# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:46:00 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(CCC(C)(C)O)c2cc(Nc3nc(ncc3Cl)n4nc(C)cc4C)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
 NQT  NQT  5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one  ligand  58  32  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NQT
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
 NQT  C11  C   CH2   0  -0.427  22.0389  -12.5624  17.0361
 NQT  C14  C   CH3   0  -0.664  22.8761  -14.6000  15.7946
 NQT  C15  C   CR5   0   0.687  22.6034  -10.9142  19.9369
 NQT  C20  C   CR6   0  -0.208  27.7966  -10.1920  13.9534
 NQT  C21  C   CR16  0   0.024  27.4223  -10.5374  12.6783
 NQT  CL   CL  CL    0  -0.095  29.4435   -9.9143  14.3692
 NQT  N6   N   N     0  -0.431  26.1552  -10.7468  12.3261
 NQT  C5   C   CR6   0   0.610  25.2785  -10.6098  13.2994
 NQT  N1   N   NR5   0  -0.448  23.9309  -10.8088  12.9819
 NQT  N    N   N     0  -0.286  23.6077  -11.6182  11.9577
 NQT  C3   C   CR5   0   0.294  22.2985  -11.6176  11.9048
 NQT  C4   C   CH3   0  -0.709  21.5577  -12.4239  10.8972
 NQT  C2   C   CR15  0  -0.552  21.7576  -10.7798  12.9083
 NQT  C1   C   CR5   0   0.424  22.8278  -10.2724  13.5926
 NQT  C    C   CH3   0  -0.705  22.8284   -9.2863  14.7064
 NQT  C6   C   CR6   0   0.642  26.7755  -10.0803  14.9184
 NQT  N2   N   N     0  -0.482  25.5208  -10.3049  14.5554
 NQT  C7   C   CR6   0   0.342  26.0709   -9.6975  17.2274
 NQT  C19  C   CR16  0  -0.297  26.0410   -8.5778  18.0525
 NQT  C18  C   CR16  0  -0.291  25.1274   -8.4738  19.0984
 NQT  C17  C   CR56  0   0.331  24.2333   -9.5087  19.2706
 NQT  C9   C   CR56  0   0.347  24.2665  -10.6328  18.4415
 NQT  C8   C   CR16  0  -0.324  25.1848  -10.7582  17.4242
 NQT  N5   N   NR5   0  -0.590  23.2097   -9.7049  20.1731
 NQT  C16  C   CH3   0  -0.513  22.8330   -8.7867  21.2138
 NQT  O1   O   O     0  -0.518  21.6609  -11.3957  20.5419
 NQT  N4   N   NR5   0  -0.598  23.2727  -11.4827  18.8782
 NQT  C10  C   CH2   0  -0.313  22.9164  -12.7424  18.2712
 NQT  C12  C   CT    0   0.189  21.6472  -13.8712  16.3339
 NQT  O    O   OH1   0  -0.678  20.9187  -14.7132  17.2266
 NQT  C13  C   CH3   0  -0.652  20.7011  -13.5520  15.1860
 NQT  H1   H   HCH2  0   0.240  22.5537  -11.9257  16.3104
 NQT  H2   H   HCH2  0   0.233  21.1330  -12.0263  17.3333
 NQT  H3   H   HCH3  0   0.214  23.5418  -14.9446  16.5898
 NQT  H4   H   HCH3  0   0.240  22.5851  -15.4781  15.2178
 NQT  H5   H   HCH3  0   0.235  23.4612  -13.9501  15.1430
 NQT  H6   H   HCR6  0   0.277  28.1726  -10.6429  11.9034
 NQT  H7   H   HCH3  0   0.242  22.2422  -12.9966  10.2753
 NQT  H8   H   HCH3  0   0.234  20.8712  -13.1212  11.3786
 NQT  H9   H   HCH3  0   0.242  20.9603  -11.7849  10.2465
 NQT  H10  H   HCR5  0   0.243  20.7182  -10.5636  13.0943
 NQT  H11  H   HCH3  0   0.266  23.2564   -9.6839  15.6238
 NQT  H12  H   HCH3  0   0.251  23.3979   -8.3923  14.4517
 NQT  H13  H   HCH3  0   0.239  21.8025   -8.9826  14.9046
 NQT  H14  H   HNH1  0   0.386  27.9820   -9.5123  16.4352
 NQT  H15  H   HCR6  0   0.243  26.7343   -7.7668  17.8763
 NQT  H16  H   HCR6  0   0.253  25.1257   -7.6002  19.7354
 NQT  H17  H   HCR6  0   0.256  25.2189  -11.6363  16.7960
 NQT  H18  H   HCH3  0   0.262  21.9434   -9.1576  21.7135
 NQT  H19  H   HCH3  0   0.245  23.6281   -8.6806  21.9516
 NQT  H20  H   HCH3  0   0.242  22.6119   -7.8045  20.7974
 NQT  H21  H   HCH2  0   0.251  22.4038  -13.3341  19.0287
 NQT  H22  H   HCH2  0   0.245  23.8433  -13.2664  18.0296
 NQT  H23  H   HOH1  0   0.427  21.5430  -15.2238  17.7495
 NQT  H24  H   HCH3  0   0.218  19.8076  -13.0306  15.5357
 NQT  H25  H   HCH3  0   0.253  21.1904  -12.9091  14.4545
 NQT  H26  H   HCH3  0   0.224  20.3853  -14.4644  14.6773
 NQT  N3   N   NH1   0  -0.771  27.0355   -9.7644  16.2018

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
 NQT  C4   C3   single    1.488  0.020  1.488
 NQT  C3   N    aromatic  1.310  0.020  1.310
 NQT  C3   C2   aromatic  1.415  0.020  1.415
 NQT  N    N1   aromatic  1.345  0.020  1.345
 NQT  N6   C21  aromatic  1.332  0.020  1.332
 NQT  N6   C5   aromatic  1.317  0.020  1.317
 NQT  C2   C1   aromatic  1.368  0.020  1.368
 NQT  N1   C5   single    1.399  0.020  1.399
 NQT  N1   C1   aromatic  1.370  0.020  1.370
 NQT  C21  C20  aromatic  1.373  0.020  1.373
 NQT  C5   N2   aromatic  1.315  0.020  1.315
 NQT  C1   C    single    1.488  0.020  1.488
 NQT  C20  CL   single    1.721  0.020  1.721
 NQT  C20  C6   aromatic  1.409  0.020  1.409
 NQT  N2   C6   aromatic  1.325  0.020  1.325
 NQT  C6   N3   single    1.347  0.020  1.347
 NQT  N3   C7   single    1.409  0.020  1.409
 NQT  C7   C19  aromatic  1.391  0.020  1.391
 NQT  C7   C8   aromatic  1.396  0.020  1.396
 NQT  C19  C18  aromatic  1.393  0.020  1.393
 NQT  C8   C9   aromatic  1.376  0.020  1.376
 NQT  C13  C12  single    1.521  0.020  1.521
 NQT  C18  C17  aromatic  1.378  0.020  1.378
 NQT  C14  C12  single    1.527  0.020  1.527
 NQT  C11  C12  single    1.536  0.020  1.536
 NQT  C11  C10  single    1.526  0.020  1.526
 NQT  C9   C17  aromatic  1.397  0.020  1.397
 NQT  C9   N4   single    1.379  0.020  1.379
 NQT  C12  O    single    1.427  0.020  1.427
 NQT  C17  N5   single    1.379  0.020  1.379
 NQT  N4   C10  single    1.443  0.020  1.443
 NQT  N4   C15  single    1.375  0.020  1.375
 NQT  N5   C15  single    1.373  0.020  1.373
 NQT  N5   C16  single    1.438  0.020  1.438
 NQT  C15  O1   double    1.219  0.020  1.219
 NQT  C11  H1   single    0.970  0.020  1.090
 NQT  C11  H2   single    0.970  0.020  1.090
 NQT  C14  H3   single    0.970  0.020  1.090
 NQT  C14  H4   single    0.970  0.020  1.090
 NQT  C14  H5   single    0.970  0.020  1.090
 NQT  C21  H6   single    0.930  0.020  1.080
 NQT  C4   H7   single    0.970  0.020  1.090
 NQT  C4   H8   single    0.970  0.020  1.090
 NQT  C4   H9   single    0.970  0.020  1.090
 NQT  C2   H10  single    0.930  0.020  1.080
 NQT  C    H11  single    0.970  0.020  1.090
 NQT  C    H12  single    0.970  0.020  1.090
 NQT  C    H13  single    0.970  0.020  1.090
 NQT  N3   H14  single    0.860  0.020  1.020
 NQT  C19  H15  single    0.930  0.020  1.080
 NQT  C18  H16  single    0.930  0.020  1.080
 NQT  C8   H17  single    0.930  0.020  1.080
 NQT  C16  H18  single    0.970  0.020  1.090
 NQT  C16  H19  single    0.970  0.020  1.090
 NQT  C16  H20  single    0.970  0.020  1.090
 NQT  C10  H21  single    0.970  0.020  1.090
 NQT  C10  H22  single    0.970  0.020  1.090
 NQT  O    H23  single    0.850  0.020  0.980
 NQT  C13  H24  single    0.970  0.020  1.090
 NQT  C13  H25  single    0.970  0.020  1.090
 NQT  C13  H26  single    0.970  0.020  1.090

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
 NQT  H2   C11  H1   106.54  3.000
 NQT  H2   C11  C12  109.31  3.000
 NQT  H1   C11  C12  108.22  3.000
 NQT  H2   C11  C10  108.31  3.000
 NQT  H1   C11  C10  109.57  3.000
 NQT  C12  C11  C10  114.59  3.000
 NQT  H5   C14  H4   107.88  3.000
 NQT  H5   C14  H3   107.21  3.000
 NQT  H4   C14  H3   107.07  3.000
 NQT  H5   C14  C12  111.00  3.000
 NQT  H4   C14  C12  110.88  3.000
 NQT  H3   C14  C12  112.56  3.000
 NQT  N4   C15  O1   126.51  3.000
 NQT  O1   C15  N5   127.14  3.000
 NQT  N4   C15  N5   106.35  3.000
 NQT  C6   C20  CL   121.00  3.000
 NQT  C6   C20  C21  117.28  3.000
 NQT  CL   C20  C21  121.72  3.000
 NQT  H6   C21  N6   117.02  3.000
 NQT  H6   C21  C20  119.99  3.000
 NQT  N6   C21  C20  122.99  3.000
 NQT  C5   N6   C21  114.93  3.000
 NQT  N2   C5   N1   115.30  3.000
 NQT  N2   C5   N6   127.39  3.000
 NQT  N1   C5   N6   117.31  3.000
 NQT  C1   N1   N    112.42  3.000
 NQT  C1   N1   C5   128.23  3.000
 NQT  N    N1   C5   119.35  3.000
 NQT  C3   N    N1   105.70  3.000
 NQT  C2   C3   C4   127.65  3.000
 NQT  C2   C3   N    110.71  3.000
 NQT  C4   C3   N    121.63  3.000
 NQT  H9   C4   H8   107.06  3.000
 NQT  H9   C4   H7   108.19  3.000
 NQT  H8   C4   H7   108.17  3.000
 NQT  H9   C4   C3   111.06  3.000
 NQT  H8   C4   C3   111.16  3.000
 NQT  H7   C4   C3   111.05  3.000
 NQT  H10  C2   C1   126.42  3.000
 NQT  H10  C2   C3   127.59  3.000
 NQT  C1   C2   C3   105.98  3.000
 NQT  C    C1   C2   128.37  3.000
 NQT  C    C1   N1   126.36  3.000
 NQT  C2   C1   N1   105.17  3.000
 NQT  H13  C    H12  107.83  3.000
 NQT  H13  C    H11  108.63  3.000
 NQT  H12  C    H11  106.94  3.000
 NQT  H13  C    C1   108.72  3.000
 NQT  H12  C    C1   111.64  3.000
 NQT  H11  C    C1   112.92  3.000
 NQT  N3   C6   N2   118.91  3.000
 NQT  N3   C6   C20  122.08  3.000
 NQT  N2   C6   C20  119.01  3.000
 NQT  C6   N2   C5   118.38  3.000
 NQT  C8   C7   C19  120.94  3.000
 NQT  C8   C7   N3   120.06  3.000
 NQT  C19  C7   N3   118.98  3.000
 NQT  H15  C19  C18  119.14  3.000
 NQT  H15  C19  C7   119.55  3.000
 NQT  C18  C19  C7   121.31  3.000
 NQT  H16  C18  C17  122.14  3.000
 NQT  H16  C18  C19  120.26  3.000
 NQT  C17  C18  C19  117.60  3.000
 NQT  N5   C17  C9   106.96  3.000
 NQT  N5   C17  C18  132.08  3.000
 NQT  C9   C17  C18  120.96  3.000
 NQT  N4   C9   C8   131.22  3.000
 NQT  N4   C9   C17  106.91  3.000
 NQT  C8   C9   C17  121.86  3.000
 NQT  H17  C8   C9   121.67  3.000
 NQT  H17  C8   C7   121.03  3.000
 NQT  C9   C8   C7   117.29  3.000
 NQT  C16  N5   C17  125.27  3.000
 NQT  C16  N5   C15  124.82  3.000
 NQT  C17  N5   C15  109.90  3.000
 NQT  H20  C16  H19  108.61  3.000
 NQT  H20  C16  H18  108.52  3.000
 NQT  H19  C16  H18  108.63  3.000
 NQT  H20  C16  N5   110.62  3.000
 NQT  H19  C16  N5   111.16  3.000
 NQT  H18  C16  N5   109.24  3.000
 NQT  C10  N4   C9   125.66  3.000
 NQT  C10  N4   C15  124.36  3.000
 NQT  C9   N4   C15  109.87  3.000
 NQT  H22  C10  H21  107.01  3.000
 NQT  H22  C10  N4   107.60  3.000
 NQT  H21  C10  N4   107.33  3.000
 NQT  H22  C10  C11  111.45  3.000
 NQT  H21  C10  C11  110.88  3.000
 NQT  N4   C10  C11  112.31  3.000
 NQT  C13  C12  O    106.16  3.000
 NQT  O    C12  C14  110.49  3.000
 NQT  C13  C12  C14  109.52  3.000
 NQT  O    C12  C11  110.31  3.000
 NQT  C14  C12  C11  111.27  3.000
 NQT  C13  C12  C11  108.95  3.000
 NQT  H23  O    C12  108.80  3.000
 NQT  H26  C13  H25  108.07  3.000
 NQT  H26  C13  H24  108.16  3.000
 NQT  H25  C13  H24  107.50  3.000
 NQT  H26  C13  C12  110.87  3.000
 NQT  H25  C13  C12  110.55  3.000
 NQT  H24  C13  C12  111.55  3.000
 NQT  H14  N3   C7   117.56  3.000
 NQT  H14  N3   C6   117.45  3.000
 NQT  C7   N3   C6   124.91  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
 NQT  CONST_01  C5   N6   C21  C20     0.00   0.0  0
 NQT  CONST_02  C5   N2   C6   C20     0.00   0.0  0
 NQT  CONST_03  N1   C5   N6   C21   180.00   0.0  0
 NQT  CONST_04  N2   C5   N6   C21     0.00   0.0  0
 NQT  CONST_05  N2   C6   C20  C21     0.00   0.0  0
 NQT  CONST_06  C6   C20  C21  N6      0.00   0.0  0
 NQT  CONST_09  C6   N2   C5   N6      0.00   0.0  0
 NQT  CONST_10  C3   N    N1   C5    180.00   0.0  0
 NQT  CONST_11  C2   C1   N1   C5    180.00   0.0  0
 NQT  CONST_12  C2   C3   N    N1      0.00   0.0  0
 NQT  CONST_13  C6   N2   C5   N1    180.00   0.0  0
 NQT  CONST_14  C3   C2   C1   N1      0.00   0.0  0
 NQT  CONST_15  C1   C2   C3   N       0.00   0.0  0
 NQT  CONST_17  C2   C1   N1   N       0.00   0.0  0
 NQT  CONST_18  C1   N1   N    C3      0.00   0.0  0
 NQT  CONST_20  C17  C18  C19  C7      0.00   0.0  0
 NQT  CONST_21  C17  C9   C8   C7      0.00   0.0  0
 NQT  CONST_22  C9   C8   C7   C19     0.00   0.0  0
 NQT  CONST_23  C9   C17  C18  C19     0.00   0.0  0
 NQT  CONST_24  C8   C7   C19  C18     0.00   0.0  0
 NQT  CONST_25  C8   C9   C17  C18     0.00   0.0  0
 NQT  CONST_26  C17  C9   N4   C15     0.00   0.0  0
 NQT  CONST_27  C9   C17  N5   C15     0.00   0.0  0
 NQT  CONST_28  N4   C15  N5   C17     0.00   0.0  0
 NQT  CONST_29  N5   C15  N4   C9      0.00   0.0  0
 NQT  CONST_30  N4   C9   C17  N5      0.00   0.0  0
 NQT  CONST_31  N3   C6   C20  C21   180.00   0.0  0
 NQT  CONST_32  N6   C21  C20  CL    180.00   0.0  0
 NQT  CONST_33  N2   C6   C20  CL    180.00   0.0  0
 NQT  CONST_34  C    C1   N1   C5      0.00   0.0  0
 NQT  CONST_35  N3   C6   N2   C5    180.00   0.0  0
 NQT  CONST_36  C4   C3   N    N1    180.00   0.0  0
 NQT  CONST_37  C    C1   N1   N     180.00   0.0  0
 NQT  CONST_38  C    C1   C2   C3    180.00   0.0  0
 NQT  CONST_39  C1   C2   C3   C4    180.00   0.0  0
 NQT  CONST_40  C18  C19  C7   N3    180.00   0.0  0
 NQT  CONST_41  C9   C8   C7   N3    180.00   0.0  0
 NQT  CONST_42  C10  N4   C9   C17   180.00   0.0  0
 NQT  CONST_43  O1   C15  N5   C17   180.00   0.0  0
 NQT  CONST_44  C16  N5   C17  C9    180.00   0.0  0
 NQT  CONST_45  O1   C15  N4   C9    180.00   0.0  0
 NQT  CONST_46  C10  N4   C15  N5    180.00   0.0  0
 NQT  CONST_47  N4   C15  N5   C16   180.00   0.0  0
 NQT  CONST_48  H6   C21  N6   C5    180.00   0.0  0
 NQT  CONST_49  H10  C2   C1   N1    180.00   0.0  0
 NQT  CONST_50  H16  C18  C19  C7    180.00   0.0  0
 NQT  CONST_51  H17  C8   C7   C19   180.00   0.0  0
 NQT  CONST_52  H15  C19  C18  C17   180.00   0.0  0
 NQT  CONST_53  O1   C15  N5   C16     0.00   0.0  0
 NQT  CONST_54  C10  N4   C15  O1      0.00   0.0  0
 NQT  Var_01    C7   N3   C6   C20  -176.91  30.0  2
 NQT  Var_02    C19  C7   N3   C6   -131.18  30.0  2
 NQT  Var_03    C9   N4   C10  C11   -79.59  30.0  2
 NQT  Var_04    H18  C16  N5   C15    -5.31  30.0  3
 NQT  Var_05    H11  C    C1   N1    -64.88  30.0  2
 NQT  Var_06    H7   C4   C3   N       1.58  30.0  2
 NQT  Var_07    C12  C11  C10  N4    179.04  30.0  1
 NQT  Var_08    C10  C11  C12  C14   -63.03  30.0  3
 NQT  Var_09    H24  C13  C12  C11   -58.18  30.0  3
 NQT  Var_10    H3   C14  C12  C11    65.38  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
 NQT  plan-1  C5   0.020
 NQT  plan-1  N1   0.020
 NQT  plan-1  N    0.020
 NQT  plan-1  C3   0.020
 NQT  plan-1  C4   0.020
 NQT  plan-1  C2   0.020
 NQT  plan-1  C1   0.020
 NQT  plan-1  C    0.020
 NQT  plan-1  H10  0.020
 NQT  plan-2  C20  0.020
 NQT  plan-2  C21  0.020
 NQT  plan-2  CL   0.020
 NQT  plan-2  N6   0.020
 NQT  plan-2  C5   0.020
 NQT  plan-2  N1   0.020
 NQT  plan-2  C6   0.020
 NQT  plan-2  N2   0.020
 NQT  plan-2  H6   0.020
 NQT  plan-2  N3   0.020
 NQT  plan-3  C15  0.020
 NQT  plan-3  C7   0.020
 NQT  plan-3  C19  0.020
 NQT  plan-3  C18  0.020
 NQT  plan-3  C17  0.020
 NQT  plan-3  C9   0.020
 NQT  plan-3  C8   0.020
 NQT  plan-3  N5   0.020
 NQT  plan-3  C16  0.020
 NQT  plan-3  O1   0.020
 NQT  plan-3  N4   0.020
 NQT  plan-3  C10  0.020
 NQT  plan-3  H15  0.020
 NQT  plan-3  H16  0.020
 NQT  plan-3  H17  0.020
 NQT  plan-3  N3   0.020

