# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:31:18 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-D-arabinofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[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
 BXY  BXY  'alpha-D-arabinofuranose  '  D-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_BXY
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
 BXY  O5   O  OH1   0  -0.660  4.7885  35.4340  -0.0215
 BXY  C5   C  CH2   0  -0.207  5.5946  36.2594   0.7828
 BXY  C4   C  CR15  0   0.005  6.1409  37.4857   0.0767
 BXY  C3   C  CR15  0  -0.016  5.1119  38.4277  -0.5491
 BXY  O3   O  OH1   0  -0.660  4.5071  39.3152   0.3505
 BXY  C2   C  CR15  0  -0.047  5.9848  39.1650  -1.5491
 BXY  O2   O  OH1   0  -0.660  5.3209  39.7590  -2.6284
 BXY  C1   C  CR15  0   0.289  6.9156  38.0636  -2.0460
 BXY  O4   O  O     0  -0.507  6.9623  37.0985  -1.0161
 BXY  HO5  H  HOH1  0   0.451  3.9083  35.8160  -0.0774
 BXY  H51  H  HCH2  0   0.211  5.0707  36.5997   1.6850
 BXY  H52  H  HCH2  0   0.235  6.4356  35.6510   1.1258
 BXY  H4   H  HCR5  0   0.211  6.7252  38.0490   0.8215
 BXY  H3   H  HCR5  0   0.217  4.3632  37.8434  -1.1048
 BXY  HO3  H  HOH1  0   0.457  3.7868  38.8616   0.7985
 BXY  H2   H  HCR5  0   0.222  6.5872  39.9008  -0.9926
 BXY  HO2  H  HOH1  0   0.455  4.8290  40.5186  -2.3015
 BXY  O1   O  OH1   0  -0.656  8.1683  38.5904  -2.3180
 BXY  H1   H  HCR5  0   0.202  6.4958  37.5827  -2.9406
 BXY  HO1  H  HOH1  0   0.459  8.6587  37.9765  -2.8745

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
 BXY  O5  C5   single  1.406  0.020  1.406
 BXY  O5  HO5  single  0.850  0.020  0.980
 BXY  C5  H51  single  0.970  0.020  1.090
 BXY  C5  H52  single  0.970  0.020  1.090
 BXY  C4  C5   single  1.517  0.020  1.517
 BXY  C4  H4   single  0.970  0.020  1.090
 BXY  C3  C4   single  1.529  0.020  1.529
 BXY  C3  O3   single  1.401  0.020  1.401
 BXY  C3  H3   single  0.970  0.020  1.090
 BXY  O3  HO3  single  0.850  0.020  0.980
 BXY  C2  C3   single  1.518  0.020  1.518
 BXY  C2  H2   single  0.970  0.020  1.090
 BXY  O2  C2   single  1.399  0.020  1.399
 BXY  O2  HO2  single  0.850  0.020  0.980
 BXY  C1  C2   single  1.525  0.020  1.525
 BXY  C1  O4   single  1.412  0.020  1.412
 BXY  C1  O1   single  1.386  0.020  1.386
 BXY  O4  C4   single  1.421  0.020  1.421
 BXY  C1  H1   single  0.970  0.020  1.090
 BXY  O1  HO1  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
 BXY  HO5  O5  C5   108.96  3.000
 BXY  H52  C5  H51  106.38  3.000
 BXY  H52  C5  C4   108.60  3.000
 BXY  H51  C5  C4   107.70  3.000
 BXY  C4   C5  O5   114.49  3.000
 BXY  H52  C5  O5   107.08  3.000
 BXY  H51  C5  O5   112.24  3.000
 BXY  H4   C4  O4   110.65  3.000
 BXY  O4   C4  C3   104.01  3.000
 BXY  H4   C4  C3   108.58  3.000
 BXY  O4   C4  C5   110.24  3.000
 BXY  C3   C4  C5   116.50  3.000
 BXY  H4   C4  C5   106.84  3.000
 BXY  H3   C3  C2   108.45  3.000
 BXY  C2   C3  O3   111.31  3.000
 BXY  H3   C3  O3   111.53  3.000
 BXY  C2   C3  C4   100.48  3.000
 BXY  H3   C3  C4   109.72  3.000
 BXY  O3   C3  C4   114.71  3.000
 BXY  HO3  O3  C3   108.88  3.000
 BXY  H2   C2  C1   108.25  3.000
 BXY  C1   C2  O2   110.17  3.000
 BXY  H2   C2  O2   111.44  3.000
 BXY  C1   C2  C3   102.40  3.000
 BXY  O2   C2  C3   116.18  3.000
 BXY  H2   C2  C3   107.82  3.000
 BXY  HO2  O2  C2   108.40  3.000
 BXY  H1   C1  O1   110.60  3.000
 BXY  H1   C1  O4   107.89  3.000
 BXY  O1   C1  O4   111.90  3.000
 BXY  H1   C1  C2   110.37  3.000
 BXY  O1   C1  C2   109.94  3.000
 BXY  O4   C1  C2   106.03  3.000
 BXY  C1   O4  C4   110.82  3.000
 BXY  HO1  O1  C1   109.36  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
 BXY  chir_01  C4  C5  C3  O4  positiv
 BXY  chir_02  C3  O3  C2  C4  negativ
 BXY  chir_03  C2  O2  C1  C3  positiv
 BXY  chir_04  C1  O1  O4  C2  negativ

