# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 01:54:19 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c(F)cc1Nc2ncc(c(NC3CC3)n2)C(F)(F)F)C(=O)N4CCOCC4
#
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
 4K5  4K5  (4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone  ligand  53  32  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4K5
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
 4K5  C4   C  CR6   0   0.585   4.1957  -0.1338  -0.0403
 4K5  C5   C  CR6   0  -0.447   4.2194   1.2604  -0.3375
 4K5  C6   C  CR16  0   0.006   2.9998   1.8977  -0.3292
 4K5  N1   N  N     0  -0.500   1.8458   1.2930  -0.0768
 4K5  N3   N  N     0  -0.508   3.0416  -0.7349   0.2100
 4K5  CAL  C  CH2   0  -0.517   6.2943  -3.1524  -0.3275
 4K5  CAM  C  CH2   0  -0.475   4.8503  -3.2673  -0.7097
 4K5  CBD  C  CH1   0  -0.085   5.2743  -2.2805   0.3281
 4K5  NAS  N  NH1   0  -0.677   5.3016  -0.8921  -0.0024
 4K5  CBF  C  CT    0   1.074   5.4687   1.9910  -0.6629
 4K5  FAE  F  F     0  -0.322   6.3736   1.9296   0.3335
 4K5  FAF  F  F     0  -0.318   6.0856   1.4869  -1.7468
 4K5  FAD  F  F     0  -0.299   5.2532   3.2851  -0.9067
 4K5  C2   C  CR6   0   0.626   1.9285  -0.0086   0.1742
 4K5  NAR  N  NH1   0  -0.760   0.8008  -0.7240   0.4337
 4K5  CAY  C  CR6   0   0.298  -0.5271  -0.3422   0.5080
 4K5  CAZ  C  CR6   0   0.329  -1.4498  -1.3626   0.8453
 4K5  CAI  C  CR16  0  -0.360  -2.7969  -1.0765   0.9398
 4K5  OAT  O  O2    0  -0.484  -0.9091  -2.5788   1.0554
 4K5  CAA  C  CH3   0  -0.435  -1.7643  -3.6602   1.3713
 4K5  CAH  C  CR16  0  -0.492  -1.0072   0.9398   0.2738
 4K5  CAW  C  CR6   0   0.568  -2.3624   1.1894   0.3898
 4K5  FAC  F  F     0  -0.309  -2.7926   2.4380   0.1439
 4K5  CBA  C  CR6   0  -0.309  -3.2787   0.2158   0.7116
 4K5  CAV  C  C     0   0.527  -4.7199   0.5482   0.9334
 4K5  OAB  O  O     0  -0.482  -5.0310   1.3464   1.8063
 4K5  NBE  N  NT    0  -0.455  -5.6193  -0.1067   0.1735
 4K5  CAN  C  CH2   0  -0.331  -7.0472   0.0502   0.3997
 4K5  CAJ  C  CH2   0  -0.184  -7.7064   0.6382  -0.8356
 4K5  OAU  O  O2    0  -0.481  -7.4350  -0.1377  -1.9820
 4K5  CAK  C  CH2   0  -0.174  -6.0491  -0.2398  -2.2142
 4K5  CAO  C  CH2   0  -0.330  -5.3202  -0.8613  -1.0325
 4K5  H1   H  HCR6  0   0.283   2.9315   2.9587  -0.5380
 4K5  H3   H  HCH2  0   0.259   6.9687  -2.6917  -1.0391
 4K5  H4   H  HCH2  0   0.256   4.5520  -2.8790  -1.6746
 4K5  H5   H  HCH2  0   0.256   4.2917  -4.1324  -0.3777
 4K5  H6   H  HCH1  0   0.270   5.0130  -2.5038   1.3576
 4K5  H7   H  HNH1  0   0.403   6.2079  -0.4587  -0.0422
 4K5  H8   H  HNH1  0   0.415   0.9804  -1.7010   0.6125
 4K5  H9   H  HCR6  0   0.299  -3.5049  -1.8531   1.1987
 4K5  H10  H  HCH3  0   0.267  -1.1281  -4.5341   1.4810
 4K5  H11  H  HCH3  0   0.235  -2.2996  -3.4911   2.3087
 4K5  H12  H  HCH3  0   0.232  -2.4887  -3.8477   0.5749
 4K5  H13  H  HCR6  0   0.311  -0.3319   1.7368   0.0062
 4K5  H14  H  HCH2  0   0.255  -7.4748  -0.9330   0.6202
 4K5  H15  H  HCH2  0   0.271  -7.2201   0.6937   1.2586
 4K5  H16  H  HCH2  0   0.246  -8.7889   0.6593  -0.7030
 4K5  H17  H  HCH2  0   0.212  -7.3606   1.6718  -0.9770
 4K5  H18  H  HCH2  0   0.248  -5.9084  -0.8625  -3.0987
 4K5  H19  H  HCH2  0   0.209  -5.6171   0.7498  -2.4205
 4K5  H20  H  HCH2  0   0.280  -4.2525  -0.8607  -1.2375
 4K5  H21  H  HCH2  0   0.253  -5.6335  -1.9009  -0.8970
 4K5  H2   H  HCH2  0   0.262   6.7404  -3.9362   0.2699

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
 4K5  FAF  CBF  single    1.345  0.020  1.345
 4K5  FAE  CBF  single    1.347  0.020  1.347
 4K5  CBF  FAD  single    1.334  0.020  1.334
 4K5  CBF  C5   single    1.483  0.020  1.483
 4K5  C5   C6   aromatic  1.376  0.020  1.376
 4K5  C5   C4   aromatic  1.426  0.020  1.426
 4K5  C6   N1   aromatic  1.327  0.020  1.327
 4K5  NAS  C4   single    1.341  0.020  1.341
 4K5  NAS  CBD  single    1.427  0.020  1.427
 4K5  C4   N3   aromatic  1.325  0.020  1.325
 4K5  N1   C2   aromatic  1.328  0.020  1.328
 4K5  CAM  CAL  single    1.498  0.020  1.498
 4K5  CAM  CBD  single    1.494  0.020  1.494
 4K5  CAL  CBD  single    1.494  0.020  1.494
 4K5  N3   C2   aromatic  1.330  0.020  1.330
 4K5  C2   NAR  single    1.360  0.020  1.360
 4K5  NAR  CAY  single    1.384  0.020  1.384
 4K5  OAT  CAA  single    1.414  0.020  1.414
 4K5  OAT  CAZ  single    1.348  0.020  1.348
 4K5  CAY  CAZ  aromatic  1.416  0.020  1.416
 4K5  CAY  CAH  aromatic  1.389  0.020  1.389
 4K5  CAZ  CAI  aromatic  1.380  0.020  1.380
 4K5  CAH  CAW  aromatic  1.383  0.020  1.383
 4K5  CAO  CAK  single    1.521  0.020  1.521
 4K5  CAO  NBE  single    1.454  0.020  1.454
 4K5  CAK  OAU  single    1.409  0.020  1.409
 4K5  CAI  CBA  aromatic  1.398  0.020  1.398
 4K5  CAW  CBA  aromatic  1.375  0.020  1.375
 4K5  CAW  FAC  single    1.343  0.020  1.343
 4K5  CBA  CAV  single    1.496  0.020  1.496
 4K5  OAU  CAJ  single    1.411  0.020  1.411
 4K5  NBE  CAV  single    1.347  0.020  1.347
 4K5  NBE  CAN  single    1.454  0.020  1.454
 4K5  CAV  OAB  double    1.223  0.020  1.223
 4K5  CAJ  CAN  single    1.519  0.020  1.519
 4K5  C6   H1   single    0.930  0.020  1.080
 4K5  CAL  H2   single    0.970  0.020  1.090
 4K5  CAL  H3   single    0.970  0.020  1.090
 4K5  CAM  H4   single    0.970  0.020  1.090
 4K5  CAM  H5   single    0.970  0.020  1.090
 4K5  CBD  H6   single    0.970  0.020  1.090
 4K5  NAS  H7   single    0.860  0.020  1.020
 4K5  NAR  H8   single    0.860  0.020  1.020
 4K5  CAI  H9   single    0.930  0.020  1.080
 4K5  CAA  H10  single    0.970  0.020  1.090
 4K5  CAA  H11  single    0.970  0.020  1.090
 4K5  CAA  H12  single    0.970  0.020  1.090
 4K5  CAH  H13  single    0.930  0.020  1.080
 4K5  CAN  H14  single    0.970  0.020  1.090
 4K5  CAN  H15  single    0.970  0.020  1.090
 4K5  CAJ  H16  single    0.970  0.020  1.090
 4K5  CAJ  H17  single    0.970  0.020  1.090
 4K5  CAK  H18  single    0.970  0.020  1.090
 4K5  CAK  H19  single    0.970  0.020  1.090
 4K5  CAO  H20  single    0.970  0.020  1.090
 4K5  CAO  H21  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
 4K5  NAS  C4   N3   117.15  3.000
 4K5  N3   C4   C5   119.83  3.000
 4K5  NAS  C4   C5   123.02  3.000
 4K5  CBF  C5   C6   121.31  3.000
 4K5  C6   C5   C4   115.90  3.000
 4K5  CBF  C5   C4   122.78  3.000
 4K5  H1   C6   N1   115.35  3.000
 4K5  H1   C6   C5   120.54  3.000
 4K5  N1   C6   C5   124.11  3.000
 4K5  C2   N1   C6   115.37  3.000
 4K5  C2   N3   C4   118.44  3.000
 4K5  H3   CAL  H2   114.47  3.000
 4K5  H3   CAL  CBD  117.73  3.000
 4K5  H2   CAL  CBD  117.53  3.000
 4K5  H3   CAL  CAM  117.71  3.000
 4K5  H2   CAL  CAM  118.87  3.000
 4K5  CBD  CAL  CAM   59.90  3.000
 4K5  H5   CAM  H4   114.72  3.000
 4K5  H5   CAM  CBD  117.49  3.000
 4K5  H4   CAM  CBD  117.44  3.000
 4K5  H5   CAM  CAL  118.73  3.000
 4K5  H4   CAM  CAL  117.76  3.000
 4K5  CBD  CAM  CAL   59.90  3.000
 4K5  H6   CBD  NAS  115.11  3.000
 4K5  H6   CBD  CAM  117.06  3.000
 4K5  NAS  CBD  CAM  119.15  3.000
 4K5  H6   CBD  CAL  117.43  3.000
 4K5  CAM  CBD  CAL   60.21  3.000
 4K5  NAS  CBD  CAL  116.94  3.000
 4K5  H7   NAS  CBD  116.47  3.000
 4K5  H7   NAS  C4   119.89  3.000
 4K5  CBD  NAS  C4   122.72  3.000
 4K5  FAD  CBF  FAF  106.88  3.000
 4K5  FAD  CBF  FAE  106.73  3.000
 4K5  FAF  CBF  FAE  105.71  3.000
 4K5  FAD  CBF  C5   112.44  3.000
 4K5  FAE  CBF  C5   112.39  3.000
 4K5  FAF  CBF  C5   112.23  3.000
 4K5  NAR  C2   N3   113.67  3.000
 4K5  NAR  C2   N1   119.99  3.000
 4K5  N3   C2   N1   126.34  3.000
 4K5  H8   NAR  CAY  115.36  3.000
 4K5  H8   NAR  C2   113.28  3.000
 4K5  CAY  NAR  C2   131.35  3.000
 4K5  CAH  CAY  CAZ  118.69  3.000
 4K5  CAH  CAY  NAR  125.27  3.000
 4K5  CAZ  CAY  NAR  116.05  3.000
 4K5  OAT  CAZ  CAI  124.61  3.000
 4K5  CAI  CAZ  CAY  120.18  3.000
 4K5  OAT  CAZ  CAY  115.21  3.000
 4K5  H9   CAI  CBA  118.48  3.000
 4K5  H9   CAI  CAZ  120.40  3.000
 4K5  CBA  CAI  CAZ  121.12  3.000
 4K5  CAA  OAT  CAZ  118.83  3.000
 4K5  H12  CAA  H11  109.09  3.000
 4K5  H12  CAA  H10  108.89  3.000
 4K5  H11  CAA  H10  108.94  3.000
 4K5  H12  CAA  OAT  111.67  3.000
 4K5  H11  CAA  OAT  111.69  3.000
 4K5  H10  CAA  OAT  106.46  3.000
 4K5  H13  CAH  CAW  120.08  3.000
 4K5  H13  CAH  CAY  120.51  3.000
 4K5  CAW  CAH  CAY  119.42  3.000
 4K5  CBA  CAW  FAC  119.17  3.000
 4K5  FAC  CAW  CAH  117.79  3.000
 4K5  CBA  CAW  CAH  123.02  3.000
 4K5  CAV  CBA  CAW  121.30  3.000
 4K5  CAV  CBA  CAI  120.89  3.000
 4K5  CAW  CBA  CAI  117.58  3.000
 4K5  NBE  CAV  OAB  123.36  3.000
 4K5  OAB  CAV  CBA  119.74  3.000
 4K5  NBE  CAV  CBA  116.85  3.000
 4K5  CAO  NBE  CAN  112.77  3.000
 4K5  CAN  NBE  CAV  121.02  3.000
 4K5  CAO  NBE  CAV  125.65  3.000
 4K5  H15  CAN  H14  108.09  3.000
 4K5  H15  CAN  CAJ  110.15  3.000
 4K5  H14  CAN  CAJ  110.01  3.000
 4K5  H15  CAN  NBE  110.05  3.000
 4K5  H14  CAN  NBE  108.54  3.000
 4K5  CAJ  CAN  NBE  109.97  3.000
 4K5  H17  CAJ  H16  108.05  3.000
 4K5  H17  CAJ  OAU  110.62  3.000
 4K5  H16  CAJ  OAU  107.48  3.000
 4K5  H17  CAJ  CAN  109.41  3.000
 4K5  H16  CAJ  CAN  109.84  3.000
 4K5  OAU  CAJ  CAN  111.38  3.000
 4K5  CAK  OAU  CAJ  111.29  3.000
 4K5  H19  CAK  H18  108.12  3.000
 4K5  H19  CAK  CAO  108.99  3.000
 4K5  H18  CAK  CAO  109.57  3.000
 4K5  H19  CAK  OAU  110.62  3.000
 4K5  H18  CAK  OAU  107.57  3.000
 4K5  CAO  CAK  OAU  111.90  3.000
 4K5  H21  CAO  H20  107.76  3.000
 4K5  H21  CAO  CAK  110.32  3.000
 4K5  H20  CAO  CAK  108.90  3.000
 4K5  H21  CAO  NBE  109.36  3.000
 4K5  H20  CAO  NBE  110.98  3.000
 4K5  CAK  CAO  NBE  109.50  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
 4K5  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 4K5  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 4K5  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 4K5  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 4K5  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 4K5  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 4K5  CONST_07  CBA  CAI  CAZ  CAY     0.00   0.0  0
 4K5  CONST_08  CBA  CAW  CAH  CAY     0.00   0.0  0
 4K5  CONST_09  CAW  CAH  CAY  CAZ     0.00   0.0  0
 4K5  CONST_10  CAW  CBA  CAI  CAZ     0.00   0.0  0
 4K5  CONST_11  CAH  CAY  CAZ  CAI     0.00   0.0  0
 4K5  CONST_12  CAH  CAW  CBA  CAI     0.00   0.0  0
 4K5  CONST_13  NAR  C2   N3   C4    180.00   0.0  0
 4K5  CONST_14  NAS  C4   C5   C6    180.00   0.0  0
 4K5  CONST_15  NAR  C2   N1   C6    180.00   0.0  0
 4K5  CONST_16  CBF  C5   C6   N1    180.00   0.0  0
 4K5  CONST_17  CBF  C5   C4   N3    180.00   0.0  0
 4K5  CONST_18  C2   N3   C4   NAS   180.00   0.0  0
 4K5  CONST_19  CAI  CAZ  CAY  NAR   180.00   0.0  0
 4K5  CONST_20  CAW  CAH  CAY  NAR   180.00   0.0  0
 4K5  CONST_21  FAC  CAW  CAH  CAY   180.00   0.0  0
 4K5  CONST_22  CAV  CBA  CAI  CAZ   180.00   0.0  0
 4K5  CONST_23  FAC  CAW  CBA  CAI   180.00   0.0  0
 4K5  CONST_24  CAH  CAY  CAZ  OAT   180.00   0.0  0
 4K5  CONST_25  CBA  CAI  CAZ  OAT   180.00   0.0  0
 4K5  CONST_26  CAV  CBA  CAW  CAH   180.00   0.0  0
 4K5  CONST_28  CAN  NBE  CAV  CBA   180.00   0.0  0
 4K5  CONST_29  CBD  NAS  C4   C5    180.00   0.0  0
 4K5  CONST_30  CBD  NAS  C4   N3      0.00   0.0  0
 4K5  CONST_31  H1   C6   C5   C4    180.00   0.0  0
 4K5  CONST_32  H9   CAI  CAZ  CAY   180.00   0.0  0
 4K5  CONST_33  H13  CAH  CAY  CAZ   180.00   0.0  0
 4K5  CONST_34  CAO  NBE  CAV  OAB   180.00   0.0  0
 4K5  CONST_35  CAN  NBE  CAV  OAB     0.00   0.0  0
 4K5  CONST_36  H7   NAS  C4   C5      0.00   0.0  0
 4K5  Var_01    OAU  CAK  CAO  NBE   -55.04  30.0  1
 4K5  Var_02    OAU  CAJ  CAN  NBE    55.23  30.0  1
 4K5  Var_03    CAK  CAO  NBE  CAN    53.01  30.0  1
 4K5  Var_04    CAO  CAK  OAU  CAJ    58.65  30.0  1
 4K5  Var_05    CAO  NBE  CAN  CAJ   -53.40  30.0  1
 4K5  Var_06    CAM  CBD  NAS  C4     78.74  30.0  3
 4K5  Var_07    CAY  NAR  C2   N1     -0.70  30.0  2
 4K5  Var_08    NAS  CBD  CAM  CAL   106.17  30.0  1
 4K5  Var_09    CAZ  CAY  NAR  C2   -178.11  30.0  2
 4K5  Var_10    NBE  CAV  CBA  CAI   -62.04  30.0  2
 4K5  Var_11    FAF  CBF  C5   C4     59.44  30.0  3
 4K5  Var_12    H10  CAA  OAT  CAZ   179.07  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
 4K5  chir_01  CBD  NAS  CAM  CAL  both

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
 4K5  plan-1  C4   0.020
 4K5  plan-1  C5   0.020
 4K5  plan-1  C6   0.020
 4K5  plan-1  N1   0.020
 4K5  plan-1  N3   0.020
 4K5  plan-1  NAS  0.020
 4K5  plan-1  CBF  0.020
 4K5  plan-1  C2   0.020
 4K5  plan-1  NAR  0.020
 4K5  plan-1  H1   0.020
 4K5  plan-2  NAR  0.020
 4K5  plan-2  CAY  0.020
 4K5  plan-2  CAZ  0.020
 4K5  plan-2  CAI  0.020
 4K5  plan-2  OAT  0.020
 4K5  plan-2  CAH  0.020
 4K5  plan-2  CAW  0.020
 4K5  plan-2  FAC  0.020
 4K5  plan-2  CBA  0.020
 4K5  plan-2  CAV  0.020
 4K5  plan-2  H9   0.020
 4K5  plan-2  H13  0.020
 4K5  plan-3  C4   0.020
 4K5  plan-3  CBD  0.020
 4K5  plan-3  NAS  0.020
 4K5  plan-3  H7   0.020
 4K5  plan-4  CBA  0.020
 4K5  plan-4  CAV  0.020
 4K5  plan-4  OAB  0.020
 4K5  plan-4  NBE  0.020
 4K5  plan-4  CAN  0.020
 4K5  plan-4  CAO  0.020

