# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:14:12 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 1-deoxy-D-tagatose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@@H](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
 TGD  TGD  '1-deoxy-D-tagatose       '  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 GRAND
;

data_comp_TGD
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
 TGD  C1   C  CH3   0  -0.774   2.9905   1.2766  -0.5427
 TGD  C2   C  C     0   0.380   2.3218   0.2075   0.2610
 TGD  C3   C  CH1   0  -0.086   1.0352  -0.4097  -0.2852
 TGD  C4   C  CH1   0  -0.018  -0.1613   0.2805   0.4024
 TGD  O2   O  O     0  -0.402   2.7732  -0.2105   1.3041
 TGD  O3   O  OH1   0  -0.654   1.0183  -1.7949  -0.0765
 TGD  O4   O  OH1   0  -0.661  -0.0561   1.6816   0.3042
 TGD  C5   C  CH1   0  -0.017  -1.5004  -0.2408  -0.1248
 TGD  O5   O  OH1   0  -0.672  -1.6534   0.0862  -1.4918
 TGD  C6   C  CH2   0  -0.182  -2.6489   0.2676   0.7286
 TGD  O6   O  OH1   0  -0.669  -3.8464  -0.3136   0.2683
 TGD  H1   H  HCH3  0   0.277   3.6000   0.7873  -1.3084
 TGD  H2   H  HCH3  0   0.254   2.2747   1.9039  -1.0697
 TGD  H3   H  HCH3  0   0.265   3.6438   1.8929   0.0716
 TGD  H4   H  HCH1  0   0.262   0.9784  -0.2476  -1.3664
 TGD  H5   H  HCH1  0   0.247  -0.1009   0.0480   1.4724
 TGD  H6   H  HOH1  0   0.446   1.2322  -1.9651   0.8489
 TGD  H7   H  HOH1  0   0.444  -0.1946   1.9360  -0.6156
 TGD  H8   H  HCH1  0   0.237  -1.4849  -1.3334  -0.0524
 TGD  H9   H  HOH1  0   0.454  -2.1976   0.8753  -1.5769
 TGD  H10  H  HCH2  0   0.210  -2.4443   0.0061   1.7745
 TGD  H11  H  HCH2  0   0.202  -2.6894   1.3645   0.6771
 TGD  H12  H  HOH1  0   0.457  -4.5704   0.0466   0.7882

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
 TGD  O5  C5   single  1.414  0.020  1.414
 TGD  O6  C6   single  1.408  0.020  1.408
 TGD  C5  C6   single  1.518  0.020  1.518
 TGD  C5  C4   single  1.531  0.020  1.531
 TGD  O4  C4   single  1.409  0.020  1.409
 TGD  C4  C3   single  1.543  0.020  1.543
 TGD  C3  C2   single  1.528  0.020  1.528
 TGD  C3  O3   single  1.401  0.020  1.401
 TGD  C1  C2   single  1.495  0.020  1.495
 TGD  C2  O2   double  1.211  0.020  1.211
 TGD  C1  H1   single  0.970  0.020  1.090
 TGD  C1  H2   single  0.970  0.020  1.090
 TGD  C1  H3   single  0.970  0.020  1.090
 TGD  C3  H4   single  0.970  0.020  1.090
 TGD  C4  H5   single  0.970  0.020  1.090
 TGD  O3  H6   single  0.850  0.020  0.980
 TGD  O4  H7   single  0.850  0.020  0.980
 TGD  C5  H8   single  0.970  0.020  1.090
 TGD  O5  H9   single  0.850  0.020  0.980
 TGD  C6  H10  single  0.970  0.020  1.090
 TGD  C6  H11  single  0.970  0.020  1.090
 TGD  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
 TGD  H3   C1  H2   109.99  3.000
 TGD  H3   C1  H1   108.30  3.000
 TGD  H2   C1  H1   106.58  3.000
 TGD  H3   C1  C2   111.71  3.000
 TGD  H2   C1  C2   112.23  3.000
 TGD  H1   C1  C2   107.79  3.000
 TGD  O2   C2  C3   118.84  3.000
 TGD  O2   C2  C1   122.89  3.000
 TGD  C3   C2  C1   118.25  3.000
 TGD  H4   C3  O3   107.03  3.000
 TGD  H4   C3  C4   109.49  3.000
 TGD  O3   C3  C4   111.50  3.000
 TGD  H4   C3  C2   109.69  3.000
 TGD  O3   C3  C2   110.88  3.000
 TGD  C4   C3  C2   108.24  3.000
 TGD  H5   C4  C5   108.18  3.000
 TGD  H5   C4  O4   105.95  3.000
 TGD  C5   C4  O4   112.34  3.000
 TGD  H5   C4  C3   107.29  3.000
 TGD  O4   C4  C3   110.85  3.000
 TGD  C5   C4  C3   111.88  3.000
 TGD  H6   O3  C3   108.33  3.000
 TGD  H7   O4  C4   108.55  3.000
 TGD  H8   C5  C6   107.91  3.000
 TGD  H8   C5  O5   107.23  3.000
 TGD  C6   C5  O5   112.59  3.000
 TGD  H8   C5  C4   107.74  3.000
 TGD  C6   C5  C4   110.74  3.000
 TGD  O5   C5  C4   110.42  3.000
 TGD  H9   O5  C5   109.65  3.000
 TGD  H11  C6  H10  106.82  3.000
 TGD  H11  C6  O6   111.42  3.000
 TGD  H10  C6  O6   111.82  3.000
 TGD  H11  C6  C5   109.62  3.000
 TGD  H10  C6  C5   108.35  3.000
 TGD  O6   C6  C5   108.74  3.000
 TGD  H12  O6  C6   108.00  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
 TGD  Var_01  H1  C1  C2  C3  -82.72  30.0  3

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
 TGD  chir_01  C3  C4  C2  O3  negativ
 TGD  chir_02  C4  O4  C3  C5  positiv
 TGD  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
 TGD  plan-1  C1  0.020
 TGD  plan-1  C2  0.020
 TGD  plan-1  C3  0.020
 TGD  plan-1  O2  0.020

