# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:49:55 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-L-arabinopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[C@@H](O)[C@H](O)[C@H]1O
#
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
 ARA  ARA  'alpha-L-arabinopyranose  '  L-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ARA
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
 ARA  C1   C  CH1   0   0.283  14.3661  56.6832  55.1070
 ARA  C2   C  CH1   0  -0.000  12.9502  57.1711  54.8119
 ARA  C3   C  CH1   0  -0.007  12.3927  56.3886  53.6249
 ARA  C4   C  CH1   0  -0.011  13.3307  56.4724  52.4233
 ARA  C5   C  CH2   0  -0.233  14.7166  56.0341  52.8792
 ARA  O1   O  OH1   0  -0.654  14.9064  57.4564  56.1111
 ARA  O2   O  OH1   0  -0.669  12.1746  56.9668  55.9658
 ARA  O3   O  OH1   0  -0.668  11.1001  56.8808  53.3675
 ARA  O4   O  OH1   0  -0.664  13.3188  57.7911  51.9347
 ARA  O5   O  O2    0  -0.485  15.1720  56.8144  53.9608
 ARA  H1   H  HCH1  0   0.181  14.3203  55.6169  55.3966
 ARA  H2   H  HCH1  0   0.213  13.0026  58.2385  54.5490
 ARA  H3   H  HCH1  0   0.218  12.3530  55.3286  53.9193
 ARA  H4   H  HCH1  0   0.220  12.9889  55.7593  51.6575
 ARA  H51  H  HCH2  0   0.211  14.6896  54.9667  53.1434
 ARA  H52  H  HCH2  0   0.251  15.4430  56.1488  52.0716
 ARA  HO1  H  HOH1  0   0.460  15.6737  57.0066  56.4806
 ARA  HO2  H  HOH1  0   0.448  11.2593  57.1658  55.7414
 ARA  HO3  H  HOH1  0   0.455  10.6243  56.2376  52.8331
 ARA  HO4  H  HOH1  0   0.451  13.8861  57.8330  51.1583

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
 ARA  C1  C2   single  1.526  0.020  1.526
 ARA  C1  O1   single  1.378  0.020  1.378
 ARA  C1  O5   single  1.407  0.020  1.407
 ARA  C1  H1   single  0.970  0.020  1.090
 ARA  C2  C3   single  1.527  0.020  1.527
 ARA  C2  O2   single  1.405  0.020  1.405
 ARA  C2  H2   single  0.970  0.020  1.090
 ARA  C3  C4   single  1.527  0.020  1.527
 ARA  C3  O3   single  1.407  0.020  1.407
 ARA  C3  H3   single  0.970  0.020  1.090
 ARA  C4  C5   single  1.523  0.020  1.523
 ARA  C4  O4   single  1.406  0.020  1.406
 ARA  C4  H4   single  0.970  0.020  1.090
 ARA  C5  O5   single  1.409  0.020  1.409
 ARA  C5  H51  single  0.970  0.020  1.090
 ARA  C5  H52  single  0.970  0.020  1.090
 ARA  O1  HO1  single  0.850  0.020  0.980
 ARA  O2  HO2  single  0.850  0.020  0.980
 ARA  O3  HO3  single  0.850  0.020  0.980
 ARA  O4  HO4  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
 ARA  H1   C1  O5   109.08  3.000
 ARA  H1   C1  O1   111.50  3.000
 ARA  O5   C1  O1   108.46  3.000
 ARA  H1   C1  C2   108.69  3.000
 ARA  O5   C1  C2   110.12  3.000
 ARA  O1   C1  C2   108.98  3.000
 ARA  H2   C2  O2   111.31  3.000
 ARA  H2   C2  C3   109.19  3.000
 ARA  O2   C2  C3   111.24  3.000
 ARA  H2   C2  C1   108.19  3.000
 ARA  O2   C2  C1   107.87  3.000
 ARA  C3   C2  C1   108.97  3.000
 ARA  H3   C3  O3   110.66  3.000
 ARA  H3   C3  C4   106.59  3.000
 ARA  O3   C3  C4   113.66  3.000
 ARA  H3   C3  C2   107.38  3.000
 ARA  O3   C3  C2   107.36  3.000
 ARA  C4   C3  C2   111.05  3.000
 ARA  H4   C4  O4   111.29  3.000
 ARA  H4   C4  C5   107.71  3.000
 ARA  O4   C4  C5   112.42  3.000
 ARA  H4   C4  C3   108.73  3.000
 ARA  O4   C4  C3   108.65  3.000
 ARA  C5   C4  C3   107.92  3.000
 ARA  H52  C5  H51  107.21  3.000
 ARA  H52  C5  O5   107.13  3.000
 ARA  H51  C5  O5   111.15  3.000
 ARA  H52  C5  C4   110.70  3.000
 ARA  H51  C5  C4   109.19  3.000
 ARA  O5   C5  C4   111.37  3.000
 ARA  HO1  O1  C1   109.27  3.000
 ARA  HO2  O2  C2   107.65  3.000
 ARA  HO3  O3  C3   108.78  3.000
 ARA  HO4  O4  C4   108.42  3.000
 ARA  C5   O5  C1   112.86  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
 ARA  Var_01  C4  C5  O5  C1  62.82  30.0  1

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
 ARA  chir_01  C1  C2  O1  O5  positiv
 ARA  chir_02  C2  O2  C1  C3  negativ
 ARA  chir_03  C3  O3  C2  C4  positiv
 ARA  chir_04  C4  O4  C3  C5  positiv

