# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul 10 02:43:48 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)CCc2c[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
 ZX5  ZX5  3-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}propanamide  ligand  50  25  .  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_ZX5
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
 ZX5  CAT   C  CR56  0   0.028   4.8091  -0.0273  -0.0404
 ZX5  CAI   C  CR16  0  -0.376   4.8914  -1.3378   0.4447
 ZX5  CAG   C  CR16  0  -0.269   5.9761  -1.6983   1.2203
 ZX5  CAF   C  CR16  0  -0.285   6.9877  -0.7718   1.5256
 ZX5  CAH   C  CR16  0  -0.306   6.9348   0.5283   1.0603
 ZX5  CAS   C  CR56  0   0.354   5.8384   0.8875   0.2770
 ZX5  NAP   N  NR15  0  -0.687   5.5241   2.0732  -0.3174
 ZX5  CAJ   C  CR15  0  -0.089   4.3426   1.9400  -0.9944
 ZX5  CAR   C  CR5   0   0.013   3.8600   0.6693  -0.8582
 ZX5  CAL   C  CH2   0  -0.529   2.5797   0.1231  -1.3996
 ZX5  CAK   C  CH2   0  -0.583   1.5048   0.0402  -0.3185
 ZX5  CAQ   C  C     0   0.555   0.1896  -0.5312  -0.8097
 ZX5  OAB   O  O     0  -0.498  -0.1130  -0.5580  -1.9940
 ZX5  NAN   N  NH1   0  -0.648  -0.6170  -0.9774   0.1728
 ZX5  CAM   C  CH2   0  -0.276  -1.9468  -1.5104  -0.0160
 ZX5  CAV   C  CH1   0  -0.115  -3.0218  -0.5925   0.5631
 ZX5  NAO   N  NH1   0  -0.609  -2.9934   0.6857  -0.1203
 ZX5  CAU   C  CH1   0  -0.094  -3.9280   1.6579   0.4236
 ZX5  CAA   C  CH3   0  -0.673  -3.7268   3.0054  -0.2491
 ZX5  CAW   C  CH1   0   0.042  -5.3519   1.1350   0.2725
 ZX5  OAC   O  OH1   0  -0.672  -5.7017   1.0769  -1.0886
 ZX5  CAY   C  CH1   0  -0.036  -5.4576  -0.2386   0.9337
 ZX5  OAE   O  OH1   0  -0.676  -6.7268  -0.8233   0.7087
 ZX5  CAX   C  CH1   0   0.086  -4.4100  -1.2029   0.3908
 ZX5  OAD   O  OH1   0  -0.680  -4.4472  -2.4315   1.0793
 ZX5  HAI   H  HCR6  0   0.238   4.1187  -2.0618   0.2145
 ZX5  HAG   H  HCR6  0   0.245   6.0518  -2.7087   1.6015
 ZX5  HAF   H  HCR6  0   0.248   7.8260  -1.0829   2.1357
 ZX5  HAH   H  HCR6  0   0.257   7.7150   1.2411   1.2966
 ZX5  HNAP  H  HNR5  0   0.407   6.0675   2.9181  -0.2656
 ZX5  HAJ   H  HCR5  0   0.279   3.9239   2.7755  -1.5340
 ZX5  HAL   H  HCH2  0   0.248   2.2283   0.7509  -2.2198
 ZX5  HALA  H  HCH2  0   0.238   2.7507  -0.8703  -1.8238
 ZX5  HAK   H  HCH2  0   0.262   1.8660  -0.5421   0.5335
 ZX5  HAKA  H  HCH2  0   0.276   1.3068   1.0444   0.0707
 ZX5  HNAN  H  HNH1  0   0.399  -0.2694  -0.9439   1.1185
 ZX5  HAM   H  HCH2  0   0.243  -2.1177  -1.6432  -1.0840
 ZX5  HAMA  H  HCH2  0   0.256  -2.0058  -2.4915   0.4553
 ZX5  HAV   H  HCH1  0   0.201  -2.8401  -0.4840   1.6495
 ZX5  HNAO  H  HNH1  0   0.353  -2.0579   1.0679  -0.0575
 ZX5  HAU   H  HCH1  0   0.205  -3.7749   1.7966   1.5089
 ZX5  HAA   H  HCH3  0   0.229  -3.8711   2.9384  -1.3267
 ZX5  HAAA  H  HCH3  0   0.228  -4.4260   3.7429   0.1465
 ZX5  HAAB  H  HCH3  0   0.231  -2.7180   3.3791  -0.0645
 ZX5  HAW   H  HCH1  0   0.209  -6.0164   1.8258   0.8164
 ZX5  HOAC  H  HOH1  0   0.444  -6.5240   0.5781  -1.1494
 ZX5  HAY   H  HCH1  0   0.217  -5.2733  -0.1097   2.0104
 ZX5  HOAE  H  HOH1  0   0.460  -7.3630  -0.4258   1.3117
 ZX5  HAX   H  HCH1  0   0.201  -4.5846  -1.3495  -0.6861
 ZX5  HOAD  H  HOH1  0   0.450  -5.3462  -2.7716   1.0246

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
 ZX5  CAT  CAI   aromatic  1.400  0.020  1.400
 ZX5  CAT  CAS   aromatic  1.413  0.020  1.413
 ZX5  CAT  CAR   aromatic  1.434  0.020  1.434
 ZX5  CAI  CAG   aromatic  1.381  0.020  1.381
 ZX5  CAG  CAF   aromatic  1.405  0.020  1.405
 ZX5  CAF  CAH   aromatic  1.382  0.020  1.382
 ZX5  CAH  CAS   aromatic  1.395  0.020  1.395
 ZX5  CAS  NAP   aromatic  1.363  0.020  1.363
 ZX5  NAP  CAJ   aromatic  1.368  0.020  1.368
 ZX5  CAJ  CAR   aromatic  1.366  0.020  1.366
 ZX5  CAR  CAL   single    1.493  0.020  1.493
 ZX5  CAL  CAK   single    1.527  0.020  1.527
 ZX5  CAK  CAQ   single    1.516  0.020  1.516
 ZX5  CAQ  OAB   double    1.223  0.020  1.223
 ZX5  CAQ  NAN   single    1.347  0.020  1.347
 ZX5  NAN  CAM   single    1.445  0.020  1.445
 ZX5  CAM  CAV   single    1.528  0.020  1.528
 ZX5  CAV  NAO   single    1.450  0.020  1.450
 ZX5  CAV  CAX   single    1.526  0.020  1.526
 ZX5  NAO  CAU   single    1.454  0.020  1.454
 ZX5  CAU  CAA   single    1.519  0.020  1.519
 ZX5  CAU  CAW   single    1.524  0.020  1.524
 ZX5  CAW  OAC   single    1.407  0.020  1.407
 ZX5  CAW  CAY   single    1.528  0.020  1.528
 ZX5  CAY  OAE   single    1.415  0.020  1.415
 ZX5  CAY  CAX   single    1.524  0.020  1.524
 ZX5  CAX  OAD   single    1.409  0.020  1.409
 ZX5  CAI  HAI   single    0.930  0.020  1.080
 ZX5  CAG  HAG   single    0.930  0.020  1.080
 ZX5  CAF  HAF   single    0.930  0.020  1.080
 ZX5  CAH  HAH   single    0.930  0.020  1.080
 ZX5  NAP  HNAP  single    0.860  0.020  1.020
 ZX5  CAJ  HAJ   single    0.930  0.020  1.080
 ZX5  CAL  HAL   single    0.970  0.020  1.090
 ZX5  CAL  HALA  single    0.970  0.020  1.090
 ZX5  CAK  HAK   single    0.970  0.020  1.090
 ZX5  CAK  HAKA  single    0.970  0.020  1.090
 ZX5  NAN  HNAN  single    0.860  0.020  1.020
 ZX5  CAM  HAM   single    0.970  0.020  1.090
 ZX5  CAM  HAMA  single    0.970  0.020  1.090
 ZX5  CAV  HAV   single    0.970  0.020  1.090
 ZX5  NAO  HNAO  single    0.890  0.020  1.040
 ZX5  CAU  HAU   single    0.970  0.020  1.090
 ZX5  CAA  HAA   single    0.970  0.020  1.090
 ZX5  CAA  HAAA  single    0.970  0.020  1.090
 ZX5  CAA  HAAB  single    0.970  0.020  1.090
 ZX5  CAW  HAW   single    0.970  0.020  1.090
 ZX5  OAC  HOAC  single    0.850  0.020  0.980
 ZX5  CAY  HAY   single    0.970  0.020  1.090
 ZX5  OAE  HOAE  single    0.850  0.020  0.980
 ZX5  CAX  HAX   single    0.970  0.020  1.090
 ZX5  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
 ZX5  CAR   CAT  CAS   107.21  3.000
 ZX5  CAR   CAT  CAI   133.75  3.000
 ZX5  CAS   CAT  CAI   119.04  3.000
 ZX5  HAI   CAI  CAG   120.32  3.000
 ZX5  HAI   CAI  CAT   120.66  3.000
 ZX5  CAG   CAI  CAT   119.02  3.000
 ZX5  HAG   CAG  CAF   119.25  3.000
 ZX5  HAG   CAG  CAI   119.75  3.000
 ZX5  CAF   CAG  CAI   121.00  3.000
 ZX5  HAF   CAF  CAH   119.33  3.000
 ZX5  HAF   CAF  CAG   119.36  3.000
 ZX5  CAH   CAF  CAG   121.31  3.000
 ZX5  HAH   CAH  CAS   121.29  3.000
 ZX5  HAH   CAH  CAF   121.22  3.000
 ZX5  CAS   CAH  CAF   117.49  3.000
 ZX5  NAP   CAS  CAH   130.57  3.000
 ZX5  NAP   CAS  CAT   107.29  3.000
 ZX5  CAH   CAS  CAT   122.14  3.000
 ZX5  HNAP  NAP  CAJ   125.02  3.000
 ZX5  HNAP  NAP  CAS   125.70  3.000
 ZX5  CAJ   NAP  CAS   109.28  3.000
 ZX5  HAJ   CAJ  CAR   129.27  3.000
 ZX5  HAJ   CAJ  NAP   120.47  3.000
 ZX5  CAR   CAJ  NAP   110.27  3.000
 ZX5  CAL   CAR  CAJ   127.37  3.000
 ZX5  CAL   CAR  CAT   126.63  3.000
 ZX5  CAJ   CAR  CAT   105.96  3.000
 ZX5  HALA  CAL  HAL   106.35  3.000
 ZX5  HALA  CAL  CAK   109.60  3.000
 ZX5  HAL   CAL  CAK   109.68  3.000
 ZX5  HALA  CAL  CAR   109.80  3.000
 ZX5  HAL   CAL  CAR   109.77  3.000
 ZX5  CAK   CAL  CAR   111.52  3.000
 ZX5  HAKA  CAK  HAK   105.73  3.000
 ZX5  HAKA  CAK  CAQ   107.70  3.000
 ZX5  HAK   CAK  CAQ   109.78  3.000
 ZX5  HAKA  CAK  CAL   109.22  3.000
 ZX5  HAK   CAK  CAL   110.37  3.000
 ZX5  CAQ   CAK  CAL   113.70  3.000
 ZX5  NAN   CAQ  OAB   123.43  3.000
 ZX5  NAN   CAQ  CAK   114.09  3.000
 ZX5  OAB   CAQ  CAK   122.48  3.000
 ZX5  HNAN  NAN  CAM   116.88  3.000
 ZX5  HNAN  NAN  CAQ   117.81  3.000
 ZX5  CAM   NAN  CAQ   125.30  3.000
 ZX5  HAMA  CAM  HAM   107.79  3.000
 ZX5  HAMA  CAM  CAV   109.80  3.000
 ZX5  HAM   CAM  CAV   109.53  3.000
 ZX5  HAMA  CAM  NAN   108.99  3.000
 ZX5  HAM   CAM  NAN   108.51  3.000
 ZX5  CAV   CAM  NAN   112.11  3.000
 ZX5  HAV   CAV  CAX   107.42  3.000
 ZX5  HAV   CAV  NAO   111.90  3.000
 ZX5  CAX   CAV  NAO   108.49  3.000
 ZX5  HAV   CAV  CAM   108.39  3.000
 ZX5  CAX   CAV  CAM   110.91  3.000
 ZX5  NAO   CAV  CAM   109.71  3.000
 ZX5  HNAO  NAO  CAU   108.56  3.000
 ZX5  HNAO  NAO  CAV   108.76  3.000
 ZX5  CAU   NAO  CAV   113.61  3.000
 ZX5  HAU   CAU  CAW   105.66  3.000
 ZX5  HAU   CAU  CAA   107.77  3.000
 ZX5  CAW   CAU  CAA   112.58  3.000
 ZX5  HAU   CAU  NAO   111.24  3.000
 ZX5  CAW   CAU  NAO   109.51  3.000
 ZX5  CAA   CAU  NAO   110.01  3.000
 ZX5  HAAB  CAA  HAAA  107.44  3.000
 ZX5  HAAB  CAA  HAA   108.11  3.000
 ZX5  HAAA  CAA  HAA   108.39  3.000
 ZX5  HAAB  CAA  CAU   110.56  3.000
 ZX5  HAAA  CAA  CAU   110.75  3.000
 ZX5  HAA   CAA  CAU   111.46  3.000
 ZX5  HAW   CAW  CAY   107.95  3.000
 ZX5  HAW   CAW  OAC   110.70  3.000
 ZX5  CAY   CAW  OAC   111.37  3.000
 ZX5  HAW   CAW  CAU   107.42  3.000
 ZX5  CAY   CAW  CAU   109.27  3.000
 ZX5  OAC   CAW  CAU   110.02  3.000
 ZX5  HOAC  OAC  CAW   107.13  3.000
 ZX5  HAY   CAY  CAX   107.92  3.000
 ZX5  HAY   CAY  OAE   110.75  3.000
 ZX5  CAX   CAY  OAE   107.37  3.000
 ZX5  HAY   CAY  CAW   107.85  3.000
 ZX5  CAX   CAY  CAW   111.53  3.000
 ZX5  OAE   CAY  CAW   111.38  3.000
 ZX5  HOAE  OAE  CAY   108.82  3.000
 ZX5  HAX   CAX  OAD   110.96  3.000
 ZX5  HAX   CAX  CAY   108.89  3.000
 ZX5  OAD   CAX  CAY   111.07  3.000
 ZX5  HAX   CAX  CAV   107.94  3.000
 ZX5  OAD   CAX  CAV   108.52  3.000
 ZX5  CAY   CAX  CAV   109.39  3.000
 ZX5  HOAD  OAD  CAX   107.75  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
 ZX5  CONST_01  CAF   CAG  CAI  CAT     0.00   0.0  0
 ZX5  CONST_02  CAF   CAH  CAS  CAT     0.00   0.0  0
 ZX5  CONST_03  CAJ   NAP  CAS  CAT     0.00   0.0  0
 ZX5  CONST_04  NAP   CAJ  CAR  CAT     0.00   0.0  0
 ZX5  CONST_05  CAH   CAS  CAT  CAI     0.00   0.0  0
 ZX5  CONST_06  NAP   CAS  CAT  CAI   180.00   0.0  0
 ZX5  CONST_07  CAJ   CAR  CAT  CAI   180.00   0.0  0
 ZX5  CONST_08  CAH   CAF  CAG  CAI     0.00   0.0  0
 ZX5  CONST_09  CAS   CAT  CAI  CAG     0.00   0.0  0
 ZX5  CONST_10  CAR   CAT  CAI  CAG   180.00   0.0  0
 ZX5  CONST_11  CAS   CAH  CAF  CAG     0.00   0.0  0
 ZX5  CONST_12  NAP   CAS  CAH  CAF   180.00   0.0  0
 ZX5  CONST_13  CAR   CAT  CAS  CAH   180.00   0.0  0
 ZX5  CONST_14  CAJ   NAP  CAS  CAH   180.00   0.0  0
 ZX5  CONST_15  CAJ   CAR  CAT  CAS     0.00   0.0  0
 ZX5  CONST_16  CAR   CAJ  NAP  CAS     0.00   0.0  0
 ZX5  CONST_17  CAR   CAT  CAS  NAP     0.00   0.0  0
 ZX5  CONST_18  CAL   CAR  CAT  CAI     0.00   0.0  0
 ZX5  CONST_19  CAL   CAR  CAT  CAS   180.00   0.0  0
 ZX5  CONST_20  CAL   CAR  CAJ  NAP   180.00   0.0  0
 ZX5  CONST_21  HAG   CAG  CAI  CAT   180.00   0.0  0
 ZX5  CONST_22  HAH   CAH  CAS  CAT   180.00   0.0  0
 ZX5  CONST_23  HNAP  NAP  CAS  CAT   180.00   0.0  0
 ZX5  CONST_24  HAJ   CAJ  CAR  CAT   180.00   0.0  0
 ZX5  CONST_25  HAF   CAF  CAG  CAI   180.00   0.0  0
 ZX5  CONST_26  HAI   CAI  CAG  CAF   180.00   0.0  0
 ZX5  CONST_27  CAM   NAN  CAQ  CAK   180.00   0.0  0
 ZX5  CONST_28  CAM   NAN  CAQ  OAB     0.00   0.0  0
 ZX5  CONST_29  HNAN  NAN  CAQ  CAK     0.00   0.0  0
 ZX5  Var_01    CAK   CAL  CAR  CAT    75.81  30.0  2
 ZX5  Var_02    CAQ   CAK  CAL  CAR  -179.00  30.0  3
 ZX5  Var_03    CAV   CAM  NAN  CAQ  -111.84  30.0  3
 ZX5  Var_04    OAB   CAQ  CAK  CAL   -19.94  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
 ZX5  chir_01  CAV  CAM  NAO  CAX  negativ
 ZX5  chir_02  CAU  NAO  CAA  CAW  negativ
 ZX5  chir_03  CAW  OAC  CAU  CAY  positiv
 ZX5  chir_04  CAY  OAE  CAW  CAX  positiv
 ZX5  chir_05  CAX  OAD  CAY  CAV  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
 ZX5  plan-1  CAT   0.020
 ZX5  plan-1  CAI   0.020
 ZX5  plan-1  CAG   0.020
 ZX5  plan-1  CAF   0.020
 ZX5  plan-1  CAH   0.020
 ZX5  plan-1  CAS   0.020
 ZX5  plan-1  NAP   0.020
 ZX5  plan-1  CAJ   0.020
 ZX5  plan-1  CAR   0.020
 ZX5  plan-1  CAL   0.020
 ZX5  plan-1  HAI   0.020
 ZX5  plan-1  HAG   0.020
 ZX5  plan-1  HAF   0.020
 ZX5  plan-1  HAH   0.020
 ZX5  plan-1  HNAP  0.020
 ZX5  plan-1  HAJ   0.020
 ZX5  plan-2  CAK   0.020
 ZX5  plan-2  CAQ   0.020
 ZX5  plan-2  OAB   0.020
 ZX5  plan-2  NAN   0.020
 ZX5  plan-2  CAM   0.020
 ZX5  plan-2  HNAN  0.020

