# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:37:02 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-deoxy-2-fluoro-alpha-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
 X2F  X2F  2-deoxy-2-fluoro-alpha-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_X2F
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
 X2F  C1   C  CH1   0   0.192  21.5813  68.4728  36.8801
 X2F  C2   C  CH1   0   0.169  20.8583  69.4776  37.7768
 X2F  C3   C  CH1   0  -0.027  20.1586  68.8023  38.9388
 X2F  C4   C  CH1   0  -0.014  19.2427  67.7178  38.3807
 X2F  C5   C  CH2   0  -0.222  20.0390  66.7800  37.4796
 X2F  O1   O  OH1   0  -0.658  22.6441  67.9390  37.5942
 X2F  O3   O  OH1   0  -0.665  19.4460  69.7843  39.6461
 X2F  O4   O  OH1   0  -0.664  18.6846  67.0315  39.4759
 X2F  O5   O  O2    0  -0.490  20.6725  67.5020  36.4377
 X2F  F2   F  F     0  -0.372  21.7739  70.4089  38.2487
 X2F  H1   H  HCH1  0   0.245  21.9243  68.9740  35.9675
 X2F  H2   H  HCH1  0   0.227  20.1229  70.0155  37.1700
 X2F  H3   H  HCH1  0   0.222  20.9100  68.3194  39.5825
 X2F  H4   H  HCH1  0   0.222  18.4620  68.2060  37.7797
 X2F  H51  H  HCH2  0   0.218  20.7615  66.2127  38.0779
 X2F  H52  H  HCH2  0   0.245  19.3739  66.0614  36.9975
 X2F  HO1  H  HOH1  0   0.464  23.2350  67.4803  36.9868
 X2F  HO3  H  HOH1  0   0.451  18.9877  69.3498  40.3733
 X2F  HO4  H  HOH1  0   0.459  17.8830  66.5851  39.1866

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
 X2F  C1  C2   single  1.528  0.020  1.528
 X2F  C1  O1   single  1.387  0.020  1.387
 X2F  C1  O5   single  1.402  0.020  1.402
 X2F  C1  H1   single  0.970  0.020  1.090
 X2F  C2  C3   single  1.515  0.020  1.515
 X2F  C2  F2   single  1.389  0.020  1.389
 X2F  C2  H2   single  0.970  0.020  1.090
 X2F  C3  C4   single  1.525  0.020  1.525
 X2F  C3  O3   single  1.404  0.020  1.404
 X2F  C3  H3   single  0.970  0.020  1.090
 X2F  C4  C5   single  1.525  0.020  1.525
 X2F  C4  O4   single  1.408  0.020  1.408
 X2F  C4  H4   single  0.970  0.020  1.090
 X2F  C5  O5   single  1.417  0.020  1.417
 X2F  C5  H51  single  0.970  0.020  1.090
 X2F  C5  H52  single  0.970  0.020  1.090
 X2F  O1  HO1  single  0.850  0.020  0.980
 X2F  O3  HO3  single  0.850  0.020  0.980
 X2F  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
 X2F  H1   C1  O5   104.89  3.000
 X2F  H1   C1  O1   111.40  3.000
 X2F  O5   C1  O1   113.12  3.000
 X2F  H1   C1  C2   109.62  3.000
 X2F  O5   C1  C2   109.50  3.000
 X2F  O1   C1  C2   108.26  3.000
 X2F  H2   C2  F2   107.56  3.000
 X2F  H2   C2  C3   109.50  3.000
 X2F  F2   C2  C3   110.04  3.000
 X2F  H2   C2  C1   108.40  3.000
 X2F  F2   C2  C1   109.17  3.000
 X2F  C3   C2  C1   112.05  3.000
 X2F  H3   C3  O3   111.01  3.000
 X2F  H3   C3  C4   108.17  3.000
 X2F  O3   C3  C4   112.13  3.000
 X2F  H3   C3  C2   109.19  3.000
 X2F  O3   C3  C2   108.00  3.000
 X2F  C4   C3  C2   108.27  3.000
 X2F  H4   C4  O4   111.11  3.000
 X2F  H4   C4  C5   108.72  3.000
 X2F  O4   C4  C5   111.52  3.000
 X2F  H4   C4  C3   108.10  3.000
 X2F  O4   C4  C3   107.46  3.000
 X2F  C5   C4  C3   109.87  3.000
 X2F  H52  C5  H51  107.58  3.000
 X2F  H52  C5  O5   106.45  3.000
 X2F  H51  C5  O5   111.73  3.000
 X2F  H52  C5  C4   110.35  3.000
 X2F  H51  C5  C4   109.87  3.000
 X2F  O5   C5  C4   110.76  3.000
 X2F  HO1  O1  C1   109.18  3.000
 X2F  HO3  O3  C3   107.83  3.000
 X2F  HO4  O4  C4   108.82  3.000
 X2F  C5   O5  C1   114.26  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
 X2F  Var_01  C4  C5  O5  C1  60.52  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
 X2F  chir_01  C1  C2  O1  O5  negativ
 X2F  chir_02  C2  F2  C3  C1  positiv
 X2F  chir_03  C3  O3  C2  C4  positiv
 X2F  chir_04  C4  O4  C3  C5  negativ

