# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:08:15 2021
#   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  23  12  .  2021-08-11  2022-11-17
;
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  OH1   0  -0.592  328.3109  -40.5182  -23.9263
 IDJ  C6   C  C     0   0.540  328.8755  -41.5904  -24.4633
 IDJ  O6A  O  O     0  -0.433  328.3278  -42.6580  -24.5604
 IDJ  C5   C  CR16  0  -0.240  330.2682  -41.2832  -24.9616
 IDJ  N5   N  NR16  0  -0.623  330.8284  -42.4071  -25.6749
 IDJ  C4   C  CR16  0   0.059  331.1877  -40.9471  -23.7715
 IDJ  O4   O  OH1   0  -0.672  330.7450  -41.6597  -22.6364
 IDJ  C3   C  CR16  0   0.002  332.6376  -41.3062  -24.1245
 IDJ  O3   O  OH1   0  -0.679  333.5507  -40.5211  -23.3843
 IDJ  C2   C  CR16  0   0.007  332.8844  -41.0637  -25.6091
 IDJ  O2   O  OH1   0  -0.671  334.2239  -41.2873  -25.9713
 IDJ  C1   C  C     0  -0.302  332.0042  -42.0080  -26.4363
 IDJ  H1   H  HOH1  0   0.484  327.4293  -40.7390  -23.5904
 IDJ  H2   H  HCR6  0   0.273  330.1845  -40.3818  -25.5924
 IDJ  H3   H  HNR6  0   0.362  330.1473  -42.8252  -26.2937
 IDJ  H5   H  HCR6  0   0.227  331.1346  -39.8661  -23.5989
 IDJ  H6   H  HOH1  0   0.459  331.0407  -41.1969  -21.8470
 IDJ  H7   H  HCR6  0   0.226  332.7872  -42.3731  -23.9165
 IDJ  H8   H  HOH1  0   0.459  333.8135  -41.0039  -22.5967
 IDJ  H9   H  HCR6  0   0.209  332.6032  -40.0216  -25.8298
 IDJ  H10  H  HOH1  0   0.446  334.7708  -40.6955  -25.4434
 IDJ  H11  H  H     0   0.236  332.5817  -42.9045  -26.6749
 IDJ  H12  H  H     0   0.223  331.7467  -41.5212  -27.3860

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  1.457  0.020  1.457
 IDJ  C1   C2   single  1.533  0.020  1.533
 IDJ  N5   C5   single  1.444  0.020  1.444
 IDJ  O2   C2   single  1.405  0.020  1.405
 IDJ  C2   C3   single  1.524  0.020  1.524
 IDJ  C5   C6   single  1.511  0.020  1.511
 IDJ  C5   C4   single  1.541  0.020  1.541
 IDJ  C6   O6A  double  1.204  0.020  1.204
 IDJ  C6   O6B  single  1.325  0.020  1.325
 IDJ  C3   C4   single  1.535  0.020  1.535
 IDJ  C3   O3   single  1.414  0.020  1.414
 IDJ  C4   O4   single  1.411  0.020  1.411
 IDJ  O6B  H1   single  0.850  0.020  0.980
 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  H1   O6B  C6   110.10  3.000
 IDJ  C5   C6   O6A  124.97  3.000
 IDJ  O6A  C6   O6B  123.80  3.000
 IDJ  C5   C6   O6B  111.21  3.000
 IDJ  H2   C5   C4   107.98  3.000
 IDJ  H2   C5   N5   112.51  3.000
 IDJ  C4   C5   N5   108.64  3.000
 IDJ  H2   C5   C6   106.54  3.000
 IDJ  C4   C5   C6   109.86  3.000
 IDJ  N5   C5   C6   111.24  3.000
 IDJ  H3   N5   C1   109.71  3.000
 IDJ  H3   N5   C5   111.28  3.000
 IDJ  C1   N5   C5   110.98  3.000
 IDJ  H5   C4   C3   108.23  3.000
 IDJ  H5   C4   O4   110.86  3.000
 IDJ  C3   C4   O4   111.30  3.000
 IDJ  H5   C4   C5   107.92  3.000
 IDJ  O4   C4   C5   108.89  3.000
 IDJ  C3   C4   C5   109.57  3.000
 IDJ  H6   O4   C4   108.71  3.000
 IDJ  H7   C3   C2   108.50  3.000
 IDJ  H7   C3   O3   110.65  3.000
 IDJ  C2   C3   O3   108.48  3.000
 IDJ  H7   C3   C4   108.22  3.000
 IDJ  O3   C3   C4   111.09  3.000
 IDJ  C2   C3   C4   109.86  3.000
 IDJ  H8   O3   C3   109.08  3.000
 IDJ  H9   C2   C1   109.15  3.000
 IDJ  H9   C2   O2   110.00  3.000
 IDJ  C1   C2   O2   108.07  3.000
 IDJ  H9   C2   C3   107.71  3.000
 IDJ  O2   C2   C3   112.33  3.000
 IDJ  C1   C2   C3   109.54  3.000
 IDJ  H10  O2   C2   107.59  3.000
 IDJ  H12  C1   H11  107.38  3.000
 IDJ  H12  C1   C2   109.16  3.000
 IDJ  H11  C1   C2   108.64  3.000
 IDJ  H12  C1   N5   112.61  3.000
 IDJ  H11  C1   N5   108.42  3.000
 IDJ  C2   C1   N5   110.50  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  CONST_01  H1  O6B  C6  C5  180.00   0.0  0
 IDJ  Var_01    C2  C1   N5  C5   42.14  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
 IDJ  plan-1  H1   0.020

