# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:52:27 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: methyl alpha-D-arabinofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO)[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
 AXR  AXR  'methyl alpha-D-arabinofuranoside'  D-saccharide  23  11  .  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_AXR
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
 AXR  O5   O  OH1   0  -0.660  12.7865  38.6428  -1.7200
 AXR  C5   C  CH2   0  -0.166  14.0891  38.1256  -1.5969
 AXR  C4   C  CH1   0  -0.029  15.1715  39.1414  -1.8899
 AXR  O4   O  O2    0  -0.513  15.1629  40.1534  -0.8915
 AXR  C3   C  CH1   0  -0.020  16.5886  38.5783  -1.8168
 AXR  O3   O  OH1   0  -0.652  16.9832  37.7920  -2.9034
 AXR  C2   C  CH1   0  -0.061  17.3909  39.8560  -1.5909
 AXR  O2   O  OH1   0  -0.659  18.6350  39.6994  -0.9709
 AXR  C1   C  CH1   0   0.325  16.4612  40.6759  -0.7007
 AXR  O1   O  O2    0  -0.485  16.5386  42.0136  -1.0471
 AXR  C6   C  CH3   0  -0.409  15.9044  42.8886  -0.1382
 AXR  HO5  H  HOH1  0   0.447  12.6503  39.2893  -1.0206
 AXR  H51  H  HCH2  0   0.200  14.2667  37.6929  -0.6031
 AXR  H52  H  HCH2  0   0.225  14.1789  37.3140  -2.3224
 AXR  H4   H  HCH1  0   0.220  14.9935  39.5801  -2.8854
 AXR  H3   H  HCH1  0   0.245  16.6774  37.9407  -0.9285
 AXR  HO3  H  HOH1  0   0.447  16.9277  38.3202  -3.7082
 AXR  H2   H  HCH1  0   0.223  17.4843  40.3723  -2.5604
 AXR  HO2  H  HOH1  0   0.456  19.2249  39.2498  -1.5842
 AXR  H1   H  HCH1  0   0.203  16.7198  40.5453   0.3616
 AXR  H6   H  HCH3  0   0.210  16.2557  42.7296   0.8873
 AXR  H6A  H  HCH3  0   0.237  16.1551  43.9060  -0.4334
 AXR  H6B  H  HCH3  0   0.215  14.8162  42.7842  -0.1488

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
 AXR  C5  O5   single  1.407  0.020  1.407
 AXR  O5  HO5  single  0.850  0.020  0.980
 AXR  C4  C5   single  1.513  0.020  1.513
 AXR  C5  H51  single  0.970  0.020  1.090
 AXR  C5  H52  single  0.970  0.020  1.090
 AXR  C4  C3   single  1.527  0.020  1.527
 AXR  C4  O4   single  1.422  0.020  1.422
 AXR  C4  H4   single  0.970  0.020  1.090
 AXR  O4  C1   single  1.412  0.020  1.412
 AXR  O3  C3   single  1.398  0.020  1.398
 AXR  C3  C2   single  1.525  0.020  1.525
 AXR  C3  H3   single  0.970  0.020  1.090
 AXR  O3  HO3  single  0.850  0.020  0.980
 AXR  C2  O2   single  1.399  0.020  1.399
 AXR  C2  C1   single  1.526  0.020  1.526
 AXR  C2  H2   single  0.970  0.020  1.090
 AXR  O2  HO2  single  0.850  0.020  0.980
 AXR  O1  C1   single  1.384  0.020  1.384
 AXR  C1  H1   single  0.970  0.020  1.090
 AXR  O1  C6   single  1.412  0.020  1.412
 AXR  C6  H6   single  0.970  0.020  1.090
 AXR  C6  H6A  single  0.970  0.020  1.090
 AXR  C6  H6B  single  0.970  0.020  1.090

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
 AXR  HO5  O5  C5   108.33  3.000
 AXR  H52  C5  H51  107.15  3.000
 AXR  H52  C5  C4   108.15  3.000
 AXR  H51  C5  C4   108.91  3.000
 AXR  H52  C5  O5   106.92  3.000
 AXR  H51  C5  O5   111.94  3.000
 AXR  C4   C5  O5   113.49  3.000
 AXR  H4   C4  C3   109.87  3.000
 AXR  H4   C4  O4   110.48  3.000
 AXR  C3   C4  O4   103.56  3.000
 AXR  H4   C4  C5   109.06  3.000
 AXR  O4   C4  C5   109.73  3.000
 AXR  C3   C4  C5   114.03  3.000
 AXR  C1   O4  C4   110.65  3.000
 AXR  H3   C3  C2   108.92  3.000
 AXR  H3   C3  O3   106.24  3.000
 AXR  C2   C3  O3   115.96  3.000
 AXR  H3   C3  C4   109.16  3.000
 AXR  C2   C3  C4   100.74  3.000
 AXR  O3   C3  C4   115.61  3.000
 AXR  HO3  O3  C3   108.93  3.000
 AXR  H2   C2  C1   108.24  3.000
 AXR  H2   C2  O2   111.52  3.000
 AXR  C1   C2  O2   110.09  3.000
 AXR  H2   C2  C3   107.86  3.000
 AXR  C1   C2  C3   102.47  3.000
 AXR  O2   C2  C3   116.08  3.000
 AXR  HO2  O2  C2   108.37  3.000
 AXR  H1   C1  O1   110.06  3.000
 AXR  H1   C1  C2   110.85  3.000
 AXR  O1   C1  C2   109.83  3.000
 AXR  H1   C1  O4   107.60  3.000
 AXR  O1   C1  O4   112.03  3.000
 AXR  C2   C1  O4   106.41  3.000
 AXR  C6   O1  C1   114.38  3.000
 AXR  H6B  C6  H6A  108.41  3.000
 AXR  H6B  C6  H6   108.32  3.000
 AXR  H6A  C6  H6   108.40  3.000
 AXR  H6B  C6  O1   112.43  3.000
 AXR  H6A  C6  O1   107.53  3.000
 AXR  H6   C6  O1   111.63  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
 AXR  Var_01  H6  C6  O1  C1  53.07  30.0  3

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

