# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:42:31 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](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
 SDY  SDY  (2~{R},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)oxane-2,3,4,5-tetrol  D-saccharide  24  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_SDY
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
 SDY  C1   C  CH1   0   0.271  20.5616  -8.7730  -1.4759
 SDY  O1   O  OH1   0  -0.659  21.4461  -9.8105  -1.2708
 SDY  C2   C  CH1   0  -0.010  19.1371  -9.2983  -1.3525
 SDY  O2   O  OH1   0  -0.670  19.0023  -9.9822  -0.1364
 SDY  C3   C  CH1   0  -0.000  18.1819  -8.1140  -1.4834
 SDY  O3   O  OH1   0  -0.669  16.8800  -8.6109  -1.3037
 SDY  C4   C  CH1   0  -0.033  18.5270  -6.9703  -0.5262
 SDY  O4   O  OH1   0  -0.667  18.2095  -7.3361   0.7948
 SDY  C5   C  CH1   0  -0.007  20.0092  -6.6277  -0.7062
 SDY  O5   O  O2    0  -0.496  20.8129  -7.7723  -0.5203
 SDY  C6   C  CH2   0  -0.167  20.4698  -5.5549   0.2556
 SDY  O6   O  OH1   0  -0.669  21.7708  -5.1510  -0.0987
 SDY  H1   H  HCH1  0   0.188  20.6731  -8.3407  -2.4866
 SDY  H2   H  HCH1  0   0.223  18.9568  -9.9708  -2.2064
 SDY  H3   H  HCH1  0   0.224  18.3134  -7.7128  -2.4999
 SDY  H4   H  HCH1  0   0.240  17.9467  -6.0891  -0.8363
 SDY  HO4  H  HOH1  0   0.457  17.9927  -6.5415   1.2893
 SDY  H5   H  HCH1  0   0.216  20.1297  -6.2435  -1.7341
 SDY  H61  H  HCH2  0   0.204  19.7565  -4.7214   0.1994
 SDY  H62  H  HCH2  0   0.203  20.4332  -5.9429   1.2810
 SDY  HO6  H  HOH1  0   0.456  22.0618  -4.4956   0.5413
 SDY  HO3  H  HOH1  0   0.457  16.2589  -7.8754  -1.2883
 SDY  HO1  H  HOH1  0   0.463  22.3155  -9.5490  -1.5920
 SDY  HO2  H  HOH1  0   0.449  18.0723  -9.9668   0.1117

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
 SDY  C1  C2   single  1.523  0.020  1.523
 SDY  C1  O1   single  1.379  0.020  1.379
 SDY  C1  O5   single  1.406  0.020  1.406
 SDY  C3  C2   single  1.527  0.020  1.527
 SDY  C3  O3   single  1.405  0.020  1.405
 SDY  C3  C4   single  1.531  0.020  1.531
 SDY  C2  O2   single  1.402  0.020  1.402
 SDY  C5  C4   single  1.532  0.020  1.532
 SDY  C5  O5   single  1.411  0.020  1.411
 SDY  C5  C6   single  1.513  0.020  1.513
 SDY  C4  O4   single  1.407  0.020  1.407
 SDY  O6  C6   single  1.408  0.020  1.408
 SDY  C1  H1   single  0.970  0.020  1.090
 SDY  C2  H2   single  0.970  0.020  1.090
 SDY  C3  H3   single  0.970  0.020  1.090
 SDY  C4  H4   single  0.970  0.020  1.090
 SDY  O4  HO4  single  0.850  0.020  0.980
 SDY  C5  H5   single  0.970  0.020  1.090
 SDY  C6  H61  single  0.970  0.020  1.090
 SDY  C6  H62  single  0.970  0.020  1.090
 SDY  O6  HO6  single  0.850  0.020  0.980
 SDY  O3  HO3  single  0.850  0.020  0.980
 SDY  O1  HO1  single  0.850  0.020  0.980
 SDY  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
 SDY  H1   C1  O5   108.97  3.000
 SDY  H1   C1  C2   107.66  3.000
 SDY  O5   C1  C2   110.94  3.000
 SDY  H1   C1  O1   111.45  3.000
 SDY  O5   C1  O1   108.65  3.000
 SDY  C2   C1  O1   109.17  3.000
 SDY  HO1  O1  C1   108.98  3.000
 SDY  H2   C2  C3   107.73  3.000
 SDY  H2   C2  O2   111.03  3.000
 SDY  C3   C2  O2   113.11  3.000
 SDY  H2   C2  C1   107.50  3.000
 SDY  O2   C2  C1   109.18  3.000
 SDY  C3   C2  C1   108.09  3.000
 SDY  HO2  O2  C2   107.98  3.000
 SDY  H3   C3  C4   106.15  3.000
 SDY  H3   C3  O3   110.96  3.000
 SDY  C4   C3  O3   113.15  3.000
 SDY  H3   C3  C2   106.68  3.000
 SDY  C4   C3  C2   112.63  3.000
 SDY  O3   C3  C2   107.12  3.000
 SDY  HO3  O3  C3   109.25  3.000
 SDY  H4   C4  C5   107.35  3.000
 SDY  H4   C4  O4   110.74  3.000
 SDY  C5   C4  O4   112.76  3.000
 SDY  H4   C4  C3   107.66  3.000
 SDY  O4   C4  C3   109.99  3.000
 SDY  C5   C4  C3   108.16  3.000
 SDY  HO4  O4  C4   108.61  3.000
 SDY  H5   C5  C6   108.18  3.000
 SDY  H5   C5  O5   110.06  3.000
 SDY  C6   C5  O5   108.55  3.000
 SDY  H5   C5  C4   107.03  3.000
 SDY  C6   C5  C4   112.24  3.000
 SDY  O5   C5  C4   110.75  3.000
 SDY  C5   O5  C1   112.70  3.000
 SDY  H62  C6  H61  107.13  3.000
 SDY  H62  C6  O6   111.57  3.000
 SDY  H61  C6  O6   111.69  3.000
 SDY  H62  C6  C5   109.47  3.000
 SDY  H61  C6  C5   107.93  3.000
 SDY  O6   C6  C5   108.96  3.000
 SDY  HO6  O6  C6   107.94  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
 SDY  chir_01  C1  C2  O1  O5  positiv
 SDY  chir_02  C2  O2  C1  C3  positiv
 SDY  chir_03  C3  O3  C2  C4  positiv
 SDY  chir_04  C4  O4  C5  C3  negativ
 SDY  chir_05  C5  O5  C4  C6  negativ

