# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:45:32 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-deoxy-beta-D-xylo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 Z9D  Z9D  4-deoxy-beta-D-xylo-hexopyranose  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_Z9D
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
 Z9D  C1   C  CH1   0   0.277  22.0247  53.8519  65.9598
 Z9D  C2   C  CH1   0   0.006  22.2325  52.5006  65.2833
 Z9D  C3   C  CH1   0   0.008  22.4185  51.4301  66.3527
 Z9D  C4   C  CH2   0  -0.482  23.5342  51.8258  67.3096
 Z9D  C5   C  CH1   0   0.007  23.2589  53.2139  67.8697
 Z9D  C6   C  CH2   0  -0.172  24.3772  53.7489  68.7472
 Z9D  O1   O  OH1   0  -0.657  21.9625  54.8315  64.9926
 Z9D  O2   O  OH1   0  -0.673  21.1115  52.2451  64.4761
 Z9D  O3   O  OH1   0  -0.675  22.6747  50.2152  65.6815
 Z9D  O5   O  O2    0  -0.505  23.1098  54.1393  66.8084
 Z9D  O6   O  OH1   0  -0.671  24.5221  52.8842  69.8486
 Z9D  HO1  H  HOH1  0   0.463  21.5480  55.6181  65.3625
 Z9D  H1   H  HCH1  0   0.185  21.0969  53.8150  66.5587
 Z9D  H2   H  HCH1  0   0.209  23.1566  52.5570  64.6837
 Z9D  H3   H  HCH1  0   0.209  21.4789  51.3623  66.9227
 Z9D  H41  H  HCH2  0   0.249  23.6020  51.0976  68.1204
 Z9D  H42  H  HCH2  0   0.229  24.4950  51.8272  66.7833
 Z9D  H5   H  HCH1  0   0.216  22.3312  53.1838  68.4644
 Z9D  H61  H  HCH2  0   0.197  25.2988  53.8123  68.1530
 Z9D  H62  H  HCH2  0   0.214  24.1216  54.7683  69.0634
 Z9D  HO2  H  HOH1  0   0.450  21.1881  51.3438  64.1456
 Z9D  HO3  H  HOH1  0   0.456  22.5508  49.4903  66.3017
 Z9D  HO6  H  HOH1  0   0.460  25.2257  53.2271  70.4060

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
 Z9D  C1   C2   single  1.525  0.020  1.525
 Z9D  C1   O1   single  1.378  0.020  1.378
 Z9D  C1   O5   single  1.407  0.020  1.407
 Z9D  C1   H1   single  0.970  0.020  1.090
 Z9D  C2   C3   single  1.525  0.020  1.525
 Z9D  C2   O2   single  1.405  0.020  1.405
 Z9D  C2   H2   single  0.970  0.020  1.090
 Z9D  C3   C4   single  1.522  0.020  1.522
 Z9D  C3   O3   single  1.411  0.020  1.411
 Z9D  C3   H3   single  0.970  0.020  1.090
 Z9D  C4   C5   single  1.522  0.020  1.522
 Z9D  C4   H41  single  0.970  0.020  1.090
 Z9D  C4   H42  single  0.970  0.020  1.090
 Z9D  C5   C6   single  1.519  0.020  1.519
 Z9D  C5   O5   single  1.416  0.020  1.416
 Z9D  C5   H5   single  0.970  0.020  1.090
 Z9D  C6   O6   single  1.408  0.020  1.408
 Z9D  C6   H61  single  0.970  0.020  1.090
 Z9D  C6   H62  single  0.970  0.020  1.090
 Z9D  O2   HO2  single  0.850  0.020  0.980
 Z9D  O3   HO3  single  0.850  0.020  0.980
 Z9D  O6   HO6  single  0.850  0.020  0.980
 Z9D  HO1  O1   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
 Z9D  H1   C1  O5   109.11  3.000
 Z9D  H1   C1  O1   111.48  3.000
 Z9D  O5   C1  O1   108.23  3.000
 Z9D  H1   C1  C2   108.98  3.000
 Z9D  O5   C1  C2   110.08  3.000
 Z9D  O1   C1  C2   108.95  3.000
 Z9D  H2   C2  O2   111.44  3.000
 Z9D  H2   C2  C3   108.36  3.000
 Z9D  O2   C2  C3   111.88  3.000
 Z9D  H2   C2  C1   108.05  3.000
 Z9D  O2   C2  C1   107.89  3.000
 Z9D  C3   C2  C1   109.12  3.000
 Z9D  H3   C3  O3   110.37  3.000
 Z9D  H3   C3  C4   108.42  3.000
 Z9D  O3   C3  C4   112.93  3.000
 Z9D  H3   C3  C2   107.60  3.000
 Z9D  O3   C3  C2   107.04  3.000
 Z9D  C4   C3  C2   110.36  3.000
 Z9D  H42  C4  H41  107.65  3.000
 Z9D  H42  C4  C5   109.53  3.000
 Z9D  H41  C4  C5   110.26  3.000
 Z9D  H42  C4  C3   109.95  3.000
 Z9D  H41  C4  C3   109.82  3.000
 Z9D  C5   C4  C3   109.62  3.000
 Z9D  H5   C5  O5   109.49  3.000
 Z9D  H5   C5  C6   108.52  3.000
 Z9D  O5   C5  C6   106.28  3.000
 Z9D  H5   C5  C4   109.02  3.000
 Z9D  O5   C5  C4   109.83  3.000
 Z9D  C6   C5  C4   113.62  3.000
 Z9D  H62  C6  H61  107.32  3.000
 Z9D  H62  C6  O6   111.66  3.000
 Z9D  H61  C6  O6   111.86  3.000
 Z9D  H62  C6  C5   108.79  3.000
 Z9D  H61  C6  C5   109.00  3.000
 Z9D  O6   C6  C5   108.14  3.000
 Z9D  HO1  O1  C1   109.30  3.000
 Z9D  HO2  O2  C2   107.70  3.000
 Z9D  HO3  O3  C3   108.58  3.000
 Z9D  C5   O5  C1   113.56  3.000
 Z9D  HO6  O6  C6   108.06  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
 Z9D  chir_01  C1  C2  O1  O5  positiv
 Z9D  chir_02  C2  O2  C1  C3  negativ
 Z9D  chir_03  C3  O3  C2  C4  positiv
 Z9D  chir_04  C5  O5  C6  C4  positiv

