# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:00:09 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2R,3S)-2,3-dihydroxy-5-oxohexanedioate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC(=O)C([O-])=O)[C@@H](O)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
 GLR  GLR  '(2R,3S)-2,3-dihydroxy-5-oxohexanedioate (non-preferred name)'  ligand  19  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GLR
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
 GLR  O1B   O  O      0  -0.670   3.2089  -1.1212  -0.9886
 GLR  O1A   O  OC    -1  -0.634   3.8769   0.3543   0.5527
 GLR  C1    C  C      0   0.389   3.0590  -0.1254  -0.2660
 GLR  C2    C  CH1    0  -0.121   1.7245   0.6467  -0.3699
 GLR  O2    O  OH1    0  -0.554   1.7542   1.7384   0.5179
 GLR  C3    C  CH1    0  -0.036   0.5417  -0.2658  -0.0528
 GLR  O3    O  OH1    0  -0.644   0.6585  -0.7901   1.2541
 GLR  C4    C  CH2    0  -0.578  -0.7856   0.4548  -0.2424
 GLR  O5    O  O      0  -0.457  -1.9128  -1.6438  -0.1288
 GLR  C5    C  C      0   0.290  -1.9960  -0.4385  -0.1608
 GLR  C6    C  C      0   0.364  -3.3929   0.2539  -0.1602
 GLR  O6A   O  O      0  -0.612  -4.3688  -0.5088  -0.1739
 GLR  O6B   O  OC    -1  -0.639  -3.3767   1.4967  -0.1511
 GLR  H21   H  HCH1   0   0.203   1.6179   0.9975  -1.4075
 GLR  HO21  H  HOH1   0   0.423   2.6375   1.6401   0.9252
 GLR  H31   H  HCH1   0   0.266   0.5895  -1.1176  -0.7353
 GLR  HO31  H  HOH1   0   0.428   0.7865  -0.0403   1.8465
 GLR  H41   H  HCH2   0   0.306  -0.8942   1.2730   0.4742
 GLR  H42   H  HCH2   0   0.276  -0.8160   0.9416  -1.2249

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
 GLR  O1B  C1    double  1.239  0.020  1.239
 GLR  O1A  C1    single  1.253  0.020  1.253
 GLR  C1   C2    single  1.545  0.020  1.545
 GLR  C2   O2    single  1.407  0.020  1.407
 GLR  C2   C3    single  1.527  0.020  1.527
 GLR  C2   H21   single  0.970  0.020  1.090
 GLR  O2   HO21  single  0.850  0.020  0.980
 GLR  C3   O3    single  1.413  0.020  1.413
 GLR  C3   C4    single  1.522  0.020  1.522
 GLR  C3   H31   single  0.970  0.020  1.090
 GLR  O3   HO31  single  0.850  0.020  0.980
 GLR  C4   C5    single  1.507  0.020  1.507
 GLR  C4   H41   single  0.970  0.020  1.090
 GLR  C4   H42   single  0.970  0.020  1.090
 GLR  O5   C5    double  1.209  0.020  1.209
 GLR  C5   C6    single  1.559  0.020  1.559
 GLR  C6   O6A   double  1.239  0.020  1.239
 GLR  C6   O6B   single  1.243  0.020  1.243

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
 GLR  C2    C1  O1A  114.61  3.000
 GLR  C2    C1  O1B  117.82  3.000
 GLR  O1A   C1  O1B  127.57  3.000
 GLR  H21   C2  C3   108.13  3.000
 GLR  H21   C2  O2   110.46  3.000
 GLR  C3    C2  O2   110.42  3.000
 GLR  H21   C2  C1   107.83  3.000
 GLR  C3    C2  C1   110.88  3.000
 GLR  O2    C2  C1   109.08  3.000
 GLR  HO21  O2  C2   101.77  3.000
 GLR  H31   C3  C4   109.23  3.000
 GLR  H31   C3  O3   106.55  3.000
 GLR  C4    C3  O3   111.28  3.000
 GLR  H31   C3  C2   107.59  3.000
 GLR  C4    C3  C2   111.51  3.000
 GLR  O3    C3  C2   110.47  3.000
 GLR  HO31  O3  C3   106.90  3.000
 GLR  H42   C4  H41  104.61  3.000
 GLR  H42   C4  C5   106.82  3.000
 GLR  H41   C4  C5   109.18  3.000
 GLR  H42   C4  C3   110.23  3.000
 GLR  H41   C4  C3   111.06  3.000
 GLR  C5    C4  C3   114.41  3.000
 GLR  C6    C5  O5   120.30  3.000
 GLR  C6    C5  C4   117.17  3.000
 GLR  O5    C5  C4   122.50  3.000
 GLR  O6B   C6  O6A  128.76  3.000
 GLR  O6B   C6  C5   115.61  3.000
 GLR  O6A   C6  C5   115.63  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
 GLR  Var_01  O5   C5  C4  C3   -9.48  30.0  3
 GLR  Var_02  O6A  C6  C5  C4  175.81  30.0  2

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
 GLR  chir_01  C2  C1  O2  C3  positiv
 GLR  chir_02  C3  O3  C2  C4  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
 GLR  plan-1  C4   0.020
 GLR  plan-1  O5   0.020
 GLR  plan-1  C5   0.020
 GLR  plan-1  C6   0.020
 GLR  plan-2  O1B  0.020
 GLR  plan-2  O1A  0.020
 GLR  plan-2  C1   0.020
 GLR  plan-2  C2   0.020
 GLR  plan-3  C5   0.020
 GLR  plan-3  C6   0.020
 GLR  plan-3  O6A  0.020
 GLR  plan-3  O6B  0.020

