# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 07:36:31 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 6-[[4-[(3-methylsulfonylphenyl)methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,4-dihydro-1~{H}-quinolin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(CNc2nc(Nc3ccc4NC(=O)CCc4c3)ncc2C(F)(F)F)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
 P4N  P4N  6-[[4-[(3-methylsulfonylphenyl)methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]-3,4-dihydro-1~{H}-quinolin-2-one  ligand  54  34  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P4N
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
 P4N  C1   C  CR16  0  -0.231  -16.0849  -0.7953  16.9054
 P4N  C2   C  CR16  0  -0.248  -14.7866  -1.1608  16.5855
 P4N  C3   C  CR6   0  -0.184  -14.3201  -2.3918  17.0247
 P4N  C10  C  CH3   0  -0.789  -12.9007  -3.7865  15.0652
 P4N  C13  C  CR6   0   0.605  -16.1125  -4.1561  20.9646
 P4N  C15  C  CR6   0   0.594  -16.1085  -2.4557  22.4823
 P4N  N23  N  NH1   0  -0.754  -16.5835  -1.2553  22.8972
 P4N  C24  C  CR6   0   0.351  -17.6419  -0.5161  22.3472
 P4N  C27  C  CR16  0  -0.293  -17.7904  -0.3141  20.9781
 P4N  C30  C  CH2   0  -0.490  -20.6774   1.4013  23.6427
 P4N  C31  C  CH2   0  -0.592  -21.2144   2.7018  23.0589
 P4N  C32  C  C     0   0.501  -21.6406   2.5554  21.6190
 P4N  C4   C  CR16  0  -0.272  -15.1128  -3.2473  17.7755
 P4N  C5   C  CR6   0   0.103  -16.4152  -2.8785  18.0914
 P4N  C6   C  CR16  0  -0.292  -16.8901  -1.6487  17.6465
 P4N  S7   S  S     0   1.214  -12.6714  -2.9009  16.5911
 P4N  O8   O  OS    0  -0.662  -11.8789  -1.7047  16.3181
 P4N  O9   O  OS    0  -0.663  -12.1942  -3.8482  17.5960
 P4N  N12  N  NH1   0  -0.679  -16.6077  -4.6367  19.8113
 P4N  N14  N  N     0  -0.507  -16.5293  -2.9492  21.3286
 P4N  N16  N  N     0  -0.484  -15.2394  -3.0392  23.3179
 P4N  C17  C  CR16  0  -0.032  -14.8029  -4.2271  22.9413
 P4N  C18  C  CR6   0  -0.445  -15.1965  -4.8704  21.7812
 P4N  F20  F  F     0  -0.322  -15.6021  -7.1344  21.2760
 P4N  F21  F  F     0  -0.319  -14.0105  -6.1641  20.2153
 P4N  F22  F  F     0  -0.300  -13.7670  -6.6562  22.2961
 P4N  C25  C  CR16  0  -0.399  -18.5628   0.0678  23.2166
 P4N  C26  C  CR16  0  -0.329  -18.8572   0.4264  20.4960
 P4N  C28  C  CR6   0   0.359  -19.7816   0.9854  21.3691
 P4N  C29  C  CR6   0   0.071  -19.6303   0.8132  22.7447
 P4N  N33  N  NH1   0  -0.732  -20.8769   1.7040  20.8844
 P4N  O34  O  O     0  -0.460  -22.5714   3.1656  21.1250
 P4N  H1   H  HCR6  0   0.272  -16.4691   0.1623  16.5805
 P4N  H2   H  HCR6  0   0.282  -14.1579  -0.4954  16.0098
 P4N  H3   H  HCH3  0   0.308  -11.9201  -4.1327  14.7391
 P4N  H4   H  HCH3  0   0.294  -13.5584  -4.6353  15.2393
 P4N  H5   H  HCH3  0   0.294  -13.3300  -3.1207  14.3199
 P4N  H6   H  HCH2  0   0.273  -18.0933  -3.2343  19.3770
 P4N  H7   H  HCH2  0   0.289  -17.8269  -4.4817  18.1762
 P4N  H8   H  HNH1  0   0.406  -16.3065  -1.0109  23.8365
 P4N  H9   H  HCR6  0   0.273  -17.0751  -0.7247  20.2826
 P4N  H10  H  HCH2  0   0.262  -21.4979   0.6853  23.7580
 P4N  H11  H  HCH2  0   0.269  -20.2769   1.5766  24.6414
 P4N  H12  H  HCH2  0   0.279  -20.4372   3.4735  23.0921
 P4N  H13  H  HCH2  0   0.277  -22.0588   3.0762  23.6358
 P4N  H14  H  HCR6  0   0.271  -14.7153  -4.1945  18.1179
 P4N  H15  H  HCR6  0   0.276  -17.9037  -1.3497  17.8882
 P4N  H16  H  HNH1  0   0.410  -16.3556  -5.5570  19.4963
 P4N  H17  H  HCR6  0   0.280  -14.0912  -4.6964  23.6108
 P4N  H18  H  HCR6  0   0.264  -18.4560  -0.0764  24.2864
 P4N  H19  H  HCR6  0   0.268  -18.9620   0.5748  19.4276
 P4N  H20  H  HNH1  0   0.404  -21.0817   1.6452  19.8960
 P4N  C11  C  CH2   0  -0.345  -17.3191  -3.8093  18.8691
 P4N  C19  C  CT    0   1.074  -14.6461  -6.1942  21.4032

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
 P4N  C10  S7   single    1.779  0.020  1.779
 P4N  C2   C1   aromatic  1.386  0.020  1.386
 P4N  C2   C3   aromatic  1.388  0.020  1.388
 P4N  C1   C6   aromatic  1.388  0.020  1.388
 P4N  S7   C3   single    1.779  0.020  1.779
 P4N  S7   O8   double    1.461  0.020  1.461
 P4N  S7   O9   double    1.461  0.020  1.461
 P4N  C3   C4   aromatic  1.387  0.020  1.387
 P4N  C6   C5   aromatic  1.391  0.020  1.391
 P4N  C4   C5   aromatic  1.390  0.020  1.390
 P4N  C5   C11  single    1.513  0.020  1.513
 P4N  C11  N12  single    1.442  0.020  1.442
 P4N  N12  C13  single    1.344  0.020  1.344
 P4N  F21  C19  single    1.348  0.020  1.348
 P4N  C26  C27  aromatic  1.385  0.020  1.385
 P4N  C26  C28  aromatic  1.389  0.020  1.389
 P4N  N33  C28  single    1.397  0.020  1.397
 P4N  N33  C32  single    1.359  0.020  1.359
 P4N  C27  C24  aromatic  1.392  0.020  1.392
 P4N  O34  C32  double    1.218  0.020  1.218
 P4N  C13  N14  aromatic  1.328  0.020  1.328
 P4N  C13  C18  aromatic  1.420  0.020  1.420
 P4N  F20  C19  single    1.347  0.020  1.347
 P4N  C19  C18  single    1.483  0.020  1.483
 P4N  C19  F22  single    1.336  0.020  1.336
 P4N  C28  C29  aromatic  1.394  0.020  1.394
 P4N  N14  C15  aromatic  1.323  0.020  1.323
 P4N  C32  C31  single    1.509  0.020  1.509
 P4N  C18  C17  aromatic  1.384  0.020  1.384
 P4N  C24  N23  single    1.403  0.020  1.403
 P4N  C24  C25  aromatic  1.395  0.020  1.395
 P4N  C15  N23  single    1.356  0.020  1.356
 P4N  C15  N16  aromatic  1.339  0.020  1.339
 P4N  C29  C25  aromatic  1.385  0.020  1.385
 P4N  C29  C30  single    1.500  0.020  1.500
 P4N  C31  C30  single    1.523  0.020  1.523
 P4N  C17  N16  aromatic  1.320  0.020  1.320
 P4N  C1   H1   single    0.930  0.020  1.080
 P4N  C2   H2   single    0.930  0.020  1.080
 P4N  C10  H3   single    0.970  0.020  1.090
 P4N  C10  H4   single    0.970  0.020  1.090
 P4N  C10  H5   single    0.970  0.020  1.090
 P4N  C11  H6   single    0.970  0.020  1.090
 P4N  C11  H7   single    0.970  0.020  1.090
 P4N  N23  H8   single    0.860  0.020  1.020
 P4N  C27  H9   single    0.930  0.020  1.080
 P4N  C30  H10  single    0.970  0.020  1.090
 P4N  C30  H11  single    0.970  0.020  1.090
 P4N  C31  H12  single    0.970  0.020  1.090
 P4N  C31  H13  single    0.970  0.020  1.090
 P4N  C4   H14  single    0.930  0.020  1.080
 P4N  C6   H15  single    0.930  0.020  1.080
 P4N  N12  H16  single    0.860  0.020  1.020
 P4N  C17  H17  single    0.930  0.020  1.080
 P4N  C25  H18  single    0.930  0.020  1.080
 P4N  C26  H19  single    0.930  0.020  1.080
 P4N  N33  H20  single    0.860  0.020  1.020

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
 P4N  H1   C1   C6   119.92  3.000
 P4N  H1   C1   C2   119.78  3.000
 P4N  C6   C1   C2   120.30  3.000
 P4N  H2   C2   C3   121.25  3.000
 P4N  H2   C2   C1   120.34  3.000
 P4N  C3   C2   C1   118.41  3.000
 P4N  S7   C3   C4   119.01  3.000
 P4N  C4   C3   C2   121.75  3.000
 P4N  S7   C3   C2   119.22  3.000
 P4N  H5   C10  H4   110.41  3.000
 P4N  H5   C10  H3   110.16  3.000
 P4N  H4   C10  H3   110.12  3.000
 P4N  H5   C10  S7   109.50  3.000
 P4N  H4   C10  S7   109.21  3.000
 P4N  H3   C10  S7   107.38  3.000
 P4N  C18  C13  N14  120.14  3.000
 P4N  C18  C13  N12  123.46  3.000
 P4N  N14  C13  N12  116.40  3.000
 P4N  N16  C15  N14  125.99  3.000
 P4N  N16  C15  N23  114.97  3.000
 P4N  N14  C15  N23  119.04  3.000
 P4N  H8   N23  C24  116.37  3.000
 P4N  H8   N23  C15  113.76  3.000
 P4N  C24  N23  C15  127.64  3.000
 P4N  C25  C24  C27  118.81  3.000
 P4N  C25  C24  N23  118.31  3.000
 P4N  C27  C24  N23  122.85  3.000
 P4N  H9   C27  C26  119.31  3.000
 P4N  H9   C27  C24  120.54  3.000
 P4N  C26  C27  C24  120.14  3.000
 P4N  H11  C30  H10  106.50  3.000
 P4N  H11  C30  C29  110.80  3.000
 P4N  H10  C30  C29  109.25  3.000
 P4N  H11  C30  C31  110.08  3.000
 P4N  H10  C30  C31  109.54  3.000
 P4N  C29  C30  C31  110.57  3.000
 P4N  H13  C31  H12  106.97  3.000
 P4N  H13  C31  C32  108.66  3.000
 P4N  H12  C31  C32  107.32  3.000
 P4N  H13  C31  C30  111.33  3.000
 P4N  H12  C31  C30  109.85  3.000
 P4N  C32  C31  C30  112.49  3.000
 P4N  O34  C32  N33  121.60  3.000
 P4N  O34  C32  C31  123.68  3.000
 P4N  N33  C32  C31  114.70  3.000
 P4N  H14  C4   C5   120.28  3.000
 P4N  H14  C4   C3   120.06  3.000
 P4N  C5   C4   C3   119.66  3.000
 P4N  C6   C5   C4   118.79  3.000
 P4N  C4   C5   C11  120.90  3.000
 P4N  C6   C5   C11  120.28  3.000
 P4N  H15  C6   C5   119.45  3.000
 P4N  H15  C6   C1   119.47  3.000
 P4N  C5   C6   C1   121.08  3.000
 P4N  O9   S7   O8   118.84  3.000
 P4N  O9   S7   C10  108.01  3.000
 P4N  O8   S7   C10  108.50  3.000
 P4N  O9   S7   C3   108.69  3.000
 P4N  O8   S7   C3   108.30  3.000
 P4N  C10  S7   C3   103.41  3.000
 P4N  H16  N12  C13  120.27  3.000
 P4N  H16  N12  C11  116.40  3.000
 P4N  C13  N12  C11  122.50  3.000
 P4N  C15  N14  C13  118.56  3.000
 P4N  C17  N16  C15  115.37  3.000
 P4N  H17  C17  C18  120.23  3.000
 P4N  H17  C17  N16  115.49  3.000
 P4N  C18  C17  N16  124.29  3.000
 P4N  C17  C18  C19  121.55  3.000
 P4N  C17  C18  C13  115.58  3.000
 P4N  C19  C18  C13  122.82  3.000
 P4N  H18  C25  C29  118.91  3.000
 P4N  H18  C25  C24  119.61  3.000
 P4N  C29  C25  C24  121.46  3.000
 P4N  H19  C26  C28  120.01  3.000
 P4N  H19  C26  C27  119.40  3.000
 P4N  C28  C26  C27  120.59  3.000
 P4N  N33  C28  C29  119.40  3.000
 P4N  C29  C28  C26  119.88  3.000
 P4N  N33  C28  C26  120.71  3.000
 P4N  C28  C29  C25  119.09  3.000
 P4N  C25  C29  C30  123.04  3.000
 P4N  C28  C29  C30  117.81  3.000
 P4N  H20  N33  C28  117.92  3.000
 P4N  H20  N33  C32  116.80  3.000
 P4N  C28  N33  C32  125.11  3.000
 P4N  H7   C11  H6   106.89  3.000
 P4N  H7   C11  N12  106.91  3.000
 P4N  H6   C11  N12  110.41  3.000
 P4N  H7   C11  C5   109.32  3.000
 P4N  H6   C11  C5   109.84  3.000
 P4N  N12  C11  C5   113.22  3.000
 P4N  F22  C19  F21  106.66  3.000
 P4N  F22  C19  F20  106.79  3.000
 P4N  F21  C19  F20  105.50  3.000
 P4N  F22  C19  C18  112.51  3.000
 P4N  F20  C19  C18  112.58  3.000
 P4N  F21  C19  C18  112.32  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
 P4N  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 P4N  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 P4N  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 P4N  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 P4N  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 P4N  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 P4N  CONST_07  N16  C15  N14  C13     0.00   0.0  0
 P4N  CONST_08  N16  C17  C18  C13     0.00   0.0  0
 P4N  CONST_09  C18  C13  N14  C15     0.00   0.0  0
 P4N  CONST_10  C18  C17  N16  C15     0.00   0.0  0
 P4N  CONST_11  C28  C26  C27  C24     0.00   0.0  0
 P4N  CONST_12  C28  C29  C25  C24     0.00   0.0  0
 P4N  CONST_13  C29  C28  C26  C27     0.00   0.0  0
 P4N  CONST_14  C29  C25  C24  C27     0.00   0.0  0
 P4N  CONST_15  C17  C18  C13  N14     0.00   0.0  0
 P4N  CONST_16  C17  N16  C15  N14     0.00   0.0  0
 P4N  CONST_17  C26  C27  C24  C25     0.00   0.0  0
 P4N  CONST_18  C26  C28  C29  C25     0.00   0.0  0
 P4N  CONST_19  C28  N33  C32  C31     0.00   0.0  0
 P4N  CONST_20  S7   C3   C2   C1    180.00   0.0  0
 P4N  CONST_21  C11  C5   C6   C1    180.00   0.0  0
 P4N  CONST_22  C11  C5   C4   C3    180.00   0.0  0
 P4N  CONST_23  N23  C15  N14  C13   180.00   0.0  0
 P4N  CONST_24  N12  C13  N14  C15   180.00   0.0  0
 P4N  CONST_25  N14  C13  C18  C19   180.00   0.0  0
 P4N  CONST_26  N16  C17  C18  C19   180.00   0.0  0
 P4N  CONST_27  C26  C27  C24  N23   180.00   0.0  0
 P4N  CONST_28  C29  C25  C24  N23   180.00   0.0  0
 P4N  CONST_29  C17  N16  C15  N23   180.00   0.0  0
 P4N  CONST_30  S7   C3   C4   C5    180.00   0.0  0
 P4N  CONST_31  C17  C18  C13  N12   180.00   0.0  0
 P4N  CONST_32  O34  C32  N33  C28   180.00   0.0  0
 P4N  CONST_33  H15  C6   C1   C2    180.00   0.0  0
 P4N  CONST_34  H14  C4   C3   C2    180.00   0.0  0
 P4N  CONST_35  H1   C1   C2   C3    180.00   0.0  0
 P4N  CONST_36  H17  C17  C18  C13   180.00   0.0  0
 P4N  CONST_37  H19  C26  C27  C24   180.00   0.0  0
 P4N  CONST_38  H18  C25  C24  C27   180.00   0.0  0
 P4N  CONST_39  H2   C2   C3   C4    180.00   0.0  0
 P4N  CONST_40  H9   C27  C24  C25   180.00   0.0  0
 P4N  CONST_41  H20  N33  C32  C31   180.00   0.0  0
 P4N  CONST_42  N14  C13  N12  C11     0.00   0.0  0
 P4N  CONST_43  C18  C13  N12  C11   180.00   0.0  0
 P4N  CONST_44  H16  N12  C13  N14   180.00   0.0  0
 P4N  Var_01    N33  C32  C31  C30   -35.26  30.0  1
 P4N  Var_02    C28  C29  C30  C31   -34.10  30.0  1
 P4N  Var_03    C26  C28  N33  C32  -162.82  30.0  1
 P4N  Var_04    C29  C30  C31  C32    50.80  30.0  1
 P4N  Var_05    C27  C24  N23  C15   -45.49  30.0  2
 P4N  Var_06    N14  C15  N23  C24    10.18  30.0  1
 P4N  Var_07    C10  S7   C3   C2    -90.91  30.0  1
 P4N  Var_08    C5   C11  N12  C13    74.21  30.0  2
 P4N  Var_09    F21  C19  C18  C13    57.32  30.0  2
 P4N  Var_10    N12  C11  C5   C4     32.02  30.0  2
 P4N  Var_11    H3   C10  S7   C3   -179.89  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
 P4N  plan-1  C1   0.020
 P4N  plan-1  C2   0.020
 P4N  plan-1  C3   0.020
 P4N  plan-1  C4   0.020
 P4N  plan-1  C5   0.020
 P4N  plan-1  C6   0.020
 P4N  plan-1  S7   0.020
 P4N  plan-1  H1   0.020
 P4N  plan-1  H2   0.020
 P4N  plan-1  H14  0.020
 P4N  plan-1  H15  0.020
 P4N  plan-1  C11  0.020
 P4N  plan-2  C13  0.020
 P4N  plan-2  C15  0.020
 P4N  plan-2  N23  0.020
 P4N  plan-2  N12  0.020
 P4N  plan-2  N14  0.020
 P4N  plan-2  N16  0.020
 P4N  plan-2  C17  0.020
 P4N  plan-2  C18  0.020
 P4N  plan-2  H17  0.020
 P4N  plan-2  C19  0.020
 P4N  plan-3  N23  0.020
 P4N  plan-3  C24  0.020
 P4N  plan-3  C27  0.020
 P4N  plan-3  C30  0.020
 P4N  plan-3  C25  0.020
 P4N  plan-3  C26  0.020
 P4N  plan-3  C28  0.020
 P4N  plan-3  C29  0.020
 P4N  plan-3  N33  0.020
 P4N  plan-3  H9   0.020
 P4N  plan-3  H18  0.020
 P4N  plan-3  H19  0.020
 P4N  plan-4  C13  0.020
 P4N  plan-4  N12  0.020
 P4N  plan-4  H16  0.020
 P4N  plan-4  C11  0.020
 P4N  plan-5  C31  0.020
 P4N  plan-5  C32  0.020
 P4N  plan-5  C28  0.020
 P4N  plan-5  N33  0.020
 P4N  plan-5  O34  0.020
 P4N  plan-5  H20  0.020

