# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:53:33 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@H](OC(=O)[C@@H]1O)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
 GCB  GCB  '(2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxotetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  D-saccharide  21  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_GCB
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
 GCB  C1   C  C     0   0.531   1.1747  -1.3964   0.1222
 GCB  C2   C  CH1   0  -0.125   1.8133  -0.1020  -0.3528
 GCB  C3   C  CH1   0   0.024   1.1317   1.1259   0.2329
 GCB  C4   C  CH1   0  -0.029  -0.3490   1.0513  -0.0976
 GCB  C5   C  CH1   0  -0.063  -0.9270  -0.2474   0.5146
 GCB  C6   C  C     0   0.511  -2.2879  -0.5743  -0.0741
 GCB  O1   O  O     0  -0.414   1.7923  -2.4153   0.2563
 GCB  O2   O  OH1   0  -0.654   3.1657  -0.0578  -0.0179
 GCB  O3   O  OH1   0  -0.657   1.6426   2.3005  -0.3265
 GCB  O4   O  OH1   0  -0.650  -0.9793   2.1644   0.4593
 GCB  O5   O  O2    0  -0.438  -0.1426  -1.4125   0.3169
 GCB  O6A  O  OH1   0  -0.587  -3.1958   0.3045   0.3167
 GCB  O6B  O  O     0  -0.412  -2.4991  -1.4970  -0.8112
 GCB  HC2  H  HCH1  0   0.277   1.6624  -0.0791  -1.4446
 GCB  HC3  H  HCH1  0   0.240   1.2524   1.1167   1.3286
 GCB  HC4  H  HCH1  0   0.260  -0.4606   1.0244  -1.1907
 GCB  HC5  H  HCH1  0   0.303  -1.0292  -0.0860   1.5931
 GCB  HO2  H  HOH1  0   0.467   3.6545  -0.6686  -0.5783
 GCB  HO3  H  HOH1  0   0.458   2.5864   2.3411  -0.1379
 GCB  HO4  H  HOH1  0   0.464  -1.8051   2.3338  -0.0035
 GCB  HO6  H  HOH1  0   0.494  -4.0517   0.1132  -0.0977

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
 GCB  C1   C2   single  1.520  0.020  1.520
 GCB  C1   O1   double  1.199  0.020  1.199
 GCB  C1   O5   single  1.332  0.020  1.332
 GCB  C2   C3   single  1.522  0.020  1.522
 GCB  C2   O2   single  1.394  0.020  1.394
 GCB  C2   HC2  single  0.970  0.020  1.090
 GCB  C3   C4   single  1.519  0.020  1.519
 GCB  C3   O3   single  1.398  0.020  1.398
 GCB  C3   HC3  single  0.970  0.020  1.090
 GCB  C4   C5   single  1.548  0.020  1.548
 GCB  C4   O4   single  1.395  0.020  1.395
 GCB  C4   HC4  single  0.970  0.020  1.090
 GCB  C5   C6   single  1.518  0.020  1.518
 GCB  C5   O5   single  1.418  0.020  1.418
 GCB  C5   HC5  single  0.970  0.020  1.090
 GCB  C6   O6A  single  1.323  0.020  1.323
 GCB  C6   O6B  double  1.200  0.020  1.200
 GCB  O2   HO2  single  0.850  0.020  0.980
 GCB  O3   HO3  single  0.850  0.020  0.980
 GCB  O4   HO4  single  0.850  0.020  0.980
 GCB  O6A  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
 GCB  O5   C1   O1   118.87  3.000
 GCB  O5   C1   C2   118.14  3.000
 GCB  O1   C1   C2   122.85  3.000
 GCB  HC2  C2   O2   111.73  3.000
 GCB  HC2  C2   C3   107.64  3.000
 GCB  O2   C2   C3   108.45  3.000
 GCB  HC2  C2   C1   105.65  3.000
 GCB  O2   C2   C1   111.08  3.000
 GCB  C3   C2   C1   112.26  3.000
 GCB  HC3  C3   O3   111.39  3.000
 GCB  HC3  C3   C4   108.82  3.000
 GCB  O3   C3   C4   108.09  3.000
 GCB  HC3  C3   C2   109.07  3.000
 GCB  O3   C3   C2   111.12  3.000
 GCB  C4   C3   C2   108.26  3.000
 GCB  HC4  C4   O4   111.76  3.000
 GCB  HC4  C4   C5   109.57  3.000
 GCB  O4   C4   C5   110.05  3.000
 GCB  HC4  C4   C3   108.45  3.000
 GCB  O4   C4   C3   108.32  3.000
 GCB  C5   C4   C3   108.61  3.000
 GCB  HC5  C5   O5   108.06  3.000
 GCB  HC5  C5   C6   109.26  3.000
 GCB  O5   C5   C6   105.35  3.000
 GCB  HC5  C5   C4   107.50  3.000
 GCB  O5   C5   C4   115.32  3.000
 GCB  C6   C5   C4   111.22  3.000
 GCB  O6B  C6   O6A  124.87  3.000
 GCB  O6B  C6   C5   124.17  3.000
 GCB  O6A  C6   C5   110.95  3.000
 GCB  HO2  O2   C2   109.44  3.000
 GCB  HO3  O3   C3   108.37  3.000
 GCB  HO4  O4   C4   109.66  3.000
 GCB  C5   O5   C1   123.88  3.000
 GCB  HO6  O6A  C6   110.39  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
 GCB  CONST_01  HO6  O6A  C6  C5  180.00   0.0  0
 GCB  Var_01    O1   C1   O5  C5  163.80  30.0  1

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
 GCB  chir_01  C2  C1  C3  O2  negativ
 GCB  chir_02  C3  O3  C2  C4  positiv
 GCB  chir_03  C4  O4  C3  C5  negativ
 GCB  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
 GCB  plan-1  C5   0.020
 GCB  plan-1  C6   0.020
 GCB  plan-1  O6A  0.020
 GCB  plan-1  O6B  0.020
 GCB  plan-1  HO6  0.020
 GCB  plan-2  C1   0.020
 GCB  plan-2  C2   0.020
 GCB  plan-2  O1   0.020
 GCB  plan-2  O5   0.020

