# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:18:29 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 YYK  YYK  6-deoxy-beta-D-glucopyranose  D-saccharide  23  11  .  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_YYK
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
 YYK  C1   C  CH1   0   0.280  34.3743  30.4595  27.2494
 YYK  C2   C  CH1   0   0.004  33.0328  31.1613  27.4232
 YYK  C3   C  CH1   0  -0.017  33.2752  32.6310  27.7460
 YYK  C4   C  CH1   0   0.017  34.2198  32.7774  28.9321
 YYK  C5   C  CH1   0   0.006  35.5000  31.9813  28.6619
 YYK  C6   C  CH3   0  -0.694  36.4734  32.0058  29.8211
 YYK  O1   O  OH1   0  -0.657  34.1530  29.1118  27.0690
 YYK  O2   O  OH1   0  -0.671  32.3008  31.0031  26.2351
 YYK  O3   O  OH1   0  -0.674  32.0184  33.2194  27.9838
 YYK  O4   O  OH1   0  -0.674  34.4789  34.1534  29.0924
 YYK  O5   O  O2    0  -0.502  35.1526  30.6317  28.4097
 YYK  H1   H  HCH1  0   0.186  34.9069  30.9030  26.3887
 YYK  HO1  H  HOH1  0   0.463  34.9565  28.7014  26.7316
 YYK  H2   H  HCH1  0   0.213  32.5145  30.6968  28.2783
 YYK  HO2  H  HOH1  0   0.452  31.4951  31.5254  26.3095
 YYK  H3   H  HCH1  0   0.211  33.7608  33.0958  26.8719
 YYK  HO3  H  HOH1  0   0.455  32.1372  34.1723  28.0492
 YYK  H4   H  HCH1  0   0.216  33.7349  32.3592  29.8269
 YYK  HO4  H  HOH1  0   0.460  34.7386  34.3193  30.0030
 YYK  H5   H  HCH1  0   0.212  35.9925  32.4097  27.7734
 YYK  H63  H  HCH3  0   0.231  36.0239  31.5929  30.7259
 YYK  H61  H  HCH3  0   0.246  37.3682  31.4295  29.5857
 YYK  H62  H  HCH3  0   0.235  36.7913  33.0259  30.0347

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
 YYK  C1  C2   single  1.524  0.020  1.524
 YYK  C1  O5   single  1.408  0.020  1.408
 YYK  C1  O1   single  1.378  0.020  1.378
 YYK  C1  H1   single  0.970  0.020  1.090
 YYK  C2  C3   single  1.524  0.020  1.524
 YYK  C2  O2   single  1.404  0.020  1.404
 YYK  C2  H2   single  0.970  0.020  1.090
 YYK  C3  C4   single  1.523  0.020  1.523
 YYK  C3  O3   single  1.408  0.020  1.408
 YYK  C3  H3   single  0.970  0.020  1.090
 YYK  C4  C5   single  1.532  0.020  1.532
 YYK  C4  O4   single  1.409  0.020  1.409
 YYK  C4  H4   single  0.970  0.020  1.090
 YYK  C5  O5   single  1.416  0.020  1.416
 YYK  C5  H5   single  0.970  0.020  1.090
 YYK  C5  C6   single  1.514  0.020  1.514
 YYK  C6  H61  single  0.970  0.020  1.090
 YYK  C6  H62  single  0.970  0.020  1.090
 YYK  C6  H63  single  0.970  0.020  1.090
 YYK  O1  HO1  single  0.850  0.020  0.980
 YYK  O2  HO2  single  0.850  0.020  0.980
 YYK  O3  HO3  single  0.850  0.020  0.980
 YYK  O4  HO4  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
 YYK  H1   C1  O5   109.06  3.000
 YYK  H1   C1  O1   111.59  3.000
 YYK  O5   C1  O1   108.45  3.000
 YYK  H1   C1  C2   109.16  3.000
 YYK  O1   C1  C2   108.91  3.000
 YYK  O5   C1  C2   109.66  3.000
 YYK  H2   C2  O2   111.32  3.000
 YYK  H2   C2  C3   108.47  3.000
 YYK  O2   C2  C3   111.76  3.000
 YYK  H2   C2  C1   107.96  3.000
 YYK  O2   C2  C1   108.09  3.000
 YYK  C3   C2  C1   109.16  3.000
 YYK  H3   C3  O3   110.54  3.000
 YYK  H3   C3  C4   107.68  3.000
 YYK  O3   C3  C4   112.45  3.000
 YYK  H3   C3  C2   107.98  3.000
 YYK  O3   C3  C2   107.27  3.000
 YYK  C4   C3  C2   110.87  3.000
 YYK  H4   C4  O4   111.07  3.000
 YYK  H4   C4  C5   108.32  3.000
 YYK  O4   C4  C5   111.95  3.000
 YYK  H4   C4  C3   108.87  3.000
 YYK  O4   C4  C3   107.24  3.000
 YYK  C5   C4  C3   109.33  3.000
 YYK  H5   C5  O5   109.66  3.000
 YYK  H5   C5  C6   108.88  3.000
 YYK  O5   C5  C6   108.03  3.000
 YYK  C6   C5  C4   113.20  3.000
 YYK  H5   C5  C4   108.28  3.000
 YYK  O5   C5  C4   108.76  3.000
 YYK  H62  C6  H61  107.33  3.000
 YYK  H62  C6  H63  108.17  3.000
 YYK  H61  C6  H63  108.48  3.000
 YYK  H63  C6  C5   111.34  3.000
 YYK  H62  C6  C5   110.66  3.000
 YYK  H61  C6  C5   110.72  3.000
 YYK  HO1  O1  C1   109.19  3.000
 YYK  HO2  O2  C2   108.03  3.000
 YYK  HO3  O3  C3   108.36  3.000
 YYK  HO4  O4  C4   109.02  3.000
 YYK  C5   O5  C1   113.51  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
 YYK  chir_01  C1  C2  O5  O1  negativ
 YYK  chir_02  C2  O2  C1  C3  negativ
 YYK  chir_03  C3  O3  C2  C4  positiv
 YYK  chir_04  C4  O4  C5  C3  positiv
 YYK  chir_05  C5  O5  C4  C6  negativ

