# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:21:44 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(4-hydroxyphenyl)-1H-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2[nH]c(nc12)c3ccc(O)cc3
#
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
 NU3  NU3  2-(4-hydroxyphenyl)-1H-benzimidazole-4-carboxamide  ligand  30  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NU3
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
 NU3  C    C  C     0   0.463  -3.2329   1.7325   0.2727
 NU3  N    N  NH2   0  -0.802  -4.2734   2.1848  -0.4463
 NU3  O    O  O     0  -0.475  -2.5544   2.4513   0.9913
 NU3  C1   C  CR6   0  -0.147  -2.9679   0.2687   0.1512
 NU3  N1   N  NR15  0  -0.736  -0.0827  -1.7543   0.0264
 NU3  O1   O  OH1   0  -0.621   5.9606   0.5375   0.0195
 NU3  C2   C  CR16  0  -0.297  -4.0027  -0.6571   0.1012
 NU3  N2   N  N     0  -0.468  -0.4572   0.4285   0.1437
 NU3  C3   C  CR16  0  -0.273  -3.7622  -2.0346   0.0417
 NU3  C4   C  CR16  0  -0.309  -2.4746  -2.5411   0.0154
 NU3  C5   C  CR56  0   0.344  -1.4423  -1.6153   0.0563
 NU3  C6   C  CR5   0   0.489   0.4585  -0.5069   0.0778
 NU3  C7   C  CR6   0  -0.012   1.8933  -0.2510   0.0600
 NU3  C8   C  CR16  0  -0.275   2.3533   1.0607   0.1859
 NU3  C9   C  CR16  0  -0.366   3.7044   1.3484   0.1735
 NU3  C10  C  CR6   0   0.357   4.6362   0.3198   0.0343
 NU3  C11  C  CR16  0  -0.322   4.1906  -0.9949  -0.0956
 NU3  C12  C  CR16  0  -0.287   2.8364  -1.2706  -0.0823
 NU3  C13  C  CR56  0   0.163  -1.6568  -0.2268   0.1364
 NU3  HN   H  HNH2  0   0.403  -4.5263   3.1589  -0.4104
 NU3  HNA  H  HNH2  0   0.410  -4.7408   1.6107  -1.1260
 NU3  HN1  H  HNR5  0   0.424   0.4134  -2.6292  -0.0303
 NU3  HO1  H  HOH1  0   0.479   6.1510   1.4773   0.1207
 NU3  H2   H  HCR6  0   0.261  -5.0297  -0.3153   0.1332
 NU3  H3   H  HCR6  0   0.262  -4.6023  -2.7153   0.0185
 NU3  H4   H  HCR6  0   0.272  -2.2869  -3.6055  -0.0353
 NU3  H8   H  HCR6  0   0.264   1.6401   1.8663   0.2959
 NU3  H9   H  HCR6  0   0.278   4.0350   2.3756   0.2745
 NU3  H11  H  HCR6  0   0.273   4.9078  -1.7978  -0.2065
 NU3  H12  H  HCR6  0   0.248   2.5325  -2.3040  -0.1897

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
 NU3  C    N    single    1.343  0.020  1.343
 NU3  C    O    double    1.222  0.020  1.222
 NU3  C    C1   single    1.492  0.020  1.492
 NU3  C1   C2   aromatic  1.389  0.020  1.389
 NU3  C1   C13  aromatic  1.402  0.020  1.402
 NU3  N1   C5   aromatic  1.367  0.020  1.367
 NU3  N1   C6   aromatic  1.361  0.020  1.361
 NU3  O1   C10  single    1.342  0.020  1.342
 NU3  C2   C3   aromatic  1.400  0.020  1.400
 NU3  N2   C6   aromatic  1.311  0.020  1.311
 NU3  N2   C13  aromatic  1.367  0.020  1.367
 NU3  C3   C4   aromatic  1.384  0.020  1.384
 NU3  C4   C5   aromatic  1.387  0.020  1.387
 NU3  C5   C13  aromatic  1.407  0.020  1.407
 NU3  C6   C7   single    1.458  0.020  1.458
 NU3  C7   C8   aromatic  1.396  0.020  1.396
 NU3  C7   C12  aromatic  1.396  0.020  1.396
 NU3  C8   C9   aromatic  1.381  0.020  1.381
 NU3  C9   C10  aromatic  1.395  0.020  1.395
 NU3  C10  C11  aromatic  1.394  0.020  1.394
 NU3  C11  C12  aromatic  1.382  0.020  1.382
 NU3  N    HN   single    0.860  0.020  1.020
 NU3  N    HNA  single    0.860  0.020  1.020
 NU3  N1   HN1  single    0.860  0.020  1.020
 NU3  O1   HO1  single    0.850  0.020  0.980
 NU3  C2   H2   single    0.930  0.020  1.080
 NU3  C3   H3   single    0.930  0.020  1.080
 NU3  C4   H4   single    0.930  0.020  1.080
 NU3  C8   H8   single    0.930  0.020  1.080
 NU3  C9   H9   single    0.930  0.020  1.080
 NU3  C11  H11  single    0.930  0.020  1.080
 NU3  C12  H12  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
 NU3  C1   C    O    121.75  3.000
 NU3  C1   C    N    115.10  3.000
 NU3  O    C    N    123.14  3.000
 NU3  HNA  N    HN   117.38  3.000
 NU3  HNA  N    C    122.00  3.000
 NU3  HN   N    C    120.08  3.000
 NU3  C13  C1   C2   117.43  3.000
 NU3  C13  C1   C    120.91  3.000
 NU3  C2   C1   C    121.62  3.000
 NU3  HN1  N1   C6   127.05  3.000
 NU3  HN1  N1   C5   125.40  3.000
 NU3  C6   N1   C5   107.55  3.000
 NU3  HO1  O1   C10  110.60  3.000
 NU3  H2   C2   C3   118.35  3.000
 NU3  H2   C2   C1   119.66  3.000
 NU3  C3   C2   C1   121.97  3.000
 NU3  C13  N2   C6   105.71  3.000
 NU3  H3   C3   C4   119.47  3.000
 NU3  H3   C3   C2   119.14  3.000
 NU3  C4   C3   C2   121.39  3.000
 NU3  H4   C4   C5   121.93  3.000
 NU3  H4   C4   C3   121.49  3.000
 NU3  C5   C4   C3   116.58  3.000
 NU3  C13  C5   C4   123.14  3.000
 NU3  C13  C5   N1   104.67  3.000
 NU3  C4   C5   N1   132.19  3.000
 NU3  C7   C6   N2   124.27  3.000
 NU3  C7   C6   N1   123.50  3.000
 NU3  N2   C6   N1   112.23  3.000
 NU3  C12  C7   C8   118.22  3.000
 NU3  C12  C7   C6   122.54  3.000
 NU3  C8   C7   C6   119.23  3.000
 NU3  H8   C8   C9   119.39  3.000
 NU3  H8   C8   C7   119.46  3.000
 NU3  C9   C8   C7   121.15  3.000
 NU3  H9   C9   C10  120.30  3.000
 NU3  H9   C9   C8   119.66  3.000
 NU3  C10  C9   C8   120.04  3.000
 NU3  C11  C10  C9   119.41  3.000
 NU3  C11  C10  O1   117.86  3.000
 NU3  C9   C10  O1   122.72  3.000
 NU3  H11  C11  C12  120.15  3.000
 NU3  H11  C11  C10  119.82  3.000
 NU3  C12  C11  C10  120.03  3.000
 NU3  H12  C12  C11  117.68  3.000
 NU3  H12  C12  C7   121.18  3.000
 NU3  C11  C12  C7   121.14  3.000
 NU3  C5   C13  N2   109.85  3.000
 NU3  C5   C13  C1   119.47  3.000
 NU3  N2   C13  C1   130.64  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
 NU3  CONST_01  C4   C3   C2   C1    0.00   0.0  0
 NU3  CONST_02  C6   N2   C13  C1  180.00   0.0  0
 NU3  CONST_03  N1   C5   C13  C1  180.00   0.0  0
 NU3  CONST_04  C4   C5   C13  C1    0.00   0.0  0
 NU3  CONST_05  C3   C4   C5   N1  180.00   0.0  0
 NU3  CONST_06  N2   C13  C5   N1    0.00   0.0  0
 NU3  CONST_07  C13  N2   C6   N1    0.00   0.0  0
 NU3  CONST_08  C8   C7   C6   N1  180.00   0.0  0
 NU3  CONST_09  C12  C7   C6   N1    0.00   0.0  0
 NU3  CONST_10  N2   C13  C1   C2  180.00   0.0  0
 NU3  CONST_11  C5   C13  C1   C2    0.00   0.0  0
 NU3  CONST_12  C5   C4   C3   C2    0.00   0.0  0
 NU3  CONST_13  C5   N1   C6   N2    0.00   0.0  0
 NU3  CONST_14  C8   C7   C6   N2    0.00   0.0  0
 NU3  CONST_15  C12  C7   C6   N2  180.00   0.0  0
 NU3  CONST_16  C4   C5   C13  N2  180.00   0.0  0
 NU3  CONST_17  C13  C1   C2   C3    0.00   0.0  0
 NU3  CONST_18  C13  C5   C4   C3    0.00   0.0  0
 NU3  CONST_19  C6   N1   C5   C4  180.00   0.0  0
 NU3  CONST_20  C7   C6   N1   C5  180.00   0.0  0
 NU3  CONST_21  C6   N2   C13  C5    0.00   0.0  0
 NU3  CONST_22  C13  C5   N1   C6    0.00   0.0  0
 NU3  CONST_23  C9   C8   C7   C6  180.00   0.0  0
 NU3  CONST_24  C11  C12  C7   C6  180.00   0.0  0
 NU3  CONST_25  C13  N2   C6   C7  180.00   0.0  0
 NU3  CONST_26  C10  C9   C8   C7    0.00   0.0  0
 NU3  CONST_27  C10  C11  C12  C7    0.00   0.0  0
 NU3  CONST_28  C11  C12  C7   C8    0.00   0.0  0
 NU3  CONST_29  C11  C10  C9   C8    0.00   0.0  0
 NU3  CONST_30  C12  C7   C8   C9    0.00   0.0  0
 NU3  CONST_31  C12  C11  C10  C9    0.00   0.0  0
 NU3  CONST_32  C3   C2   C1   C   180.00   0.0  0
 NU3  CONST_33  N2   C13  C1   C     0.00   0.0  0
 NU3  CONST_34  C5   C13  C1   C   180.00   0.0  0
 NU3  CONST_35  C8   C9   C10  O1  180.00   0.0  0
 NU3  CONST_36  C12  C11  C10  O1  180.00   0.0  0
 NU3  CONST_37  H3   C3   C2   C1  180.00   0.0  0
 NU3  CONST_38  H4   C4   C5   N1    0.00   0.0  0
 NU3  CONST_39  HN1  N1   C6   N2  180.00   0.0  0
 NU3  CONST_40  H2   C2   C3   C4  180.00   0.0  0
 NU3  CONST_41  H8   C8   C7   C6    0.00   0.0  0
 NU3  CONST_42  H12  C12  C7   C6    0.00   0.0  0
 NU3  CONST_43  H9   C9   C8   C7  180.00   0.0  0
 NU3  CONST_44  H11  C11  C12  C7  180.00   0.0  0
 NU3  CONST_45  HN   N    C    C1  180.00   0.0  0
 NU3  CONST_46  HNA  N    C    C1    0.00   0.0  0
 NU3  Var_01    C2   C1   C    N   -39.59  30.0  2

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
 NU3  plan-1  O1   0.020
 NU3  plan-1  C6   0.020
 NU3  plan-1  C7   0.020
 NU3  plan-1  C8   0.020
 NU3  plan-1  C9   0.020
 NU3  plan-1  C10  0.020
 NU3  plan-1  C11  0.020
 NU3  plan-1  C12  0.020
 NU3  plan-1  H8   0.020
 NU3  plan-1  H9   0.020
 NU3  plan-1  H11  0.020
 NU3  plan-1  H12  0.020
 NU3  plan-2  C    0.020
 NU3  plan-2  C1   0.020
 NU3  plan-2  N1   0.020
 NU3  plan-2  C2   0.020
 NU3  plan-2  N2   0.020
 NU3  plan-2  C3   0.020
 NU3  plan-2  C4   0.020
 NU3  plan-2  C5   0.020
 NU3  plan-2  C6   0.020
 NU3  plan-2  C7   0.020
 NU3  plan-2  C13  0.020
 NU3  plan-2  HN1  0.020
 NU3  plan-2  H2   0.020
 NU3  plan-2  H3   0.020
 NU3  plan-2  H4   0.020
 NU3  plan-3  C    0.020
 NU3  plan-3  N    0.020
 NU3  plan-3  O    0.020
 NU3  plan-3  C1   0.020
 NU3  plan-3  HN   0.020
 NU3  plan-3  HNA  0.020

