# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:21:09 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: ~{N}-(3-imidazol-1-ylpropyl)-8-(4-methoxyphenyl)-1,6-naphthyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2cncc3ccc(nc23)C(=O)NCCCn4ccnc4
#
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
 QKQ  QKQ  ~{N}-(3-imidazol-1-ylpropyl)-8-(4-methoxyphenyl)-1,6-naphthyridine-2-carboxamide  ligand  50  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QKQ
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
 QKQ  N1   N  N     0  -0.394   3.2879  26.7503  55.3718
 QKQ  N3   N  NR5   0  -0.394  -5.8401  32.0037  54.5391
 QKQ  C4   C  CR16  0  -0.287   1.2824  29.3760  52.5298
 QKQ  C5   C  CR6   0   0.054   1.1678  29.4868  53.9174
 QKQ  C6   C  CR6   0  -0.037   1.6088  28.3865  54.7918
 QKQ  C7   C  CR16  0  -0.129   2.8336  27.7827  54.6307
 QKQ  C8   C  CR16  0  -0.098   2.5254  26.2769  56.3179
 QKQ  C10  C  CR16  0  -0.174   0.3999  26.2792  57.6077
 QKQ  C15  C  CH2   0  -0.454  -4.9545  29.8016  55.2261
 QKQ  C17  C  CR15  0  -0.105  -5.2895  32.2971  53.3232
 QKQ  C20  C  CR66  0   0.288   0.7704  27.8689  55.8181
 QKQ  C21  C  CR16  0  -0.274   0.6123  30.6562  54.4312
 QKQ  C22  C  CR16  0  -0.373   0.1622  31.6726  53.6017
 QKQ  C1   C  CH3   0  -0.434  -0.8373  33.5995  51.8190
 QKQ  C11  C  CR16  0  -0.297  -0.8355  26.8338  57.7949
 QKQ  C12  C  CR6   0   0.127  -1.2137  27.9034  56.9587
 QKQ  C14  C  CH2   0  -0.288  -3.9750  30.3688  56.2477
 QKQ  C16  C  CH2   0  -0.324  -6.1808  30.6826  55.0343
 QKQ  C18  C  CR15  0  -0.213  -5.0887  33.6484  53.3279
 QKQ  C19  C  CR15  0   0.089  -5.9397  33.1679  55.2154
 QKQ  C2   C  CR6   0   0.376   0.2618  31.5356  52.2180
 QKQ  C3   C  CR16  0  -0.330   0.8394  30.3801  51.6892
 QKQ  C9   C  CR66  0  -0.012   1.2411  26.7922  56.5997
 QKQ  N2   N  NH1   0  -0.644  -2.7564  29.6014  56.3252
 QKQ  N4   N  N     0  -0.455  -5.4996  34.1828  54.5157
 QKQ  N5   N  N     0  -0.474  -0.4516  28.3901  56.0171
 QKQ  O1   O  O2    0  -0.468  -0.1678  32.4524  51.3328
 QKQ  O2   O  O     0  -0.475  -3.3775  28.1242  57.9360
 QKQ  H1   H  HCR6  0   0.257   1.6990  28.4765  52.0942
 QKQ  H2   H  HCR6  0   0.270   3.5155  28.1464  53.8698
 QKQ  H3   H  HCR6  0   0.277   2.9083  25.4484  56.9062
 QKQ  H4   H  HCR6  0   0.282   0.7374  25.4514  58.2189
 QKQ  H5   H  HCH2  0   0.243  -4.4461  29.6613  54.2687
 QKQ  H6   H  HCH2  0   0.258  -5.2935  28.8146  55.5480
 QKQ  H7   H  HCR5  0   0.290  -5.0988  31.5433  52.5775
 QKQ  H8   H  HCR6  0   0.258   0.5304  30.7931  55.5009
 QKQ  H9   H  HCR6  0   0.282  -0.2602  32.5596  54.0533
 QKQ  H10  H  HCH3  0   0.263  -1.1094  34.1904  50.9482
 QKQ  H11  H  HCH3  0   0.219  -1.7487  33.3375  52.3643
 QKQ  H12  H  HCH3  0   0.232  -0.1998  34.2036  52.4692
 QKQ  H13  H  HCR6  0   0.281  -1.5087  26.4659  58.5553
 QKQ  H14  H  HCH2  0   0.252  -4.4382  30.4145  57.2344
 QKQ  H15  H  HCH2  0   0.257  -3.6947  31.3887  55.9810
 QKQ  H16  H  HCH2  0   0.268  -6.7131  30.8133  55.9771
 QKQ  H17  H  HCH2  0   0.280  -6.8728  30.2111  54.3365
 QKQ  H18  H  HCR5  0   0.248  -4.6772  34.2576  52.5375
 QKQ  H19  H  HCR5  0   0.280  -6.3477  33.2146  56.2144
 QKQ  H20  H  HCR6  0   0.265   0.9212  30.2658  50.6155
 QKQ  H21  H  HNH1  0   0.409  -2.0059  29.8124  55.6828
 QKQ  C13  C  C     0   0.531  -2.5684  28.5495  57.1243

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
 QKQ  O1   C1   single    1.414  0.020  1.414
 QKQ  O1   C2   single    1.345  0.020  1.345
 QKQ  C3   C2   aromatic  1.396  0.020  1.396
 QKQ  C3   C4   aromatic  1.382  0.020  1.382
 QKQ  C2   C22  aromatic  1.394  0.020  1.394
 QKQ  C4   C5   aromatic  1.397  0.020  1.397
 QKQ  N4   C19  aromatic  1.309  0.020  1.309
 QKQ  N4   C18  aromatic  1.366  0.020  1.366
 QKQ  C19  N3   aromatic  1.350  0.020  1.350
 QKQ  C22  C21  aromatic  1.387  0.020  1.387
 QKQ  C18  C17  aromatic  1.366  0.020  1.366
 QKQ  C5   C21  aromatic  1.393  0.020  1.393
 QKQ  C5   C6   single    1.473  0.020  1.473
 QKQ  N2   C14  single    1.442  0.020  1.442
 QKQ  N2   C13  single    1.334  0.020  1.334
 QKQ  C14  C15  single    1.525  0.020  1.525
 QKQ  N3   C17  aromatic  1.367  0.020  1.367
 QKQ  N3   C16  single    1.451  0.020  1.451
 QKQ  C6   C20  aromatic  1.423  0.020  1.423
 QKQ  C6   C7   aromatic  1.375  0.020  1.375
 QKQ  C13  O2   double    1.222  0.020  1.222
 QKQ  C13  C12  single    1.510  0.020  1.510
 QKQ  N5   C20  aromatic  1.343  0.020  1.343
 QKQ  N5   C12  aromatic  1.306  0.020  1.306
 QKQ  C16  C15  single    1.522  0.020  1.522
 QKQ  C20  C9   aromatic  1.411  0.020  1.411
 QKQ  C12  C11  aromatic  1.409  0.020  1.409
 QKQ  C7   N1   aromatic  1.350  0.020  1.350
 QKQ  C9   C8   aromatic  1.412  0.020  1.412
 QKQ  C9   C10  aromatic  1.410  0.020  1.410
 QKQ  N1   C8   aromatic  1.304  0.020  1.304
 QKQ  C11  C10  aromatic  1.367  0.020  1.367
 QKQ  C4   H1   single    0.930  0.020  1.080
 QKQ  C7   H2   single    0.930  0.020  1.080
 QKQ  C8   H3   single    0.930  0.020  1.080
 QKQ  C10  H4   single    0.930  0.020  1.080
 QKQ  C15  H5   single    0.970  0.020  1.090
 QKQ  C15  H6   single    0.970  0.020  1.090
 QKQ  C17  H7   single    0.930  0.020  1.080
 QKQ  C21  H8   single    0.930  0.020  1.080
 QKQ  C22  H9   single    0.930  0.020  1.080
 QKQ  C1   H10  single    0.970  0.020  1.090
 QKQ  C1   H11  single    0.970  0.020  1.090
 QKQ  C1   H12  single    0.970  0.020  1.090
 QKQ  C11  H13  single    0.930  0.020  1.080
 QKQ  C14  H14  single    0.970  0.020  1.090
 QKQ  C14  H15  single    0.970  0.020  1.090
 QKQ  C16  H16  single    0.970  0.020  1.090
 QKQ  C16  H17  single    0.970  0.020  1.090
 QKQ  C18  H18  single    0.930  0.020  1.080
 QKQ  C19  H19  single    0.930  0.020  1.080
 QKQ  C3   H20  single    0.930  0.020  1.080
 QKQ  N2   H21  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
 QKQ  C8   N1   C7   118.64  3.000
 QKQ  C19  N3   C16  126.63  3.000
 QKQ  C16  N3   C17  126.41  3.000
 QKQ  C19  N3   C17  106.87  3.000
 QKQ  H1   C4   C3   118.81  3.000
 QKQ  H1   C4   C5   119.81  3.000
 QKQ  C3   C4   C5   121.35  3.000
 QKQ  C21  C5   C6   121.84  3.000
 QKQ  C6   C5   C4   120.40  3.000
 QKQ  C21  C5   C4   117.75  3.000
 QKQ  C20  C6   C7   116.72  3.000
 QKQ  C7   C6   C5   121.68  3.000
 QKQ  C20  C6   C5   121.57  3.000
 QKQ  H2   C7   C6   119.67  3.000
 QKQ  H2   C7   N1   115.48  3.000
 QKQ  C6   C7   N1   124.85  3.000
 QKQ  H3   C8   C9   119.40  3.000
 QKQ  H3   C8   N1   117.64  3.000
 QKQ  C9   C8   N1   122.96  3.000
 QKQ  H4   C10  C9   119.72  3.000
 QKQ  H4   C10  C11  120.96  3.000
 QKQ  C9   C10  C11  119.32  3.000
 QKQ  H6   C15  H5   106.65  3.000
 QKQ  H6   C15  C16  108.07  3.000
 QKQ  H5   C15  C16  109.79  3.000
 QKQ  H6   C15  C14  109.77  3.000
 QKQ  H5   C15  C14  109.62  3.000
 QKQ  C16  C15  C14  112.75  3.000
 QKQ  H7   C17  C18  131.95  3.000
 QKQ  H7   C17  N3   122.47  3.000
 QKQ  C18  C17  N3   105.58  3.000
 QKQ  N5   C20  C9   121.15  3.000
 QKQ  C9   C20  C6   118.72  3.000
 QKQ  N5   C20  C6   120.12  3.000
 QKQ  H8   C21  C22  118.31  3.000
 QKQ  H8   C21  C5   120.08  3.000
 QKQ  C22  C21  C5   121.61  3.000
 QKQ  H9   C22  C2   121.54  3.000
 QKQ  H9   C22  C21  118.57  3.000
 QKQ  C2   C22  C21  119.89  3.000
 QKQ  H12  C1   H11  108.77  3.000
 QKQ  H12  C1   H10  108.80  3.000
 QKQ  H11  C1   H10  108.72  3.000
 QKQ  H12  C1   O1   112.13  3.000
 QKQ  H11  C1   O1   111.81  3.000
 QKQ  H10  C1   O1   106.50  3.000
 QKQ  H13  C11  C12  120.59  3.000
 QKQ  H13  C11  C10  121.43  3.000
 QKQ  C12  C11  C10  117.98  3.000
 QKQ  N5   C12  C11  123.65  3.000
 QKQ  C11  C12  C13  120.03  3.000
 QKQ  N5   C12  C13  116.32  3.000
 QKQ  H15  C14  H14  106.92  3.000
 QKQ  H15  C14  N2   107.07  3.000
 QKQ  H14  C14  N2   109.42  3.000
 QKQ  H15  C14  C15  110.43  3.000
 QKQ  H14  C14  C15  110.41  3.000
 QKQ  N2   C14  C15  112.39  3.000
 QKQ  H17  C16  H16  107.18  3.000
 QKQ  H17  C16  C15  109.98  3.000
 QKQ  H16  C16  C15  110.71  3.000
 QKQ  H17  C16  N3   108.92  3.000
 QKQ  H16  C16  N3   107.49  3.000
 QKQ  C15  C16  N3   112.38  3.000
 QKQ  H18  C18  N4   122.04  3.000
 QKQ  H18  C18  C17  127.72  3.000
 QKQ  N4   C18  C17  110.24  3.000
 QKQ  H19  C19  N4   126.01  3.000
 QKQ  H19  C19  N3   121.91  3.000
 QKQ  N4   C19  N3   112.09  3.000
 QKQ  O1   C2   C3   116.56  3.000
 QKQ  C3   C2   C22  119.14  3.000
 QKQ  O1   C2   C22  124.30  3.000
 QKQ  H20  C3   C2   119.62  3.000
 QKQ  H20  C3   C4   120.14  3.000
 QKQ  C2   C3   C4   120.23  3.000
 QKQ  C20  C9   C10  118.34  3.000
 QKQ  C10  C9   C8   123.55  3.000
 QKQ  C20  C9   C8   118.11  3.000
 QKQ  H21  N2   C14  118.84  3.000
 QKQ  H21  N2   C13  116.16  3.000
 QKQ  C14  N2   C13  124.80  3.000
 QKQ  C19  N4   C18  105.23  3.000
 QKQ  C12  N5   C20  119.56  3.000
 QKQ  C2   O1   C1   118.54  3.000
 QKQ  O2   C13  N2   125.35  3.000
 QKQ  O2   C13  C12  121.19  3.000
 QKQ  N2   C13  C12  113.45  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
 QKQ  CONST_01  C5   C6   C7   N1    180.00   0.0  0
 QKQ  CONST_02  C20  C6   C7   N1      0.00   0.0  0
 QKQ  CONST_03  C20  C9   C8   N1      0.00   0.0  0
 QKQ  CONST_04  C10  C9   C8   N1    180.00   0.0  0
 QKQ  CONST_05  C18  N4   C19  N3      0.00   0.0  0
 QKQ  CONST_06  N4   C18  C17  N3      0.00   0.0  0
 QKQ  CONST_07  C22  C2   C3   C4      0.00   0.0  0
 QKQ  CONST_08  C22  C21  C5   C4      0.00   0.0  0
 QKQ  CONST_11  C2   C3   C4   C5      0.00   0.0  0
 QKQ  CONST_12  C2   C22  C21  C5      0.00   0.0  0
 QKQ  CONST_13  N5   C20  C6   C5      0.00   0.0  0
 QKQ  CONST_14  C9   C20  C6   C5    180.00   0.0  0
 QKQ  CONST_15  C3   C4   C5   C6    180.00   0.0  0
 QKQ  CONST_16  C22  C21  C5   C6    180.00   0.0  0
 QKQ  CONST_17  C12  N5   C20  C6    180.00   0.0  0
 QKQ  CONST_18  C8   C9   C20  C6      0.00   0.0  0
 QKQ  CONST_19  C10  C9   C20  C6    180.00   0.0  0
 QKQ  CONST_20  C8   N1   C7   C6      0.00   0.0  0
 QKQ  CONST_22  N5   C20  C6   C7    180.00   0.0  0
 QKQ  CONST_23  C9   C20  C6   C7      0.00   0.0  0
 QKQ  CONST_24  C9   C8   N1   C7      0.00   0.0  0
 QKQ  CONST_25  N5   C20  C9   C8    180.00   0.0  0
 QKQ  CONST_26  C11  C10  C9   C8    180.00   0.0  0
 QKQ  CONST_27  N5   C20  C9   C10     0.00   0.0  0
 QKQ  CONST_28  N5   C12  C11  C10     0.00   0.0  0
 QKQ  CONST_29  C19  N4   C18  C17     0.00   0.0  0
 QKQ  CONST_30  N4   C19  N3   C17     0.00   0.0  0
 QKQ  CONST_32  C11  C12  N5   C20     0.00   0.0  0
 QKQ  CONST_33  C11  C10  C9   C20     0.00   0.0  0
 QKQ  CONST_34  C3   C2   C22  C21     0.00   0.0  0
 QKQ  CONST_35  C3   C4   C5   C21     0.00   0.0  0
 QKQ  CONST_36  C9   C20  N5   C12     0.00   0.0  0
 QKQ  CONST_37  C9   C10  C11  C12     0.00   0.0  0
 QKQ  CONST_38  C19  N3   C17  C18     0.00   0.0  0
 QKQ  CONST_39  O1   C2   C3   C4    180.00   0.0  0
 QKQ  CONST_40  C13  C12  C11  C10   180.00   0.0  0
 QKQ  CONST_41  C20  N5   C12  C13   180.00   0.0  0
 QKQ  CONST_42  O1   C2   C22  C21   180.00   0.0  0
 QKQ  CONST_43  N4   C19  N3   C16   180.00   0.0  0
 QKQ  CONST_44  C18  C17  N3   C16   180.00   0.0  0
 QKQ  CONST_45  H18  C18  C17  N3    180.00   0.0  0
 QKQ  CONST_46  H8   C21  C5   C4    180.00   0.0  0
 QKQ  CONST_47  H20  C3   C4   C5    180.00   0.0  0
 QKQ  CONST_48  H9   C22  C21  C5    180.00   0.0  0
 QKQ  CONST_49  H2   C7   C6   C5      0.00   0.0  0
 QKQ  CONST_50  H1   C4   C5   C6      0.00   0.0  0
 QKQ  CONST_51  H3   C8   N1   C7    180.00   0.0  0
 QKQ  CONST_52  H4   C10  C9   C8      0.00   0.0  0
 QKQ  CONST_53  H19  C19  N3   C17   180.00   0.0  0
 QKQ  CONST_54  H7   C17  N3   C19   180.00   0.0  0
 QKQ  CONST_55  H13  C11  C10  C9    180.00   0.0  0
 QKQ  CONST_56  C14  N2   C13  C12   180.00   0.0  0
 QKQ  CONST_57  H21  N2   C13  C12     0.00   0.0  0
 QKQ  CONST_58  O2   C13  N2   C14     0.00   0.0  0
 QKQ  Var_01    C19  N3   C16  C15  -111.19  30.0  3
 QKQ  Var_02    C3   C2   O1   C1    175.98  30.0  2
 QKQ  Var_03    N2   C13  C12  C11   175.93  30.0  2
 QKQ  Var_04    C14  C15  C16  N3     61.41  30.0  3
 QKQ  Var_05    H10  C1   O1   C2   -179.03  30.0  3
 QKQ  Var_06    C15  C14  N2   C13   -88.57  30.0  3
 QKQ  Var_07    N2   C14  C15  C16  -174.14  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
 QKQ  plan-1  N3   0.020
 QKQ  plan-1  C17  0.020
 QKQ  plan-1  C16  0.020
 QKQ  plan-1  C18  0.020
 QKQ  plan-1  C19  0.020
 QKQ  plan-1  N4   0.020
 QKQ  plan-1  H7   0.020
 QKQ  plan-1  H18  0.020
 QKQ  plan-1  H19  0.020
 QKQ  plan-2  C4   0.020
 QKQ  plan-2  C5   0.020
 QKQ  plan-2  C6   0.020
 QKQ  plan-2  C21  0.020
 QKQ  plan-2  C22  0.020
 QKQ  plan-2  C2   0.020
 QKQ  plan-2  C3   0.020
 QKQ  plan-2  O1   0.020
 QKQ  plan-2  H1   0.020
 QKQ  plan-2  H8   0.020
 QKQ  plan-2  H9   0.020
 QKQ  plan-2  H20  0.020
 QKQ  plan-3  N1   0.020
 QKQ  plan-3  C5   0.020
 QKQ  plan-3  C6   0.020
 QKQ  plan-3  C7   0.020
 QKQ  plan-3  C8   0.020
 QKQ  plan-3  C10  0.020
 QKQ  plan-3  C20  0.020
 QKQ  plan-3  C11  0.020
 QKQ  plan-3  C12  0.020
 QKQ  plan-3  C9   0.020
 QKQ  plan-3  N5   0.020
 QKQ  plan-3  H2   0.020
 QKQ  plan-3  H3   0.020
 QKQ  plan-3  H4   0.020
 QKQ  plan-3  H13  0.020
 QKQ  plan-3  C13  0.020
 QKQ  plan-4  C12  0.020
 QKQ  plan-4  C14  0.020
 QKQ  plan-4  N2   0.020
 QKQ  plan-4  O2   0.020
 QKQ  plan-4  H21  0.020
 QKQ  plan-4  C13  0.020

