# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 21:04:16 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OCC(=O)C(=C1)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
 AY9  AY9  (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one  D-saccharide  18  10  .  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_AY9
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
 AY9  C1    C  C     0  -0.294  -0.4003  -1.5785  -0.3349
 AY9  C2    C  CR6   0   0.297  -1.5547  -0.6457  -0.0674
 AY9  C3    C  CR6   0   0.282  -1.2172   0.7872   0.0069
 AY9  C4    C  CR16  0  -0.346   0.0412   1.1758  -0.2200
 AY9  C5    C  CR16  0  -0.012   1.1508   0.1818  -0.3857
 AY9  C6    C  CH2   0  -0.160   2.4052   0.6771   0.3082
 AY9  O2    O  O     0  -0.406  -2.7071  -1.0185   0.0092
 AY9  O3    O  OH1   0  -0.625  -2.2272   1.6461   0.2172
 AY9  O5    O  O     0  -0.478   0.8059  -1.0705   0.1604
 AY9  O6    O  OH1   0  -0.668   3.4578  -0.2099   0.0293
 AY9  H11C  H  H     0   0.283  -0.5877  -2.5396   0.1458
 AY9  H12C  H  H     0   0.253  -0.3592  -1.7560  -1.4216
 AY9  H4    H  HCR6  0   0.285   0.2838   2.2304  -0.2950
 AY9  H3    H  HOH1  0   0.470  -3.0579   1.1510   0.2497
 AY9  H5    H  HCR6  0   0.239   1.3709   0.0748  -1.4628
 AY9  H61C  H  HCH2  0   0.210   2.6129   1.6889  -0.0620
 AY9  H62C  H  HCH2  0   0.210   2.2070   0.7615   1.3847
 AY9  H6    H  HOH1  0   0.459   4.2313   0.0805   0.5207

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
 AY9  C1  C2    single  1.508  0.020  1.508
 AY9  C1  O5    single  1.399  0.020  1.399
 AY9  C2  C3    single  1.474  0.020  1.474
 AY9  C2  O2    double  1.214  0.020  1.214
 AY9  C3  C4    double  1.336  0.020  1.336
 AY9  C3  O3    single  1.342  0.020  1.342
 AY9  C4  C5    single  1.499  0.020  1.499
 AY9  C5  C6    single  1.517  0.020  1.517
 AY9  C5  O5    single  1.409  0.020  1.409
 AY9  C6  O6    single  1.404  0.020  1.404
 AY9  C1  H11C  single  0.970  0.020  1.090
 AY9  C1  H12C  single  0.970  0.020  1.090
 AY9  C4  H4    single  0.930  0.020  1.080
 AY9  O3  H3    single  0.850  0.020  0.980
 AY9  C5  H5    single  0.970  0.020  1.090
 AY9  C6  H61C  single  0.970  0.020  1.090
 AY9  C6  H62C  single  0.970  0.020  1.090
 AY9  O6  H6    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
 AY9  H12C  C1  H11C  107.40  3.000
 AY9  H12C  C1  O5    112.05  3.000
 AY9  H11C  C1  O5    108.18  3.000
 AY9  H12C  C1  C2    107.64  3.000
 AY9  H11C  C1  C2    109.60  3.000
 AY9  O5    C1  C2    111.86  3.000
 AY9  O2    C2  C3    120.86  3.000
 AY9  O2    C2  C1    123.23  3.000
 AY9  C3    C2  C1    115.79  3.000
 AY9  O3    C3  C4    123.30  3.000
 AY9  O3    C3  C2    117.23  3.000
 AY9  C4    C3  C2    119.32  3.000
 AY9  H4    C4  C5    118.13  3.000
 AY9  H4    C4  C3    120.34  3.000
 AY9  C5    C4  C3    121.53  3.000
 AY9  H5    C5  O5    109.91  3.000
 AY9  H5    C5  C6    108.24  3.000
 AY9  O5    C5  C6    108.38  3.000
 AY9  H5    C5  C4    108.64  3.000
 AY9  O5    C5  C4    111.42  3.000
 AY9  C6    C5  C4    110.19  3.000
 AY9  H62C  C6  H61C  107.11  3.000
 AY9  H62C  C6  O6    112.25  3.000
 AY9  H61C  C6  O6    111.93  3.000
 AY9  H62C  C6  C5    108.93  3.000
 AY9  H61C  C6  C5    107.65  3.000
 AY9  O6    C6  C5    108.83  3.000
 AY9  H3    O3  C3    108.89  3.000
 AY9  C5    O5  C1    113.36  3.000
 AY9  H6    O6  C6    108.11  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
 AY9  Var_01  C4  C3  C2  C1   2.96  30.0  1
 AY9  Var_02  C5  C4  C3  C2  -7.46  30.0  1
 AY9  Var_03  O5  C1  C2  C3  29.10  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
 AY9  chir_01  C5  C4  C6  O5  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
 AY9  plan-1  C1  0.020
 AY9  plan-1  C2  0.020
 AY9  plan-1  C3  0.020
 AY9  plan-1  O2  0.020

