# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:15:45 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: alpha-D-threo-hexo-2,5-diulo-2,6-pyranosyl fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@]1(F)OCC(=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
 5DI  5DI  'alpha-D-threo-hexo-2,5-diulo-2,6-pyranosyl fluoride'  D-saccharide  21  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 OK (reasonable std)
;

data_comp_5DI
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
 5DI  C1    C  CH2   0  -0.290  -1.2023   1.0038   1.1485
 5DI  C2    C  C     0   0.367  -1.9306  -0.0108   0.2953
 5DI  O2    O  O     0  -0.374  -3.0647  -0.3459   0.5341
 5DI  C3    C  CH1   0  -0.107  -1.1761  -0.4730  -0.9422
 5DI  O3    O  OH1   0  -0.649  -1.2162   0.5641  -1.8902
 5DI  C4    C  CH1   0  -0.059   0.2670  -0.7935  -0.5508
 5DI  O4    O  OH1   0  -0.666   0.2396  -1.8949   0.3239
 5DI  C5    C  CT    0   0.598   0.9146   0.3438   0.2460
 5DI  O5    O  O2    0  -0.497   0.1667   0.6922   1.3459
 5DI  C6    C  CH2   0  -0.207   2.3097   0.0228   0.7615
 5DI  O6    O  OH1   0  -0.671   3.1097  -0.3381  -0.3332
 5DI  F1    F  F     0  -0.374   1.0192   1.4385  -0.6030
 5DI  H11C  H  HCH2  0   0.267  -1.3234   1.9897   0.6830
 5DI  H12C  H  HCH2  0   0.282  -1.6565   1.0501   2.1374
 5DI  H3C   H  HCH1  0   0.266  -1.6423  -1.3901  -1.3248
 5DI  H3O   H  HOH1  0   0.466  -2.0864   0.5649  -2.3023
 5DI  H4C   H  HCH1  0   0.265   0.8550  -0.9903  -1.4535
 5DI  H4O   H  HOH1  0   0.467   0.0942  -2.6940  -0.1921
 5DI  H61C  H  HCH2  0   0.226   2.6919   0.9160   1.2740
 5DI  H62C  H  HCH2  0   0.226   2.2374  -0.7737   1.5068
 5DI  H6O   H  HOH1  0   0.465   3.9264  -0.7170   0.0028

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
 5DI  C1  C2    single  1.513  0.020  1.513
 5DI  C1  O5    single  1.418  0.020  1.418
 5DI  C2  O2    double  1.206  0.020  1.206
 5DI  C2  C3    single  1.521  0.020  1.521
 5DI  C3  O3    single  1.406  0.020  1.406
 5DI  C3  C4    single  1.529  0.020  1.529
 5DI  C4  O4    single  1.407  0.020  1.407
 5DI  C4  C5    single  1.532  0.020  1.532
 5DI  C5  O5    single  1.375  0.020  1.375
 5DI  C5  C6    single  1.522  0.020  1.522
 5DI  C5  F1    single  1.389  0.020  1.389
 5DI  C6  O6    single  1.403  0.020  1.403
 5DI  C1  H11C  single  0.970  0.020  1.090
 5DI  C1  H12C  single  0.970  0.020  1.090
 5DI  C3  H3C   single  0.970  0.020  1.090
 5DI  O3  H3O   single  0.850  0.020  0.980
 5DI  C4  H4C   single  0.970  0.020  1.090
 5DI  O4  H4O   single  0.850  0.020  0.980
 5DI  C6  H61C  single  0.970  0.020  1.090
 5DI  C6  H62C  single  0.970  0.020  1.090
 5DI  O6  H6O   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
 5DI  H12C  C1  H11C  107.52  3.000
 5DI  H12C  C1  O5    106.59  3.000
 5DI  H11C  C1  O5    111.29  3.000
 5DI  H12C  C1  C2    109.87  3.000
 5DI  H11C  C1  C2    108.08  3.000
 5DI  O5    C1  C2    113.33  3.000
 5DI  C3    C2  O2    122.88  3.000
 5DI  C3    C2  C1    115.08  3.000
 5DI  O2    C2  C1    121.83  3.000
 5DI  H3C   C3  C4    108.36  3.000
 5DI  H3C   C3  O3    111.67  3.000
 5DI  C4    C3  O3    110.74  3.000
 5DI  H3C   C3  C2    109.07  3.000
 5DI  C4    C3  C2    108.88  3.000
 5DI  O3    C3  C2    108.08  3.000
 5DI  H3O   O3  C3    108.37  3.000
 5DI  H4C   C4  C5    109.58  3.000
 5DI  H4C   C4  O4    112.47  3.000
 5DI  C5    C4  O4    105.43  3.000
 5DI  H4C   C4  C3    109.47  3.000
 5DI  C5    C4  C3    112.11  3.000
 5DI  O4    C4  C3    107.75  3.000
 5DI  H4O   O4  C4    108.65  3.000
 5DI  F1    C5  C6    107.71  3.000
 5DI  F1    C5  O5    109.28  3.000
 5DI  C6    C5  O5    106.33  3.000
 5DI  F1    C5  C4    107.39  3.000
 5DI  C6    C5  C4    114.02  3.000
 5DI  O5    C5  C4    111.97  3.000
 5DI  C5    O5  C1    118.00  3.000
 5DI  H62C  C6  H61C  107.30  3.000
 5DI  H62C  C6  O6    112.47  3.000
 5DI  H61C  C6  O6    112.01  3.000
 5DI  H62C  C6  C5    108.91  3.000
 5DI  H61C  C6  C5    107.79  3.000
 5DI  O6    C6  C5    108.23  3.000
 5DI  H6O   O6  C6    108.25  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 5DI  Var_01  O5  C1  C2  C3  -43.80  30.0  1

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
 5DI  chir_01  C3  C2  O3  C4  negativ
 5DI  chir_02  C4  O4  C5  C3  positiv
 5DI  chir_03  C5  O5  C6  C4  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 5DI  plan-1  C1  0.020
 5DI  plan-1  C2  0.020
 5DI  plan-1  O2  0.020
 5DI  plan-1  C3  0.020

