# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:31:29 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 3-amino-N-(3-fluorophenyl)-6-thiophen-2-ylthieno[2,3-b]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1c(sc2nc(ccc12)c3sccc3)C(=O)Nc4cccc(F)c4
#
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
 DZ9  DZ9  3-amino-N-(3-fluorophenyl)-6-thiophen-2-ylthieno[2,3-b]pyridine-2-carboxamide  ligand  37  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZ9
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
 DZ9  CAL   C  CR16  0  -0.490   5.3795  -0.2668   0.0496
 DZ9  CAR   C  CR6   0   0.556   6.7019   0.1355   0.0288
 DZ9  FAC   F  F     0  -0.318   7.6412  -0.8137   0.1792
 DZ9  CAG   C  CR16  0  -0.433   7.1034   1.4439  -0.1383
 DZ9  CAE   C  CR16  0  -0.227   6.1058   2.3984  -0.2911
 DZ9  CAH   C  CR16  0  -0.372   4.7700   2.0429  -0.2770
 DZ9  CAS   C  CR6   0   0.406   4.3912   0.7061  -0.1069
 DZ9  NAN   N  NH1   0  -0.787   3.0226   0.4457  -0.0962
 DZ9  CAQ   C  C     0   0.602   2.3721  -0.7532  -0.0165
 DZ9  OAB   O  O     0  -0.489   2.9655  -1.8274   0.0199
 DZ9  CAW   C  CR5   0  -0.462   0.9208  -0.6932   0.0123
 DZ9  CAT   C  CR5   0   0.397   0.0952  -1.8016  -0.0565
 DZ9  NAA   N  NH2   0  -0.849   0.4723  -3.0923  -0.0877
 DZ9  SAP   S  S2    0   0.176   0.0219   0.8192   0.1147
 DZ9  CAY   C  CR56  0  -0.029  -1.4805  -0.0345   0.0215
 DZ9  NAM   N  N     0  -0.456  -2.6427   0.5823   0.0443
 DZ9  CAX   C  CR56  0   0.102  -1.2954  -1.4199  -0.0588
 DZ9  CAK   C  CR16  0  -0.177  -2.4466  -2.2028  -0.1188
 DZ9  CAJ   C  CR16  0  -0.321  -3.6718  -1.5749  -0.1018
 DZ9  CAU   C  CR6   0   0.267  -3.7364  -0.1720  -0.0189
 DZ9  CAV   C  CR5   0  -0.246  -5.0062   0.5441   0.0061
 DZ9  CAI   C  CR15  0  -0.209  -5.1869   1.8987   0.1056
 DZ9  CAD   C  CR15  0  -0.167  -6.5505   2.2759   0.1050
 DZ9  CAF   C  CR15  0  -0.457  -7.3886   1.2050   0.0047
 DZ9  SAO   S  S2    0   0.229  -6.5274  -0.2669  -0.0906
 DZ9  HAL   H  HCR6  0   0.300   5.1431  -1.3092   0.1838
 DZ9  HAG   H  HCR6  0   0.278   8.1516   1.7095  -0.1507
 DZ9  HAE   H  HCR6  0   0.272   6.3757   3.4372  -0.4252
 DZ9  HAH   H  HCR6  0   0.276   4.0112   2.8063  -0.3984
 DZ9  HNAN  H  HNH1  0   0.420   2.4588   1.2730  -0.2181
 DZ9  HNAA  H  HNH2  0   0.408   1.4482  -3.3029  -0.2129
 DZ9  HNAB  H  HNH2  0   0.402  -0.1807  -3.7864  -0.4078
 DZ9  HAK   H  HCR6  0   0.276  -2.3975  -3.2827  -0.1754
 DZ9  HAJ   H  HCR6  0   0.278  -4.5727  -2.1716  -0.1471
 DZ9  HAI   H  HCR5  0   0.270  -4.3659   2.5966   0.1769
 DZ9  HAD   H  HCR5  0   0.273  -6.8948   3.2972   0.1768
 DZ9  HAF   H  HCR5  0   0.304  -8.4673   1.2030  -0.0186

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
 DZ9  CAR  CAL   aromatic  1.382  0.020  1.382
 DZ9  CAS  CAL   aromatic  1.396  0.020  1.396
 DZ9  CAL  HAL   single    0.930  0.020  1.080
 DZ9  CAG  CAR   aromatic  1.379  0.020  1.379
 DZ9  CAR  FAC   single    1.344  0.020  1.344
 DZ9  CAE  CAG   aromatic  1.389  0.020  1.389
 DZ9  CAG  HAG   single    0.930  0.020  1.080
 DZ9  CAE  CAH   aromatic  1.382  0.020  1.382
 DZ9  CAE  HAE   single    0.930  0.020  1.080
 DZ9  CAH  CAS   aromatic  1.400  0.020  1.400
 DZ9  CAH  HAH   single    0.930  0.020  1.080
 DZ9  CAS  NAN   single    1.393  0.020  1.393
 DZ9  NAN  CAQ   single    1.366  0.020  1.366
 DZ9  NAN  HNAN  single    0.860  0.020  1.020
 DZ9  CAQ  OAB   double    1.228  0.020  1.228
 DZ9  CAQ  CAW   single    1.453  0.020  1.453
 DZ9  CAW  CAT   aromatic  1.384  0.020  1.384
 DZ9  CAW  SAP   aromatic  1.762  0.020  1.762
 DZ9  NAA  CAT   single    1.345  0.020  1.345
 DZ9  CAT  CAX   aromatic  1.442  0.020  1.442
 DZ9  NAA  HNAA  single    0.890  0.020  1.040
 DZ9  NAA  HNAB  single    0.890  0.020  1.040
 DZ9  SAP  CAY   aromatic  1.731  0.020  1.731
 DZ9  CAX  CAY   aromatic  1.400  0.020  1.400
 DZ9  CAY  NAM   aromatic  1.316  0.020  1.316
 DZ9  NAM  CAU   aromatic  1.330  0.020  1.330
 DZ9  CAX  CAK   aromatic  1.394  0.020  1.394
 DZ9  CAK  CAJ   aromatic  1.377  0.020  1.377
 DZ9  CAK  HAK   single    0.930  0.020  1.080
 DZ9  CAJ  CAU   aromatic  1.407  0.020  1.407
 DZ9  CAJ  HAJ   single    0.930  0.020  1.080
 DZ9  CAU  CAV   single    1.458  0.020  1.458
 DZ9  CAI  CAV   aromatic  1.370  0.020  1.370
 DZ9  CAV  SAO   aromatic  1.727  0.020  1.727
 DZ9  CAI  CAD   aromatic  1.415  0.020  1.415
 DZ9  CAI  HAI   single    0.930  0.020  1.080
 DZ9  CAD  CAF   aromatic  1.363  0.020  1.363
 DZ9  CAD  HAD   single    0.930  0.020  1.080
 DZ9  SAO  CAF   aromatic  1.708  0.020  1.708
 DZ9  CAF  HAF   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
 DZ9  HAL   CAL  CAS   122.21  3.000
 DZ9  HAL   CAL  CAR   119.56  3.000
 DZ9  CAS   CAL  CAR   118.22  3.000
 DZ9  CAG   CAR  FAC   118.70  3.000
 DZ9  FAC   CAR  CAL   117.48  3.000
 DZ9  CAG   CAR  CAL   123.82  3.000
 DZ9  HAG   CAG  CAE   121.74  3.000
 DZ9  HAG   CAG  CAR   121.11  3.000
 DZ9  CAE   CAG  CAR   117.14  3.000
 DZ9  HAE   CAE  CAH   119.30  3.000
 DZ9  HAE   CAE  CAG   119.63  3.000
 DZ9  CAH   CAE  CAG   121.08  3.000
 DZ9  HAH   CAH  CAS   119.81  3.000
 DZ9  HAH   CAH  CAE   119.64  3.000
 DZ9  CAS   CAH  CAE   120.55  3.000
 DZ9  NAN   CAS  CAH   116.44  3.000
 DZ9  NAN   CAS  CAL   124.37  3.000
 DZ9  CAH   CAS  CAL   119.19  3.000
 DZ9  HNAN  NAN  CAQ   117.43  3.000
 DZ9  HNAN  NAN  CAS   113.26  3.000
 DZ9  CAQ   NAN  CAS   129.21  3.000
 DZ9  CAW   CAQ  OAB   121.22  3.000
 DZ9  CAW   CAQ  NAN   116.14  3.000
 DZ9  OAB   CAQ  NAN   122.64  3.000
 DZ9  SAP   CAW  CAT   112.70  3.000
 DZ9  SAP   CAW  CAQ   123.10  3.000
 DZ9  CAT   CAW  CAQ   124.19  3.000
 DZ9  CAX   CAT  NAA   121.62  3.000
 DZ9  CAX   CAT  CAW   111.31  3.000
 DZ9  NAA   CAT  CAW   127.05  3.000
 DZ9  HNAB  NAA  HNAA  116.48  3.000
 DZ9  HNAB  NAA  CAT   119.20  3.000
 DZ9  HNAA  NAA  CAT   118.40  3.000
 DZ9  CAY   SAP  CAW    90.94  3.000
 DZ9  CAX   CAY  NAM   125.56  3.000
 DZ9  NAM   CAY  SAP   122.32  3.000
 DZ9  CAX   CAY  SAP   112.11  3.000
 DZ9  CAU   NAM  CAY   117.36  3.000
 DZ9  CAK   CAX  CAY   116.69  3.000
 DZ9  CAK   CAX  CAT   130.39  3.000
 DZ9  CAY   CAX  CAT   112.91  3.000
 DZ9  HAK   CAK  CAJ   119.74  3.000
 DZ9  HAK   CAK  CAX   121.69  3.000
 DZ9  CAJ   CAK  CAX   118.58  3.000
 DZ9  HAJ   CAJ  CAU   120.95  3.000
 DZ9  HAJ   CAJ  CAK   119.28  3.000
 DZ9  CAU   CAJ  CAK   119.77  3.000
 DZ9  CAV   CAU  CAJ   122.06  3.000
 DZ9  CAV   CAU  NAM   115.90  3.000
 DZ9  CAJ   CAU  NAM   122.04  3.000
 DZ9  SAO   CAV  CAI   110.62  3.000
 DZ9  SAO   CAV  CAU   122.39  3.000
 DZ9  CAI   CAV  CAU   126.99  3.000
 DZ9  HAI   CAI  CAD   124.09  3.000
 DZ9  HAI   CAI  CAV   122.91  3.000
 DZ9  CAD   CAI  CAV   113.00  3.000
 DZ9  HAD   CAD  CAF   123.47  3.000
 DZ9  HAD   CAD  CAI   124.00  3.000
 DZ9  CAF   CAD  CAI   112.52  3.000
 DZ9  HAF   CAF  SAO   120.08  3.000
 DZ9  HAF   CAF  CAD   128.14  3.000
 DZ9  SAO   CAF  CAD   111.78  3.000
 DZ9  CAF   SAO  CAV    92.08  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
 DZ9  CONST_01  CAE   CAG  CAR  CAL    0.00   0.0  0
 DZ9  CONST_02  CAE   CAH  CAS  CAL    0.00   0.0  0
 DZ9  CONST_03  CAH   CAS  CAL  CAR    0.00   0.0  0
 DZ9  CONST_04  CAH   CAE  CAG  CAR    0.00   0.0  0
 DZ9  CONST_05  CAS   CAL  CAR  CAG    0.00   0.0  0
 DZ9  CONST_06  CAS   CAH  CAE  CAG    0.00   0.0  0
 DZ9  CONST_07  CAY   CAX  CAT  CAW    0.00   0.0  0
 DZ9  CONST_08  CAK   CAX  CAT  CAW  180.00   0.0  0
 DZ9  CONST_09  CAX   CAY  SAP  CAW    0.00   0.0  0
 DZ9  CONST_10  NAM   CAY  SAP  CAW  180.00   0.0  0
 DZ9  CONST_11  CAY   SAP  CAW  CAT    0.00   0.0  0
 DZ9  CONST_12  SAP   CAY  CAX  CAT    0.00   0.0  0
 DZ9  CONST_13  NAM   CAY  CAX  CAT  180.00   0.0  0
 DZ9  CONST_14  CAJ   CAK  CAX  CAT  180.00   0.0  0
 DZ9  CONST_15  CAX   CAT  CAW  SAP    0.00   0.0  0
 DZ9  CONST_16  CAK   CAX  CAY  SAP  180.00   0.0  0
 DZ9  CONST_17  CAU   NAM  CAY  SAP  180.00   0.0  0
 DZ9  CONST_18  CAJ   CAK  CAX  CAY    0.00   0.0  0
 DZ9  CONST_19  CAJ   CAU  NAM  CAY    0.00   0.0  0
 DZ9  CONST_20  CAV   CAU  NAM  CAY  180.00   0.0  0
 DZ9  CONST_21  CAK   CAX  CAY  NAM    0.00   0.0  0
 DZ9  CONST_22  CAK   CAJ  CAU  NAM    0.00   0.0  0
 DZ9  CONST_23  CAI   CAV  CAU  NAM    0.00   0.0  0
 DZ9  CONST_24  SAO   CAV  CAU  NAM  180.00   0.0  0
 DZ9  CONST_25  CAU   NAM  CAY  CAX    0.00   0.0  0
 DZ9  CONST_26  CAU   CAJ  CAK  CAX    0.00   0.0  0
 DZ9  CONST_27  CAV   CAU  CAJ  CAK  180.00   0.0  0
 DZ9  CONST_28  CAI   CAV  CAU  CAJ  180.00   0.0  0
 DZ9  CONST_29  SAO   CAV  CAU  CAJ    0.00   0.0  0
 DZ9  CONST_30  CAD   CAI  CAV  CAU  180.00   0.0  0
 DZ9  CONST_31  CAF   SAO  CAV  CAU  180.00   0.0  0
 DZ9  CONST_32  CAF   CAD  CAI  CAV    0.00   0.0  0
 DZ9  CONST_33  CAD   CAF  SAO  CAV    0.00   0.0  0
 DZ9  CONST_34  CAF   SAO  CAV  CAI    0.00   0.0  0
 DZ9  CONST_35  SAO   CAF  CAD  CAI    0.00   0.0  0
 DZ9  CONST_36  SAO   CAV  CAI  CAD    0.00   0.0  0
 DZ9  CONST_37  NAN   CAS  CAL  CAR  180.00   0.0  0
 DZ9  CONST_38  CAS   CAL  CAR  FAC  180.00   0.0  0
 DZ9  CONST_39  CAE   CAG  CAR  FAC  180.00   0.0  0
 DZ9  CONST_40  NAN   CAS  CAH  CAE  180.00   0.0  0
 DZ9  CONST_41  CAX   CAT  CAW  CAQ  180.00   0.0  0
 DZ9  CONST_42  CAY   SAP  CAW  CAQ  180.00   0.0  0
 DZ9  CONST_43  SAP   CAW  CAT  NAA  180.00   0.0  0
 DZ9  CONST_44  CAY   CAX  CAT  NAA  180.00   0.0  0
 DZ9  CONST_45  CAK   CAX  CAT  NAA    0.00   0.0  0
 DZ9  CONST_46  HAG   CAG  CAR  CAL  180.00   0.0  0
 DZ9  CONST_47  HAH   CAH  CAS  CAL  180.00   0.0  0
 DZ9  CONST_48  HAE   CAE  CAG  CAR  180.00   0.0  0
 DZ9  CONST_49  HAL   CAL  CAR  CAG  180.00   0.0  0
 DZ9  CONST_50  HAK   CAK  CAX  CAT    0.00   0.0  0
 DZ9  CONST_51  HAJ   CAJ  CAU  NAM  180.00   0.0  0
 DZ9  CONST_52  HAI   CAI  CAV  CAU    0.00   0.0  0
 DZ9  CONST_53  HAD   CAD  CAI  CAV  180.00   0.0  0
 DZ9  CONST_54  HAF   CAF  SAO  CAV  180.00   0.0  0
 DZ9  CONST_55  CAW   CAQ  NAN  CAS  180.00   0.0  0
 DZ9  CONST_56  CAQ   NAN  CAS  CAL    0.00   0.0  0
 DZ9  CONST_57  CAQ   NAN  CAS  CAH  180.00   0.0  0
 DZ9  CONST_58  HNAN  NAN  CAS  CAL  180.00   0.0  0
 DZ9  CONST_59  HNAA  NAA  CAT  CAW    0.00   0.0  0
 DZ9  CONST_61  OAB   CAQ  NAN  CAS    0.00   0.0  0
 DZ9  Var_01    CAT   CAW  CAQ  NAN  172.61  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
 DZ9  plan-1  CAU   0.020
 DZ9  plan-1  CAV   0.020
 DZ9  plan-1  CAI   0.020
 DZ9  plan-1  CAD   0.020
 DZ9  plan-1  CAF   0.020
 DZ9  plan-1  SAO   0.020
 DZ9  plan-1  HAI   0.020
 DZ9  plan-1  HAD   0.020
 DZ9  plan-1  HAF   0.020
 DZ9  plan-2  CAL   0.020
 DZ9  plan-2  CAR   0.020
 DZ9  plan-2  FAC   0.020
 DZ9  plan-2  CAG   0.020
 DZ9  plan-2  CAE   0.020
 DZ9  plan-2  CAH   0.020
 DZ9  plan-2  CAS   0.020
 DZ9  plan-2  NAN   0.020
 DZ9  plan-2  HAL   0.020
 DZ9  plan-2  HAG   0.020
 DZ9  plan-2  HAE   0.020
 DZ9  plan-2  HAH   0.020
 DZ9  plan-3  CAQ   0.020
 DZ9  plan-3  CAW   0.020
 DZ9  plan-3  CAT   0.020
 DZ9  plan-3  NAA   0.020
 DZ9  plan-3  SAP   0.020
 DZ9  plan-3  CAY   0.020
 DZ9  plan-3  NAM   0.020
 DZ9  plan-3  CAX   0.020
 DZ9  plan-3  CAK   0.020
 DZ9  plan-3  CAJ   0.020
 DZ9  plan-3  CAU   0.020
 DZ9  plan-3  CAV   0.020
 DZ9  plan-3  HAK   0.020
 DZ9  plan-3  HAJ   0.020
 DZ9  plan-4  CAS   0.020
 DZ9  plan-4  NAN   0.020
 DZ9  plan-4  CAQ   0.020
 DZ9  plan-4  OAB   0.020
 DZ9  plan-4  CAW   0.020
 DZ9  plan-4  HNAN  0.020
 DZ9  plan-5  CAT   0.020
 DZ9  plan-5  NAA   0.020
 DZ9  plan-5  HNAA  0.020
 DZ9  plan-5  HNAB  0.020

