# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 22:29:51 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1OC(=O)[C@@H](O)[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
 8S0  8S0  (3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-one  L-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_8S0
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
 8S0  C1   C  C     0   0.525   0.6306  -1.5028   0.0561
 8S0  C2   C  CH1   0  -0.114   1.5945  -0.3609   0.3466
 8S0  C3   C  CH1   0   0.003   1.1330   0.9437  -0.2793
 8S0  C4   C  CH1   0  -0.009  -0.2968   1.2034   0.1660
 8S0  C5   C  CH1   0  -0.003  -1.2017   0.0721  -0.3099
 8S0  C6   C  CH2   0  -0.152  -2.5661   0.1306   0.3421
 8S0  O1   O  O     0  -0.427   0.9962  -2.6459  -0.0085
 8S0  O2   O  OH1   0  -0.655   2.8787  -0.6563  -0.1093
 8S0  O3   O  OH1   0  -0.667   1.9117   2.0283   0.1516
 8S0  O4   O  OH1   0  -0.664  -0.8140   2.3818  -0.3900
 8S0  O5   O  O2    0  -0.442  -0.6647  -1.2325  -0.0384
 8S0  O6   O  OH1   0  -0.668  -3.3857  -0.8523  -0.2380
 8S0  H1   H  HCH1  0   0.267   1.5713  -0.2323   1.4418
 8S0  H2   H  HCH1  0   0.241   1.1546   0.8492  -1.3758
 8S0  H3   H  HCH1  0   0.229  -0.3149   1.2441   1.2673
 8S0  H4   H  HCH1  0   0.263  -1.3099   0.1535  -1.3974
 8S0  H5   H  HCH2  0   0.207  -2.4465  -0.0165   1.4241
 8S0  H6   H  HCH2  0   0.221  -2.9663   1.1390   0.1938
 8S0  H7   H  HOH1  0   0.463   3.2337  -1.3920   0.4006
 8S0  H8   H  HOH1  0   0.463   2.7657   1.9960  -0.2907
 8S0  H9   H  HOH1  0   0.459  -0.2432   3.1127  -0.1292
 8S0  H10  H  HOH1  0   0.460  -4.2675  -0.7638   0.1342

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
 8S0  O1  C1   double  1.202  0.020  1.202
 8S0  C1  O5   single  1.327  0.020  1.327
 8S0  C1  C2   single  1.522  0.020  1.522
 8S0  O2  C2   single  1.394  0.020  1.394
 8S0  O5  C5   single  1.437  0.020  1.437
 8S0  C2  C3   single  1.519  0.020  1.519
 8S0  O6  C6   single  1.405  0.020  1.405
 8S0  C5  C6   single  1.513  0.020  1.513
 8S0  C5  C4   single  1.525  0.020  1.525
 8S0  C3  C4   single  1.520  0.020  1.520
 8S0  C3  O3   single  1.403  0.020  1.403
 8S0  C4  O4   single  1.402  0.020  1.402
 8S0  C2  H1   single  0.970  0.020  1.090
 8S0  C3  H2   single  0.970  0.020  1.090
 8S0  C4  H3   single  0.970  0.020  1.090
 8S0  C5  H4   single  0.970  0.020  1.090
 8S0  C6  H5   single  0.970  0.020  1.090
 8S0  C6  H6   single  0.970  0.020  1.090
 8S0  O2  H7   single  0.850  0.020  0.980
 8S0  O3  H8   single  0.850  0.020  0.980
 8S0  O4  H9   single  0.850  0.020  0.980
 8S0  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
 8S0  O5   C1  O1  119.14  3.000
 8S0  O5   C1  C2  118.62  3.000
 8S0  O1   C1  C2  122.08  3.000
 8S0  H1   C2  O2  111.64  3.000
 8S0  H1   C2  C3  107.62  3.000
 8S0  O2   C2  C3  109.10  3.000
 8S0  H1   C2  C1  105.28  3.000
 8S0  C3   C2  C1  111.92  3.000
 8S0  O2   C2  C1  111.21  3.000
 8S0  H2   C3  O3  111.18  3.000
 8S0  H2   C3  C4  108.97  3.000
 8S0  O3   C3  C4  107.46  3.000
 8S0  H2   C3  C2  109.32  3.000
 8S0  O3   C3  C2  111.64  3.000
 8S0  C4   C3  C2  108.17  3.000
 8S0  H3   C4  O4  111.06  3.000
 8S0  H3   C4  C5  109.24  3.000
 8S0  O4   C4  C5  106.31  3.000
 8S0  H3   C4  C3  108.33  3.000
 8S0  O4   C4  C3  111.99  3.000
 8S0  C5   C4  C3  109.87  3.000
 8S0  H4   C5  O5  106.98  3.000
 8S0  H4   C5  C6  109.61  3.000
 8S0  O5   C5  C6  106.90  3.000
 8S0  H4   C5  C4  108.25  3.000
 8S0  C6   C5  C4  111.83  3.000
 8S0  O5   C5  C4  113.14  3.000
 8S0  H6   C6  H5  107.25  3.000
 8S0  H6   C6  O6  112.03  3.000
 8S0  H5   C6  O6  112.12  3.000
 8S0  H6   C6  C5  107.87  3.000
 8S0  H5   C6  C5  108.73  3.000
 8S0  O6   C6  C5  108.72  3.000
 8S0  H7   O2  C2  109.16  3.000
 8S0  H8   O3  C3  108.99  3.000
 8S0  H9   O4  C4  108.17  3.000
 8S0  C5   O5  C1  124.29  3.000
 8S0  H10  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
 8S0  Var_01  O1  C1  O5  C5  -163.76  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
 8S0  chir_01  C2  C1  O2  C3  negativ
 8S0  chir_02  C3  O3  C2  C4  negativ
 8S0  chir_03  C4  O4  C3  C5  positiv
 8S0  chir_04  C5  O5  C4  C6  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
 8S0  plan-1  C1  0.020
 8S0  plan-1  C2  0.020
 8S0  plan-1  O1  0.020
 8S0  plan-1  O5  0.020

