# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:38:40 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: alpha-D-glucopyranosyl fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](F)[C@H](O)[C@@H](O)[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
 GLF  GLF  'alpha-D-glucopyranosyl fluoride'  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 PERFECT
;

data_comp_GLF
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
 GLF  C1   C  CH1   0   0.369   1.5864  -0.2437  -0.4880
 GLF  C2   C  CH1   0  -0.052   0.5509  -0.5301  -1.5699
 GLF  C3   C  CH1   0  -0.008  -0.7542   0.1885  -1.2579
 GLF  C4   C  CH1   0   0.024  -1.2069  -0.1653   0.1527
 GLF  C5   C  CH1   0  -0.022  -0.0938   0.1422   1.1527
 GLF  C6   C  CH2   0  -0.158  -0.4382  -0.3456   2.5440
 GLF  F1   F  F     0  -0.380   1.9717   1.0897  -0.5753
 GLF  O2   O  OH1   0  -0.667   0.9918  -0.1252  -2.8394
 GLF  O3   O  OH1   0  -0.672  -1.7833  -0.1963  -2.1374
 GLF  O4   O  OH1   0  -0.670  -2.3372   0.5782   0.5328
 GLF  O5   O  O2    0  -0.490   1.1138  -0.5120   0.7704
 GLF  O6   O  OH1   0  -0.670   0.5789   0.0563   3.4296
 GLF  H1   H  HCH1  0   0.236   2.4883  -0.8456  -0.6249
 GLF  H2   H  HCH1  0   0.236   0.3620  -1.6121  -1.5391
 GLF  H3   H  HCH1  0   0.223  -0.5881   1.2754  -1.3058
 GLF  H4   H  HCH1  0   0.216  -1.4149  -1.2471   0.1865
 GLF  H5   H  HCH1  0   0.239   0.0604   1.2288   1.1852
 GLF  H61  H  HCH2  0   0.199  -0.5544  -1.4381   2.5209
 GLF  H62  H  HCH2  0   0.216  -1.4083   0.0771   2.8241
 GLF  HO2  H  HOH1  0   0.462   1.5826  -0.7963  -3.1939
 GLF  HO3  H  HOH1  0   0.457  -1.5771   0.1397  -3.0153
 GLF  HO4  H  HOH1  0   0.456  -3.0419   0.3976  -0.0983
 GLF  HO6  H  HOH1  0   0.458   0.3233  -0.2126   4.3164

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
 GLF  C1  C2   single  1.525  0.020  1.525
 GLF  C1  F1   single  1.391  0.020  1.391
 GLF  C1  O5   single  1.371  0.020  1.371
 GLF  C1  H1   single  0.970  0.020  1.090
 GLF  C2  C3   single  1.522  0.020  1.522
 GLF  C2  O2   single  1.404  0.020  1.404
 GLF  C2  H2   single  0.970  0.020  1.090
 GLF  C3  C4   single  1.523  0.020  1.523
 GLF  C3  O3   single  1.407  0.020  1.407
 GLF  C3  H3   single  0.970  0.020  1.090
 GLF  C4  C5   single  1.528  0.020  1.528
 GLF  C4  O4   single  1.405  0.020  1.405
 GLF  C4  H4   single  0.970  0.020  1.090
 GLF  C5  C6   single  1.514  0.020  1.514
 GLF  C5  O5   single  1.426  0.020  1.426
 GLF  C5  H5   single  0.970  0.020  1.090
 GLF  C6  O6   single  1.407  0.020  1.407
 GLF  C6  H61  single  0.970  0.020  1.090
 GLF  C6  H62  single  0.970  0.020  1.090
 GLF  O2  HO2  single  0.850  0.020  0.980
 GLF  O3  HO3  single  0.850  0.020  0.980
 GLF  O4  HO4  single  0.850  0.020  0.980
 GLF  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
 GLF  H1   C1  O5   106.95  3.000
 GLF  H1   C1  F1   106.95  3.000
 GLF  O5   C1  F1   109.93  3.000
 GLF  H1   C1  C2   111.60  3.000
 GLF  O5   C1  C2   112.37  3.000
 GLF  F1   C1  C2   108.89  3.000
 GLF  H2   C2  O2   111.31  3.000
 GLF  H2   C2  C3   108.17  3.000
 GLF  O2   C2  C3   108.57  3.000
 GLF  H2   C2  C1   106.37  3.000
 GLF  O2   C2  C1   111.98  3.000
 GLF  C3   C2  C1   110.38  3.000
 GLF  H3   C3  O3   110.68  3.000
 GLF  H3   C3  C4   108.33  3.000
 GLF  O3   C3  C4   107.33  3.000
 GLF  H3   C3  C2   109.14  3.000
 GLF  O3   C3  C2   111.70  3.000
 GLF  C4   C3  C2   109.57  3.000
 GLF  H4   C4  O4   111.06  3.000
 GLF  H4   C4  C5   108.36  3.000
 GLF  O4   C4  C5   107.61  3.000
 GLF  H4   C4  C3   108.21  3.000
 GLF  O4   C4  C3   111.51  3.000
 GLF  C5   C4  C3   110.06  3.000
 GLF  H5   C5  O5   110.07  3.000
 GLF  H5   C5  C6   108.88  3.000
 GLF  O5   C5  C6   106.94  3.000
 GLF  H5   C5  C4   108.71  3.000
 GLF  O5   C5  C4   110.45  3.000
 GLF  C6   C5  C4   111.77  3.000
 GLF  H62  C6  H61  107.19  3.000
 GLF  H62  C6  O6   111.67  3.000
 GLF  H61  C6  O6   111.93  3.000
 GLF  H62  C6  C5   108.20  3.000
 GLF  H61  C6  C5   108.97  3.000
 GLF  O6   C6  C5   108.78  3.000
 GLF  HO2  O2  C2   108.97  3.000
 GLF  HO3  O3  C3   108.54  3.000
 GLF  HO4  O4  C4   108.18  3.000
 GLF  C5   O5  C1   116.64  3.000
 GLF  HO6  O6  C6   107.97  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
 GLF  chir_01  C1  C2  F1  O5  negativ
 GLF  chir_02  C2  O2  C1  C3  negativ
 GLF  chir_03  C3  O3  C2  C4  positiv
 GLF  chir_04  C4  O4  C5  C3  positiv
 GLF  chir_05  C5  O5  C4  C6  negativ

