# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 10:41:49 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (2R,3R,4R,5R,6S)-2-(aminomethyl)-6-methylpiperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CN)[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
 ZWZ  ZWZ  (2R,3R,4R,5R,6S)-2-(aminomethyl)-6-methylpiperidine-3,4,5-triol  ligand  28  12  .  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_ZWZ
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
 ZWZ  OAE   O  OH1   0  -0.681  -0.6369   2.4534   0.2591
 ZWZ  CAK   C  CH1   0   0.077  -0.1468   1.1946  -0.1480
 ZWZ  CAJ   C  CH1   0  -0.030   1.2022   0.9074   0.5024
 ZWZ  OAD   O  OH1   0  -0.677   2.1090   1.8916   0.0358
 ZWZ  CAI   C  CH1   0   0.029   1.6992  -0.4997   0.1833
 ZWZ  OAC   O  OH1   0  -0.676   1.9872  -0.6405  -1.1893
 ZWZ  CAH   C  CH1   0  -0.124   0.6216  -1.5116   0.5738
 ZWZ  CAA   C  CH3   0  -0.663   1.0337  -2.9442   0.2722
 ZWZ  NAG   N  NH1   0  -0.569  -0.6666  -1.2239  -0.0319
 ZWZ  CAL   C  CH1   0  -0.135  -1.1619   0.1119   0.2435
 ZWZ  CAF   C  CH2   0  -0.275  -2.5005   0.3354  -0.4522
 ZWZ  NAB   N  NH2   0  -0.794  -3.5068  -0.6183  -0.0090
 ZWZ  HOAE  H  HOH1  0   0.447   0.0330   3.1132   0.0508
 ZWZ  HAK   H  HCH1  0   0.191  -0.0225   1.1624  -1.2423
 ZWZ  HAJ   H  HCH1  0   0.216   1.0742   0.9827   1.5924
 ZWZ  HOAD  H  HOH1  0   0.458   2.8575   1.9362   0.6391
 ZWZ  HAI   H  HCH1  0   0.205   2.5984  -0.6945   0.7914
 ZWZ  HOAC  H  HOH1  0   0.445   2.5103   0.1242  -1.4545
 ZWZ  HAH   H  HCH1  0   0.227   0.4945  -1.4168   1.6598
 ZWZ  HAA   H  HCH3  0   0.226   1.9844  -3.1850   0.7494
 ZWZ  HAAA  H  HCH3  0   0.232   0.2838  -3.6416   0.6455
 ZWZ  HAAB  H  HCH3  0   0.225   1.1469  -3.1121  -0.7996
 ZWZ  HNAG  H  HNH1  0   0.331  -0.6107  -1.3654  -1.0355
 ZWZ  HAL   H  HCH1  0   0.220  -1.3184   0.1882   1.3299
 ZWZ  HAF   H  HCH2  0   0.210  -2.7987   1.3795  -0.3041
 ZWZ  HAFA  H  HCH2  0   0.208  -2.3546   0.2070  -1.5308
 ZWZ  HNAB  H  HNH2  0   0.334  -3.6679  -0.4902   0.9831
 ZWZ  HNAA  H  HNH2  0   0.344  -4.3875  -0.3900  -0.4529

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
 ZWZ  OAE  CAK   single  1.411  0.020  1.411
 ZWZ  CAK  CAJ   single  1.525  0.020  1.525
 ZWZ  CAK  CAL   single  1.535  0.020  1.535
 ZWZ  CAJ  OAD   single  1.417  0.020  1.417
 ZWZ  CAJ  CAI   single  1.526  0.020  1.526
 ZWZ  CAI  OAC   single  1.410  0.020  1.410
 ZWZ  CAI  CAH   single  1.529  0.020  1.529
 ZWZ  CAH  CAA   single  1.521  0.020  1.521
 ZWZ  CAH  NAG   single  1.452  0.020  1.452
 ZWZ  NAG  CAL   single  1.451  0.020  1.451
 ZWZ  CAL  CAF   single  1.525  0.020  1.525
 ZWZ  CAF  NAB   single  1.456  0.020  1.456
 ZWZ  OAE  HOAE  single  0.850  0.020  0.980
 ZWZ  CAK  HAK   single  0.970  0.020  1.090
 ZWZ  CAJ  HAJ   single  0.970  0.020  1.090
 ZWZ  OAD  HOAD  single  0.850  0.020  0.980
 ZWZ  CAI  HAI   single  0.970  0.020  1.090
 ZWZ  OAC  HOAC  single  0.850  0.020  0.980
 ZWZ  CAH  HAH   single  0.970  0.020  1.090
 ZWZ  CAA  HAA   single  0.970  0.020  1.090
 ZWZ  CAA  HAAA  single  0.970  0.020  1.090
 ZWZ  CAA  HAAB  single  0.970  0.020  1.090
 ZWZ  NAG  HNAG  single  0.890  0.020  1.040
 ZWZ  CAL  HAL   single  0.970  0.020  1.090
 ZWZ  CAF  HAF   single  0.970  0.020  1.090
 ZWZ  CAF  HAFA  single  0.970  0.020  1.090
 ZWZ  NAB  HNAB  single  0.890  0.020  1.040
 ZWZ  NAB  HNAA  single  0.890  0.020  1.040

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
 ZWZ  HOAE  OAE  CAK   107.89  3.000
 ZWZ  HAK   CAK  CAL   107.90  3.000
 ZWZ  HAK   CAK  CAJ   108.56  3.000
 ZWZ  CAL   CAK  CAJ   110.08  3.000
 ZWZ  HAK   CAK  OAE   110.60  3.000
 ZWZ  CAL   CAK  OAE   109.03  3.000
 ZWZ  CAJ   CAK  OAE   110.63  3.000
 ZWZ  HAJ   CAJ  CAI   107.95  3.000
 ZWZ  HAJ   CAJ  OAD   110.68  3.000
 ZWZ  CAI   CAJ  OAD   111.29  3.000
 ZWZ  HAJ   CAJ  CAK   107.87  3.000
 ZWZ  CAI   CAJ  CAK   111.88  3.000
 ZWZ  OAD   CAJ  CAK   107.15  3.000
 ZWZ  HOAD  OAD  CAJ   108.87  3.000
 ZWZ  HAI   CAI  CAH   108.47  3.000
 ZWZ  HAI   CAI  OAC   110.65  3.000
 ZWZ  CAH   CAI  OAC   109.06  3.000
 ZWZ  HAI   CAI  CAJ   108.25  3.000
 ZWZ  CAH   CAI  CAJ   109.11  3.000
 ZWZ  OAC   CAI  CAJ   111.24  3.000
 ZWZ  HOAC  OAC  CAI   107.43  3.000
 ZWZ  HAH   CAH  NAG   107.03  3.000
 ZWZ  HAH   CAH  CAA   108.00  3.000
 ZWZ  NAG   CAH  CAA   110.13  3.000
 ZWZ  HAH   CAH  CAI   106.09  3.000
 ZWZ  NAG   CAH  CAI   112.80  3.000
 ZWZ  CAA   CAH  CAI   112.45  3.000
 ZWZ  HAAB  CAA  HAAA  108.03  3.000
 ZWZ  HAAB  CAA  HAA   107.79  3.000
 ZWZ  HAAA  CAA  HAA   107.97  3.000
 ZWZ  HAAB  CAA  CAH   111.59  3.000
 ZWZ  HAAA  CAA  CAH   110.39  3.000
 ZWZ  HAA   CAA  CAH   110.93  3.000
 ZWZ  HNAG  NAG  CAL   109.56  3.000
 ZWZ  HNAG  NAG  CAH   109.63  3.000
 ZWZ  CAL   NAG  CAH   113.95  3.000
 ZWZ  HAL   CAL  CAF   108.38  3.000
 ZWZ  HAL   CAL  NAG   107.45  3.000
 ZWZ  CAF   CAL  NAG   110.36  3.000
 ZWZ  HAL   CAL  CAK   107.28  3.000
 ZWZ  CAF   CAL  CAK   111.14  3.000
 ZWZ  NAG   CAL  CAK   112.04  3.000
 ZWZ  HAFA  CAF  HAF   106.31  3.000
 ZWZ  HAFA  CAF  NAB   108.35  3.000
 ZWZ  HAF   CAF  NAB   113.26  3.000
 ZWZ  HAFA  CAF  CAL   108.36  3.000
 ZWZ  HAF   CAF  CAL   108.47  3.000
 ZWZ  NAB   CAF  CAL   111.84  3.000
 ZWZ  HNAA  NAB  HNAB  105.22  3.000
 ZWZ  HNAA  NAB  CAF   108.68  3.000
 ZWZ  HNAB  NAB  CAF   108.98  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
 ZWZ  Var_01  HNAB  NAB  CAF  CAL  62.19  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
 ZWZ  chir_01  CAK  OAE  CAJ  CAL  negativ
 ZWZ  chir_02  CAJ  OAD  CAK  CAI  negativ
 ZWZ  chir_03  CAI  OAC  CAJ  CAH  negativ
 ZWZ  chir_04  CAH  NAG  CAI  CAA  positiv
 ZWZ  chir_05  CAL  NAG  CAF  CAK  positiv

