# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:58:56 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-[4-(4-aminothieno[2,3-d]pyrimidin-5-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2scc(c3ccc(NC(=O)Nc4cc(ccc4F)C(F)(F)F)cc3)c12
#
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
 T6E  T6E  1-[4-(4-aminothieno[2,3-d]pyrimidin-5-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea  ligand  44  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T6E
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
 T6E  C4    C  CR6   0   0.442   5.6310  -0.9250  -1.4846
 T6E  C5    C  CR56  0  -0.028   5.6271  -0.1741  -0.2774
 T6E  C6    C  CR56  0  -0.007   6.8762   0.3156   0.1027
 T6E  N1    N  N     0  -0.438   8.0300   0.0869  -0.5219
 T6E  N3    N  N     0  -0.460   6.7879  -1.1721  -2.1025
 T6E  NBF   N  NH2   0  -0.820   4.5233  -1.4063  -2.0547
 T6E  C2    C  CR16  0   0.043   7.9053  -0.6714  -1.5924
 T6E  CBB   C  CR5   0   0.229   4.5755   0.2454   0.6134
 T6E  CAZ   C  CR6   0  -0.020   3.1567  -0.1458   0.5401
 T6E  CAO   C  CR16  0  -0.304   2.7766  -1.4879   0.5932
 T6E  CAM   C  CR16  0  -0.330   1.4442  -1.8497   0.5591
 T6E  CAN   C  CR16  0  -0.275   2.1499   0.8113   0.4662
 T6E  CAL   C  CR16  0  -0.302   0.8073   0.4633   0.4371
 T6E  CAX   C  CR6   0   0.373   0.4375  -0.8818   0.4780
 T6E  NAT   N  NH1   0  -0.789  -0.8746  -1.3500   0.4581
 T6E  CAV   C  C     0   0.738  -2.0251  -0.6416   0.2607
 T6E  OAD   O  O     0  -0.487  -2.0737   0.5618   0.0907
 T6E  NAU   N  NH1   0  -0.784  -3.1444  -1.4379   0.2830
 T6E  CAY   C  CR6   0   0.215  -4.4298  -0.9621   0.0255
 T6E  CAP   C  CR16  0  -0.298  -4.9363   0.1983   0.5973
 T6E  CAJ   C  CR6   0   0.510  -5.2700  -1.6871  -0.8165
 T6E  CAH   C  CR16  0  -0.402  -6.5597  -1.2947  -1.0950
 T6E  CAK   C  CR16  0  -0.281  -7.0440  -0.1223  -0.5363
 T6E  CBA   C  CR6   0  -0.204  -6.2293   0.6185   0.3080
 T6E  CBG   C  CT    0   1.053  -6.7093   1.9023   0.9071
 T6E  FAF   F  F     0  -0.314  -6.1330   2.9642   0.3228
 T6E  FAG   F  F     0  -0.302  -8.0298   2.0620   0.7858
 T6E  FAE   F  F     0  -0.311  -6.4204   1.9867   2.2128
 T6E  F1    F  F     0  -0.300  -4.7953  -2.8108  -1.3654
 T6E  S     S  S2    0   0.226   6.7615   1.3089   1.5132
 T6E  C8    C  CR15  0  -0.550   5.0568   1.0468   1.5971
 T6E  HBF1  H  HNH2  0   0.419   3.6044  -1.1771  -1.7216
 T6E  HBF2  H  HNH2  0   0.405   4.5960  -1.8704  -2.9446
 T6E  H2    H  HCR6  0   0.258   8.8183  -0.9058  -2.1290
 T6E  H8    H  HCR5  0   0.301   4.4909   1.4829   2.4065
 T6E  HAO   H  HCR6  0   0.270   3.5286  -2.2633   0.6723
 T6E  HAN   H  HCR6  0   0.257   2.4139   1.8604   0.4206
 T6E  HAM   H  HCR6  0   0.275   1.1813  -2.8999   0.6031
 T6E  HAL   H  HCR6  0   0.285   0.0667   1.2427   0.3811
 T6E  HAT   H  HNH1  0   0.417  -0.9615  -2.3496   0.5595
 T6E  HAU   H  HNH1  0   0.416  -3.0256  -2.4398   0.2852
 T6E  HAP   H  HCR6  0   0.291  -4.3153   0.7604   1.2794
 T6E  HAH   H  HCR6  0   0.296  -7.1750  -1.8898  -1.7559
 T6E  HAK   H  HCR6  0   0.283  -8.0521   0.1894  -0.7682

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
 T6E  C4   C5    aromatic  1.422  0.020  1.422
 T6E  C4   N3    aromatic  1.335  0.020  1.335
 T6E  C4   NBF   single    1.336  0.020  1.336
 T6E  C5   C6    aromatic  1.394  0.020  1.394
 T6E  C5   CBB   aromatic  1.441  0.020  1.441
 T6E  C6   N1    aromatic  1.332  0.020  1.332
 T6E  C6   S     aromatic  1.729  0.020  1.729
 T6E  N1   C2    aromatic  1.318  0.020  1.318
 T6E  N3   C2    aromatic  1.326  0.020  1.326
 T6E  CBB  CAZ   single    1.474  0.020  1.474
 T6E  CBB  C8    aromatic  1.357  0.020  1.357
 T6E  CAZ  CAO   aromatic  1.396  0.020  1.396
 T6E  CAZ  CAN   aromatic  1.391  0.020  1.391
 T6E  CAO  CAM   aromatic  1.381  0.020  1.381
 T6E  CAM  CAX   aromatic  1.399  0.020  1.399
 T6E  CAN  CAL   aromatic  1.387  0.020  1.387
 T6E  CAL  CAX   aromatic  1.396  0.020  1.396
 T6E  CAX  NAT   single    1.393  0.020  1.393
 T6E  NAT  CAV   single    1.365  0.020  1.365
 T6E  CAV  OAD   double    1.216  0.020  1.216
 T6E  CAV  NAU   single    1.374  0.020  1.374
 T6E  NAU  CAY   single    1.395  0.020  1.395
 T6E  CAY  CAP   aromatic  1.389  0.020  1.389
 T6E  CAY  CAJ   aromatic  1.393  0.020  1.393
 T6E  CAP  CBA   aromatic  1.390  0.020  1.390
 T6E  CAJ  CAH   aromatic  1.377  0.020  1.377
 T6E  CAJ  F1    single    1.338  0.020  1.338
 T6E  CAH  CAK   aromatic  1.386  0.020  1.386
 T6E  CAK  CBA   aromatic  1.388  0.020  1.388
 T6E  CBA  CBG   single    1.496  0.020  1.496
 T6E  CBG  FAF   single    1.342  0.020  1.342
 T6E  CBG  FAG   single    1.336  0.020  1.336
 T6E  CBG  FAE   single    1.340  0.020  1.340
 T6E  S    C8    aromatic  1.727  0.020  1.727
 T6E  NBF  HBF1  single    0.860  0.020  1.020
 T6E  NBF  HBF2  single    0.860  0.020  1.020
 T6E  C2   H2    single    0.930  0.020  1.080
 T6E  C8   H8    single    0.930  0.020  1.080
 T6E  CAO  HAO   single    0.930  0.020  1.080
 T6E  CAN  HAN   single    0.930  0.020  1.080
 T6E  CAM  HAM   single    0.930  0.020  1.080
 T6E  CAL  HAL   single    0.930  0.020  1.080
 T6E  NAT  HAT   single    0.860  0.020  1.020
 T6E  NAU  HAU   single    0.860  0.020  1.020
 T6E  CAP  HAP   single    0.930  0.020  1.080
 T6E  CAH  HAH   single    0.930  0.020  1.080
 T6E  CAK  HAK   single    0.930  0.020  1.080

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
 T6E  NBF   C4   N3    117.04  3.000
 T6E  NBF   C4   C5    123.40  3.000
 T6E  N3    C4   C5    119.56  3.000
 T6E  CBB   C5   C6    112.52  3.000
 T6E  CBB   C5   C4    132.91  3.000
 T6E  C6    C5   C4    114.49  3.000
 T6E  S     C6   N1    122.60  3.000
 T6E  S     C6   C5    111.39  3.000
 T6E  N1    C6   C5    126.01  3.000
 T6E  C2    N1   C6    113.44  3.000
 T6E  C2    N3   C4    118.84  3.000
 T6E  HBF2  NBF  HBF1  117.71  3.000
 T6E  HBF2  NBF  C4    118.93  3.000
 T6E  HBF1  NBF  C4    122.36  3.000
 T6E  H2    C2   N3    115.93  3.000
 T6E  H2    C2   N1    116.52  3.000
 T6E  N3    C2   N1    127.54  3.000
 T6E  C8    CBB  CAZ   122.30  3.000
 T6E  C8    CBB  C5    111.17  3.000
 T6E  CAZ   CBB  C5    126.50  3.000
 T6E  CAN   CAZ  CAO   117.80  3.000
 T6E  CAN   CAZ  CBB   121.12  3.000
 T6E  CAO   CAZ  CBB   121.04  3.000
 T6E  HAO   CAO  CAM   118.96  3.000
 T6E  HAO   CAO  CAZ   120.13  3.000
 T6E  CAM   CAO  CAZ   120.91  3.000
 T6E  HAM   CAM  CAX   119.90  3.000
 T6E  HAM   CAM  CAO   119.14  3.000
 T6E  CAX   CAM  CAO   120.96  3.000
 T6E  HAN   CAN  CAL   118.56  3.000
 T6E  HAN   CAN  CAZ   119.50  3.000
 T6E  CAL   CAN  CAZ   121.93  3.000
 T6E  HAL   CAL  CAX   121.14  3.000
 T6E  HAL   CAL  CAN   119.02  3.000
 T6E  CAX   CAL  CAN   119.84  3.000
 T6E  NAT   CAX  CAL   124.96  3.000
 T6E  NAT   CAX  CAM   116.49  3.000
 T6E  CAL   CAX  CAM   118.55  3.000
 T6E  HAT   NAT  CAV   117.14  3.000
 T6E  HAT   NAT  CAX   114.38  3.000
 T6E  CAV   NAT  CAX   128.40  3.000
 T6E  NAU   CAV  OAD   122.90  3.000
 T6E  NAU   CAV  NAT   112.54  3.000
 T6E  OAD   CAV  NAT   124.55  3.000
 T6E  HAU   NAU  CAY   116.60  3.000
 T6E  HAU   NAU  CAV   118.67  3.000
 T6E  CAY   NAU  CAV   123.38  3.000
 T6E  CAJ   CAY  CAP   117.62  3.000
 T6E  CAJ   CAY  NAU   119.34  3.000
 T6E  CAP   CAY  NAU   123.03  3.000
 T6E  HAP   CAP  CBA   120.60  3.000
 T6E  HAP   CAP  CAY   119.00  3.000
 T6E  CBA   CAP  CAY   120.40  3.000
 T6E  F1    CAJ  CAH   119.27  3.000
 T6E  F1    CAJ  CAY   118.11  3.000
 T6E  CAH   CAJ  CAY   122.62  3.000
 T6E  HAH   CAH  CAK   120.87  3.000
 T6E  HAH   CAH  CAJ   119.98  3.000
 T6E  CAK   CAH  CAJ   119.14  3.000
 T6E  HAK   CAK  CBA   121.63  3.000
 T6E  HAK   CAK  CAH   118.92  3.000
 T6E  CBA   CAK  CAH   119.45  3.000
 T6E  CBG   CBA  CAK   120.90  3.000
 T6E  CBG   CBA  CAP   118.33  3.000
 T6E  CAK   CBA  CAP   120.76  3.000
 T6E  FAE   CBG  FAG   107.10  3.000
 T6E  FAE   CBG  FAF   106.37  3.000
 T6E  FAG   CBG  FAF   106.88  3.000
 T6E  FAE   CBG  CBA   112.03  3.000
 T6E  FAG   CBG  CBA   112.55  3.000
 T6E  FAF   CBG  CBA   111.53  3.000
 T6E  C8    S    C6     91.02  3.000
 T6E  H8    C8   S     119.51  3.000
 T6E  H8    C8   CBB   126.59  3.000
 T6E  S     C8   CBB   113.87  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
 T6E  CONST_01  N1    C6   C5   C4     0.00   0.0  0
 T6E  CONST_02  S     C6   C5   C4   180.00   0.0  0
 T6E  CONST_03  CAZ   CBB  C5   C4     0.00   0.0  0
 T6E  CONST_04  C8    CBB  C5   C4   180.00   0.0  0
 T6E  CONST_05  N1    C2   N3   C4     0.00   0.0  0
 T6E  CONST_06  C2    N3   C4   C5     0.00   0.0  0
 T6E  CONST_07  C2    N1   C6   C5     0.00   0.0  0
 T6E  CONST_08  C8    S    C6   C5     0.00   0.0  0
 T6E  CONST_11  S     C8   CBB  C5     0.00   0.0  0
 T6E  CONST_12  N3    C4   C5   C6     0.00   0.0  0
 T6E  CONST_13  CAZ   CBB  C5   C6   180.00   0.0  0
 T6E  CONST_14  C8    CBB  C5   C6     0.00   0.0  0
 T6E  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 T6E  CONST_16  CBB   C8   S    C6     0.00   0.0  0
 T6E  CONST_17  CBB   C5   C6   N1   180.00   0.0  0
 T6E  CONST_18  C8    S    C6   N1   180.00   0.0  0
 T6E  CONST_19  CBB   C5   C4   N3   180.00   0.0  0
 T6E  CONST_20  S     C6   N1   C2   180.00   0.0  0
 T6E  CONST_21  S     C6   C5   CBB    0.00   0.0  0
 T6E  CONST_22  CAM   CAO  CAZ  CBB  180.00   0.0  0
 T6E  CONST_23  CAL   CAN  CAZ  CBB  180.00   0.0  0
 T6E  CONST_24  S     C8   CBB  CAZ  180.00   0.0  0
 T6E  CONST_25  CAX   CAM  CAO  CAZ    0.00   0.0  0
 T6E  CONST_26  CAX   CAL  CAN  CAZ    0.00   0.0  0
 T6E  CONST_28  CAL   CAN  CAZ  CAO    0.00   0.0  0
 T6E  CONST_29  CAL   CAX  CAM  CAO    0.00   0.0  0
 T6E  CONST_30  CAN   CAZ  CAO  CAM    0.00   0.0  0
 T6E  CONST_31  CAN   CAL  CAX  CAM    0.00   0.0  0
 T6E  CONST_33  CAK   CBA  CAP  CAY    0.00   0.0  0
 T6E  CONST_34  CAK   CAH  CAJ  CAY    0.00   0.0  0
 T6E  CONST_35  CAH   CAJ  CAY  CAP    0.00   0.0  0
 T6E  CONST_36  CAH   CAK  CBA  CAP    0.00   0.0  0
 T6E  CONST_37  CBA   CAP  CAY  CAJ    0.00   0.0  0
 T6E  CONST_38  CBA   CAK  CAH  CAJ    0.00   0.0  0
 T6E  CONST_39  NBF   C4   C5   C6   180.00   0.0  0
 T6E  CONST_40  CBB   C5   C4   NBF    0.00   0.0  0
 T6E  CONST_41  C2    N3   C4   NBF  180.00   0.0  0
 T6E  CONST_42  NAT   CAX  CAM  CAO  180.00   0.0  0
 T6E  CONST_43  NAT   CAX  CAL  CAN  180.00   0.0  0
 T6E  CONST_44  CBA   CAP  CAY  NAU  180.00   0.0  0
 T6E  CONST_45  CAH   CAJ  CAY  NAU  180.00   0.0  0
 T6E  CONST_46  CBG   CBA  CAP  CAY  180.00   0.0  0
 T6E  CONST_47  F1    CAJ  CAY  CAP  180.00   0.0  0
 T6E  CONST_48  CBG   CBA  CAK  CAH  180.00   0.0  0
 T6E  CONST_49  F1    CAJ  CAH  CAK  180.00   0.0  0
 T6E  CONST_50  H2    C2   N3   C4   180.00   0.0  0
 T6E  CONST_51  H8    C8   CBB  C5   180.00   0.0  0
 T6E  CONST_52  HAO   CAO  CAZ  CBB    0.00   0.0  0
 T6E  CONST_53  HAN   CAN  CAZ  CBB    0.00   0.0  0
 T6E  CONST_54  HAM   CAM  CAO  CAZ  180.00   0.0  0
 T6E  CONST_55  HAL   CAL  CAN  CAZ  180.00   0.0  0
 T6E  CONST_56  HAH   CAH  CAJ  CAY  180.00   0.0  0
 T6E  CONST_57  HAK   CAK  CBA  CAP  180.00   0.0  0
 T6E  CONST_58  HAP   CAP  CAY  CAJ  180.00   0.0  0
 T6E  CONST_59  CAV   NAT  CAX  CAM  180.00   0.0  0
 T6E  CONST_60  CAV   NAT  CAX  CAL    0.00   0.0  0
 T6E  CONST_63  HBF1  NBF  C4   C5     0.00   0.0  0
 T6E  CONST_64  HBF2  NBF  C4   C5   180.00   0.0  0
 T6E  CONST_65  HAT   NAT  CAX  CAM    0.00   0.0  0
 T6E  CONST_67  OAD   CAV  NAT  CAX    0.00   0.0  0
 T6E  CONST_68  CAY   NAU  CAV  OAD    0.00   0.0  0
 T6E  CONST_69  NAU   CAV  NAT  CAX  180.00   0.0  0
 T6E  CONST_70  CAY   NAU  CAV  NAT  180.00   0.0  0
 T6E  Var_01    FAF   CBG  CBA  CAP   72.68  30.0  2

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
 T6E  plan-1  CBB   0.020
 T6E  plan-1  CAZ   0.020
 T6E  plan-1  CAO   0.020
 T6E  plan-1  CAM   0.020
 T6E  plan-1  CAN   0.020
 T6E  plan-1  CAL   0.020
 T6E  plan-1  CAX   0.020
 T6E  plan-1  NAT   0.020
 T6E  plan-1  HAO   0.020
 T6E  plan-1  HAN   0.020
 T6E  plan-1  HAM   0.020
 T6E  plan-1  HAL   0.020
 T6E  plan-2  NAU   0.020
 T6E  plan-2  CAY   0.020
 T6E  plan-2  CAP   0.020
 T6E  plan-2  CAJ   0.020
 T6E  plan-2  CAH   0.020
 T6E  plan-2  CAK   0.020
 T6E  plan-2  CBA   0.020
 T6E  plan-2  CBG   0.020
 T6E  plan-2  F1    0.020
 T6E  plan-2  HAP   0.020
 T6E  plan-2  HAH   0.020
 T6E  plan-2  HAK   0.020
 T6E  plan-3  C4    0.020
 T6E  plan-3  C5    0.020
 T6E  plan-3  C6    0.020
 T6E  plan-3  N1    0.020
 T6E  plan-3  N3    0.020
 T6E  plan-3  NBF   0.020
 T6E  plan-3  C2    0.020
 T6E  plan-3  CBB   0.020
 T6E  plan-3  CAZ   0.020
 T6E  plan-3  S     0.020
 T6E  plan-3  C8    0.020
 T6E  plan-3  H2    0.020
 T6E  plan-3  H8    0.020
 T6E  plan-4  CAX   0.020
 T6E  plan-4  NAT   0.020
 T6E  plan-4  CAV   0.020
 T6E  plan-4  OAD   0.020
 T6E  plan-4  NAU   0.020
 T6E  plan-4  CAY   0.020
 T6E  plan-4  HAT   0.020
 T6E  plan-4  HAU   0.020
 T6E  plan-5  C4    0.020
 T6E  plan-5  NBF   0.020
 T6E  plan-5  HBF1  0.020
 T6E  plan-5  HBF2  0.020

