# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 11:25:03 2019
#
#   Ligand name: 1-O-phosphono-alpha-D-ribofuranose
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[P](O)(O)=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
R1P        R1P '1-O-phosphono-alpha-D-ribofuranose' saccharide 23 14 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_R1P
#
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
R1P        C5'     C   CH2    0    .      -2.5651    0.6196   -0.3886
R1P        O5'     O   OH1    0    .      -3.0011    1.7185    0.3623
R1P        C4'     C   CH1    0    .      -1.0368    0.5773   -0.3899
R1P        O4'     O   O2     0    .      -0.5845    0.5577    0.8407
R1P        C1'     C   CH1    0    .       0.7458   -0.3405    0.8009
R1P        C2'     C   CH1    0    .       0.4928   -1.3343   -0.0823
R1P        O2'     O   OH1    0    .       1.7304   -1.6965   -0.8077
R1P        C3'     C   CH1    0    .      -0.5301   -0.7666   -1.0485
R1P        O3'     O   OH1    0    .       0.0482   -0.5114   -2.2432
R1P        O1'     O   O2     0    .       1.8042    0.4067    0.3762
R1P         P      P   P      0    .       2.8012    1.0710    1.5082
R1P         O1P    O   O      0    .       1.9720    1.6965    2.6043
R1P         O2P    O   OP    -1    .       3.6618    2.1299    0.8616
R1P         O3P    O   OP    -1    .       3.6830   -0.0047    2.0958
R1P        H5'1    H   HCH2   0    .      -2.9252    0.7123   -1.4077
R1P        H5'2    H   HCH2   0    .      -2.9518   -0.2942    0.0498
R1P        HO5'    H   HOH1   0    .      -3.9217    1.8608    0.2069
R1P        H4'     H   HCH1   0    .      -0.6321    1.4308   -0.9234
R1P        H1'     H   HCH1   0    .       0.9436   -0.7559    1.7817
R1P        H2'     H   HCH1   0    .       0.0846   -2.1965    0.4312
R1P        HO2'    H   HOH1   0    .       2.0206   -2.5490   -0.5280
R1P        H3'     H   HCH1   0    .      -1.3556   -1.4583   -1.1658
R1P        HO3'    H   HOH1   0    .      -0.4842   -0.8731   -2.9345
#
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
R1P  C5'     O5'    single        1.401 0.020     1.401
R1P  C5'     C4'    single        1.529 0.020     1.529
R1P  C5'     H5'1   single        0.970 0.020     1.090
R1P  C5'     H5'2   single        0.970 0.020     1.090
R1P  O5'     HO5'   single        0.850 0.020     0.980
R1P  C4'     O4'    single        1.311 0.020     1.311
R1P  C4'     C3'    single        1.580 0.020     1.580
R1P  C4'     H4'    single        0.970 0.020     1.090
R1P  O4'     C1'    single        1.606 0.020     1.606
R1P  C1'     C2'    single        1.353 0.020     1.353
R1P  C1'     O1'    single        1.363 0.020     1.363
R1P  C1'     H1'    single        0.970 0.020     1.090
R1P  C2'     O2'    single        1.480 0.020     1.480
R1P  C2'     C3'    single        1.517 0.020     1.517
R1P  C2'     H2'    single        0.970 0.020     1.090
R1P  O2'     HO2'   single        0.850 0.020     0.980
R1P  C3'     O3'    single        1.352 0.020     1.352
R1P  C3'     H3'    single        0.970 0.020     1.090
R1P  O3'     HO3'   single        0.850 0.020     0.980
R1P  O1'      P     single        1.648 0.020     1.648
R1P   P       O1P   deloc         1.510 0.020     1.510
R1P   P       O2P   deloc         1.510 0.020     1.510
R1P   P       O3P   deloc         1.510 0.020     1.510
#
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
R1P  H5'2    C5'     H5'1         109.47 3.000
R1P  H5'2    C5'     C4'          109.47 3.000
R1P  H5'1    C5'     C4'          109.47 3.000
R1P  H5'2    C5'     O5'          109.47 3.000
R1P  H5'1    C5'     O5'          109.47 3.000
R1P  C4'     C5'     O5'          109.47 3.000
R1P  HO5'    O5'     C5'          109.47 3.000
R1P  H4'     C4'     C3'          110.15 3.000
R1P  H4'     C4'     O4'          110.15 3.000
R1P  C3'     C4'     O4'          105.53 3.000
R1P  H4'     C4'     C5'          110.59 3.000
R1P  C3'     C4'     C5'          110.15 3.000
R1P  O4'     C4'     C5'          110.15 3.000
R1P  C1'     O4'     C4'          105.72 3.000
R1P  H1'     C1'     O1'          110.51 3.000
R1P  H1'     C1'     C2'          110.08 3.000
R1P  O1'     C1'     C2'          110.14 3.000
R1P  H1'     C1'     O4'          110.08 3.000
R1P  O1'     C1'     O4'          110.14 3.000
R1P  C2'     C1'     O4'          105.79 3.000
R1P  H2'     C2'     C3'          110.22 3.000
R1P  H2'     C2'     O2'          110.65 3.000
R1P  C3'     C2'     O2'          110.08 3.000
R1P  H2'     C2'     C1'          110.22 3.000
R1P  C3'     C2'     C1'          105.48 3.000
R1P  O2'     C2'     C1'          110.08 3.000
R1P  HO2'    O2'     C2'          109.47 3.000
R1P  H3'     C3'     O3'          110.54 3.000
R1P  H3'     C3'     C2'          110.11 3.000
R1P  O3'     C3'     C2'          110.19 3.000
R1P  H3'     C3'     C4'          110.11 3.000
R1P  O3'     C3'     C4'          110.19 3.000
R1P  C2'     C3'     C4'          105.60 3.000
R1P  HO3'    O3'     C3'          109.47 3.000
R1P   P      O1'     C1'          118.46 3.000
R1P   O3P     P       O2P         109.47 3.000
R1P   O3P     P       O1P         109.47 3.000
R1P   O2P     P       O1P         109.47 3.000
R1P   O3P     P      O1'          109.47 3.000
R1P   O2P     P      O1'          109.47 3.000
R1P   O1P     P      O1'          109.47 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
R1P Var_01         O1P     P      O1'     C1'          -45.18  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
R1P chir_01  C4'     C5'     O4'     C3'    negativ
R1P chir_02  C1'     O4'     O1'     C2'    positiv
R1P chir_03  C2'     O2'     C1'     C3'    negativ
R1P chir_04  C3'     O3'     C2'     C4'    negativ
