# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:58:43 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-deoxy-3-fluoro-beta-D-galactopyranose
#   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
 2H5  2H5  3-deoxy-3-fluoro-beta-D-galactopyranose  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_2H5
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
 2H5  C2   C  CH1   0  -0.037  -1.5245  -0.3901   0.1492
 2H5  C6   C  CH2   0  -0.155   2.6635   0.4813   0.0429
 2H5  C3   C  CH1   0   0.162  -1.1108   0.9126  -0.5022
 2H5  C4   C  CH1   0  -0.044   0.2896   1.3350  -0.0814
 2H5  C5   C  CH1   0  -0.026   1.2394   0.1766  -0.3704
 2H5  C1   C  CH1   0   0.254  -0.4456  -1.4385  -0.1428
 2H5  O1   O  OH1   0  -0.659  -0.7712  -2.5875   0.5463
 2H5  O2   O  OH1   0  -0.667  -2.7639  -0.7746  -0.3837
 2H5  F3   F  F     0  -0.375  -2.0147   1.9150  -0.1540
 2H5  O4   O  OH1   0  -0.667   0.3546   1.6422   1.2882
 2H5  O5   O  O2    0  -0.492   0.8111  -0.9899   0.2984
 2H5  O6   O  OH1   0  -0.670   3.4967  -0.5445  -0.4424
 2H5  H1   H  HCH1  0   0.230  -1.5753  -0.2476   1.2383
 2H5  H2   H  HCH2  0   0.204   2.9334   1.4575  -0.3802
 2H5  H3   H  HCH2  0   0.209   2.7235   0.5723   1.1331
 2H5  H4   H  HCH1  0   0.223  -1.1447   0.8076  -1.5919
 2H5  H5   H  HCH1  0   0.248   0.5976   2.1907  -0.6989
 2H5  H6   H  HCH1  0   0.232   1.2289   0.0151  -1.4612
 2H5  H7   H  HCH1  0   0.192  -0.4085  -1.6155  -1.2328
 2H5  H8   H  HOH1  0   0.468  -0.3363  -3.3438   0.1387
 2H5  H9   H  HOH1  0   0.455  -3.0805  -1.5386   0.1088
 2H5  H10  H  HOH1  0   0.457  -0.2004   2.4103   1.4558
 2H5  H11  H  HOH1  0   0.457   4.3936  -0.3622  -0.1487

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
 2H5  O6  C6   single  1.408  0.020  1.408
 2H5  C6  C5   single  1.514  0.020  1.514
 2H5  C5  C4   single  1.526  0.020  1.526
 2H5  C5  O5   single  1.411  0.020  1.411
 2H5  C4  C3   single  1.522  0.020  1.522
 2H5  C4  O4   single  1.405  0.020  1.405
 2H5  O5  C1   single  1.405  0.020  1.405
 2H5  C3  C2   single  1.514  0.020  1.514
 2H5  C3  F3   single  1.394  0.020  1.394
 2H5  C1  C2   single  1.532  0.020  1.532
 2H5  C1  O1   single  1.379  0.020  1.379
 2H5  C2  O2   single  1.403  0.020  1.403
 2H5  C2  H1   single  0.970  0.020  1.090
 2H5  C6  H2   single  0.970  0.020  1.090
 2H5  C6  H3   single  0.970  0.020  1.090
 2H5  C3  H4   single  0.970  0.020  1.090
 2H5  C4  H5   single  0.970  0.020  1.090
 2H5  C5  H6   single  0.970  0.020  1.090
 2H5  C1  H7   single  0.970  0.020  1.090
 2H5  O1  H8   single  0.850  0.020  0.980
 2H5  O2  H9   single  0.850  0.020  0.980
 2H5  O4  H10  single  0.850  0.020  0.980
 2H5  O6  H11  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
 2H5  H1   C2  O2  111.77  3.000
 2H5  H1   C2  C1  108.06  3.000
 2H5  O2   C2  C1  111.23  3.000
 2H5  H1   C2  C3  109.10  3.000
 2H5  O2   C2  C3  108.29  3.000
 2H5  C1   C2  C3  108.32  3.000
 2H5  H3   C6  H2  107.23  3.000
 2H5  H3   C6  O6  111.79  3.000
 2H5  H2   C6  O6  111.69  3.000
 2H5  H3   C6  C5  109.87  3.000
 2H5  H2   C6  C5  107.76  3.000
 2H5  O6   C6  C5  108.42  3.000
 2H5  H4   C3  F3  107.30  3.000
 2H5  H4   C3  C4  109.28  3.000
 2H5  F3   C3  C4  109.15  3.000
 2H5  H4   C3  C2  109.70  3.000
 2H5  F3   C3  C2  109.52  3.000
 2H5  C4   C3  C2  111.79  3.000
 2H5  H5   C4  O4  111.37  3.000
 2H5  H5   C4  C5  108.08  3.000
 2H5  O4   C4  C5  108.78  3.000
 2H5  H5   C4  C3  108.57  3.000
 2H5  O4   C4  C3  111.88  3.000
 2H5  C5   C4  C3  108.04  3.000
 2H5  H6   C5  O5  110.17  3.000
 2H5  H6   C5  C4  107.02  3.000
 2H5  O5   C5  C4  110.42  3.000
 2H5  H6   C5  C6  107.97  3.000
 2H5  O5   C5  C6  108.81  3.000
 2H5  C4   C5  C6  112.40  3.000
 2H5  H7   C1  O5  109.32  3.000
 2H5  H7   C1  O1  111.57  3.000
 2H5  O5   C1  O1  108.68  3.000
 2H5  H7   C1  C2  108.73  3.000
 2H5  O1   C1  C2  107.98  3.000
 2H5  O5   C1  C2  110.57  3.000
 2H5  H8   O1  C1  109.65  3.000
 2H5  H9   O2  C2  108.29  3.000
 2H5  H10  O4  C4  108.52  3.000
 2H5  C1   O5  C5  112.73  3.000
 2H5  H11  O6  C6  107.99  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
 2H5  chir_01  C2  C3  C1  O2  positiv
 2H5  chir_02  C3  F3  C4  C2  negativ
 2H5  chir_03  C4  O4  C5  C3  negativ
 2H5  chir_04  C5  O5  C4  C6  negativ
 2H5  chir_05  C1  O5  O1  C2  negativ

