# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 13:13:18 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 4,6-dideoxy-alpha-D-xylo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](O)[C@@H](O)[C@@H](O)O1
#
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
 GLD  GLD  4,6-dideoxy-alpha-D-xylo-hexopyranose  D-saccharide  22  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_GLD
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
 GLD  C1   C  CH1   0   0.233  49.6487  89.6322  45.9442
 GLD  C2   C  CH1   0   0.019  49.9004  88.1296  45.8161
 GLD  C3   C  CH1   0   0.017  49.0588  87.5427  44.6918
 GLD  C4   C  CH2   0  -0.488  47.5978  87.8934  44.9426
 GLD  C5   C  CH1   0   0.034  47.4236  89.3971  45.1042
 GLD  C6   C  CH3   0  -0.677  46.0085  89.7765  45.4869
 GLD  O1   O  OH1   0  -0.662  50.1689  90.2644  44.8177
 GLD  O2   O  OH1   0  -0.669  51.2777  87.9246  45.6395
 GLD  O3   O  OH1   0  -0.672  49.2910  86.1496  44.6859
 GLD  O5   O  O2    0  -0.500  48.2854  89.8885  46.1285
 GLD  H1   H  HCH1  0   0.228  50.1288  90.0038  46.8582
 GLD  H2   H  HCH1  0   0.208  49.5538  87.6756  46.7585
 GLD  H3   H  HCH1  0   0.207  49.3759  87.9888  43.7386
 GLD  H4   H  HCH2  0   0.242  46.9767  87.5448  44.1128
 GLD  H42  H  HCH2  0   0.226  47.2512  87.3823  45.8474
 GLD  H5   H  HCH1  0   0.210  47.6721  89.8829  44.1520
 GLD  H61  H  HCH3  0   0.236  45.9019  90.8570  45.5892
 GLD  H62  H  HCH3  0   0.230  45.3127  89.4446  44.7164
 GLD  H63  H  HCH3  0   0.224  45.7165  89.3089  46.4287
 GLD  HO1  H  HOH1  0   0.457  50.1809  91.2153  44.9717
 GLD  HO2  H  HOH1  0   0.447  51.4236  86.9762  45.5650
 GLD  HO3  H  HOH1  0   0.452  48.9042  85.7794  43.8864

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
 GLD  C1  C2   single  1.529  0.020  1.529
 GLD  C1  O1   single  1.392  0.020  1.392
 GLD  C1  O5   single  1.399  0.020  1.399
 GLD  C1  H1   single  0.970  0.020  1.090
 GLD  C2  C3   single  1.522  0.020  1.522
 GLD  C2  O2   single  1.404  0.020  1.404
 GLD  C2  H2   single  0.970  0.020  1.090
 GLD  C3  C4   single  1.523  0.020  1.523
 GLD  C3  O3   single  1.412  0.020  1.412
 GLD  C3  H3   single  0.970  0.020  1.090
 GLD  C4  C5   single  1.522  0.020  1.522
 GLD  C4  H4   single  0.970  0.020  1.090
 GLD  C4  H42  single  0.970  0.020  1.090
 GLD  C5  C6   single  1.514  0.020  1.514
 GLD  C5  O5   single  1.426  0.020  1.426
 GLD  C5  H5   single  0.970  0.020  1.090
 GLD  C6  H61  single  0.970  0.020  1.090
 GLD  C6  H62  single  0.970  0.020  1.090
 GLD  C6  H63  single  0.970  0.020  1.090
 GLD  O1  HO1  single  0.850  0.020  0.980
 GLD  O2  HO2  single  0.850  0.020  0.980
 GLD  O3  HO3  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
 GLD  H1   C1  O5   104.74  3.000
 GLD  H1   C1  O1   110.90  3.000
 GLD  O5   C1  O1   112.79  3.000
 GLD  H1   C1  C2   109.30  3.000
 GLD  O5   C1  C2   110.57  3.000
 GLD  O1   C1  C2   108.48  3.000
 GLD  H2   C2  O2   110.86  3.000
 GLD  H2   C2  C3   107.39  3.000
 GLD  O2   C2  C3   113.17  3.000
 GLD  H2   C2  C1   106.34  3.000
 GLD  O2   C2  C1   108.40  3.000
 GLD  C3   C2  C1   110.47  3.000
 GLD  H3   C3  O3   110.44  3.000
 GLD  H3   C3  C4   109.03  3.000
 GLD  O3   C3  C4   112.68  3.000
 GLD  H3   C3  C2   108.93  3.000
 GLD  O3   C3  C2   107.01  3.000
 GLD  C4   C3  C2   108.66  3.000
 GLD  H42  C4  H4   107.36  3.000
 GLD  H42  C4  C5   109.69  3.000
 GLD  H4   C4  C5   109.29  3.000
 GLD  H42  C4  C3   109.39  3.000
 GLD  H4   C4  C3   110.27  3.000
 GLD  C5   C4  C3   110.77  3.000
 GLD  H5   C5  O5   109.50  3.000
 GLD  H5   C5  C6   108.67  3.000
 GLD  O5   C5  C6   107.27  3.000
 GLD  H5   C5  C4   108.61  3.000
 GLD  O5   C5  C4   110.33  3.000
 GLD  C6   C5  C4   112.41  3.000
 GLD  H63  C6  H62  107.99  3.000
 GLD  H63  C6  H61  108.51  3.000
 GLD  H62  C6  H61  107.79  3.000
 GLD  H63  C6  C5   111.15  3.000
 GLD  H62  C6  C5   109.98  3.000
 GLD  H61  C6  C5   111.30  3.000
 GLD  HO1  O1  C1   108.88  3.000
 GLD  HO2  O2  C2   107.60  3.000
 GLD  HO3  O3  C3   108.48  3.000
 GLD  C5   O5  C1   115.53  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
 GLD  chir_01  C1  C2  O1  O5  negativ
 GLD  chir_02  C2  O2  C1  C3  negativ
 GLD  chir_03  C3  O3  C2  C4  positiv
 GLD  chir_04  C5  O5  C6  C4  positiv

