# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:58:09 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: 5-[[5-chloranyl-2-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-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: C[C@@H]1CN(C[C@H](C)O1)c2ncc(Cl)c(Nc3ccc4N(C)C(=O)N(CCC(C)(C)O)c4c3)n2
#
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
 NQW  NQW  5-[[5-chloranyl-2-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-yl]pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one  ligand  64  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NQW
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
 NQW  CL   CL  CL    0  -0.127  -28.1015  11.8701  13.6374
 NQW  C21  C   CR6   0  -0.258  -27.0155  10.6237  13.1292
 NQW  C22  C   CR16  0   0.014  -26.9945  10.1797  11.8295
 NQW  N5   N   N     0  -0.501  -26.1837   9.2245  11.3985
 NQW  C6   C   CR6   0   0.648  -25.3605   8.6981  12.3128
 NQW  N    N   NT    0  -0.515  -24.5143   7.7227  11.9140
 NQW  C2   C   CH2   0  -0.304  -23.6401   7.0125  12.8228
 NQW  C3   C   CH2   0  -0.300  -24.4968   7.1896  10.5686
 NQW  C4   C   CH1   0   0.040  -24.7986   5.6961  10.5947
 NQW  C5   C   CH3   0  -0.689  -24.6493   5.0741   9.2228
 NQW  O    O   O2    0  -0.498  -23.9188   5.0273  11.4794
 NQW  C1   C   CH1   0   0.038  -23.9740   5.5255  12.8032
 NQW  C    C   CH3   0  -0.685  -23.0129   4.7226  13.6530
 NQW  C7   C   CR6   0   0.618  -26.1084  10.0179  14.0252
 NQW  N1   N   N     0  -0.523  -25.2980   9.0699  13.5931
 NQW  N2   N   NH1   0  -0.770  -26.0565  10.4015  15.3207
 NQW  C8   C   CR6   0   0.340  -25.1634   9.9392  16.3031
 NQW  C13  C   CR16  0  -0.299  -24.8792   8.5834  16.4684
 NQW  C12  C   CR16  0  -0.319  -24.0054   8.1488  17.4614
 NQW  C11  C   CR56  0   0.325  -23.4449   9.0957  18.2943
 NQW  N3   N   NR5   0  -0.587  -22.5642   8.9935  19.3495
 NQW  C14  C   CH3   0  -0.535  -22.0093   7.7637  19.8520
 NQW  C15  C   CR5   0   0.668  -22.3177  10.2393  19.8740
 NQW  O1   O   O     0  -0.504  -21.5889  10.5113  20.8117
 NQW  N4   N   NR5   0  -0.594  -23.0642  11.1266  19.1299
 NQW  C10  C   CR56  0   0.352  -23.7536  10.4500  18.1489
 NQW  C9   C   CR16  0  -0.402  -24.5996  10.8946  17.1542
 NQW  C16  C   CH2   0  -0.333  -23.0732  12.5573  19.3292
 NQW  C17  C   CH2   0  -0.438  -22.1727  13.2841  18.3346
 NQW  C18  C   CT    0   0.195  -22.2158  14.8174  18.4382
 NQW  O2   O   OH1   0  -0.679  -21.8307  15.2376  19.7419
 NQW  C20  C   CH3   0  -0.656  -21.1821  15.4020  17.4837
 NQW  C19  C   CH3   0  -0.688  -23.6015  15.3613  18.0922
 NQW  H1   H   HCR6  0   0.282  -27.6693  10.6161  11.1003
 NQW  H2   H   HCH2  0   0.236  -22.5985   7.1576  12.5109
 NQW  H3   H   HCH2  0   0.275  -23.7464   7.4111  13.8281
 NQW  H4   H   HCH2  0   0.235  -23.5058   7.3575  10.1294
 NQW  H5   H   HCH2  0   0.272  -25.2286   7.7078   9.9556
 NQW  H6   H   HCH1  0   0.206  -25.8353   5.5685  10.9448
 NQW  H7   H   HCH3  0   0.243  -24.8752   4.0081   9.2486
 NQW  H8   H   HCH3  0   0.234  -25.3371   5.5429   8.5188
 NQW  H9   H   HCH3  0   0.229  -23.6351   5.2024   8.8407
 NQW  H10  H   HCH1  0   0.206  -24.9960   5.4036  13.1962
 NQW  H11  H   HCH3  0   0.230  -23.0741   5.0409  14.6939
 NQW  H12  H   HCH3  0   0.243  -23.2539   3.6601  13.6171
 NQW  H13  H   HCH3  0   0.229  -21.9818   4.8527  13.3202
 NQW  H14  H   HNH1  0   0.405  -26.5872  11.2234  15.5648
 NQW  H15  H   HCR6  0   0.263  -25.3457   7.8547  15.8239
 NQW  H16  H   HCR6  0   0.275  -23.7897   7.0944  17.5727
 NQW  H17  H   HCH3  0   0.268  -21.2644   7.9906  20.6089
 NQW  H18  H   HCH3  0   0.255  -22.7831   7.1399  20.2993
 NQW  H19  H   HCH3  0   0.256  -21.5278   7.2078  19.0487
 NQW  H20  H   HCR6  0   0.276  -24.8215  11.9463  17.0224
 NQW  H21  H   HCH2  0   0.267  -22.7515  12.7446  20.3531
 NQW  H22  H   HCH2  0   0.262  -24.1088  12.8943  19.2543
 NQW  H23  H   HCH2  0   0.233  -22.4473  12.9955  17.3158
 NQW  H24  H   HCH2  0   0.244  -21.1430  12.9467  18.4878
 NQW  H25  H   HOH1  0   0.446  -22.5583  15.0788  20.3518
 NQW  H26  H   HCH3  0   0.233  -20.1769  15.0557  17.7305
 NQW  H27  H   HCH3  0   0.227  -21.3959  15.1026  16.4574
 NQW  H28  H   HCH3  0   0.233  -21.1884  16.4927  17.5227
 NQW  H29  H   HCH3  0   0.232  -24.3663  15.0253  18.7965
 NQW  H30  H   HCH3  0   0.241  -23.5990  16.4523  18.1102
 NQW  H31  H   HCH3  0   0.231  -23.9114  15.0445  17.0954

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
 NQW  C5   C4   single    1.514  0.020  1.514
 NQW  C3   C4   single    1.524  0.020  1.524
 NQW  C3   N    single    1.447  0.020  1.447
 NQW  C4   O    single    1.416  0.020  1.416
 NQW  N5   C22  aromatic  1.325  0.020  1.325
 NQW  N5   C6   aromatic  1.338  0.020  1.338
 NQW  O    C1   single    1.416  0.020  1.416
 NQW  C22  C21  aromatic  1.374  0.020  1.374
 NQW  N    C6   single    1.351  0.020  1.351
 NQW  N    C2   single    1.447  0.020  1.447
 NQW  C6   N1   aromatic  1.335  0.020  1.335
 NQW  C2   C1   single    1.524  0.020  1.524
 NQW  C1   C    single    1.513  0.020  1.513
 NQW  C21  CL   single    1.729  0.020  1.729
 NQW  C21  C7   aromatic  1.412  0.020  1.412
 NQW  N1   C7   aromatic  1.320  0.020  1.320
 NQW  C7   N2   single    1.352  0.020  1.352
 NQW  N2   C8   single    1.406  0.020  1.406
 NQW  C8   C13  aromatic  1.395  0.020  1.395
 NQW  C8   C9   aromatic  1.398  0.020  1.398
 NQW  C13  C12  aromatic  1.392  0.020  1.392
 NQW  C20  C18  single    1.524  0.020  1.524
 NQW  C9   C10  aromatic  1.379  0.020  1.379
 NQW  C12  C11  aromatic  1.380  0.020  1.380
 NQW  C19  C18  single    1.528  0.020  1.528
 NQW  C17  C18  single    1.537  0.020  1.537
 NQW  C17  C16  single    1.526  0.020  1.526
 NQW  C18  O2   single    1.423  0.020  1.423
 NQW  C10  C11  aromatic  1.397  0.020  1.397
 NQW  C10  N4   single    1.377  0.020  1.377
 NQW  C11  N3   single    1.378  0.020  1.378
 NQW  N4   C16  single    1.445  0.020  1.445
 NQW  N4   C15  single    1.378  0.020  1.378
 NQW  N3   C14  single    1.440  0.020  1.440
 NQW  N3   C15  single    1.374  0.020  1.374
 NQW  C15  O1   double    1.218  0.020  1.218
 NQW  C22  H1   single    0.930  0.020  1.080
 NQW  C2   H2   single    0.970  0.020  1.090
 NQW  C2   H3   single    0.970  0.020  1.090
 NQW  C3   H4   single    0.970  0.020  1.090
 NQW  C3   H5   single    0.970  0.020  1.090
 NQW  C4   H6   single    0.970  0.020  1.090
 NQW  C5   H7   single    0.970  0.020  1.090
 NQW  C5   H8   single    0.970  0.020  1.090
 NQW  C5   H9   single    0.970  0.020  1.090
 NQW  C1   H10  single    0.970  0.020  1.090
 NQW  C    H11  single    0.970  0.020  1.090
 NQW  C    H12  single    0.970  0.020  1.090
 NQW  C    H13  single    0.970  0.020  1.090
 NQW  N2   H14  single    0.860  0.020  1.020
 NQW  C13  H15  single    0.930  0.020  1.080
 NQW  C12  H16  single    0.930  0.020  1.080
 NQW  C14  H17  single    0.970  0.020  1.090
 NQW  C14  H18  single    0.970  0.020  1.090
 NQW  C14  H19  single    0.970  0.020  1.090
 NQW  C9   H20  single    0.930  0.020  1.080
 NQW  C16  H21  single    0.970  0.020  1.090
 NQW  C16  H22  single    0.970  0.020  1.090
 NQW  C17  H23  single    0.970  0.020  1.090
 NQW  C17  H24  single    0.970  0.020  1.090
 NQW  O2   H25  single    0.850  0.020  0.980
 NQW  C20  H26  single    0.970  0.020  1.090
 NQW  C20  H27  single    0.970  0.020  1.090
 NQW  C20  H28  single    0.970  0.020  1.090
 NQW  C19  H29  single    0.970  0.020  1.090
 NQW  C19  H30  single    0.970  0.020  1.090
 NQW  C19  H31  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
 NQW  C7   C21  C22  116.87  3.000
 NQW  C7   C21  CL   121.75  3.000
 NQW  C22  C21  CL   121.37  3.000
 NQW  H1   C22  N5   116.86  3.000
 NQW  H1   C22  C21  119.76  3.000
 NQW  N5   C22  C21  123.38  3.000
 NQW  C6   N5   C22  115.96  3.000
 NQW  N1   C6   N    117.06  3.000
 NQW  N1   C6   N5   125.07  3.000
 NQW  N    C6   N5   117.87  3.000
 NQW  C3   N    C2   113.31  3.000
 NQW  C2   N    C6   123.17  3.000
 NQW  C3   N    C6   123.21  3.000
 NQW  H3   C2   H2   107.90  3.000
 NQW  H3   C2   C1   110.39  3.000
 NQW  H2   C2   C1   109.48  3.000
 NQW  H3   C2   N    109.98  3.000
 NQW  H2   C2   N    109.28  3.000
 NQW  C1   C2   N    109.78  3.000
 NQW  H5   C3   H4   108.05  3.000
 NQW  H5   C3   C4   110.11  3.000
 NQW  H4   C3   C4   109.62  3.000
 NQW  H5   C3   N    109.92  3.000
 NQW  H4   C3   N    109.07  3.000
 NQW  C4   C3   N    110.04  3.000
 NQW  H6   C4   O    109.37  3.000
 NQW  H6   C4   C5   109.47  3.000
 NQW  O    C4   C5   108.12  3.000
 NQW  H6   C4   C3   107.77  3.000
 NQW  O    C4   C3   110.53  3.000
 NQW  C5   C4   C3   111.57  3.000
 NQW  H9   C5   H8   108.04  3.000
 NQW  H9   C5   H7   108.41  3.000
 NQW  H8   C5   H7   107.76  3.000
 NQW  H9   C5   C4   111.14  3.000
 NQW  H8   C5   C4   110.27  3.000
 NQW  H7   C5   C4   111.10  3.000
 NQW  C1   O    C4   113.20  3.000
 NQW  H10  C1   C    109.27  3.000
 NQW  H10  C1   O    109.32  3.000
 NQW  C    C1   O    108.28  3.000
 NQW  H10  C1   C2   107.86  3.000
 NQW  C    C1   C2   111.79  3.000
 NQW  O    C1   C2   110.29  3.000
 NQW  H13  C    H12  108.36  3.000
 NQW  H13  C    H11  108.02  3.000
 NQW  H12  C    H11  107.67  3.000
 NQW  H13  C    C1   111.44  3.000
 NQW  H12  C    C1   110.99  3.000
 NQW  H11  C    C1   110.22  3.000
 NQW  N2   C7   N1   119.60  3.000
 NQW  N2   C7   C21  120.73  3.000
 NQW  N1   C7   C21  119.67  3.000
 NQW  C7   N1   C6   119.04  3.000
 NQW  H14  N2   C8   115.67  3.000
 NQW  H14  N2   C7   116.30  3.000
 NQW  C8   N2   C7   126.91  3.000
 NQW  C9   C8   C13  120.65  3.000
 NQW  C9   C8   N2   117.18  3.000
 NQW  C13  C8   N2   122.12  3.000
 NQW  H15  C13  C12  119.12  3.000
 NQW  H15  C13  C8   119.84  3.000
 NQW  C12  C13  C8   121.04  3.000
 NQW  H16  C12  C11  121.71  3.000
 NQW  H16  C12  C13  120.17  3.000
 NQW  C11  C12  C13  118.12  3.000
 NQW  C10  C11  N3   107.03  3.000
 NQW  N3   C11  C12  132.12  3.000
 NQW  C10  C11  C12  120.85  3.000
 NQW  C15  N3   C14  124.90  3.000
 NQW  C15  N3   C11  109.85  3.000
 NQW  C14  N3   C11  125.23  3.000
 NQW  H19  C14  H18  108.93  3.000
 NQW  H19  C14  H17  108.51  3.000
 NQW  H18  C14  H17  108.70  3.000
 NQW  H19  C14  N3   110.42  3.000
 NQW  H18  C14  N3   111.01  3.000
 NQW  H17  C14  N3   109.22  3.000
 NQW  N4   C15  O1   126.58  3.000
 NQW  O1   C15  N3   127.12  3.000
 NQW  N4   C15  N3   106.30  3.000
 NQW  C16  N4   C10  125.59  3.000
 NQW  C16  N4   C15  124.52  3.000
 NQW  C10  N4   C15  109.85  3.000
 NQW  C9   C10  N4   131.49  3.000
 NQW  N4   C10  C11  106.96  3.000
 NQW  C9   C10  C11  121.54  3.000
 NQW  H20  C9   C10  121.77  3.000
 NQW  H20  C9   C8   120.46  3.000
 NQW  C10  C9   C8   117.78  3.000
 NQW  H22  C16  H21  106.95  3.000
 NQW  H22  C16  C17  111.60  3.000
 NQW  H21  C16  C17  110.89  3.000
 NQW  H22  C16  N4   107.59  3.000
 NQW  H21  C16  N4   107.34  3.000
 NQW  C17  C16  N4   112.22  3.000
 NQW  H24  C17  H23  106.57  3.000
 NQW  H24  C17  C18  108.93  3.000
 NQW  H23  C17  C18  108.59  3.000
 NQW  H24  C17  C16  108.50  3.000
 NQW  H23  C17  C16  109.47  3.000
 NQW  C18  C17  C16  114.49  3.000
 NQW  C19  C18  C20  109.68  3.000
 NQW  C19  C18  O2   110.35  3.000
 NQW  C20  C18  O2   106.09  3.000
 NQW  O2   C18  C17  110.40  3.000
 NQW  C19  C18  C17  111.41  3.000
 NQW  C20  C18  C17  108.76  3.000
 NQW  H25  O2   C18  109.10  3.000
 NQW  H28  C20  H27  107.87  3.000
 NQW  H28  C20  H26  108.32  3.000
 NQW  H27  C20  H26  107.83  3.000
 NQW  H28  C20  C18  110.93  3.000
 NQW  H27  C20  C18  110.57  3.000
 NQW  H26  C20  C18  111.19  3.000
 NQW  H31  C19  H30  107.82  3.000
 NQW  H31  C19  H29  107.51  3.000
 NQW  H30  C19  H29  107.36  3.000
 NQW  H31  C19  C18  111.17  3.000
 NQW  H30  C19  C18  110.49  3.000
 NQW  H29  C19  C18  112.29  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
 NQW  CONST_01  C6   N5   C22  C21     0.00   0.0  0
 NQW  CONST_02  C6   N1   C7   C21     0.00   0.0  0
 NQW  CONST_03  N1   C6   N5   C22     0.00   0.0  0
 NQW  CONST_04  N1   C7   C21  C22     0.00   0.0  0
 NQW  CONST_05  C7   C21  C22  N5      0.00   0.0  0
 NQW  CONST_06  C7   N1   C6   N5      0.00   0.0  0
 NQW  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 NQW  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 NQW  CONST_09  C10  C9   C8   C13     0.00   0.0  0
 NQW  CONST_10  C10  C11  C12  C13     0.00   0.0  0
 NQW  CONST_11  C9   C8   C13  C12     0.00   0.0  0
 NQW  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 NQW  CONST_13  N    C6   N5   C22   180.00   0.0  0
 NQW  CONST_14  C7   N1   C6   N     180.00   0.0  0
 NQW  CONST_15  C15  N4   C10  C11     0.00   0.0  0
 NQW  CONST_16  N4   C15  N3   C11     0.00   0.0  0
 NQW  CONST_17  N4   C10  C11  N3      0.00   0.0  0
 NQW  CONST_18  C10  N4   C15  N3      0.00   0.0  0
 NQW  CONST_19  C10  C11  N3   C15     0.00   0.0  0
 NQW  CONST_20  N5   C22  C21  CL    180.00   0.0  0
 NQW  CONST_21  N1   C7   C21  CL    180.00   0.0  0
 NQW  CONST_22  N2   C7   C21  C22   180.00   0.0  0
 NQW  CONST_23  N2   C7   N1   C6    180.00   0.0  0
 NQW  CONST_24  C12  C13  C8   N2    180.00   0.0  0
 NQW  CONST_25  C10  C9   C8   N2    180.00   0.0  0
 NQW  CONST_26  C16  N4   C10  C11   180.00   0.0  0
 NQW  CONST_27  O1   C15  N3   C11   180.00   0.0  0
 NQW  CONST_28  C16  N4   C15  N3    180.00   0.0  0
 NQW  CONST_29  C10  C11  N3   C14   180.00   0.0  0
 NQW  CONST_30  N4   C15  N3   C14   180.00   0.0  0
 NQW  CONST_31  C10  N4   C15  O1    180.00   0.0  0
 NQW  CONST_32  H1   C22  N5   C6    180.00   0.0  0
 NQW  CONST_33  H16  C12  C13  C8    180.00   0.0  0
 NQW  CONST_34  H20  C9   C8   C13   180.00   0.0  0
 NQW  CONST_35  H15  C13  C12  C11   180.00   0.0  0
 NQW  CONST_36  O1   C15  N3   C14     0.00   0.0  0
 NQW  CONST_37  C16  N4   C15  O1      0.00   0.0  0
 NQW  Var_01    C3   N    C6   N5     -2.58  30.0  2
 NQW  Var_02    C4   C3   N    C6   -119.80  30.0  1
 NQW  Var_03    C1   C2   N    C6    119.31  30.0  1
 NQW  Var_04    C8   N2   C7   C21  -176.48  30.0  2
 NQW  Var_05    C13  C8   N2   C7    -45.59  30.0  2
 NQW  Var_06    C17  C16  N4   C15    99.42  30.0  3
 NQW  Var_07    H17  C14  N3   C11   173.64  30.0  3
 NQW  Var_08    C18  C17  C16  N4    176.09  30.0  2
 NQW  Var_09    C20  C18  C17  C16   174.84  30.0  3
 NQW  Var_10    H26  C20  C18  C17   -59.86  30.0  3
 NQW  Var_11    H29  C19  C18  C17    63.66  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 NQW  chir_01  C4  C5  C3  O  positiv
 NQW  chir_02  C1  O   C2  C  positiv

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
 NQW  plan-1  CL   0.020
 NQW  plan-1  C21  0.020
 NQW  plan-1  C22  0.020
 NQW  plan-1  N5   0.020
 NQW  plan-1  C6   0.020
 NQW  plan-1  N    0.020
 NQW  plan-1  C7   0.020
 NQW  plan-1  N1   0.020
 NQW  plan-1  N2   0.020
 NQW  plan-1  H1   0.020
 NQW  plan-2  N2   0.020
 NQW  plan-2  C8   0.020
 NQW  plan-2  C13  0.020
 NQW  plan-2  C12  0.020
 NQW  plan-2  C11  0.020
 NQW  plan-2  N3   0.020
 NQW  plan-2  C14  0.020
 NQW  plan-2  C15  0.020
 NQW  plan-2  O1   0.020
 NQW  plan-2  N4   0.020
 NQW  plan-2  C10  0.020
 NQW  plan-2  C9   0.020
 NQW  plan-2  C16  0.020
 NQW  plan-2  H15  0.020
 NQW  plan-2  H16  0.020
 NQW  plan-2  H20  0.020

