# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:12:22 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (1R,2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
#
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
 MIG  MIG  (1R,2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol  ligand  31  14  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MIG
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
 MIG  OAA   O  OH1   0  -0.657   2.5943   0.9885   1.6147
 MIG  OAC   O  OH1   0  -0.676  -2.8146   1.8382   0.2960
 MIG  OAD   O  OH1   0  -0.679  -3.2409  -0.9549  -0.0773
 MIG  OAE   O  OH1   0  -0.675  -1.0098  -2.5657   0.3442
 MIG  CAF   C  CH2   0  -0.166   2.4466   1.9090   0.5586
 MIG  CAG   C  CH2   0  -0.188   1.4873  -1.6904  -0.7232
 MIG  CAH   C  CH2   0  -0.334   1.8626   1.2420  -0.6785
 MIG  CAI   C  CH2   0  -0.327  -0.4209   1.4914   0.0416
 MIG  CAJ   C  CH1   0   0.038  -1.8273   1.0191  -0.2910
 MIG  CAK   C  CH1   0   0.003  -1.9985  -0.3789   0.2632
 MIG  CAL   C  CH1   0   0.043  -0.9156  -1.3029  -0.2763
 MIG  CAM   C  CH1   0  -0.072   0.4994  -0.7541  -0.0274
 MIG  NAN   N  NT    0  -0.443   0.5614   0.6084  -0.5473
 MIG  HOAA  H  HOH1  0   0.449   2.7667   1.4890   2.4169
 MIG  HOAB  H  HOH1  0   0.450   3.3246  -2.2644  -0.5780
 MIG  HOAC  H  HOH1  0   0.455  -2.8365   2.6754  -0.1770
 MIG  HOAD  H  HOH1  0   0.454  -3.9346  -0.4804   0.3908
 MIG  HOAE  H  HOH1  0   0.450  -1.9026  -2.8962   0.2006
 MIG  HAF   H  HCH2  0   0.193   1.8074   2.7498   0.8565
 MIG  HAFA  H  HCH2  0   0.195   3.4101   2.3507   0.2649
 MIG  HAG   H  HCH2  0   0.194   1.5221  -1.4187  -1.7877
 MIG  HAGA  H  HCH2  0   0.226   1.0984  -2.7117  -0.6698
 MIG  HAH   H  HCH2  0   0.228   1.7701   2.0354  -1.4289
 MIG  HAHA  H  HCH2  0   0.252   2.5765   0.5294  -1.0854
 MIG  HAI   H  HCH2  0   0.241  -0.2752   2.4963  -0.3664
 MIG  HAIA  H  HCH2  0   0.200  -0.3220   1.5765   1.1371
 MIG  HAJ   H  HCH1  0   0.203  -1.9360   0.9877  -1.3846
 MIG  HAK   H  HCH1  0   0.202  -1.8821  -0.3261   1.3586
 MIG  HAL   H  HCH1  0   0.199  -1.0529  -1.3906  -1.3670
 MIG  HAM   H  HCH1  0   0.207   0.6832  -0.7949   1.0583
 MIG  OAB   O  OH1   0  -0.664   2.7637  -1.6301  -0.1225

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
 MIG  OAA  CAF   single  1.409  0.020  1.409
 MIG  OAB  CAG   single  1.412  0.020  1.412
 MIG  OAC  CAJ   single  1.411  0.020  1.411
 MIG  OAD  CAK   single  1.411  0.020  1.411
 MIG  OAE  CAL   single  1.410  0.020  1.410
 MIG  CAF  CAH   single  1.522  0.020  1.522
 MIG  CAG  CAM   single  1.529  0.020  1.529
 MIG  CAH  NAN   single  1.453  0.020  1.453
 MIG  CAI  CAJ   single  1.520  0.020  1.520
 MIG  CAI  NAN   single  1.446  0.020  1.446
 MIG  CAJ  CAK   single  1.514  0.020  1.514
 MIG  CAK  CAL   single  1.522  0.020  1.522
 MIG  CAL  CAM   single  1.538  0.020  1.538
 MIG  CAM  NAN   single  1.460  0.020  1.460
 MIG  OAA  HOAA  single  0.850  0.020  0.980
 MIG  OAB  HOAB  single  0.850  0.020  0.980
 MIG  OAC  HOAC  single  0.850  0.020  0.980
 MIG  OAD  HOAD  single  0.850  0.020  0.980
 MIG  OAE  HOAE  single  0.850  0.020  0.980
 MIG  CAF  HAF   single  0.970  0.020  1.090
 MIG  CAF  HAFA  single  0.970  0.020  1.090
 MIG  CAG  HAG   single  0.970  0.020  1.090
 MIG  CAG  HAGA  single  0.970  0.020  1.090
 MIG  CAH  HAH   single  0.970  0.020  1.090
 MIG  CAH  HAHA  single  0.970  0.020  1.090
 MIG  CAI  HAI   single  0.970  0.020  1.090
 MIG  CAI  HAIA  single  0.970  0.020  1.090
 MIG  CAJ  HAJ   single  0.970  0.020  1.090
 MIG  CAK  HAK   single  0.970  0.020  1.090
 MIG  CAL  HAL   single  0.970  0.020  1.090
 MIG  CAM  HAM   single  0.970  0.020  1.090

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
 MIG  HOAA  OAA  CAF  107.72  3.000
 MIG  HOAC  OAC  CAJ  108.46  3.000
 MIG  HOAD  OAD  CAK  108.43  3.000
 MIG  HOAE  OAE  CAL  107.68  3.000
 MIG  HAFA  CAF  HAF  105.97  3.000
 MIG  HAFA  CAF  CAH  107.17  3.000
 MIG  HAF   CAF  CAH  109.45  3.000
 MIG  HAFA  CAF  OAA  111.76  3.000
 MIG  HAF   CAF  OAA  110.98  3.000
 MIG  CAH   CAF  OAA  111.30  3.000
 MIG  HAGA  CAG  HAG  106.81  3.000
 MIG  HAGA  CAG  CAM  108.65  3.000
 MIG  HAG   CAG  CAM  108.04  3.000
 MIG  HAGA  CAG  OAB  109.91  3.000
 MIG  HAG   CAG  OAB  111.89  3.000
 MIG  CAM   CAG  OAB  111.37  3.000
 MIG  HAHA  CAH  HAH  105.87  3.000
 MIG  HAHA  CAH  NAN  109.62  3.000
 MIG  HAH   CAH  NAN  107.57  3.000
 MIG  HAHA  CAH  CAF  109.84  3.000
 MIG  HAH   CAH  CAF  105.76  3.000
 MIG  NAN   CAH  CAF  117.48  3.000
 MIG  HAIA  CAI  HAI  106.71  3.000
 MIG  HAIA  CAI  NAN  112.99  3.000
 MIG  HAI   CAI  NAN  108.57  3.000
 MIG  HAIA  CAI  CAJ  108.91  3.000
 MIG  HAI   CAI  CAJ  109.08  3.000
 MIG  NAN   CAI  CAJ  110.46  3.000
 MIG  HAJ   CAJ  CAK  109.06  3.000
 MIG  HAJ   CAJ  CAI  108.54  3.000
 MIG  CAK   CAJ  CAI  108.15  3.000
 MIG  HAJ   CAJ  OAC  111.18  3.000
 MIG  CAK   CAJ  OAC  107.75  3.000
 MIG  CAI   CAJ  OAC  112.09  3.000
 MIG  HAK   CAK  CAL  107.82  3.000
 MIG  HAK   CAK  CAJ  107.91  3.000
 MIG  CAL   CAK  CAJ  110.52  3.000
 MIG  HAK   CAK  OAD  110.61  3.000
 MIG  CAL   CAK  OAD  107.04  3.000
 MIG  CAJ   CAK  OAD  112.85  3.000
 MIG  HAL   CAL  CAM  107.63  3.000
 MIG  HAL   CAL  CAK  108.07  3.000
 MIG  CAM   CAL  CAK  112.36  3.000
 MIG  HAL   CAL  OAE  110.84  3.000
 MIG  CAM   CAL  OAE  108.05  3.000
 MIG  CAK   CAL  OAE  109.88  3.000
 MIG  HAM   CAM  NAN  112.24  3.000
 MIG  HAM   CAM  CAL  107.44  3.000
 MIG  NAN   CAM  CAL  108.34  3.000
 MIG  HAM   CAM  CAG  108.53  3.000
 MIG  NAN   CAM  CAG  112.47  3.000
 MIG  CAL   CAM  CAG  107.60  3.000
 MIG  CAM   NAN  CAI  113.33  3.000
 MIG  CAM   NAN  CAH  118.50  3.000
 MIG  CAI   NAN  CAH  112.25  3.000
 MIG  HOAB  OAB  CAG  107.31  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
 MIG  Var_01  CAM  NAN  CAI  CAJ  -63.06  30.0  1
 MIG  Var_02  CAI  NAN  CAH  CAF   51.37  30.0  3
 MIG  Var_03  NAN  CAH  CAF  OAA   58.96  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
 MIG  chir_01  CAJ  OAC  CAI  CAK  negativ
 MIG  chir_02  CAK  OAD  CAJ  CAL  positiv
 MIG  chir_03  CAL  OAE  CAK  CAM  negativ
 MIG  chir_04  CAM  NAN  CAL  CAG  negativ

