# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:37:59 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1COC(=C[C@@H]1O)C(O)=O
#
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
 GAD  GAD  '2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid'  L-saccharide  18  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_GAD
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
 GAD  C1   C  CH2    0  -0.222   1.5639  -0.3270   0.8855
 GAD  C2   C  CH1    0  -0.010   0.5189   0.2477   1.8353
 GAD  O2   O  OH1    0  -0.670   0.7986  -0.1183   3.1639
 GAD  C3   C  CH1    0   0.049  -0.8362  -0.3033   1.4412
 GAD  O3   O  OH1    0  -0.671  -1.8366   0.4624   2.0817
 GAD  C4   C  C1     0  -0.431  -0.9625  -0.2510  -0.0553
 GAD  C5   C  C      0   0.180   0.0640  -0.0529  -0.8849
 GAD  C6   C  C      0   0.376  -0.0916   0.0768  -2.3974
 GAD  O6A  O  O      0  -0.591  -1.2509  -0.0178  -2.8398
 GAD  O6B  O  OC    -1  -0.596   0.9539   0.2677  -3.0395
 GAD  O5   O  O2     0  -0.469   1.3436   0.0611  -0.4579
 GAD  H11  H  HCH2   0   0.246   2.5605   0.0268   1.1542
 GAD  H12  H  HCH2   0   0.219   1.5612  -1.4226   0.9623
 GAD  H2   H  HCH1   0   0.220   0.4972   1.3407   1.7143
 GAD  HO2  H  HOH1   0   0.455   1.5696   0.3741   3.4625
 GAD  H3   H  HCH1   0   0.213  -0.8909  -1.3506   1.7786
 GAD  HO3  H  HOH1   0   0.451  -2.6908   0.0692   1.8775
 GAD  H4   H  H      0   0.252  -1.9470  -0.3676  -0.4889

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
 GAD  C1  C2   single  1.525  0.020  1.525
 GAD  C1  O5   single  1.416  0.020  1.416
 GAD  C1  H11  single  0.970  0.020  1.090
 GAD  C1  H12  single  0.970  0.020  1.090
 GAD  C2  O2   single  1.406  0.020  1.406
 GAD  C2  C3   single  1.515  0.020  1.515
 GAD  C2  H2   single  0.970  0.020  1.090
 GAD  O2  HO2  single  0.850  0.020  0.980
 GAD  C3  O3   single  1.413  0.020  1.413
 GAD  C3  C4   single  1.503  0.020  1.503
 GAD  C3  H3   single  0.970  0.020  1.090
 GAD  O3  HO3  single  0.850  0.020  0.980
 GAD  C4  C5   double  1.335  0.020  1.335
 GAD  C4  H4   single  0.930  0.020  1.080
 GAD  C5  C6   single  1.526  0.020  1.526
 GAD  C5  O5   single  1.354  0.020  1.354
 GAD  C6  O6A  deloc   1.244  0.020  1.244
 GAD  C6  O6B  deloc   1.242  0.020  1.242

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
 GAD  H12  C1  H11  107.96  3.000
 GAD  H12  C1  O5   109.85  3.000
 GAD  H11  C1  O5   106.67  3.000
 GAD  H12  C1  C2   109.32  3.000
 GAD  H11  C1  C2   110.51  3.000
 GAD  O5   C1  C2   112.41  3.000
 GAD  H2   C2  C3   108.37  3.000
 GAD  H2   C2  O2   111.50  3.000
 GAD  C3   C2  O2   109.21  3.000
 GAD  H2   C2  C1   108.64  3.000
 GAD  C3   C2  C1   108.29  3.000
 GAD  O2   C2  C1   110.74  3.000
 GAD  HO2  O2  C2   108.62  3.000
 GAD  H3   C3  C4   109.51  3.000
 GAD  H3   C3  O3   109.95  3.000
 GAD  C4   C3  O3   111.90  3.000
 GAD  H3   C3  C2   108.09  3.000
 GAD  C4   C3  C2   108.76  3.000
 GAD  O3   C3  C2   108.55  3.000
 GAD  HO3  O3  C3   108.10  3.000
 GAD  H4   C4  C5   117.82  3.000
 GAD  H4   C4  C3   118.15  3.000
 GAD  C5   C4  C3   124.03  3.000
 GAD  O5   C5  C6   113.69  3.000
 GAD  O5   C5  C4   122.92  3.000
 GAD  C6   C5  C4   123.39  3.000
 GAD  O6B  C6  O6A  127.75  3.000
 GAD  O6B  C6  C5   116.09  3.000
 GAD  O6A  C6  C5   116.16  3.000
 GAD  C5   O5  C1   115.05  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
 GAD  Var_01  C4   C5  O5  C1  13.02  30.0  1
 GAD  Var_02  O5   C5  C4  C3   3.13  30.0  1
 GAD  Var_03  O6A  C6  C5  C4  -0.27  30.0  2

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
 GAD  chir_01  C2  C1  O2  C3  positiv
 GAD  chir_02  C3  O3  C2  C4  positiv

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
 GAD  plan-1  C5   0.020
 GAD  plan-1  C6   0.020
 GAD  plan-1  O6A  0.020
 GAD  plan-1  O6B  0.020

