# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:00:37 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1-deoxy-alpha-D-xylo-hex-3-ulofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@]1(O)OC[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
 TGR  TGR  1-deoxy-alpha-D-xylo-hex-3-ulofuranose  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_TGR
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
 TGR  C1   C  CH3   0  -0.708   2.7308   1.0339   0.2469
 TGR  C2   C  CH1   0   0.011   1.7633  -0.1428   0.2969
 TGR  O2   O  OH1   0  -0.667   2.2375  -1.2367  -0.4576
 TGR  C3   C  CT    0   0.435   0.3462   0.2299  -0.1665
 TGR  O3   O  OH1   0  -0.668   0.3564   0.6435  -1.5045
 TGR  C4   C  CH1   0   0.016  -0.6852  -0.9047  -0.0739
 TGR  O4   O  OH1   0  -0.668  -0.4301  -1.6265   1.1027
 TGR  C5   C  CH1   0  -0.067  -1.9985  -0.1264   0.0586
 TGR  O5   O  OH1   0  -0.666  -2.4912   0.1857  -1.2200
 TGR  C6   C  CH2   0  -0.171  -1.5526   1.0928   0.8695
 TGR  O6   O  O2    0  -0.520  -0.1477   1.2336   0.6774
 TGR  H1   H  HCH3  0   0.239   2.3754   1.8756   0.8408
 TGR  H2   H  HCH3  0   0.248   3.6977   0.7317   0.6490
 TGR  H3   H  HCH3  0   0.219   2.9050   1.3888  -0.7721
 TGR  H4   H  HCH1  0   0.237   1.7053  -0.4915   1.3287
 TGR  H5   H  HOH1  0   0.439   2.2780  -0.9665  -1.3819
 TGR  H6   H  HOH1  0   0.451   0.8528   1.4677  -1.5728
 TGR  H7   H  HCH1  0   0.239  -0.6734  -1.5412  -0.9654
 TGR  H8   H  HOH1  0   0.459  -1.0948  -2.3169   1.1877
 TGR  H9   H  HCH1  0   0.239  -2.7323  -0.7128   0.6259
 TGR  H10  H  HOH1  0   0.453  -3.3467   0.6123  -1.1156
 TGR  H11  H  HCH2  0   0.228  -2.0726   2.0012   0.5523
 TGR  H12  H  HCH2  0   0.223  -1.7473   0.9479   1.9349

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
 TGR  O4  C4   single  1.404  0.020  1.404
 TGR  O2  C2   single  1.411  0.020  1.411
 TGR  C2  C1   single  1.524  0.020  1.524
 TGR  C2  C3   single  1.537  0.020  1.537
 TGR  C4  C5   single  1.532  0.020  1.532
 TGR  C4  C3   single  1.536  0.020  1.536
 TGR  C5  C6   single  1.531  0.020  1.531
 TGR  C5  O5   single  1.405  0.020  1.405
 TGR  C6  O6   single  1.425  0.020  1.425
 TGR  C3  O6   single  1.401  0.020  1.401
 TGR  C3  O3   single  1.401  0.020  1.401
 TGR  C1  H1   single  0.970  0.020  1.090
 TGR  C1  H2   single  0.970  0.020  1.090
 TGR  C1  H3   single  0.970  0.020  1.090
 TGR  C2  H4   single  0.970  0.020  1.090
 TGR  O2  H5   single  0.850  0.020  0.980
 TGR  O3  H6   single  0.850  0.020  0.980
 TGR  C4  H7   single  0.970  0.020  1.090
 TGR  O4  H8   single  0.850  0.020  0.980
 TGR  C5  H9   single  0.970  0.020  1.090
 TGR  O5  H10  single  0.850  0.020  0.980
 TGR  C6  H11  single  0.970  0.020  1.090
 TGR  C6  H12  single  0.970  0.020  1.090

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
 TGR  H3   C1  H2   107.01  3.000
 TGR  H3   C1  H1   108.02  3.000
 TGR  H2   C1  H1   107.60  3.000
 TGR  H3   C1  C2   112.49  3.000
 TGR  H2   C1  C2   109.69  3.000
 TGR  H1   C1  C2   111.80  3.000
 TGR  H4   C2  C3   108.28  3.000
 TGR  H4   C2  O2   106.01  3.000
 TGR  C3   C2  O2   109.67  3.000
 TGR  H4   C2  C1   108.16  3.000
 TGR  C3   C2  C1   112.84  3.000
 TGR  O2   C2  C1   111.57  3.000
 TGR  H5   O2  C2   108.03  3.000
 TGR  O6   C3  C4   104.84  3.000
 TGR  O6   C3  O3   111.49  3.000
 TGR  C4   C3  O3   106.30  3.000
 TGR  O3   C3  C2   110.67  3.000
 TGR  O6   C3  C2   108.49  3.000
 TGR  C4   C3  C2   114.96  3.000
 TGR  H6   O3  C3   108.89  3.000
 TGR  H7   C4  C5   112.01  3.000
 TGR  H7   C4  O4   112.42  3.000
 TGR  C5   C4  O4   110.15  3.000
 TGR  H7   C4  C3   111.89  3.000
 TGR  C5   C4  C3   101.86  3.000
 TGR  O4   C4  C3   107.95  3.000
 TGR  H8   O4  C4   108.51  3.000
 TGR  H9   C5  C6   110.28  3.000
 TGR  H9   C5  O5   110.77  3.000
 TGR  C6   C5  O5   114.03  3.000
 TGR  H9   C5  C4   110.27  3.000
 TGR  O5   C5  C4   109.54  3.000
 TGR  C6   C5  C4   101.58  3.000
 TGR  H10  O5  C5   108.15  3.000
 TGR  H12  C6  H11  107.94  3.000
 TGR  H12  C6  O6   108.68  3.000
 TGR  H11  C6  O6   110.35  3.000
 TGR  H12  C6  C5   111.04  3.000
 TGR  H11  C6  C5   111.68  3.000
 TGR  O6   C6  C5   107.13  3.000
 TGR  C6   O6  C3   110.97  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 TGR  Var_01  C5  C6  O6  C3  -0.19  30.0  1

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
 TGR  chir_01  C2  O2  C1  C3  negativ
 TGR  chir_02  C3  O6  C4  C2  positiv
 TGR  chir_03  C4  O4  C5  C3  negativ
 TGR  chir_04  C5  O5  C4  C6  negativ

