# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:57:13 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 9-oxo-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-9H-fluorene-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)c2cccc3c4ccccc4C(=O)c23)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 TA9  TA9  9-oxo-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-9H-fluorene-1-carboxamide  ligand  50  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TA9
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
 TA9  CAK   C  CR56  0  -0.095   2.2189   0.0986   0.9595
 TA9  CAQ   C  CR5   0   0.342   1.8917   0.1997  -0.4887
 TA9  OBB   O  O     0  -0.362   0.8537  -0.1028  -1.0289
 TA9  CAN   C  CR56  0  -0.071   3.1065   0.7643  -1.1289
 TA9  CAS   C  CR16  0  -0.273   3.3426   1.0547  -2.4568
 TA9  CAH   C  CR16  0  -0.261   4.5831   1.5911  -2.7977
 TA9  CAC   C  CR16  0  -0.233   5.5428   1.8229  -1.8195
 TA9  CAR   C  CR16  0  -0.342   5.2980   1.5280  -0.4771
 TA9  CAM   C  CR56  0   0.139   4.0697   0.9953  -0.1423
 TA9  CAL   C  CR56  0   0.150   3.5144   0.5862   1.1604
 TA9  CAO   C  CR16  0  -0.352   4.0594   0.6264   2.4270
 TA9  CAT   C  CR16  0  -0.225   3.2807   0.1739   3.4919
 TA9  CAP   C  CR16  0  -0.291   1.9942  -0.3084   3.2928
 TA9  CAJ   C  CR6   0  -0.034   1.4445  -0.3534   2.0106
 TA9  CAI   C  C     0   0.469   0.0806  -0.9499   1.8020
 TA9  OAZ   O  O     0  -0.468  -0.0435  -2.1260   1.5039
 TA9  NAV   N  NH1   0  -0.618  -0.9261  -0.0940   2.0174
 TA9  CAD   C  CH2   0  -0.280  -2.3328  -0.4329   1.9657
 TA9  CAA   C  CH1   0  -0.114  -3.0398   0.2196   0.7805
 TA9  NAW   N  NH1   0  -0.624  -2.5029  -0.3002  -0.4608
 TA9  CAE   C  CH1   0  -0.094  -3.0644   0.3307  -1.6444
 TA9  CAU   C  CH3   0  -0.678  -2.3455  -0.1609  -2.8904
 TA9  CAG   C  CH1   0   0.040  -4.5651   0.0680  -1.6983
 TA9  OAX   O  OH1   0  -0.673  -4.8048  -1.3014  -1.9137
 TA9  CAF   C  CH1   0  -0.035  -5.2106   0.5457  -0.3986
 TA9  OAY   O  OH1   0  -0.676  -6.5817   0.1983  -0.3462
 TA9  CAB   C  CH1   0   0.086  -4.5382  -0.0723   0.8209
 TA9  OBA   O  OH1   0  -0.680  -5.0660   0.4612   2.0134
 TA9  HAS   H  HCR6  0   0.269   2.5897   0.8725  -3.2131
 TA9  HAH   H  HCR6  0   0.271   4.8030   1.8285  -3.8297
 TA9  HAC   H  HCR6  0   0.274   6.4990   2.2414  -2.1043
 TA9  HAR   H  HCR6  0   0.261   6.0579   1.7163   0.2706
 TA9  HAO   H  HCR6  0   0.263   5.0594   0.9999   2.6046
 TA9  HAT   H  HCR6  0   0.277   3.6846   0.2003   4.4951
 TA9  HAP   H  HCR6  0   0.274   1.4167  -0.6521   4.1412
 TA9  HAV   H  HNH1  0   0.410  -0.6920   0.8541   2.2682
 TA9  HAD1  H  HCH2  0   0.249  -2.4263  -1.5163   1.8981
 TA9  HAD2  H  HCH2  0   0.265  -2.7965  -0.1138   2.8986
 TA9  HAA   H  HCH1  0   0.203  -2.9108   1.3156   0.8637
 TA9  HAW   H  HNH1  0   0.363  -1.4973  -0.1769  -0.4716
 TA9  HAB   H  HCH1  0   0.201  -4.6703  -1.1642   0.7848
 TA9  HAE   H  HCH1  0   0.204  -2.9555   1.4291  -1.6035
 TA9  HAU1  H  HCH3  0   0.228  -2.4201  -1.2432  -2.9903
 TA9  HAU2  H  HCH3  0   0.227  -2.7694   0.2969  -3.7848
 TA9  HAU3  H  HCH3  0   0.233  -1.2877   0.1020  -2.8535
 TA9  HAG   H  HCH1  0   0.209  -4.9770   0.6693  -2.5256
 TA9  HAX   H  HOH1  0   0.444  -5.7484  -1.4488  -1.7855
 TA9  HAF   H  HCH1  0   0.217  -5.0819   1.6360  -0.3373
 TA9  HAY   H  HOH1  0   0.460  -7.0832   0.8300  -0.8709
 TA9  HBA   H  HOH1  0   0.450  -6.0188   0.3223   2.0024

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
 TA9  CAK  CAQ   single    1.488  0.020  1.488
 TA9  CAK  CAL   aromatic  1.399  0.020  1.399
 TA9  CAK  CAJ   aromatic  1.382  0.020  1.382
 TA9  CAQ  OBB   double    1.209  0.020  1.209
 TA9  CAQ  CAN   single    1.485  0.020  1.485
 TA9  CAN  CAS   aromatic  1.380  0.020  1.380
 TA9  CAN  CAM   aromatic  1.398  0.020  1.398
 TA9  CAS  CAH   aromatic  1.394  0.020  1.394
 TA9  CAH  CAC   aromatic  1.390  0.020  1.390
 TA9  CAC  CAR   aromatic  1.396  0.020  1.396
 TA9  CAR  CAM   aromatic  1.380  0.020  1.380
 TA9  CAM  CAL   aromatic  1.474  0.020  1.474
 TA9  CAL  CAO   aromatic  1.380  0.020  1.380
 TA9  CAO  CAT   aromatic  1.395  0.020  1.395
 TA9  CAT  CAP   aromatic  1.388  0.020  1.388
 TA9  CAP  CAJ   aromatic  1.396  0.020  1.396
 TA9  CAJ  CAI   single    1.503  0.020  1.503
 TA9  CAI  OAZ   double    1.220  0.020  1.220
 TA9  CAI  NAV   single    1.339  0.020  1.339
 TA9  NAV  CAD   single    1.448  0.020  1.448
 TA9  CAD  CAA   single    1.527  0.020  1.527
 TA9  CAA  NAW   single    1.449  0.020  1.449
 TA9  CAA  CAB   single    1.527  0.020  1.527
 TA9  NAW  CAE   single    1.454  0.020  1.454
 TA9  CAE  CAU   single    1.520  0.020  1.520
 TA9  CAE  CAG   single    1.525  0.020  1.525
 TA9  CAG  OAX   single    1.407  0.020  1.407
 TA9  CAG  CAF   single    1.528  0.020  1.528
 TA9  CAF  OAY   single    1.415  0.020  1.415
 TA9  CAF  CAB   single    1.523  0.020  1.523
 TA9  CAB  OBA   single    1.409  0.020  1.409
 TA9  CAS  HAS   single    0.930  0.020  1.080
 TA9  CAH  HAH   single    0.930  0.020  1.080
 TA9  CAC  HAC   single    0.930  0.020  1.080
 TA9  CAR  HAR   single    0.930  0.020  1.080
 TA9  CAO  HAO   single    0.930  0.020  1.080
 TA9  CAT  HAT   single    0.930  0.020  1.080
 TA9  CAP  HAP   single    0.930  0.020  1.080
 TA9  NAV  HAV   single    0.860  0.020  1.020
 TA9  CAD  HAD1  single    0.970  0.020  1.090
 TA9  CAD  HAD2  single    0.970  0.020  1.090
 TA9  CAA  HAA   single    0.970  0.020  1.090
 TA9  NAW  HAW   single    0.890  0.020  1.040
 TA9  CAB  HAB   single    0.970  0.020  1.090
 TA9  CAE  HAE   single    0.970  0.020  1.090
 TA9  CAU  HAU1  single    0.970  0.020  1.090
 TA9  CAU  HAU2  single    0.970  0.020  1.090
 TA9  CAU  HAU3  single    0.970  0.020  1.090
 TA9  CAG  HAG   single    0.970  0.020  1.090
 TA9  OAX  HAX   single    0.850  0.020  0.980
 TA9  CAF  HAF   single    0.970  0.020  1.090
 TA9  OAY  HAY   single    0.850  0.020  0.980
 TA9  OBA  HBA   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
 TA9  CAJ   CAK  CAL   121.60  3.000
 TA9  CAJ   CAK  CAQ   129.74  3.000
 TA9  CAL   CAK  CAQ   108.64  3.000
 TA9  CAN   CAQ  OBB   127.24  3.000
 TA9  CAN   CAQ  CAK   105.40  3.000
 TA9  OBB   CAQ  CAK   127.35  3.000
 TA9  CAM   CAN  CAS   121.77  3.000
 TA9  CAM   CAN  CAQ   108.80  3.000
 TA9  CAS   CAN  CAQ   129.43  3.000
 TA9  HAS   CAS  CAH   120.86  3.000
 TA9  HAS   CAS  CAN   121.19  3.000
 TA9  CAH   CAS  CAN   117.95  3.000
 TA9  HAH   CAH  CAC   119.64  3.000
 TA9  HAH   CAH  CAS   119.93  3.000
 TA9  CAC   CAH  CAS   120.44  3.000
 TA9  HAC   CAC  CAR   119.33  3.000
 TA9  HAC   CAC  CAH   119.31  3.000
 TA9  CAR   CAC  CAH   121.36  3.000
 TA9  HAR   CAR  CAM   121.62  3.000
 TA9  HAR   CAR  CAC   120.29  3.000
 TA9  CAM   CAR  CAC   118.09  3.000
 TA9  CAL   CAM  CAR   131.06  3.000
 TA9  CAL   CAM  CAN   108.56  3.000
 TA9  CAR   CAM  CAN   120.38  3.000
 TA9  CAO   CAL  CAM   130.88  3.000
 TA9  CAO   CAL  CAK   120.53  3.000
 TA9  CAM   CAL  CAK   108.59  3.000
 TA9  HAO   CAO  CAT   120.18  3.000
 TA9  HAO   CAO  CAL   121.72  3.000
 TA9  CAT   CAO  CAL   118.10  3.000
 TA9  HAT   CAT  CAP   119.17  3.000
 TA9  HAT   CAT  CAO   119.45  3.000
 TA9  CAP   CAT  CAO   121.38  3.000
 TA9  HAP   CAP  CAJ   119.98  3.000
 TA9  HAP   CAP  CAT   119.50  3.000
 TA9  CAJ   CAP  CAT   120.52  3.000
 TA9  CAI   CAJ  CAP   119.84  3.000
 TA9  CAI   CAJ  CAK   122.20  3.000
 TA9  CAP   CAJ  CAK   117.88  3.000
 TA9  NAV   CAI  OAZ   125.40  3.000
 TA9  NAV   CAI  CAJ   113.97  3.000
 TA9  OAZ   CAI  CAJ   120.60  3.000
 TA9  HAV   NAV  CAD   117.03  3.000
 TA9  HAV   NAV  CAI   117.82  3.000
 TA9  CAD   NAV  CAI   125.11  3.000
 TA9  HAD2  CAD  HAD1  107.92  3.000
 TA9  HAD2  CAD  CAA   110.03  3.000
 TA9  HAD1  CAD  CAA   109.70  3.000
 TA9  HAD2  CAD  NAV   108.32  3.000
 TA9  HAD1  CAD  NAV   108.56  3.000
 TA9  CAA   CAD  NAV   112.19  3.000
 TA9  HAA   CAA  CAB   107.56  3.000
 TA9  HAA   CAA  NAW   112.12  3.000
 TA9  CAB   CAA  NAW   108.53  3.000
 TA9  HAA   CAA  CAD   108.12  3.000
 TA9  CAB   CAA  CAD   110.62  3.000
 TA9  NAW   CAA  CAD   109.89  3.000
 TA9  HAW   NAW  CAE   108.77  3.000
 TA9  HAW   NAW  CAA   109.47  3.000
 TA9  CAE   NAW  CAA   113.49  3.000
 TA9  HAE   CAE  CAG   105.65  3.000
 TA9  HAE   CAE  CAU   107.78  3.000
 TA9  CAG   CAE  CAU   112.38  3.000
 TA9  HAE   CAE  NAW   111.30  3.000
 TA9  CAG   CAE  NAW   109.52  3.000
 TA9  CAU   CAE  NAW   110.14  3.000
 TA9  HAU3  CAU  HAU2  107.67  3.000
 TA9  HAU3  CAU  HAU1  107.99  3.000
 TA9  HAU2  CAU  HAU1  108.38  3.000
 TA9  HAU3  CAU  CAE   110.67  3.000
 TA9  HAU2  CAU  CAE   110.66  3.000
 TA9  HAU1  CAU  CAE   111.34  3.000
 TA9  HAG   CAG  CAF   108.06  3.000
 TA9  HAG   CAG  OAX   110.63  3.000
 TA9  CAF   CAG  OAX   111.26  3.000
 TA9  HAG   CAG  CAE   107.48  3.000
 TA9  CAF   CAG  CAE   109.39  3.000
 TA9  OAX   CAG  CAE   109.93  3.000
 TA9  HAX   OAX  CAG   107.18  3.000
 TA9  HAF   CAF  CAB   107.82  3.000
 TA9  HAF   CAF  OAY   110.77  3.000
 TA9  CAB   CAF  OAY   107.36  3.000
 TA9  HAF   CAF  CAG   107.94  3.000
 TA9  CAB   CAF  CAG   111.57  3.000
 TA9  OAY   CAF  CAG   111.34  3.000
 TA9  HAY   OAY  CAF   108.88  3.000
 TA9  HAB   CAB  OBA   111.01  3.000
 TA9  HAB   CAB  CAF   108.86  3.000
 TA9  OBA   CAB  CAF   111.01  3.000
 TA9  HAB   CAB  CAA   107.85  3.000
 TA9  OBA   CAB  CAA   108.52  3.000
 TA9  CAF   CAB  CAA   109.53  3.000
 TA9  HBA   OBA  CAB   107.84  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
 TA9  CONST_01  CAN  CAM  CAL  CAK     0.00   0.0  0
 TA9  CONST_02  CAR  CAM  CAL  CAK   180.00   0.0  0
 TA9  CONST_03  CAT  CAO  CAL  CAK     0.00   0.0  0
 TA9  CONST_04  CAT  CAP  CAJ  CAK     0.00   0.0  0
 TA9  CONST_05  CAC  CAH  CAS  CAN     0.00   0.0  0
 TA9  CONST_06  CAC  CAR  CAM  CAN     0.00   0.0  0
 TA9  CONST_07  CAO  CAL  CAM  CAN   180.00   0.0  0
 TA9  CONST_08  CAR  CAM  CAN  CAS     0.00   0.0  0
 TA9  CONST_09  CAL  CAM  CAN  CAS   180.00   0.0  0
 TA9  CONST_10  CAR  CAC  CAH  CAS     0.00   0.0  0
 TA9  CONST_11  CAM  CAN  CAS  CAH     0.00   0.0  0
 TA9  CONST_12  CAM  CAR  CAC  CAH     0.00   0.0  0
 TA9  CONST_13  CAL  CAM  CAR  CAC   180.00   0.0  0
 TA9  CONST_14  CAO  CAL  CAM  CAR     0.00   0.0  0
 TA9  CONST_15  CAJ  CAK  CAL  CAM   180.00   0.0  0
 TA9  CONST_16  CAT  CAO  CAL  CAM   180.00   0.0  0
 TA9  CONST_17  CAP  CAJ  CAK  CAL     0.00   0.0  0
 TA9  CONST_18  CAP  CAT  CAO  CAL     0.00   0.0  0
 TA9  CONST_19  CAJ  CAK  CAL  CAO     0.00   0.0  0
 TA9  CONST_20  CAJ  CAP  CAT  CAO     0.00   0.0  0
 TA9  CONST_21  CAI  CAJ  CAK  CAQ     0.00   0.0  0
 TA9  CONST_22  CAI  CAJ  CAK  CAL   180.00   0.0  0
 TA9  CONST_23  CAI  CAJ  CAP  CAT   180.00   0.0  0
 TA9  CONST_24  HAO  CAO  CAL  CAK   180.00   0.0  0
 TA9  CONST_25  HAP  CAP  CAJ  CAK   180.00   0.0  0
 TA9  CONST_26  HAS  CAS  CAN  CAQ     0.00   0.0  0
 TA9  CONST_27  HAH  CAH  CAS  CAN   180.00   0.0  0
 TA9  CONST_28  HAR  CAR  CAM  CAN   180.00   0.0  0
 TA9  CONST_29  HAC  CAC  CAH  CAS   180.00   0.0  0
 TA9  CONST_30  HAT  CAT  CAO  CAL   180.00   0.0  0
 TA9  CONST_31  CAD  NAV  CAI  CAJ   180.00   0.0  0
 TA9  CONST_32  HAV  NAV  CAI  CAJ     0.00   0.0  0
 TA9  CONST_33  CAD  NAV  CAI  OAZ     0.00   0.0  0
 TA9  Var_01    CAL  CAK  CAQ  OBB  -178.51  30.0  1
 TA9  Var_02    CAS  CAN  CAQ  OBB    -0.92  30.0  1
 TA9  Var_03    OAZ  CAI  CAJ  CAK    83.33  30.0  2
 TA9  Var_04    CAA  CAD  NAV  CAI  -111.64  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
 TA9  chir_01  CAA  CAD  NAW  CAB  negativ
 TA9  chir_02  CAE  NAW  CAU  CAG  negativ
 TA9  chir_03  CAG  OAX  CAE  CAF  positiv
 TA9  chir_04  CAF  OAY  CAG  CAB  positiv
 TA9  chir_05  CAB  OBA  CAF  CAA  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
 TA9  plan-1  CAJ  0.020
 TA9  plan-1  CAI  0.020
 TA9  plan-1  OAZ  0.020
 TA9  plan-1  NAV  0.020
 TA9  plan-1  CAD  0.020
 TA9  plan-1  HAV  0.020
 TA9  plan-2  CAK  0.020
 TA9  plan-2  CAQ  0.020
 TA9  plan-2  CAN  0.020
 TA9  plan-2  CAS  0.020
 TA9  plan-2  CAH  0.020
 TA9  plan-2  CAC  0.020
 TA9  plan-2  CAR  0.020
 TA9  plan-2  CAM  0.020
 TA9  plan-2  CAL  0.020
 TA9  plan-2  CAO  0.020
 TA9  plan-2  CAT  0.020
 TA9  plan-2  CAP  0.020
 TA9  plan-2  CAJ  0.020
 TA9  plan-2  CAI  0.020
 TA9  plan-2  HAS  0.020
 TA9  plan-2  HAH  0.020
 TA9  plan-2  HAC  0.020
 TA9  plan-2  HAR  0.020
 TA9  plan-2  HAO  0.020
 TA9  plan-2  HAT  0.020
 TA9  plan-2  HAP  0.020
 TA9  plan-3  CAK  0.020
 TA9  plan-3  CAQ  0.020
 TA9  plan-3  OBB  0.020
 TA9  plan-3  CAN  0.020

