# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:58:59 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-deoxy-2-fluoro-beta-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](O)[C@H](F)[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
 BXF  BXF  2-deoxy-2-fluoro-beta-D-xylopyranose  D-saccharide  19  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_BXF
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
 BXF  C1   C  CH1   0   0.242  -11.5667  -10.2172  -5.0974
 BXF  O1   O  OH1   0  -0.653  -12.4192  -10.1754  -6.1752
 BXF  C2   C  CH1   0   0.153  -10.4417  -11.1997  -5.4047
 BXF  F    F  F     0  -0.372  -10.9891  -12.4695  -5.5431
 BXF  C3   C  CH1   0  -0.031   -9.4204  -11.2140  -4.2854
 BXF  O3   O  OH1   0  -0.662   -8.3760  -12.0743  -4.6536
 BXF  C4   C  CH1   0  -0.010   -8.9423   -9.7889  -4.0225
 BXF  O4   O  OH1   0  -0.663   -8.0996   -9.8304  -2.8966
 BXF  C5   C  CH2   0  -0.226  -10.1500   -8.8854  -3.7899
 BXF  O5   O  O2    0  -0.486  -11.0214   -8.9358  -4.8980
 BXF  H1   H  HCH1  0   0.198  -12.0826  -10.5419  -4.1764
 BXF  H2   H  HCH1  0   0.226   -9.9662  -10.9317  -6.3550
 BXF  H3   H  HCH1  0   0.219   -9.9244  -11.5690  -3.3704
 BXF  H4   H  HCH1  0   0.223   -8.4026   -9.4332  -4.9117
 BXF  HO4  H  HOH1  0   0.459   -7.5788   -9.0217  -2.8694
 BXF  H51  H  HCH2  0   0.215  -10.6625   -9.1876  -2.8651
 BXF  H52  H  HCH2  0   0.252   -9.8373   -7.8466  -3.6729
 BXF  HO1  H  HOH1  0   0.465  -13.2700   -9.8174  -5.8995
 BXF  HO3  H  HOH1  0   0.452   -7.7524  -12.1143  -3.9210

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
 BXF  C1  O1   single  1.375  0.020  1.375
 BXF  C1  C2   single  1.525  0.020  1.525
 BXF  C1  O5   single  1.407  0.020  1.407
 BXF  C2  F    single  1.390  0.020  1.390
 BXF  C2  C3   single  1.515  0.020  1.515
 BXF  C3  O3   single  1.402  0.020  1.402
 BXF  C3  C4   single  1.526  0.020  1.526
 BXF  C4  O4   single  1.407  0.020  1.407
 BXF  C4  C5   single  1.526  0.020  1.526
 BXF  C5  O5   single  1.411  0.020  1.411
 BXF  C1  H1   single  0.970  0.020  1.090
 BXF  C2  H2   single  0.970  0.020  1.090
 BXF  C3  H3   single  0.970  0.020  1.090
 BXF  C4  H4   single  0.970  0.020  1.090
 BXF  O4  HO4  single  0.850  0.020  0.980
 BXF  C5  H51  single  0.970  0.020  1.090
 BXF  C5  H52  single  0.970  0.020  1.090
 BXF  O1  HO1  single  0.850  0.020  0.980
 BXF  O3  HO3  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
 BXF  H1   C1  O5   109.31  3.000
 BXF  H1   C1  C2   108.86  3.000
 BXF  O5   C1  C2   109.24  3.000
 BXF  H1   C1  O1   111.90  3.000
 BXF  O5   C1  O1   108.90  3.000
 BXF  C2   C1  O1   108.61  3.000
 BXF  HO1  O1  C1   109.55  3.000
 BXF  H2   C2  C3   110.51  3.000
 BXF  H2   C2  F    107.94  3.000
 BXF  C3   C2  F    109.29  3.000
 BXF  H2   C2  C1   109.72  3.000
 BXF  C3   C2  C1   110.76  3.000
 BXF  F    C2  C1   108.55  3.000
 BXF  H3   C3  C4   107.51  3.000
 BXF  H3   C3  O3   111.14  3.000
 BXF  C4   C3  O3   112.63  3.000
 BXF  H3   C3  C2   107.93  3.000
 BXF  C4   C3  C2   109.24  3.000
 BXF  O3   C3  C2   108.29  3.000
 BXF  HO3  O3  C3   107.94  3.000
 BXF  H4   C4  C5   108.68  3.000
 BXF  H4   C4  O4   111.27  3.000
 BXF  C5   C4  O4   111.68  3.000
 BXF  H4   C4  C3   108.46  3.000
 BXF  C5   C4  C3   109.34  3.000
 BXF  O4   C4  C3   107.34  3.000
 BXF  HO4  O4  C4   108.79  3.000
 BXF  H52  C5  H51  107.75  3.000
 BXF  H52  C5  O5   107.18  3.000
 BXF  H51  C5  O5   111.28  3.000
 BXF  H52  C5  C4   110.69  3.000
 BXF  H51  C5  C4   109.53  3.000
 BXF  O5   C5  C4   110.37  3.000
 BXF  C5   O5  C1   112.54  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
 BXF  Var_01  C4  C5  O5  C1  63.41  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
 BXF  chir_01  C1  O1  C2  O5  negativ
 BXF  chir_02  C2  F   C3  C1  positiv
 BXF  chir_03  C3  O3  C2  C4  positiv
 BXF  chir_04  C4  O4  C3  C5  negativ

