# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:45:07 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: D-arabinonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 D8T  D8T  'D-arabinonic acid        '  ligand  20  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D8T
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
 D8T  OAA   O  O      0  -0.608   3.1339   0.1054  -0.7035
 D8T  OAB   O  OH1    0  -0.672   0.0096  -1.3646  -0.9124
 D8T  OAC   O  OH1    0  -0.664  -1.7260   1.2391   1.0030
 D8T  CAD   C  C      0   0.408   2.3306  -0.0532   0.2444
 D8T  CAE   C  CH1    0  -0.124   0.9601   0.6330   0.0467
 D8T  CAF   C  CH1    0  -0.014  -0.1644  -0.3987   0.1032
 D8T  CAG   C  CH1    0  -0.015  -1.5597   0.2432   0.0168
 D8T  CAH   C  CH2    0  -0.158  -2.6520  -0.8115   0.0997
 D8T  OAI   O  OH1    0  -0.672  -3.9049  -0.1852  -0.0586
 D8T  OAJ   O  OC    -1  -0.593   2.5175  -0.6762   1.2994
 D8T  OAK   O  OH1    0  -0.700   0.9481   1.2855  -1.2006
 D8T  HAE   H  HCH1   0   0.214   0.8223   1.3545   0.8623
 D8T  HAF   H  HCH1   0   0.225  -0.0879  -0.9345   1.0566
 D8T  HAG   H  HCH1   0   0.225  -1.6475   0.7623  -0.9448
 D8T  HAH   H  HCH2   0   0.204  -2.4791  -1.5674  -0.6727
 D8T  HAHA  H  HCH2   0   0.184  -2.5777  -1.3249   1.0715
 D8T  HOAI  H  HOH1   0   0.453  -4.5816  -0.8669  -0.0317
 D8T  HOAK  H  HOH1   0   0.431   1.8436   1.0850  -1.5381
 D8T  HOAB  H  HOH1   0   0.435   0.1248  -0.8846  -1.7414
 D8T  HOAC  H  HOH1   0   0.442  -1.6693   0.8228   1.8704

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
 D8T  OAA  CAD   deloc   1.253  0.020  1.253
 D8T  CAF  OAB   single  1.412  0.020  1.412
 D8T  OAB  HOAB  single  0.850  0.020  0.980
 D8T  OAC  CAG   single  1.411  0.020  1.411
 D8T  OAC  HOAC  single  0.850  0.020  0.980
 D8T  CAE  CAD   single  1.545  0.020  1.545
 D8T  CAD  OAJ   deloc   1.239  0.020  1.239
 D8T  CAF  CAE   single  1.527  0.020  1.527
 D8T  CAE  OAK   single  1.408  0.020  1.408
 D8T  CAE  HAE   single  0.970  0.020  1.090
 D8T  CAG  CAF   single  1.538  0.020  1.538
 D8T  CAF  HAF   single  0.970  0.020  1.090
 D8T  CAH  CAG   single  1.521  0.020  1.521
 D8T  CAG  HAG   single  0.970  0.020  1.090
 D8T  OAI  CAH   single  1.410  0.020  1.410
 D8T  CAH  HAH   single  0.970  0.020  1.090
 D8T  CAH  HAHA  single  0.970  0.020  1.090
 D8T  OAI  HOAI  single  0.850  0.020  0.980
 D8T  OAK  HOAK  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
 D8T  HOAB  OAB  CAF  106.99  3.000
 D8T  HOAC  OAC  CAG  108.49  3.000
 D8T  OAJ   CAD  CAE  117.77  3.000
 D8T  OAJ   CAD  OAA  127.67  3.000
 D8T  CAE   CAD  OAA  114.56  3.000
 D8T  HAE   CAE  OAK  110.65  3.000
 D8T  HAE   CAE  CAF  108.92  3.000
 D8T  OAK   CAE  CAF  109.85  3.000
 D8T  HAE   CAE  CAD  107.95  3.000
 D8T  OAK   CAE  CAD  109.07  3.000
 D8T  CAF   CAE  CAD  110.38  3.000
 D8T  HAF   CAF  CAG  108.42  3.000
 D8T  HAF   CAF  CAE  108.12  3.000
 D8T  CAG   CAF  CAE  112.58  3.000
 D8T  HAF   CAF  OAB  106.41  3.000
 D8T  CAG   CAF  OAB  110.90  3.000
 D8T  CAE   CAF  OAB  110.17  3.000
 D8T  HAG   CAG  CAH  108.59  3.000
 D8T  HAG   CAG  CAF  108.63  3.000
 D8T  CAH   CAG  CAF  111.04  3.000
 D8T  HAG   CAG  OAC  105.63  3.000
 D8T  CAH   CAG  OAC  111.51  3.000
 D8T  CAF   CAG  OAC  111.23  3.000
 D8T  HAHA  CAH  HAH  106.86  3.000
 D8T  HAHA  CAH  OAI  111.47  3.000
 D8T  HAH   CAH  OAI  111.60  3.000
 D8T  HAHA  CAH  CAG  108.84  3.000
 D8T  HAH   CAH  CAG  109.10  3.000
 D8T  OAI   CAH  CAG  108.91  3.000
 D8T  HOAI  OAI  CAH  107.91  3.000
 D8T  HOAK  OAK  CAE  101.71  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
 D8T  chir_01  CAE  CAD  CAF  OAK  positiv
 D8T  chir_02  CAF  OAB  CAE  CAG  negativ
 D8T  chir_03  CAG  OAC  CAF  CAH  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
 D8T  plan-1  OAA  0.020
 D8T  plan-1  CAD  0.020
 D8T  plan-1  CAE  0.020
 D8T  plan-1  OAJ  0.020

