# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:11:50 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 3,6-dideoxy-alpha-D-ribo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O)[C@H](O)C[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
 PZU  PZU  3,6-dideoxy-alpha-D-ribo-hexopyranose  D-saccharide  22  10  .  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_PZU
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
 PZU  C1   C  CH1   0   0.226  -1.1078   0.9793  -0.1695
 PZU  C2   C  CH1   0   0.023  -1.3784  -0.4831  -0.5334
 PZU  O2   O  OH1   0  -0.667  -2.6743  -0.8966  -0.1800
 PZU  C3   C  CH2   0  -0.525  -0.3648  -1.3809   0.1556
 PZU  C4   C  CH1   0   0.057   1.0494  -0.9297  -0.1935
 PZU  O4   O  OH1   0  -0.675   2.0281  -1.6522   0.5179
 PZU  C5   C  CH1   0   0.032   1.2303   0.5487   0.1464
 PZU  O5   O  O2    0  -0.510   0.2167   1.3126  -0.4984
 PZU  C6   C  CH3   0  -0.686   2.5625   1.1042  -0.3135
 PZU  H1   H  HCH1  0   0.226  -1.7183   1.6420  -0.7969
 PZU  O1   O  OH1   0  -0.664  -1.3928   1.1646   1.1778
 PZU  H2   H  HCH1  0   0.215  -1.2270  -0.5610  -1.6198
 PZU  HO2  H  HOH1  0   0.451  -3.3050  -0.4478  -0.7518
 PZU  H3   H  HCH2  0   0.235  -0.5008  -1.3483   1.2408
 PZU  H3A  H  HCH2  0   0.248  -0.5156  -2.4166  -0.1637
 PZU  H4   H  HCH1  0   0.197   1.1937  -1.0431  -1.2796
 PZU  HO4  H  HOH1  0   0.453   1.9645  -2.5779   0.2632
 PZU  H5   H  HCH1  0   0.210   1.1509   0.6623   1.2363
 PZU  H6   H  HCH3  0   0.223   2.6894   0.9851  -1.3913
 PZU  H6A  H  HCH3  0   0.237   2.6424   2.1654  -0.0754
 PZU  H6B  H  HCH3  0   0.235   3.3840   0.5918   0.1837
 PZU  HO1  H  HOH1  0   0.459  -1.3969   2.1083   1.3695

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
 PZU  C1  C2   single  1.531  0.020  1.531
 PZU  C1  O5   single  1.405  0.020  1.405
 PZU  C1  H1   single  0.970  0.020  1.090
 PZU  C1  O1   single  1.390  0.020  1.390
 PZU  C2  O2   single  1.406  0.020  1.406
 PZU  C2  C3   single  1.519  0.020  1.519
 PZU  C2  H2   single  0.970  0.020  1.090
 PZU  O2  HO2  single  0.850  0.020  0.980
 PZU  C3  C4   single  1.525  0.020  1.525
 PZU  C3  H3   single  0.970  0.020  1.090
 PZU  C3  H3A  single  0.970  0.020  1.090
 PZU  C4  O4   single  1.409  0.020  1.409
 PZU  C4  C5   single  1.528  0.020  1.528
 PZU  C4  H4   single  0.970  0.020  1.090
 PZU  O4  HO4  single  0.850  0.020  0.980
 PZU  C5  O5   single  1.424  0.020  1.424
 PZU  C5  C6   single  1.515  0.020  1.515
 PZU  C5  H5   single  0.970  0.020  1.090
 PZU  C6  H6   single  0.970  0.020  1.090
 PZU  C6  H6A  single  0.970  0.020  1.090
 PZU  C6  H6B  single  0.970  0.020  1.090
 PZU  O1  HO1  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
 PZU  O1   C1  H1   111.08  3.000
 PZU  O1   C1  O5   112.88  3.000
 PZU  H1   C1  O5   104.32  3.000
 PZU  O1   C1  C2   108.75  3.000
 PZU  H1   C1  C2   110.02  3.000
 PZU  O5   C1  C2   109.73  3.000
 PZU  H2   C2  C3   108.32  3.000
 PZU  H2   C2  O2   110.76  3.000
 PZU  C3   C2  O2   109.10  3.000
 PZU  H2   C2  C1   106.15  3.000
 PZU  C3   C2  C1   109.80  3.000
 PZU  O2   C2  C1   112.59  3.000
 PZU  HO2  O2  C2   108.52  3.000
 PZU  H3A  C3  H3   107.49  3.000
 PZU  H3A  C3  C4   109.94  3.000
 PZU  H3   C3  C4   109.48  3.000
 PZU  H3A  C3  C2   109.58  3.000
 PZU  H3   C3  C2   110.44  3.000
 PZU  C4   C3  C2   109.88  3.000
 PZU  H4   C4  C5   107.67  3.000
 PZU  H4   C4  O4   110.73  3.000
 PZU  C5   C4  O4   107.56  3.000
 PZU  H4   C4  C3   108.46  3.000
 PZU  C5   C4  C3   110.20  3.000
 PZU  O4   C4  C3   112.14  3.000
 PZU  HO4  O4  C4   108.29  3.000
 PZU  H5   C5  C6   109.07  3.000
 PZU  H5   C5  O5   110.03  3.000
 PZU  C6   C5  O5   106.97  3.000
 PZU  H5   C5  C4   108.19  3.000
 PZU  C6   C5  C4   113.04  3.000
 PZU  O5   C5  C4   109.52  3.000
 PZU  C5   O5  C1   115.97  3.000
 PZU  H6B  C6  H6A  107.64  3.000
 PZU  H6B  C6  H6   108.17  3.000
 PZU  H6A  C6  H6   108.25  3.000
 PZU  H6B  C6  C5   110.64  3.000
 PZU  H6A  C6  C5   110.79  3.000
 PZU  H6   C6  C5   111.22  3.000
 PZU  HO1  O1  C1   108.94  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
 PZU  chir_01  C1  C2  O5  O1  positiv
 PZU  chir_02  C2  O2  C1  C3  negativ
 PZU  chir_03  C4  O4  C3  C5  negativ
 PZU  chir_04  C5  O5  C4  C6  negativ

