# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 07:25:00 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: D-galacturonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C=O)[C@@H](O)[C@@H](O)[C@H](O)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
 DGU  DGU  'D-galacturonic acid      '  D-saccharide  22  13  .  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_DGU
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
 DGU  OAA   O  O      0  -0.380  -4.3582   0.0016  -0.3033
 DGU  OAB   O  OH1    0  -0.670  -2.2093   1.6122  -0.1648
 DGU  OAC   O  OH1    0  -0.698   1.6265  -1.7836   0.5056
 DGU  CAE   C  C1     0   0.152  -3.4001  -0.4210   0.2951
 DGU  CAF   C  CH1    0  -0.075  -2.1364   0.3716   0.4754
 DGU  CAG   C  CH1    0  -0.023  -0.9694  -0.4629  -0.0659
 DGU  CAH   C  CH1    0   0.003   0.3845   0.2407   0.1239
 DGU  CAI   C  CH1    0  -0.131   1.5505  -0.6438  -0.3159
 DGU  CAJ   C  C      0   0.408   2.8822   0.1367  -0.2231
 DGU  OAK   O  OH1    0  -0.664  -1.1956  -0.7955  -1.4160
 DGU  OAL   O  OH1    0  -0.672   0.5505   0.6465   1.4628
 DGU  OAM   O  O      0  -0.607   3.7380  -0.3842   0.5279
 DGU  HAE   H  H      0   0.218  -3.3999  -1.4197   0.7612
 DGU  HAF   H  HCH1   0   0.259  -2.0053   0.4885   1.5618
 DGU  HAG   H  HCH1   0   0.250  -0.9564  -1.4088   0.4872
 DGU  HAH   H  HCH1   0   0.238   0.3983   1.1478  -0.4879
 DGU  HAI   H  HCH1   0   0.218   1.3998  -0.9308  -1.3649
 DGU  HOAK  H  HOH1   0   0.444  -1.2430   0.0228  -1.9239
 DGU  HOAL  H  HOH1   0   0.437   0.7421  -0.1456   1.9791
 DGU  HOAB  H  HOH1   0   0.450  -3.0867   1.6957  -0.5612
 DGU  OAD   O  OC    -1  -0.592   2.9900   1.1764  -0.8886
 DGU  HOAC  H  HOH1   0   0.433   2.5257  -1.7000   0.8811

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
 DGU  OAA  CAE   double  1.206  0.020  1.206
 DGU  OAB  CAF   single  1.398  0.020  1.398
 DGU  OAB  HOAB  single  0.850  0.020  0.980
 DGU  CAI  OAC   single  1.407  0.020  1.407
 DGU  OAC  HOAC  single  0.850  0.020  0.980
 DGU  CAJ  OAD   deloc   1.239  0.020  1.239
 DGU  CAE  CAF   single  1.503  0.020  1.503
 DGU  CAE  HAE   single  0.930  0.020  1.080
 DGU  CAF  CAG   single  1.533  0.020  1.533
 DGU  CAF  HAF   single  0.970  0.020  1.090
 DGU  CAG  OAK   single  1.409  0.020  1.409
 DGU  CAG  CAH   single  1.538  0.020  1.538
 DGU  CAG  HAG   single  0.970  0.020  1.090
 DGU  OAL  CAH   single  1.409  0.020  1.409
 DGU  CAH  CAI   single  1.528  0.020  1.528
 DGU  CAH  HAH   single  0.970  0.020  1.090
 DGU  CAI  CAJ   single  1.546  0.020  1.546
 DGU  CAI  HAI   single  0.970  0.020  1.090
 DGU  OAM  CAJ   deloc   1.252  0.020  1.252
 DGU  OAK  HOAK  single  0.850  0.020  0.980
 DGU  OAL  HOAL  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
 DGU  HOAB  OAB  CAF  108.17  3.000
 DGU  HOAC  OAC  CAI  101.81  3.000
 DGU  HAE   CAE  CAF  115.28  3.000
 DGU  HAE   CAE  OAA  121.83  3.000
 DGU  CAF   CAE  OAA  122.88  3.000
 DGU  HAF   CAF  CAG  108.40  3.000
 DGU  HAF   CAF  CAE  105.94  3.000
 DGU  CAG   CAF  CAE  108.10  3.000
 DGU  HAF   CAF  OAB  111.35  3.000
 DGU  CAG   CAF  OAB  111.16  3.000
 DGU  CAE   CAF  OAB  111.67  3.000
 DGU  HAG   CAG  OAK  106.37  3.000
 DGU  HAG   CAG  CAH  108.80  3.000
 DGU  OAK   CAG  CAH  111.58  3.000
 DGU  HAG   CAG  CAF  107.49  3.000
 DGU  CAH   CAG  CAF  112.18  3.000
 DGU  OAK   CAG  CAF  110.16  3.000
 DGU  HAH   CAH  OAL  106.92  3.000
 DGU  HAH   CAH  CAI  108.01  3.000
 DGU  OAL   CAH  CAI  110.51  3.000
 DGU  HAH   CAH  CAG  108.75  3.000
 DGU  CAI   CAH  CAG  111.81  3.000
 DGU  OAL   CAH  CAG  110.67  3.000
 DGU  HAI   CAI  CAJ  107.91  3.000
 DGU  HAI   CAI  CAH  108.76  3.000
 DGU  CAJ   CAI  CAH  110.35  3.000
 DGU  HAI   CAI  OAC  110.70  3.000
 DGU  CAJ   CAI  OAC  109.11  3.000
 DGU  CAH   CAI  OAC  110.00  3.000
 DGU  OAM   CAJ  CAI  114.50  3.000
 DGU  OAM   CAJ  OAD  127.72  3.000
 DGU  CAI   CAJ  OAD  117.78  3.000
 DGU  HOAK  OAK  CAG  108.20  3.000
 DGU  HOAL  OAL  CAH  107.19  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
 DGU  chir_01  CAF  OAB  CAE  CAG  negativ
 DGU  chir_02  CAG  OAK  CAF  CAH  positiv
 DGU  chir_03  CAH  OAL  CAG  CAI  positiv
 DGU  chir_04  CAI  OAC  CAH  CAJ  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
 DGU  plan-1  CAI  0.020
 DGU  plan-1  CAJ  0.020
 DGU  plan-1  OAM  0.020
 DGU  plan-1  OAD  0.020
 DGU  plan-2  OAA  0.020
 DGU  plan-2  CAE  0.020
 DGU  plan-2  CAF  0.020
 DGU  plan-2  HAE  0.020

