# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:33:59 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 1-deoxy-D-xylo-hex-3-ulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)C(=O)[C@@H](O)[C@H](O)CO
#
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
 TGS  TGS  1-deoxy-D-xylo-hex-3-ulose  ligand  23  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TGS
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
 TGS  C1   C  CH3   0  -0.708   2.1423   1.1226  -1.3571
 TGS  C2   C  CH1   0  -0.062   1.9198   0.6342   0.0742
 TGS  O2   O  OH1   0  -0.659   3.1235   0.4011   0.7503
 TGS  C3   C  C     0   0.373   1.1396  -0.6617   0.0904
 TGS  O3   O  O     0  -0.387   1.5698  -1.6614   0.6138
 TGS  C4   C  CH1   0  -0.094  -0.2213  -0.7126  -0.5946
 TGS  O4   O  OH1   0  -0.671  -0.7814  -1.9849  -0.4401
 TGS  C5   C  CH1   0  -0.033  -1.1578   0.3496  -0.0086
 TGS  O5   O  OH1   0  -0.658  -1.2226   0.2376   1.3919
 TGS  C6   C  CH2   0  -0.149  -2.5263   0.2915  -0.6702
 TGS  O6   O  OH1   0  -0.669  -3.2793   1.3928  -0.2225
 TGS  H1   H  HCH3  0   0.236   1.2070   1.3816  -1.8519
 TGS  H2   H  HCH3  0   0.259   2.7545   2.0249  -1.3431
 TGS  H3   H  HCH3  0   0.248   2.6528   0.3701  -1.9589
 TGS  H4   H  HCH1  0   0.254   1.3121   1.3832   0.6035
 TGS  H5   H  HOH1  0   0.459   3.5854   1.2421   0.8256
 TGS  H6   H  HCH1  0   0.255  -0.0661  -0.4915  -1.6613
 TGS  H7   H  HOH1  0   0.451  -0.1286  -2.5364   0.0153
 TGS  H8   H  HCH1  0   0.245  -0.7338   1.3369  -0.2192
 TGS  H9   H  HOH1  0   0.445  -1.5789  -0.6320   1.6087
 TGS  H10  H  HCH2  0   0.198  -2.3865   0.3108  -1.7597
 TGS  H11  H  HCH2  0   0.207  -3.0152  -0.6597  -0.4259
 TGS  H12  H  HOH1  0   0.457  -4.1774   1.2926  -0.5495

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
 TGS  O3  C3   double  1.208  0.020  1.208
 TGS  O4  C4   single  1.399  0.020  1.399
 TGS  O2  C2   single  1.400  0.020  1.400
 TGS  C3  C4   single  1.524  0.020  1.524
 TGS  C3  C2   single  1.513  0.020  1.513
 TGS  C4  C5   single  1.533  0.020  1.533
 TGS  C2  C1   single  1.529  0.020  1.529
 TGS  O5  C5   single  1.406  0.020  1.406
 TGS  C5  C6   single  1.521  0.020  1.521
 TGS  C6  O6   single  1.407  0.020  1.407
 TGS  C1  H1   single  0.970  0.020  1.090
 TGS  C1  H2   single  0.970  0.020  1.090
 TGS  C1  H3   single  0.970  0.020  1.090
 TGS  C2  H4   single  0.970  0.020  1.090
 TGS  O2  H5   single  0.850  0.020  0.980
 TGS  C4  H6   single  0.970  0.020  1.090
 TGS  O4  H7   single  0.850  0.020  0.980
 TGS  C5  H8   single  0.970  0.020  1.090
 TGS  O5  H9   single  0.850  0.020  0.980
 TGS  C6  H10  single  0.970  0.020  1.090
 TGS  C6  H11  single  0.970  0.020  1.090
 TGS  O6  H12  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
 TGS  H3   C1  H2   108.38  3.000
 TGS  H3   C1  H1   108.39  3.000
 TGS  H2   C1  H1   106.92  3.000
 TGS  H3   C1  C2   111.37  3.000
 TGS  H2   C1  C2   109.51  3.000
 TGS  H1   C1  C2   112.10  3.000
 TGS  H4   C2  C3   107.05  3.000
 TGS  H4   C2  O2   110.85  3.000
 TGS  C3   C2  O2   107.19  3.000
 TGS  H4   C2  C1   108.26  3.000
 TGS  C3   C2  C1   111.03  3.000
 TGS  O2   C2  C1   112.34  3.000
 TGS  H5   O2  C2   107.76  3.000
 TGS  C4   C3  O3   119.02  3.000
 TGS  C4   C3  C2   118.96  3.000
 TGS  O3   C3  C2   122.01  3.000
 TGS  H6   C4  C5   108.51  3.000
 TGS  H6   C4  O4   110.26  3.000
 TGS  C5   C4  O4   110.09  3.000
 TGS  H6   C4  C3   107.64  3.000
 TGS  C5   C4  C3   110.52  3.000
 TGS  O4   C4  C3   109.77  3.000
 TGS  H7   O4  C4   107.45  3.000
 TGS  H8   C5  C6   107.40  3.000
 TGS  H8   C5  O5   106.33  3.000
 TGS  C6   C5  O5   112.86  3.000
 TGS  H8   C5  C4   108.35  3.000
 TGS  C6   C5  C4   110.92  3.000
 TGS  O5   C5  C4   110.71  3.000
 TGS  H9   O5  C5   108.23  3.000
 TGS  H11  C6  H10  107.03  3.000
 TGS  H11  C6  O6   111.67  3.000
 TGS  H10  C6  O6   111.71  3.000
 TGS  H11  C6  C5   109.70  3.000
 TGS  H10  C6  C5   108.43  3.000
 TGS  O6   C6  C5   108.25  3.000
 TGS  H12  O6  C6   108.07  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
 TGS  chir_01  C2  O2  C3  C1  positiv
 TGS  chir_02  C4  O4  C3  C5  positiv
 TGS  chir_03  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 TGS  plan-1  C2  0.020
 TGS  plan-1  C3  0.020
 TGS  plan-1  O3  0.020
 TGS  plan-1  C4  0.020

