# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 15:50:57 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-(2,6-dichlorophenyl)-8-methyl-2-{[3-(methylsulfanyl)phenyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1cccc(Nc2ncc3C=C(C(=O)N(C)c3n2)c4c(Cl)cccc4Cl)c1
#
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
 P17  P17  6-(2,6-dichlorophenyl)-8-methyl-2-{[3-(methylsulfanyl)phenyl]amino}pyrido[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_P17
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
 P17  S2   S   S2    0   0.040   2.3586  -0.6738   6.4654
 P17  C3   C   CR6   0  -0.095   0.6614  -0.3213   6.1513
 P17  C8   C   CR16  0  -0.322   0.3144  -0.1912   4.8042
 P17  C7   C   CR6   0   0.380  -1.0014   0.0883   4.4475
 P17  N9   N   NH1   0  -0.765  -1.4540   0.2586   3.1415
 P17  C10  C   CR6   0   0.624  -0.8447   0.1118   1.9410
 P17  N15  N   N     0  -0.504  -1.6180   0.4060   0.8958
 P17  C14  C   CR66  0   0.568  -1.0847   0.2780  -0.3037
 P17  N19  N   NR6   0  -0.586  -1.8562   0.5837  -1.3876
 P17  C20  C   CH3   0  -0.538  -3.2224   1.0370  -1.1549
 P17  C18  C   CR6   0   0.570  -1.3846   0.4850  -2.6933
 P17  O21  O   OC    0  -0.449  -2.0896   0.7785  -3.6427
 P17  C17  C   CR6   0  -0.223  -0.0125   0.0164  -2.8613
 P17  C22  C   CR6   0   0.279   0.4778  -0.0974  -4.2478
 P17  C27  C   CR6   0  -0.121   0.1157  -1.1740  -5.0554
 P17  C26  C   CR16  0  -0.188   0.5720  -1.3107  -6.3553
 P17  C25  C   CR16  0  -0.286   1.4171  -0.3428  -6.8755
 P17  C24  C   CR16  0  -0.185   1.7965   0.7472  -6.1097
 P17  C23  C   CR6   0  -0.134   1.3207   0.8574  -4.8122
 P17  CL2  CL  CL    0  -0.111  -0.9345  -2.3850  -4.4078
 P17  C16  C   CR16  0  -0.142   0.7611  -0.2823  -1.7996
 P17  C13  C   CR66  0  -0.110   0.2414  -0.1564  -0.4856
 P17  C12  C   CR16  0  -0.010   0.9435  -0.4303   0.6826
 P17  N11  N   N     0  -0.475   0.4257  -0.3016   1.8856
 P17  C6   C   CR16  0  -0.367  -1.9662   0.2355   5.4532
 P17  C5   C   CR16  0  -0.227  -1.6070   0.1053   6.7791
 P17  C4   C   CR16  0  -0.289  -0.2960  -0.1742   7.1475
 P17  C1   C   CH3   0  -0.795   2.4619  -0.7253   8.2624
 P17  H10  H   HCR6  0   0.292   1.0681  -0.3055   4.0409
 P17  H1   H   HNH1  0   0.416  -2.4180   0.5468   3.0602
 P17  H4   H   HCH3  0   0.272  -3.6899   1.2469  -2.1085
 P17  H5   H   HCH3  0   0.260  -3.7913   0.2681  -0.6372
 P17  H6   H   HCH3  0   0.260  -3.2213   1.9395  -0.5481
 P17  H7   H   HCR6  0   0.287   0.2726  -2.1594  -6.9541
 P17  H8   H   HCR6  0   0.281   1.7819  -0.4393  -7.8888
 P17  H9   H   HCR6  0   0.288   2.4512   1.5043  -6.5177
 P17  H3   H   HCR6  0   0.285   1.7812  -0.6218  -1.9351
 P17  H2   H   HCR6  0   0.286   1.9734  -0.7681   0.6246
 P17  H16  H   HCR6  0   0.271  -2.9943   0.4523   5.1893
 P17  H15  H   HCR6  0   0.263  -2.3608   0.2212   7.5468
 P17  H14  H   HCR6  0   0.264  -0.0462  -0.2726   8.1940
 P17  H11  H   HCH3  0   0.295   3.5056  -0.9273   8.4950
 P17  H12  H   HCH3  0   0.274   2.1842   0.2274   8.7098
 P17  H13  H   HCH3  0   0.274   1.8528  -1.5245   8.6804
 P17  CL1  CL  CL    0  -0.112   1.7825   2.2373  -3.8767

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
 P17  S2   C3   single    1.762  0.020  1.762
 P17  S2   C1   single    1.801  0.020  1.801
 P17  C3   C8   aromatic  1.397  0.020  1.397
 P17  C3   C4   aromatic  1.389  0.020  1.389
 P17  C8   C7   aromatic  1.392  0.020  1.392
 P17  C8   H10  single    0.930  0.020  1.080
 P17  C7   N9   single    1.393  0.020  1.393
 P17  C7   C6   aromatic  1.401  0.020  1.401
 P17  N9   C10  single    1.354  0.020  1.354
 P17  N9   H1   single    0.860  0.020  1.020
 P17  C10  N15  aromatic  1.333  0.020  1.333
 P17  C10  N11  aromatic  1.337  0.020  1.337
 P17  N15  C14  aromatic  1.319  0.020  1.319
 P17  C14  N19  aromatic  1.365  0.020  1.365
 P17  C14  C13  aromatic  1.407  0.020  1.407
 P17  N19  C20  single    1.458  0.020  1.458
 P17  N19  C18  aromatic  1.392  0.020  1.392
 P17  C20  H4   single    0.970  0.020  1.090
 P17  C20  H5   single    0.970  0.020  1.090
 P17  C20  H6   single    0.970  0.020  1.090
 P17  C18  O21  double    1.218  0.020  1.218
 P17  C18  C17  aromatic  1.460  0.020  1.460
 P17  C17  C22  single    1.475  0.020  1.475
 P17  C17  C16  aromatic  1.347  0.020  1.347
 P17  C22  C27  aromatic  1.394  0.020  1.394
 P17  C22  C23  aromatic  1.393  0.020  1.393
 P17  C27  C26  aromatic  1.384  0.020  1.384
 P17  C27  CL2  single    1.729  0.020  1.729
 P17  CL1  C23  single    1.730  0.020  1.730
 P17  C26  C25  aromatic  1.386  0.020  1.386
 P17  C26  H7   single    0.930  0.020  1.080
 P17  C25  C24  aromatic  1.385  0.020  1.385
 P17  C25  H8   single    0.930  0.020  1.080
 P17  C24  C23  aromatic  1.386  0.020  1.386
 P17  C24  H9   single    0.930  0.020  1.080
 P17  C16  C13  aromatic  1.419  0.020  1.419
 P17  C16  H3   single    0.930  0.020  1.080
 P17  C13  C12  aromatic  1.390  0.020  1.390
 P17  C12  N11  aromatic  1.316  0.020  1.316
 P17  C12  H2   single    0.930  0.020  1.080
 P17  C6   C5   aromatic  1.380  0.020  1.380
 P17  C6   H16  single    0.930  0.020  1.080
 P17  C5   C4   aromatic  1.390  0.020  1.390
 P17  C5   H15  single    0.930  0.020  1.080
 P17  C4   H14  single    0.930  0.020  1.080
 P17  C1   H11  single    0.970  0.020  1.090
 P17  C1   H12  single    0.970  0.020  1.090
 P17  C1   H13  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
 P17  C1   S2   C3   103.82  3.000
 P17  C4   C3   C8   120.68  3.000
 P17  C4   C3   S2   123.86  3.000
 P17  C8   C3   S2   115.45  3.000
 P17  H10  C8   C7   120.04  3.000
 P17  H10  C8   C3   119.92  3.000
 P17  C7   C8   C3   120.04  3.000
 P17  C6   C7   N9   115.88  3.000
 P17  C6   C7   C8   119.22  3.000
 P17  N9   C7   C8   124.90  3.000
 P17  H1   N9   C10  112.91  3.000
 P17  H1   N9   C7   114.88  3.000
 P17  C10  N9   C7   132.21  3.000
 P17  N11  C10  N15  125.93  3.000
 P17  N11  C10  N9   119.85  3.000
 P17  N15  C10  N9   114.22  3.000
 P17  C14  N15  C10  117.21  3.000
 P17  C13  C14  N19  119.94  3.000
 P17  C13  C14  N15  121.90  3.000
 P17  N19  C14  N15  118.16  3.000
 P17  C18  N19  C20  119.29  3.000
 P17  C18  N19  C14  122.51  3.000
 P17  C20  N19  C14  118.19  3.000
 P17  H6   C20  H5   108.76  3.000
 P17  H6   C20  H4   109.32  3.000
 P17  H5   C20  H4   109.30  3.000
 P17  H6   C20  N19  110.25  3.000
 P17  H5   C20  N19  110.26  3.000
 P17  H4   C20  N19  108.92  3.000
 P17  C17  C18  O21  122.11  3.000
 P17  C17  C18  N19  116.70  3.000
 P17  O21  C18  N19  121.19  3.000
 P17  C16  C17  C22  122.20  3.000
 P17  C16  C17  C18  121.35  3.000
 P17  C22  C17  C18  116.45  3.000
 P17  C23  C22  C27  116.86  3.000
 P17  C23  C22  C17  121.94  3.000
 P17  C27  C22  C17  121.20  3.000
 P17  CL2  C27  C26  118.86  3.000
 P17  CL2  C27  C22  118.81  3.000
 P17  C26  C27  C22  122.33  3.000
 P17  H7   C26  C25  120.61  3.000
 P17  H7   C26  C27  120.42  3.000
 P17  C25  C26  C27  118.96  3.000
 P17  H8   C25  C24  119.73  3.000
 P17  H8   C25  C26  119.67  3.000
 P17  C24  C25  C26  120.60  3.000
 P17  H9   C24  C23  120.36  3.000
 P17  H9   C24  C25  120.56  3.000
 P17  C23  C24  C25  119.08  3.000
 P17  C24  C23  CL1  118.55  3.000
 P17  C24  C23  C22  122.16  3.000
 P17  CL1  C23  C22  119.29  3.000
 P17  H3   C16  C13  119.24  3.000
 P17  H3   C16  C17  120.76  3.000
 P17  C13  C16  C17  120.00  3.000
 P17  C12  C13  C16  125.16  3.000
 P17  C12  C13  C14  115.35  3.000
 P17  C16  C13  C14  119.49  3.000
 P17  H2   C12  N11  116.91  3.000
 P17  H2   C12  C13  119.71  3.000
 P17  N11  C12  C13  123.38  3.000
 P17  C12  N11  C10  116.23  3.000
 P17  H16  C6   C5   120.01  3.000
 P17  H16  C6   C7   119.97  3.000
 P17  C5   C6   C7   120.03  3.000
 P17  H15  C5   C4   119.37  3.000
 P17  H15  C5   C6   119.35  3.000
 P17  C4   C5   C6   121.27  3.000
 P17  H14  C4   C5   119.54  3.000
 P17  H14  C4   C3   121.70  3.000
 P17  C5   C4   C3   118.76  3.000
 P17  H13  C1   H12  110.01  3.000
 P17  H13  C1   H11  108.57  3.000
 P17  H12  C1   H11  108.62  3.000
 P17  H13  C1   S2   111.85  3.000
 P17  H12  C1   S2   111.75  3.000
 P17  H11  C1   S2   105.88  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
 P17  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 P17  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 P17  CONST_03  C5   C4   C3   C8      0.00   0.0  0
 P17  CONST_04  C5   C6   C7   C8      0.00   0.0  0
 P17  CONST_05  C4   C3   C8   C7      0.00   0.0  0
 P17  CONST_06  C4   C5   C6   C7      0.00   0.0  0
 P17  CONST_07  N19  C14  N15  C10   180.00   0.0  0
 P17  CONST_08  C13  C14  N15  C10     0.00   0.0  0
 P17  CONST_09  C13  C12  N11  C10     0.00   0.0  0
 P17  CONST_10  C12  N11  C10  N15     0.00   0.0  0
 P17  CONST_11  C18  N19  C14  N15   180.00   0.0  0
 P17  CONST_12  C16  C13  C14  N15   180.00   0.0  0
 P17  CONST_13  C12  C13  C14  N15     0.00   0.0  0
 P17  CONST_14  N11  C10  N15  C14     0.00   0.0  0
 P17  CONST_15  C17  C18  N19  C14     0.00   0.0  0
 P17  CONST_16  C17  C16  C13  C14     0.00   0.0  0
 P17  CONST_17  N11  C12  C13  C14     0.00   0.0  0
 P17  CONST_18  C16  C13  C14  N19     0.00   0.0  0
 P17  CONST_19  C12  C13  C14  N19   180.00   0.0  0
 P17  CONST_20  C22  C17  C18  N19   180.00   0.0  0
 P17  CONST_21  C16  C17  C18  N19     0.00   0.0  0
 P17  CONST_22  C13  C14  N19  C18     0.00   0.0  0
 P17  CONST_25  C13  C16  C17  C18     0.00   0.0  0
 P17  CONST_26  C26  C27  C22  C17   180.00   0.0  0
 P17  CONST_27  C24  C23  C22  C17   180.00   0.0  0
 P17  CONST_28  C12  C13  C16  C17   180.00   0.0  0
 P17  CONST_29  C13  C16  C17  C22   180.00   0.0  0
 P17  CONST_30  C25  C26  C27  C22     0.00   0.0  0
 P17  CONST_31  C25  C24  C23  C22     0.00   0.0  0
 P17  CONST_33  C24  C23  C22  C27     0.00   0.0  0
 P17  CONST_34  C24  C25  C26  C27     0.00   0.0  0
 P17  CONST_35  C23  C22  C27  C26     0.00   0.0  0
 P17  CONST_36  C23  C24  C25  C26     0.00   0.0  0
 P17  CONST_38  N11  C12  C13  C16   180.00   0.0  0
 P17  CONST_39  C7   C8   C3   S2    180.00   0.0  0
 P17  CONST_40  C5   C4   C3   S2    180.00   0.0  0
 P17  CONST_41  N9   C7   C8   C3    180.00   0.0  0
 P17  CONST_42  C5   C6   C7   N9    180.00   0.0  0
 P17  CONST_43  C14  N15  C10  N9    180.00   0.0  0
 P17  CONST_44  C12  N11  C10  N9    180.00   0.0  0
 P17  CONST_45  C20  N19  C14  N15     0.00   0.0  0
 P17  CONST_46  O21  C18  N19  C14   180.00   0.0  0
 P17  CONST_47  C13  C14  N19  C20   180.00   0.0  0
 P17  CONST_48  C17  C18  N19  C20   180.00   0.0  0
 P17  CONST_49  C22  C17  C18  O21     0.00   0.0  0
 P17  CONST_50  C16  C17  C18  O21   180.00   0.0  0
 P17  CONST_51  CL2  C27  C22  C17     0.00   0.0  0
 P17  CONST_52  CL1  C23  C22  C17     0.00   0.0  0
 P17  CONST_53  CL1  C23  C22  C27   180.00   0.0  0
 P17  CONST_54  C25  C24  C23  CL1   180.00   0.0  0
 P17  CONST_55  CL2  C27  C26  C25   180.00   0.0  0
 P17  CONST_56  CL2  C27  C22  C23   180.00   0.0  0
 P17  CONST_57  H15  C5   C4   C3    180.00   0.0  0
 P17  CONST_58  H14  C4   C3   C8    180.00   0.0  0
 P17  CONST_59  H16  C6   C7   C8    180.00   0.0  0
 P17  CONST_60  H2   C12  N11  C10   180.00   0.0  0
 P17  CONST_61  H3   C16  C13  C14   180.00   0.0  0
 P17  CONST_62  H7   C26  C27  C22   180.00   0.0  0
 P17  CONST_63  H9   C24  C23  C22   180.00   0.0  0
 P17  CONST_64  H8   C25  C26  C27   180.00   0.0  0
 P17  CONST_65  H10  C8   C7   C6    180.00   0.0  0
 P17  CONST_66  O21  C18  N19  C20     0.00   0.0  0
 P17  Var_01    C10  N9   C7   C8      5.76  30.0  2
 P17  Var_02    N15  C10  N9   C7   -178.36  30.0  2
 P17  Var_03    H4   C20  N19  C14   179.33  30.0  2
 P17  Var_04    H11  C1   S2   C3   -179.17  30.0  3

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
 P17  plan-1  S2   0.020
 P17  plan-1  C3   0.020
 P17  plan-1  C8   0.020
 P17  plan-1  C7   0.020
 P17  plan-1  N9   0.020
 P17  plan-1  C6   0.020
 P17  plan-1  C5   0.020
 P17  plan-1  C4   0.020
 P17  plan-1  H10  0.020
 P17  plan-1  H16  0.020
 P17  plan-1  H15  0.020
 P17  plan-1  H14  0.020
 P17  plan-2  C17  0.020
 P17  plan-2  C22  0.020
 P17  plan-2  C27  0.020
 P17  plan-2  C26  0.020
 P17  plan-2  C25  0.020
 P17  plan-2  C24  0.020
 P17  plan-2  C23  0.020
 P17  plan-2  CL2  0.020
 P17  plan-2  H7   0.020
 P17  plan-2  H8   0.020
 P17  plan-2  H9   0.020
 P17  plan-2  CL1  0.020
 P17  plan-3  N9   0.020
 P17  plan-3  C10  0.020
 P17  plan-3  N15  0.020
 P17  plan-3  C14  0.020
 P17  plan-3  N19  0.020
 P17  plan-3  C20  0.020
 P17  plan-3  C18  0.020
 P17  plan-3  O21  0.020
 P17  plan-3  C17  0.020
 P17  plan-3  C22  0.020
 P17  plan-3  C16  0.020
 P17  plan-3  C13  0.020
 P17  plan-3  C12  0.020
 P17  plan-3  N11  0.020
 P17  plan-3  H3   0.020
 P17  plan-3  H2   0.020

