# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 18:09:49 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)c2oc3ccccc3c2)[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
 ZX8  ZX8  N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-1-benzofuran-2-carboxamide  ligand  43  23  .  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_ZX8
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
 ZX8  CAJ   C  CR15  0  -0.360  -3.5101  -0.7965   1.2591
 ZX8  CAQ   C  CR56  0   0.058  -4.5452  -0.1033   0.5525
 ZX8  CAH   C  CR16  0  -0.331  -5.8937   0.1750   0.7895
 ZX8  CAF   C  CR16  0  -0.260  -6.5858   0.8989  -0.1626
 ZX8  CAG   C  CR16  0  -0.267  -5.9597   1.3452  -1.3361
 ZX8  CAI   C  CR16  0  -0.339  -4.6250   1.0806  -1.5930
 ZX8  CAR   C  CR56  0   0.375  -3.9509   0.3526  -0.6272
 ZX8  OAN   O  O     0  -0.467  -2.6544  -0.0206  -0.6668
 ZX8  CAP   C  CR5   0   0.238  -2.4092  -0.7128   0.4796
 ZX8  CAO   C  C     0   0.490  -1.0583  -1.2590   0.7194
 ZX8  OAB   O  O     0  -0.478  -0.8178  -1.8162   1.7814
 ZX8  NAL   N  NH1   0  -0.661  -0.1779  -1.0957  -0.2798
 ZX8  CAK   C  CH2   0  -0.266   1.1895  -1.5680  -0.2472
 ZX8  CAT   C  CH1   0  -0.125   2.1699  -0.4349  -0.5365
 ZX8  NAM   N  NH1   0  -0.608   2.0533   0.5892   0.4820
 ZX8  CAS   C  CH1   0  -0.096   2.8846   1.7542   0.2218
 ZX8  CAA   C  CH3   0  -0.672   2.5941   2.8427   1.2420
 ZX8  CAU   C  CH1   0   0.040   4.3509   1.3387   0.2128
 ZX8  OAC   O  OH1   0  -0.671   4.7417   0.9394   1.5033
 ZX8  CAW   C  CH1   0  -0.032   4.5544   0.2154  -0.8036
 ZX8  OAE   O  OH1   0  -0.675   5.8751  -0.2891  -0.7551
 ZX8  CAV   C  CH1   0   0.086   3.6073  -0.9495  -0.5447
 ZX8  OAD   O  OH1   0  -0.679   3.7233  -1.9339  -1.5451
 ZX8  HAJ   H  HCR5  0   0.276  -3.5814  -1.2933   2.2128
 ZX8  HAH   H  HCR6  0   0.264  -6.3813  -0.1682   1.6925
 ZX8  HAF   H  HCR6  0   0.261  -7.6307   1.1295  -0.0040
 ZX8  HAG   H  HCR6  0   0.266  -6.5328   1.9103  -2.0590
 ZX8  HAI   H  HCR6  0   0.276  -4.1392   1.4241  -2.4963
 ZX8  HNAL  H  HNH1  0   0.410  -0.4954  -0.6879  -1.1461
 ZX8  HAK   H  HCH2  0   0.250   1.3896  -1.9838   0.7390
 ZX8  HAKA  H  HCH2  0   0.262   1.3140  -2.3654  -0.9807
 ZX8  HAT   H  HCH1  0   0.206   1.9513  -0.0390  -1.5466
 ZX8  HNAM  H  HNH1  0   0.352   1.0871   0.8879   0.5406
 ZX8  HAS   H  HCH1  0   0.206   2.6856   2.1675  -0.7833
 ZX8  HAA   H  HCH3  0   0.230   2.7721   2.4928   2.2582
 ZX8  HAAA  H  HCH3  0   0.228   3.2229   3.7155   1.0625
 ZX8  HAAB  H  HCH3  0   0.231   1.5548   3.1686   1.1721
 ZX8  HAU   H  HCH1  0   0.210   4.9400   2.2084  -0.1216
 ZX8  HOAC  H  HOH1  0   0.444   5.6208   0.5518   1.4303
 ZX8  HAW   H  HCH1  0   0.216   4.3248   0.6156  -1.8019
 ZX8  HOAE  H  HOH1  0   0.460   6.4563   0.3219  -1.2186
 ZX8  HAV   H  HCH1  0   0.203   3.8231  -1.3669   0.4499
 ZX8  HOAD  H  HOH1  0   0.451   4.6378  -2.2341  -1.5621

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
 ZX8  CAJ  CAQ   aromatic  1.432  0.020  1.432
 ZX8  CAJ  CAP   aromatic  1.352  0.020  1.352
 ZX8  CAQ  CAH   aromatic  1.397  0.020  1.397
 ZX8  CAQ  CAR   aromatic  1.397  0.020  1.397
 ZX8  CAH  CAF   aromatic  1.382  0.020  1.382
 ZX8  CAF  CAG   aromatic  1.403  0.020  1.403
 ZX8  CAG  CAI   aromatic  1.385  0.020  1.385
 ZX8  CAI  CAR   aromatic  1.385  0.020  1.385
 ZX8  CAR  OAN   aromatic  1.350  0.020  1.350
 ZX8  OAN  CAP   aromatic  1.361  0.020  1.361
 ZX8  CAP  CAO   single    1.477  0.020  1.477
 ZX8  CAO  OAB   double    1.223  0.020  1.223
 ZX8  CAO  NAL   single    1.342  0.020  1.342
 ZX8  NAL  CAK   single    1.447  0.020  1.447
 ZX8  CAK  CAT   single    1.526  0.020  1.526
 ZX8  CAT  NAM   single    1.449  0.020  1.449
 ZX8  CAT  CAV   single    1.527  0.020  1.527
 ZX8  NAM  CAS   single    1.455  0.020  1.455
 ZX8  CAS  CAA   single    1.520  0.020  1.520
 ZX8  CAS  CAU   single    1.524  0.020  1.524
 ZX8  CAU  OAC   single    1.406  0.020  1.406
 ZX8  CAU  CAW   single    1.529  0.020  1.529
 ZX8  CAW  OAE   single    1.415  0.020  1.415
 ZX8  CAW  CAV   single    1.523  0.020  1.523
 ZX8  CAV  OAD   single    1.408  0.020  1.408
 ZX8  CAJ  HAJ   single    0.930  0.020  1.080
 ZX8  CAH  HAH   single    0.930  0.020  1.080
 ZX8  CAF  HAF   single    0.930  0.020  1.080
 ZX8  CAG  HAG   single    0.930  0.020  1.080
 ZX8  CAI  HAI   single    0.930  0.020  1.080
 ZX8  NAL  HNAL  single    0.860  0.020  1.020
 ZX8  CAK  HAK   single    0.970  0.020  1.090
 ZX8  CAK  HAKA  single    0.970  0.020  1.090
 ZX8  CAT  HAT   single    0.970  0.020  1.090
 ZX8  NAM  HNAM  single    0.890  0.020  1.040
 ZX8  CAS  HAS   single    0.970  0.020  1.090
 ZX8  CAA  HAA   single    0.970  0.020  1.090
 ZX8  CAA  HAAA  single    0.970  0.020  1.090
 ZX8  CAA  HAAB  single    0.970  0.020  1.090
 ZX8  CAU  HAU   single    0.970  0.020  1.090
 ZX8  OAC  HOAC  single    0.850  0.020  0.980
 ZX8  CAW  HAW   single    0.970  0.020  1.090
 ZX8  OAE  HOAE  single    0.850  0.020  0.980
 ZX8  CAV  HAV   single    0.970  0.020  1.090
 ZX8  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
 ZX8  HAJ   CAJ  CAP   126.35  3.000
 ZX8  HAJ   CAJ  CAQ   127.73  3.000
 ZX8  CAP   CAJ  CAQ   105.92  3.000
 ZX8  CAR   CAQ  CAH   119.25  3.000
 ZX8  CAR   CAQ  CAJ   105.49  3.000
 ZX8  CAH   CAQ  CAJ   135.26  3.000
 ZX8  HAH   CAH  CAF   121.02  3.000
 ZX8  HAH   CAH  CAQ   120.88  3.000
 ZX8  CAF   CAH  CAQ   118.09  3.000
 ZX8  HAF   CAF  CAG   119.07  3.000
 ZX8  HAF   CAF  CAH   119.63  3.000
 ZX8  CAG   CAF  CAH   121.30  3.000
 ZX8  HAG   CAG  CAI   119.11  3.000
 ZX8  HAG   CAG  CAF   119.26  3.000
 ZX8  CAI   CAG  CAF   121.64  3.000
 ZX8  HAI   CAI  CAR   122.07  3.000
 ZX8  HAI   CAI  CAG   121.81  3.000
 ZX8  CAR   CAI  CAG   116.12  3.000
 ZX8  OAN   CAR  CAI   126.33  3.000
 ZX8  OAN   CAR  CAQ   110.06  3.000
 ZX8  CAI   CAR  CAQ   123.60  3.000
 ZX8  CAP   OAN  CAR   106.79  3.000
 ZX8  CAO   CAP  OAN   119.31  3.000
 ZX8  CAO   CAP  CAJ   128.95  3.000
 ZX8  OAN   CAP  CAJ   111.74  3.000
 ZX8  NAL   CAO  OAB   124.96  3.000
 ZX8  NAL   CAO  CAP   115.74  3.000
 ZX8  OAB   CAO  CAP   119.30  3.000
 ZX8  HNAL  NAL  CAK   116.66  3.000
 ZX8  HNAL  NAL  CAO   118.83  3.000
 ZX8  CAK   NAL  CAO   124.30  3.000
 ZX8  HAKA  CAK  HAK   108.00  3.000
 ZX8  HAKA  CAK  CAT   110.00  3.000
 ZX8  HAK   CAK  CAT   109.70  3.000
 ZX8  HAKA  CAK  NAL   109.36  3.000
 ZX8  HAK   CAK  NAL   108.59  3.000
 ZX8  CAT   CAK  NAL   111.13  3.000
 ZX8  HAT   CAT  CAV   107.56  3.000
 ZX8  HAT   CAT  NAM   111.89  3.000
 ZX8  CAV   CAT  NAM   108.52  3.000
 ZX8  HAT   CAT  CAK   108.16  3.000
 ZX8  CAV   CAT  CAK   110.83  3.000
 ZX8  NAM   CAT  CAK   109.87  3.000
 ZX8  HNAM  NAM  CAS   108.61  3.000
 ZX8  HNAM  NAM  CAT   109.01  3.000
 ZX8  CAS   NAM  CAT   113.22  3.000
 ZX8  HAS   CAS  CAU   105.66  3.000
 ZX8  HAS   CAS  CAA   107.96  3.000
 ZX8  CAU   CAS  CAA   112.53  3.000
 ZX8  HAS   CAS  NAM   111.06  3.000
 ZX8  CAU   CAS  NAM   109.42  3.000
 ZX8  CAA   CAS  NAM   110.14  3.000
 ZX8  HAAB  CAA  HAAA  107.43  3.000
 ZX8  HAAB  CAA  HAA   108.13  3.000
 ZX8  HAAA  CAA  HAA   108.44  3.000
 ZX8  HAAB  CAA  CAS   110.66  3.000
 ZX8  HAAA  CAA  CAS   110.64  3.000
 ZX8  HAA   CAA  CAS   111.41  3.000
 ZX8  HAU   CAU  CAW   107.88  3.000
 ZX8  HAU   CAU  OAC   110.72  3.000
 ZX8  CAW   CAU  OAC   111.38  3.000
 ZX8  HAU   CAU  CAS   107.51  3.000
 ZX8  CAW   CAU  CAS   109.41  3.000
 ZX8  OAC   CAU  CAS   109.84  3.000
 ZX8  HOAC  OAC  CAU   107.35  3.000
 ZX8  HAW   CAW  CAV   107.63  3.000
 ZX8  HAW   CAW  OAE   110.84  3.000
 ZX8  CAV   CAW  OAE   107.57  3.000
 ZX8  HAW   CAW  CAU   107.96  3.000
 ZX8  CAV   CAW  CAU   111.48  3.000
 ZX8  OAE   CAW  CAU   111.32  3.000
 ZX8  HOAE  OAE  CAW   108.72  3.000
 ZX8  HAV   CAV  OAD   111.16  3.000
 ZX8  HAV   CAV  CAW   108.77  3.000
 ZX8  OAD   CAV  CAW   111.26  3.000
 ZX8  HAV   CAV  CAT   107.93  3.000
 ZX8  OAD   CAV  CAT   108.48  3.000
 ZX8  CAW   CAV  CAT   109.17  3.000
 ZX8  HOAD  OAD  CAV   107.99  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
 ZX8  CONST_01  CAF   CAH  CAQ  CAJ   180.00   0.0  0
 ZX8  CONST_02  CAI   CAR  CAQ  CAJ   180.00   0.0  0
 ZX8  CONST_03  OAN   CAR  CAQ  CAJ     0.00   0.0  0
 ZX8  CONST_04  CAR   OAN  CAP  CAJ     0.00   0.0  0
 ZX8  CONST_05  OAN   CAP  CAJ  CAQ     0.00   0.0  0
 ZX8  CONST_06  CAG   CAF  CAH  CAQ     0.00   0.0  0
 ZX8  CONST_07  CAG   CAI  CAR  CAQ     0.00   0.0  0
 ZX8  CONST_08  CAP   OAN  CAR  CAQ     0.00   0.0  0
 ZX8  CONST_09  CAP   CAJ  CAQ  CAH   180.00   0.0  0
 ZX8  CONST_10  CAI   CAR  CAQ  CAH     0.00   0.0  0
 ZX8  CONST_11  OAN   CAR  CAQ  CAH   180.00   0.0  0
 ZX8  CONST_12  CAI   CAG  CAF  CAH     0.00   0.0  0
 ZX8  CONST_13  CAR   CAQ  CAH  CAF     0.00   0.0  0
 ZX8  CONST_14  CAR   CAI  CAG  CAF     0.00   0.0  0
 ZX8  CONST_15  OAN   CAR  CAI  CAG   180.00   0.0  0
 ZX8  CONST_16  CAP   OAN  CAR  CAI   180.00   0.0  0
 ZX8  CONST_17  CAP   CAJ  CAQ  CAR     0.00   0.0  0
 ZX8  CONST_18  CAO   CAP  CAJ  CAQ   180.00   0.0  0
 ZX8  CONST_19  CAO   CAP  OAN  CAR   180.00   0.0  0
 ZX8  CONST_20  HAH   CAH  CAQ  CAJ     0.00   0.0  0
 ZX8  CONST_21  HAF   CAF  CAH  CAQ   180.00   0.0  0
 ZX8  CONST_22  HAI   CAI  CAR  CAQ   180.00   0.0  0
 ZX8  CONST_23  HAJ   CAJ  CAQ  CAH     0.00   0.0  0
 ZX8  CONST_24  HAG   CAG  CAF  CAH   180.00   0.0  0
 ZX8  CONST_25  CAK   NAL  CAO  CAP   180.00   0.0  0
 ZX8  CONST_26  HNAL  NAL  CAO  CAP     0.00   0.0  0
 ZX8  CONST_27  CAK   NAL  CAO  OAB     0.00   0.0  0
 ZX8  Var_01    OAB   CAO  CAP  CAJ    -4.24  30.0  2
 ZX8  Var_02    CAT   CAK  NAL  CAO  -125.73  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
 ZX8  chir_01  CAT  CAK  NAM  CAV  negativ
 ZX8  chir_02  CAS  NAM  CAA  CAU  negativ
 ZX8  chir_03  CAU  OAC  CAS  CAW  positiv
 ZX8  chir_04  CAW  OAE  CAU  CAV  positiv
 ZX8  chir_05  CAV  OAD  CAW  CAT  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
 ZX8  plan-1  CAJ   0.020
 ZX8  plan-1  CAQ   0.020
 ZX8  plan-1  CAH   0.020
 ZX8  plan-1  CAF   0.020
 ZX8  plan-1  CAG   0.020
 ZX8  plan-1  CAI   0.020
 ZX8  plan-1  CAR   0.020
 ZX8  plan-1  OAN   0.020
 ZX8  plan-1  CAP   0.020
 ZX8  plan-1  CAO   0.020
 ZX8  plan-1  HAJ   0.020
 ZX8  plan-1  HAH   0.020
 ZX8  plan-1  HAF   0.020
 ZX8  plan-1  HAG   0.020
 ZX8  plan-1  HAI   0.020
 ZX8  plan-2  CAP   0.020
 ZX8  plan-2  CAO   0.020
 ZX8  plan-2  OAB   0.020
 ZX8  plan-2  NAL   0.020
 ZX8  plan-2  CAK   0.020
 ZX8  plan-2  HNAL  0.020

