# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 05:00:20 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)Cc2c[nH]c3ccccc23)[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
 ZX6  ZX6  2-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}acetamide  ligand  47  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZX6
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
 ZX6  CAS   C  CR56  0   0.029   2.4820  -0.2030  -0.7902
 ZX6  CAI   C  CR16  0  -0.363   1.5858  -0.7761  -1.7016
 ZX6  CAG   C  CR16  0  -0.260   1.5046  -2.1520  -1.7878
 ZX6  CAF   C  CR16  0  -0.280   2.3055  -2.9758  -0.9795
 ZX6  CAH   C  CR16  0  -0.306   3.1991  -2.4409  -0.0720
 ZX6  CAR   C  CR56  0   0.358   3.2758  -1.0517   0.0140
 ZX6  NAO   N  NR15  0  -0.686   4.0548  -0.2551   0.8005
 ZX6  CAJ   C  CR15  0  -0.072   3.7852   1.0554   0.5263
 ZX6  CAQ   C  CR5   0   0.000   2.8299   1.1446  -0.4454
 ZX6  CAL   C  CH2   0  -0.682   2.2117   2.3925  -0.9873
 ZX6  CAP   C  C     0   0.518   0.8387   2.5750  -0.3602
 ZX6  OAB   O  O     0  -0.486   0.7118   2.9102   0.8071
 ZX6  NAM   N  NH1   0  -0.633  -0.1953   2.2780  -1.1689
 ZX6  CAK   C  CH2   0  -0.276  -1.5751   2.1875  -0.7503
 ZX6  CAU   C  CH1   0  -0.113  -2.0413   0.7348  -0.6377
 ZX6  NAN   N  NH1   0  -0.615  -1.2360   0.0315   0.3409
 ZX6  CAT   C  CH1   0  -0.090  -1.5657  -1.3778   0.4696
 ZX6  CAA   C  CH3   0  -0.678  -0.5746  -2.0575   1.4001
 ZX6  CAV   C  CH1   0   0.043  -3.0079  -1.5206   0.9398
 ZX6  OAC   O  OH1   0  -0.673  -3.1355  -1.0273   2.2510
 ZX6  CAX   C  CH1   0  -0.038  -3.9292  -0.7770  -0.0260
 ZX6  OAE   O  OH1   0  -0.676  -5.2659  -0.7685   0.4422
 ZX6  CAW   C  CH1   0   0.088  -3.5027   0.6738  -0.2036
 ZX6  OAD   O  OH1   0  -0.681  -4.2854   1.3171  -1.1829
 ZX6  HAI   H  HCR6  0   0.235   0.9710  -0.1536  -2.3399
 ZX6  HAG   H  HCR6  0   0.246   0.8160  -2.6058  -2.4889
 ZX6  HAF   H  HCR6  0   0.249   2.2194  -4.0510  -1.0694
 ZX6  HAH   H  HCR6  0   0.260   3.8166  -3.0776   0.5488
 ZX6  HNAO  H  HNR5  0   0.410   4.7318  -0.5753   1.4723
 ZX6  HAJ   H  HCR5  0   0.283   4.3006   1.8440   1.0517
 ZX6  HAL   H  HCH2  0   0.282   2.8250   3.2578  -0.7314
 ZX6  HALA  H  HCH2  0   0.265   2.1536   2.3502  -2.0781
 ZX6  HNAM  H  HNH1  0   0.402  -0.0008   2.0731  -2.1353
 ZX6  HAK   H  HCH2  0   0.245  -1.6816   2.6877   0.2118
 ZX6  HAKA  H  HCH2  0   0.260  -2.1951   2.7184  -1.4719
 ZX6  HAU   H  HCH1  0   0.199  -1.9705   0.2738  -1.6412
 ZX6  HNAN  H  HNH1  0   0.363  -0.2601   0.1018   0.0790
 ZX6  HAT   H  HCH1  0   0.202  -1.5161  -1.8965  -0.5046
 ZX6  HAA   H  HCH3  0   0.226  -0.5628  -1.5851   2.3818
 ZX6  HAAA  H  HCH3  0   0.223  -0.8284  -3.1107   1.5290
 ZX6  HAAB  H  HCH3  0   0.244   0.4338  -2.0133   0.9836
 ZX6  HAV   H  HCH1  0   0.208  -3.2677  -2.5913   0.9000
 ZX6  HOAC  H  HOH1  0   0.443  -4.0777  -0.9693   2.4443
 ZX6  HAX   H  HCH1  0   0.218  -3.8653  -1.2736  -1.0048
 ZX6  HOAE  H  HOH1  0   0.460  -5.6684  -1.6194   0.2427
 ZX6  HAW   H  HCH1  0   0.199  -3.5865   1.1879   0.7659
 ZX6  HOAD  H  HOH1  0   0.449  -5.2105   1.2063  -0.9398

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
 ZX6  CAS  CAI   aromatic  1.401  0.020  1.401
 ZX6  CAS  CAR   aromatic  1.413  0.020  1.413
 ZX6  CAS  CAQ   aromatic  1.434  0.020  1.434
 ZX6  CAI  CAG   aromatic  1.381  0.020  1.381
 ZX6  CAG  CAF   aromatic  1.405  0.020  1.405
 ZX6  CAF  CAH   aromatic  1.381  0.020  1.381
 ZX6  CAH  CAR   aromatic  1.394  0.020  1.394
 ZX6  CAR  NAO   aromatic  1.364  0.020  1.364
 ZX6  NAO  CAJ   aromatic  1.366  0.020  1.366
 ZX6  CAJ  CAQ   aromatic  1.366  0.020  1.366
 ZX6  CAQ  CAL   single    1.494  0.020  1.494
 ZX6  CAL  CAP   single    1.520  0.020  1.520
 ZX6  CAP  OAB   double    1.221  0.020  1.221
 ZX6  CAP  NAM   single    1.346  0.020  1.346
 ZX6  NAM  CAK   single    1.445  0.020  1.445
 ZX6  CAK  CAU   single    1.530  0.020  1.530
 ZX6  CAU  NAN   single    1.449  0.020  1.449
 ZX6  CAU  CAW   single    1.526  0.020  1.526
 ZX6  NAN  CAT   single    1.453  0.020  1.453
 ZX6  CAT  CAA   single    1.520  0.020  1.520
 ZX6  CAT  CAV   single    1.524  0.020  1.524
 ZX6  CAV  OAC   single    1.407  0.020  1.407
 ZX6  CAV  CAX   single    1.528  0.020  1.528
 ZX6  CAX  OAE   single    1.416  0.020  1.416
 ZX6  CAX  CAW   single    1.523  0.020  1.523
 ZX6  CAW  OAD   single    1.409  0.020  1.409
 ZX6  CAI  HAI   single    0.930  0.020  1.080
 ZX6  CAG  HAG   single    0.930  0.020  1.080
 ZX6  CAF  HAF   single    0.930  0.020  1.080
 ZX6  CAH  HAH   single    0.930  0.020  1.080
 ZX6  NAO  HNAO  single    0.860  0.020  1.020
 ZX6  CAJ  HAJ   single    0.930  0.020  1.080
 ZX6  CAL  HAL   single    0.970  0.020  1.090
 ZX6  CAL  HALA  single    0.970  0.020  1.090
 ZX6  NAM  HNAM  single    0.860  0.020  1.020
 ZX6  CAK  HAK   single    0.970  0.020  1.090
 ZX6  CAK  HAKA  single    0.970  0.020  1.090
 ZX6  CAU  HAU   single    0.970  0.020  1.090
 ZX6  NAN  HNAN  single    0.890  0.020  1.040
 ZX6  CAT  HAT   single    0.970  0.020  1.090
 ZX6  CAA  HAA   single    0.970  0.020  1.090
 ZX6  CAA  HAAA  single    0.970  0.020  1.090
 ZX6  CAA  HAAB  single    0.970  0.020  1.090
 ZX6  CAV  HAV   single    0.970  0.020  1.090
 ZX6  OAC  HOAC  single    0.850  0.020  0.980
 ZX6  CAX  HAX   single    0.970  0.020  1.090
 ZX6  OAE  HOAE  single    0.850  0.020  0.980
 ZX6  CAW  HAW   single    0.970  0.020  1.090
 ZX6  OAD  HOAD  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
 ZX6  CAQ   CAS  CAR   106.93  3.000
 ZX6  CAQ   CAS  CAI   134.12  3.000
 ZX6  CAR   CAS  CAI   118.94  3.000
 ZX6  HAI   CAI  CAG   120.16  3.000
 ZX6  HAI   CAI  CAS   120.77  3.000
 ZX6  CAG   CAI  CAS   119.07  3.000
 ZX6  HAG   CAG  CAF   119.31  3.000
 ZX6  HAG   CAG  CAI   119.71  3.000
 ZX6  CAF   CAG  CAI   120.98  3.000
 ZX6  HAF   CAF  CAH   119.39  3.000
 ZX6  HAF   CAF  CAG   119.30  3.000
 ZX6  CAH   CAF  CAG   121.31  3.000
 ZX6  HAH   CAH  CAR   121.28  3.000
 ZX6  HAH   CAH  CAF   121.19  3.000
 ZX6  CAR   CAH  CAF   117.52  3.000
 ZX6  NAO   CAR  CAH   130.48  3.000
 ZX6  NAO   CAR  CAS   107.35  3.000
 ZX6  CAH   CAR  CAS   122.17  3.000
 ZX6  HNAO  NAO  CAJ   124.91  3.000
 ZX6  HNAO  NAO  CAR   125.70  3.000
 ZX6  CAJ   NAO  CAR   109.39  3.000
 ZX6  HAJ   CAJ  CAQ   129.28  3.000
 ZX6  HAJ   CAJ  NAO   120.63  3.000
 ZX6  CAQ   CAJ  NAO   110.10  3.000
 ZX6  CAL   CAQ  CAJ   127.02  3.000
 ZX6  CAL   CAQ  CAS   126.67  3.000
 ZX6  CAJ   CAQ  CAS   106.23  3.000
 ZX6  HALA  CAL  HAL   107.13  3.000
 ZX6  HALA  CAL  CAP   111.61  3.000
 ZX6  HAL   CAL  CAP   108.41  3.000
 ZX6  HALA  CAL  CAQ   110.58  3.000
 ZX6  HAL   CAL  CAQ   110.16  3.000
 ZX6  CAP   CAL  CAQ   108.92  3.000
 ZX6  NAM   CAP  OAB   123.72  3.000
 ZX6  NAM   CAP  CAL   114.80  3.000
 ZX6  OAB   CAP  CAL   121.41  3.000
 ZX6  HNAM  NAM  CAK   116.74  3.000
 ZX6  HNAM  NAM  CAP   118.24  3.000
 ZX6  CAK   NAM  CAP   125.00  3.000
 ZX6  HAKA  CAK  HAK   107.79  3.000
 ZX6  HAKA  CAK  CAU   109.76  3.000
 ZX6  HAK   CAK  CAU   109.95  3.000
 ZX6  HAKA  CAK  NAM   108.72  3.000
 ZX6  HAK   CAK  NAM   108.68  3.000
 ZX6  CAU   CAK  NAM   111.83  3.000
 ZX6  HAU   CAU  CAW   107.61  3.000
 ZX6  HAU   CAU  NAN   112.00  3.000
 ZX6  CAW   CAU  NAN   108.71  3.000
 ZX6  HAU   CAU  CAK   108.02  3.000
 ZX6  CAW   CAU  CAK   110.53  3.000
 ZX6  NAN   CAU  CAK   109.95  3.000
 ZX6  HNAN  NAN  CAT   107.99  3.000
 ZX6  HNAN  NAN  CAU   109.09  3.000
 ZX6  CAT   NAN  CAU   113.85  3.000
 ZX6  HAT   CAT  CAV   105.70  3.000
 ZX6  HAT   CAT  CAA   107.49  3.000
 ZX6  CAV   CAT  CAA   112.73  3.000
 ZX6  HAT   CAT  NAN   111.53  3.000
 ZX6  CAV   CAT  NAN   109.45  3.000
 ZX6  CAA   CAT  NAN   109.88  3.000
 ZX6  HAAB  CAA  HAAA  107.40  3.000
 ZX6  HAAB  CAA  HAA   108.43  3.000
 ZX6  HAAA  CAA  HAA   108.34  3.000
 ZX6  HAAB  CAA  CAT   110.52  3.000
 ZX6  HAAA  CAA  CAT   110.63  3.000
 ZX6  HAA   CAA  CAT   111.39  3.000
 ZX6  HAV   CAV  CAX   107.92  3.000
 ZX6  HAV   CAV  OAC   110.66  3.000
 ZX6  CAX   CAV  OAC   111.34  3.000
 ZX6  HAV   CAV  CAT   107.63  3.000
 ZX6  CAX   CAV  CAT   109.27  3.000
 ZX6  OAC   CAV  CAT   109.91  3.000
 ZX6  HOAC  OAC  CAV   107.26  3.000
 ZX6  HAX   CAX  CAW   108.08  3.000
 ZX6  HAX   CAX  OAE   110.60  3.000
 ZX6  CAW   CAX  OAE   107.29  3.000
 ZX6  HAX   CAX  CAV   107.93  3.000
 ZX6  CAW   CAX  CAV   111.63  3.000
 ZX6  OAE   CAX  CAV   111.28  3.000
 ZX6  HOAE  OAE  CAX   108.72  3.000
 ZX6  HAW   CAW  OAD   110.90  3.000
 ZX6  HAW   CAW  CAX   108.72  3.000
 ZX6  OAD   CAW  CAX   111.13  3.000
 ZX6  HAW   CAW  CAU   107.75  3.000
 ZX6  OAD   CAW  CAU   108.43  3.000
 ZX6  CAX   CAW  CAU   109.85  3.000
 ZX6  HOAD  OAD  CAW   107.80  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
 ZX6  CONST_01  CAF   CAG  CAI  CAS     0.00   0.0  0
 ZX6  CONST_02  CAF   CAH  CAR  CAS     0.00   0.0  0
 ZX6  CONST_03  CAJ   NAO  CAR  CAS     0.00   0.0  0
 ZX6  CONST_04  NAO   CAJ  CAQ  CAS     0.00   0.0  0
 ZX6  CONST_05  CAH   CAR  CAS  CAI     0.00   0.0  0
 ZX6  CONST_06  NAO   CAR  CAS  CAI   180.00   0.0  0
 ZX6  CONST_07  CAJ   CAQ  CAS  CAI   180.00   0.0  0
 ZX6  CONST_08  CAH   CAF  CAG  CAI     0.00   0.0  0
 ZX6  CONST_09  CAR   CAS  CAI  CAG     0.00   0.0  0
 ZX6  CONST_10  CAQ   CAS  CAI  CAG   180.00   0.0  0
 ZX6  CONST_11  CAR   CAH  CAF  CAG     0.00   0.0  0
 ZX6  CONST_12  NAO   CAR  CAH  CAF   180.00   0.0  0
 ZX6  CONST_13  CAQ   CAS  CAR  CAH   180.00   0.0  0
 ZX6  CONST_14  CAJ   NAO  CAR  CAH   180.00   0.0  0
 ZX6  CONST_15  CAJ   CAQ  CAS  CAR     0.00   0.0  0
 ZX6  CONST_16  CAQ   CAJ  NAO  CAR     0.00   0.0  0
 ZX6  CONST_17  CAQ   CAS  CAR  NAO     0.00   0.0  0
 ZX6  CONST_18  CAL   CAQ  CAS  CAI     0.00   0.0  0
 ZX6  CONST_19  CAL   CAQ  CAS  CAR   180.00   0.0  0
 ZX6  CONST_20  CAL   CAQ  CAJ  NAO   180.00   0.0  0
 ZX6  CONST_21  HAG   CAG  CAI  CAS   180.00   0.0  0
 ZX6  CONST_22  HAH   CAH  CAR  CAS   180.00   0.0  0
 ZX6  CONST_23  HNAO  NAO  CAR  CAS   180.00   0.0  0
 ZX6  CONST_24  HAJ   CAJ  CAQ  CAS   180.00   0.0  0
 ZX6  CONST_25  HAF   CAF  CAG  CAI   180.00   0.0  0
 ZX6  CONST_26  HAI   CAI  CAG  CAF   180.00   0.0  0
 ZX6  CONST_27  CAK   NAM  CAP  CAL   180.00   0.0  0
 ZX6  CONST_28  CAK   NAM  CAP  OAB     0.00   0.0  0
 ZX6  CONST_29  HNAM  NAM  CAP  CAL     0.00   0.0  0
 ZX6  Var_01    CAP   CAL  CAQ  CAS    74.66  30.0  2
 ZX6  Var_02    OAB   CAP  CAL  CAQ    72.46  30.0  3
 ZX6  Var_03    CAU   CAK  NAM  CAP  -104.17  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
 ZX6  chir_01  CAU  CAK  NAN  CAW  negativ
 ZX6  chir_02  CAT  NAN  CAA  CAV  negativ
 ZX6  chir_03  CAV  OAC  CAT  CAX  positiv
 ZX6  chir_04  CAX  OAE  CAV  CAW  positiv
 ZX6  chir_05  CAW  OAD  CAX  CAU  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
 ZX6  plan-1  CAS   0.020
 ZX6  plan-1  CAI   0.020
 ZX6  plan-1  CAG   0.020
 ZX6  plan-1  CAF   0.020
 ZX6  plan-1  CAH   0.020
 ZX6  plan-1  CAR   0.020
 ZX6  plan-1  NAO   0.020
 ZX6  plan-1  CAJ   0.020
 ZX6  plan-1  CAQ   0.020
 ZX6  plan-1  CAL   0.020
 ZX6  plan-1  HAI   0.020
 ZX6  plan-1  HAG   0.020
 ZX6  plan-1  HAF   0.020
 ZX6  plan-1  HAH   0.020
 ZX6  plan-1  HNAO  0.020
 ZX6  plan-1  HAJ   0.020
 ZX6  plan-2  CAL   0.020
 ZX6  plan-2  CAP   0.020
 ZX6  plan-2  OAB   0.020
 ZX6  plan-2  NAM   0.020
 ZX6  plan-2  CAK   0.020
 ZX6  plan-2  HNAM  0.020

