# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:26:04 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanedioate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@H](O)[C@H](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
 GKR  GKR  '(2R,3S,4S,5S)-2,3,4,5-tetrahydroxyhexanedioate (non-preferred name)'  ligand  22  14  .  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_GKR
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
 GKR  O1B   O  O      0  -0.716   3.1747  -1.5760  -0.6995
 GKR  O1A   O  OC    -1  -0.604   4.1348   0.2330   0.1951
 GKR  C1    C  C      0   0.399   3.1803  -0.3959  -0.3178
 GKR  C2    C  CH1    0  -0.080   1.8848   0.4317  -0.4999
 GKR  O2    O  OH1    0  -0.629   2.1048   1.7276  -0.0073
 GKR  C3    C  CH1    0  -0.019   0.7080  -0.2542   0.1997
 GKR  O3    O  OH1    0  -0.654   0.8758  -0.2201   1.5987
 GKR  C4    C  CH1    0  -0.032  -0.6552   0.2917  -0.2214
 GKR  O4    O  OH1    0  -0.671  -0.7852   1.6252   0.2032
 GKR  O5    O  OH1    0  -0.691  -1.6832  -1.9041  -0.0347
 GKR  C5    C  CH1    0  -0.137  -1.8096  -0.5600   0.3434
 GKR  C6    C  C      0   0.386  -3.1668  -0.0157  -0.1474
 GKR  O6A   O  O      0  -0.773  -3.9186  -0.8410  -0.6969
 GKR  O6B   O  OC    -1  -0.480  -3.3945   1.2026   0.0367
 GKR  H21   H  HCH1   0   0.245   1.6653   0.4582  -1.5795
 GKR  HO21  H  HOH1   0   0.423   3.0338   1.6675   0.2900
 GKR  H31   H  HCH1   0   0.256   0.7379  -1.3041  -0.0995
 GKR  HO31  H  HOH1   0   0.430   0.8958   0.7107   1.8478
 GKR  H42   H  HCH1   0   0.284  -0.7027   0.2130  -1.3232
 GKR  H41   H  HOH1   0   0.412  -1.7520   1.7876   0.2197
 GKR  HO51  H  HOH1   0   0.428  -2.5237  -2.0825  -0.4925
 GKR  H51   H  HCH1   0   0.224  -1.7910  -0.4647   1.4400

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
 GKR  O1B  C1    double  1.240  0.020  1.240
 GKR  O1A  C1    single  1.253  0.020  1.253
 GKR  C1   C2    single  1.548  0.020  1.548
 GKR  C2   O2    single  1.404  0.020  1.404
 GKR  C2   C3    single  1.531  0.020  1.531
 GKR  C2   H21   single  0.970  0.020  1.090
 GKR  O2   HO21  single  0.850  0.020  0.980
 GKR  C3   O3    single  1.409  0.020  1.409
 GKR  C3   C4    single  1.528  0.020  1.528
 GKR  C3   H31   single  0.970  0.020  1.090
 GKR  O3   HO31  single  0.850  0.020  0.980
 GKR  C4   O4    single  1.405  0.020  1.405
 GKR  C4   C5    single  1.542  0.020  1.542
 GKR  C4   H42   single  0.970  0.020  1.090
 GKR  O4   H41   single  0.850  0.020  0.980
 GKR  O5   C5    single  1.402  0.020  1.402
 GKR  O5   HO51  single  0.850  0.020  0.980
 GKR  C5   C6    single  1.542  0.020  1.542
 GKR  C5   H51   single  0.970  0.020  1.090
 GKR  C6   O6A   double  1.244  0.020  1.244
 GKR  C6   O6B   single  1.253  0.020  1.253

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
 GKR  C2    C1  O1A  114.67  3.000
 GKR  C2    C1  O1B  117.95  3.000
 GKR  O1A   C1  O1B  127.37  3.000
 GKR  H21   C2  C3   107.78  3.000
 GKR  H21   C2  O2   110.66  3.000
 GKR  C3    C2  O2   111.94  3.000
 GKR  H21   C2  C1   107.15  3.000
 GKR  C3    C2  C1   110.48  3.000
 GKR  O2    C2  C1   108.73  3.000
 GKR  HO21  O2  C2   101.48  3.000
 GKR  H31   C3  C4   107.01  3.000
 GKR  H31   C3  O3   106.97  3.000
 GKR  C4    C3  O3   111.79  3.000
 GKR  H31   C3  C2   106.52  3.000
 GKR  C4    C3  C2   113.56  3.000
 GKR  O3    C3  C2   110.56  3.000
 GKR  HO31  O3  C3   106.40  3.000
 GKR  H42   C4  C5   107.07  3.000
 GKR  H42   C4  O4   111.39  3.000
 GKR  C5    C4  O4   110.13  3.000
 GKR  H42   C4  C3   106.72  3.000
 GKR  C5    C4  C3   111.70  3.000
 GKR  O4    C4  C3   109.77  3.000
 GKR  H41   O4  C4   104.68  3.000
 GKR  HO51  O5  C5   102.99  3.000
 GKR  H51   C5  C6   107.53  3.000
 GKR  H51   C5  O5   110.49  3.000
 GKR  C6    C5  O5   109.38  3.000
 GKR  H51   C5  C4   107.73  3.000
 GKR  C6    C5  C4   110.32  3.000
 GKR  O5    C5  C4   111.31  3.000
 GKR  O6B   C6  O6A  126.87  3.000
 GKR  O6B   C6  C5   117.15  3.000
 GKR  O6A   C6  C5   115.98  3.000

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
 GKR  chir_01  C2  C1  O2  C3  positiv
 GKR  chir_02  C3  O3  C2  C4  positiv
 GKR  chir_03  C4  O4  C3  C5  negativ
 GKR  chir_04  C5  O5  C4  C6  negativ

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
 GKR  plan-1  O1B  0.020
 GKR  plan-1  O1A  0.020
 GKR  plan-1  C1   0.020
 GKR  plan-1  C2   0.020
 GKR  plan-2  C5   0.020
 GKR  plan-2  C6   0.020
 GKR  plan-2  O6A  0.020
 GKR  plan-2  O6B  0.020

