# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:43:29 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-cyclopropyl-4-methyl-3-[8-methyl-7-oxo-2-(tetrahydro-2H-pyran-4-ylamino)-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Cc2cnc(NC3CCOCC3)nc12)c4cc(ccc4C)C(=O)NC5CC5
#
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
 FKL  FKL  N-cyclopropyl-4-methyl-3-[8-methyl-7-oxo-2-(tetrahydro-2H-pyran-4-ylamino)-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl]benzamide  ligand  59  32  .  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_FKL
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
 FKL  N1    N  N     0  -0.468   3.4622  -0.6437  -0.9240
 FKL  N3    N  N     0  -0.512   2.9564   1.0830   0.6431
 FKL  C4    C  CR16  0  -0.033   2.2023  -0.6528  -1.2877
 FKL  C5    C  CR66  0  -0.117   1.2310   0.1791  -0.7324
 FKL  C6    C  CR66  0   0.566   1.6921   1.0578   0.2662
 FKL  C8    C  CR6   0   0.565  -0.5520   1.9265   0.5479
 FKL  C10   C  CR16  0  -0.170  -0.1368   0.1893  -1.1051
 FKL  C15   C  CR16  0  -0.307  -3.2285  -0.0415  -0.5270
 FKL  C17   C  CR16  0  -0.293  -5.1469   0.9819  -1.5227
 FKL  C24   C  CH1   0  -0.079  -7.5338  -2.2706  -0.0043
 FKL  C26   C  CH2   0  -0.519  -8.7545  -1.9834   0.8060
 FKL  C28   C  CH2   0  -0.470   7.4806   0.0231   0.1735
 FKL  O22   O  O     0  -0.486  -4.7837  -2.3666  -0.2033
 FKL  N23   N  NH1   0  -0.662  -6.6866  -1.1736  -0.3382
 FKL  C25   C  CH2   0  -0.481  -7.6093  -2.7310   1.4176
 FKL  C16   C  CR6   0  -0.032  -4.5854  -0.0898  -0.8365
 FKL  C18   C  CR16  0  -0.283  -4.3644   2.0702  -1.8757
 FKL  C19   C  CR6   0   0.079  -3.0131   2.1351  -1.5512
 FKL  C14   C  CR6   0   0.095  -2.4448   1.0547  -0.8603
 FKL  C9    C  CR6   0  -0.227  -1.0071   1.0351  -0.5117
 FKL  O13   O  O     0  -0.465  -1.3035   2.6696   1.1599
 FKL  N7    N  NR6   0  -0.586   0.8019   1.9063   0.8658
 FKL  C12   C  CH3   0  -0.541   1.2358   2.8219   1.9140
 FKL  C2    C  CR6   0   0.623   3.7947   0.2377   0.0392
 FKL  N11   N  NH1   0  -0.655   5.0764   0.2879   0.4234
 FKL  C27   C  CH1   0  -0.066   6.1128  -0.6228  -0.0145
 FKL  C32   C  CH2   0  -0.456   6.0708  -1.9574   0.7296
 FKL  C31   C  CH2   0  -0.185   7.2553  -2.8218   0.3266
 FKL  O30   O  O2    0  -0.483   8.4845  -2.1629   0.5415
 FKL  C29   C  CH2   0  -0.183   8.5770  -0.9651  -0.1969
 FKL  H4    H  HCR6  0   0.278   1.9199  -1.3573  -2.0645
 FKL  H10   H  HCR6  0   0.274  -0.4739  -0.4861  -1.8830
 FKL  H15   H  HCR6  0   0.252  -2.7732  -0.8722  -0.0031
 FKL  H17   H  HCR6  0   0.256  -6.1877   0.9784  -1.8220
 FKL  H20   H  HCH3  0   0.256  -1.9631   3.9534  -1.0991
 FKL  H20A  H  HCH3  0   0.247  -1.2471   3.0248  -2.4056
 FKL  H20B  H  HCH3  0   0.252  -2.7316   3.9379  -2.6810
 FKL  H24   H  HCH1  0   0.269  -7.6184  -3.0334  -0.7718
 FKL  H26   H  HCH2  0   0.259  -8.9190  -0.9617   1.1258
 FKL  H26A  H  HCH2  0   0.260  -9.6584  -2.5242   0.5595
 FKL  H28   H  HCH2  0   0.250   7.5725   0.9141  -0.4517
 FKL  H28A  H  HCH2  0   0.232   7.6052   0.3373   1.2155
 FKL  HN23  H  HNH1  0   0.409  -7.1178  -0.2826  -0.5203
 FKL  H25   H  HCH2  0   0.255  -7.7187  -3.7926   1.5970
 FKL  H25A  H  HCH2  0   0.255  -6.9976  -2.2103   2.1428
 FKL  H18   H  HCR6  0   0.257  -4.8158   2.8851  -2.4280
 FKL  H12   H  HCH3  0   0.256   0.9327   3.8373   1.6712
 FKL  H12A  H  HCH3  0   0.256   0.7959   2.5423   2.8696
 FKL  H12B  H  HCH3  0   0.274   2.3143   2.7797   1.9949
 FKL  HN11  H  HNH1  0   0.394   5.2809   0.8973   1.2005
 FKL  H27   H  HCH1  0   0.248   5.9627  -0.8132  -1.0805
 FKL  H32   H  HCH2  0   0.227   6.0938  -1.7732   1.8080
 FKL  H32A  H  HCH2  0   0.244   5.1424  -2.4868   0.5054
 FKL  H31   H  HCH2  0   0.239   7.2774  -3.7400   0.9155
 FKL  H31A  H  HCH2  0   0.200   7.1571  -3.1116  -0.7303
 FKL  H29   H  HCH2  0   0.200   8.5268  -1.1771  -1.2753
 FKL  H29A  H  HCH2  0   0.241   9.5595  -0.5373   0.0068
 FKL  C20   C  CH3   0  -0.746  -2.1963   3.3234  -1.9587
 FKL  C21   C  C     0   0.537  -5.3522  -1.3087  -0.4364

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
 FKL  N1   C4    aromatic  1.311  0.020  1.311
 FKL  N1   C2    aromatic  1.347  0.020  1.347
 FKL  N3   C6    aromatic  1.319  0.020  1.319
 FKL  N3   C2    aromatic  1.335  0.020  1.335
 FKL  C4   C5    aromatic  1.394  0.020  1.394
 FKL  C5   C6    aromatic  1.408  0.020  1.408
 FKL  C5   C10   single    1.418  0.020  1.418
 FKL  C6   N7    single    1.368  0.020  1.368
 FKL  C8   C9    single    1.458  0.020  1.458
 FKL  C8   O13   double    1.221  0.020  1.221
 FKL  C8   N7    single    1.391  0.020  1.391
 FKL  C10  C9    double    1.351  0.020  1.351
 FKL  C15  C16   aromatic  1.393  0.020  1.393
 FKL  C15  C14   aromatic  1.388  0.020  1.388
 FKL  C17  C16   aromatic  1.391  0.020  1.391
 FKL  C17  C18   aromatic  1.386  0.020  1.386
 FKL  C20  C19   single    1.498  0.020  1.498
 FKL  C21  O22   double    1.223  0.020  1.223
 FKL  C21  N23   single    1.345  0.020  1.345
 FKL  C21  C16   single    1.495  0.020  1.495
 FKL  C24  C26   single    1.493  0.020  1.493
 FKL  C24  N23   single    1.426  0.020  1.426
 FKL  C24  C25   single    1.497  0.020  1.497
 FKL  C26  C25   single    1.498  0.020  1.498
 FKL  C28  C27   single    1.524  0.020  1.524
 FKL  C28  C29   single    1.522  0.020  1.522
 FKL  C18  C19   aromatic  1.391  0.020  1.391
 FKL  C19  C14   aromatic  1.403  0.020  1.403
 FKL  C14  C9    single    1.480  0.020  1.480
 FKL  N7   C12   single    1.458  0.020  1.458
 FKL  C2   N11   single    1.339  0.020  1.339
 FKL  N11  C27   single    1.448  0.020  1.448
 FKL  C27  C32   single    1.529  0.020  1.529
 FKL  C32  C31   single    1.521  0.020  1.521
 FKL  C31  O30   single    1.411  0.020  1.411
 FKL  O30  C29   single    1.410  0.020  1.410
 FKL  C4   H4    single    0.930  0.020  1.080
 FKL  C10  H10   single    0.930  0.020  1.080
 FKL  C15  H15   single    0.930  0.020  1.080
 FKL  C17  H17   single    0.930  0.020  1.080
 FKL  C20  H20   single    0.970  0.020  1.090
 FKL  C20  H20A  single    0.970  0.020  1.090
 FKL  C20  H20B  single    0.970  0.020  1.090
 FKL  C24  H24   single    0.970  0.020  1.090
 FKL  C26  H26   single    0.970  0.020  1.090
 FKL  C26  H26A  single    0.970  0.020  1.090
 FKL  C28  H28   single    0.970  0.020  1.090
 FKL  C28  H28A  single    0.970  0.020  1.090
 FKL  N23  HN23  single    0.860  0.020  1.020
 FKL  C25  H25   single    0.970  0.020  1.090
 FKL  C25  H25A  single    0.970  0.020  1.090
 FKL  C18  H18   single    0.930  0.020  1.080
 FKL  C12  H12   single    0.970  0.020  1.090
 FKL  C12  H12A  single    0.970  0.020  1.090
 FKL  C12  H12B  single    0.970  0.020  1.090
 FKL  N11  HN11  single    0.860  0.020  1.020
 FKL  C27  H27   single    0.970  0.020  1.090
 FKL  C32  H32   single    0.970  0.020  1.090
 FKL  C32  H32A  single    0.970  0.020  1.090
 FKL  C31  H31   single    0.970  0.020  1.090
 FKL  C31  H31A  single    0.970  0.020  1.090
 FKL  C29  H29   single    0.970  0.020  1.090
 FKL  C29  H29A  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
 FKL  C2    N1   C4    116.10  3.000
 FKL  C2    N3   C6    117.41  3.000
 FKL  H4    C4   C5    119.39  3.000
 FKL  H4    C4   N1    116.91  3.000
 FKL  C5    C4   N1    123.69  3.000
 FKL  C10   C5   C6    119.87  3.000
 FKL  C10   C5   C4    124.87  3.000
 FKL  C6    C5   C4    115.26  3.000
 FKL  N7    C6   C5    119.00  3.000
 FKL  N7    C6   N3    119.10  3.000
 FKL  C5    C6   N3    121.90  3.000
 FKL  N7    C8   O13   119.55  3.000
 FKL  N7    C8   C9    117.47  3.000
 FKL  O13   C8   C9    122.98  3.000
 FKL  H10   C10  C9    120.33  3.000
 FKL  H10   C10  C5    118.96  3.000
 FKL  C9    C10  C5    120.70  3.000
 FKL  H15   C15  C14   119.00  3.000
 FKL  H15   C15  C16   119.39  3.000
 FKL  C14   C15  C16   121.60  3.000
 FKL  H17   C17  C18   118.34  3.000
 FKL  H17   C17  C16   121.45  3.000
 FKL  C18   C17  C16   120.18  3.000
 FKL  H24   C24  C25   116.85  3.000
 FKL  H24   C24  N23   114.93  3.000
 FKL  C25   C24  N23   119.29  3.000
 FKL  H24   C24  C26   117.08  3.000
 FKL  C25   C24  C26    60.15  3.000
 FKL  N23   C24  C26   117.71  3.000
 FKL  H26A  C26  H26   114.33  3.000
 FKL  H26A  C26  C25   118.83  3.000
 FKL  H26   C26  C25   117.80  3.000
 FKL  H26A  C26  C24   117.60  3.000
 FKL  H26   C26  C24   117.77  3.000
 FKL  C25   C26  C24    60.04  3.000
 FKL  H28A  C28  H28   107.51  3.000
 FKL  H28A  C28  C29   109.62  3.000
 FKL  H28   C28  C29   109.25  3.000
 FKL  H28A  C28  C27   109.94  3.000
 FKL  H28   C28  C27   110.52  3.000
 FKL  C29   C28  C27   109.95  3.000
 FKL  HN23  N23  C24   117.97  3.000
 FKL  HN23  N23  C21   120.05  3.000
 FKL  C24   N23  C21   121.97  3.000
 FKL  H25A  C25  H25   114.71  3.000
 FKL  H25A  C25  C26   117.74  3.000
 FKL  H25   C25  C26   118.68  3.000
 FKL  H25A  C25  C24   117.40  3.000
 FKL  H25   C25  C24   117.67  3.000
 FKL  C26   C25  C24    59.81  3.000
 FKL  C21   C16  C17   123.59  3.000
 FKL  C21   C16  C15   117.95  3.000
 FKL  C17   C16  C15   118.45  3.000
 FKL  H18   C18  C19   119.26  3.000
 FKL  H18   C18  C17   119.03  3.000
 FKL  C19   C18  C17   121.70  3.000
 FKL  C14   C19  C18   118.19  3.000
 FKL  C14   C19  C20   121.60  3.000
 FKL  C18   C19  C20   120.20  3.000
 FKL  C9    C14  C19   121.33  3.000
 FKL  C9    C14  C15   118.79  3.000
 FKL  C19   C14  C15   119.86  3.000
 FKL  C14   C9   C10   122.06  3.000
 FKL  C14   C9   C8    117.81  3.000
 FKL  C10   C9   C8    120.07  3.000
 FKL  C12   N7   C8    116.42  3.000
 FKL  C12   N7   C6    120.73  3.000
 FKL  C8    N7   C6    122.83  3.000
 FKL  H12B  C12  H12A  109.09  3.000
 FKL  H12B  C12  H12   109.33  3.000
 FKL  H12A  C12  H12   108.87  3.000
 FKL  H12B  C12  N7    109.01  3.000
 FKL  H12A  C12  N7    110.46  3.000
 FKL  H12   C12  N7    110.07  3.000
 FKL  N11   C2   N3    116.59  3.000
 FKL  N11   C2   N1    117.77  3.000
 FKL  N3    C2   N1    125.64  3.000
 FKL  HN11  N11  C27   117.91  3.000
 FKL  HN11  N11  C2    115.97  3.000
 FKL  C27   N11  C2    125.10  3.000
 FKL  H27   C27  C32   108.59  3.000
 FKL  H27   C27  N11   107.84  3.000
 FKL  C32   C27  N11   112.48  3.000
 FKL  H27   C27  C28   108.50  3.000
 FKL  C32   C27  C28   109.55  3.000
 FKL  N11   C27  C28   109.79  3.000
 FKL  H32A  C32  H32   107.57  3.000
 FKL  H32A  C32  C31   109.41  3.000
 FKL  H32   C32  C31   109.91  3.000
 FKL  H32A  C32  C27   110.28  3.000
 FKL  H32   C32  C27   109.40  3.000
 FKL  C31   C32  C27   110.23  3.000
 FKL  H31A  C31  H31   107.38  3.000
 FKL  H31A  C31  O30   110.30  3.000
 FKL  H31   C31  O30   107.04  3.000
 FKL  H31A  C31  C32   109.56  3.000
 FKL  H31   C31  C32   110.56  3.000
 FKL  O30   C31  C32   111.88  3.000
 FKL  C29   O30  C31   111.96  3.000
 FKL  H29A  C29  H29   107.44  3.000
 FKL  H29A  C29  O30   107.13  3.000
 FKL  H29   C29  O30   110.28  3.000
 FKL  H29A  C29  C28   110.41  3.000
 FKL  H29   C29  C28   109.32  3.000
 FKL  O30   C29  C28   112.14  3.000
 FKL  H20B  C20  H20A  108.09  3.000
 FKL  H20B  C20  H20   107.56  3.000
 FKL  H20A  C20  H20   107.15  3.000
 FKL  H20B  C20  C19   111.10  3.000
 FKL  H20A  C20  C19   111.63  3.000
 FKL  H20   C20  C19   111.11  3.000
 FKL  C16   C21  N23   116.53  3.000
 FKL  C16   C21  O22   121.18  3.000
 FKL  N23   C21  O22   122.28  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
 FKL  CONST_01  C6    C5   C4   N1      0.00   0.0  0
 FKL  CONST_02  C6    N3   C2   N1      0.00   0.0  0
 FKL  CONST_03  C4    C5   C6   N3      0.00   0.0  0
 FKL  CONST_04  C4    N1   C2   N3      0.00   0.0  0
 FKL  CONST_05  C2    N1   C4   C5      0.00   0.0  0
 FKL  CONST_06  C2    N3   C6   C5      0.00   0.0  0
 FKL  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 FKL  CONST_08  C18   C19  C14  C15     0.00   0.0  0
 FKL  CONST_09  C14   C15  C16  C17     0.00   0.0  0
 FKL  CONST_10  C14   C19  C18  C17     0.00   0.0  0
 FKL  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 FKL  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 FKL  CONST_13  C9    C14  C15  C16   180.00   0.0  0
 FKL  CONST_14  C9    C14  C19  C18   180.00   0.0  0
 FKL  CONST_15  C9    C8   N7   C6      0.00   0.0  0
 FKL  CONST_16  N11   C2   N1   C4    180.00   0.0  0
 FKL  CONST_17  N11   C2   N3   C6    180.00   0.0  0
 FKL  CONST_18  C20   C19  C14  C15   180.00   0.0  0
 FKL  CONST_19  C20   C19  C18  C17   180.00   0.0  0
 FKL  CONST_20  C9    C14  C19  C20     0.00   0.0  0
 FKL  CONST_21  C14   C15  C16  C21   180.00   0.0  0
 FKL  CONST_22  C18   C17  C16  C21   180.00   0.0  0
 FKL  CONST_23  C27   N11  C2   N1      0.00   0.0  0
 FKL  CONST_24  C27   N11  C2   N3    180.00   0.0  0
 FKL  CONST_25  O13   C8   N7   C6    180.00   0.0  0
 FKL  CONST_26  C12   N7   C8   C9    180.00   0.0  0
 FKL  CONST_27  H4    C4   C5   C6    180.00   0.0  0
 FKL  CONST_28  H17   C17  C16  C15   180.00   0.0  0
 FKL  CONST_29  H15   C15  C16  C17   180.00   0.0  0
 FKL  CONST_30  H18   C18  C17  C16   180.00   0.0  0
 FKL  CONST_31  C16   C21  N23  C24   180.00   0.0  0
 FKL  CONST_32  C12   N7   C8   O13     0.00   0.0  0
 FKL  CONST_33  HN11  N11  C2   N1    180.00   0.0  0
 FKL  CONST_34  O22   C21  N23  C24     0.00   0.0  0
 FKL  CONST_35  HN23  N23  C21  C16     0.00   0.0  0
 FKL  Var_01    C15   C14  C9   C8   -109.59  30.0  3
 FKL  Var_02    O30   C29  C28  C27   -56.32  30.0  1
 FKL  Var_03    O30   C31  C32  C27    56.04  30.0  1
 FKL  Var_04    N23   C24  C25  C26   107.02  30.0  1
 FKL  Var_05    H25   C25  C26  C24  -107.11  30.0  1
 FKL  Var_06    O22   C21  C16  C15   -20.50  30.0  2
 FKL  Var_07    C26   C24  N23  C21   146.19  30.0  3
 FKL  Var_08    H12   C12  N7   C6    127.14  30.0  3
 FKL  Var_09    H20   C20  C19  C18   107.10  30.0  2

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
 FKL  chir_02  C27  C28  N11  C32  positiv
 FKL  chir_03  C24  C26  N23  C25  both

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
 FKL  plan-1  C15   0.020
 FKL  plan-1  C17   0.020
 FKL  plan-1  C16   0.020
 FKL  plan-1  C18   0.020
 FKL  plan-1  C19   0.020
 FKL  plan-1  C14   0.020
 FKL  plan-1  C9    0.020
 FKL  plan-1  H15   0.020
 FKL  plan-1  H17   0.020
 FKL  plan-1  H18   0.020
 FKL  plan-1  C20   0.020
 FKL  plan-1  C21   0.020
 FKL  plan-2  C2    0.020
 FKL  plan-2  N11   0.020
 FKL  plan-2  C27   0.020
 FKL  plan-2  HN11  0.020
 FKL  plan-3  C24   0.020
 FKL  plan-3  O22   0.020
 FKL  plan-3  N23   0.020
 FKL  plan-3  C16   0.020
 FKL  plan-3  HN23  0.020
 FKL  plan-3  C21   0.020
 FKL  plan-4  N1    0.020
 FKL  plan-4  N3    0.020
 FKL  plan-4  C4    0.020
 FKL  plan-4  C5    0.020
 FKL  plan-4  C6    0.020
 FKL  plan-4  C8    0.020
 FKL  plan-4  C10   0.020
 FKL  plan-4  C14   0.020
 FKL  plan-4  C9    0.020
 FKL  plan-4  O13   0.020
 FKL  plan-4  N7    0.020
 FKL  plan-4  C12   0.020
 FKL  plan-4  C2    0.020
 FKL  plan-4  N11   0.020
 FKL  plan-4  H4    0.020
 FKL  plan-4  H10   0.020

