# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 31 12:55:35 2019
#
#   Ligand name: 2-deoxy-5-O-phosphono-alpha-D-erythro-pentofuranose
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@H](O)[C@@H](CO[P](O)(O)=O)O1
#
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
ORP        ORP '2-deoxy-5-O-phosphono-alpha-D-erythro-pentofuranose' saccharide 22 13 .
2019-10-31 2019-10-31
;
CIF prepared directly in eLBOW
;
#
data_comp_ORP
#
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
ORP         C1     C   CH1    0    .      -1.0099   -0.8251   -1.5300
ORP         O1     O   OH1    0    .      -1.7552   -1.7420   -2.2955
ORP         C2     C   CH2    0    .       0.5351   -1.1567   -1.6341
ORP         C3     C   CH1    0    .       1.0443   -1.1703   -0.2110
ORP         O3     O   OH1    0    .       1.3113   -2.5693    0.2226
ORP         C4     C   CH1    0    .       0.0549   -0.6385    0.5288
ORP         O4     O   O2     0    .      -1.3071   -0.9469   -0.2745
ORP         C5     C   CH2    0    .       0.2498    0.8414    0.6658
ORP         O5     O   O2     0    .      -0.8299    1.3942    1.3930
ORP         P      P   P      0    .      -0.5791    2.8069    2.2306
ORP         O1P    O   O      0    .      -1.9115    3.4643    2.5228
ORP         O2P    O   OP    -1    .       0.2685    3.7365    1.4036
ORP         O3P    O   OP    -1    .       0.1289    2.5026    3.5322
ORP         H1     H   HCH1   0    .      -1.1973    0.1889   -1.8613
ORP         HO1    H   HOH1   0    .      -2.4031   -1.2736   -2.8093
ORP         H21    H   HCH2   0    .       1.0431   -0.3895   -2.2045
ORP         H22    H   HCH2   0    .       0.6791   -2.1334   -2.0932
ORP         H3     H   HCH1   0    .       1.9427   -0.5651   -0.1277
ORP         HO3    H   HOH1   0    .       2.2368   -2.7461    0.1628
ORP         H4     H   HCH1   0    .       0.0259   -1.1098    1.5057
ORP         H51    H   HCH2   0    .       0.2916    1.2942   -0.3213
ORP         H52    H   HCH2   0    .       1.1811    1.0373    1.1944
#
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
ORP   C1      O1    single        1.408 0.020     1.408
ORP   C1      C2    single        1.584 0.020     1.584
ORP   C1      O4    single        1.296 0.020     1.296
ORP   C1      H1    single        0.970 0.020     1.090
ORP   O1      HO1   single        0.850 0.020     0.980
ORP   C2      C3    single        1.512 0.020     1.512
ORP   C2      H21   single        0.970 0.020     1.090
ORP   C2      H22   single        0.970 0.020     1.090
ORP   C3      O3    single        1.489 0.020     1.489
ORP   C3      C4    single        1.345 0.020     1.345
ORP   C3      H3    single        0.970 0.020     1.090
ORP   O3      HO3   single        0.850 0.020     0.980
ORP   C4      O4    single        1.611 0.020     1.611
ORP   C4      C5    single        1.499 0.020     1.499
ORP   C4      H4    single        0.970 0.020     1.090
ORP   C5      O5    single        1.414 0.020     1.414
ORP   C5      H51   single        0.970 0.020     1.090
ORP   C5      H52   single        0.970 0.020     1.090
ORP   O5      P     single        1.661 0.020     1.661
ORP   P       O1P   deloc         1.514 0.020     1.514
ORP   P       O2P   deloc         1.505 0.020     1.505
ORP   P       O3P   deloc         1.513 0.020     1.513
#
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
ORP   H1      C1      O4          110.16 3.000
ORP   H1      C1      C2          110.17 3.000
ORP   O4      C1      C2          105.53 3.000
ORP   H1      C1      O1          110.60 3.000
ORP   O4      C1      O1          110.13 3.000
ORP   C2      C1      O1          110.14 3.000
ORP   HO1     O1      C1          109.50 3.000
ORP   H22     C2      H21         110.58 3.000
ORP   H22     C2      C3          110.15 3.000
ORP   H21     C2      C3          110.14 3.000
ORP   H22     C2      C1          110.16 3.000
ORP   H21     C2      C1          110.13 3.000
ORP   C3      C2      C1          105.59 3.000
ORP   H3      C3      C4          110.23 3.000
ORP   H3      C3      O3          110.66 3.000
ORP   C4      C3      O3          110.07 3.000
ORP   H3      C3      C2          110.23 3.000
ORP   C4      C3      C2          105.46 3.000
ORP   O3      C3      C2          110.06 3.000
ORP   HO3     O3      C3          109.47 3.000
ORP   H4      C4      C5          110.49 3.000
ORP   H4      C4      O4          110.07 3.000
ORP   C5      C4      O4          110.15 3.000
ORP   H4      C4      C3          110.07 3.000
ORP   C5      C4      C3          110.18 3.000
ORP   O4      C4      C3          105.78 3.000
ORP   C4      O4      C1          105.73 3.000
ORP   H52     C5      H51         109.46 3.000
ORP   H52     C5      O5          109.45 3.000
ORP   H51     C5      O5          109.48 3.000
ORP   H52     C5      C4          109.47 3.000
ORP   H51     C5      C4          109.48 3.000
ORP   O5      C5      C4          109.49 3.000
ORP   P       O5      C5          118.45 3.000
ORP   O3P     P       O2P         109.47 3.000
ORP   O3P     P       O1P         109.46 3.000
ORP   O2P     P       O1P         109.47 3.000
ORP   O3P     P       O5          109.48 3.000
ORP   O2P     P       O5          109.46 3.000
ORP   O1P     P       O5          109.49 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
ORP Var_01         O1P     P       O5      C5          160.59  30.0 3
ORP Var_02         H51     C5      O5      P           -85.78  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
ORP chir_01   C1      O1      C2      O4    positiv
ORP chir_02   C3      O3      C4      C2    positiv
ORP chir_03   C4      O4      C3      C5    negativ
