# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:35:14 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  20  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_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   0.519   1.1629  -1.4180   0.0243
 GCB  C2   C  CH1    0  -0.121   1.8445  -0.1026  -0.3344
 GCB  C3   C  CH1    0   0.024   1.1166   1.1177   0.2093
 GCB  C4   C  CH1    0   0.002  -0.3400   1.0087  -0.1933
 GCB  C5   C  CH1    0  -0.148  -0.9263  -0.2733   0.4133
 GCB  C6   C  C      0   0.443  -2.3790  -0.5023  -0.0526
 GCB  O1   O  O      0  -0.432   1.7834  -2.4441   0.1248
 GCB  O2   O  OH1    0  -0.658   3.1636  -0.0763   0.1232
 GCB  O3   O  OH1    0  -0.664   1.6465   2.3019  -0.3216
 GCB  O4   O  OH1    0  -0.692  -1.0495   2.1157   0.2778
 GCB  O5   O  O2     0  -0.433  -0.1572  -1.4441   0.1238
 GCB  O6A  O  OC    -1  -0.610  -3.1021   0.5230   0.0428
 GCB  O6B  O  O      0  -0.552  -2.7101  -1.6185  -0.4497
 GCB  HC2  H  HCH1   0   0.265   1.7964  -0.0492  -1.4351
 GCB  HC3  H  HCH1   0   0.224   1.1792   1.1118   1.3096
 GCB  HC4  H  HCH1   0   0.211  -0.3921   0.9360  -1.2940
 GCB  HC5  H  HCH1   0   0.264  -0.9343  -0.1495   1.5041
 GCB  HO2  H  HOH1   0   0.462   3.6750  -0.7431  -0.3461
 GCB  HO3  H  HOH1   0   0.454   2.5716   2.3653  -0.0621
 GCB  HO4  H  HOH1   0   0.442  -1.9878   1.8162   0.2461

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  1.524  0.020  1.524
 GCB  C1  O1   double  1.203  0.020  1.203
 GCB  C1  O5   single  1.324  0.020  1.324
 GCB  C2  C3   single  1.521  0.020  1.521
 GCB  C2  O2   single  1.396  0.020  1.396
 GCB  C2  HC2  single  0.970  0.020  1.090
 GCB  C3  C4   single  1.515  0.020  1.515
 GCB  C3  O3   single  1.402  0.020  1.402
 GCB  C3  HC3  single  0.970  0.020  1.090
 GCB  C4  C5   single  1.535  0.020  1.535
 GCB  C4  O4   single  1.397  0.020  1.397
 GCB  C4  HC4  single  0.970  0.020  1.090
 GCB  C5  C6   single  1.543  0.020  1.543
 GCB  C5  O5   single  1.430  0.020  1.430
 GCB  C5  HC5  single  0.970  0.020  1.090
 GCB  C6  O6A  deloc   1.258  0.020  1.258
 GCB  C6  O6B  deloc   1.230  0.020  1.230
 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

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   119.40  3.000
 GCB  O5   C1  C2   118.72  3.000
 GCB  O1   C1  C2   121.67  3.000
 GCB  HC2  C2  O2   111.55  3.000
 GCB  HC2  C2  C3   107.27  3.000
 GCB  O2   C2  C3   108.65  3.000
 GCB  HC2  C2  C1   104.90  3.000
 GCB  O2   C2  C1   111.19  3.000
 GCB  C3   C2  C1   113.21  3.000
 GCB  HC3  C3  O3   111.18  3.000
 GCB  HC3  C3  C4   108.63  3.000
 GCB  O3   C3  C4   108.88  3.000
 GCB  HC3  C3  C2   108.98  3.000
 GCB  O3   C3  C2   111.19  3.000
 GCB  C4   C3  C2   107.89  3.000
 GCB  HC4  C4  O4   111.37  3.000
 GCB  HC4  C4  C5   108.72  3.000
 GCB  O4   C4  C5   109.55  3.000
 GCB  HC4  C4  C3   108.35  3.000
 GCB  O4   C4  C3   109.98  3.000
 GCB  C5   C4  C3   108.81  3.000
 GCB  HC5  C5  O5   107.30  3.000
 GCB  HC5  C5  C6   108.05  3.000
 GCB  O5   C5  C6   108.89  3.000
 GCB  HC5  C5  C4   107.54  3.000
 GCB  O5   C5  C4   113.48  3.000
 GCB  C6   C5  C4   111.37  3.000
 GCB  O6B  C6  O6A  127.53  3.000
 GCB  O6B  C6  C5   119.05  3.000
 GCB  O6A  C6  C5   113.41  3.000
 GCB  HO2  O2  C2   109.21  3.000
 GCB  HO3  O3  C3   108.47  3.000
 GCB  HO4  O4  C4   103.40  3.000
 GCB  C5   O5  C1   122.35  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  Var_01  O1  C1  O5  C5  160.93  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-2  C1   0.020
 GCB  plan-2  C2   0.020
 GCB  plan-2  O1   0.020
 GCB  plan-2  O5   0.020

