# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 10:45:07 2019
#
#   Ligand name: 1-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)O[P@](O)(=O)O[P](O)(O)=O
#
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
PRP        PRP '1-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-5-O-phosphono-alpha-D-ribofuranose' saccharide 30 22 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_PRP
#
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
PRP         C1     C   CH1    0    .       0.2201    0.2047   -1.1773
PRP         C2     C   CH1    0    .       1.5472    0.1900   -1.2001
PRP         C3     C   CH1    0    .       1.9850    0.2127    0.2831
PRP         C4     C   CH1    0    .       0.6719    0.5660    1.1124
PRP         C5     C   CH2    0    .       0.9714    1.7059    2.1240
PRP         O1     O   O2     0    .      -0.2637   -1.0606   -1.1913
PRP         O2     O   OH1    0    .       2.0290   -1.0399   -1.8506
PRP         O3     O   OH1    0    .       2.4543   -0.9822    0.6463
PRP         O4     O   O2     0    .      -0.1963    0.9596    0.2361
PRP         O5     O   O2     0    .      -0.2538    2.1625    2.7076
PRP         P      P   P      0    .      -0.1758    3.2104    4.0217
PRP         O1P    O   O      0    .       0.6338    2.5718    5.1318
PRP         O2P    O   OP    -1    .       0.4848    4.5053    3.5955
PRP         O3P    O   OP    -1    .      -1.5667    3.4960    4.5180
PRP         PA     P   P      0    .      -1.6694   -1.3739   -2.0758
PRP         O1A    O   O      0    .      -1.5375   -0.7730   -3.4657
PRP         O2A    O   OP    -1    .      -2.8714   -0.7502   -1.3638
PRP         O3A    O   O2     0    .      -1.8912   -3.0117   -2.1997
PRP         PB     P   P      0    .      -3.3037   -3.7005   -2.6755
PRP         O1B    O   O      0    .      -4.1489   -3.9961   -1.4697
PRP         O2B    O   OP    -1    .      -3.0146   -4.9847   -3.4141
PRP         O3B    O   OP    -1    .      -4.0420   -2.7515   -3.5855
PRP         H1     H   HCH1   0    .      -0.1575    0.7615   -2.0190
PRP         H2     H   HCH1   0    .       1.9210    1.0638   -1.7122
PRP         H3     H   HCH1   0    .       2.7451    0.9856    0.4382
PRP         H4     H   HCH1   0    .       0.3099   -0.3085    1.6244
PRP         H51    H   HCH2   0    .       1.4525    2.5247    1.6102
PRP         H52    H   HCH2   0    .       1.6273    1.3327    2.9045
PRP         HO2    H   HOH1   0    .       2.6818   -0.8245   -2.4741
PRP         HO3    H   HOH1   0    .       3.3573   -0.8958    0.9206
#
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
PRP   C1      C2    single        1.327 0.020     1.327
PRP   C1      O1    single        1.355 0.020     1.355
PRP   C1      O4    single        1.656 0.020     1.656
PRP   C1      H1    single        0.970 0.020     1.090
PRP   C2      C3    single        1.547 0.020     1.547
PRP   C2      O2    single        1.472 0.020     1.472
PRP   C2      H2    single        0.970 0.020     1.090
PRP   C3      C4    single        1.593 0.020     1.593
PRP   C3      O3    single        1.334 0.020     1.334
PRP   C3      H3    single        0.970 0.020     1.090
PRP   C4      C5    single        1.553 0.020     1.553
PRP   C4      O4    single        1.295 0.020     1.295
PRP   C4      H4    single        0.970 0.020     1.090
PRP   C5      O5    single        1.432 0.020     1.432
PRP   C5      H51   single        0.970 0.020     1.090
PRP   C5      H52   single        0.970 0.020     1.090
PRP   O1      PA    single        1.690 0.020     1.690
PRP   O2      HO2   single        0.850 0.020     0.980
PRP   O3      HO3   single        0.850 0.020     0.980
PRP   O5      P     single        1.683 0.020     1.683
PRP   P       O1P   deloc         1.515 0.020     1.515
PRP   P       O2P   deloc         1.515 0.020     1.515
PRP   P       O3P   deloc         1.504 0.020     1.504
PRP   PA      O1A   deloc         1.520 0.020     1.520
PRP   PA      O2A   deloc         1.530 0.020     1.530
PRP   PA      O3A   single        1.657 0.020     1.657
PRP   O3A     PB    single        1.642 0.020     1.642
PRP   PB      O1B   deloc         1.502 0.020     1.502
PRP   PB      O2B   deloc         1.509 0.020     1.509
PRP   PB      O3B   deloc         1.508 0.020     1.508
#
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
PRP   H1      C1      O4          110.07 3.000
PRP   H1      C1      O1          110.45 3.000
PRP   O4      C1      O1          110.18 3.000
PRP   H1      C1      C2          110.04 3.000
PRP   O4      C1      C2          105.73 3.000
PRP   O1      C1      C2          110.27 3.000
PRP   H2      C2      O2          110.68 3.000
PRP   H2      C2      C3          110.18 3.000
PRP   O2      C2      C3          110.08 3.000
PRP   H2      C2      C1          110.20 3.000
PRP   O2      C2      C1          110.12 3.000
PRP   C3      C2      C1          105.45 3.000
PRP   H3      C3      O3          110.45 3.000
PRP   H3      C3      C4          109.99 3.000
PRP   O3      C3      C4          110.30 3.000
PRP   H3      C3      C2          110.04 3.000
PRP   O3      C3      C2          110.33 3.000
PRP   C4      C3      C2          105.61 3.000
PRP   H4      C4      O4          110.09 3.000
PRP   H4      C4      C5          110.57 3.000
PRP   O4      C4      C5          110.30 3.000
PRP   H4      C4      C3          110.17 3.000
PRP   O4      C4      C3          105.54 3.000
PRP   C5      C4      C3          110.06 3.000
PRP   H52     C5      H51         109.48 3.000
PRP   H52     C5      O5          109.49 3.000
PRP   H51     C5      O5          109.48 3.000
PRP   H52     C5      C4          109.41 3.000
PRP   H51     C5      C4          109.42 3.000
PRP   O5      C5      C4          109.54 3.000
PRP   PA      O1      C1          118.40 3.000
PRP   HO2     O2      C2          109.46 3.000
PRP   HO3     O3      C3          109.41 3.000
PRP   C4      O4      C1          105.69 3.000
PRP   P       O5      C5          118.51 3.000
PRP   O3P     P       O2P         109.49 3.000
PRP   O3P     P       O1P         109.41 3.000
PRP   O2P     P       O1P         109.48 3.000
PRP   O3P     P       O5          109.46 3.000
PRP   O2P     P       O5          109.44 3.000
PRP   O1P     P       O5          109.54 3.000
PRP   O3A     PA      O2A         109.42 3.000
PRP   O3A     PA      O1A         109.50 3.000
PRP   O2A     PA      O1A         109.43 3.000
PRP   O3A     PA      O1          109.49 3.000
PRP   O2A     PA      O1          109.53 3.000
PRP   O1A     PA      O1          109.45 3.000
PRP   PB      O3A     PA          123.46 3.000
PRP   O3B     PB      O2B         109.51 3.000
PRP   O3B     PB      O1B         109.45 3.000
PRP   O2B     PB      O1B         109.47 3.000
PRP   O3B     PB      O3A         109.39 3.000
PRP   O2B     PB      O3A         109.51 3.000
PRP   O1B     PB      O3A         109.51 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
PRP Var_01         O1A     PA      O1      C1           48.54  30.0 3
PRP Var_02         O1P     P       O5      C5          -56.87  30.0 3
PRP Var_03         O1B     PB      O3A     PA          -91.87  30.0 3
PRP Var_04         H51     C5      O5      P           -70.22  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
PRP chir_01   C1      C2      O1      O4    negativ
PRP chir_02   C2      O2      C3      C1    positiv
PRP chir_03   C3      O3      C2      C4    negativ
PRP chir_04   C4      O4      C3      C5    negativ
