# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:13:37 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: (2S,3R,4R)-4-(hydroxymethyl)oxolane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)CO[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
 XXM  XXM  (2S,3R,4R)-4-(hydroxymethyl)oxolane-2,3,4-triol  D-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XXM
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
 XXM  O5   O  OH1   0  -0.666  23.4824  21.8493  20.9882
 XXM  C5   C  CH2   0  -0.156  24.5939  21.3764  21.7086
 XXM  C3   C  CT    0   0.107  25.7215  21.0806  20.7332
 XXM  O3   O  OH1   0  -0.666  25.3494  20.0885  19.8079
 XXM  C4   C  CH2   0  -0.141  26.1848  22.3124  19.9639
 XXM  O4   O  O2    0  -0.498  27.5918  22.1807  19.7655
 XXM  C1   C  CH1   0   0.290  28.1121  21.0973  20.4626
 XXM  O1   O  OH1   0  -0.662  28.4196  20.0833  19.5541
 XXM  C2   C  CH1   0  -0.068  27.0201  20.6907  21.4626
 XXM  O2   O  OH1   0  -0.664  27.0876  19.3229  21.7629
 XXM  HO5  H  HOH1  0   0.455  22.7840  22.0581  21.6151
 XXM  H51  H  HCH2  0   0.205  24.3581  20.4591  22.2683
 XXM  H52  H  HCH2  0   0.197  24.9448  22.1126  22.4439
 XXM  HO3  H  HOH1  0   0.441  25.3843  19.2363  20.2588
 XXM  H41  H  HCH2  0   0.221  25.9919  23.2259  20.5346
 XXM  H42  H  HCH2  0   0.236  25.6830  22.4071  18.9989
 XXM  H1   H  HCH1  0   0.198  29.0238  21.4297  20.9788
 XXM  HO1  H  HOH1  0   0.447  28.4621  19.2485  20.0359
 XXM  H2   H  HCH1  0   0.253  27.1288  21.3087  22.3607
 XXM  HO2  H  HOH1  0   0.471  27.0131  19.1928  22.7119

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
 XXM  O1  C1   single  1.396  0.020  1.396
 XXM  C4  O4   single  1.427  0.020  1.427
 XXM  C4  C3   single  1.524  0.020  1.524
 XXM  O3  C3   single  1.407  0.020  1.407
 XXM  O4  C1   single  1.389  0.020  1.389
 XXM  C1  C2   single  1.536  0.020  1.536
 XXM  C3  C2   single  1.540  0.020  1.540
 XXM  C3  C5   single  1.520  0.020  1.520
 XXM  O5  C5   single  1.406  0.020  1.406
 XXM  C2  O2   single  1.402  0.020  1.402
 XXM  O5  HO5  single  0.850  0.020  0.980
 XXM  C5  H51  single  0.970  0.020  1.090
 XXM  C5  H52  single  0.970  0.020  1.090
 XXM  O3  HO3  single  0.850  0.020  0.980
 XXM  C4  H41  single  0.970  0.020  1.090
 XXM  C4  H42  single  0.970  0.020  1.090
 XXM  C1  H1   single  0.970  0.020  1.090
 XXM  O1  HO1  single  0.850  0.020  0.980
 XXM  C2  H2   single  0.970  0.020  1.090
 XXM  O2  HO2  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
 XXM  HO5  O5  C5   108.25  3.000
 XXM  H52  C5  H51  106.67  3.000
 XXM  H52  C5  C3   108.85  3.000
 XXM  H51  C5  C3   108.86  3.000
 XXM  H52  C5  O5   111.73  3.000
 XXM  H51  C5  O5   111.81  3.000
 XXM  C3   C5  O5   108.85  3.000
 XXM  C2   C3  C4   100.80  3.000
 XXM  C2   C3  O3   110.86  3.000
 XXM  C4   C3  O3   108.57  3.000
 XXM  C2   C3  C5   111.77  3.000
 XXM  O3   C3  C5   111.29  3.000
 XXM  C4   C3  C5   113.08  3.000
 XXM  HO3  O3  C3   107.82  3.000
 XXM  H42  C4  H41  107.91  3.000
 XXM  H42  C4  O4   109.77  3.000
 XXM  H41  C4  O4   108.87  3.000
 XXM  H42  C4  C3   112.11  3.000
 XXM  H41  C4  C3   110.97  3.000
 XXM  O4   C4  C3   107.17  3.000
 XXM  C1   O4  C4   111.80  3.000
 XXM  H1   C1  C2   111.35  3.000
 XXM  H1   C1  O1   110.04  3.000
 XXM  C2   C1  O1   112.84  3.000
 XXM  H1   C1  O4   108.08  3.000
 XXM  C2   C1  O4   105.48  3.000
 XXM  O1   C1  O4   108.81  3.000
 XXM  HO1  O1  C1   108.26  3.000
 XXM  H2   C2  O2   111.71  3.000
 XXM  H2   C2  C1   108.30  3.000
 XXM  O2   C2  C1   111.32  3.000
 XXM  H2   C2  C3   109.22  3.000
 XXM  O2   C2  C3   112.90  3.000
 XXM  C1   C2  C3   102.96  3.000
 XXM  HO2  O2  C2   109.87  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
 XXM  Var_01  H41  C4  O4  C1  112.43  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
 XXM  chir_01  C3  C4  C2  C5  negativ
 XXM  chir_02  C1  O4  O1  C2  positiv
 XXM  chir_03  C2  O2  C1  C3  negativ

