# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 23:38:57 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: D-glucuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C=O)[C@@H](O)[C@H](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
 REL  REL  'D-glucuronic acid        '  D-saccharide  22  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_REL
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
 REL  O6A  O  O      0  -0.572  -3.6900  -0.4881  -0.6417
 REL  C6   C  C      0   0.437  -2.8122   0.1143  -0.0040
 REL  O6B  O  OC    -1  -0.601  -2.8831   1.2736   0.4704
 REL  C5   C  CH1    0  -0.126  -1.4901  -0.6474   0.2229
 REL  O5   O  OH1    0  -0.689  -1.5065  -1.8584  -0.4809
 REL  C4   C  CH1    0   0.002  -0.2874   0.2164  -0.2054
 REL  O4   O  OH1    0  -0.703  -0.2885   1.4362   0.4930
 REL  C3   C  CH1    0  -0.007   1.0376  -0.4951   0.0915
 REL  O3   O  OH1    0  -0.666   1.3301  -0.4472   1.4686
 REL  C2   C  CH1    0  -0.081   2.2116   0.0573  -0.7329
 REL  O2   O  OH1    0  -0.635   2.4429   1.4260  -0.6039
 REL  C1   C  C1     0   0.173   3.4308  -0.7665  -0.4007
 REL  O1   O  O      0  -0.365   4.4573  -0.3105   0.0333
 REL  H5   H  HCH1   0   0.218  -1.4022  -0.8352   1.3047
 REL  HO5  H  HOH1   0   0.439  -2.3788  -1.8630  -0.9116
 REL  H4   H  HCH1   0   0.201  -0.3626   0.3683  -1.2939
 REL  HO4  H  HOH1   0   0.444  -1.2432   1.6432   0.6366
 REL  H3   H  HCH1   0   0.239   0.9308  -1.5473  -0.1925
 REL  HO3  H  HOH1   0   0.432   0.9655   0.3855   1.7991
 REL  H2   H  HCH1   0   0.259   1.9839  -0.1398  -1.7890
 REL  HO2  H  HOH1   0   0.425   2.7376   1.6120   0.2941
 REL  H1   H  H      0   0.172   3.3132  -1.8496  -0.5844

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
 REL  O6A  C6   deloc   1.241  0.020  1.241
 REL  O4   C4   single  1.406  0.020  1.406
 REL  C6   O6B  deloc   1.255  0.020  1.255
 REL  C6   C5   single  1.543  0.020  1.543
 REL  C5   C4   single  1.541  0.020  1.541
 REL  C5   O5   single  1.401  0.020  1.401
 REL  C4   C3   single  1.533  0.020  1.533
 REL  O3   C3   single  1.409  0.020  1.409
 REL  C3   C2   single  1.537  0.020  1.537
 REL  C2   O2   single  1.394  0.020  1.394
 REL  C2   C1   single  1.509  0.020  1.509
 REL  C1   O1   double  1.204  0.020  1.204
 REL  C5   H5   single  0.970  0.020  1.090
 REL  O5   HO5  single  0.850  0.020  0.980
 REL  C4   H4   single  0.970  0.020  1.090
 REL  O4   HO4  single  0.850  0.020  0.980
 REL  C3   H3   single  0.970  0.020  1.090
 REL  O3   HO3  single  0.850  0.020  0.980
 REL  C2   H2   single  0.970  0.020  1.090
 REL  O2   HO2  single  0.850  0.020  0.980
 REL  C1   H1   single  0.930  0.020  1.080

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
 REL  C5   C6  O6B  116.68  3.000
 REL  C5   C6  O6A  116.24  3.000
 REL  O6B  C6  O6A  127.08  3.000
 REL  H5   C5  C4   107.83  3.000
 REL  H5   C5  O5   110.30  3.000
 REL  C4   C5  O5   110.73  3.000
 REL  H5   C5  C6   107.28  3.000
 REL  O5   C5  C6   110.06  3.000
 REL  C4   C5  C6   110.56  3.000
 REL  HO5  O5  C5   103.71  3.000
 REL  H4   C4  C3   108.33  3.000
 REL  H4   C4  O4   111.79  3.000
 REL  C3   C4  O4   107.90  3.000
 REL  H4   C4  C5   107.37  3.000
 REL  C3   C4  C5   111.13  3.000
 REL  O4   C4  C5   110.34  3.000
 REL  HO4  O4  C4   104.77  3.000
 REL  H3   C3  C2   106.30  3.000
 REL  H3   C3  O3   107.85  3.000
 REL  C2   C3  O3   110.70  3.000
 REL  H3   C3  C4   108.14  3.000
 REL  C2   C3  C4   112.92  3.000
 REL  O3   C3  C4   110.67  3.000
 REL  HO3  O3  C3   106.57  3.000
 REL  H2   C2  C1   106.34  3.000
 REL  H2   C2  O2   107.43  3.000
 REL  C1   C2  O2   112.44  3.000
 REL  H2   C2  C3   107.03  3.000
 REL  C1   C2  C3   107.63  3.000
 REL  O2   C2  C3   115.46  3.000
 REL  HO2  O2  C2   109.06  3.000
 REL  H1   C1  O1   121.46  3.000
 REL  H1   C1  C2   114.38  3.000
 REL  O1   C1  C2   124.16  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
 REL  chir_01  C5  C6  C4  O5  positiv
 REL  chir_02  C4  O4  C5  C3  positiv
 REL  chir_03  C3  O3  C4  C2  negativ
 REL  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
 REL  plan-1  O6A  0.020
 REL  plan-1  C6   0.020
 REL  plan-1  O6B  0.020
 REL  plan-1  C5   0.020
 REL  plan-2  C2   0.020
 REL  plan-2  C1   0.020
 REL  plan-2  O1   0.020
 REL  plan-2  H1   0.020

