# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:34:14 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3R,4R,5S,6R)-6-fluoro-6-(hydroxymethyl)tetrahydro-2H-pyran-2,3,4,5-tetrol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@]1(F)O[C@@H](O)[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
 B9D  B9D  '(2R,3R,4R,5S,6R)-6-fluoro-6-(hydroxymethyl)tetrahydro-2H-pyran-2,3,4,5-tetrol (non-preferred name)'  L-saccharide  24  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B9D
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
 B9D  O1   O  OH1   0  -0.647  12.5008  17.5840  46.3056
 B9D  O5   O  O2    0  -0.505  13.0264  16.3696  44.4863
 B9D  C5   C  CH1   0   0.278  12.1246  17.3427  45.0048
 B9D  F1   F  F     0  -0.366  14.1828  15.3667  42.9339
 B9D  C4   C  CH1   0  -0.013  12.2349  18.6394  44.2161
 B9D  O4   O  OH1   0  -0.665  11.2633  19.5195  44.7145
 B9D  C3   C  CH1   0  -0.025  12.0400  18.3619  42.7332
 B9D  O3   O  OH1   0  -0.667  12.2380  19.5811  42.0565
 B9D  C2   C  CH1   0  -0.068  13.0422  17.3124  42.2687
 B9D  O2   O  OH1   0  -0.661  12.8007  17.0447  40.9138
 B9D  C1   C  CT    0   0.570  12.9915  16.0451  43.1379
 B9D  C6   C  CH2   0  -0.209  11.9194  15.0186  42.7881
 B9D  O6   O  OH1   0  -0.660  10.6482  15.5948  42.9360
 B9D  HO1  H  HOH1  0   0.464  12.1370  16.9007  46.8785
 B9D  H5   H  HCH1  0   0.211  11.0981  16.9620  44.9465
 B9D  H4   H  HCH1  0   0.215  13.2526  19.0384  44.3621
 B9D  HO4  H  HOH1  0   0.451  11.2682  20.3093  44.1634
 B9D  H3   H  HCH1  0   0.233  11.0191  17.9938  42.5721
 B9D  HO3  H  HOH1  0   0.455  11.9106  19.4881  41.1567
 B9D  H2   H  HCH1  0   0.246  14.0474  17.7377  42.4132
 B9D  HO2  H  HOH1  0   0.459  13.5994  16.6853  40.5154
 B9D  H6   H  HCH2  0   0.215  12.0920  14.6643  41.7661
 B9D  H6A  H  HCH2  0   0.224  12.0601  14.1612  43.4588
 B9D  HO6  H  HOH1  0   0.467   9.9860  14.9204  42.7585

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
 B9D  C5  O1   single  1.375  0.020  1.375
 B9D  O1  HO1  single  0.850  0.020  0.980
 B9D  C1  O5   single  1.387  0.020  1.387
 B9D  O5  C5   single  1.424  0.020  1.424
 B9D  C4  C5   single  1.522  0.020  1.522
 B9D  C5  H5   single  0.970  0.020  1.090
 B9D  F1  C1   single  1.386  0.020  1.386
 B9D  C3  C4   single  1.521  0.020  1.521
 B9D  C4  O4   single  1.403  0.020  1.403
 B9D  C4  H4   single  0.970  0.020  1.090
 B9D  O4  HO4  single  0.850  0.020  0.980
 B9D  O3  C3   single  1.408  0.020  1.408
 B9D  C2  C3   single  1.524  0.020  1.524
 B9D  C3  H3   single  0.970  0.020  1.090
 B9D  O3  HO3  single  0.850  0.020  0.980
 B9D  O2  C2   single  1.402  0.020  1.402
 B9D  C2  C1   single  1.538  0.020  1.538
 B9D  C2  H2   single  0.970  0.020  1.090
 B9D  O2  HO2  single  0.850  0.020  0.980
 B9D  C6  C1   single  1.525  0.020  1.525
 B9D  C6  O6   single  1.404  0.020  1.404
 B9D  C6  H6   single  0.970  0.020  1.090
 B9D  C6  H6A  single  0.970  0.020  1.090
 B9D  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
 B9D  HO1  O1  C5  109.56  3.000
 B9D  C1   O5  C5  119.85  3.000
 B9D  H5   C5  C4  109.65  3.000
 B9D  H5   C5  O5  109.64  3.000
 B9D  C4   C5  O5  110.34  3.000
 B9D  H5   C5  O1  111.55  3.000
 B9D  C4   C5  O1  108.71  3.000
 B9D  O5   C5  O1  106.92  3.000
 B9D  H4   C4  C3  108.25  3.000
 B9D  H4   C4  O4  111.42  3.000
 B9D  C3   C4  O4  111.85  3.000
 B9D  H4   C4  C5  107.86  3.000
 B9D  O4   C4  C5  107.48  3.000
 B9D  C3   C4  C5  109.91  3.000
 B9D  HO4  O4  C4  107.92  3.000
 B9D  H3   C3  C2  109.65  3.000
 B9D  H3   C3  O3  110.53  3.000
 B9D  C2   C3  O3  110.94  3.000
 B9D  H3   C3  C4  108.88  3.000
 B9D  C2   C3  C4  109.79  3.000
 B9D  O3   C3  C4  107.00  3.000
 B9D  HO3  O3  C3  108.54  3.000
 B9D  H2   C2  C1  105.92  3.000
 B9D  H2   C2  O2  110.97  3.000
 B9D  C1   C2  O2  112.54  3.000
 B9D  H2   C2  C3  107.12  3.000
 B9D  C1   C2  C3  111.94  3.000
 B9D  O2   C2  C3  108.23  3.000
 B9D  HO2  O2  C2  109.17  3.000
 B9D  C6   C1  C2  116.63  3.000
 B9D  C6   C1  F1  103.95  3.000
 B9D  C2   C1  F1  106.97  3.000
 B9D  C6   C1  O5  113.46  3.000
 B9D  C2   C1  O5  110.85  3.000
 B9D  F1   C1  O5  103.65  3.000
 B9D  H6A  C6  H6  107.30  3.000
 B9D  H6A  C6  O6  111.87  3.000
 B9D  H6   C6  O6  111.95  3.000
 B9D  H6A  C6  C1  107.19  3.000
 B9D  H6   C6  C1  108.72  3.000
 B9D  O6   C6  C1  109.64  3.000
 B9D  HO6  O6  C6  108.44  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
 B9D  chir_01  C5  O1  O5  C4  positiv
 B9D  chir_02  C4  O4  C5  C3  negativ
 B9D  chir_03  C3  O3  C4  C2  positiv
 B9D  chir_04  C2  O2  C3  C1  negativ
 B9D  chir_05  C1  O5  C6  C2  negativ

