# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:49:20 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: 8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[4-[6-[bis(fluoranyl)methyl]pyridin-2-yl]-2-chloranyl-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)c5cccc(n5)C(F)F
#
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
 SQE  SQE  8-[(5-azanyl-1,3-dioxan-2-yl)methyl]-6-[4-[6-[bis(fluoranyl)methyl]pyridin-2-yl]-2-chloranyl-phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one  ligand  60  37  .  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_SQE
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
 SQE  C13  C   CH1   0   0.531  -27.7535  -5.6470   7.0828
 SQE  C12  C   CR6   0   0.095  -28.7399  -6.5523   7.7652
 SQE  C10  C   CR6   0   0.052  -30.6237  -6.1325  10.8269
 SQE  C7   C   CR6   0   0.167  -31.5618  -4.9272  13.2001
 SQE  C4   C   CR66  0  -0.112  -32.5359  -4.2762  16.7909
 SQE  C3   C   CR66  0   0.583  -32.9636  -2.9403  16.7156
 SQE  C2   C   CR16  0  -0.047  -32.6186  -4.8593  18.0604
 SQE  C1   C   CR6   0   0.604  -33.4517  -2.9495  18.9248
 SQE  N    N   NH1   0  -0.634  -33.8966  -2.2939  19.9978
 SQE  C    C   CH3   0  -0.509  -34.3316  -0.9202  19.9679
 SQE  C11  C   CR6   0   0.236  -30.1246  -6.7505   9.5791
 SQE  C14  C   CR16  0  -0.325  -29.1220  -7.7768   7.2426
 SQE  C15  C   CR16  0  -0.139  -30.0543  -8.5120   7.9604
 SQE  C16  C   CR16  0  -0.328  -30.5620  -8.0019   9.1407
 SQE  C17  C   CR16  0  -0.260  -29.8939  -5.1204  11.4518
 SQE  C18  C   CR16  0  -0.282  -30.3600  -4.5345  12.6127
 SQE  C19  C   CR6   0   0.563  -32.4545  -2.8956  14.3447
 SQE  C21  C   CH1   0   0.319  -32.1897   0.0729  15.4762
 SQE  C22  C   CH2   0  -0.193  -30.3535   0.7288  16.7310
 SQE  C23  C   CH1   0  -0.145  -30.8440   2.1764  16.7289
 SQE  C24  C   CH2   0  -0.187  -31.7585   2.3633  15.5243
 SQE  C5   C   CR16  0  -0.160  -32.0742  -4.9344  15.6265
 SQE  C6   C   CR6   0  -0.209  -32.0309  -4.2847  14.4422
 SQE  C8   C   CR6   0  -0.098  -32.2820  -5.9317  12.5603
 SQE  C9   C   CR16  0  -0.259  -31.8299  -6.5303  11.3947
 SQE  F    F   F     0  -0.344  -28.4182  -4.5926   6.5295
 SQE  F1   F   F     0  -0.334  -27.1239  -6.2882   6.0661
 SQE  N1   N   N     0  -0.463  -33.0572  -4.2300  19.1194
 SQE  N2   N   N     0  -0.492  -33.4291  -2.2946  17.7674
 SQE  N3   N   N     0  -0.447  -29.2209  -6.0580   8.8948
 SQE  N4   N   NR6   0  -0.597  -32.9151  -2.2900  15.5109
 SQE  N5   N   NH2   0  -0.794  -29.7871   3.1658  16.6940
 SQE  O1   O   O2    0  -0.477  -31.4404  -0.1723  16.6231
 SQE  O2   O   O2    0  -0.495  -32.7494   1.3521  15.4861
 SQE  CL   CL  CL    0  -0.120  -33.8081  -6.4475  13.1998
 SQE  H1   H   HCH1  0   0.212  -27.0042  -5.2552   7.7711
 SQE  H2   H   HCR6  0   0.280  -32.3059  -5.8910  18.1926
 SQE  H3   H   HNH1  0   0.404  -33.9118  -2.7968  20.8690
 SQE  H4   H   HCH3  0   0.253  -34.5683  -0.6162  20.9832
 SQE  H5   H   HCH3  0   0.241  -33.5526  -0.2644  19.5779
 SQE  H6   H   HCH3  0   0.237  -35.2208  -0.7888  19.3495
 SQE  H7   H   HCR6  0   0.283  -28.7111  -8.1561   6.3185
 SQE  H8   H   HCR6  0   0.284  -30.3769  -9.4811   7.6049
 SQE  H9   H   HCR6  0   0.278  -31.2698  -8.5824   9.7147
 SQE  H10  H   HCR6  0   0.261  -28.9540  -4.7976  11.0268
 SQE  H11  H   HCR6  0   0.263  -29.7728  -3.7602  13.0893
 SQE  H12  H   HCH2  0   0.289  -34.0299  -0.7111  16.2498
 SQE  H13  H   HCH2  0   0.283  -33.8969  -0.7670  14.4896
 SQE  H14  H   HCH1  0   0.196  -31.5396  -0.0318  14.5893
 SQE  H15  H   HCH2  0   0.199  -29.6495   0.5830  15.8960
 SQE  H16  H   HCH2  0   0.243  -29.8259   0.4932  17.6569
 SQE  H17  H   HCH1  0   0.242  -31.4339   2.3417  17.6358
 SQE  H18  H   HCH2  0   0.204  -31.1608   2.3433  14.5994
 SQE  H19  H   HCH2  0   0.249  -32.2721   3.3242  15.5671
 SQE  H20  H   HCR6  0   0.280  -31.7538  -5.9675  15.7007
 SQE  H21  H   HCR6  0   0.277  -32.4445  -7.2875  10.9273
 SQE  H22  H   HNH2  0   0.355  -29.2374   3.1179  17.5424
 SQE  H23  H   HNH2  0   0.343  -29.1474   2.9702  15.9324
 SQE  O    O   O     0  -0.464  -32.4250  -2.2654  13.2991
 SQE  C20  C   CH2   0  -0.392  -33.3531  -0.9044  15.4217

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
 SQE  F1   C13  single    1.357  0.020  1.357
 SQE  F    C13  single    1.364  0.020  1.364
 SQE  C13  C12  single    1.503  0.020  1.503
 SQE  C14  C12  aromatic  1.385  0.020  1.385
 SQE  C14  C15  aromatic  1.387  0.020  1.387
 SQE  C12  N3   aromatic  1.324  0.020  1.324
 SQE  C15  C16  aromatic  1.382  0.020  1.382
 SQE  N3   C11  aromatic  1.328  0.020  1.328
 SQE  C16  C11  aromatic  1.396  0.020  1.396
 SQE  C11  C10  single    1.479  0.020  1.479
 SQE  C10  C9   aromatic  1.391  0.020  1.391
 SQE  C10  C17  aromatic  1.396  0.020  1.396
 SQE  C9   C8   aromatic  1.386  0.020  1.386
 SQE  C17  C18  aromatic  1.381  0.020  1.381
 SQE  C8   CL   single    1.733  0.020  1.733
 SQE  C8   C7   aromatic  1.392  0.020  1.392
 SQE  C18  C7   aromatic  1.394  0.020  1.394
 SQE  C7   C6   single    1.475  0.020  1.475
 SQE  O    C19  double    1.221  0.020  1.221
 SQE  C19  C6   single    1.456  0.020  1.456
 SQE  C19  N4   single    1.392  0.020  1.392
 SQE  C24  O2   single    1.416  0.020  1.416
 SQE  C24  C23  single    1.524  0.020  1.524
 SQE  C6   C5   double    1.351  0.020  1.351
 SQE  O2   C21  single    1.396  0.020  1.396
 SQE  N5   C23  single    1.448  0.020  1.448
 SQE  C21  C20  single    1.520  0.020  1.520
 SQE  C21  O1   single    1.392  0.020  1.392
 SQE  C23  C22  single    1.528  0.020  1.528
 SQE  C20  N4   single    1.456  0.020  1.456
 SQE  N4   C3   single    1.370  0.020  1.370
 SQE  C5   C4   single    1.415  0.020  1.415
 SQE  C22  O1   single    1.416  0.020  1.416
 SQE  C3   C4   aromatic  1.405  0.020  1.405
 SQE  C3   N2   aromatic  1.319  0.020  1.319
 SQE  C4   C2   aromatic  1.399  0.020  1.399
 SQE  N2   C1   aromatic  1.330  0.020  1.330
 SQE  C2   N1   aromatic  1.308  0.020  1.308
 SQE  C1   N1   aromatic  1.354  0.020  1.354
 SQE  C1   N    single    1.334  0.020  1.334
 SQE  N    C    single    1.441  0.020  1.441
 SQE  C13  H1   single    0.970  0.020  1.090
 SQE  C2   H2   single    0.930  0.020  1.080
 SQE  N    H3   single    0.860  0.020  1.020
 SQE  C    H4   single    0.970  0.020  1.090
 SQE  C    H5   single    0.970  0.020  1.090
 SQE  C    H6   single    0.970  0.020  1.090
 SQE  C14  H7   single    0.930  0.020  1.080
 SQE  C15  H8   single    0.930  0.020  1.080
 SQE  C16  H9   single    0.930  0.020  1.080
 SQE  C17  H10  single    0.930  0.020  1.080
 SQE  C18  H11  single    0.930  0.020  1.080
 SQE  C20  H12  single    0.970  0.020  1.090
 SQE  C20  H13  single    0.970  0.020  1.090
 SQE  C21  H14  single    0.970  0.020  1.090
 SQE  C22  H15  single    0.970  0.020  1.090
 SQE  C22  H16  single    0.970  0.020  1.090
 SQE  C23  H17  single    0.970  0.020  1.090
 SQE  C24  H18  single    0.970  0.020  1.090
 SQE  C24  H19  single    0.970  0.020  1.090
 SQE  C5   H20  single    0.930  0.020  1.080
 SQE  C9   H21  single    0.930  0.020  1.080
 SQE  N5   H22  single    0.890  0.020  1.040
 SQE  N5   H23  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
 SQE  H1   C13  F1   108.90  3.000
 SQE  H1   C13  F    108.25  3.000
 SQE  F1   C13  F    106.71  3.000
 SQE  H1   C13  C12  112.40  3.000
 SQE  F    C13  C12  109.27  3.000
 SQE  F1   C13  C12  111.11  3.000
 SQE  N3   C12  C14  123.50  3.000
 SQE  N3   C12  C13  113.64  3.000
 SQE  C14  C12  C13  122.84  3.000
 SQE  C9   C10  C17  118.55  3.000
 SQE  C17  C10  C11  120.29  3.000
 SQE  C9   C10  C11  121.15  3.000
 SQE  C8   C7   C6   122.47  3.000
 SQE  C6   C7   C18  120.41  3.000
 SQE  C8   C7   C18  117.11  3.000
 SQE  C5   C4   C2   124.89  3.000
 SQE  C2   C4   C3   115.27  3.000
 SQE  C5   C4   C3   119.84  3.000
 SQE  N4   C3   N2   118.78  3.000
 SQE  N2   C3   C4   122.02  3.000
 SQE  N4   C3   C4   119.19  3.000
 SQE  H2   C2   N1   117.07  3.000
 SQE  H2   C2   C4   119.29  3.000
 SQE  N1   C2   C4   123.64  3.000
 SQE  N2   C1   N1   125.86  3.000
 SQE  N1   C1   N    116.52  3.000
 SQE  N2   C1   N    117.63  3.000
 SQE  H3   N    C    119.33  3.000
 SQE  H3   N    C1   117.13  3.000
 SQE  C    N    C1   123.53  3.000
 SQE  H6   C    H5   107.89  3.000
 SQE  H6   C    H4   108.58  3.000
 SQE  H5   C    H4   108.76  3.000
 SQE  H6   C    N    111.87  3.000
 SQE  H5   C    N    111.41  3.000
 SQE  H4   C    N    108.25  3.000
 SQE  N3   C11  C16  121.23  3.000
 SQE  C16  C11  C10  122.26  3.000
 SQE  N3   C11  C10  116.50  3.000
 SQE  H7   C14  C15  120.81  3.000
 SQE  H7   C14  C12  121.89  3.000
 SQE  C15  C14  C12  117.30  3.000
 SQE  H8   C15  C16  120.12  3.000
 SQE  H8   C15  C14  120.34  3.000
 SQE  C16  C15  C14  119.54  3.000
 SQE  H9   C16  C15  119.73  3.000
 SQE  H9   C16  C11  121.32  3.000
 SQE  C15  C16  C11  118.94  3.000
 SQE  H10  C17  C18  119.81  3.000
 SQE  H10  C17  C10  119.69  3.000
 SQE  C18  C17  C10  120.50  3.000
 SQE  H11  C18  C17  119.37  3.000
 SQE  H11  C18  C7   118.92  3.000
 SQE  C17  C18  C7   121.70  3.000
 SQE  N4   C19  C6   117.08  3.000
 SQE  N4   C19  O    120.04  3.000
 SQE  C6   C19  O    122.87  3.000
 SQE  H14  C21  O2   109.17  3.000
 SQE  H14  C21  O1   109.16  3.000
 SQE  O2   C21  O1   111.80  3.000
 SQE  H14  C21  C20  111.14  3.000
 SQE  O1   C21  C20  109.16  3.000
 SQE  O2   C21  C20  106.40  3.000
 SQE  H16  C22  H15  107.79  3.000
 SQE  H16  C22  O1   107.35  3.000
 SQE  H15  C22  O1   110.40  3.000
 SQE  H16  C22  C23  111.15  3.000
 SQE  H15  C22  C23  109.23  3.000
 SQE  O1   C22  C23  110.87  3.000
 SQE  H17  C23  N5   108.07  3.000
 SQE  H17  C23  C24  108.24  3.000
 SQE  N5   C23  C24  109.58  3.000
 SQE  H17  C23  C22  108.36  3.000
 SQE  N5   C23  C22  114.38  3.000
 SQE  C24  C23  C22  108.05  3.000
 SQE  H19  C24  H18  107.73  3.000
 SQE  H19  C24  O2   107.50  3.000
 SQE  H18  C24  O2   110.12  3.000
 SQE  H19  C24  C23  111.09  3.000
 SQE  H18  C24  C23  109.63  3.000
 SQE  O2   C24  C23  110.71  3.000
 SQE  H20  C5   C6   120.57  3.000
 SQE  H20  C5   C4   118.90  3.000
 SQE  C6   C5   C4   120.53  3.000
 SQE  C5   C6   C19  120.54  3.000
 SQE  C5   C6   C7   122.60  3.000
 SQE  C19  C6   C7   116.86  3.000
 SQE  CL   C8   C9   117.97  3.000
 SQE  CL   C8   C7   120.06  3.000
 SQE  C9   C8   C7   121.97  3.000
 SQE  H21  C9   C8   118.71  3.000
 SQE  H21  C9   C10  121.10  3.000
 SQE  C8   C9   C10  120.17  3.000
 SQE  C1   N1   C2   115.88  3.000
 SQE  C1   N2   C3   117.31  3.000
 SQE  C11  N3   C12  119.48  3.000
 SQE  C20  N4   C19  117.52  3.000
 SQE  C20  N4   C3   119.67  3.000
 SQE  C19  N4   C3   122.81  3.000
 SQE  H23  N5   H22  106.14  3.000
 SQE  H23  N5   C23  110.29  3.000
 SQE  H22  N5   C23  110.11  3.000
 SQE  C22  O1   C21  111.34  3.000
 SQE  C24  O2   C21  111.95  3.000
 SQE  H13  C20  H12  108.61  3.000
 SQE  H13  C20  N4   108.85  3.000
 SQE  H12  C20  N4   108.06  3.000
 SQE  H13  C20  C21  109.39  3.000
 SQE  H12  C20  C21  109.56  3.000
 SQE  N4   C20  C21  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
 SQE  CONST_01  C16  C15  C14  C12     0.00   0.0  0
 SQE  CONST_02  C16  C11  N3   C12     0.00   0.0  0
 SQE  CONST_03  C10  C11  N3   C12   180.00   0.0  0
 SQE  CONST_04  C15  C16  C11  C10   180.00   0.0  0
 SQE  CONST_05  C7   C8   C9   C10     0.00   0.0  0
 SQE  CONST_06  C7   C18  C17  C10     0.00   0.0  0
 SQE  CONST_07  C1   N2   C3   C4      0.00   0.0  0
 SQE  CONST_08  C1   N1   C2   C4      0.00   0.0  0
 SQE  CONST_09  N1   C2   C4   C3      0.00   0.0  0
 SQE  CONST_10  N1   C1   N2   C3      0.00   0.0  0
 SQE  CONST_11  N2   C3   C4   C2      0.00   0.0  0
 SQE  CONST_12  N2   C1   N1   C2      0.00   0.0  0
 SQE  CONST_13  C14  C12  N3   C11     0.00   0.0  0
 SQE  CONST_14  C14  C15  C16  C11     0.00   0.0  0
 SQE  CONST_15  C8   C9   C10  C11   180.00   0.0  0
 SQE  CONST_16  C18  C17  C10  C11   180.00   0.0  0
 SQE  CONST_17  N3   C12  C14  C15     0.00   0.0  0
 SQE  CONST_18  N3   C11  C16  C15     0.00   0.0  0
 SQE  CONST_22  C8   C9   C10  C17     0.00   0.0  0
 SQE  CONST_23  C8   C7   C18  C17     0.00   0.0  0
 SQE  CONST_24  C9   C10  C17  C18     0.00   0.0  0
 SQE  CONST_25  C9   C8   C7   C18     0.00   0.0  0
 SQE  CONST_27  C6   C7   C18  C17   180.00   0.0  0
 SQE  CONST_28  C9   C8   C7   C6    180.00   0.0  0
 SQE  CONST_29  C6   C19  N4   C3      0.00   0.0  0
 SQE  CONST_30  C15  C14  C12  C13   180.00   0.0  0
 SQE  CONST_31  C11  N3   C12  C13   180.00   0.0  0
 SQE  CONST_32  CL   C8   C9   C10   180.00   0.0  0
 SQE  CONST_33  N    C1   N2   C3    180.00   0.0  0
 SQE  CONST_34  N    C1   N1   C2    180.00   0.0  0
 SQE  CONST_35  CL   C8   C7   C18   180.00   0.0  0
 SQE  CONST_36  CL   C8   C7   C6      0.00   0.0  0
 SQE  CONST_37  O    C19  N4   C3    180.00   0.0  0
 SQE  CONST_38  C6   C19  N4   C20   180.00   0.0  0
 SQE  CONST_39  H8   C15  C14  C12   180.00   0.0  0
 SQE  CONST_40  H9   C16  C11  C10     0.00   0.0  0
 SQE  CONST_41  H11  C18  C17  C10   180.00   0.0  0
 SQE  CONST_42  H21  C9   C8   C7    180.00   0.0  0
 SQE  CONST_43  H10  C17  C18  C7    180.00   0.0  0
 SQE  CONST_44  H2   C2   C4   C3    180.00   0.0  0
 SQE  CONST_45  H7   C14  C15  C16   180.00   0.0  0
 SQE  CONST_46  N2   C1   N    C       0.00   0.0  0
 SQE  CONST_47  N1   C1   N    C     180.00   0.0  0
 SQE  CONST_48  C20  N4   C19  O       0.00   0.0  0
 SQE  CONST_49  H3   N    C1   N1      0.00   0.0  0
 SQE  Var_01    C19  C6   C7   C18    69.06  30.0  2
 SQE  Var_02    C23  C24  O2   C21   -56.45  30.0  1
 SQE  Var_03    C23  C22  O1   C21    57.28  30.0  1
 SQE  Var_04    C21  C20  N4   C3     98.07  30.0  3
 SQE  Var_05    F1   C13  C12  C14   -11.60  30.0  3
 SQE  Var_06    H4   C    N    C1   -175.72  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
 SQE  chir_01  C21  O2  C20  O1   positiv
 SQE  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
 SQE  plan-1  C10  0.020
 SQE  plan-1  C7   0.020
 SQE  plan-1  C11  0.020
 SQE  plan-1  C17  0.020
 SQE  plan-1  C18  0.020
 SQE  plan-1  C6   0.020
 SQE  plan-1  C8   0.020
 SQE  plan-1  C9   0.020
 SQE  plan-1  CL   0.020
 SQE  plan-1  H10  0.020
 SQE  plan-1  H11  0.020
 SQE  plan-1  H21  0.020
 SQE  plan-2  C13  0.020
 SQE  plan-2  C12  0.020
 SQE  plan-2  C10  0.020
 SQE  plan-2  C11  0.020
 SQE  plan-2  C14  0.020
 SQE  plan-2  C15  0.020
 SQE  plan-2  C16  0.020
 SQE  plan-2  N3   0.020
 SQE  plan-2  H7   0.020
 SQE  plan-2  H8   0.020
 SQE  plan-2  H9   0.020
 SQE  plan-3  C7   0.020
 SQE  plan-3  C4   0.020
 SQE  plan-3  C3   0.020
 SQE  plan-3  C2   0.020
 SQE  plan-3  C1   0.020
 SQE  plan-3  N    0.020
 SQE  plan-3  C19  0.020
 SQE  plan-3  C5   0.020
 SQE  plan-3  C6   0.020
 SQE  plan-3  N1   0.020
 SQE  plan-3  N2   0.020
 SQE  plan-3  N4   0.020
 SQE  plan-3  H2   0.020
 SQE  plan-3  H20  0.020
 SQE  plan-3  O    0.020
 SQE  plan-3  C20  0.020
 SQE  plan-4  C1   0.020
 SQE  plan-4  N    0.020
 SQE  plan-4  C    0.020
 SQE  plan-4  H3   0.020

