# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:54:11 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: D-gluconic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](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
 GCO  GCO  'D-gluconic acid          '  D-saccharide  24  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_GCO
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
 GCO  C1   C  C      0   0.408  -0.4401   0.2858  -2.8583
 GCO  C2   C  CH1    0  -0.141   0.4797   0.4560  -1.6229
 GCO  C3   C  CH1    0   0.014  -0.1570  -0.1560  -0.3700
 GCO  C4   C  CH1    0  -0.023   0.4347   0.3926   0.9312
 GCO  C5   C  CH1    0  -0.021  -0.2925  -0.1498   2.1751
 GCO  C6   C  CH2    0  -0.158   0.2702   0.4595   3.4498
 GCO  O11  O  O      0  -0.609   0.1058  -0.2803  -3.8335
 GCO  O12  O  OC    -1  -0.587  -1.5958   0.7256  -2.7875
 GCO  O2   O  OH1    0  -0.691   1.7147  -0.1576  -1.9019
 GCO  O3   O  OH1    0  -0.684  -0.0613  -1.5639  -0.4282
 GCO  O4   O  OH1    0  -0.664   1.8257   0.1764   1.0306
 GCO  O5   O  OH1    0  -0.663  -1.6871   0.0440   2.0827
 GCO  O6   O  OH1    0  -0.672  -0.3665  -0.1348   4.5582
 GCO  H2   H  HCH1   0   0.218   0.6063   1.5361  -1.4560
 GCO  H3   H  HCH1   0   0.230  -1.2162   0.1107  -0.3820
 GCO  H4   H  HCH1   0   0.224   0.3060   1.4832   0.9078
 GCO  H5   H  HCH1   0   0.225  -0.1480  -1.2357   2.2155
 GCO  H61  H  HCH2   0   0.185   0.1073   1.5486   3.4270
 GCO  H62  H  HCH2   0   0.205   1.3532   0.3032   3.4776
 GCO  HO2  H  HOH1   0   0.433   1.5823  -0.4467  -2.8291
 GCO  HO3  H  HOH1   0   0.436   0.7537  -1.7595  -0.9098
 GCO  HO4  H  HOH1   0   0.438   1.9893  -0.7716   0.9786
 GCO  HO5  H  HOH1   0   0.442  -1.8650   0.9912   2.0790
 GCO  HO6  H  HOH1   0   0.453   0.0343   0.2227   5.3553

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
 GCO  C1  C2   single  1.550  0.020  1.550
 GCO  C1  O11  deloc   1.253  0.020  1.253
 GCO  C1  O12  deloc   1.239  0.020  1.239
 GCO  C2  C3   single  1.533  0.020  1.533
 GCO  C2  O2   single  1.407  0.020  1.407
 GCO  C2  H2   single  0.970  0.020  1.090
 GCO  C3  C4   single  1.531  0.020  1.531
 GCO  C3  O3   single  1.412  0.020  1.412
 GCO  C3  H3   single  0.970  0.020  1.090
 GCO  C4  C5   single  1.540  0.020  1.540
 GCO  C4  O4   single  1.411  0.020  1.411
 GCO  C4  H4   single  0.970  0.020  1.090
 GCO  C5  C6   single  1.521  0.020  1.521
 GCO  C5  O5   single  1.411  0.020  1.411
 GCO  C5  H5   single  0.970  0.020  1.090
 GCO  C6  O6   single  1.410  0.020  1.410
 GCO  C6  H61  single  0.970  0.020  1.090
 GCO  C6  H62  single  0.970  0.020  1.090
 GCO  O2  HO2  single  0.850  0.020  0.980
 GCO  O3  HO3  single  0.850  0.020  0.980
 GCO  O4  HO4  single  0.850  0.020  0.980
 GCO  O5  HO5  single  0.850  0.020  0.980
 GCO  O6  HO6  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
 GCO  O12  C1  O11  127.70  3.000
 GCO  O12  C1  C2   117.99  3.000
 GCO  O11  C1  C2   114.30  3.000
 GCO  H2   C2  O2   110.93  3.000
 GCO  H2   C2  C3   108.40  3.000
 GCO  O2   C2  C3   110.65  3.000
 GCO  H2   C2  C1   107.28  3.000
 GCO  O2   C2  C1   108.37  3.000
 GCO  C3   C2  C1   111.17  3.000
 GCO  H3   C3  O3   107.98  3.000
 GCO  H3   C3  C4   107.25  3.000
 GCO  O3   C3  C4   111.47  3.000
 GCO  H3   C3  C2   107.24  3.000
 GCO  O3   C3  C2   109.64  3.000
 GCO  C4   C3  C2   113.02  3.000
 GCO  H4   C4  O4   105.62  3.000
 GCO  H4   C4  C5   108.16  3.000
 GCO  O4   C4  C5   110.77  3.000
 GCO  H4   C4  C3   107.00  3.000
 GCO  O4   C4  C3   112.70  3.000
 GCO  C5   C4  C3   112.20  3.000
 GCO  H5   C5  O5   105.59  3.000
 GCO  H5   C5  C6   108.49  3.000
 GCO  O5   C5  C6   111.44  3.000
 GCO  H5   C5  C4   108.46  3.000
 GCO  O5   C5  C4   111.44  3.000
 GCO  C6   C5  C4   111.18  3.000
 GCO  H62  C6  H61  106.74  3.000
 GCO  H62  C6  O6   111.52  3.000
 GCO  H61  C6  O6   111.49  3.000
 GCO  H62  C6  C5   109.28  3.000
 GCO  H61  C6  C5   108.91  3.000
 GCO  O6   C6  C5   108.85  3.000
 GCO  HO2  O2  C2   101.40  3.000
 GCO  HO3  O3  C3   106.22  3.000
 GCO  HO4  O4  C4   108.32  3.000
 GCO  HO5  O5  C5   108.52  3.000
 GCO  HO6  O6  C6   107.88  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
 GCO  chir_01  C2  C1  C3  O2  negativ
 GCO  chir_02  C3  O3  C2  C4  positiv
 GCO  chir_03  C4  O4  C3  C5  negativ
 GCO  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
 GCO  plan-1  C1   0.020
 GCO  plan-1  C2   0.020
 GCO  plan-1  O11  0.020
 GCO  plan-1  O12  0.020

