# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:26:55 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: D-fructosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)C(=O)C(O)=O
#
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
 8YV  8YV  'D-fructosonic acid       '  D-saccharide  22  13  .  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_8YV
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
 8YV  C2   C  CH1    0  -0.035  -0.6047  -0.0164   0.2936
 8YV  C4   C  C      0   0.222   1.7800  -0.5413  -0.1632
 8YV  O4   O  OH1    0  -0.663  -0.4822  -0.6976   1.5221
 8YV  O1   O  O      0  -0.574   1.9533   1.7706  -0.5531
 8YV  C5   C  C      0   0.352   2.4063   0.8397   0.1340
 8YV  O2   O  OC    -1  -0.572   3.2893   0.8558   0.9995
 8YV  O    O  O      0  -0.398   2.3911  -1.5712   0.0138
 8YV  C3   C  CH1    0  -0.061   0.3755  -0.5954  -0.7354
 8YV  O3   O  OH1    0  -0.678   0.0260  -1.9183  -1.0444
 8YV  C1   C  CH1    0  -0.019  -2.0542  -0.0310  -0.2184
 8YV  O5   O  OH1    0  -0.660  -2.1487   0.5633  -1.4926
 8YV  C    C  CH2    0  -0.159  -2.9814   0.6352   0.7865
 8YV  O6   O  OH1    0  -0.671  -4.3070   0.5346   0.3206
 8YV  H1   H  HCH1   0   0.250  -0.3184   1.0217   0.4908
 8YV  H2   H  HOH1   0   0.443  -0.6788  -1.6294   1.3697
 8YV  H4   H  HCH1   0   0.250   0.3594   0.0287  -1.6353
 8YV  H5   H  HOH1   0   0.445   0.7617  -2.4796  -0.7590
 8YV  H6   H  HCH1   0   0.234  -2.3717  -1.0714  -0.3509
 8YV  H7   H  HOH1   0   0.444  -1.9568   1.5041  -1.4103
 8YV  H8   H  HCH2   0   0.208  -2.8592   0.1531   1.7619
 8YV  H9   H  HCH2   0   0.188  -2.6750   1.6861   0.9108
 8YV  H10  H  HOH1   0   0.455  -4.8869   0.8758   1.0068

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
 8YV  O3  C3   single  1.403  0.020  1.403
 8YV  O4  C2   single  1.410  0.020  1.410
 8YV  C3  C2   single  1.535  0.020  1.535
 8YV  C3  C4   single  1.518  0.020  1.518
 8YV  C2  C1   single  1.537  0.020  1.537
 8YV  O1  C5   deloc   1.243  0.020  1.243
 8YV  C4  C5   single  1.545  0.020  1.545
 8YV  C4  O    double  1.210  0.020  1.210
 8YV  C5  O2   deloc   1.236  0.020  1.236
 8YV  C1  C    single  1.521  0.020  1.521
 8YV  C1  O5   single  1.409  0.020  1.409
 8YV  C   O6   single  1.409  0.020  1.409
 8YV  C2  H1   single  0.970  0.020  1.090
 8YV  O4  H2   single  0.850  0.020  0.980
 8YV  C3  H4   single  0.970  0.020  1.090
 8YV  O3  H5   single  0.850  0.020  0.980
 8YV  C1  H6   single  0.970  0.020  1.090
 8YV  O5  H7   single  0.850  0.020  0.980
 8YV  C   H8   single  0.970  0.020  1.090
 8YV  C   H9   single  0.970  0.020  1.090
 8YV  O6  H10  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
 8YV  H1   C2  C1  108.40  3.000
 8YV  H1   C2  C3  108.15  3.000
 8YV  C1   C2  C3  112.04  3.000
 8YV  H1   C2  O4  106.17  3.000
 8YV  C1   C2  O4  111.56  3.000
 8YV  C3   C2  O4  110.27  3.000
 8YV  C3   C4  O   119.47  3.000
 8YV  O    C4  C5  121.85  3.000
 8YV  C3   C4  C5  118.65  3.000
 8YV  H2   O4  C2  108.14  3.000
 8YV  O2   C5  O1  129.62  3.000
 8YV  O2   C5  C4  115.83  3.000
 8YV  O1   C5  C4  114.55  3.000
 8YV  H4   C3  O3  110.65  3.000
 8YV  H4   C3  C4  107.65  3.000
 8YV  O3   C3  C4  110.32  3.000
 8YV  H4   C3  C2  109.06  3.000
 8YV  C4   C3  C2  108.96  3.000
 8YV  O3   C3  C2  110.14  3.000
 8YV  H5   O3  C3  107.01  3.000
 8YV  H6   C1  C   108.61  3.000
 8YV  H6   C1  O5  105.76  3.000
 8YV  C    C1  O5  111.83  3.000
 8YV  H6   C1  C2  108.81  3.000
 8YV  O5   C1  C2  111.12  3.000
 8YV  C    C1  C2  110.52  3.000
 8YV  H7   O5  C1  108.73  3.000
 8YV  H9   C   H8  106.76  3.000
 8YV  H9   C   O6  111.54  3.000
 8YV  H8   C   O6  111.61  3.000
 8YV  H9   C   C1  108.83  3.000
 8YV  H8   C   C1  109.13  3.000
 8YV  O6   C   C1  108.90  3.000
 8YV  H10  O6  C   107.84  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
 8YV  Var_01  C3  C4  C5  O1  -25.84  30.0  2

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
 8YV  chir_01  C2  O4  C3  C1  negativ
 8YV  chir_02  C3  O3  C2  C4  negativ
 8YV  chir_03  C1  O5  C2  C   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
 8YV  plan-1  C4  0.020
 8YV  plan-1  C5  0.020
 8YV  plan-1  O   0.020
 8YV  plan-1  C3  0.020
 8YV  plan-2  C4  0.020
 8YV  plan-2  O1  0.020
 8YV  plan-2  C5  0.020
 8YV  plan-2  O2  0.020

