# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:32:47 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  25  13  .  2023-02-15  2023-02-16
;
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   0.510  -0.4207   0.1137  -2.9305
 GCO  C2   C  CH1   0  -0.108   0.2021   0.6946  -1.6696
 GCO  C3   C  CH1   0  -0.010  -0.2556  -0.1400  -0.4588
 GCO  C4   C  CH1   0  -0.013   0.4758   0.2707   0.8305
 GCO  C5   C  CH1   0  -0.050  -0.3465  -0.0703   2.0865
 GCO  C6   C  CH2   0  -0.156   0.3917   0.3355   3.3551
 GCO  O11  O  O     0  -0.434   0.2105  -0.4002  -3.8174
 GCO  O12  O  OH1   0  -0.590  -1.7397   0.2318  -2.9290
 GCO  O2   O  OH1   0  -0.646   1.5831   0.8301  -1.8183
 GCO  O3   O  OH1   0  -0.665  -0.1524  -1.5247  -0.6995
 GCO  O4   O  OH1   0  -0.662   1.7649  -0.3029   0.8795
 GCO  O5   O  OH1   0  -0.654  -1.6261   0.5125   2.0253
 GCO  O6   O  OH1   0  -0.668  -0.3857  -0.0387   4.4670
 GCO  H2   H  HCH1  0   0.285  -0.1901   1.7070  -1.5284
 GCO  H3   H  HCH1  0   0.263  -1.3196   0.0645  -0.3288
 GCO  H4   H  HCH1  0   0.239   0.6183   1.3584   0.8133
 GCO  H5   H  HCH1  0   0.235  -0.5154  -1.1542   2.1102
 GCO  H61  H  HCH2  0   0.193   0.5679   1.4224   3.3300
 GCO  H62  H  HCH2  0   0.205   1.3771  -0.1418   3.3764
 GCO  HO1  H  HOH1  0   0.486  -2.1157  -0.1746  -3.7246
 GCO  HO2  H  HOH1  0   0.444   1.9791  -0.0234  -2.0228
 GCO  HO3  H  HOH1  0   0.441   0.7761  -1.7835  -0.6778
 GCO  HO4  H  HOH1  0   0.453   1.7164  -1.1654   1.3058
 GCO  HO5  H  HOH1  0   0.447  -1.5319   1.4700   2.0855
 GCO  HO6  H  HOH1  0   0.456   0.1237   0.1502   5.2599

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  1.522  0.020  1.522
 GCO  C1   O11  double  1.204  0.020  1.204
 GCO  C1   O12  single  1.324  0.020  1.324
 GCO  C2   C3   single  1.540  0.020  1.540
 GCO  C2   O2   single  1.396  0.020  1.396
 GCO  C2   H2   single  0.970  0.020  1.090
 GCO  C3   C4   single  1.538  0.020  1.538
 GCO  C3   O3   single  1.409  0.020  1.409
 GCO  C3   H3   single  0.970  0.020  1.090
 GCO  C4   C5   single  1.540  0.020  1.540
 GCO  C4   O4   single  1.412  0.020  1.412
 GCO  C4   H4   single  0.970  0.020  1.090
 GCO  C5   C6   single  1.523  0.020  1.523
 GCO  C5   O5   single  1.407  0.020  1.407
 GCO  C5   H5   single  0.970  0.020  1.090
 GCO  C6   O6   single  1.407  0.020  1.407
 GCO  C6   H61  single  0.970  0.020  1.090
 GCO  C6   H62  single  0.970  0.020  1.090
 GCO  O12  HO1  single  0.850  0.020  0.980
 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  124.13  3.000
 GCO  O12  C1   C2   111.88  3.000
 GCO  O11  C1   C2   123.98  3.000
 GCO  H2   C2   O2   106.17  3.000
 GCO  H2   C2   C3   107.05  3.000
 GCO  O2   C2   C3   115.50  3.000
 GCO  H2   C2   C1   108.25  3.000
 GCO  O2   C2   C1   110.72  3.000
 GCO  C3   C2   C1   108.84  3.000
 GCO  H3   C3   O3   106.02  3.000
 GCO  H3   C3   C4   108.28  3.000
 GCO  O3   C3   C4   111.76  3.000
 GCO  H3   C3   C2   106.37  3.000
 GCO  O3   C3   C2   112.12  3.000
 GCO  C4   C3   C2   111.90  3.000
 GCO  H4   C4   O4   106.55  3.000
 GCO  H4   C4   C5   107.56  3.000
 GCO  O4   C4   C5   111.68  3.000
 GCO  H4   C4   C3   108.26  3.000
 GCO  O4   C4   C3   110.78  3.000
 GCO  C5   C4   C3   111.76  3.000
 GCO  H5   C5   O5   105.67  3.000
 GCO  H5   C5   C6   108.66  3.000
 GCO  O5   C5   C6   111.51  3.000
 GCO  H5   C5   C4   108.58  3.000
 GCO  O5   C5   C4   111.00  3.000
 GCO  C6   C5   C4   111.20  3.000
 GCO  H62  C6   H61  106.65  3.000
 GCO  H62  C6   O6   111.45  3.000
 GCO  H61  C6   O6   111.64  3.000
 GCO  H62  C6   C5   109.65  3.000
 GCO  H61  C6   C5   108.76  3.000
 GCO  O6   C6   C5   108.63  3.000
 GCO  HO1  O12  C1   110.37  3.000
 GCO  HO2  O2   C2   110.09  3.000
 GCO  HO3  O3   C3   109.29  3.000
 GCO  HO4  O4   C4   109.46  3.000
 GCO  HO5  O5   C5   108.65  3.000
 GCO  HO6  O6   C6   107.86  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
 GCO  CONST_01  HO1  O12  C1  C2  180.00  0.0  0

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
 GCO  plan-1  HO1  0.020

