# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:20:50 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  20  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  OH1   0  -0.582  -2.7615  -1.2399   0.7521
 DXL  OAB   O  OH1   0  -0.644  -1.4286   1.8997   0.0425
 DXL  OAC   O  OH1   0  -0.642   1.4355   1.6569   0.7847
 DXL  CAF   C  C     0   0.519  -2.4575  -0.2636  -0.0852
 DXL  CAG   C  CH1   0  -0.100  -1.2586   0.5558   0.3760
 DXL  CAH   C  CH1   0  -0.030   0.0164  -0.0544  -0.2570
 DXL  CAI   C  CH1   0  -0.087   1.2756   0.2903   0.5589
 DXL  CAJ   C  C     0   0.514   2.4860  -0.2752  -0.1756
 DXL  OAK   O  O     0  -0.440   3.0041   0.2974  -1.1009
 DXL  OAL   O  OH1   0  -0.649  -0.0745  -1.4421  -0.4430
 DXL  HOAA  H  HOH1  0   0.486  -3.4973  -1.7666   0.4032
 DXL  HOAC  H  HOH1  0   0.450   1.4603   2.1220  -0.0594
 DXL  HOAD  H  HOH1  0   0.486   3.6364  -1.7764  -0.2164
 DXL  HAG   H  HCH1  0   0.284  -1.1911   0.5035   1.4667
 DXL  HAH   H  HCH1  0   0.266   0.1151   0.3700  -1.2635
 DXL  HAI   H  HCH1  0   0.282   1.1899  -0.1799   1.5437
 DXL  HOAL  H  HOH1  0   0.456  -0.1082  -1.8872   0.4118
 DXL  HOAB  H  HOH1  0   0.449  -1.6033   1.9654  -0.9039
 DXL  OAD   O  OH1   0  -0.579   2.8885  -1.4391   0.3013
 DXL  OAE   O  O     0  -0.439  -3.0545  -0.0314  -1.1055

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   single  1.322  0.020  1.322
 DXL  OAA  HOAA  single  0.850  0.020  0.980
 DXL  CAG  OAB   single  1.395  0.020  1.395
 DXL  OAB  HOAB  single  0.850  0.020  0.980
 DXL  CAI  OAC   single  1.394  0.020  1.394
 DXL  OAC  HOAC  single  0.850  0.020  0.980
 DXL  OAD  CAJ   single  1.321  0.020  1.321
 DXL  OAD  HOAD  single  0.850  0.020  0.980
 DXL  OAE  CAF   double  1.205  0.020  1.205
 DXL  CAF  CAG   single  1.524  0.020  1.524
 DXL  CAH  CAG   single  1.549  0.020  1.549
 DXL  CAG  HAG   single  0.970  0.020  1.090
 DXL  CAI  CAH   single  1.540  0.020  1.540
 DXL  CAH  OAL   single  1.403  0.020  1.403
 DXL  CAH  HAH   single  0.970  0.020  1.090
 DXL  CAJ  CAI   single  1.525  0.020  1.525
 DXL  CAI  HAI   single  0.970  0.020  1.090
 DXL  OAK  CAJ   double  1.205  0.020  1.205
 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  HOAA  OAA  CAF  110.35  3.000
 DXL  HOAB  OAB  CAG  108.80  3.000
 DXL  HOAC  OAC  CAI  109.51  3.000
 DXL  CAG   CAF  OAE  122.86  3.000
 DXL  CAG   CAF  OAA  112.74  3.000
 DXL  OAE   CAF  OAA  124.40  3.000
 DXL  HAG   CAG  CAH  109.75  3.000
 DXL  HAG   CAG  CAF  108.94  3.000
 DXL  CAH   CAG  CAF  108.19  3.000
 DXL  HAG   CAG  OAB  106.97  3.000
 DXL  CAH   CAG  OAB  112.47  3.000
 DXL  CAF   CAG  OAB  110.48  3.000
 DXL  HAH   CAH  OAL  105.48  3.000
 DXL  HAH   CAH  CAI  109.03  3.000
 DXL  OAL   CAH  CAI  110.16  3.000
 DXL  HAH   CAH  CAG  107.26  3.000
 DXL  OAL   CAH  CAG  112.99  3.000
 DXL  CAI   CAH  CAG  111.63  3.000
 DXL  HAI   CAI  CAJ  109.65  3.000
 DXL  HAI   CAI  CAH  108.45  3.000
 DXL  CAJ   CAI  CAH  108.12  3.000
 DXL  HAI   CAI  OAC  106.52  3.000
 DXL  CAJ   CAI  OAC  110.52  3.000
 DXL  CAH   CAI  OAC  113.52  3.000
 DXL  OAK   CAJ  CAI  122.34  3.000
 DXL  OAK   CAJ  OAD  124.40  3.000
 DXL  CAI   CAJ  OAD  113.26  3.000
 DXL  HOAL  OAL  CAH  109.96  3.000
 DXL  HOAD  OAD  CAJ  110.41  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
 DXL  CONST_01  HOAA  OAA  CAF  OAE    0.00  0.0  0
 DXL  CONST_02  HOAD  OAD  CAJ  CAI  180.00  0.0  0

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  HOAA  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  HOAD  0.020
 DXL  plan-2  OAD   0.020

