# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:15:00 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-(1H-benzimidazol-2-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NN=C(N1)c2[nH]c3ccccc3n2
#
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
 0BQ  0BQ  "5-(1H-benzimidazol-2-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one"
  ligand  22  15  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0BQ
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
 0BQ  N3   N  NR15  0  -0.506  17.0787  4.8434   2.0907
 0BQ  C6   C  CR5   0   0.415  18.9013  5.2860   1.1672
 0BQ  C13  C  CR16  0  -0.273  23.4081  6.3324  -2.5183
 0BQ  C15  C  CR16  0  -0.334  21.2235  5.4374  -3.0982
 0BQ  O1   O  O     0  -0.485  17.6185  5.2139   4.3299
 0BQ  C2   C  CR5   0   0.612  17.8786  5.1770   3.1434
 0BQ  N5   N  N     0  -0.246  17.6955  4.9097   0.8957
 0BQ  N7   N  NR15  0  -0.727  19.0694  5.4636   2.5104
 0BQ  C9   C  CR5   0   0.467  19.9111  5.4808   0.1419
 0BQ  N10  N  NR15  0  -0.716  21.1544  5.9738   0.3843
 0BQ  C11  C  CR56  0   0.338  21.8061  6.0188  -0.8169
 0BQ  C12  C  CR16  0  -0.306  23.0849  6.4302  -1.1781
 0BQ  C14  C  CR16  0  -0.265  22.4908  5.8441  -3.4650
 0BQ  C16  C  CR56  0   0.144  20.8755  5.5288  -1.7487
 0BQ  N17  N  N     0  -0.457  19.7059  5.2031  -1.1175
 0BQ  H1   H  HNR5  0   0.432  16.1095  4.5718   2.1456
 0BQ  H3   H  HCR6  0   0.257  20.5182  5.0633  -3.8288
 0BQ  H4   H  HNR5  0   0.438  19.9056  5.7332   3.0065
 0BQ  H5   H  HNR5  0   0.429  21.5429  6.2652   1.2683
 0BQ  H6   H  HCR6  0   0.268  23.7916  6.8058  -0.4504
 0BQ  H7   H  HCR6  0   0.255  22.7890  5.7883  -4.5038
 0BQ  H2   H  HCR6  0   0.258  24.3908  6.6417  -2.8492

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
 0BQ  C14  C15  aromatic  1.380  0.020  1.380
 0BQ  C14  C13  aromatic  1.406  0.020  1.406
 0BQ  C15  C16  aromatic  1.397  0.020  1.397
 0BQ  C13  C12  aromatic  1.382  0.020  1.382
 0BQ  C16  N17  aromatic  1.368  0.020  1.368
 0BQ  C16  C11  aromatic  1.405  0.020  1.405
 0BQ  C12  C11  aromatic  1.391  0.020  1.391
 0BQ  N17  C9   aromatic  1.306  0.020  1.306
 0BQ  C11  N10  aromatic  1.367  0.020  1.367
 0BQ  C9   N10  aromatic  1.359  0.020  1.359
 0BQ  C9   C6   single    1.452  0.020  1.452
 0BQ  N5   C6   double    1.292  0.020  1.292
 0BQ  N5   N3   single    1.346  0.020  1.346
 0BQ  C6   N7   single    1.365  0.020  1.365
 0BQ  N3   C2   single    1.364  0.020  1.364
 0BQ  N7   C2   single    1.379  0.020  1.379
 0BQ  C2   O1   double    1.215  0.020  1.215
 0BQ  N3   H1   single    0.860  0.020  1.020
 0BQ  C13  H2   single    0.930  0.020  1.080
 0BQ  C15  H3   single    0.930  0.020  1.080
 0BQ  N7   H4   single    0.860  0.020  1.020
 0BQ  N10  H5   single    0.860  0.020  1.020
 0BQ  C12  H6   single    0.930  0.020  1.080
 0BQ  C14  H7   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
 0BQ  H1   N3   N5   120.14  3.000
 0BQ  H1   N3   C2   126.01  3.000
 0BQ  N5   N3   C2   113.85  3.000
 0BQ  C9   C6   N7   126.27  3.000
 0BQ  N7   C6   N5   111.07  3.000
 0BQ  C9   C6   N5   122.66  3.000
 0BQ  H2   C13  C14  119.08  3.000
 0BQ  H2   C13  C12  119.25  3.000
 0BQ  C14  C13  C12  121.67  3.000
 0BQ  H3   C15  C16  120.83  3.000
 0BQ  H3   C15  C14  121.38  3.000
 0BQ  C16  C15  C14  117.78  3.000
 0BQ  N7   C2   O1   128.82  3.000
 0BQ  O1   C2   N3   129.47  3.000
 0BQ  N7   C2   N3   101.72  3.000
 0BQ  C6   N5   N3   104.80  3.000
 0BQ  H4   N7   C2   123.07  3.000
 0BQ  H4   N7   C6   128.35  3.000
 0BQ  C2   N7   C6   108.56  3.000
 0BQ  N17  C9   N10  113.13  3.000
 0BQ  N10  C9   C6   123.97  3.000
 0BQ  N17  C9   C6   122.90  3.000
 0BQ  H5   N10  C11  125.23  3.000
 0BQ  H5   N10  C9   127.83  3.000
 0BQ  C11  N10  C9   106.93  3.000
 0BQ  C16  C11  C12  122.67  3.000
 0BQ  C12  C11  N10  132.53  3.000
 0BQ  C16  C11  N10  104.80  3.000
 0BQ  H6   C12  C11  121.91  3.000
 0BQ  H6   C12  C13  121.61  3.000
 0BQ  C11  C12  C13  116.48  3.000
 0BQ  H7   C14  C15  119.53  3.000
 0BQ  H7   C14  C13  118.98  3.000
 0BQ  C15  C14  C13  121.50  3.000
 0BQ  N17  C16  C11  110.07  3.000
 0BQ  C11  C16  C15  119.91  3.000
 0BQ  N17  C16  C15  130.02  3.000
 0BQ  C16  N17  C9   105.07  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
 0BQ  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 0BQ  CONST_02  C16  C11  C12  C13    0.00   0.0  0
 0BQ  CONST_03  N10  C11  C12  C13  180.00   0.0  0
 0BQ  CONST_04  C12  C13  C14  C15    0.00   0.0  0
 0BQ  CONST_05  C9   N17  C16  C15  180.00   0.0  0
 0BQ  CONST_06  C12  C11  C16  C15    0.00   0.0  0
 0BQ  CONST_07  N10  C11  C16  C15  180.00   0.0  0
 0BQ  CONST_08  C11  C16  N17  C9     0.00   0.0  0
 0BQ  CONST_09  C16  C11  N10  C9     0.00   0.0  0
 0BQ  CONST_10  C12  C11  N10  C9   180.00   0.0  0
 0BQ  CONST_11  N17  C16  C11  N10    0.00   0.0  0
 0BQ  CONST_12  C16  N17  C9   N10    0.00   0.0  0
 0BQ  CONST_13  C14  C15  C16  C11    0.00   0.0  0
 0BQ  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 0BQ  CONST_15  N17  C9   N10  C11    0.00   0.0  0
 0BQ  CONST_16  N17  C16  C11  C12  180.00   0.0  0
 0BQ  CONST_17  N17  C16  C15  C14  180.00   0.0  0
 0BQ  CONST_18  C16  N17  C9   C6   180.00   0.0  0
 0BQ  CONST_19  C11  N10  C9   C6   180.00   0.0  0
 0BQ  CONST_20  C9   C6   N5   N3   180.00   0.0  0
 0BQ  CONST_21  N7   C6   N5   N3     0.00   0.0  0
 0BQ  CONST_22  C6   N7   C2   N3     0.00   0.0  0
 0BQ  CONST_23  C2   N3   N5   C6     0.00   0.0  0
 0BQ  CONST_24  C9   C6   N7   C2   180.00   0.0  0
 0BQ  CONST_25  N5   C6   N7   C2     0.00   0.0  0
 0BQ  CONST_26  N7   C2   N3   N5     0.00   0.0  0
 0BQ  CONST_27  O1   C2   N7   C6   180.00   0.0  0
 0BQ  CONST_28  N5   N3   C2   O1   180.00   0.0  0
 0BQ  CONST_29  H5   N10  C9   C6     0.00   0.0  0
 0BQ  CONST_30  H3   C15  C14  C13  180.00   0.0  0
 0BQ  CONST_31  H2   C13  C14  C15  180.00   0.0  0
 0BQ  CONST_32  H6   C12  C11  N10    0.00   0.0  0
 0BQ  CONST_33  H3   C15  C16  C11  180.00   0.0  0
 0BQ  CONST_34  H2   C13  C12  C11  180.00   0.0  0
 0BQ  CONST_35  H7   C14  C13  C12  180.00   0.0  0
 0BQ  CONST_36  H5   N10  C11  C12    0.00   0.0  0
 0BQ  CONST_37  H6   C12  C13  C14  180.00   0.0  0
 0BQ  CONST_38  H7   C14  C15  C16  180.00   0.0  0
 0BQ  CONST_39  H6   C12  C11  C16  180.00   0.0  0
 0BQ  CONST_40  H5   N10  C11  C16  180.00   0.0  0
 0BQ  CONST_41  H3   C15  C16  N17    0.00   0.0  0
 0BQ  CONST_42  H5   N10  C9   N17  180.00   0.0  0
 0BQ  CONST_43  H4   N7   C2   N3   180.00   0.0  0
 0BQ  CONST_44  H1   N3   N5   C6   180.00   0.0  0
 0BQ  CONST_45  H4   N7   C6   N5   180.00   0.0  0
 0BQ  CONST_46  H1   N3   C2   N7   180.00   0.0  0
 0BQ  CONST_47  H4   N7   C6   C9     0.00   0.0  0
 0BQ  CONST_48  H1   N3   C2   O1     0.00   0.0  0
 0BQ  CONST_49  H4   N7   C2   O1     0.00   0.0  0
 0BQ  Var_01    N17  C9   C6   N5    -4.86  30.0  1
 0BQ  Var_02    N10  C9   C6   N5   174.72  30.0  1
 0BQ  Var_03    N17  C9   C6   N7   175.12  30.0  1
 0BQ  Var_04    N10  C9   C6   N7    -5.30  30.0  1

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
 0BQ  plan-1  C6   0.020
 0BQ  plan-1  C13  0.020
 0BQ  plan-1  C15  0.020
 0BQ  plan-1  C9   0.020
 0BQ  plan-1  N10  0.020
 0BQ  plan-1  C11  0.020
 0BQ  plan-1  C12  0.020
 0BQ  plan-1  C14  0.020
 0BQ  plan-1  C16  0.020
 0BQ  plan-1  N17  0.020
 0BQ  plan-1  H3   0.020
 0BQ  plan-1  H5   0.020
 0BQ  plan-1  H6   0.020
 0BQ  plan-1  H7   0.020
 0BQ  plan-1  H2   0.020
 0BQ  plan-2  N3   0.020
 0BQ  plan-2  C6   0.020
 0BQ  plan-2  O1   0.020
 0BQ  plan-2  C2   0.020
 0BQ  plan-2  N5   0.020
 0BQ  plan-2  N7   0.020
 0BQ  plan-2  C9   0.020
 0BQ  plan-2  H1   0.020
 0BQ  plan-2  H4   0.020

