# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 14:29:29 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 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(C)=O)[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
 ZXA  ZXA  N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}acetamide  ligand  33  15  .  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_ZXA
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
 ZXA  CAA   C  CH3   0  -0.780   4.5632  -1.2013  -0.3448
 ZXA  CAJ   C  C     0   0.510   3.4474  -0.4838   0.3750
 ZXA  OAC   O  O     0  -0.504   3.3944  -0.4364   1.5965
 ZXA  NAH   N  NH1   0  -0.633   2.5482   0.1113  -0.4315
 ZXA  CAG   C  CH2   0  -0.269   1.4420   0.9247   0.0195
 ZXA  CAL   C  CH1   0  -0.117   0.1033   0.3777  -0.4689
 ZXA  NAI   N  NH1   0  -0.609  -0.1077  -0.9512   0.0684
 ZXA  CAK   C  CH1   0  -0.093  -1.3174  -1.5882  -0.4247
 ZXA  CAB   C  CH3   0  -0.673  -1.3774  -3.0305   0.0504
 ZXA  CAM   C  CH1   0   0.041  -2.5309  -0.7760   0.0112
 ZXA  OAD   O  OH1   0  -0.672  -2.6752  -0.8424   1.4087
 ZXA  CAO   C  CH1   0  -0.032  -2.3721   0.6682  -0.4653
 ZXA  OAF   O  OH1   0  -0.676  -3.4065   1.4932   0.0372
 ZXA  CAN   C  CH1   0   0.086  -1.0479   1.2711  -0.0133
 ZXA  OAE   O  OH1   0  -0.680  -0.8621   2.5541  -0.5658
 ZXA  HAA   H  HCH3  0   0.262   4.8068  -2.1247   0.1769
 ZXA  HAAA  H  HCH3  0   0.249   4.3270  -1.4348  -1.3816
 ZXA  HAAB  H  HCH3  0   0.269   5.4563  -0.5740  -0.3363
 ZXA  HNAH  H  HNH1  0   0.400   2.7020   0.0602  -1.4261
 ZXA  HAG   H  HCH2  0   0.244   1.4535   0.9423   1.1087
 ZXA  HAGA  H  HCH2  0   0.255   1.5764   1.9482  -0.3328
 ZXA  HAL   H  HCH1  0   0.201   0.1105   0.3806  -1.5758
 ZXA  HNAI  H  HNH1  0   0.351   0.6876  -1.5322  -0.1681
 ZXA  HAK   H  HCH1  0   0.204  -1.3449  -1.5947  -1.5291
 ZXA  HAB   H  HCH3  0   0.229  -1.3464  -3.0940   1.1375
 ZXA  HABA  H  HCH3  0   0.228  -2.2908  -3.5153  -0.2964
 ZXA  HABB  H  HCH3  0   0.231  -0.5337  -3.5991  -0.3453
 ZXA  HAM   H  HCH1  0   0.209  -3.4139  -1.2028  -0.4919
 ZXA  HOAD  H  HOH1  0   0.443  -3.3461  -0.1969   1.6569
 ZXA  HAO   H  HCH1  0   0.215  -2.3799   0.6650  -1.5651
 ZXA  HOAF  H  HOH1  0   0.459  -4.2056   1.3331  -0.4749
 ZXA  HAN   H  HCH1  0   0.201  -1.0307   1.3086   1.0863
 ZXA  HOAE  H  HOH1  0   0.450  -1.6039   3.1040  -0.2936

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
 ZXA  CAA  CAJ   single  1.509  0.020  1.509
 ZXA  CAJ  OAC   double  1.224  0.020  1.224
 ZXA  CAJ  NAH   single  1.347  0.020  1.347
 ZXA  NAH  CAG   single  1.445  0.020  1.445
 ZXA  CAG  CAL   single  1.526  0.020  1.526
 ZXA  CAL  NAI   single  1.449  0.020  1.449
 ZXA  CAL  CAN   single  1.527  0.020  1.527
 ZXA  NAI  CAK   single  1.453  0.020  1.453
 ZXA  CAK  CAB   single  1.520  0.020  1.520
 ZXA  CAK  CAM   single  1.524  0.020  1.524
 ZXA  CAM  OAD   single  1.406  0.020  1.406
 ZXA  CAM  CAO   single  1.529  0.020  1.529
 ZXA  CAO  OAF   single  1.415  0.020  1.415
 ZXA  CAO  CAN   single  1.524  0.020  1.524
 ZXA  CAN  OAE   single  1.409  0.020  1.409
 ZXA  CAA  HAA   single  0.970  0.020  1.090
 ZXA  CAA  HAAA  single  0.970  0.020  1.090
 ZXA  CAA  HAAB  single  0.970  0.020  1.090
 ZXA  NAH  HNAH  single  0.860  0.020  1.020
 ZXA  CAG  HAG   single  0.970  0.020  1.090
 ZXA  CAG  HAGA  single  0.970  0.020  1.090
 ZXA  CAL  HAL   single  0.970  0.020  1.090
 ZXA  NAI  HNAI  single  0.890  0.020  1.040
 ZXA  CAK  HAK   single  0.970  0.020  1.090
 ZXA  CAB  HAB   single  0.970  0.020  1.090
 ZXA  CAB  HABA  single  0.970  0.020  1.090
 ZXA  CAB  HABB  single  0.970  0.020  1.090
 ZXA  CAM  HAM   single  0.970  0.020  1.090
 ZXA  OAD  HOAD  single  0.850  0.020  0.980
 ZXA  CAO  HAO   single  0.970  0.020  1.090
 ZXA  OAF  HOAF  single  0.850  0.020  0.980
 ZXA  CAN  HAN   single  0.970  0.020  1.090
 ZXA  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
 ZXA  HAAB  CAA  HAAA  107.96  3.000
 ZXA  HAAB  CAA  HAA   107.50  3.000
 ZXA  HAAA  CAA  HAA   108.85  3.000
 ZXA  HAAB  CAA  CAJ   109.15  3.000
 ZXA  HAAA  CAA  CAJ   113.31  3.000
 ZXA  HAA   CAA  CAJ   109.89  3.000
 ZXA  NAH   CAJ  OAC   123.49  3.000
 ZXA  NAH   CAJ  CAA   114.72  3.000
 ZXA  OAC   CAJ  CAA   121.78  3.000
 ZXA  HNAH  NAH  CAG   116.96  3.000
 ZXA  HNAH  NAH  CAJ   117.83  3.000
 ZXA  CAG   NAH  CAJ   124.96  3.000
 ZXA  HAGA  CAG  HAG   107.84  3.000
 ZXA  HAGA  CAG  CAL   109.94  3.000
 ZXA  HAG   CAG  CAL   109.57  3.000
 ZXA  HAGA  CAG  NAH   109.45  3.000
 ZXA  HAG   CAG  NAH   108.25  3.000
 ZXA  CAL   CAG  NAH   111.70  3.000
 ZXA  HAL   CAL  CAN   107.56  3.000
 ZXA  HAL   CAL  NAI   111.97  3.000
 ZXA  CAN   CAL  NAI   108.43  3.000
 ZXA  HAL   CAL  CAG   108.26  3.000
 ZXA  CAN   CAL  CAG   110.86  3.000
 ZXA  NAI   CAL  CAG   109.74  3.000
 ZXA  HNAI  NAI  CAK   108.84  3.000
 ZXA  HNAI  NAI  CAL   108.98  3.000
 ZXA  CAK   NAI  CAL   113.42  3.000
 ZXA  HAK   CAK  CAM   105.62  3.000
 ZXA  HAK   CAK  CAB   107.81  3.000
 ZXA  CAM   CAK  CAB   112.65  3.000
 ZXA  HAK   CAK  NAI   111.25  3.000
 ZXA  CAM   CAK  NAI   109.40  3.000
 ZXA  CAB   CAK  NAI   110.05  3.000
 ZXA  HABB  CAB  HABA  107.49  3.000
 ZXA  HABB  CAB  HAB   108.02  3.000
 ZXA  HABA  CAB  HAB   108.37  3.000
 ZXA  HABB  CAB  CAK   110.52  3.000
 ZXA  HABA  CAB  CAK   110.82  3.000
 ZXA  HAB   CAB  CAK   111.48  3.000
 ZXA  HAM   CAM  CAO   107.86  3.000
 ZXA  HAM   CAM  OAD   110.67  3.000
 ZXA  CAO   CAM  OAD   111.40  3.000
 ZXA  HAM   CAM  CAK   107.51  3.000
 ZXA  CAO   CAM  CAK   109.36  3.000
 ZXA  OAD   CAM  CAK   109.92  3.000
 ZXA  HOAD  OAD  CAM   107.20  3.000
 ZXA  HAO   CAO  CAN   107.70  3.000
 ZXA  HAO   CAO  OAF   110.57  3.000
 ZXA  CAN   CAO  OAF   107.41  3.000
 ZXA  HAO   CAO  CAM   107.95  3.000
 ZXA  CAN   CAO  CAM   111.82  3.000
 ZXA  OAF   CAO  CAM   111.35  3.000
 ZXA  HOAF  OAF  CAO   108.72  3.000
 ZXA  HAN   CAN  OAE   111.03  3.000
 ZXA  HAN   CAN  CAO   108.88  3.000
 ZXA  OAE   CAN  CAO   111.01  3.000
 ZXA  HAN   CAN  CAL   107.84  3.000
 ZXA  OAE   CAN  CAL   108.44  3.000
 ZXA  CAO   CAN  CAL   109.59  3.000
 ZXA  HOAE  OAE  CAN   107.91  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
 ZXA  CONST_01  CAG   NAH  CAJ  CAA   180.00   0.0  0
 ZXA  CONST_02  CAG   NAH  CAJ  OAC     0.00   0.0  0
 ZXA  CONST_03  HNAH  NAH  CAJ  CAA     0.00   0.0  0
 ZXA  Var_01    CAL   CAG  NAH  CAJ  -122.32  30.0  3
 ZXA  Var_02    HAA   CAA  CAJ  OAC    39.69  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
 ZXA  chir_01  CAL  CAG  NAI  CAN  negativ
 ZXA  chir_02  CAK  NAI  CAB  CAM  negativ
 ZXA  chir_03  CAM  OAD  CAK  CAO  positiv
 ZXA  chir_04  CAO  OAF  CAM  CAN  positiv
 ZXA  chir_05  CAN  OAE  CAO  CAL  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
 ZXA  plan-1  CAA   0.020
 ZXA  plan-1  CAJ   0.020
 ZXA  plan-1  OAC   0.020
 ZXA  plan-1  NAH   0.020
 ZXA  plan-1  CAG   0.020
 ZXA  plan-1  HNAH  0.020

