# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:32:20 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-fluoranyl-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncc2C=C(C(=O)N(C[C@@H]3OC[C@@H](N)CO3)c2n1)c4ccc(cc4Cl)c5nc(C)ccc5F
#
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
 SQK  SQK  8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[2-chloranyl-4-(3-fluoranyl-6-methyl-pyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one  ligand  60  36  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SQK
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
 SQK  C1   C   CR6   0   0.604  -33.6371  -2.9623  18.8969
 SQK  O1   O   O2    0  -0.477  -31.5206  -0.2286  16.6737
 SQK  C2   C   CR16  0  -0.047  -32.8648  -4.8889  18.0133
 SQK  C3   C   CR66  0   0.583  -33.1295  -2.9407  16.6924
 SQK  C4   C   CR66  0  -0.111  -32.7495  -4.2917  16.7530
 SQK  C5   C   CR16  0  -0.163  -32.2980  -4.9490  15.5844
 SQK  C6   C   CR6   0  -0.207  -32.2202  -4.2863  14.4086
 SQK  C7   C   CR6   0   0.174  -31.7558  -4.9310  13.1661
 SQK  C8   C   CR6   0  -0.104  -32.4685  -5.9492  12.5389
 SQK  C9   C   CR16  0  -0.241  -32.0124  -6.5628  11.3818
 SQK  C10  C   CR6   0   0.068  -30.8132  -6.1552  10.8068
 SQK  C11  C   CR6   0   0.016  -30.3030  -6.7507   9.5537
 SQK  C12  C   CR6   0   0.470  -30.3784  -8.1055   9.2657
 SQK  N    N   NH1   0  -0.634  -34.0657  -2.3052  19.9756
 SQK  C    C   CH3   0  -0.509  -34.4422  -0.9140  19.9636
 SQK  C13  C   CR16  0  -0.292  -29.8803  -8.6030   8.0781
 SQK  C14  C   CR16  0  -0.310  -29.2988  -7.7136   7.1973
 SQK  C15  C   CR6   0   0.227  -29.2253  -6.3636   7.5450
 SQK  C16  C   CH3   0  -0.729  -28.5788  -5.3709   6.6272
 SQK  C17  C   CR16  0  -0.263  -30.0949  -5.1238  11.4119
 SQK  C18  C   CR16  0  -0.285  -30.5611  -4.5303  12.5689
 SQK  C19  C   CR6   0   0.562  -32.5937  -2.8814  14.3270
 SQK  C21  C   CH1   0   0.319  -32.2374   0.0587  15.5162
 SQK  C22  C   CH2   0  -0.193  -30.4040   0.6300  16.8159
 SQK  C23  C   CH1   0  -0.145  -30.8402   2.0948  16.8234
 SQK  C24  C   CH2   0  -0.187  -31.7234   2.3305  15.6041
 SQK  F    F   F     0  -0.301  -30.9144  -8.9578  10.1503
 SQK  N1   N   N     0  -0.464  -33.2906  -4.2588  19.0770
 SQK  N2   N   N     0  -0.492  -33.5815  -2.2931  17.7487
 SQK  N3   N   N     0  -0.431  -29.7182  -5.9187   8.6915
 SQK  N4   N   NR6   0  -0.597  -33.0462  -2.2767  15.4973
 SQK  N5   N   NH2   0  -0.794  -29.7464   3.0441  16.8194
 SQK  O2   O   O2    0  -0.495  -32.7504   1.3575  15.5331
 SQK  CL   CL  CL    0  -0.123  -33.9922  -6.4692  13.1827
 SQK  H1   H   HCR6  0   0.280  -32.5899  -5.9327  18.1342
 SQK  H2   H   HCR6  0   0.280  -32.0113  -5.9926  15.6488
 SQK  H3   H   HCR6  0   0.276  -32.6208  -7.3281  10.9215
 SQK  H4   H   HNH1  0   0.404  -34.1067  -2.8193  20.8392
 SQK  H5   H   HCH3  0   0.253  -34.6696  -0.6146  20.9824
 SQK  H6   H   HCH3  0   0.241  -33.6346  -0.2867  19.5854
 SQK  H7   H   HCH3  0   0.237  -35.3226  -0.7357  19.3445
 SQK  H8   H   HCR6  0   0.296  -29.9411  -9.6610   7.8579
 SQK  H9   H   HCR6  0   0.277  -28.8989  -8.0601   6.2539
 SQK  H10  H   HCH3  0   0.251  -28.6686  -4.3621   7.0239
 SQK  H11  H   HCH3  0   0.254  -27.5192  -5.5956   6.4957
 SQK  H12  H   HCH3  0   0.252  -29.0358  -5.3959   5.6372
 SQK  H13  H   HCR6  0   0.261  -29.1625  -4.7934  10.9751
 SQK  H14  H   HCR6  0   0.262  -29.9796  -3.7450  13.0340
 SQK  H15  H   HCH2  0   0.289  -34.1202  -0.6713  16.2413
 SQK  H16  H   HCH2  0   0.284  -33.9525  -0.7032  14.4831
 SQK  H17  H   HCH1  0   0.196  -31.5739  -0.0576  14.6406
 SQK  H18  H   HCH2  0   0.199  -29.6890   0.4701  15.9929
 SQK  H19  H   HCH2  0   0.243  -29.9048   0.3619  17.7486
 SQK  H20  H   HCH1  0   0.242  -31.4408   2.2724  17.7209
 SQK  H21  H   HCH2  0   0.204  -31.1094   2.2996  14.6902
 SQK  H22  H   HCH2  0   0.249  -32.2014   3.3094  15.6498
 SQK  H23  H   HNH2  0   0.355  -29.2244   2.9778  17.6838
 SQK  H24  H   HNH2  0   0.343  -29.0918   2.8229  16.0777
 SQK  O    O   O     0  -0.464  -32.5298  -2.2365  13.2921
 SQK  C20  C   CH2   0  -0.391  -33.4338  -0.8753  15.4235

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
 SQK  C16  C15  single    1.499  0.020  1.499
 SQK  C14  C15  aromatic  1.396  0.020  1.396
 SQK  C14  C13  aromatic  1.380  0.020  1.380
 SQK  C15  N3   aromatic  1.325  0.020  1.325
 SQK  C13  C12  aromatic  1.381  0.020  1.381
 SQK  N3   C11  aromatic  1.333  0.020  1.333
 SQK  C12  C11  aromatic  1.387  0.020  1.387
 SQK  C12  F    single    1.340  0.020  1.340
 SQK  C11  C10  single    1.478  0.020  1.478
 SQK  C10  C9   aromatic  1.391  0.020  1.391
 SQK  C10  C17  aromatic  1.395  0.020  1.395
 SQK  C9   C8   aromatic  1.387  0.020  1.387
 SQK  C17  C18  aromatic  1.381  0.020  1.381
 SQK  C8   CL   single    1.734  0.020  1.734
 SQK  C8   C7   aromatic  1.392  0.020  1.392
 SQK  C18  C7   aromatic  1.395  0.020  1.395
 SQK  C7   C6   single    1.475  0.020  1.475
 SQK  O    C19  double    1.221  0.020  1.221
 SQK  C19  C6   single    1.456  0.020  1.456
 SQK  C19  N4   single    1.393  0.020  1.393
 SQK  C6   C5   double    1.352  0.020  1.352
 SQK  C24  O2   single    1.417  0.020  1.417
 SQK  C24  C23  single    1.524  0.020  1.524
 SQK  O2   C21  single    1.397  0.020  1.397
 SQK  N5   C23  single    1.448  0.020  1.448
 SQK  C21  C20  single    1.521  0.020  1.521
 SQK  C21  O1   single    1.391  0.020  1.391
 SQK  C5   C4   single    1.415  0.020  1.415
 SQK  N4   C20  single    1.456  0.020  1.456
 SQK  N4   C3   single    1.370  0.020  1.370
 SQK  C23  C22  single    1.528  0.020  1.528
 SQK  C22  O1   single    1.416  0.020  1.416
 SQK  C3   C4   aromatic  1.405  0.020  1.405
 SQK  C3   N2   aromatic  1.319  0.020  1.319
 SQK  C4   C2   aromatic  1.399  0.020  1.399
 SQK  N2   C1   aromatic  1.330  0.020  1.330
 SQK  C2   N1   aromatic  1.308  0.020  1.308
 SQK  C1   N1   aromatic  1.354  0.020  1.354
 SQK  C1   N    single    1.334  0.020  1.334
 SQK  N    C    single    1.441  0.020  1.441
 SQK  C2   H1   single    0.930  0.020  1.080
 SQK  C5   H2   single    0.930  0.020  1.080
 SQK  C9   H3   single    0.930  0.020  1.080
 SQK  N    H4   single    0.860  0.020  1.020
 SQK  C    H5   single    0.970  0.020  1.090
 SQK  C    H6   single    0.970  0.020  1.090
 SQK  C    H7   single    0.970  0.020  1.090
 SQK  C13  H8   single    0.930  0.020  1.080
 SQK  C14  H9   single    0.930  0.020  1.080
 SQK  C16  H10  single    0.970  0.020  1.090
 SQK  C16  H11  single    0.970  0.020  1.090
 SQK  C16  H12  single    0.970  0.020  1.090
 SQK  C17  H13  single    0.930  0.020  1.080
 SQK  C18  H14  single    0.930  0.020  1.080
 SQK  C20  H15  single    0.970  0.020  1.090
 SQK  C20  H16  single    0.970  0.020  1.090
 SQK  C21  H17  single    0.970  0.020  1.090
 SQK  C22  H18  single    0.970  0.020  1.090
 SQK  C22  H19  single    0.970  0.020  1.090
 SQK  C23  H20  single    0.970  0.020  1.090
 SQK  C24  H21  single    0.970  0.020  1.090
 SQK  C24  H22  single    0.970  0.020  1.090
 SQK  N5   H23  single    0.890  0.020  1.040
 SQK  N5   H24  single    0.890  0.020  1.040

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
 SQK  N2   C1   N1   125.86  3.000
 SQK  N1   C1   N    116.51  3.000
 SQK  N2   C1   N    117.63  3.000
 SQK  C22  O1   C21  111.38  3.000
 SQK  H1   C2   N1   117.06  3.000
 SQK  H1   C2   C4   119.31  3.000
 SQK  N1   C2   C4   123.63  3.000
 SQK  N4   C3   N2   118.79  3.000
 SQK  N2   C3   C4   122.04  3.000
 SQK  N4   C3   C4   119.17  3.000
 SQK  C5   C4   C3   119.84  3.000
 SQK  C3   C4   C2   115.28  3.000
 SQK  C5   C4   C2   124.89  3.000
 SQK  H2   C5   C6   120.55  3.000
 SQK  H2   C5   C4   118.85  3.000
 SQK  C6   C5   C4   120.60  3.000
 SQK  C19  C6   C7   117.09  3.000
 SQK  C19  C6   C5   120.46  3.000
 SQK  C7   C6   C5   122.45  3.000
 SQK  C18  C7   C8   117.12  3.000
 SQK  C18  C7   C6   120.33  3.000
 SQK  C8   C7   C6   122.55  3.000
 SQK  CL   C8   C9   117.78  3.000
 SQK  CL   C8   C7   120.13  3.000
 SQK  C9   C8   C7   122.08  3.000
 SQK  H3   C9   C10  121.12  3.000
 SQK  H3   C9   C8   118.92  3.000
 SQK  C10  C9   C8   119.92  3.000
 SQK  C17  C10  C11  119.19  3.000
 SQK  C17  C10  C9   118.77  3.000
 SQK  C11  C10  C9   122.01  3.000
 SQK  N3   C11  C12  119.94  3.000
 SQK  C12  C11  C10  123.41  3.000
 SQK  N3   C11  C10  116.63  3.000
 SQK  F    C12  C13  118.87  3.000
 SQK  F    C12  C11  120.39  3.000
 SQK  C13  C12  C11  120.73  3.000
 SQK  H4   N    C    119.33  3.000
 SQK  H4   N    C1   117.11  3.000
 SQK  C    N    C1   123.56  3.000
 SQK  H7   C    H6   107.87  3.000
 SQK  H7   C    H5   108.56  3.000
 SQK  H6   C    H5   108.78  3.000
 SQK  H7   C    N    111.92  3.000
 SQK  H6   C    N    111.39  3.000
 SQK  H5   C    N    108.25  3.000
 SQK  H8   C13  C14  121.58  3.000
 SQK  H8   C13  C12  120.47  3.000
 SQK  C14  C13  C12  117.95  3.000
 SQK  H9   C14  C15  120.50  3.000
 SQK  H9   C14  C13  120.39  3.000
 SQK  C15  C14  C13  119.10  3.000
 SQK  N3   C15  C16  117.90  3.000
 SQK  N3   C15  C14  121.38  3.000
 SQK  C16  C15  C14  120.72  3.000
 SQK  H12  C16  H11  107.02  3.000
 SQK  H12  C16  H10  108.53  3.000
 SQK  H11  C16  H10  108.37  3.000
 SQK  H12  C16  C15  111.10  3.000
 SQK  H11  C16  C15  110.87  3.000
 SQK  H10  C16  C15  110.82  3.000
 SQK  H13  C17  C18  119.87  3.000
 SQK  H13  C17  C10  119.65  3.000
 SQK  C18  C17  C10  120.48  3.000
 SQK  H14  C18  C17  119.37  3.000
 SQK  H14  C18  C7   118.99  3.000
 SQK  C17  C18  C7   121.63  3.000
 SQK  N4   C19  O    119.99  3.000
 SQK  N4   C19  C6   117.08  3.000
 SQK  O    C19  C6   122.93  3.000
 SQK  H17  C21  O2   109.16  3.000
 SQK  H17  C21  C20  111.08  3.000
 SQK  O2   C21  C20  106.43  3.000
 SQK  H17  C21  O1   109.16  3.000
 SQK  C20  C21  O1   109.22  3.000
 SQK  O2   C21  O1   111.79  3.000
 SQK  H19  C22  H18  107.81  3.000
 SQK  H19  C22  C23  111.21  3.000
 SQK  H18  C22  C23  109.14  3.000
 SQK  H19  C22  O1   107.32  3.000
 SQK  H18  C22  O1   110.41  3.000
 SQK  C23  C22  O1   110.89  3.000
 SQK  H20  C23  N5   108.08  3.000
 SQK  H20  C23  C24  108.24  3.000
 SQK  N5   C23  C24  109.52  3.000
 SQK  H20  C23  C22  108.43  3.000
 SQK  N5   C23  C22  114.37  3.000
 SQK  C24  C23  C22  108.04  3.000
 SQK  H22  C24  H21  107.72  3.000
 SQK  H22  C24  O2   107.51  3.000
 SQK  H21  C24  O2   110.08  3.000
 SQK  H22  C24  C23  111.06  3.000
 SQK  H21  C24  C23  109.66  3.000
 SQK  O2   C24  C23  110.74  3.000
 SQK  C2   N1   C1   115.88  3.000
 SQK  C3   N2   C1   117.30  3.000
 SQK  C15  N3   C11  120.88  3.000
 SQK  C20  N4   C19  117.51  3.000
 SQK  C20  N4   C3   119.65  3.000
 SQK  C19  N4   C3   122.84  3.000
 SQK  H24  N5   H23  106.12  3.000
 SQK  H24  N5   C23  110.28  3.000
 SQK  H23  N5   C23  110.14  3.000
 SQK  C24  O2   C21  111.91  3.000
 SQK  H16  C20  H15  108.64  3.000
 SQK  H16  C20  N4   108.85  3.000
 SQK  H15  C20  N4   108.10  3.000
 SQK  H16  C20  C21  109.31  3.000
 SQK  H15  C20  C21  109.62  3.000
 SQK  N4   C20  C21  112.25  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
 SQK  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 SQK  CONST_02  C4   C2   N1   C1      0.00   0.0  0
 SQK  CONST_03  N2   C3   C4   C2      0.00   0.0  0
 SQK  CONST_04  N2   C1   N1   C2      0.00   0.0  0
 SQK  CONST_05  N1   C2   C4   C3      0.00   0.0  0
 SQK  CONST_06  N1   C1   N2   C3      0.00   0.0  0
 SQK  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 SQK  CONST_08  C10  C17  C18  C7      0.00   0.0  0
 SQK  CONST_09  C11  C10  C9   C8    180.00   0.0  0
 SQK  CONST_10  C17  C10  C9   C8      0.00   0.0  0
 SQK  CONST_11  C17  C18  C7   C8      0.00   0.0  0
 SQK  CONST_14  C18  C17  C10  C9      0.00   0.0  0
 SQK  CONST_15  C18  C7   C8   C9      0.00   0.0  0
 SQK  CONST_16  C15  N3   C11  C10   180.00   0.0  0
 SQK  CONST_17  C13  C12  C11  C10   180.00   0.0  0
 SQK  CONST_18  C14  C15  N3   C11     0.00   0.0  0
 SQK  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 SQK  CONST_20  C18  C17  C10  C11   180.00   0.0  0
 SQK  CONST_21  C15  C14  C13  C12     0.00   0.0  0
 SQK  CONST_22  C15  N3   C11  C12     0.00   0.0  0
 SQK  CONST_24  N3   C15  C14  C13     0.00   0.0  0
 SQK  CONST_25  N3   C11  C12  C13     0.00   0.0  0
 SQK  CONST_27  C9   C8   C7   C6    180.00   0.0  0
 SQK  CONST_28  C17  C18  C7   C6    180.00   0.0  0
 SQK  CONST_29  C6   C19  N4   C3      0.00   0.0  0
 SQK  CONST_30  N    C1   N1   C2    180.00   0.0  0
 SQK  CONST_31  N    C1   N2   C3    180.00   0.0  0
 SQK  CONST_32  CL   C8   C7   C6      0.00   0.0  0
 SQK  CONST_33  F    C12  C11  C10     0.00   0.0  0
 SQK  CONST_34  CL   C8   C9   C10   180.00   0.0  0
 SQK  CONST_35  C16  C15  N3   C11   180.00   0.0  0
 SQK  CONST_36  C16  C15  C14  C13   180.00   0.0  0
 SQK  CONST_37  F    C12  C13  C14   180.00   0.0  0
 SQK  CONST_38  CL   C8   C7   C18   180.00   0.0  0
 SQK  CONST_39  N3   C11  C12  F     180.00   0.0  0
 SQK  CONST_40  O    C19  N4   C3    180.00   0.0  0
 SQK  CONST_41  C20  N4   C19  C6    180.00   0.0  0
 SQK  CONST_42  H1   C2   N1   C1    180.00   0.0  0
 SQK  CONST_43  H14  C18  C7   C6      0.00   0.0  0
 SQK  CONST_44  H3   C9   C8   C7    180.00   0.0  0
 SQK  CONST_45  H13  C17  C18  C7    180.00   0.0  0
 SQK  CONST_46  H8   C13  C12  C11   180.00   0.0  0
 SQK  CONST_47  H9   C14  C13  C12   180.00   0.0  0
 SQK  CONST_48  N2   C1   N    C       0.00   0.0  0
 SQK  CONST_49  N1   C1   N    C     180.00   0.0  0
 SQK  CONST_50  C20  N4   C19  O       0.00   0.0  0
 SQK  CONST_51  H4   N    C1   N1      0.00   0.0  0
 SQK  Var_01    C8   C7   C6   C5     66.39  30.0  3
 SQK  Var_02    C23  C24  O2   C21   -56.48  30.0  1
 SQK  Var_03    C23  C22  O1   C21    57.23  30.0  1
 SQK  Var_04    C21  C20  N4   C3     97.52  30.0  3
 SQK  Var_05    H10  C16  C15  C14   176.24  30.0  2
 SQK  Var_06    H5   C    N    C1   -175.30  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
 SQK  chir_01  C21  O2  C20  O1   positiv
 SQK  chir_02  C23  N5  C22  C24  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
 SQK  plan-1  C6   0.020
 SQK  plan-1  C7   0.020
 SQK  plan-1  C8   0.020
 SQK  plan-1  C9   0.020
 SQK  plan-1  C10  0.020
 SQK  plan-1  C11  0.020
 SQK  plan-1  C17  0.020
 SQK  plan-1  C18  0.020
 SQK  plan-1  CL   0.020
 SQK  plan-1  H3   0.020
 SQK  plan-1  H13  0.020
 SQK  plan-1  H14  0.020
 SQK  plan-2  C10  0.020
 SQK  plan-2  C11  0.020
 SQK  plan-2  C12  0.020
 SQK  plan-2  C13  0.020
 SQK  plan-2  C14  0.020
 SQK  plan-2  C15  0.020
 SQK  plan-2  C16  0.020
 SQK  plan-2  F    0.020
 SQK  plan-2  N3   0.020
 SQK  plan-2  H8   0.020
 SQK  plan-2  H9   0.020
 SQK  plan-3  C1   0.020
 SQK  plan-3  C2   0.020
 SQK  plan-3  C3   0.020
 SQK  plan-3  C4   0.020
 SQK  plan-3  C5   0.020
 SQK  plan-3  C6   0.020
 SQK  plan-3  C7   0.020
 SQK  plan-3  N    0.020
 SQK  plan-3  C19  0.020
 SQK  plan-3  N1   0.020
 SQK  plan-3  N2   0.020
 SQK  plan-3  N4   0.020
 SQK  plan-3  H1   0.020
 SQK  plan-3  H2   0.020
 SQK  plan-3  O    0.020
 SQK  plan-3  C20  0.020
 SQK  plan-4  C1   0.020
 SQK  plan-4  N    0.020
 SQK  plan-4  C    0.020
 SQK  plan-4  H4   0.020

