# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:35:20 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-deoxy-3-fluoro-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](F)[C@@H]1O
#
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
 G3F  G3F  3-deoxy-3-fluoro-beta-D-glucopyranose  D-saccharide  23  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G3F
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
 G3F  C1   C  CH1   0   0.254   0.5857  -1.4354   0.2259
 G3F  O1   O  OH1   0  -0.658   1.0208  -2.6440  -0.2733
 G3F  C2   C  CH1   0  -0.051   1.5671  -0.3507  -0.2228
 G3F  O2   O  OH1   0  -0.665   2.8370  -0.5374   0.3413
 G3F  C3   C  CH1   0   0.163   1.0361   0.9880   0.2403
 G3F  F3   F  F     0  -0.376   1.8367   2.0086  -0.2712
 G3F  C4   C  CH1   0  -0.018  -0.3999   1.2201  -0.2045
 G3F  O4   O  OH1   0  -0.668  -0.9387   2.3744   0.3887
 G3F  C5   C  CH1   0  -0.025  -1.2576   0.0222   0.2154
 G3F  O5   O  O2    0  -0.494  -0.6909  -1.1635  -0.2969
 G3F  C6   C  CH2   0  -0.154  -2.6724   0.1332  -0.3115
 G3F  O6   O  OH1   0  -0.670  -3.4232  -0.9487   0.1847
 G3F  H1   H  HCH1  0   0.197   0.5367  -1.4454   1.3285
 G3F  HO1  H  HOH1  0   0.469   0.6801  -3.3609   0.2716
 G3F  H2   H  HCH1  0   0.231   1.6041  -0.3626  -1.3233
 G3F  HO2  H  HOH1  0   0.456   3.2114  -1.3470  -0.0211
 G3F  H3   H  HCH1  0   0.220   1.0922   1.0500   1.3338
 G3F  H4   H  HCH1  0   0.230  -0.4202   1.2898  -1.3022
 G3F  HO4  H  HOH1  0   0.461  -0.5648   3.1493  -0.0415
 G3F  H5   H  HCH1  0   0.228  -1.2889  -0.0182   1.3171
 G3F  H6   H  HCH2  0   0.215  -3.0861   1.0947   0.0082
 G3F  H6A  H  HCH2  0   0.198  -2.6438   0.1423  -1.4102
 G3F  HO6  H  HOH1  0   0.457  -4.3367  -0.8241  -0.0866

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
 G3F  O1  C1   single  1.378  0.020  1.378
 G3F  C2  C1   single  1.530  0.020  1.530
 G3F  C1  O5   single  1.406  0.020  1.406
 G3F  C1  H1   single  0.970  0.020  1.090
 G3F  O1  HO1  single  0.850  0.020  0.980
 G3F  O2  C2   single  1.402  0.020  1.402
 G3F  C2  C3   single  1.513  0.020  1.513
 G3F  C2  H2   single  0.970  0.020  1.090
 G3F  O2  HO2  single  0.850  0.020  0.980
 G3F  F3  C3   single  1.394  0.020  1.394
 G3F  C3  C4   single  1.521  0.020  1.521
 G3F  C3  H3   single  0.970  0.020  1.090
 G3F  C4  C5   single  1.532  0.020  1.532
 G3F  C4  O4   single  1.405  0.020  1.405
 G3F  C4  H4   single  0.970  0.020  1.090
 G3F  O4  HO4  single  0.850  0.020  0.980
 G3F  O5  C5   single  1.410  0.020  1.410
 G3F  C5  C6   single  1.514  0.020  1.514
 G3F  C5  H5   single  0.970  0.020  1.090
 G3F  C6  O6   single  1.407  0.020  1.407
 G3F  C6  H6   single  0.970  0.020  1.090
 G3F  C6  H6A  single  0.970  0.020  1.090
 G3F  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
 G3F  H1   C1  O5  109.44  3.000
 G3F  H1   C1  C2  109.14  3.000
 G3F  O5   C1  C2  109.65  3.000
 G3F  H1   C1  O1  111.59  3.000
 G3F  O5   C1  O1  108.76  3.000
 G3F  C2   C1  O1  108.24  3.000
 G3F  HO1  O1  C1  109.65  3.000
 G3F  H2   C2  C3  109.10  3.000
 G3F  H2   C2  O2  111.73  3.000
 G3F  C3   C2  O2  108.22  3.000
 G3F  H2   C2  C1  107.88  3.000
 G3F  C3   C2  C1  108.21  3.000
 G3F  O2   C2  C1  111.63  3.000
 G3F  HO2  O2  C2  108.23  3.000
 G3F  H3   C3  C4  109.34  3.000
 G3F  H3   C3  F3  107.17  3.000
 G3F  C4   C3  F3  108.85  3.000
 G3F  H3   C3  C2  109.71  3.000
 G3F  C4   C3  C2  112.14  3.000
 G3F  F3   C3  C2  109.50  3.000
 G3F  H4   C4  C5  108.22  3.000
 G3F  H4   C4  O4  111.23  3.000
 G3F  C5   C4  O4  108.17  3.000
 G3F  H4   C4  C3  108.60  3.000
 G3F  O4   C4  C3  111.34  3.000
 G3F  C5   C4  C3  109.22  3.000
 G3F  HO4  O4  C4  108.90  3.000
 G3F  H5   C5  C6  108.90  3.000
 G3F  H5   C5  O5  110.09  3.000
 G3F  C6   C5  O5  108.10  3.000
 G3F  H5   C5  C4  108.56  3.000
 G3F  C6   C5  C4  111.75  3.000
 G3F  O5   C5  C4  109.44  3.000
 G3F  C5   O5  C1  113.10  3.000
 G3F  H6A  C6  H6  107.13  3.000
 G3F  H6A  C6  O6  111.89  3.000
 G3F  H6   C6  O6  111.76  3.000
 G3F  H6A  C6  C5  108.92  3.000
 G3F  H6   C6  C5  108.42  3.000
 G3F  O6   C6  C5  108.63  3.000
 G3F  HO6  O6  C6  107.93  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
 G3F  chir_01  C1  O1  C2  O5  negativ
 G3F  chir_02  C2  O2  C1  C3  negativ
 G3F  chir_03  C3  F3  C4  C2  negativ
 G3F  chir_04  C4  O4  C3  C5  negativ
 G3F  chir_05  C5  O5  C4  C6  negativ

