# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:17:04 2019
#
#   Ligand name: 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1F
#
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
RF5        RF5 '2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose' saccharide 22 14 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_RF5
#
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
RF5         P      P   P      0    .      -3.5232   -1.3169   -0.1824
RF5         C1     C   CH1    0    .       1.9776    0.2071   -1.1292
RF5         O1     O   OH1    0    .       3.2795   -0.1030   -0.7967
RF5         C2     C   CH1    0    .       1.5700    1.2654   -0.4459
RF5         F2     F   F      0    .       0.6239    1.9876   -1.1942
RF5         C3     C   CH1    0    .       0.8809    0.6794    0.9106
RF5         O3     O   OH1    0    .       1.8793    0.3742    1.8716
RF5         C4     C   CH1    0    .       0.2310   -0.4557    0.5355
RF5         O4     O   O2     0    .       0.9935   -0.9823   -0.6885
RF5         C5     C   CH2    0    .      -1.2085   -0.1354    0.1586
RF5         O5     O   O2     0    .      -1.8750   -1.3169   -0.1824
RF5         OP1    O   O      0    .      -4.0266   -1.3169    1.2412
RF5         OP2    O   OP    -1    .      -4.0266   -0.0839   -0.8942
RF5         OP3    O   OP    -1    .      -4.0266   -2.5498   -0.8942
RF5         H1     H   HCH1   0    .       1.8887    0.3916   -2.1930
RF5         HO1    H   HOH1   0    .       3.7055   -0.5050   -1.5355
RF5         H2     H   HCH1   0    .       2.4152    1.8942   -0.1930
RF5         H3     H   HCH1   0    .       0.1755    1.3978    1.3103
RF5         HO3    H   HOH1   0    .       1.7294    0.8811    2.6524
RF5         H4     H   HCH1   0    .       0.2616   -1.1849    1.3361
RF5         H5     H   HCH2   0    .      -1.2183    0.5417   -0.6870
RF5         H5A    H   HCH2   0    .      -1.7070    0.3304    1.0000
#
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
RF5   OP1     P     deloc         1.510 0.020     1.510
RF5   OP2     P     deloc         1.510 0.020     1.510
RF5   P       OP3   deloc         1.510 0.020     1.510
RF5   P       O5    single        1.648 0.020     1.648
RF5   O4      C1    single        1.605 0.020     1.605
RF5   C1      O1    single        1.379 0.020     1.379
RF5   C1      C2    single        1.324 0.020     1.324
RF5   C1      H1    single        0.970 0.020     1.090
RF5   O1      HO1   single        0.850 0.020     0.980
RF5   C3      C2    single        1.630 0.020     1.630
RF5   C2      F2    single        1.406 0.020     1.406
RF5   C2      H2    single        0.970 0.020     1.090
RF5   C4      C3    single        1.361 0.020     1.361
RF5   C3      O3    single        1.419 0.020     1.419
RF5   C3      H3    single        0.970 0.020     1.090
RF5   O3      HO3   single        0.850 0.020     0.980
RF5   C5      C4    single        1.522 0.020     1.522
RF5   C4      O4    single        1.535 0.020     1.535
RF5   C4      H4    single        0.970 0.020     1.090
RF5   O5      C5    single        1.399 0.020     1.399
RF5   C5      H5    single        0.970 0.020     1.090
RF5   C5      H5A   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
RF5   OP3     P       OP2         109.47 3.000
RF5   OP3     P       OP1         109.47 3.000
RF5   OP2     P       OP1         109.47 3.000
RF5   OP3     P       O5          109.47 3.000
RF5   OP2     P       O5          109.47 3.000
RF5   OP1     P       O5          109.47 3.000
RF5   H1      C1      O4          110.20 3.000
RF5   H1      C1      C2          110.21 3.000
RF5   O4      C1      C2          105.18 3.000
RF5   H1      C1      O1          110.65 3.000
RF5   C2      C1      O1          110.24 3.000
RF5   O4      C1      O1          110.24 3.000
RF5   HO1     O1      C1          109.48 3.000
RF5   H2      C2      C3          110.13 3.000
RF5   H2      C2      F2          110.56 3.000
RF5   C3      C2      F2          110.06 3.000
RF5   H2      C2      C1          110.13 3.000
RF5   F2      C2      C1          110.06 3.000
RF5   C3      C2      C1          105.79 3.000
RF5   H3      C3      C4          110.12 3.000
RF5   H3      C3      O3          110.54 3.000
RF5   C4      C3      O3          110.08 3.000
RF5   H3      C3      C2          110.11 3.000
RF5   O3      C3      C2          110.08 3.000
RF5   C4      C3      C2          105.81 3.000
RF5   HO3     O3      C3          109.48 3.000
RF5   H4      C4      C5          110.57 3.000
RF5   H4      C4      O4          110.14 3.000
RF5   C5      C4      O4          110.15 3.000
RF5   H4      C4      C3          110.14 3.000
RF5   O4      C4      C3          105.58 3.000
RF5   C5      C4      C3          110.15 3.000
RF5   C4      O4      C1          105.62 3.000
RF5   H5A     C5      H5          109.47 3.000
RF5   H5A     C5      O5          109.47 3.000
RF5   H5      C5      O5          109.47 3.000
RF5   H5A     C5      C4          109.47 3.000
RF5   H5      C5      C4          109.48 3.000
RF5   O5      C5      C4          109.47 3.000
RF5   C5      O5      P           118.46 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
RF5 Var_01         C4      C5      O5      P           161.68  30.0 3
RF5 Var_02         OP1     P       O5      C5          -73.90  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
RF5 chir_01   C1      O4      O1      C2    positiv
RF5 chir_02   C2      F2      C3      C1    negativ
RF5 chir_03   C3      O3      C2      C4    negativ
RF5 chir_04   C4      O4      C3      C5    negativ
