# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:27:22 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (5R)-5-[(1R)-1,2-dihydroxyethyl]-3,4-dihydroxyfuran-2(5H)-one (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H]1OC(=O)C(=C1O)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
 ISD  ISD  '(5R)-5-[(1R)-1,2-dihydroxyethyl]-3,4-dihydroxyfuran-2(5H)-one (non-preferred name)'  D-saccharide  20  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 PERFECT
;

data_comp_ISD
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
 ISD  O6    O  O     0  -0.447   2.1703  -2.1417  -0.2560
 ISD  C5    C  CR5   0   0.486   1.5216  -1.1524  -0.0291
 ISD  C4    C  CR5   0   0.049   1.8801   0.2401  -0.2233
 ISD  O8    O  OH1   0  -0.626   3.0452   0.6645  -0.7497
 ISD  C3    C  CR5   0   0.312   0.8552   0.9966   0.1950
 ISD  O7    O  OH1   0  -0.578   0.7217   2.3099   0.2623
 ISD  O1    O  O     0  -0.459   0.2864  -1.2105   0.5055
 ISD  C2    C  CR15  0  -0.085  -0.2608   0.0997   0.6342
 ISD  C9    C  CH1   0  -0.007  -1.5388   0.2048  -0.2157
 ISD  O11   O  OH1   0  -0.645  -2.0180   1.5209  -0.2144
 ISD  C13   C  CH2   0  -0.166  -2.5864  -0.7918   0.2599
 ISD  O14   O  OH1   0  -0.667  -3.6969  -0.7004  -0.5973
 ISD  HO8   H  HOH1  0   0.478   3.7512   0.0431  -0.5351
 ISD  HO7   H  HOH1  0   0.489   1.5355   2.7497  -0.0176
 ISD  H2    H  HCR5  0   0.293  -0.4972   0.2707   1.6915
 ISD  H9    H  HCH1  0   0.252  -1.2717  -0.0229  -1.2535
 ISD  HO11  H  HOH1  0   0.450  -2.3513   1.7372   0.6637
 ISD  H131  H  HCH2  0   0.213  -2.1573  -1.7999   0.2618
 ISD  H132  H  HCH2  0   0.200  -2.8537  -0.5560   1.3013
 ISD  HO14  H  HOH1  0   0.459  -4.3632  -1.3204  -0.2881

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
 ISD  O6   C5    double  1.205  0.020  1.205
 ISD  C5   C4    single  1.451  0.020  1.451
 ISD  C5   O1    single  1.347  0.020  1.347
 ISD  C4   O8    single  1.347  0.020  1.347
 ISD  C4   C3    double  1.341  0.020  1.341
 ISD  O8   HO8   single  0.850  0.020  0.980
 ISD  C3   O7    single  1.322  0.020  1.322
 ISD  C3   C2    single  1.498  0.020  1.498
 ISD  O7   HO7   single  0.850  0.020  0.980
 ISD  O1   C2    single  1.426  0.020  1.426
 ISD  C2   C9    single  1.538  0.020  1.538
 ISD  C2   H2    single  0.970  0.020  1.090
 ISD  C9   O11   single  1.401  0.020  1.401
 ISD  C9   C13   single  1.522  0.020  1.522
 ISD  C9   H9    single  0.970  0.020  1.090
 ISD  O11  HO11  single  0.850  0.020  0.980
 ISD  C13  O14   single  1.406  0.020  1.406
 ISD  C13  H131  single  0.970  0.020  1.090
 ISD  C13  H132  single  0.970  0.020  1.090
 ISD  O14  HO14  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
 ISD  O1    C5   C4    108.72  3.000
 ISD  O1    C5   O6    122.21  3.000
 ISD  C4    C5   O6    129.05  3.000
 ISD  C3    C4   O8    127.25  3.000
 ISD  C3    C4   C5    108.11  3.000
 ISD  O8    C4   C5    124.63  3.000
 ISD  HO8   O8   C4    110.07  3.000
 ISD  C2    C3   O7    120.32  3.000
 ISD  C2    C3   C4    108.86  3.000
 ISD  O7    C3   C4    130.82  3.000
 ISD  HO7   O7   C3    110.63  3.000
 ISD  C2    O1   C5    110.37  3.000
 ISD  H2    C2   C9    110.05  3.000
 ISD  H2    C2   O1    108.24  3.000
 ISD  C9    C2   O1    109.38  3.000
 ISD  H2    C2   C3    110.48  3.000
 ISD  C9    C2   C3    114.59  3.000
 ISD  O1    C2   C3    103.76  3.000
 ISD  H9    C9   C13   109.12  3.000
 ISD  H9    C9   O11   106.24  3.000
 ISD  C13   C9   O11   112.30  3.000
 ISD  H9    C9   C2    107.86  3.000
 ISD  C13   C9   C2    110.75  3.000
 ISD  O11   C9   C2    110.36  3.000
 ISD  HO11  O11  C9    109.28  3.000
 ISD  H132  C13  H131  106.89  3.000
 ISD  H132  C13  O14   111.78  3.000
 ISD  H131  C13  O14   111.73  3.000
 ISD  H132  C13  C9    108.81  3.000
 ISD  H131  C13  C9    109.48  3.000
 ISD  O14   C13  C9    108.10  3.000
 ISD  HO14  O14  C13   108.03  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
 ISD  Var_01  C2  C3  C4  C5  -2.46  30.0  1
 ISD  Var_02  O1  C5  C4  C3  -0.10  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
 ISD  chir_01  C2  C3   O1  C9   positiv
 ISD  chir_02  C9  O11  C2  C13  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
 ISD  plan-1  O6  0.020
 ISD  plan-1  C5  0.020
 ISD  plan-1  C4  0.020
 ISD  plan-1  O1  0.020

