# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:19:10 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CNC[C@@H]([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
 SJ5  SJ5  '(3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid'  ligand  21  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SJ5
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
 SJ5  C2   C  CH2    0  -0.353   2.0470   1.1512   0.3819
 SJ5  C3   C  CH1    0   0.022   1.8137  -0.2132  -0.2700
 SJ5  O3   O  OH1    0  -0.680   2.7340  -1.1801   0.1997
 SJ5  N    N  NH1    0  -0.578   1.0529   2.1421   0.0193
 SJ5  C7   C  CH2    0  -0.307  -0.2942   1.6634   0.2820
 SJ5  C5   C  CH1    0  -0.397  -0.6264   0.3147  -0.3710
 SJ5  C6   C  C      0   0.419  -2.0528  -0.1270   0.0112
 SJ5  O62  O  OC    -1  -0.612  -2.9177  -0.1113  -0.8871
 SJ5  C4   C  CH1    0   0.065   0.4126  -0.7115   0.0517
 SJ5  O4   O  OH1    0  -0.680   0.1275  -1.9275  -0.6087
 SJ5  O61  O  O      0  -0.616  -2.2343  -0.4318   1.2080
 SJ5  H1   H  HCH2   0   0.218   2.0371   1.0275   1.4711
 SJ5  H2   H  HCH2   0   0.237   3.0395   1.5256   0.1156
 SJ5  H3   H  HCH1   0   0.193   1.8967  -0.0975  -1.3625
 SJ5  H4   H  HOH1   0   0.453   3.6103  -0.9486  -0.1231
 SJ5  H5   H  HNH1   0   0.341   1.1440   2.3616  -0.9659
 SJ5  H7   H  HCH2   0   0.215  -0.4163   1.5709   1.3660
 SJ5  H8   H  HCH2   0   0.236  -1.0042   2.4229  -0.0533
 SJ5  H9   H  HCH1   0   0.202  -0.5654   0.4428  -1.4590
 SJ5  H11  H  HCH1   0   0.182   0.3400  -0.8390   1.1438
 SJ5  H12  H  HOH1   0   0.442   0.7882  -2.5734  -0.3389

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
 SJ5  O61  C6   deloc   1.248  0.020  1.248
 SJ5  O4   C4   single  1.413  0.020  1.413
 SJ5  O62  C6   deloc   1.247  0.020  1.247
 SJ5  C6   C5   single  1.541  0.020  1.541
 SJ5  C4   C5   single  1.520  0.020  1.520
 SJ5  C4   C3   single  1.521  0.020  1.521
 SJ5  O3   C3   single  1.415  0.020  1.415
 SJ5  C5   C7   single  1.535  0.020  1.535
 SJ5  C7   N    single  1.454  0.020  1.454
 SJ5  C3   C2   single  1.530  0.020  1.530
 SJ5  C2   N    single  1.450  0.020  1.450
 SJ5  C2   H1   single  0.970  0.020  1.090
 SJ5  C2   H2   single  0.970  0.020  1.090
 SJ5  C3   H3   single  0.970  0.020  1.090
 SJ5  O3   H4   single  0.850  0.020  0.980
 SJ5  N    H5   single  0.890  0.020  1.040
 SJ5  C7   H7   single  0.970  0.020  1.090
 SJ5  C7   H8   single  0.970  0.020  1.090
 SJ5  C5   H9   single  0.970  0.020  1.090
 SJ5  C4   H11  single  0.970  0.020  1.090
 SJ5  O4   H12  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
 SJ5  H2   C2  H1   106.79  3.000
 SJ5  H2   C2  N    109.11  3.000
 SJ5  H1   C2  N    108.63  3.000
 SJ5  H2   C2  C3   109.87  3.000
 SJ5  H1   C2  C3   108.74  3.000
 SJ5  N    C2  C3   113.48  3.000
 SJ5  H3   C3  C4   108.26  3.000
 SJ5  H3   C3  O3   110.61  3.000
 SJ5  C4   C3  O3   107.75  3.000
 SJ5  H3   C3  C2   108.50  3.000
 SJ5  O3   C3  C2   111.64  3.000
 SJ5  C4   C3  C2   110.02  3.000
 SJ5  H4   O3  C3   108.45  3.000
 SJ5  H5   N   C7   109.30  3.000
 SJ5  H5   N   C2   109.24  3.000
 SJ5  C7   N   C2   111.42  3.000
 SJ5  H8   C7  H7   106.87  3.000
 SJ5  H8   C7  C5   109.86  3.000
 SJ5  H7   C7  C5   108.83  3.000
 SJ5  H8   C7  N    108.53  3.000
 SJ5  H7   C7  N    108.07  3.000
 SJ5  C5   C7  N    114.40  3.000
 SJ5  H9   C5  C4   108.45  3.000
 SJ5  H9   C5  C6   109.31  3.000
 SJ5  C4   C5  C6   111.72  3.000
 SJ5  H9   C5  C7   107.89  3.000
 SJ5  C4   C5  C7   109.08  3.000
 SJ5  C6   C5  C7   110.28  3.000
 SJ5  O61  C6  O62  126.36  3.000
 SJ5  O62  C6  C5   117.36  3.000
 SJ5  O61  C6  C5   116.25  3.000
 SJ5  H11  C4  O4   110.52  3.000
 SJ5  H11  C4  C5   107.98  3.000
 SJ5  O4   C4  C5   108.24  3.000
 SJ5  H11  C4  C3   107.94  3.000
 SJ5  C5   C4  C3   110.45  3.000
 SJ5  O4   C4  C3   111.65  3.000
 SJ5  H12  O4  C4   107.93  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
 SJ5  Var_01  C5  C7  N   C2  -54.14  30.0  1
 SJ5  Var_02  C7  N   C2  C3   53.87  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
 SJ5  chir_01  C3  C4  O3  C2  positiv
 SJ5  chir_02  C5  C6  C4  C7  positiv
 SJ5  chir_03  C4  O4  C5  C3  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
 SJ5  plan-1  C5   0.020
 SJ5  plan-1  C6   0.020
 SJ5  plan-1  O62  0.020
 SJ5  plan-1  O61  0.020

