# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:43:09 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 8-[4-[1-(cyclobutylmethyl)piperidin-4-yl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2c1ccnc2n3cc(cn3)C4CCN(CC4)CC5CCC5
#
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
 FQK  FQK  8-[4-[1-(cyclobutylmethyl)piperidin-4-yl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  51  27  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FQK
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
 FQK  C1   C  CR16  0  -0.064  -4.6850   2.3601   0.3314
 FQK  C2   C  CR6   0   0.438  -3.1063   0.7111   0.2662
 FQK  C3   C  CR66  0   0.156  -4.0717  -0.2968   0.0419
 FQK  C4   C  CR66  0  -0.017  -5.4068   0.1207   0.0283
 FQK  C5   C  CR6   0   0.580  -6.4606  -0.8769  -0.1825
 FQK  C6   C  CR16  0   0.151  -4.6353  -2.4373  -0.3910
 FQK  C7   C  CR15  0  -0.081   0.0120  -0.5625   0.9901
 FQK  C8   C  CR5   0  -0.078   0.4403   0.4915   0.1473
 FQK  C10  C  CH1   0  -0.362   1.8364   0.8684  -0.2280
 FQK  C11  C  CH2   0  -0.413   2.5975  -0.2936  -0.8659
 FQK  C13  C  CH2   0  -0.280   4.0631   1.7105   0.5767
 FQK  C14  C  CH2   0  -0.413   2.6313   1.3865   0.9718
 FQK  O    O  O     0  -0.433  -7.6509  -0.6404  -0.1914
 FQK  C    C  CR16  0  -0.355  -5.7219   1.4692   0.1809
 FQK  N1   N  NR16  0  -0.659  -5.9598  -2.1413  -0.3793
 FQK  N2   N  N     0  -0.430  -3.6934  -1.5924  -0.1903
 FQK  N    N  N     0  -0.398  -3.4063   1.9789   0.3858
 FQK  N3   N  NR5   0  -0.369  -1.7415   0.3956   0.3383
 FQK  C9   C  CR15  0   0.004  -0.7284   1.0911  -0.2395
 FQK  N4   N  N     0  -0.267  -1.2968  -0.6098   1.0972
 FQK  N5   N  NT    0  -0.411   4.7303   0.5566   0.0034
 FQK  C12  C  CH2   0  -0.283   4.0336   0.0946  -1.1826
 FQK  C15  C  CH2   0  -0.255   6.1349   0.8262  -0.2396
 FQK  H1   H  HCR6  0   0.282  -4.8735   3.4214   0.4282
 FQK  H2   H  HCR6  0   0.307  -4.3994  -3.4747  -0.5908
 FQK  H3   H  HCR5  0   0.259   0.6202  -1.2791   1.5228
 FQK  H4   H  HCH1  0   0.234   1.7800   1.6781  -0.9663
 FQK  H5   H  HCH2  0   0.217   2.6017  -1.1514  -0.1858
 FQK  H6   H  HCH2  0   0.235   2.0965  -0.6140  -1.7822
 FQK  H7   H  HCH2  0   0.182   4.0592   2.5661  -0.1247
 FQK  H8   H  HCH2  0   0.233   4.6207   2.0329   1.4597
 FQK  H9   H  HCH2  0   0.235   2.1546   2.2798   1.3817
 FQK  H10  H  HCH2  0   0.218   2.6359   0.6323   1.7654
 FQK  H11  H  HCR6  0   0.286  -6.7479   1.8091   0.1693
 FQK  H12  H  HNR6  0   0.440  -6.6208  -2.8899  -0.5449
 FQK  H13  H  HCR5  0   0.291  -0.9122   1.9356  -0.8839
 FQK  H15  H  HCH2  0   0.240   4.5517  -0.7743  -1.5911
 FQK  H16  H  HCH2  0   0.182   4.0366   0.8664  -1.9756
 FQK  H17  H  HCH2  0   0.190   6.2781   1.5789  -1.0369
 FQK  H19  H  HCH2  0   0.214   6.5464   1.2665   0.6748
 FQK  C16  C  C     0  -0.258   6.9313  -0.4206  -0.5601
 FQK  C17  C  C     0  -0.431   8.4661  -0.3654  -0.4105
 FQK  C18  C  C     0  -0.455   8.4135  -1.7904   0.1745
 FQK  C19  C  C     0  -0.427   6.9160  -1.5697   0.4634
 FQK  H18  H  H     0   0.216   6.7494  -1.1923   1.4749
 FQK  H14  H  H     0   0.223   6.2289  -2.3983   0.2887
 FQK  H24  H  H     0   0.222   8.5692  -2.5474  -0.5960
 FQK  H25  H  H     0   0.225   9.0672  -2.0173   1.0172
 FQK  H23  H  H     0   0.226   9.0624  -0.2016  -1.3088
 FQK  H22  H  H     0   0.217   8.7663   0.3665   0.3432
 FQK  H21  H  H     0   0.233   6.6835  -0.8050  -1.5534

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
 FQK  C12  C11  single    1.521  0.020  1.521
 FQK  C12  N5   single    1.451  0.020  1.451
 FQK  C11  C10  single    1.529  0.020  1.529
 FQK  C7   N4   aromatic  1.314  0.020  1.314
 FQK  C7   C8   aromatic  1.416  0.020  1.416
 FQK  C10  C8   single    1.494  0.020  1.494
 FQK  C10  C14  single    1.530  0.020  1.530
 FQK  N4   N3   aromatic  1.336  0.020  1.336
 FQK  C8   C9   aromatic  1.369  0.020  1.369
 FQK  C15  N5   single    1.451  0.020  1.451
 FQK  N5   C13  single    1.451  0.020  1.451
 FQK  N3   C9   aromatic  1.358  0.020  1.358
 FQK  N3   C2   single    1.403  0.020  1.403
 FQK  N    C2   aromatic  1.308  0.020  1.308
 FQK  N    C1   aromatic  1.335  0.020  1.335
 FQK  C2   C3   aromatic  1.414  0.020  1.414
 FQK  C13  C14  single    1.520  0.020  1.520
 FQK  N2   C3   single    1.369  0.020  1.369
 FQK  N2   C6   double    1.281  0.020  1.281
 FQK  C3   C4   aromatic  1.399  0.020  1.399
 FQK  C1   C    aromatic  1.375  0.020  1.375
 FQK  C6   N1   single    1.357  0.020  1.357
 FQK  C4   C    aromatic  1.393  0.020  1.393
 FQK  C4   C5   single    1.466  0.020  1.466
 FQK  N1   C5   single    1.374  0.020  1.374
 FQK  C5   O    double    1.214  0.020  1.214
 FQK  C1   H1   single    0.930  0.020  1.080
 FQK  C6   H2   single    0.930  0.020  1.080
 FQK  C7   H3   single    0.930  0.020  1.080
 FQK  C10  H4   single    0.970  0.020  1.090
 FQK  C11  H5   single    0.970  0.020  1.090
 FQK  C11  H6   single    0.970  0.020  1.090
 FQK  C13  H7   single    0.970  0.020  1.090
 FQK  C13  H8   single    0.970  0.020  1.090
 FQK  C14  H9   single    0.970  0.020  1.090
 FQK  C14  H10  single    0.970  0.020  1.090
 FQK  C    H11  single    0.930  0.020  1.080
 FQK  N1   H12  single    0.860  0.020  1.020
 FQK  C9   H13  single    0.930  0.020  1.080
 FQK  C12  H15  single    0.970  0.020  1.090
 FQK  C12  H16  single    0.970  0.020  1.090
 FQK  C15  H17  single    0.970  0.020  1.090
 FQK  C15  H19  single    0.970  0.020  1.090
 FQK  C15  C16  single    1.514  0.020  1.514
 FQK  C16  C17  single    1.543  0.020  1.543
 FQK  C17  C18  single    1.541  0.020  1.541
 FQK  C18  C19  single    1.541  0.020  1.541
 FQK  C19  C16  single    1.539  0.020  1.539
 FQK  C19  H18  single    0.970  0.020  1.090
 FQK  C19  H14  single    0.970  0.020  1.090
 FQK  C18  H24  single    0.970  0.020  1.090
 FQK  C18  H25  single    0.970  0.020  1.090
 FQK  C17  H23  single    0.970  0.020  1.090
 FQK  C17  H22  single    0.970  0.020  1.090
 FQK  C16  H21  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
 FQK  H1   C1   N    116.30  3.000
 FQK  H1   C1   C    120.91  3.000
 FQK  N    C1   C    122.78  3.000
 FQK  N3   C2   N    115.87  3.000
 FQK  N    C2   C3   123.29  3.000
 FQK  N3   C2   C3   120.82  3.000
 FQK  N2   C3   C4   122.98  3.000
 FQK  C4   C3   C2   116.14  3.000
 FQK  N2   C3   C2   120.84  3.000
 FQK  C    C4   C5   120.79  3.000
 FQK  C5   C4   C3   118.96  3.000
 FQK  C    C4   C3   120.24  3.000
 FQK  N1   C5   O    122.39  3.000
 FQK  O    C5   C4   124.98  3.000
 FQK  N1   C5   C4   112.63  3.000
 FQK  H2   C6   N2   120.04  3.000
 FQK  H2   C6   N1   115.04  3.000
 FQK  N2   C6   N1   124.91  3.000
 FQK  H3   C7   N4   119.78  3.000
 FQK  H3   C7   C8   128.10  3.000
 FQK  N4   C7   C8   112.12  3.000
 FQK  C9   C8   C10  128.04  3.000
 FQK  C9   C8   C7   103.65  3.000
 FQK  C10  C8   C7   128.31  3.000
 FQK  H4   C10  C14  107.73  3.000
 FQK  H4   C10  C11  107.81  3.000
 FQK  C14  C10  C11  109.03  3.000
 FQK  H4   C10  C8   107.88  3.000
 FQK  C14  C10  C8   111.97  3.000
 FQK  C11  C10  C8   112.23  3.000
 FQK  H6   C11  H5   107.04  3.000
 FQK  H6   C11  C12  109.46  3.000
 FQK  H5   C11  C12  109.01  3.000
 FQK  H6   C11  C10  110.16  3.000
 FQK  H5   C11  C10  109.77  3.000
 FQK  C12  C11  C10  111.28  3.000
 FQK  H8   C13  H7   106.61  3.000
 FQK  H8   C13  N5   108.62  3.000
 FQK  H7   C13  N5   111.48  3.000
 FQK  H8   C13  C14  109.47  3.000
 FQK  H7   C13  C14  109.04  3.000
 FQK  N5   C13  C14  111.48  3.000
 FQK  H10  C14  H9   107.04  3.000
 FQK  H10  C14  C13  109.34  3.000
 FQK  H9   C14  C13  109.53  3.000
 FQK  H10  C14  C10  109.72  3.000
 FQK  H9   C14  C10  110.16  3.000
 FQK  C13  C14  C10  110.96  3.000
 FQK  H11  C    C4   121.18  3.000
 FQK  H11  C    C1   120.87  3.000
 FQK  C4   C    C1   117.94  3.000
 FQK  H12  N1   C6   118.33  3.000
 FQK  H12  N1   C5   117.77  3.000
 FQK  C6   N1   C5   123.89  3.000
 FQK  C6   N2   C3   116.57  3.000
 FQK  C2   N    C1   119.50  3.000
 FQK  N4   N3   C9   112.26  3.000
 FQK  C9   N3   C2   126.08  3.000
 FQK  N4   N3   C2   121.49  3.000
 FQK  H13  C9   N3   121.89  3.000
 FQK  H13  C9   C8   131.10  3.000
 FQK  N3   C9   C8   107.00  3.000
 FQK  N3   N4   C7   104.96  3.000
 FQK  C15  N5   C12  112.77  3.000
 FQK  C15  N5   C13  111.32  3.000
 FQK  C12  N5   C13  110.82  3.000
 FQK  H16  C12  H15  106.61  3.000
 FQK  H16  C12  N5   111.24  3.000
 FQK  H15  C12  N5   109.37  3.000
 FQK  H16  C12  C11  109.26  3.000
 FQK  H15  C12  C11  108.85  3.000
 FQK  N5   C12  C11  111.37  3.000
 FQK  C16  C15  H19  108.07  3.000
 FQK  C16  C15  H17  109.87  3.000
 FQK  H19  C15  H17  106.24  3.000
 FQK  C16  C15  N5   113.07  3.000
 FQK  H19  C15  N5   107.38  3.000
 FQK  H17  C15  N5   111.88  3.000
 FQK  H21  C16  C19  109.83  3.000
 FQK  H21  C16  C17  109.03  3.000
 FQK  C19  C16  C17   88.40  3.000
 FQK  H21  C16  C15  111.26  3.000
 FQK  C19  C16  C15  117.97  3.000
 FQK  C17  C16  C15  118.25  3.000
 FQK  H22  C17  H23  108.51  3.000
 FQK  H22  C17  C18  111.52  3.000
 FQK  H23  C17  C18  118.04  3.000
 FQK  H22  C17  C16  111.35  3.000
 FQK  H23  C17  C16  117.99  3.000
 FQK  C18  C17  C16   88.27  3.000
 FQK  H25  C18  H24  108.41  3.000
 FQK  H25  C18  C19  117.87  3.000
 FQK  H24  C18  C19  111.74  3.000
 FQK  H25  C18  C17  117.72  3.000
 FQK  H24  C18  C17  111.62  3.000
 FQK  C19  C18  C17   88.39  3.000
 FQK  H14  C19  H18  108.35  3.000
 FQK  H14  C19  C18  118.26  3.000
 FQK  H18  C19  C18  111.80  3.000
 FQK  H14  C19  C16  117.85  3.000
 FQK  H18  C19  C16  111.06  3.000
 FQK  C18  C19  C16   88.43  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
 FQK  CONST_01  N3   C2   N    C1   180.00   0.0  0
 FQK  CONST_02  C3   C2   N    C1     0.00   0.0  0
 FQK  CONST_03  C3   C4   C    C1     0.00   0.0  0
 FQK  CONST_04  C7   N4   N3   C2   180.00   0.0  0
 FQK  CONST_05  C8   C9   N3   C2   180.00   0.0  0
 FQK  CONST_06  C    C1   N    C2     0.00   0.0  0
 FQK  CONST_07  C    C4   C3   C2     0.00   0.0  0
 FQK  CONST_10  N3   C2   C3   C4   180.00   0.0  0
 FQK  CONST_11  N    C2   C3   C4     0.00   0.0  0
 FQK  CONST_12  N    C1   C    C4     0.00   0.0  0
 FQK  CONST_13  C9   N3   N4   C7     0.00   0.0  0
 FQK  CONST_14  N3   C9   C8   C7     0.00   0.0  0
 FQK  CONST_15  N3   N4   C7   C8     0.00   0.0  0
 FQK  CONST_16  N4   N3   C9   C8     0.00   0.0  0
 FQK  CONST_19  N4   C7   C8   C9     0.00   0.0  0
 FQK  CONST_20  N4   C7   C8   C10  180.00   0.0  0
 FQK  CONST_21  N3   C9   C8   C10  180.00   0.0  0
 FQK  CONST_22  N3   C2   C3   N2     0.00   0.0  0
 FQK  CONST_23  N1   C6   N2   C3     0.00   0.0  0
 FQK  CONST_24  C6   N1   C5   C4     0.00   0.0  0
 FQK  CONST_25  N2   C6   N1   C5     0.00   0.0  0
 FQK  CONST_26  O    C5   N1   C6   180.00   0.0  0
 FQK  CONST_27  H13  C9   N3   C2     0.00   0.0  0
 FQK  CONST_28  H1   C1   N    C2   180.00   0.0  0
 FQK  CONST_29  H11  C    C4   C3   180.00   0.0  0
 FQK  CONST_30  H3   C7   C8   C10    0.00   0.0  0
 FQK  CONST_31  H2   C6   N2   C3   180.00   0.0  0
 FQK  CONST_32  H12  N1   C5   C4   180.00   0.0  0
 FQK  Var_01    N5   C12  C11  C10   56.70  30.0  1
 FQK  Var_02    N5   C13  C14  C10  -57.15  30.0  1
 FQK  Var_03    C13  N5   C12  C11  -59.41  30.0  1
 FQK  Var_04    C12  N5   C13  C14   59.78  30.0  1
 FQK  Var_05    C19  C18  C17  C16  -19.11  30.0  1
 FQK  Var_06    C16  C15  N5   C13  167.93  30.0  1

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
 FQK  chir_01  C10  C11  C8   C14  negativ
 FQK  chir_02  C16  C15  C17  C19  negativ

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
 FQK  plan-1  C2   0.020
 FQK  plan-1  C7   0.020
 FQK  plan-1  C8   0.020
 FQK  plan-1  C10  0.020
 FQK  plan-1  N3   0.020
 FQK  plan-1  C9   0.020
 FQK  plan-1  N4   0.020
 FQK  plan-1  H3   0.020
 FQK  plan-1  H13  0.020
 FQK  plan-2  C1   0.020
 FQK  plan-2  C2   0.020
 FQK  plan-2  C3   0.020
 FQK  plan-2  C4   0.020
 FQK  plan-2  C5   0.020
 FQK  plan-2  C6   0.020
 FQK  plan-2  O    0.020
 FQK  plan-2  C    0.020
 FQK  plan-2  N1   0.020
 FQK  plan-2  N2   0.020
 FQK  plan-2  N    0.020
 FQK  plan-2  N3   0.020
 FQK  plan-2  H1   0.020
 FQK  plan-2  H2   0.020
 FQK  plan-2  H11  0.020
 FQK  plan-2  H12  0.020

