# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 02:01:59 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2R)-1-(dimethylamino)-3-{4-[(6-{[2-fluoro-5-(trifluoromethyl)phenyl]amino}pyrimidin-4-yl)amino]phenoxy}propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@@H](O)COc1ccc(Nc2cc(Nc3cc(ccc3F)C(F)(F)F)ncn2)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
 3FP  3FP  (2R)-1-(dimethylamino)-3-{4-[(6-{[2-fluoro-5-(trifluoromethyl)phenyl]amino}pyrimidin-4-yl)amino]phenoxy}propan-2-ol  ligand  56  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3FP
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
 3FP  C1    C  CR6   0   0.591  -1.0299   0.0972  -3.1352
 3FP  N1    N  N     0  -0.478   0.1007   0.0435  -0.6608
 3FP  C2    C  CR16  0  -0.529  -1.8563   0.1214  -2.0179
 3FP  C7    C  CR16  0  -0.301  -0.1260  -0.0144  -8.3056
 3FP  C6    C  CR16  0  -0.392  -1.4780   0.1486  -8.0344
 3FP  C5    C  CR6   0   0.470  -1.9013   0.1939  -6.7305
 3FP  C4    C  CR6   0   0.236  -1.0352   0.0807  -5.6349
 3FP  C3    C  CR6   0   0.560  -1.2336   0.0920  -0.7694
 3FP  C11   C  CR16  0  -0.320  -2.4104  -0.6398   2.5928
 3FP  C10   C  CR6   0   0.328  -1.5775   0.0300   1.6936
 3FP  C9    C  CR16  0  -0.338   0.3181  -0.0799  -5.9246
 3FP  C8    C  CR6   0  -0.178   0.7567  -0.1285  -7.2452
 3FP  C12   C  CR16  0  -0.339  -2.1002  -0.7118   3.9362
 3FP  C16   C  CH2   0  -0.176   0.4487   0.3542   6.3001
 3FP  C14   C  CR16  0  -0.379  -0.0987   0.5463   3.5346
 3FP  C13   C  CR6   0   0.375  -0.9314  -0.1263   4.4231
 3FP  C15   C  CR16  0  -0.276  -0.4239   0.6305   2.1853
 3FP  C     C  CR16  0   0.085   0.7754   0.0254  -1.7914
 3FP  N     N  N     0  -0.499   0.3009   0.0498  -3.0240
 3FP  N2    N  NH1   0  -0.786  -1.6037   0.1265  -4.3747
 3FP  N3    N  NH1   0  -0.771  -1.9892   0.1050   0.3555
 3FP  O     O  O2    0  -0.478  -0.6967  -0.2619   5.7446
 3FP  C21   C  CT    0   1.048   2.2265  -0.2785  -7.4833
 3FP  F2    F  F     0  -0.303   2.5167  -0.5218  -8.7645
 3FP  F3    F  F     0  -0.315   2.9008   0.8288  -7.1353
 3FP  F4    F  F     0  -0.313   2.7516  -1.2817  -6.7660
 3FP  C17   C  CH1   0   0.005   0.4900   0.0325   7.7764
 3FP  C18   C  CH2   0  -0.308   1.7956   0.5497   8.3832
 3FP  C19   C  CH3   0  -0.527   1.9313  -0.8572  10.3379
 3FP  C20   C  CH3   0  -0.515   2.6194   1.4296  10.4709
 3FP  N4    N  NT    0  -0.435   1.7242   0.4864   9.8319
 3FP  O1    O  OH1   0  -0.680  -0.6018   0.6304   8.4297
 3FP  H2    H  HCR6  0   0.286  -2.9345   0.1561  -2.1100
 3FP  H7    H  HCR6  0   0.278   0.2051  -0.0510  -9.3331
 3FP  H6    H  HCR6  0   0.294  -2.1994   0.2406  -8.8351
 3FP  H11   H  HCR6  0   0.269  -3.3181  -1.1119   2.2363
 3FP  H9    H  HCR6  0   0.313   1.0153  -0.1643  -5.1065
 3FP  H12   H  HCR6  0   0.264  -2.7615  -1.2356   4.6151
 3FP  H161  H  HCH2  0   0.224   0.4143   1.4407   6.1531
 3FP  H162  H  HCH2  0   0.226   1.3625  -0.0212   5.8237
 3FP  H14   H  HCR6  0   0.280   0.8122   1.0253   3.8666
 3FP  H15   H  HCR6  0   0.270   0.2367   1.1712   1.5256
 3FP  H     H  HCR6  0   0.255   1.8561  -0.0155  -1.7012
 3FP  HA    H  HNH1  0   0.420  -2.6104   0.1783  -4.3618
 3FP  H3    H  HNH1  0   0.411  -2.9835   0.0297   0.2083
 3FP  H17   H  HCH1  0   0.208   0.4545  -1.0632   7.8813
 3FP  H181  H  HCH2  0   0.241   1.9264   1.5972   8.0955
 3FP  H182  H  HCH2  0   0.219   2.6520  -0.0063   7.9735
 3FP  H191  H  HCH3  0   0.240   1.7820  -0.8740  11.4177
 3FP  H192  H  HCH3  0   0.241   1.2166  -1.5539   9.8997
 3FP  H193  H  HCH3  0   0.204   2.9419  -1.2368  10.1278
 3FP  H201  H  HCH3  0   0.238   2.3965   2.4433  10.1377
 3FP  H202  H  HCH3  0   0.236   2.4810   1.3942  11.5520
 3FP  H203  H  HCH3  0   0.200   3.6801   1.2284  10.2625
 3FP  H1    H  HOH1  0   0.439  -0.2854   0.7888   9.3341
 3FP  F1    F  F     0  -0.310  -3.2107   0.3509  -6.4760

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
 3FP  C1   C2    aromatic  1.390  0.020  1.390
 3FP  C1   N     aromatic  1.336  0.020  1.336
 3FP  C1   N2    single    1.366  0.020  1.366
 3FP  N1   C3    aromatic  1.340  0.020  1.340
 3FP  N1   C     aromatic  1.317  0.020  1.317
 3FP  C2   C3    aromatic  1.395  0.020  1.395
 3FP  C2   H2    single    0.930  0.020  1.080
 3FP  C7   C6    aromatic  1.388  0.020  1.388
 3FP  C7   C8    aromatic  1.384  0.020  1.384
 3FP  C7   H7    single    0.930  0.020  1.080
 3FP  C6   C5    aromatic  1.372  0.020  1.372
 3FP  C6   H6    single    0.930  0.020  1.080
 3FP  C5   C4    aromatic  1.401  0.020  1.401
 3FP  C5   F1    single    1.343  0.020  1.343
 3FP  C4   C9    aromatic  1.393  0.020  1.393
 3FP  C4   N2    single    1.383  0.020  1.383
 3FP  C3   N3    single    1.355  0.020  1.355
 3FP  C11  C10   aromatic  1.397  0.020  1.397
 3FP  C11  C12   aromatic  1.381  0.020  1.381
 3FP  C11  H11   single    0.930  0.020  1.080
 3FP  C10  C15   aromatic  1.390  0.020  1.390
 3FP  C10  N3    single    1.402  0.020  1.402
 3FP  C9   C8    aromatic  1.392  0.020  1.392
 3FP  C9   H9    single    0.930  0.020  1.080
 3FP  C8   C21   single    1.497  0.020  1.497
 3FP  C12  C13   aromatic  1.395  0.020  1.395
 3FP  C12  H12   single    0.930  0.020  1.080
 3FP  C16  O     single    1.414  0.020  1.414
 3FP  C16  C17   single    1.512  0.020  1.512
 3FP  C16  H161  single    0.970  0.020  1.090
 3FP  C16  H162  single    0.970  0.020  1.090
 3FP  C14  C13   aromatic  1.391  0.020  1.391
 3FP  C14  C15   aromatic  1.390  0.020  1.390
 3FP  C14  H14   single    0.930  0.020  1.080
 3FP  C13  O     single    1.349  0.020  1.349
 3FP  C15  H15   single    0.930  0.020  1.080
 3FP  C    N     aromatic  1.321  0.020  1.321
 3FP  C    H     single    0.930  0.020  1.080
 3FP  N2   HA    single    0.860  0.020  1.020
 3FP  N3   H3    single    0.860  0.020  1.020
 3FP  C21  F2    single    1.336  0.020  1.336
 3FP  C21  F3    single    1.342  0.020  1.342
 3FP  C21  F4    single    1.340  0.020  1.340
 3FP  C17  C18   single    1.530  0.020  1.530
 3FP  C17  O1    single    1.406  0.020  1.406
 3FP  C17  H17   single    0.970  0.020  1.090
 3FP  C18  N4    single    1.452  0.020  1.452
 3FP  C18  H181  single    0.970  0.020  1.090
 3FP  C18  H182  single    0.970  0.020  1.090
 3FP  C19  N4    single    1.451  0.020  1.451
 3FP  C19  H191  single    0.970  0.020  1.090
 3FP  C19  H192  single    0.970  0.020  1.090
 3FP  C19  H193  single    0.970  0.020  1.090
 3FP  C20  N4    single    1.449  0.020  1.449
 3FP  C20  H201  single    0.970  0.020  1.090
 3FP  C20  H202  single    0.970  0.020  1.090
 3FP  C20  H203  single    0.970  0.020  1.090
 3FP  O1   H1    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
 3FP  N2    C1   N     119.64  3.000
 3FP  N2    C1   C2    118.64  3.000
 3FP  N     C1   C2    121.72  3.000
 3FP  C     N1   C3    116.18  3.000
 3FP  H2    C2   C3    121.41  3.000
 3FP  H2    C2   C1    121.62  3.000
 3FP  C3    C2   C1    116.97  3.000
 3FP  H7    C7   C8    122.03  3.000
 3FP  H7    C7   C6    119.23  3.000
 3FP  C8    C7   C6    118.75  3.000
 3FP  H6    C6   C5    119.67  3.000
 3FP  H6    C6   C7    120.99  3.000
 3FP  C5    C6   C7    119.34  3.000
 3FP  F1    C5   C4    117.64  3.000
 3FP  F1    C5   C6    119.00  3.000
 3FP  C4    C5   C6    123.36  3.000
 3FP  N2    C4   C9    126.33  3.000
 3FP  N2    C4   C5    117.11  3.000
 3FP  C9    C4   C5    116.56  3.000
 3FP  N3    C3   C2    119.58  3.000
 3FP  N3    C3   N1    119.23  3.000
 3FP  C2    C3   N1    121.18  3.000
 3FP  H11   C11  C12   119.06  3.000
 3FP  H11   C11  C10   119.78  3.000
 3FP  C12   C11  C10   121.16  3.000
 3FP  N3    C10  C15   123.92  3.000
 3FP  N3    C10  C11   117.72  3.000
 3FP  C15   C10  C11   118.31  3.000
 3FP  H9    C9   C8    120.88  3.000
 3FP  H9    C9   C4    118.64  3.000
 3FP  C8    C9   C4    120.48  3.000
 3FP  C21   C8   C9    117.63  3.000
 3FP  C21   C8   C7    120.84  3.000
 3FP  C9    C8   C7    121.52  3.000
 3FP  H12   C12  C13   119.73  3.000
 3FP  H12   C12  C11   119.87  3.000
 3FP  C13   C12  C11   120.40  3.000
 3FP  H162  C16  H161  107.88  3.000
 3FP  H162  C16  C17   109.18  3.000
 3FP  H161  C16  C17   110.03  3.000
 3FP  H162  C16  O     110.80  3.000
 3FP  H161  C16  O     110.71  3.000
 3FP  C17   C16  O     108.24  3.000
 3FP  H14   C14  C15   117.92  3.000
 3FP  H14   C14  C13   121.48  3.000
 3FP  C15   C14  C13   120.60  3.000
 3FP  O     C13  C14   124.76  3.000
 3FP  O     C13  C12   116.46  3.000
 3FP  C14   C13  C12   118.78  3.000
 3FP  H15   C15  C14   118.72  3.000
 3FP  H15   C15  C10   120.55  3.000
 3FP  C14   C15  C10   120.74  3.000
 3FP  H     C    N     115.85  3.000
 3FP  H     C    N1    116.06  3.000
 3FP  N     C    N1    128.09  3.000
 3FP  C     N    C1    115.85  3.000
 3FP  HA    N2   C4    115.07  3.000
 3FP  HA    N2   C1    114.13  3.000
 3FP  C4    N2   C1    130.79  3.000
 3FP  H3    N3   C10   115.15  3.000
 3FP  H3    N3   C3    115.34  3.000
 3FP  C10   N3   C3    128.91  3.000
 3FP  C13   O    C16   118.81  3.000
 3FP  F4    C21  F3    106.37  3.000
 3FP  F4    C21  F2    106.97  3.000
 3FP  F3    C21  F2    106.85  3.000
 3FP  F4    C21  C8    112.00  3.000
 3FP  F3    C21  C8    111.68  3.000
 3FP  F2    C21  C8    112.59  3.000
 3FP  H17   C17  O1    110.73  3.000
 3FP  H17   C17  C18   109.03  3.000
 3FP  O1    C17  C18   109.55  3.000
 3FP  H17   C17  C16   107.69  3.000
 3FP  O1    C17  C16   110.01  3.000
 3FP  C18   C17  C16   109.80  3.000
 3FP  H182  C18  H181  107.03  3.000
 3FP  H182  C18  N4    112.82  3.000
 3FP  H181  C18  N4    108.06  3.000
 3FP  H182  C18  C17   110.23  3.000
 3FP  H181  C18  C17   108.75  3.000
 3FP  N4    C18  C17   109.82  3.000
 3FP  H193  C19  H192  107.76  3.000
 3FP  H193  C19  H191  108.04  3.000
 3FP  H192  C19  H191  107.36  3.000
 3FP  H193  C19  N4    112.60  3.000
 3FP  H192  C19  N4    110.99  3.000
 3FP  H191  C19  N4    109.90  3.000
 3FP  H203  C20  H202  107.72  3.000
 3FP  H203  C20  H201  108.03  3.000
 3FP  H202  C20  H201  107.89  3.000
 3FP  H203  C20  N4    113.16  3.000
 3FP  H202  C20  N4    109.74  3.000
 3FP  H201  C20  N4    110.14  3.000
 3FP  C20   N4   C19   111.15  3.000
 3FP  C20   N4   C18   112.42  3.000
 3FP  C19   N4   C18   112.42  3.000
 3FP  H1    O1   C17   104.42  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
 3FP  CONST_01  N1    C3   C2   C1      0.00   0.0  0
 3FP  CONST_02  N1    C    N    C1      0.00   0.0  0
 3FP  CONST_03  C     N    C1   C2      0.00   0.0  0
 3FP  CONST_04  C     N1   C3   C2      0.00   0.0  0
 3FP  CONST_05  C4    C5   C6   C7      0.00   0.0  0
 3FP  CONST_06  C4    C9   C8   C7      0.00   0.0  0
 3FP  CONST_07  C9    C8   C7   C6      0.00   0.0  0
 3FP  CONST_08  C9    C4   C5   C6      0.00   0.0  0
 3FP  CONST_09  C8    C7   C6   C5      0.00   0.0  0
 3FP  CONST_10  C8    C9   C4   C5      0.00   0.0  0
 3FP  CONST_11  N     C    N1   C3      0.00   0.0  0
 3FP  CONST_12  N     C1   C2   C3      0.00   0.0  0
 3FP  CONST_13  C14   C15  C10  C11     0.00   0.0  0
 3FP  CONST_14  C14   C13  C12  C11     0.00   0.0  0
 3FP  CONST_15  C13   C12  C11  C10     0.00   0.0  0
 3FP  CONST_16  C13   C14  C15  C10     0.00   0.0  0
 3FP  CONST_17  C15   C10  C11  C12     0.00   0.0  0
 3FP  CONST_18  C15   C14  C13  C12     0.00   0.0  0
 3FP  CONST_19  N3    C3   C2   C1    180.00   0.0  0
 3FP  CONST_20  F1    C5   C6   C7    180.00   0.0  0
 3FP  CONST_21  C21   C8   C7   C6    180.00   0.0  0
 3FP  CONST_22  N2    C4   C5   C6    180.00   0.0  0
 3FP  CONST_23  C21   C8   C9   C4    180.00   0.0  0
 3FP  CONST_24  N2    C1   C2   C3    180.00   0.0  0
 3FP  CONST_25  O     C13  C12  C11   180.00   0.0  0
 3FP  CONST_26  F1    C5   C4   C9    180.00   0.0  0
 3FP  CONST_27  N2    C4   C9   C8    180.00   0.0  0
 3FP  CONST_28  N3    C10  C11  C12   180.00   0.0  0
 3FP  CONST_29  N3    C10  C15  C14   180.00   0.0  0
 3FP  CONST_30  O     C13  C14  C15   180.00   0.0  0
 3FP  CONST_31  N3    C3   N1   C     180.00   0.0  0
 3FP  CONST_32  N2    C1   N    C     180.00   0.0  0
 3FP  CONST_33  H     C    N    C1    180.00   0.0  0
 3FP  CONST_34  H2    C2   C3   N1    180.00   0.0  0
 3FP  CONST_35  H9    C9   C8   C7    180.00   0.0  0
 3FP  CONST_36  H7    C7   C6   C5    180.00   0.0  0
 3FP  CONST_37  H6    C6   C5   C4    180.00   0.0  0
 3FP  CONST_38  H15   C15  C10  C11   180.00   0.0  0
 3FP  CONST_39  H12   C12  C11  C10   180.00   0.0  0
 3FP  CONST_40  H14   C14  C15  C10   180.00   0.0  0
 3FP  CONST_41  H11   C11  C12  C13   180.00   0.0  0
 3FP  Var_01    C5    C4   N2   C1   -177.08  30.0  2
 3FP  Var_02    C10   N3   C3   N1     -2.32  30.0  2
 3FP  Var_03    C4    N2   C1   C2   -178.24  30.0  2
 3FP  Var_04    C11   C10  N3   C3   -145.86  30.0  2
 3FP  Var_05    F2    C21  C8   C7    -11.08  30.0  2
 3FP  Var_06    C14   C13  O    C16     2.30  30.0  3
 3FP  Var_07    C17   C16  O    C13  -179.07  30.0  1
 3FP  Var_08    C19   N4   C18  C17    77.90  30.0  3
 3FP  Var_09    H191  C19  N4   C18  -175.00  30.0  3
 3FP  Var_10    H201  C20  N4   C18    57.47  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
 3FP  chir_01  C17  C16  C18  O1  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
 3FP  plan-1  C1   0.020
 3FP  plan-1  N1   0.020
 3FP  plan-1  C2   0.020
 3FP  plan-1  C3   0.020
 3FP  plan-1  C    0.020
 3FP  plan-1  N    0.020
 3FP  plan-1  N2   0.020
 3FP  plan-1  N3   0.020
 3FP  plan-1  H2   0.020
 3FP  plan-1  H    0.020
 3FP  plan-2  C7   0.020
 3FP  plan-2  C6   0.020
 3FP  plan-2  C5   0.020
 3FP  plan-2  C4   0.020
 3FP  plan-2  C9   0.020
 3FP  plan-2  C8   0.020
 3FP  plan-2  N2   0.020
 3FP  plan-2  C21  0.020
 3FP  plan-2  H7   0.020
 3FP  plan-2  H6   0.020
 3FP  plan-2  H9   0.020
 3FP  plan-2  F1   0.020
 3FP  plan-3  C11  0.020
 3FP  plan-3  C10  0.020
 3FP  plan-3  C12  0.020
 3FP  plan-3  C14  0.020
 3FP  plan-3  C13  0.020
 3FP  plan-3  C15  0.020
 3FP  plan-3  N3   0.020
 3FP  plan-3  O    0.020
 3FP  plan-3  H11  0.020
 3FP  plan-3  H12  0.020
 3FP  plan-3  H14  0.020
 3FP  plan-3  H15  0.020

