# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:26:19 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: D-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
 RAT  RAT  'D-arabinaric acid        '  D-saccharide  18  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RAT
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
 RAT  O1A  O  OC    -1  -0.651  -2.4487  -1.4595  -0.2183
 RAT  C1   C  C      0   0.375  -2.4492  -0.2468   0.1014
 RAT  O1B  O  O      0  -0.726  -3.3132   0.3472   0.7704
 RAT  C2   C  CH1    0  -0.091  -1.2137   0.5796  -0.3086
 RAT  O2   O  OH1    0  -0.565  -1.3059   1.8745   0.2221
 RAT  C3   C  CH1    0  -0.071   0.0727  -0.1203   0.1583
 RAT  O3   O  OH1    0  -0.639   0.1597  -1.4097  -0.3992
 RAT  C4   C  CH1    0  -0.092   1.3254   0.6696  -0.2158
 RAT  O4   O  OH1    0  -0.615   1.3915   0.9270  -1.5947
 RAT  C5   C  C      0   0.328   2.5814  -0.1172   0.2221
 RAT  O5A  O  O      0  -0.651   3.3376  -0.4692  -0.7116
 RAT  O5B  O  OC    -1  -0.601   2.7192  -0.3539   1.4332
 RAT  H2   H  HCH1   0   0.216  -1.1904   0.6187  -1.4075
 RAT  HO2  H  HOH1   0   0.444  -2.1273   1.8500   0.7425
 RAT  H3   H  HCH1   0   0.236   0.0437  -0.1526   1.2603
 RAT  HO3  H  HOH1   0   0.436  -0.7658  -1.7216  -0.4631
 RAT  H4   H  HCH1   0   0.232   1.2993   1.6170   0.3371
 RAT  HO4  H  HOH1   0   0.436   2.1569   0.3895  -1.8709

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
 RAT  C1   O1A  deloc   1.254  0.020  1.254
 RAT  C2   C1   single  1.542  0.020  1.542
 RAT  O1B  C1   deloc   1.244  0.020  1.244
 RAT  O2   C2   single  1.402  0.020  1.402
 RAT  C3   C2   single  1.537  0.020  1.537
 RAT  C2   H2   single  0.970  0.020  1.090
 RAT  O2   HO2  single  0.850  0.020  0.980
 RAT  C4   C3   single  1.527  0.020  1.527
 RAT  O3   C3   single  1.407  0.020  1.407
 RAT  C3   H3   single  0.970  0.020  1.090
 RAT  O3   HO3  single  0.850  0.020  0.980
 RAT  C5   C4   single  1.545  0.020  1.545
 RAT  C4   O4   single  1.404  0.020  1.404
 RAT  C4   H4   single  0.970  0.020  1.090
 RAT  O4   HO4  single  0.850  0.020  0.980
 RAT  O5A  C5   deloc   1.252  0.020  1.252
 RAT  O5B  C5   deloc   1.242  0.020  1.242

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
 RAT  C2   C1  O1B  116.34  3.000
 RAT  O1B  C1  O1A  126.82  3.000
 RAT  C2   C1  O1A  116.75  3.000
 RAT  H2   C2  C3   107.58  3.000
 RAT  H2   C2  O2   110.29  3.000
 RAT  C3   C2  O2   111.13  3.000
 RAT  H2   C2  C1   107.56  3.000
 RAT  C3   C2  C1   110.22  3.000
 RAT  O2   C2  C1   109.97  3.000
 RAT  HO2  O2  C2   103.57  3.000
 RAT  H3   C3  C4   106.34  3.000
 RAT  H3   C3  O3   111.75  3.000
 RAT  C4   C3  O3   109.03  3.000
 RAT  H3   C3  C2   107.15  3.000
 RAT  O3   C3  C2   110.40  3.000
 RAT  C4   C3  C2   112.11  3.000
 RAT  HO3  O3  C3   105.03  3.000
 RAT  H4   C4  C5   108.43  3.000
 RAT  H4   C4  O4   109.73  3.000
 RAT  C5   C4  O4   109.47  3.000
 RAT  H4   C4  C3   107.68  3.000
 RAT  O4   C4  C3   111.95  3.000
 RAT  C5   C4  C3   109.50  3.000
 RAT  HO4  O4  C4   102.36  3.000
 RAT  O5B  C5  O5A  127.36  3.000
 RAT  O5B  C5  C4   117.62  3.000
 RAT  O5A  C5  C4   115.00  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
 RAT  chir_01  C2  C1  O2  C3  negativ
 RAT  chir_02  C4  O4  C3  C5  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
 RAT  plan-1  O1A  0.020
 RAT  plan-1  C1   0.020
 RAT  plan-1  O1B  0.020
 RAT  plan-1  C2   0.020
 RAT  plan-2  C4   0.020
 RAT  plan-2  C5   0.020
 RAT  plan-2  O5A  0.020
 RAT  plan-2  O5B  0.020

