# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:13:23 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2R,3R,4R,5S,6R)-6-fluoro-3,4,5-trihydroxytetrahydro-2H-pyran-2-olate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H]([O-])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
 XYF  XYF  '(2R,3R,4R,5S,6R)-6-fluoro-3,4,5-trihydroxytetrahydro-2H-pyran-2-olate (non-preferred name)'  D-saccharide  19  11  .  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_XYF
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
 XYF  O3   O  OH1    0  -0.678  1.9162  -1.6836  -0.6484
 XYF  C3   C  CH1    0  -0.036  2.1167  -0.3435  -0.2403
 XYF  C4   C  CH1    0  -0.046  2.3828   0.5453  -1.4587
 XYF  O4   O  OH1    0  -0.676  3.5888   0.2118  -2.1023
 XYF  C5   C  CH1    0   0.405  2.4656   1.9975  -1.0145
 XYF  F5   F  F      0  -0.372  2.5836   2.8050  -2.1331
 XYF  O5   O  O2     0  -0.539  1.3364   2.3931  -0.3573
 XYF  C1   C  CH1    0   0.217  1.1068   1.6485   0.9240
 XYF  C2   C  CH1    0   0.004  0.9014   0.1763   0.4963
 XYF  O2   O  OH1    0  -0.686  0.6684  -0.5956   1.6509
 XYF  O1   O  OC    -1  -0.718  0.1171   2.1418   1.5889
 XYF  HO3  H  HOH1   0   0.453  2.7503  -2.1553  -0.5854
 XYF  H3   H  HCH1   0   0.208  2.9848  -0.2778   0.4325
 XYF  H4   H  HCH1   0   0.212  1.5258   0.4511  -2.1440
 XYF  HO4  H  HOH1   0   0.450  3.4876  -0.6585  -2.4992
 XYF  H5   H  HCH1   0   0.155  3.3784   2.1571  -0.4146
 XYF  H1   H  HCH1   0   0.053  2.1139   1.6940   1.4371
 XYF  H2   H  HCH1   0   0.169  0.0269   0.1435  -0.1775
 XYF  HO2  H  HOH1   0   0.423  0.1316  -0.0205   2.2148

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
 XYF  O3  C3   single  1.415  0.020  1.415
 XYF  O3  HO3  single  0.850  0.020  0.980
 XYF  C3  C4   single  1.531  0.020  1.531
 XYF  C3  C2   single  1.513  0.020  1.513
 XYF  C3  H3   single  0.970  0.020  1.090
 XYF  C4  O4   single  1.407  0.020  1.407
 XYF  C4  C5   single  1.521  0.020  1.521
 XYF  C4  H4   single  0.970  0.020  1.090
 XYF  O4  HO4  single  0.850  0.020  0.980
 XYF  C5  F5   single  1.385  0.020  1.385
 XYF  C5  O5   single  1.365  0.020  1.365
 XYF  C5  H5   single  0.970  0.020  1.090
 XYF  O5  C1   single  1.500  0.020  1.500
 XYF  C1  C2   single  1.547  0.020  1.547
 XYF  C1  O1   single  1.290  0.020  1.290
 XYF  C1  H1   single  0.970  0.020  1.090
 XYF  C2  O2   single  1.408  0.020  1.408
 XYF  C2  H2   single  0.970  0.020  1.090
 XYF  O2  HO2  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
 XYF  HO3  O3  C3  108.86  3.000
 XYF  H3   C3  C2  108.39  3.000
 XYF  H3   C3  C4  108.34  3.000
 XYF  C2   C3  C4  109.12  3.000
 XYF  H3   C3  O3  110.16  3.000
 XYF  C2   C3  O3  110.61  3.000
 XYF  C4   C3  O3  110.17  3.000
 XYF  H4   C4  C5  107.80  3.000
 XYF  H4   C4  O4  111.22  3.000
 XYF  C5   C4  O4  108.25  3.000
 XYF  H4   C4  C3  108.07  3.000
 XYF  C5   C4  C3  109.35  3.000
 XYF  O4   C4  C3  112.05  3.000
 XYF  HO4  O4  C4  108.24  3.000
 XYF  H5   C5  O5  112.36  3.000
 XYF  H5   C5  F5  106.51  3.000
 XYF  O5   C5  F5  106.89  3.000
 XYF  H5   C5  C4  109.98  3.000
 XYF  O5   C5  C4  111.86  3.000
 XYF  F5   C5  C4  109.00  3.000
 XYF  C1   O5  C5  113.21  3.000
 XYF  H1   C1  O1  115.71  3.000
 XYF  H1   C1  C2  106.38  3.000
 XYF  O1   C1  C2  113.86  3.000
 XYF  H1   C1  O5  103.37  3.000
 XYF  O1   C1  O5  111.58  3.000
 XYF  C2   C1  O5  104.87  3.000
 XYF  H2   C2  O2  110.67  3.000
 XYF  H2   C2  C1  107.58  3.000
 XYF  O2   C2  C1  108.48  3.000
 XYF  H2   C2  C3  109.19  3.000
 XYF  O2   C2  C3  110.10  3.000
 XYF  C1   C2  C3  110.79  3.000
 XYF  HO2  O2  C2  104.11  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
 XYF  chir_01  C3  O3  C4  C2  negativ
 XYF  chir_02  C4  O4  C3  C5  negativ
 XYF  chir_03  C5  F5  O5  C4  negativ
 XYF  chir_04  C1  O5  O1  C2  negativ
 XYF  chir_05  C2  O2  C1  C3  negativ

