# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:33:27 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  19  11  .  2023-02-15  2023-02-16
;
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  -0.229   1.5453  -0.3114   0.8569
 GAD  C2   C  CH1   0  -0.012   0.4931   0.2424   1.8124
 GAD  O2   O  OH1   0  -0.665   0.7805  -0.1381   3.1323
 GAD  C3   C  CH1   0   0.038  -0.8608  -0.3217   1.4233
 GAD  O3   O  OH1   0  -0.663  -1.8669   0.4258   2.0647
 GAD  C4   C  C1    0  -0.377  -1.0032  -0.2679  -0.0724
 GAD  C5   C  C     0   0.239   0.0287  -0.0610  -0.8903
 GAD  C6   C  C     0   0.507  -0.1667   0.0330  -2.3629
 GAD  O6A  O  O     0  -0.432  -1.2435  -0.0574  -2.8989
 GAD  O6B  O  OH1   0  -0.586   0.9697   0.2276  -3.0077
 GAD  O5   O  O2    0  -0.470   1.3061   0.0807  -0.4879
 GAD  H11  H  HCH2  0   0.260   2.5356   0.0635   1.1148
 GAD  H12  H  HCH2  0   0.235   1.5648  -1.4065   0.9211
 GAD  H2   H  HCH1  0   0.232   0.4579   1.3357   1.7023
 GAD  HO2  H  HOH1  0   0.459   1.5249   0.3830   3.4494
 GAD  H3   H  HCH1  0   0.236  -0.8980  -1.3747   1.7412
 GAD  HO3  H  HOH1  0   0.458  -2.6985  -0.0521   1.9858
 GAD  H4   H  H     0   0.282  -1.9890  -0.4002  -0.4984
 GAD  H6B  H  HOH1  0   0.489   0.8007   0.2839  -3.9603

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  1.421  0.020  1.421
 GAD  C1   H11  single  0.970  0.020  1.090
 GAD  C1   H12  single  0.970  0.020  1.090
 GAD  C2   O2   single  1.403  0.020  1.403
 GAD  C2   C3   single  1.518  0.020  1.518
 GAD  C2   H2   single  0.970  0.020  1.090
 GAD  O2   HO2  single  0.850  0.020  0.980
 GAD  C3   O3   single  1.408  0.020  1.408
 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  1.333  0.020  1.333
 GAD  C4   H4   single  0.930  0.020  1.080
 GAD  C5   C6   single  1.488  0.020  1.488
 GAD  C5   O5   single  1.347  0.020  1.347
 GAD  C6   O6A  double  1.206  0.020  1.206
 GAD  C6   O6B  single  1.321  0.020  1.321
 GAD  O6B  H6B  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
 GAD  H12  C1   H11  108.26  3.000
 GAD  H12  C1   O5   109.49  3.000
 GAD  H11  C1   O5   106.37  3.000
 GAD  H12  C1   C2   109.75  3.000
 GAD  H11  C1   C2   110.72  3.000
 GAD  O5   C1   C2   112.12  3.000
 GAD  H2   C2   C3   108.38  3.000
 GAD  H2   C2   O2   111.74  3.000
 GAD  C3   C2   O2   108.85  3.000
 GAD  H2   C2   C1   108.69  3.000
 GAD  C3   C2   C1   108.65  3.000
 GAD  O2   C2   C1   110.45  3.000
 GAD  HO2  O2   C2   108.75  3.000
 GAD  H3   C3   C4   108.57  3.000
 GAD  H3   C3   O3   110.62  3.000
 GAD  C4   C3   O3   111.50  3.000
 GAD  H3   C3   C2   108.16  3.000
 GAD  C4   C3   C2   109.04  3.000
 GAD  O3   C3   C2   108.87  3.000
 GAD  HO3  O3   C3   108.45  3.000
 GAD  H4   C4   C5   118.86  3.000
 GAD  H4   C4   C3   118.26  3.000
 GAD  C5   C4   C3   122.87  3.000
 GAD  O5   C5   C6   114.42  3.000
 GAD  O5   C5   C4   124.56  3.000
 GAD  C6   C5   C4   121.02  3.000
 GAD  O6B  C6   O6A  124.20  3.000
 GAD  O6B  C6   C5   112.29  3.000
 GAD  O6A  C6   C5   123.50  3.000
 GAD  H6B  O6B  C6   109.77  3.000
 GAD  C5   O5   C1   114.42  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  CONST_01  H6B  O6B  C6  C5  180.00   0.0  0
 GAD  Var_01    C4   C5   O5  C1   13.95  30.0  1
 GAD  Var_02    O5   C5   C4  C3    2.14  30.0  1
 GAD  Var_03    O6A  C6   C5  C4    0.66  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
 GAD  plan-1  H6B  0.020

