# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 18:59:22 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2S)-2-cyclopentyl-2-phenyl-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)[C@@H](C2CCCC2)c3ccccc3)[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
 ZX9  ZX9  (2S)-2-cyclopentyl-2-phenyl-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}ethanamide  ligand  56  26  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZX9
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
 ZX9  CAI   C  CR16  0  -0.324  -1.9492   0.0830  -2.2608
 ZX9  CAG   C  CR16  0  -0.239  -1.9888   1.3350  -2.8619
 ZX9  CAF   C  CR16  0  -0.268  -2.1022   2.4775  -2.0830
 ZX9  CAH   C  CR16  0  -0.238  -2.1756   2.3578  -0.7004
 ZX9  CAJ   C  CR16  0  -0.295  -2.1330   1.1067  -0.1027
 ZX9  CAS   C  CR6   0   0.168  -2.0236  -0.0478  -0.8775
 ZX9  CAZ   C  CH1   0  -0.492  -1.9652  -1.4166  -0.2315
 ZX9  CAX   C  CR15  0  -0.203  -3.1946  -1.7320   0.6138
 ZX9  CAM   C  CH2   0  -0.438  -3.1777  -3.1463   1.2183
 ZX9  CAK   C  CH2   0  -0.444  -4.6563  -3.5775   1.3391
 ZX9  CAL   C  CH2   0  -0.448  -5.4794  -2.4275   0.7338
 ZX9  CAN   C  CH2   0  -0.422  -4.5002  -1.6987  -0.1800
 ZX9  CAR   C  C     0   0.575  -0.6707  -1.4801   0.5727
 ZX9  OAB   O  O     0  -0.485  -0.6189  -1.1783   1.7554
 ZX9  NAP   N  NH1   0  -0.640   0.4032  -1.8382  -0.1545
 ZX9  CAO   C  CH2   0  -0.277   1.7717  -1.7719   0.3027
 ZX9  CAY   C  CH1   0  -0.116   2.5351  -0.6287  -0.3674
 ZX9  NAQ   N  NH1   0  -0.610   1.8773   0.6348  -0.0961
 ZX9  CAT   C  CH1   0  -0.094   2.4956   1.7665  -0.7686
 ZX9  CAA   C  CH3   0  -0.679   1.6599   3.0169  -0.5528
 ZX9  CAU   C  CH1   0   0.039   3.9294   1.9304  -0.2782
 ZX9  OAC   O  OH1   0  -0.672   3.9313   2.3133   1.0753
 ZX9  CAV   C  CH1   0  -0.034   4.6886   0.6210  -0.4879
 ZX9  OAD   O  OH1   0  -0.676   5.9857   0.6807   0.0761
 ZX9  CAW   C  CH1   0   0.086   3.9654  -0.5525   0.1603
 ZX9  OAE   O  OH1   0  -0.681   4.6121  -1.7707  -0.1265
 ZX9  HAI   H  HCR6  0   0.251  -1.8675  -0.8037  -2.8786
 ZX9  HAG   H  HCR6  0   0.255  -1.9337   1.4151  -3.9399
 ZX9  HAF   H  HCR6  0   0.255  -2.1348   3.4543  -2.5481
 ZX9  HAH   H  HCR6  0   0.255  -2.2614   3.2429  -0.0830
 ZX9  HAJ   H  HCR6  0   0.251  -2.1874   1.0310   0.9761
 ZX9  HAZ   H  HCH1  0   0.268  -1.9129  -2.1620  -1.0335
 ZX9  HAX   H  HCR5  0   0.234  -3.2701  -0.9998   1.4242
 ZX9  HAM   H  HCH2  0   0.222  -2.6382  -3.8264   0.5529
 ZX9  HAMA  H  HCH2  0   0.235  -2.6562  -3.1683   2.1749
 ZX9  HAK   H  HCH2  0   0.225  -4.8296  -4.5034   0.7884
 ZX9  HAKA  H  HCH2  0   0.228  -4.9422  -3.7730   2.3731
 ZX9  HAL   H  HCH2  0   0.229  -6.3716  -2.7769   0.2122
 ZX9  HALA  H  HCH2  0   0.219  -5.8171  -1.7504   1.5227
 ZX9  HAN   H  HCH2  0   0.235  -4.8198  -0.6876  -0.4375
 ZX9  HANA  H  HCH2  0   0.211  -4.3776  -2.2491  -1.1200
 ZX9  HNAP  H  HNH1  0   0.399   0.2564  -2.0915  -1.1192
 ZX9  HAO   H  HCH2  0   0.245   1.7706  -1.6340   1.3835
 ZX9  HAOA  H  HCH2  0   0.258   2.2632  -2.7204   0.0869
 ZX9  HAY   H  HCH1  0   0.203   2.5881  -0.8396  -1.4522
 ZX9  HNAQ  H  HNH1  0   0.350   0.9085   0.5781  -0.3879
 ZX9  HAT   H  HCH1  0   0.205   2.5709   1.5930  -1.8572
 ZX9  HAA   H  HCH3  0   0.228   1.5567   3.2462   0.5070
 ZX9  HAAA  H  HCH3  0   0.228   2.1121   3.8753  -1.0502
 ZX9  HAAB  H  HCH3  0   0.237   0.6584   2.8848  -0.9668
 ZX9  HAU   H  HCH1  0   0.210   4.4059   2.7039  -0.9021
 ZX9  HOAC  H  HOH1  0   0.444   4.8423   2.2617   1.3849
 ZX9  HAV   H  HCH1  0   0.217   4.7435   0.4300  -1.5695
 ZX9  HOAD  H  HOH1  0   0.460   6.5619   1.1657  -0.5228
 ZX9  HAW   H  HCH1  0   0.201   3.9150  -0.3794   1.2461
 ZX9  HOAE  H  HOH1  0   0.450   5.5315  -1.6880   0.1474

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
 ZX9  CAI  CAG   aromatic  1.389  0.020  1.389
 ZX9  CAI  CAS   aromatic  1.392  0.020  1.392
 ZX9  CAG  CAF   aromatic  1.387  0.020  1.387
 ZX9  CAF  CAH   aromatic  1.390  0.020  1.390
 ZX9  CAH  CAJ   aromatic  1.387  0.020  1.387
 ZX9  CAJ  CAS   aromatic  1.395  0.020  1.395
 ZX9  CAS  CAZ   single    1.515  0.020  1.515
 ZX9  CAZ  CAX   single    1.525  0.020  1.525
 ZX9  CAZ  CAR   single    1.525  0.020  1.525
 ZX9  CAX  CAM   single    1.538  0.020  1.538
 ZX9  CAX  CAN   single    1.528  0.020  1.528
 ZX9  CAM  CAK   single    1.545  0.020  1.545
 ZX9  CAK  CAL   single    1.538  0.020  1.538
 ZX9  CAL  CAN   single    1.525  0.020  1.525
 ZX9  CAR  OAB   double    1.222  0.020  1.222
 ZX9  CAR  NAP   single    1.346  0.020  1.346
 ZX9  NAP  CAO   single    1.444  0.020  1.444
 ZX9  CAO  CAY   single    1.529  0.020  1.529
 ZX9  CAY  NAQ   single    1.450  0.020  1.450
 ZX9  CAY  CAW   single    1.526  0.020  1.526
 ZX9  NAQ  CAT   single    1.454  0.020  1.454
 ZX9  CAT  CAA   single    1.519  0.020  1.519
 ZX9  CAT  CAU   single    1.524  0.020  1.524
 ZX9  CAU  OAC   single    1.407  0.020  1.407
 ZX9  CAU  CAV   single    1.528  0.020  1.528
 ZX9  CAV  OAD   single    1.416  0.020  1.416
 ZX9  CAV  CAW   single    1.523  0.020  1.523
 ZX9  CAW  OAE   single    1.409  0.020  1.409
 ZX9  CAI  HAI   single    0.930  0.020  1.080
 ZX9  CAG  HAG   single    0.930  0.020  1.080
 ZX9  CAF  HAF   single    0.930  0.020  1.080
 ZX9  CAH  HAH   single    0.930  0.020  1.080
 ZX9  CAJ  HAJ   single    0.930  0.020  1.080
 ZX9  CAZ  HAZ   single    0.970  0.020  1.090
 ZX9  CAX  HAX   single    0.970  0.020  1.090
 ZX9  CAM  HAM   single    0.970  0.020  1.090
 ZX9  CAM  HAMA  single    0.970  0.020  1.090
 ZX9  CAK  HAK   single    0.970  0.020  1.090
 ZX9  CAK  HAKA  single    0.970  0.020  1.090
 ZX9  CAL  HAL   single    0.970  0.020  1.090
 ZX9  CAL  HALA  single    0.970  0.020  1.090
 ZX9  CAN  HAN   single    0.970  0.020  1.090
 ZX9  CAN  HANA  single    0.970  0.020  1.090
 ZX9  NAP  HNAP  single    0.860  0.020  1.020
 ZX9  CAO  HAO   single    0.970  0.020  1.090
 ZX9  CAO  HAOA  single    0.970  0.020  1.090
 ZX9  CAY  HAY   single    0.970  0.020  1.090
 ZX9  NAQ  HNAQ  single    0.890  0.020  1.040
 ZX9  CAT  HAT   single    0.970  0.020  1.090
 ZX9  CAA  HAA   single    0.970  0.020  1.090
 ZX9  CAA  HAAA  single    0.970  0.020  1.090
 ZX9  CAA  HAAB  single    0.970  0.020  1.090
 ZX9  CAU  HAU   single    0.970  0.020  1.090
 ZX9  OAC  HOAC  single    0.850  0.020  0.980
 ZX9  CAV  HAV   single    0.970  0.020  1.090
 ZX9  OAD  HOAD  single    0.850  0.020  0.980
 ZX9  CAW  HAW   single    0.970  0.020  1.090
 ZX9  OAE  HOAE  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
 ZX9  HAI   CAI  CAS   119.59  3.000
 ZX9  HAI   CAI  CAG   119.53  3.000
 ZX9  CAS   CAI  CAG   120.88  3.000
 ZX9  HAG   CAG  CAF   120.16  3.000
 ZX9  HAG   CAG  CAI   119.74  3.000
 ZX9  CAF   CAG  CAI   120.10  3.000
 ZX9  HAF   CAF  CAH   120.24  3.000
 ZX9  HAF   CAF  CAG   120.29  3.000
 ZX9  CAH   CAF  CAG   119.47  3.000
 ZX9  HAH   CAH  CAJ   119.61  3.000
 ZX9  HAH   CAH  CAF   120.08  3.000
 ZX9  CAJ   CAH  CAF   120.31  3.000
 ZX9  HAJ   CAJ  CAS   119.97  3.000
 ZX9  HAJ   CAJ  CAH   119.39  3.000
 ZX9  CAS   CAJ  CAH   120.64  3.000
 ZX9  CAZ   CAS  CAJ   120.94  3.000
 ZX9  CAZ   CAS  CAI   120.45  3.000
 ZX9  CAJ   CAS  CAI   118.60  3.000
 ZX9  HAZ   CAZ  CAR   108.48  3.000
 ZX9  HAZ   CAZ  CAX   107.66  3.000
 ZX9  CAR   CAZ  CAX   112.54  3.000
 ZX9  HAZ   CAZ  CAS   107.71  3.000
 ZX9  CAR   CAZ  CAS   107.17  3.000
 ZX9  CAX   CAZ  CAS   113.09  3.000
 ZX9  HAX   CAX  CAN   108.12  3.000
 ZX9  HAX   CAX  CAM   108.96  3.000
 ZX9  CAN   CAX  CAM   103.51  3.000
 ZX9  HAX   CAX  CAZ   109.12  3.000
 ZX9  CAN   CAX  CAZ   113.35  3.000
 ZX9  CAM   CAX  CAZ   113.53  3.000
 ZX9  HAMA  CAM  HAM   106.58  3.000
 ZX9  HAMA  CAM  CAK   112.57  3.000
 ZX9  HAM   CAM  CAK   110.25  3.000
 ZX9  HAMA  CAM  CAX   111.64  3.000
 ZX9  HAM   CAM  CAX   109.76  3.000
 ZX9  CAK   CAM  CAX   106.07  3.000
 ZX9  HAKA  CAK  HAK   106.55  3.000
 ZX9  HAKA  CAK  CAL   111.52  3.000
 ZX9  HAK   CAK  CAL   110.54  3.000
 ZX9  HAKA  CAK  CAM   112.03  3.000
 ZX9  HAK   CAK  CAM   110.45  3.000
 ZX9  CAL   CAK  CAM   105.82  3.000
 ZX9  HALA  CAL  HAL   106.91  3.000
 ZX9  HALA  CAL  CAN   109.57  3.000
 ZX9  HAL   CAL  CAN   113.06  3.000
 ZX9  HALA  CAL  CAK   110.15  3.000
 ZX9  HAL   CAL  CAK   112.72  3.000
 ZX9  CAN   CAL  CAK   104.45  3.000
 ZX9  HANA  CAN  HAN   107.19  3.000
 ZX9  HANA  CAN  CAL   110.23  3.000
 ZX9  HAN   CAN  CAL   113.34  3.000
 ZX9  HANA  CAN  CAX   109.81  3.000
 ZX9  HAN   CAN  CAX   113.15  3.000
 ZX9  CAL   CAN  CAX   103.11  3.000
 ZX9  NAP   CAR  OAB   123.72  3.000
 ZX9  NAP   CAR  CAZ   113.80  3.000
 ZX9  OAB   CAR  CAZ   122.42  3.000
 ZX9  HNAP  NAP  CAO   116.90  3.000
 ZX9  HNAP  NAP  CAR   117.89  3.000
 ZX9  CAO   NAP  CAR   124.95  3.000
 ZX9  HAOA  CAO  HAO   107.88  3.000
 ZX9  HAOA  CAO  CAY   109.80  3.000
 ZX9  HAO   CAO  CAY   109.90  3.000
 ZX9  HAOA  CAO  NAP   108.95  3.000
 ZX9  HAO   CAO  NAP   108.60  3.000
 ZX9  CAY   CAO  NAP   111.63  3.000
 ZX9  HAY   CAY  CAW   107.67  3.000
 ZX9  HAY   CAY  NAQ   111.79  3.000
 ZX9  CAW   CAY  NAQ   108.48  3.000
 ZX9  HAY   CAY  CAO   108.12  3.000
 ZX9  CAW   CAY  CAO   110.71  3.000
 ZX9  NAQ   CAY  CAO   110.05  3.000
 ZX9  HNAQ  NAQ  CAT   108.47  3.000
 ZX9  HNAQ  NAQ  CAY   109.33  3.000
 ZX9  CAT   NAQ  CAY   113.50  3.000
 ZX9  HAT   CAT  CAU   105.65  3.000
 ZX9  HAT   CAT  CAA   107.86  3.000
 ZX9  CAU   CAT  CAA   112.54  3.000
 ZX9  HAT   CAT  NAQ   111.24  3.000
 ZX9  CAU   CAT  NAQ   109.56  3.000
 ZX9  CAA   CAT  NAQ   109.93  3.000
 ZX9  HAAB  CAA  HAAA  107.62  3.000
 ZX9  HAAB  CAA  HAA   107.91  3.000
 ZX9  HAAA  CAA  HAA   108.51  3.000
 ZX9  HAAB  CAA  CAT   110.56  3.000
 ZX9  HAAA  CAA  CAT   110.79  3.000
 ZX9  HAA   CAA  CAT   111.32  3.000
 ZX9  HAU   CAU  CAV   107.99  3.000
 ZX9  HAU   CAU  OAC   110.68  3.000
 ZX9  CAV   CAU  OAC   111.38  3.000
 ZX9  HAU   CAU  CAT   107.46  3.000
 ZX9  CAV   CAU  CAT   109.34  3.000
 ZX9  OAC   CAU  CAT   109.89  3.000
 ZX9  HOAC  OAC  CAU   107.21  3.000
 ZX9  HAV   CAV  CAW   107.96  3.000
 ZX9  HAV   CAV  OAD   110.70  3.000
 ZX9  CAW   CAV  OAD   107.34  3.000
 ZX9  HAV   CAV  CAU   107.97  3.000
 ZX9  CAW   CAV  CAU   111.46  3.000
 ZX9  OAD   CAV  CAU   111.37  3.000
 ZX9  HOAD  OAD  CAV   108.79  3.000
 ZX9  HAW   CAW  OAE   110.97  3.000
 ZX9  HAW   CAW  CAV   108.69  3.000
 ZX9  OAE   CAW  CAV   111.20  3.000
 ZX9  HAW   CAW  CAY   107.81  3.000
 ZX9  OAE   CAW  CAY   108.46  3.000
 ZX9  CAV   CAW  CAY   109.65  3.000
 ZX9  HOAE  OAE  CAW   107.82  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
 ZX9  CONST_01  CAH   CAF  CAG  CAI     0.00   0.0  0
 ZX9  CONST_02  CAH   CAJ  CAS  CAI     0.00   0.0  0
 ZX9  CONST_03  CAJ   CAS  CAI  CAG     0.00   0.0  0
 ZX9  CONST_04  CAJ   CAH  CAF  CAG     0.00   0.0  0
 ZX9  CONST_05  CAS   CAI  CAG  CAF     0.00   0.0  0
 ZX9  CONST_06  CAS   CAJ  CAH  CAF     0.00   0.0  0
 ZX9  CONST_07  CAZ   CAS  CAI  CAG   180.00   0.0  0
 ZX9  CONST_08  CAZ   CAS  CAJ  CAH   180.00   0.0  0
 ZX9  CONST_09  HAF   CAF  CAG  CAI   180.00   0.0  0
 ZX9  CONST_10  HAJ   CAJ  CAS  CAI   180.00   0.0  0
 ZX9  CONST_11  HAH   CAH  CAF  CAG   180.00   0.0  0
 ZX9  CONST_12  HAI   CAI  CAG  CAF   180.00   0.0  0
 ZX9  CONST_13  HAG   CAG  CAF  CAH   180.00   0.0  0
 ZX9  CONST_14  CAO   NAP  CAR  CAZ   180.00   0.0  0
 ZX9  CONST_15  CAO   NAP  CAR  OAB     0.00   0.0  0
 ZX9  CONST_16  HNAP  NAP  CAR  CAZ     0.00   0.0  0
 ZX9  Var_01    CAL   CAK  CAM  CAX     2.81  30.0  1
 ZX9  Var_02    CAK   CAL  CAN  CAX   -38.86  30.0  1
 ZX9  Var_03    CAN   CAL  CAK  CAM    22.15  30.0  1
 ZX9  Var_04    CAY   CAO  NAP  CAR  -107.19  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
 ZX9  chir_01  CAZ  CAS  CAX  CAR  positiv
 ZX9  chir_02  CAX  CAN  CAM  CAZ  negativ
 ZX9  chir_03  CAY  NAQ  CAO  CAW  positiv
 ZX9  chir_04  CAT  NAQ  CAA  CAU  negativ
 ZX9  chir_05  CAU  OAC  CAT  CAV  positiv
 ZX9  chir_06  CAV  OAD  CAU  CAW  positiv
 ZX9  chir_07  CAW  OAE  CAV  CAY  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
 ZX9  plan-1  CAI   0.020
 ZX9  plan-1  CAG   0.020
 ZX9  plan-1  CAF   0.020
 ZX9  plan-1  CAH   0.020
 ZX9  plan-1  CAJ   0.020
 ZX9  plan-1  CAS   0.020
 ZX9  plan-1  CAZ   0.020
 ZX9  plan-1  HAI   0.020
 ZX9  plan-1  HAG   0.020
 ZX9  plan-1  HAF   0.020
 ZX9  plan-1  HAH   0.020
 ZX9  plan-1  HAJ   0.020
 ZX9  plan-2  CAZ   0.020
 ZX9  plan-2  CAR   0.020
 ZX9  plan-2  OAB   0.020
 ZX9  plan-2  NAP   0.020
 ZX9  plan-2  CAO   0.020
 ZX9  plan-2  HNAP  0.020

