# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:30:17 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: D-xylaric 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
 DXL  DXL  'D-xylaric acid           '  ligand  18  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DXL
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
 DXL  OAA   O  OC    -1  -0.764  -2.1767  -1.7273  -0.2495
 DXL  OAB   O  OH1    0  -0.698  -1.4529   1.5275   0.9614
 DXL  OAC   O  OH1    0  -0.675   2.0828   1.2704  -1.0878
 DXL  CAF   C  C      0   0.358  -2.3505  -0.5340   0.1122
 DXL  CAG   C  CH1    0  -0.075  -1.1004   0.2144   0.6096
 DXL  CAH   C  CH1    0  -0.036  -0.0051   0.2253  -0.4732
 DXL  CAI   C  CH1    0  -0.103   1.3004   0.8600   0.0118
 DXL  CAJ   C  C      0   0.315   2.1320  -0.1321   0.8586
 DXL  OAK   O  O      0  -0.398   3.2365  -0.4436   0.3437
 DXL  OAL   O  OH1    0  -0.646   0.2751  -1.0727  -0.9518
 DXL  HAG   H  HCH1   0   0.277  -0.7026  -0.3158   1.4836
 DXL  HAH   H  HCH1   0   0.241  -0.3871   0.8603  -1.2936
 DXL  HAI   H  HCH1   0   0.231   1.0532   1.7322   0.6309
 DXL  HOAL  H  HOH1   0   0.426  -0.5378  -1.5944  -0.7903
 DXL  HOAB  H  HOH1   0   0.420  -2.3924   1.5799   0.7128
 DXL  OAD   O  OC    -1  -0.776   1.6721  -0.5281   1.9347
 DXL  OAE   O  O      0  -0.507  -3.4260   0.0793   0.1697
 DXL  HOAC  H  HOH1   0   0.409   2.8805   0.7154  -0.9719

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
 DXL  CAF  OAA   deloc   1.259  0.020  1.259
 DXL  CAG  OAB   single  1.404  0.020  1.404
 DXL  OAB  HOAB  single  0.850  0.020  0.980
 DXL  CAI  OAC   single  1.411  0.020  1.411
 DXL  OAC  HOAC  single  0.850  0.020  0.980
 DXL  OAD  CAJ   deloc   1.235  0.020  1.235
 DXL  OAE  CAF   deloc   1.239  0.020  1.239
 DXL  CAF  CAG   single  1.540  0.020  1.540
 DXL  CAH  CAG   single  1.540  0.020  1.540
 DXL  CAG  HAG   single  0.970  0.020  1.090
 DXL  CAI  CAH   single  1.530  0.020  1.530
 DXL  CAH  OAL   single  1.411  0.020  1.411
 DXL  CAH  HAH   single  0.970  0.020  1.090
 DXL  CAJ  CAI   single  1.547  0.020  1.547
 DXL  CAI  HAI   single  0.970  0.020  1.090
 DXL  OAK  CAJ   deloc   1.258  0.020  1.258
 DXL  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
 DXL  HOAB  OAB  CAG  103.22  3.000
 DXL  HOAC  OAC  CAI  101.23  3.000
 DXL  CAG   CAF  OAE  116.68  3.000
 DXL  CAG   CAF  OAA  116.20  3.000
 DXL  OAE   CAF  OAA  127.02  3.000
 DXL  HAG   CAG  CAH  107.80  3.000
 DXL  HAG   CAG  CAF  108.48  3.000
 DXL  CAH   CAG  CAF  110.72  3.000
 DXL  HAG   CAG  OAB  110.08  3.000
 DXL  CAH   CAG  OAB  110.37  3.000
 DXL  CAF   CAG  OAB  109.37  3.000
 DXL  HAH   CAH  OAL  110.19  3.000
 DXL  HAH   CAH  CAI  106.96  3.000
 DXL  OAL   CAH  CAI  108.64  3.000
 DXL  HAH   CAH  CAG  106.26  3.000
 DXL  OAL   CAH  CAG  111.90  3.000
 DXL  CAI   CAH  CAG  112.75  3.000
 DXL  HAI   CAI  CAJ  108.78  3.000
 DXL  HAI   CAI  CAH  108.43  3.000
 DXL  CAJ   CAI  CAH  111.47  3.000
 DXL  HAI   CAI  OAC  109.48  3.000
 DXL  CAJ   CAI  OAC  108.37  3.000
 DXL  CAH   CAI  OAC  110.29  3.000
 DXL  OAK   CAJ  CAI  114.00  3.000
 DXL  OAK   CAJ  OAD  127.17  3.000
 DXL  CAI   CAJ  OAD  118.83  3.000
 DXL  HOAL  OAL  CAH  105.63  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
 DXL  chir_01  CAG  OAB  CAF  CAH  negativ
 DXL  chir_02  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
 DXL  plan-1  OAA  0.020
 DXL  plan-1  CAF  0.020
 DXL  plan-1  CAG  0.020
 DXL  plan-1  OAE  0.020
 DXL  plan-2  CAI  0.020
 DXL  plan-2  CAJ  0.020
 DXL  plan-2  OAK  0.020
 DXL  plan-2  OAD  0.020

