# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:42:12 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN[C@H]([C@@H](O)[C@@H]1O)C(O)=O
#
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
 IDJ  IDJ  '(2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid'  ligand  22  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IDJ
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
 IDJ  O6B  O  OC    -1  -0.609  -2.5982   0.1193  -1.0175
 IDJ  C6   C  C      0   0.456  -2.2010   0.1331   0.1754
 IDJ  O6A  O  O      0  -0.590  -2.8892   0.4223   1.1663
 IDJ  C5   C  CH1    0  -0.257  -0.7214  -0.2166   0.4552
 IDJ  N5   N  NH1    0  -0.603  -0.0749   0.9753   0.9837
 IDJ  C4   C  CH1    0   0.056   0.0266  -0.7319  -0.7780
 IDJ  O4   O  OH1    0  -0.703  -0.1351   0.1036  -1.8929
 IDJ  C3   C  CH1    0   0.003   1.5208  -0.9041  -0.4978
 IDJ  O3   O  OH1    0  -0.679   1.6458  -2.0585   0.3084
 IDJ  C2   C  CH1    0   0.019   2.1433   0.3015   0.2156
 IDJ  O2   O  OH1    0  -0.666   2.3059   1.3330  -0.7285
 IDJ  C1   C  CH2    0  -0.324   1.2841   0.7124   1.4038
 IDJ  H2   H  HCH1   0   0.197  -0.7193  -1.0372   1.1962
 IDJ  H3   H  HNH1   0   0.343  -0.6131   1.3110   1.7716
 IDJ  H5   H  HCH1   0   0.185  -0.3683  -1.7398  -0.9900
 IDJ  H6   H  HOH1   0   0.435  -1.1054   0.2458  -1.9007
 IDJ  H7   H  HCH1   0   0.215   2.0362  -1.0466  -1.4595
 IDJ  H8   H  HOH1   0   0.450   2.5800  -2.2119   0.4796
 IDJ  H9   H  HCH1   0   0.203   3.1244  -0.0138   0.6085
 IDJ  H10  H  HOH1   0   0.445   2.6788   2.0939  -0.2733
 IDJ  H11  H  HCH2   0   0.235   1.6994   1.6156   1.8620
 IDJ  H12  H  HCH2   0   0.189   1.3563  -0.0816   2.1650

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
 IDJ  C1  N5   single  1.447  0.020  1.447
 IDJ  C1  C2   single  1.523  0.020  1.523
 IDJ  N5  C5   single  1.455  0.020  1.455
 IDJ  O2  C2   single  1.408  0.020  1.408
 IDJ  C2  C3   single  1.533  0.020  1.533
 IDJ  C5  C6   single  1.546  0.020  1.546
 IDJ  C5  C4   single  1.532  0.020  1.532
 IDJ  C6  O6A  deloc   1.241  0.020  1.241
 IDJ  C6  O6B  deloc   1.257  0.020  1.257
 IDJ  C3  C4   single  1.530  0.020  1.530
 IDJ  C3  O3   single  1.414  0.020  1.414
 IDJ  C4  O4   single  1.403  0.020  1.403
 IDJ  C5  H2   single  0.970  0.020  1.090
 IDJ  N5  H3   single  0.890  0.020  1.040
 IDJ  C4  H5   single  0.970  0.020  1.090
 IDJ  O4  H6   single  0.850  0.020  0.980
 IDJ  C3  H7   single  0.970  0.020  1.090
 IDJ  O3  H8   single  0.850  0.020  0.980
 IDJ  C2  H9   single  0.970  0.020  1.090
 IDJ  O2  H10  single  0.850  0.020  0.980
 IDJ  C1  H11  single  0.970  0.020  1.090
 IDJ  C1  H12  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
 IDJ  C5   C6  O6A  116.05  3.000
 IDJ  O6A  C6  O6B  125.81  3.000
 IDJ  C5   C6  O6B  118.13  3.000
 IDJ  H2   C5  C4   106.79  3.000
 IDJ  H2   C5  N5   111.33  3.000
 IDJ  C4   C5  N5   110.55  3.000
 IDJ  H2   C5  C6   106.92  3.000
 IDJ  C4   C5  C6   113.44  3.000
 IDJ  N5   C5  C6   107.80  3.000
 IDJ  H3   N5  C1   109.51  3.000
 IDJ  H3   N5  C5   108.56  3.000
 IDJ  C1   N5  C5   111.96  3.000
 IDJ  H5   C4  C3   106.37  3.000
 IDJ  H5   C4  O4   110.50  3.000
 IDJ  C3   C4  O4   108.98  3.000
 IDJ  H5   C4  C5   106.70  3.000
 IDJ  O4   C4  C5   112.54  3.000
 IDJ  C3   C4  C5   111.55  3.000
 IDJ  H6   O4  C4   101.93  3.000
 IDJ  H7   C3  C2   108.56  3.000
 IDJ  H7   C3  O3   110.57  3.000
 IDJ  C2   C3  O3   109.93  3.000
 IDJ  H7   C3  C4   108.18  3.000
 IDJ  O3   C3  C4   106.43  3.000
 IDJ  C2   C3  C4   113.16  3.000
 IDJ  H8   O3  C3   108.51  3.000
 IDJ  H9   C2  C1   107.52  3.000
 IDJ  H9   C2  O2   110.22  3.000
 IDJ  C1   C2  O2   113.00  3.000
 IDJ  H9   C2  C3   107.59  3.000
 IDJ  O2   C2  C3   108.12  3.000
 IDJ  C1   C2  C3   110.26  3.000
 IDJ  H10  O2  C2   107.88  3.000
 IDJ  H12  C1  H11  106.29  3.000
 IDJ  H12  C1  C2   107.91  3.000
 IDJ  H11  C1  C2   109.59  3.000
 IDJ  H12  C1  N5   113.14  3.000
 IDJ  H11  C1  N5   109.15  3.000
 IDJ  C2   C1  N5   110.64  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
 IDJ  Var_01  C2  C1  N5  C5  63.63  30.0  1

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
 IDJ  chir_01  C5  N5  C6  C4  negativ
 IDJ  chir_02  C4  O4  C5  C3  positiv
 IDJ  chir_03  C3  O3  C4  C2  negativ
 IDJ  chir_04  C2  O2  C3  C1  positiv

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
 IDJ  plan-1  O6B  0.020
 IDJ  plan-1  C6   0.020
 IDJ  plan-1  O6A  0.020
 IDJ  plan-1  C5   0.020

