   0.020
 V1T  plan-1  O21   0.020
 V1T  plan-1  C22   0.020
 V1T  plan-1  H07   0.020
 V1T  plan-1  H09   0.020
 V1T  plan-1  H12   0.020
 V1T  plan-2  C11   0.020
 V1T  plan-2  C22   0.020
 V1T  plan-2  N23   0.020
 V1T  plan-2  O26   0.020
 V1T  plan-2  H231  0.020
 V1T  plan-2  H232  0.020

