# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:41:21 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: L-arabinaric acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@@H](O)C(O)=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
 LY9  LY9  'L-arabinaric acid        '  ligand  18  12  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LY9
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
 LY9  OAA   O  O      0  -0.398  -3.0626   0.3193  -1.2159
 LY9  OAB   O  OH1    0  -0.691  -1.3256   1.9168  -0.2160
 LY9  OAC   O  OH1    0  -0.715   1.3482   0.6210   1.6878
 LY9  CAF   C  C      0   0.306  -2.5491  -0.1520  -0.1716
 LY9  CAG   C  CH1    0  -0.121  -1.2938   0.6083   0.3070
 LY9  CAH   C  CH1    0  -0.043  -0.0101  -0.0984  -0.1692
 LY9  CAI   C  CH1    0  -0.087   1.2500   0.6396   0.2827
 LY9  CAJ   C  C      0   0.340   2.5089  -0.0175  -0.3222
 LY9  OAK   O  O      0  -0.623   3.3434  -0.4267   0.5187
 LY9  OAL   O  OH1    0  -0.655   0.0405  -1.4465   0.2367
 LY9  HAG   H  HCH1   0   0.256  -1.2954   0.6547   1.4036
 LY9  HAH   H  HCH1   0   0.246  -0.0210  -0.1050  -1.2642
 LY9  HAI   H  HCH1   0   0.249   1.1979   1.6729  -0.0844
 LY9  HOAL  H  HOH1   0   0.427   0.1029  -1.4569   1.1980
 LY9  HOAB  H  HOH1   0   0.419  -1.9621   1.8260  -0.9483
 LY9  OAD   O  OC    -1  -0.565   2.5923  -0.0759  -1.5579
 LY9  OAE   O  OC    -1  -0.762  -2.9404  -1.1281   0.4824
 LY9  HOAC  H  HOH1   0   0.417   2.2018   0.1654   1.8218

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
 LY9  CAF  OAA   deloc   1.255  0.020  1.255
 LY9  OAB  CAG   single  1.410  0.020  1.410
 LY9  OAB  HOAB  single  0.850  0.020  0.980
 LY9  OAC  CAI   single  1.409  0.020  1.409
 LY9  OAC  HOAC  single  0.850  0.020  0.980
 LY9  CAJ  OAD   deloc   1.240  0.020  1.240
 LY9  CAF  OAE   deloc   1.238  0.020  1.238
 LY9  CAG  CAF   single  1.544  0.020  1.544
 LY9  CAH  CAG   single  1.541  0.020  1.541
 LY9  CAG  HAG   single  0.970  0.020  1.090
 LY9  CAI  CAH   single  1.529  0.020  1.529
 LY9  OAL  CAH   single  1.409  0.020  1.409
 LY9  CAH  HAH   single  0.970  0.020  1.090
 LY9  CAJ  CAI   single  1.544  0.020  1.544
 LY9  CAI  HAI   single  0.970  0.020  1.090
 LY9  OAK  CAJ   deloc   1.253  0.020  1.253
 LY9  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
 LY9  HOAB  OAB  CAG  101.95  3.000
 LY9  HOAC  OAC  CAI  101.77  3.000
 LY9  CAG   CAF  OAE  118.78  3.000
 LY9  CAG   CAF  OAA  113.93  3.000
 LY9  OAE   CAF  OAA  127.30  3.000
 LY9  HAG   CAG  CAH  109.23  3.000
 LY9  HAG   CAG  CAF  109.23  3.000
 LY9  CAH   CAG  CAF  110.84  3.000
 LY9  HAG   CAG  OAB  109.36  3.000
 LY9  CAH   CAG  OAB  109.27  3.000
 LY9  CAF   CAG  OAB  108.89  3.000
 LY9  HAH   CAH  OAL  106.42  3.000
 LY9  HAH   CAH  CAI  107.86  3.000
 LY9  OAL   CAH  CAI  110.32  3.000
 LY9  HAH   CAH  CAG  107.67  3.000
 LY9  OAL   CAH  CAG  112.32  3.000
 LY9  CAI   CAH  CAG  111.96  3.000
 LY9  HAI   CAI  CAJ  107.96  3.000
 LY9  HAI   CAI  CAH  108.45  3.000
 LY9  CAJ   CAI  CAH  110.54  3.000
 LY9  HAI   CAI  OAC  110.45  3.000
 LY9  CAJ   CAI  OAC  109.18  3.000
 LY9  CAH   CAI  OAC  110.24  3.000
 LY9  OAK   CAJ  CAI  114.77  3.000
 LY9  OAK   CAJ  OAD  127.48  3.000
 LY9  CAI   CAJ  OAD  117.75  3.000
 LY9  HOAL  OAL  CAH  107.47  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
 LY9  chir_01  CAG  OAB  CAF  CAH  negativ
 LY9  chir_02  CAI  OAC  CAH  CAJ  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
 LY9  plan-1  OAA  0.020
 LY9  plan-1  CAF  0.020
 LY9  plan-1  CAG  0.020
 LY9  plan-1  OAE  0.020
 LY9  plan-2  CAI  0.020
 LY9  plan-2  CAJ  0.020
 LY9  plan-2  OAK  0.020
 LY9  plan-2  OAD  0.020

