# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 15:50:53 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-(2,6-dichlorophenyl)-2-{[3-(hydroxymethyl)phenyl]amino}-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Cc2cnc(Nc3cccc(CO)c3)nc12)c4c(Cl)cccc4Cl
#
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
 P16  P16  6-(2,6-dichlorophenyl)-2-{[3-(hydroxymethyl)phenyl]amino}-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one  ligand  45  29  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P16
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
 P16  O1    O   OH1   0  -0.668   0.1089   1.3287  -8.7810
 P16  C2    C   CH2   0  -0.230   0.7513   0.1629  -8.3049
 P16  C3    C   CR6   0   0.103   0.0222  -0.3027  -7.0769
 P16  C4    C   CR16  0  -0.306  -1.1329  -1.0730  -7.1884
 P16  C5    C   CR16  0  -0.235  -1.8125  -1.4545  -6.0438
 P16  C6    C   CR16  0  -0.318  -1.3722  -1.0828  -4.7799
 P16  C7    C   CR6   0   0.385  -0.2174  -0.3092  -4.6580
 P16  N9    N   NH1   0  -0.765   0.3323   0.1357  -3.4568
 P16  C10   C   CR6   0   0.623  -0.0115  -0.0780  -2.1656
 P16  N11   N   N     0  -0.473  -1.0706  -0.8415  -1.8755
 P16  C12   C   CR16  0  -0.012  -1.3360  -1.0063  -0.5974
 P16  C13   C   CR66  0  -0.110  -0.5821  -0.4349   0.4215
 P16  C16   C   CR16  0  -0.141  -0.8298  -0.5942   1.8093
 P16  C17   C   CR6   0  -0.225  -0.0263   0.0051   2.7095
 P16  C18   C   CR6   0   0.571   1.0955   0.8388   2.2896
 P16  O21   O   OC    0  -0.449   1.8169   1.4052   3.0916
 P16  N19   N   NR6   0  -0.586   1.3059   0.9609   0.9191
 P16  C14   C   CR66  0   0.567   0.5053   0.3514  -0.0034
 P16  N15   N   N     0  -0.506   0.7833   0.5251  -1.2806
 P16  C20   C   CH3   0  -0.538   2.4167   1.7742   0.4390
 P16  C22   C   CR6   0   0.281  -0.2305  -0.1365   4.1634
 P16  C27   C   CR6   0  -0.122   0.5530  -1.0070   4.9186
 P16  CL28  CL  CL    0  -0.111   1.7888  -1.9176   4.1229
 P16  C26   C   CR16  0  -0.188   0.3730  -1.1722   6.2813
 P16  C25   C   CR16  0  -0.286  -0.6175  -0.4429   6.9205
 P16  C24   C   CR16  0  -0.185  -1.4133   0.4401   6.2092
 P16  C23   C   CR6   0  -0.133  -1.2082   0.5835   4.8457
 P16  CL29  CL  CL    0  -0.112  -2.1940   1.7054   3.9728
 P16  C8    C   CR16  0  -0.400   0.4643   0.0733  -5.8190
 P16  HO1   H   HOH1  0   0.456   0.5670   1.6112  -9.5788
 P16  H21   H   HCH2  0   0.210   1.8022   0.3550  -8.0582
 P16  H22   H   HCH2  0   0.210   0.7398  -0.6343  -9.0575
 P16  H4    H   HCR6  0   0.251  -1.4931  -1.3749  -8.1641
 P16  H5    H   HCR6  0   0.257  -2.7075  -2.0580  -6.1255
 P16  H6    H   HCR6  0   0.287  -1.9193  -1.3947  -3.9058
 P16  HN9   H   HNH1  0   0.415   1.1521   0.7166  -3.5533
 P16  H12   H   HCR6  0   0.285  -2.1934  -1.6242  -0.3503
 P16  H16   H   HCR6  0   0.284  -1.6657  -1.2042   2.1309
 P16  H201  H   HCH3  0   0.272   2.9468   2.1809   1.2907
 P16  H202  H   HCH3  0   0.260   3.0992   1.1686  -0.1526
 P16  H203  H   HCH3  0   0.260   2.0485   2.5911  -0.1777
 P16  H26   H   HCR6  0   0.287   0.9948  -1.8604   6.8365
 P16  H25   H   HCR6  0   0.281  -0.7698  -0.5636   7.9843
 P16  H24   H   HCR6  0   0.288  -2.1827   1.0117   6.7090
 P16  H8    H   HCR6  0   0.265   1.3633   0.6754  -5.7324

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
 P16  O1   C2    single    1.414  0.020  1.414
 P16  O1   HO1   single    0.850  0.020  0.980
 P16  C2   C3    single    1.502  0.020  1.502
 P16  C2   H21   single    0.970  0.020  1.090
 P16  C2   H22   single    0.970  0.020  1.090
 P16  C3   C4    aromatic  1.393  0.020  1.393
 P16  C3   C8    aromatic  1.385  0.020  1.385
 P16  C4   C5    aromatic  1.385  0.020  1.385
 P16  C4   H4    single    0.930  0.020  1.080
 P16  C5   C6    aromatic  1.389  0.020  1.389
 P16  C5   H5    single    0.930  0.020  1.080
 P16  C6   C7    aromatic  1.395  0.020  1.395
 P16  C6   H6    single    0.930  0.020  1.080
 P16  C7   N9    single    1.394  0.020  1.394
 P16  C7   C8    aromatic  1.400  0.020  1.400
 P16  N9   C10   single    1.353  0.020  1.353
 P16  N9   HN9   single    0.860  0.020  1.020
 P16  C10  N11   aromatic  1.337  0.020  1.337
 P16  C10  N15   aromatic  1.334  0.020  1.334
 P16  N11  C12   aromatic  1.316  0.020  1.316
 P16  C12  C13   aromatic  1.390  0.020  1.390
 P16  C12  H12   single    0.930  0.020  1.080
 P16  C13  C16   aromatic  1.419  0.020  1.419
 P16  C13  C14   aromatic  1.408  0.020  1.408
 P16  C16  C17   aromatic  1.347  0.020  1.347
 P16  C16  H16   single    0.930  0.020  1.080
 P16  C17  C18   aromatic  1.459  0.020  1.459
 P16  C17  C22   single    1.475  0.020  1.475
 P16  C18  O21   double    1.218  0.020  1.218
 P16  C18  N19   aromatic  1.392  0.020  1.392
 P16  N19  C14   aromatic  1.365  0.020  1.365
 P16  N19  C20   single    1.458  0.020  1.458
 P16  C14  N15   aromatic  1.319  0.020  1.319
 P16  C20  H201  single    0.970  0.020  1.090
 P16  C20  H202  single    0.970  0.020  1.090
 P16  C20  H203  single    0.970  0.020  1.090
 P16  C22  C27   aromatic  1.394  0.020  1.394
 P16  C22  C23   aromatic  1.393  0.020  1.393
 P16  C27  CL28  single    1.729  0.020  1.729
 P16  C27  C26   aromatic  1.384  0.020  1.384
 P16  C26  C25   aromatic  1.386  0.020  1.386
 P16  C26  H26   single    0.930  0.020  1.080
 P16  C25  C24   aromatic  1.385  0.020  1.385
 P16  C25  H25   single    0.930  0.020  1.080
 P16  C24  C23   aromatic  1.386  0.020  1.386
 P16  C24  H24   single    0.930  0.020  1.080
 P16  C23  CL29  single    1.730  0.020  1.730
 P16  C8   H8    single    0.930  0.020  1.080

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
 P16  HO1   O1   C2    107.76  3.000
 P16  H22   C2   H21   106.97  3.000
 P16  H22   C2   C3    109.31  3.000
 P16  H21   C2   C3    109.60  3.000
 P16  H22   C2   O1    111.33  3.000
 P16  H21   C2   O1    111.52  3.000
 P16  C3    C2   O1    108.08  3.000
 P16  C8    C3   C4    119.17  3.000
 P16  C8    C3   C2    120.22  3.000
 P16  C4    C3   C2    120.56  3.000
 P16  H4    C4   C5    120.31  3.000
 P16  H4    C4   C3    120.14  3.000
 P16  C5    C4   C3    119.55  3.000
 P16  H5    C5   C6    118.68  3.000
 P16  H5    C5   C4    119.80  3.000
 P16  C6    C5   C4    121.52  3.000
 P16  H6    C6   C7    120.66  3.000
 P16  H6    C6   C5    119.99  3.000
 P16  C7    C6   C5    119.35  3.000
 P16  C8    C7   N9    115.82  3.000
 P16  C8    C7   C6    118.82  3.000
 P16  N9    C7   C6    125.36  3.000
 P16  HN9   N9   C10   112.86  3.000
 P16  HN9   N9   C7    114.93  3.000
 P16  C10   N9   C7    132.20  3.000
 P16  N15   C10  N11   125.89  3.000
 P16  N15   C10  N9    114.23  3.000
 P16  N11   C10  N9    119.89  3.000
 P16  C12   N11  C10   116.23  3.000
 P16  H12   C12  C13   119.71  3.000
 P16  H12   C12  N11   116.86  3.000
 P16  C13   C12  N11   123.44  3.000
 P16  C14   C13  C16   119.53  3.000
 P16  C14   C13  C12   115.30  3.000
 P16  C16   C13  C12   125.17  3.000
 P16  H16   C16  C17   120.80  3.000
 P16  H16   C16  C13   119.22  3.000
 P16  C17   C16  C13   119.97  3.000
 P16  C22   C17  C18   116.42  3.000
 P16  C22   C17  C16   122.24  3.000
 P16  C18   C17  C16   121.35  3.000
 P16  N19   C18  O21   121.19  3.000
 P16  N19   C18  C17   116.72  3.000
 P16  O21   C18  C17   122.09  3.000
 P16  C20   N19  C14   118.25  3.000
 P16  C20   N19  C18   119.23  3.000
 P16  C14   N19  C18   122.52  3.000
 P16  N15   C14  N19   118.17  3.000
 P16  N15   C14  C13   121.93  3.000
 P16  N19   C14  C13   119.90  3.000
 P16  C14   N15  C10   117.23  3.000
 P16  H203  C20  H202  108.79  3.000
 P16  H203  C20  H201  109.25  3.000
 P16  H202  C20  H201  109.27  3.000
 P16  H203  C20  N19   110.35  3.000
 P16  H202  C20  N19   110.28  3.000
 P16  H201  C20  N19   108.88  3.000
 P16  C23   C22  C27   116.88  3.000
 P16  C23   C22  C17   122.04  3.000
 P16  C27   C22  C17   121.09  3.000
 P16  C26   C27  CL28  118.89  3.000
 P16  C26   C27  C22   122.33  3.000
 P16  CL28  C27  C22   118.78  3.000
 P16  H26   C26  C25   120.61  3.000
 P16  H26   C26  C27   120.44  3.000
 P16  C25   C26  C27   118.95  3.000
 P16  H25   C25  C24   119.69  3.000
 P16  H25   C25  C26   119.70  3.000
 P16  C24   C25  C26   120.60  3.000
 P16  H24   C24  C23   120.36  3.000
 P16  H24   C24  C25   120.57  3.000
 P16  C23   C24  C25   119.07  3.000
 P16  CL29  C23  C24   118.62  3.000
 P16  CL29  C23  C22   119.21  3.000
 P16  C24   C23  C22   122.16  3.000
 P16  H8    C8   C7    119.26  3.000
 P16  H8    C8   C3    119.17  3.000
 P16  C7    C8   C3    121.58  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
 P16  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 P16  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 P16  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 P16  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 P16  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 P16  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 P16  CONST_07  C13   C12  N11  C10     0.00   0.0  0
 P16  CONST_08  C13   C14  N15  C10     0.00   0.0  0
 P16  CONST_09  N19   C14  N15  C10   180.00   0.0  0
 P16  CONST_10  C14   N15  C10  N11     0.00   0.0  0
 P16  CONST_11  C16   C13  C12  N11   180.00   0.0  0
 P16  CONST_12  C14   C13  C12  N11     0.00   0.0  0
 P16  CONST_13  N15   C10  N11  C12     0.00   0.0  0
 P16  CONST_14  C17   C16  C13  C12   180.00   0.0  0
 P16  CONST_15  N19   C14  C13  C12   180.00   0.0  0
 P16  CONST_16  N15   C14  C13  C12     0.00   0.0  0
 P16  CONST_17  C18   C17  C16  C13     0.00   0.0  0
 P16  CONST_18  C22   C17  C16  C13   180.00   0.0  0
 P16  CONST_19  C18   N19  C14  C13     0.00   0.0  0
 P16  CONST_20  N19   C14  C13  C16     0.00   0.0  0
 P16  CONST_21  N15   C14  C13  C16   180.00   0.0  0
 P16  CONST_22  N19   C18  C17  C16     0.00   0.0  0
 P16  CONST_25  C14   C13  C16  C17     0.00   0.0  0
 P16  CONST_26  C14   N19  C18  C17     0.00   0.0  0
 P16  CONST_27  C26   C27  C22  C17   180.00   0.0  0
 P16  CONST_28  C24   C23  C22  C17   180.00   0.0  0
 P16  CONST_31  N15   C14  N19  C18   180.00   0.0  0
 P16  CONST_32  C22   C17  C18  N19   180.00   0.0  0
 P16  CONST_33  C25   C26  C27  C22     0.00   0.0  0
 P16  CONST_34  C25   C24  C23  C22     0.00   0.0  0
 P16  CONST_35  C24   C23  C22  C27     0.00   0.0  0
 P16  CONST_36  C24   C25  C26  C27     0.00   0.0  0
 P16  CONST_37  C23   C22  C27  C26     0.00   0.0  0
 P16  CONST_38  C23   C24  C25  C26     0.00   0.0  0
 P16  CONST_39  C5    C4   C3   C2    180.00   0.0  0
 P16  CONST_40  C7    C8   C3   C2    180.00   0.0  0
 P16  CONST_41  N9    C7   C8   C3    180.00   0.0  0
 P16  CONST_42  N9    C7   C6   C5    180.00   0.0  0
 P16  CONST_43  C12   N11  C10  N9    180.00   0.0  0
 P16  CONST_44  C14   N15  C10  N9    180.00   0.0  0
 P16  CONST_45  C20   N19  C14  C13   180.00   0.0  0
 P16  CONST_46  O21   C18  C17  C16   180.00   0.0  0
 P16  CONST_47  C20   N19  C18  C17   180.00   0.0  0
 P16  CONST_48  CL28  C27  C22  C17     0.00   0.0  0
 P16  CONST_49  CL29  C23  C22  C17     0.00   0.0  0
 P16  CONST_50  C22   C17  C18  O21     0.00   0.0  0
 P16  CONST_51  C14   N19  C18  O21   180.00   0.0  0
 P16  CONST_52  C20   N19  C14  N15     0.00   0.0  0
 P16  CONST_53  CL29  C23  C22  C27   180.00   0.0  0
 P16  CONST_54  C23   C22  C27  CL28  180.00   0.0  0
 P16  CONST_55  C25   C26  C27  CL28  180.00   0.0  0
 P16  CONST_56  CL29  C23  C24  C25   180.00   0.0  0
 P16  CONST_57  H5    C5   C4   C3    180.00   0.0  0
 P16  CONST_58  H8    C8   C3   C4    180.00   0.0  0
 P16  CONST_59  H6    C6   C5   C4    180.00   0.0  0
 P16  CONST_60  H4    C4   C5   C6    180.00   0.0  0
 P16  CONST_61  H12   C12  N11  C10   180.00   0.0  0
 P16  CONST_62  H16   C16  C13  C12     0.00   0.0  0
 P16  CONST_63  H26   C26  C27  C22   180.00   0.0  0
 P16  CONST_64  H24   C24  C23  C22   180.00   0.0  0
 P16  CONST_65  H25   C25  C26  C27   180.00   0.0  0
 P16  CONST_66  C20   N19  C18  O21     0.00   0.0  0
 P16  Var_01    C10   N9   C7   C6      3.45  30.0  2
 P16  Var_02    N11   C10  N9   C7     -0.45  30.0  2
 P16  Var_03    C4    C3   C2   O1     82.59  30.0  2
 P16  Var_04    H201  C20  N19  C18     0.37  30.0  2

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
 P16  plan-1  C2    0.020
 P16  plan-1  C3    0.020
 P16  plan-1  C4    0.020
 P16  plan-1  C5    0.020
 P16  plan-1  C6    0.020
 P16  plan-1  C7    0.020
 P16  plan-1  N9    0.020
 P16  plan-1  C8    0.020
 P16  plan-1  H4    0.020
 P16  plan-1  H5    0.020
 P16  plan-1  H6    0.020
 P16  plan-1  H8    0.020
 P16  plan-2  C17   0.020
 P16  plan-2  C22   0.020
 P16  plan-2  C27   0.020
 P16  plan-2  CL28  0.020
 P16  plan-2  C26   0.020
 P16  plan-2  C25   0.020
 P16  plan-2  C24   0.020
 P16  plan-2  C23   0.020
 P16  plan-2  CL29  0.020
 P16  plan-2  H26   0.020
 P16  plan-2  H25   0.020
 P16  plan-2  H24   0.020
 P16  plan-3  N9    0.020
 P16  plan-3  C10   0.020
 P16  plan-3  N11   0.020
 P16  plan-3  C12   0.020
 P16  plan-3  C13   0.020
 P16  plan-3  C16   0.020
 P16  plan-3  C17   0.020
 P16  plan-3  C18   0.020
 P16  plan-3  O21   0.020
 P16  plan-3  N19   0.020
 P16  plan-3  C14   0.020
 P16  plan-3  N15   0.020
 P16  plan-3  C20   0.020
 P16  plan-3  C22   0.020
 P16  plan-3  H12   0.020
 P16  plan-3  H16   0.020

