# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:53:35 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2R,4S,5R)-4,5-dihydroxy-2,5-bis(hydroxymethyl)oxolan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@](O)(CO)[C@@H](O)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
 FX1  FX1  (2R,4S,5R)-4,5-dihydroxy-2,5-bis(hydroxymethyl)oxolan-3-one  D-saccharide  22  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_FX1
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
 FX1  C1   C  CH2   0  -0.175  -2.1260  -0.8156  -0.8191
 FX1  O1   O  OH1   0  -0.672  -2.3261  -2.0936  -0.2633
 FX1  C2   C  CR5   0   0.416  -0.8605  -0.2288  -0.2174
 FX1  O2   O  OH1   0  -0.658  -0.8937  -0.2413   1.1682
 FX1  C3   C  CR15  0  -0.073  -0.5702   1.2052  -0.6551
 FX1  O3   O  OH1   0  -0.648  -1.3008   2.1536   0.0428
 FX1  C4   C  CR5   0   0.315   0.9271   1.2514  -0.4271
 FX1  O4   O  O     0  -0.367   1.5763   2.2183  -0.1318
 FX1  C5   C  CR15  0  -0.098   1.4318  -0.1636  -0.6129
 FX1  O5   O  O     0  -0.508   0.2531  -0.9446  -0.7231
 FX1  C6   C  CH2   0  -0.139   2.3575  -0.6061   0.5042
 FX1  O6   O  OH1   0  -0.666   2.8067  -1.9053   0.2091
 FX1  H1   H  HCH2  0   0.212  -2.0260  -0.8542  -1.9098
 FX1  H1A  H  HCH2  0   0.231  -2.9542  -0.1371  -0.5894
 FX1  HO1  H  HOH1  0   0.468  -3.2699  -2.2635  -0.2084
 FX1  HO2  H  HOH1  0   0.455  -1.2341  -1.0992   1.4560
 FX1  H3   H  HCR5  0   0.276  -0.7269   1.2578  -1.7458
 FX1  HO3  H  HOH1  0   0.466  -1.1971   3.0046  -0.3945
 FX1  H5   H  HCR5  0   0.289   1.9748  -0.2238  -1.5655
 FX1  H6   H  HCH2  0   0.207   3.1850   0.1122   0.5531
 FX1  H6A  H  HCH2  0   0.210   1.8292  -0.5625   1.4631
 FX1  HO6  H  HOH1  0   0.459   3.3799  -2.1903   0.9264

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
 FX1  C2  C1   single  1.519  0.020  1.519
 FX1  C1  O1   single  1.408  0.020  1.408
 FX1  C1  H1   single  0.970  0.020  1.090
 FX1  C1  H1A  single  0.970  0.020  1.090
 FX1  O1  HO1  single  0.850  0.020  0.980
 FX1  O2  C2   single  1.386  0.020  1.386
 FX1  O5  C2   single  1.417  0.020  1.417
 FX1  C2  C3   single  1.527  0.020  1.527
 FX1  O2  HO2  single  0.850  0.020  0.980
 FX1  C4  C3   single  1.515  0.020  1.515
 FX1  O3  C3   single  1.386  0.020  1.386
 FX1  C3  H3   single  0.970  0.020  1.090
 FX1  O3  HO3  single  0.850  0.020  0.980
 FX1  O4  C4   double  1.202  0.020  1.202
 FX1  C5  C4   single  1.514  0.020  1.514
 FX1  C6  C5   single  1.517  0.020  1.517
 FX1  C5  O5   single  1.418  0.020  1.418
 FX1  C5  H5   single  0.970  0.020  1.090
 FX1  O6  C6   single  1.406  0.020  1.406
 FX1  C6  H6   single  0.970  0.020  1.090
 FX1  C6  H6A  single  0.970  0.020  1.090
 FX1  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
 FX1  H1A  C1  H1  107.43  3.000
 FX1  H1A  C1  C2  107.92  3.000
 FX1  H1   C1  C2  109.38  3.000
 FX1  H1A  C1  O1  111.85  3.000
 FX1  H1   C1  O1  111.95  3.000
 FX1  C2   C1  O1  108.22  3.000
 FX1  HO1  O1  C1  108.83  3.000
 FX1  O5   C2  C3  102.86  3.000
 FX1  C3   C2  O2  107.43  3.000
 FX1  O5   C2  O2  111.77  3.000
 FX1  C3   C2  C1  114.05  3.000
 FX1  O5   C2  C1  108.55  3.000
 FX1  O2   C2  C1  111.87  3.000
 FX1  HO2  O2  C2  108.30  3.000
 FX1  H3   C3  C4  106.72  3.000
 FX1  H3   C3  O3  112.98  3.000
 FX1  C4   C3  O3  115.11  3.000
 FX1  H3   C3  C2  107.52  3.000
 FX1  O3   C3  C2  113.46  3.000
 FX1  C4   C3  C2   99.98  3.000
 FX1  HO3  O3  C3  108.63  3.000
 FX1  C5   C4  O4  127.03  3.000
 FX1  C5   C4  C3  106.41  3.000
 FX1  O4   C4  C3  126.54  3.000
 FX1  H5   C5  C6  108.73  3.000
 FX1  H5   C5  O5  108.26  3.000
 FX1  C6   C5  O5  113.82  3.000
 FX1  H5   C5  C4  108.82  3.000
 FX1  O5   C5  C4  104.31  3.000
 FX1  C6   C5  C4  112.69  3.000
 FX1  C5   O5  C2  110.31  3.000
 FX1  H6A  C6  H6  107.38  3.000
 FX1  H6A  C6  O6  111.99  3.000
 FX1  H6   C6  O6  111.93  3.000
 FX1  H6A  C6  C5  109.79  3.000
 FX1  H6   C6  C5  107.59  3.000
 FX1  O6   C6  C5  108.06  3.000
 FX1  HO6  O6  C6  107.93  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
 FX1  chir_01  C2  O2  O5  C3  positiv
 FX1  chir_02  C3  O3  C2  C4  positiv
 FX1  chir_03  C5  O5  C6  C4  positiv

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
 FX1  plan-1  C3  0.020
 FX1  plan-1  C4  0.020
 FX1  plan-1  O4  0.020
 FX1  plan-1  C5  0.020

