# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 05:59:41 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-2-fluoro-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](F)[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
 G2F  G2F  2-deoxy-2-fluoro-alpha-D-glucopyranose  D-saccharide  23  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G2F
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
 G2F  C1   C  CH1   0   0.189  21.4111  68.6617  36.9303
 G2F  C2   C  CH1   0   0.173  20.7570  69.5922  37.9479
 G2F  C3   C  CH1   0  -0.026  20.0269  68.8230  39.0288
 G2F  C4   C  CH1   0  -0.006  19.0432  67.8631  38.3608
 G2F  C5   C  CH1   0  -0.010  19.7884  66.9770  37.3585
 G2F  C6   C  CH2   0  -0.194  18.8984  66.0104  36.6090
 G2F  O1   O  OH1   0  -0.659  22.4545  67.9966  37.5595
 G2F  O3   O  OH1   0  -0.665  19.3738  69.7510  39.8557
 G2F  O4   O  OH1   0  -0.670  18.4423  67.1038  39.3839
 G2F  O5   O  O2    0  -0.501  20.4447  67.7982  36.4017
 G2F  O6   O  OH1   0  -0.667  17.8652  66.7099  35.9586
 G2F  F2   F  F     0  -0.372  21.7324  70.4029  38.5128
 G2F  H1   H  HCH1  0   0.245  21.7687  69.2445  36.0737
 G2F  H2   H  HCH1  0   0.227  20.0502  70.2423  37.4221
 G2F  H3   H  HCH1  0   0.221  20.7538  68.2282  39.6035
 G2F  H4   H  HCH1  0   0.228  18.2958  68.4624  37.8243
 G2F  H5   H  HCH1  0   0.230  20.5184  66.3649  37.9058
 G2F  H61  H  HCH2  0   0.218  19.5216  65.4477  35.9014
 G2F  H62  H  HCH2  0   0.207  18.5111  65.2810  37.3309
 G2F  HO1  H  HOH1  0   0.464  23.0228  67.5976  36.8917
 G2F  HO3  H  HOH1  0   0.450  18.8858  69.2577  40.5236
 G2F  HO4  H  HOH1  0   0.460  17.5613  66.8416  39.1014
 G2F  HO6  H  HOH1  0   0.457  17.2742  66.0673  35.5566

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
 G2F  C1  C2   single  1.526  0.020  1.526
 G2F  C1  O1   single  1.388  0.020  1.388
 G2F  C1  O5   single  1.400  0.020  1.400
 G2F  C1  H1   single  0.970  0.020  1.090
 G2F  C2  C3   single  1.514  0.020  1.514
 G2F  C2  F2   single  1.388  0.020  1.388
 G2F  C2  H2   single  0.970  0.020  1.090
 G2F  C3  C4   single  1.528  0.020  1.528
 G2F  C3  O3   single  1.404  0.020  1.404
 G2F  C3  H3   single  0.970  0.020  1.090
 G2F  C4  C5   single  1.531  0.020  1.531
 G2F  C4  O4   single  1.409  0.020  1.409
 G2F  C4  H4   single  0.970  0.020  1.090
 G2F  C5  C6   single  1.513  0.020  1.513
 G2F  C5  O5   single  1.421  0.020  1.421
 G2F  C5  H5   single  0.970  0.020  1.090
 G2F  C6  O6   single  1.407  0.020  1.407
 G2F  C6  H61  single  0.970  0.020  1.090
 G2F  C6  H62  single  0.970  0.020  1.090
 G2F  O1  HO1  single  0.850  0.020  0.980
 G2F  O3  HO3  single  0.850  0.020  0.980
 G2F  O4  HO4  single  0.850  0.020  0.980
 G2F  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
 G2F  H1   C1  O5   104.96  3.000
 G2F  H1   C1  O1   111.33  3.000
 G2F  O5   C1  O1   113.24  3.000
 G2F  H1   C1  C2   109.68  3.000
 G2F  O5   C1  C2   109.39  3.000
 G2F  O1   C1  C2   108.18  3.000
 G2F  H2   C2  F2   107.59  3.000
 G2F  H2   C2  C3   109.46  3.000
 G2F  F2   C2  C3   110.18  3.000
 G2F  H2   C2  C1   108.57  3.000
 G2F  F2   C2  C1   109.04  3.000
 G2F  C3   C2  C1   111.89  3.000
 G2F  H3   C3  O3   110.90  3.000
 G2F  H3   C3  C4   108.29  3.000
 G2F  O3   C3  C4   111.91  3.000
 G2F  H3   C3  C2   109.19  3.000
 G2F  O3   C3  C2   107.99  3.000
 G2F  C4   C3  C2   108.50  3.000
 G2F  H4   C4  O4   111.02  3.000
 G2F  H4   C4  C5   109.10  3.000
 G2F  O4   C4  C5   111.78  3.000
 G2F  H4   C4  C3   107.99  3.000
 G2F  O4   C4  C3   107.20  3.000
 G2F  C5   C4  C3   109.65  3.000
 G2F  H5   C5  O5   110.51  3.000
 G2F  H5   C5  C6   106.36  3.000
 G2F  O5   C5  C6   107.90  3.000
 G2F  H5   C5  C4   108.64  3.000
 G2F  O5   C5  C4   109.33  3.000
 G2F  C6   C5  C4   114.06  3.000
 G2F  H62  C6  H61  106.49  3.000
 G2F  H62  C6  O6   112.06  3.000
 G2F  H61  C6  O6   111.94  3.000
 G2F  H62  C6  C5   107.85  3.000
 G2F  H61  C6  C5   108.23  3.000
 G2F  O6   C6  C5   110.08  3.000
 G2F  HO1  O1  C1   109.13  3.000
 G2F  HO3  O3  C3   107.79  3.000
 G2F  HO4  O4  C4   108.94  3.000
 G2F  C5   O5  C1   114.89  3.000
 G2F  HO6  O6  C6   108.21  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
 G2F  chir_01  C1  C2  O1  O5  negativ
 G2F  chir_02  C2  F2  C3  C1  positiv
 G2F  chir_03  C3  O3  C2  C4  positiv
 G2F  chir_04  C4  O4  C3  C5  negativ
 G2F  chir_05  C5  O5  C4  C6  negativ

