# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:57:31 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: 1-[(5-azanyl-1,3-dioxan-2-yl)methyl]-3-[2-chloranyl-4-(3-fluoranylpyridin-2-yl)phenyl]-7-(methylamino)-1,6-naphthyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc2N(C[C@H]3OC[C@H](N)CO3)C(=O)C(=Cc2cn1)c4ccc(cc4Cl)c5ncccc5F
#
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
 SQ8  SQ8  1-[(5-azanyl-1,3-dioxan-2-yl)methyl]-3-[2-chloranyl-4-(3-fluoranylpyridin-2-yl)phenyl]-7-(methylamino)-1,6-naphthyridin-2-one  ligand  58  35  .  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_SQ8
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
 SQ8  C20  C   CR66  0  -0.092  -33.0797   -4.3032  16.5764
 SQ8  C21  C   CR16  0  -0.108  -33.3025   -4.9457  17.7981
 SQ8  C22  C   CR6   0   0.507  -33.9312   -3.0228  18.8327
 SQ8  C24  C   CR16  0  -0.488  -33.7427   -2.2692  17.6666
 SQ8  C19  C   CR66  0   0.523  -33.3176   -2.9142  16.5124
 SQ8  N4   N   NH1   0  -0.643  -34.3327   -2.4536  19.9816
 SQ8  C17  C   CH1   0  -0.147  -30.9650    2.1474  16.6357
 SQ8  O2   O   O2    0  -0.481  -31.7077   -0.1625  16.5844
 SQ8  C12  C   CR16  0  -0.286  -30.6586   -4.6866  12.5218
 SQ8  C11  C   CR16  0  -0.261  -30.1447   -5.3294  11.4130
 SQ8  C13  C   CR16  0  -0.154  -32.6210   -4.9949  15.4305
 SQ8  C15  C   CH1   0   0.321  -32.2628    0.0475  15.3246
 SQ8  C16  C   CH2   0  -0.187  -31.6820    2.3034  15.3000
 SQ8  C10  C   CR6   0   0.475  -30.3784   -8.3782   9.3582
 SQ8  O1   O   O2    0  -0.495  -32.7288    1.3552  15.1798
 SQ8  C9   C   CR16  0  -0.296  -29.8280   -8.9407   8.2261
 SQ8  N3   N   N     0  -0.459  -33.7163   -4.3546  18.8891
 SQ8  C8   C   CR16  0  -0.305  -29.1762   -8.0998   7.3404
 SQ8  C7   C   CR16  0  -0.082  -29.1037   -6.7491   7.6491
 SQ8  C6   C   CR6   0   0.022  -30.2908   -7.0103   9.5990
 SQ8  C5   C   CR6   0   0.070  -30.8574   -6.3593  10.7987
 SQ8  C2   C   CR6   0   0.177  -31.8981   -5.0327  13.0615
 SQ8  N1   N   NR6   0  -0.623  -33.1331   -2.2742  15.3059
 SQ8  C3   C   CR6   0  -0.109  -32.6049   -6.0479  12.4213
 SQ8  C4   C   CR16  0  -0.239  -32.1004   -6.7120  11.3129
 SQ8  N2   N   NH2   0  -0.794  -29.8428    3.0615  16.6917
 SQ8  C1   C   CR6   0  -0.209  -32.4016   -4.3466  14.2653
 SQ8  C18  C   CH2   0  -0.195  -30.5864    0.6759  16.8030
 SQ8  N    N   N     0  -0.405  -29.6412   -6.2275   8.7405
 SQ8  C    C   CR6   0   0.554  -32.6590   -2.9188  14.1664
 SQ8  O    O   O     0  -0.471  -32.4899   -2.2872  13.1331
 SQ8  CL   CL  CL    0  -0.123  -34.1820   -6.5034  12.9816
 SQ8  H1   H   HCR6  0   0.271  -33.1253   -6.0158  17.8609
 SQ8  H5   H   HCR6  0   0.283  -33.8918   -1.2030  17.7007
 SQ8  H6   H   HNH1  0   0.394  -34.4696   -3.0721  20.7627
 SQ8  H7   H   HCH1  0   0.244  -31.6650    2.4190  17.4318
 SQ8  H8   H   HCR6  0   0.262  -30.0782   -3.9071  12.9975
 SQ8  H9   H   HCR6  0   0.261  -29.1772   -5.0415  11.0252
 SQ8  H10  H   HCR6  0   0.274  -32.4310   -6.0594  15.5113
 SQ8  H13  H   HCH1  0   0.202  -31.5020   -0.1572  14.5510
 SQ8  H14  H   HCH2  0   0.206  -30.9627    2.1763  14.4766
 SQ8  H15  H   HCH2  0   0.250  -32.1254    3.2950  15.2075
 SQ8  H16  H   HCR6  0   0.300  -29.9021  -10.0060   8.0510
 SQ8  H17  H   HCR6  0   0.285  -28.7292   -8.4846   6.4351
 SQ8  H18  H   HCR6  0   0.271  -28.5920   -6.0618   6.9860
 SQ8  H19  H   HCR6  0   0.277  -32.7046   -7.4739  10.8413
 SQ8  H20  H   HNH2  0   0.355  -29.4349    3.0549  17.6178
 SQ8  H21  H   HNH2  0   0.344  -29.1107    2.7561  16.0605
 SQ8  H23  H   HCH2  0   0.203  -29.7806    0.4256  16.0956
 SQ8  H24  H   HCH2  0   0.246  -30.2211    0.4731  17.8109
 SQ8  C14  C   CH2   0  -0.416  -33.4652   -0.8657  15.1501
 SQ8  C23  C   CH3   0  -0.533  -34.6444   -1.0593  20.1382
 SQ8  F    F   F     0  -0.298  -30.9848   -9.1757  10.2460
 SQ8  H2   H   HCH3  0   0.270  -34.9366   -0.8858  21.1696
 SQ8  H3   H   HCH3  0   0.237  -33.7843   -0.4212  19.9219
 SQ8  H4   H   HCH3  0   0.237  -35.4702   -0.7443  19.4948
 SQ8  H11  H   HCH2  0   0.283  -34.2483   -0.5963  15.8565
 SQ8  H12  H   HCH2  0   0.297  -33.8750   -0.7146  14.1542

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
 SQ8  C8   C7   aromatic  1.387  0.020  1.387
 SQ8  C8   C9   aromatic  1.384  0.020  1.384
 SQ8  C7   N    aromatic  1.324  0.020  1.324
 SQ8  C9   C10  aromatic  1.379  0.020  1.379
 SQ8  N    C6   aromatic  1.331  0.020  1.331
 SQ8  C10  C6   aromatic  1.392  0.020  1.392
 SQ8  C10  F    single    1.339  0.020  1.339
 SQ8  C6   C5   single    1.478  0.020  1.478
 SQ8  C5   C4   aromatic  1.391  0.020  1.391
 SQ8  C5   C11  aromatic  1.395  0.020  1.395
 SQ8  C4   C3   aromatic  1.387  0.020  1.387
 SQ8  C11  C12  aromatic  1.381  0.020  1.381
 SQ8  C3   CL   single    1.734  0.020  1.734
 SQ8  C3   C2   aromatic  1.393  0.020  1.393
 SQ8  C12  C2   aromatic  1.395  0.020  1.395
 SQ8  C2   C1   single    1.474  0.020  1.474
 SQ8  O    C    double    1.223  0.020  1.223
 SQ8  C    C1   single    1.454  0.020  1.454
 SQ8  C    N1   single    1.392  0.020  1.392
 SQ8  C1   C13  double    1.351  0.020  1.351
 SQ8  C16  O1   single    1.418  0.020  1.418
 SQ8  C16  C17  single    1.524  0.020  1.524
 SQ8  O1   C15  single    1.396  0.020  1.396
 SQ8  N2   C17  single    1.448  0.020  1.448
 SQ8  C15  C14  single    1.520  0.020  1.520
 SQ8  C15  O2   single    1.393  0.020  1.393
 SQ8  C14  N1   single    1.456  0.020  1.456
 SQ8  N1   C19  single    1.378  0.020  1.378
 SQ8  C17  C18  single    1.529  0.020  1.529
 SQ8  C13  C20  single    1.415  0.020  1.415
 SQ8  C18  O2   single    1.417  0.020  1.417
 SQ8  C19  C20  aromatic  1.411  0.020  1.411
 SQ8  C19  C24  aromatic  1.389  0.020  1.389
 SQ8  C20  C21  aromatic  1.398  0.020  1.398
 SQ8  C24  C22  aromatic  1.401  0.020  1.401
 SQ8  C21  N3   aromatic  1.308  0.020  1.308
 SQ8  C22  N3   aromatic  1.350  0.020  1.350
 SQ8  C22  N4   single    1.344  0.020  1.344
 SQ8  N4   C23  single    1.437  0.020  1.437
 SQ8  C21  H1   single    0.930  0.020  1.080
 SQ8  C23  H2   single    0.970  0.020  1.090
 SQ8  C23  H3   single    0.970  0.020  1.090
 SQ8  C23  H4   single    0.970  0.020  1.090
 SQ8  C24  H5   single    0.930  0.020  1.080
 SQ8  N4   H6   single    0.860  0.020  1.020
 SQ8  C17  H7   single    0.970  0.020  1.090
 SQ8  C12  H8   single    0.930  0.020  1.080
 SQ8  C11  H9   single    0.930  0.020  1.080
 SQ8  C13  H10  single    0.930  0.020  1.080
 SQ8  C14  H11  single    0.970  0.020  1.090
 SQ8  C14  H12  single    0.970  0.020  1.090
 SQ8  C15  H13  single    0.970  0.020  1.090
 SQ8  C16  H14  single    0.970  0.020  1.090
 SQ8  C16  H15  single    0.970  0.020  1.090
 SQ8  C9   H16  single    0.930  0.020  1.080
 SQ8  C8   H17  single    0.930  0.020  1.080
 SQ8  C7   H18  single    0.930  0.020  1.080
 SQ8  C4   H19  single    0.930  0.020  1.080
 SQ8  N2   H20  single    0.890  0.020  1.040
 SQ8  N2   H21  single    0.890  0.020  1.040
 SQ8  C18  H23  single    0.970  0.020  1.090
 SQ8  C18  H24  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
 SQ8  C13  C20  C19  119.95  3.000
 SQ8  C19  C20  C21  117.72  3.000
 SQ8  C13  C20  C21  122.32  3.000
 SQ8  H1   C21  N3   116.65  3.000
 SQ8  H1   C21  C20  118.49  3.000
 SQ8  N3   C21  C20  124.85  3.000
 SQ8  N3   C22  N4   115.45  3.000
 SQ8  N4   C22  C24  121.60  3.000
 SQ8  N3   C22  C24  122.95  3.000
 SQ8  H5   C24  C19  121.90  3.000
 SQ8  H5   C24  C22  119.17  3.000
 SQ8  C19  C24  C22  118.88  3.000
 SQ8  N1   C19  C24  123.56  3.000
 SQ8  C24  C19  C20  118.11  3.000
 SQ8  N1   C19  C20  118.32  3.000
 SQ8  H6   N4   C23  118.84  3.000
 SQ8  H6   N4   C22  116.38  3.000
 SQ8  C23  N4   C22  124.67  3.000
 SQ8  H7   C17  C18  108.53  3.000
 SQ8  H7   C17  N2   108.11  3.000
 SQ8  C18  C17  N2   114.30  3.000
 SQ8  H7   C17  C16  108.13  3.000
 SQ8  C18  C17  C16  108.12  3.000
 SQ8  N2   C17  C16  109.50  3.000
 SQ8  C18  O2   C15  111.45  3.000
 SQ8  H8   C12  C2   119.02  3.000
 SQ8  H8   C12  C11  119.26  3.000
 SQ8  C2   C12  C11  121.71  3.000
 SQ8  H9   C11  C5   119.71  3.000
 SQ8  H9   C11  C12  119.80  3.000
 SQ8  C5   C11  C12  120.48  3.000
 SQ8  H10  C13  C1   120.45  3.000
 SQ8  H10  C13  C20  118.45  3.000
 SQ8  C1   C13  C20  121.09  3.000
 SQ8  H13  C15  O1   109.33  3.000
 SQ8  H13  C15  C14  110.69  3.000
 SQ8  O1   C15  C14  106.67  3.000
 SQ8  H13  C15  O2   109.34  3.000
 SQ8  C14  C15  O2   109.18  3.000
 SQ8  O1   C15  O2   111.60  3.000
 SQ8  H15  C16  H14  107.90  3.000
 SQ8  H15  C16  O1   107.51  3.000
 SQ8  H14  C16  O1   109.99  3.000
 SQ8  H15  C16  C17  111.03  3.000
 SQ8  H14  C16  C17  109.66  3.000
 SQ8  O1   C16  C17  110.69  3.000
 SQ8  F    C10  C6   119.95  3.000
 SQ8  F    C10  C9   118.84  3.000
 SQ8  C6   C10  C9   121.19  3.000
 SQ8  C16  O1   C15  111.80  3.000
 SQ8  H16  C9   C8   121.78  3.000
 SQ8  H16  C9   C10  120.47  3.000
 SQ8  C8   C9   C10  117.74  3.000
 SQ8  C22  N3   C21  117.47  3.000
 SQ8  H17  C8   C7   120.77  3.000
 SQ8  H17  C8   C9   120.96  3.000
 SQ8  C7   C8   C9   118.27  3.000
 SQ8  H18  C7   N    116.51  3.000
 SQ8  H18  C7   C8   120.40  3.000
 SQ8  N    C7   C8   123.08  3.000
 SQ8  N    C6   C5   116.85  3.000
 SQ8  C5   C6   C10  123.32  3.000
 SQ8  N    C6   C10  119.81  3.000
 SQ8  C4   C5   C6   122.08  3.000
 SQ8  C4   C5   C11  118.75  3.000
 SQ8  C6   C5   C11  119.13  3.000
 SQ8  C1   C2   C3   122.77  3.000
 SQ8  C1   C2   C12  120.25  3.000
 SQ8  C3   C2   C12  116.98  3.000
 SQ8  C    N1   C14  115.98  3.000
 SQ8  C14  N1   C19  120.84  3.000
 SQ8  C    N1   C19  123.16  3.000
 SQ8  CL   C3   C4   117.59  3.000
 SQ8  CL   C3   C2   120.29  3.000
 SQ8  C4   C3   C2   122.12  3.000
 SQ8  H19  C4   C3   118.88  3.000
 SQ8  H19  C4   C5   121.14  3.000
 SQ8  C3   C4   C5   119.94  3.000
 SQ8  H21  N2   H20  106.07  3.000
 SQ8  H21  N2   C17  110.20  3.000
 SQ8  H20  N2   C17  110.09  3.000
 SQ8  C    C1   C2   117.51  3.000
 SQ8  C    C1   C13  120.06  3.000
 SQ8  C2   C1   C13  122.43  3.000
 SQ8  H24  C18  H23  107.83  3.000
 SQ8  H24  C18  O2   107.30  3.000
 SQ8  H23  C18  O2   110.21  3.000
 SQ8  H24  C18  C17  111.28  3.000
 SQ8  H23  C18  C17  109.26  3.000
 SQ8  O2   C18  C17  110.90  3.000
 SQ8  C6   N    C7   119.89  3.000
 SQ8  O    C    C1   122.69  3.000
 SQ8  C1   C    N1   117.33  3.000
 SQ8  O    C    N1   119.97  3.000
 SQ8  H12  C14  H11  106.79  3.000
 SQ8  H12  C14  N1   108.57  3.000
 SQ8  H11  C14  N1   109.52  3.000
 SQ8  H12  C14  C15  108.65  3.000
 SQ8  H11  C14  C15  110.24  3.000
 SQ8  N1   C14  C15  112.87  3.000
 SQ8  H4   C23  H3   108.05  3.000
 SQ8  H4   C23  H2   108.04  3.000
 SQ8  H3   C23  H2   107.84  3.000
 SQ8  H4   C23  N4   112.29  3.000
 SQ8  H3   C23  N4   111.98  3.000
 SQ8  H2   C23  N4   108.47  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
 SQ8  CONST_01  C22  C24  C19  C20     0.00   0.0  0
 SQ8  CONST_02  C22  N3   C21  C20     0.00   0.0  0
 SQ8  CONST_03  C24  C19  C20  C21     0.00   0.0  0
 SQ8  CONST_04  C24  C22  N3   C21     0.00   0.0  0
 SQ8  CONST_05  N3   C21  C20  C19     0.00   0.0  0
 SQ8  CONST_06  N3   C22  C24  C19     0.00   0.0  0
 SQ8  CONST_07  C6   C5   C11  C12   180.00   0.0  0
 SQ8  CONST_08  C4   C5   C11  C12     0.00   0.0  0
 SQ8  CONST_09  C4   C3   C2   C12     0.00   0.0  0
 SQ8  CONST_12  C3   C4   C5   C11     0.00   0.0  0
 SQ8  CONST_13  C3   C2   C12  C11     0.00   0.0  0
 SQ8  CONST_14  C7   C8   C9   C10     0.00   0.0  0
 SQ8  CONST_15  C7   N    C6   C10     0.00   0.0  0
 SQ8  CONST_17  N    C7   C8   C9      0.00   0.0  0
 SQ8  CONST_18  N    C6   C10  C9      0.00   0.0  0
 SQ8  CONST_19  C5   C6   C10  C9    180.00   0.0  0
 SQ8  CONST_20  C6   N    C7   C8      0.00   0.0  0
 SQ8  CONST_21  C6   C10  C9   C8      0.00   0.0  0
 SQ8  CONST_22  C5   C6   N    C7    180.00   0.0  0
 SQ8  CONST_23  C3   C4   C5   C6    180.00   0.0  0
 SQ8  CONST_24  C2   C3   C4   C5      0.00   0.0  0
 SQ8  CONST_25  C2   C12  C11  C5      0.00   0.0  0
 SQ8  CONST_27  C1   C2   C12  C11   180.00   0.0  0
 SQ8  CONST_28  C1   C2   C3   C4    180.00   0.0  0
 SQ8  CONST_29  C1   C    N1   C19     0.00   0.0  0
 SQ8  CONST_30  N4   C22  N3   C21   180.00   0.0  0
 SQ8  CONST_31  N4   C22  C24  C19   180.00   0.0  0
 SQ8  CONST_32  CL   C3   C2   C12   180.00   0.0  0
 SQ8  CONST_33  F    C10  C9   C8    180.00   0.0  0
 SQ8  CONST_34  F    C10  C6   C5      0.00   0.0  0
 SQ8  CONST_35  CL   C3   C4   C5    180.00   0.0  0
 SQ8  CONST_36  CL   C3   C2   C1      0.00   0.0  0
 SQ8  CONST_37  F    C10  C6   N     180.00   0.0  0
 SQ8  CONST_38  O    C    N1   C19   180.00   0.0  0
 SQ8  CONST_39  C1   C    N1   C14   180.00   0.0  0
 SQ8  CONST_40  H5   C24  C19  C20   180.00   0.0  0
 SQ8  CONST_41  H1   C21  N3   C22   180.00   0.0  0
 SQ8  CONST_42  H19  C4   C5   C11   180.00   0.0  0
 SQ8  CONST_43  H17  C8   C9   C10   180.00   0.0  0
 SQ8  CONST_44  H18  C7   C8   C9    180.00   0.0  0
 SQ8  CONST_45  H16  C9   C8   C7    180.00   0.0  0
 SQ8  CONST_46  H9   C11  C5   C6      0.00   0.0  0
 SQ8  CONST_47  H8   C12  C11  C5    180.00   0.0  0
 SQ8  CONST_48  C24  C22  N4   C23     0.00   0.0  0
 SQ8  CONST_49  N3   C22  N4   C23   180.00   0.0  0
 SQ8  CONST_50  O    C    N1   C14     0.00   0.0  0
 SQ8  CONST_51  H6   N4   C22  C24   180.00   0.0  0
 SQ8  Var_01    C    C1   C2   C12    63.22  30.0  2
 SQ8  Var_02    C15  C14  N1   C19    96.18  30.0  3
 SQ8  Var_03    H14  C16  O1   C15    64.49  30.0  1
 SQ8  Var_04    H23  C18  O2   C15   -64.09  30.0  1
 SQ8  Var_05    H2   C23  N4   C22  -179.87  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
 SQ8  chir_01  C17  C16  N2  C18  positiv
 SQ8  chir_02  C15  O1   O2  C14  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
 SQ8  plan-1  C10  0.020
 SQ8  plan-1  C9   0.020
 SQ8  plan-1  C8   0.020
 SQ8  plan-1  C7   0.020
 SQ8  plan-1  C6   0.020
 SQ8  plan-1  C5   0.020
 SQ8  plan-1  N    0.020
 SQ8  plan-1  H16  0.020
 SQ8  plan-1  H17  0.020
 SQ8  plan-1  H18  0.020
 SQ8  plan-1  F    0.020
 SQ8  plan-2  C12  0.020
 SQ8  plan-2  C11  0.020
 SQ8  plan-2  C6   0.020
 SQ8  plan-2  C5   0.020
 SQ8  plan-2  C2   0.020
 SQ8  plan-2  C3   0.020
 SQ8  plan-2  C4   0.020
 SQ8  plan-2  C1   0.020
 SQ8  plan-2  CL   0.020
 SQ8  plan-2  H8   0.020
 SQ8  plan-2  H9   0.020
 SQ8  plan-2  H19  0.020
 SQ8  plan-3  C20  0.020
 SQ8  plan-3  C21  0.020
 SQ8  plan-3  C22  0.020
 SQ8  plan-3  C24  0.020
 SQ8  plan-3  C19  0.020
 SQ8  plan-3  N4   0.020
 SQ8  plan-3  C13  0.020
 SQ8  plan-3  N3   0.020
 SQ8  plan-3  C2   0.020
 SQ8  plan-3  N1   0.020
 SQ8  plan-3  C1   0.020
 SQ8  plan-3  C    0.020
 SQ8  plan-3  O    0.020
 SQ8  plan-3  H1   0.020
 SQ8  plan-3  H5   0.020
 SQ8  plan-3  H10  0.020
 SQ8  plan-3  C14  0.020
 SQ8  plan-4  C22  0.020
 SQ8  plan-4  N4   0.020
 SQ8  plan-4  H6   0.020
 SQ8  plan-4  C23  0.020

