# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 03:04:59 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  22  11  .  2021-08-23  2022-11-17
;
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  -0.356   2.0494   1.1862   0.3149
 SJ5  C3   C  CH1   0   0.019   1.7925  -0.1885  -0.3073
 SJ5  O3   O  OH1   0  -0.676   2.7266  -1.1479   0.1404
 SJ5  N    N  NH1   0  -0.574   1.0364   2.1677  -0.0172
 SJ5  C7   C  CH2   0  -0.297  -0.2935   1.7119   0.3155
 SJ5  C5   C  CH1   0  -0.435  -0.6393   0.3412  -0.3105
 SJ5  C6   C  C     0   0.561  -2.0114  -0.0884   0.1412
 SJ5  O62  O  OH1   0  -0.589  -2.9489   0.1939  -0.7554
 SJ5  C4   C  CH1   0   0.071   0.4092  -0.6886   0.0839
 SJ5  O4   O  OH1   0  -0.674   0.0771  -1.8982  -0.5563
 SJ5  O61  O  O     0  -0.444  -2.2527  -0.5819   1.2153
 SJ5  H1   H  HCH2  0   0.226   2.0917   1.0791   1.4047
 SJ5  H2   H  HCH2  0   0.247   3.0253   1.5607  -0.0039
 SJ5  H3   H  HCH1  0   0.205   1.8276  -0.0906  -1.4036
 SJ5  H4   H  HOH1  0   0.457   3.5841  -0.9417  -0.2441
 SJ5  H5   H  HNH1  0   0.351   1.0856   2.3980  -1.0022
 SJ5  H7   H  HCH2  0   0.235  -0.3729   1.6357   1.4046
 SJ5  H8   H  HCH2  0   0.262  -1.0177   2.4603  -0.0091
 SJ5  H9   H  HCH1  0   0.272  -0.6377   0.4559  -1.3992
 SJ5  H10  H  HOH1  0   0.480  -3.8220  -0.0468  -0.4097
 SJ5  H11  H  HCH1  0   0.207   0.3894  -0.8063   1.1789
 SJ5  H12  H  HOH1  0   0.451   0.7271  -2.5620  -0.3034

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   double  1.206  0.020  1.206
 SJ5  O4   C4   single  1.408  0.020  1.408
 SJ5  O62  C6   single  1.328  0.020  1.328
 SJ5  C6   C5   single  1.507  0.020  1.507
 SJ5  C4   C5   single  1.522  0.020  1.522
 SJ5  C4   C3   single  1.522  0.020  1.522
 SJ5  O3   C3   single  1.412  0.020  1.412
 SJ5  C5   C7   single  1.546  0.020  1.546
 SJ5  C7   N    single  1.445  0.020  1.445
 SJ5  C3   C2   single  1.531  0.020  1.531
 SJ5  C2   N    single  1.449  0.020  1.449
 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  O62  H10  single  0.850  0.020  0.980
 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   106.81  3.000
 SJ5  H2   C2   N    108.99  3.000
 SJ5  H1   C2   N    108.73  3.000
 SJ5  H2   C2   C3   109.82  3.000
 SJ5  H1   C2   C3   108.84  3.000
 SJ5  N    C2   C3   113.44  3.000
 SJ5  H3   C3   C4   108.30  3.000
 SJ5  H3   C3   O3   110.80  3.000
 SJ5  C4   C3   O3   107.25  3.000
 SJ5  H3   C3   C2   108.64  3.000
 SJ5  O3   C3   C2   111.74  3.000
 SJ5  C4   C3   C2   110.07  3.000
 SJ5  H4   O3   C3   108.50  3.000
 SJ5  H5   N    C7   109.91  3.000
 SJ5  H5   N    C2   110.06  3.000
 SJ5  C7   N    C2   112.15  3.000
 SJ5  H8   C7   H7   107.20  3.000
 SJ5  H8   C7   C5   109.83  3.000
 SJ5  H7   C7   C5   108.96  3.000
 SJ5  H8   C7   N    109.04  3.000
 SJ5  H7   C7   N    108.53  3.000
 SJ5  C5   C7   N    113.10  3.000
 SJ5  H9   C5   C4   109.13  3.000
 SJ5  H9   C5   C6   109.23  3.000
 SJ5  C4   C5   C6   110.90  3.000
 SJ5  H9   C5   C7   108.03  3.000
 SJ5  C4   C5   C7   109.93  3.000
 SJ5  C6   C5   C7   109.57  3.000
 SJ5  O61  C6   O62  123.16  3.000
 SJ5  O62  C6   C5   112.32  3.000
 SJ5  O61  C6   C5   124.44  3.000
 SJ5  H10  O62  C6   110.02  3.000
 SJ5  H11  C4   O4   110.85  3.000
 SJ5  H11  C4   C5   108.52  3.000
 SJ5  O4   C4   C5   107.51  3.000
 SJ5  H11  C4   C3   107.88  3.000
 SJ5  C5   C4   C3   109.71  3.000
 SJ5  O4   C4   C3   112.31  3.000
 SJ5  H12  O4   C4   108.27  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  CONST_01  H10  O62  C6  C5  180.00   0.0  0
 SJ5  Var_01    C5   C7   N   C2  -54.12  30.0  1
 SJ5  Var_02    C7   N    C2  C3   54.44  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
 SJ5  plan-1  H10  0.020

