# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:30:53 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: (4S)-6-[(4-{[(2S)-3-(dimethylamino)-2-hydroxypropyl]oxy}phenyl)amino]-4-{[2-fluoro-5-(trifluoromethyl)phenyl]amino}-1,4-dihydropyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@H](O)COc1ccc(NC2=C[C@](O)(Nc3cc(ccc3F)C(F)(F)F)N=CN2)cc1
#
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
 3FQ  3FQ  (4S)-6-[(4-{[(2S)-3-(dimethylamino)-2-hydroxypropyl]oxy}phenyl)amino]-4-{[2-fluoro-5-(trifluoromethyl)phenyl]amino}-1,4-dihydropyrimidin-4-ol  ligand  59  34  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3FQ
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
 3FQ  C1    C  CT    0   0.534  -3.0059  -0.6052  -1.1536
 3FQ  N1    N  NH1   0  -0.687  -0.5509   0.7400  -1.1313
 3FQ  C2    C  C1    0  -0.519  -1.7047  -1.2799  -1.4523
 3FQ  C7    C  CR16  0  -0.313  -7.1378  -0.2585   2.0042
 3FQ  C6    C  CR16  0  -0.396  -6.2378  -1.1824   2.5185
 3FQ  C5    C  CR6   0   0.467  -5.1089  -1.4965   1.8029
 3FQ  C4    C  CR6   0   0.241  -4.7978  -0.9353   0.5573
 3FQ  C3    C  C     0   0.607  -0.5475  -0.5943  -1.4762
 3FQ  C11   C  CR16  0  -0.285   2.0301  -0.4076   0.0271
 3FQ  C10   C  CR6   0   0.265   1.8984  -0.8043  -1.3050
 3FQ  C9    C  CR16  0  -0.333  -5.7162  -0.0097   0.0574
 3FQ  C8    C  CR6   0  -0.189  -6.8609   0.3206   0.7755
 3FQ  C12   C  CR16  0  -0.341   3.2738  -0.1088   0.5528
 3FQ  C16   C  CH2   0  -0.179   6.7888  -0.0472  -0.3714
 3FQ  C14   C  CR16  0  -0.374   4.3023  -0.6519  -1.5477
 3FQ  C13   C  CR6   0   0.377   4.4243  -0.2289  -0.2265
 3FQ  C15   C  CR16  0  -0.299   3.0475  -0.9174  -2.0785
 3FQ  C     C  C1    0   0.119  -1.7250   1.3380  -0.8038
 3FQ  N     N  N     0  -0.453  -2.8692   0.7845  -0.7825
 3FQ  N2    N  NH1   0  -0.735  -3.6577  -1.3450  -0.0918
 3FQ  N3    N  NH1   0  -0.767   0.6556  -1.1151  -1.8852
 3FQ  O     O  O2    0  -0.477   5.5929   0.0772   0.3736
 3FQ  C21   C  CT    0   1.044  -7.8154   1.2922   0.1582
 3FQ  F2    F  F     0  -0.317  -8.5003   0.7394  -0.8571
 3FQ  F3    F  F     0  -0.305  -8.7210   1.7499   1.0286
 3FQ  F4    F  F     0  -0.313  -7.1892   2.3626  -0.3519
 3FQ  C17   C  CH1   0   0.005   7.9469   0.3609   0.5095
 3FQ  C18   C  CH2   0  -0.308   9.2382   0.3713  -0.3139
 3FQ  C19   C  CH3   0  -0.515  11.5867  -0.0899  -0.0201
 3FQ  C20   C  CH3   0  -0.525  10.6103   1.8131   1.0470
 3FQ  N4    N  NT    0  -0.437  10.3846   0.4611   0.5724
 3FQ  O1    O  OH1   0  -0.680   8.0809  -0.5407   1.5791
 3FQ  O1L   O  OH1   0  -0.658  -3.8910  -0.6893  -2.2518
 3FQ  HN1   H  HNH1  0   0.425   0.2804   1.3028  -1.2183
 3FQ  H2    H  H     0   0.268  -1.7143  -2.3362  -1.6899
 3FQ  H7    H  HCR6  0   0.271  -8.0240  -0.0094   2.5693
 3FQ  H6    H  HCR6  0   0.285  -6.4137  -1.6529   3.4768
 3FQ  H11   H  HCR6  0   0.276   1.1625  -0.3417   0.6711
 3FQ  H9    H  HCR6  0   0.283  -5.5218   0.4529  -0.8976
 3FQ  H12   H  HCR6  0   0.266   3.3599   0.2039   1.5860
 3FQ  H161  H  HCH2  0   0.227   6.7632   0.6018  -1.2551
 3FQ  H162  H  HCH2  0   0.225   6.9266  -1.0800  -0.7149
 3FQ  H14   H  HCR6  0   0.282   5.1663  -0.7658  -2.1877
 3FQ  H15   H  HCR6  0   0.269   2.9659  -1.2212  -3.1148
 3FQ  H     H  H     0   0.280  -1.6321   2.3877  -0.5441
 3FQ  HA    H  HNH1  0   0.389  -3.0053  -1.8590   0.4780
 3FQ  H3    H  HNH1  0   0.405   0.5944  -2.0077  -2.3500
 3FQ  H17   H  HCH1  0   0.207   7.7467   1.3786   0.8802
 3FQ  H181  H  HCH2  0   0.221   9.2095   1.1796  -1.0595
 3FQ  H182  H  HCH2  0   0.240   9.3092  -0.5706  -0.8661
 3FQ  H191  H  HCH3  0   0.236  12.3976  -0.0796   0.7089
 3FQ  H192  H  HCH3  0   0.238  11.4187  -1.1251  -0.3176
 3FQ  H193  H  HCH3  0   0.201  11.9234   0.4677  -0.9054
 3FQ  H201  H  HCH3  0   0.240   9.7159   2.2127   1.5246
 3FQ  H202  H  HCH3  0   0.240  11.4078   1.8182   1.7902
 3FQ  H203  H  HCH3  0   0.204  10.8941   2.5015   0.2377
 3FQ  H1    H  HOH1  0   0.439   9.0296  -0.5207   1.7894
 3FQ  H1L   H  HOH1  0   0.445  -3.4954  -0.2030  -2.9836
 3FQ  F1    F  F     0  -0.318  -4.2404  -2.3891   2.3156

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
 3FQ  C1   C2    single    1.496  0.020  1.496
 3FQ  C1   N     single    1.445  0.020  1.445
 3FQ  C1   N2    single    1.449  0.020  1.449
 3FQ  C1   O1L   single    1.413  0.020  1.413
 3FQ  N1   C3    single    1.378  0.020  1.378
 3FQ  N1   C     single    1.358  0.020  1.358
 3FQ  N1   HN1   single    0.860  0.020  1.020
 3FQ  C2   C3    double    1.345  0.020  1.345
 3FQ  C2   H2    single    0.930  0.020  1.080
 3FQ  C7   C6    aromatic  1.389  0.020  1.389
 3FQ  C7   C8    aromatic  1.386  0.020  1.386
 3FQ  C7   H7    single    0.930  0.020  1.080
 3FQ  C6   C5    aromatic  1.373  0.020  1.373
 3FQ  C6   H6    single    0.930  0.020  1.080
 3FQ  C5   C4    aromatic  1.401  0.020  1.401
 3FQ  C5   F1    single    1.347  0.020  1.347
 3FQ  C4   C9    aromatic  1.396  0.020  1.396
 3FQ  C4   N2    single    1.374  0.020  1.374
 3FQ  C3   N3    single    1.373  0.020  1.373
 3FQ  C11  C10   aromatic  1.396  0.020  1.396
 3FQ  C11  C12   aromatic  1.383  0.020  1.383
 3FQ  C11  H11   single    0.930  0.020  1.080
 3FQ  C10  C15   aromatic  1.390  0.020  1.390
 3FQ  C10  N3    single    1.406  0.020  1.406
 3FQ  C9   C8    aromatic  1.391  0.020  1.391
 3FQ  C9   H9    single    0.930  0.020  1.080
 3FQ  C8   C21   single    1.495  0.020  1.495
 3FQ  C12  C13   aromatic  1.395  0.020  1.395
 3FQ  C12  H12   single    0.930  0.020  1.080
 3FQ  C16  O     single    1.414  0.020  1.414
 3FQ  C16  C17   single    1.511  0.020  1.511
 3FQ  C16  H161  single    0.970  0.020  1.090
 3FQ  C16  H162  single    0.970  0.020  1.090
 3FQ  C14  C13   aromatic  1.393  0.020  1.393
 3FQ  C14  C15   aromatic  1.388  0.020  1.388
 3FQ  C14  H14   single    0.930  0.020  1.080
 3FQ  C13  O     single    1.349  0.020  1.349
 3FQ  C15  H15   single    0.930  0.020  1.080
 3FQ  C    N     double    1.271  0.020  1.271
 3FQ  C    H     single    0.930  0.020  1.080
 3FQ  N2   HA    single    0.890  0.020  1.040
 3FQ  N3   H3    single    0.890  0.020  1.040
 3FQ  C21  F2    single    1.344  0.020  1.344
 3FQ  C21  F3    single    1.337  0.020  1.337
 3FQ  C21  F4    single    1.341  0.020  1.341
 3FQ  C17  C18   single    1.532  0.020  1.532
 3FQ  C17  O1    single    1.405  0.020  1.405
 3FQ  C17  H17   single    0.970  0.020  1.090
 3FQ  C18  N4    single    1.452  0.020  1.452
 3FQ  C18  H181  single    0.970  0.020  1.090
 3FQ  C18  H182  single    0.970  0.020  1.090
 3FQ  C19  N4    single    1.449  0.020  1.449
 3FQ  C19  H191  single    0.970  0.020  1.090
 3FQ  C19  H192  single    0.970  0.020  1.090
 3FQ  C19  H193  single    0.970  0.020  1.090
 3FQ  C20  N4    single    1.451  0.020  1.451
 3FQ  C20  H201  single    0.970  0.020  1.090
 3FQ  C20  H202  single    0.970  0.020  1.090
 3FQ  C20  H203  single    0.970  0.020  1.090
 3FQ  O1   H1    single    0.850  0.020  0.980
 3FQ  O1L  H1L   single    0.850  0.020  0.980

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
 3FQ  O1L   C1   N2    104.91  3.000
 3FQ  O1L   C1   N     108.43  3.000
 3FQ  N2    C1   N     110.21  3.000
 3FQ  O1L   C1   C2    111.28  3.000
 3FQ  N2    C1   C2    107.90  3.000
 3FQ  N     C1   C2    113.75  3.000
 3FQ  HN1   N1   C     119.23  3.000
 3FQ  HN1   N1   C3    121.14  3.000
 3FQ  C     N1   C3    119.27  3.000
 3FQ  H2    C2   C3    120.06  3.000
 3FQ  H2    C2   C1    118.43  3.000
 3FQ  C3    C2   C1    121.47  3.000
 3FQ  H7    C7   C8    122.09  3.000
 3FQ  H7    C7   C6    119.43  3.000
 3FQ  C8    C7   C6    118.48  3.000
 3FQ  H6    C6   C5    119.72  3.000
 3FQ  H6    C6   C7    120.80  3.000
 3FQ  C5    C6   C7    119.48  3.000
 3FQ  F1    C5   C4    117.43  3.000
 3FQ  F1    C5   C6    118.91  3.000
 3FQ  C4    C5   C6    123.66  3.000
 3FQ  N2    C4   C9    125.03  3.000
 3FQ  N2    C4   C5    118.99  3.000
 3FQ  C9    C4   C5    115.96  3.000
 3FQ  N3    C3   C2    124.45  3.000
 3FQ  N3    C3   N1    116.35  3.000
 3FQ  C2    C3   N1    119.13  3.000
 3FQ  H11   C11  C12   118.78  3.000
 3FQ  H11   C11  C10   120.62  3.000
 3FQ  C12   C11  C10   120.59  3.000
 3FQ  N3    C10  C15   118.89  3.000
 3FQ  N3    C10  C11   122.67  3.000
 3FQ  C15   C10  C11   118.43  3.000
 3FQ  H9    C9   C8    120.23  3.000
 3FQ  H9    C9   C4    118.86  3.000
 3FQ  C8    C9   C4    120.91  3.000
 3FQ  C21   C8   C9    117.80  3.000
 3FQ  C21   C8   C7    120.65  3.000
 3FQ  C9    C8   C7    121.52  3.000
 3FQ  H12   C12  C13   119.50  3.000
 3FQ  H12   C12  C11   119.77  3.000
 3FQ  C13   C12  C11   120.72  3.000
 3FQ  H162  C16  H161  107.92  3.000
 3FQ  H162  C16  C17   109.91  3.000
 3FQ  H161  C16  C17   109.14  3.000
 3FQ  H162  C16  O     110.73  3.000
 3FQ  H161  C16  O     110.65  3.000
 3FQ  C17   C16  O     108.49  3.000
 3FQ  H14   C14  C15   118.42  3.000
 3FQ  H14   C14  C13   121.57  3.000
 3FQ  C15   C14  C13   120.00  3.000
 3FQ  O     C13  C14   124.53  3.000
 3FQ  O     C13  C12   116.51  3.000
 3FQ  C14   C13  C12   118.95  3.000
 3FQ  H15   C15  C14   119.18  3.000
 3FQ  H15   C15  C10   119.54  3.000
 3FQ  C14   C15  C10   121.28  3.000
 3FQ  H     C    N     119.62  3.000
 3FQ  H     C    N1    114.18  3.000
 3FQ  N     C    N1    126.20  3.000
 3FQ  C     N    C1    119.98  3.000
 3FQ  HA    N2   C4    114.98  3.000
 3FQ  HA    N2   C1    112.56  3.000
 3FQ  C4    N2   C1    124.54  3.000
 3FQ  H3    N3   C10   116.07  3.000
 3FQ  H3    N3   C3    114.83  3.000
 3FQ  C10   N3   C3    124.58  3.000
 3FQ  C13   O    C16   118.57  3.000
 3FQ  F4    C21  F3    106.90  3.000
 3FQ  F4    C21  F2    106.20  3.000
 3FQ  F3    C21  F2    106.71  3.000
 3FQ  F4    C21  C8    112.18  3.000
 3FQ  F3    C21  C8    112.71  3.000
 3FQ  F2    C21  C8    111.71  3.000
 3FQ  H17   C17  O1    110.73  3.000
 3FQ  H17   C17  C18   109.14  3.000
 3FQ  O1    C17  C18   109.46  3.000
 3FQ  H17   C17  C16   107.84  3.000
 3FQ  O1    C17  C16   110.09  3.000
 3FQ  C18   C17  C16   109.54  3.000
 3FQ  H182  C18  H181  107.00  3.000
 3FQ  H182  C18  N4    108.06  3.000
 3FQ  H181  C18  N4    112.89  3.000
 3FQ  H182  C18  C17   108.67  3.000
 3FQ  H181  C18  C17   110.33  3.000
 3FQ  N4    C18  C17   109.75  3.000
 3FQ  H193  C19  H192  108.01  3.000
 3FQ  H193  C19  H191  107.81  3.000
 3FQ  H192  C19  H191  107.83  3.000
 3FQ  H193  C19  N4    112.99  3.000
 3FQ  H192  C19  N4    110.17  3.000
 3FQ  H191  C19  N4    109.87  3.000
 3FQ  H203  C20  H202  108.05  3.000
 3FQ  H203  C20  H201  107.74  3.000
 3FQ  H202  C20  H201  107.46  3.000
 3FQ  H203  C20  N4    112.51  3.000
 3FQ  H202  C20  N4    109.95  3.000
 3FQ  H201  C20  N4    110.95  3.000
 3FQ  C20   N4   C19   111.05  3.000
 3FQ  C20   N4   C18   112.35  3.000
 3FQ  C19   N4   C18   112.45  3.000
 3FQ  H1    O1   C17   104.16  3.000
 3FQ  H1L   O1L  C1    107.64  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
 3FQ  CONST_01  C4    C5   C6   C7      0.00   0.0  0
 3FQ  CONST_02  C4    C9   C8   C7      0.00   0.0  0
 3FQ  CONST_03  C9    C8   C7   C6      0.00   0.0  0
 3FQ  CONST_04  C9    C4   C5   C6      0.00   0.0  0
 3FQ  CONST_05  C8    C7   C6   C5      0.00   0.0  0
 3FQ  CONST_06  C8    C9   C4   C5      0.00   0.0  0
 3FQ  CONST_07  C14   C15  C10  C11     0.00   0.0  0
 3FQ  CONST_08  C14   C13  C12  C11     0.00   0.0  0
 3FQ  CONST_09  C13   C12  C11  C10     0.00   0.0  0
 3FQ  CONST_10  C13   C14  C15  C10     0.00   0.0  0
 3FQ  CONST_11  C15   C10  C11  C12     0.00   0.0  0
 3FQ  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 3FQ  CONST_13  N1    C    N    C1      0.00   0.0  0
 3FQ  CONST_14  C     N1   C3   C2      0.00   0.0  0
 3FQ  CONST_15  N     C    N1   C3      0.00   0.0  0
 3FQ  CONST_16  F1    C5   C6   C7    180.00   0.0  0
 3FQ  CONST_17  C21   C8   C7   C6    180.00   0.0  0
 3FQ  CONST_18  N2    C4   C5   C6    180.00   0.0  0
 3FQ  CONST_19  C21   C8   C9   C4    180.00   0.0  0
 3FQ  CONST_20  O     C13  C12  C11   180.00   0.0  0
 3FQ  CONST_21  F1    C5   C4   C9    180.00   0.0  0
 3FQ  CONST_22  N2    C4   C9   C8    180.00   0.0  0
 3FQ  CONST_23  N3    C10  C11  C12   180.00   0.0  0
 3FQ  CONST_24  N3    C10  C15  C14   180.00   0.0  0
 3FQ  CONST_25  O     C13  C14  C15   180.00   0.0  0
 3FQ  CONST_32  N3    C3   N1   C     180.00   0.0  0
 3FQ  CONST_33  H9    C9   C8   C7    180.00   0.0  0
 3FQ  CONST_34  H7    C7   C6   C5    180.00   0.0  0
 3FQ  CONST_35  H6    C6   C5   C4    180.00   0.0  0
 3FQ  CONST_36  H15   C15  C10  C11   180.00   0.0  0
 3FQ  CONST_37  H12   C12  C11  C10   180.00   0.0  0
 3FQ  CONST_38  H14   C14  C15  C10   180.00   0.0  0
 3FQ  CONST_39  H11   C11  C12  C13   180.00   0.0  0
 3FQ  CONST_40  H     C    N    C1    180.00   0.0  0
 3FQ  CONST_41  HN1   N1   C3   C2    180.00   0.0  0
 3FQ  CONST_42  HA    N2   C4   C5      0.00   0.0  0
 3FQ  Var_01    H2    C2   C3   N1   -178.06  30.0  1
 3FQ  Var_02    F2    C21  C8   C7   -105.04  30.0  2
 3FQ  Var_03    C14   C13  O    C16    -0.67  30.0  1
 3FQ  Var_04    C17   C16  O    C13   179.52  30.0  1
 3FQ  Var_05    C19   N4   C18  C17   154.89  30.0  3
 3FQ  Var_06    H191  C19  N4   C18  -175.16  30.0  3
 3FQ  Var_07    H201  C20  N4   C18    55.13  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
 3FQ  chir_01  C1   N    C2   O1L  positiv
 3FQ  chir_02  C17  C16  C18  O1   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
 3FQ  plan-1  C7   0.020
 3FQ  plan-1  C6   0.020
 3FQ  plan-1  C5   0.020
 3FQ  plan-1  C4   0.020
 3FQ  plan-1  C9   0.020
 3FQ  plan-1  C8   0.020
 3FQ  plan-1  N2   0.020
 3FQ  plan-1  C21  0.020
 3FQ  plan-1  H7   0.020
 3FQ  plan-1  H6   0.020
 3FQ  plan-1  H9   0.020
 3FQ  plan-1  F1   0.020
 3FQ  plan-2  C11  0.020
 3FQ  plan-2  C10  0.020
 3FQ  plan-2  C12  0.020
 3FQ  plan-2  C14  0.020
 3FQ  plan-2  C13  0.020
 3FQ  plan-2  C15  0.020
 3FQ  plan-2  N3   0.020
 3FQ  plan-2  O    0.020
 3FQ  plan-2  H11  0.020
 3FQ  plan-2  H12  0.020
 3FQ  plan-2  H14  0.020
 3FQ  plan-2  H15  0.020
 3FQ  plan-3  C1   0.020
 3FQ  plan-3  C4   0.020
 3FQ  plan-3  N2   0.020
 3FQ  plan-3  HA   0.020
 3FQ  plan-4  C1   0.020
 3FQ  plan-4  N1   0.020
 3FQ  plan-4  C2   0.020
 3FQ  plan-4  C3   0.020
 3FQ  plan-4  C10  0.020
 3FQ  plan-4  C    0.020
 3FQ  plan-4  N    0.020
 3FQ  plan-4  N3   0.020
 3FQ  plan-4  HN1  0.020
 3FQ  plan-4  H    0.020
 3FQ  plan-4  H3   0.020

