data_RBY
# 
_chem_comp.id                                    RBY 
_chem_comp.name                                  "METHYLENE ADP-BETA-XYLOSE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 N5 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-07-27 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        557.343 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     RBY 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2YVP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
RBY PA     PA   P 0 1 N N R 11.435 31.554 62.078 -0.682  1.870  -0.561 PA     RBY 1  
RBY "O5'"  O5*  O 0 1 N N N 11.647 32.901 61.141 0.716   1.678  0.214  "O5'"  RBY 2  
RBY "C5'"  C5*  C 0 1 N N N 11.164 33.698 60.109 1.905   2.388  -0.138 "C5'"  RBY 3  
RBY "C4'"  C4*  C 0 1 N N R 12.503 34.587 60.232 3.044   1.970  0.794  "C4'"  RBY 4  
RBY "O4'"  O4*  O 0 1 N N N 13.164 34.942 61.546 3.383   0.592  0.565  "O4'"  RBY 5  
RBY "C3'"  C3*  C 0 1 N N S 13.751 35.012 59.314 4.302   2.807  0.493  "C3'"  RBY 6  
RBY "O3'"  O3*  O 0 1 N N N 13.475 35.493 58.132 4.698   3.548  1.649  "O3'"  RBY 7  
RBY "C2'"  C2*  C 0 1 N N R 14.843 35.893 60.173 5.379   1.757  0.127  "C2'"  RBY 8  
RBY "O2'"  O2*  O 0 1 N N N 15.463 36.982 59.572 6.641   2.098  0.704  "O2'"  RBY 9  
RBY "C1'"  C1*  C 0 1 N N R 14.070 36.257 61.437 4.806   0.468  0.771  "C1'"  RBY 10 
RBY N9     N9   N 0 1 Y N N 14.925 36.294 62.515 5.325   -0.722 0.092  N9     RBY 11 
RBY C8     C8   C 0 1 Y N N 15.121 35.150 63.288 4.716   -1.401 -0.922 C8     RBY 12 
RBY N7     N7   N 0 1 Y N N 15.985 35.414 64.217 5.455   -2.407 -1.289 N7     RBY 13 
RBY C5     C5   C 0 1 Y N N 16.370 36.719 64.097 6.581   -2.438 -0.537 C5     RBY 14 
RBY C6     C6   C 0 1 Y N N 17.278 37.567 64.807 7.711   -3.272 -0.483 C6     RBY 15 
RBY N6     N6   N 0 1 N N N 18.008 37.122 65.847 7.836   -4.351 -1.339 N6     RBY 16 
RBY N1     N1   N 0 1 Y N N 17.431 38.825 64.443 8.658   -2.999 0.410  N1     RBY 17 
RBY C2     C2   C 0 1 Y N N 16.773 39.379 63.419 8.547   -1.970 1.231  C2     RBY 18 
RBY N3     N3   N 0 1 Y N N 15.909 38.665 62.683 7.507   -1.163 1.216  N3     RBY 19 
RBY C4     C4   C 0 1 Y N N 15.686 37.320 63.000 6.514   -1.354 0.354  C4     RBY 20 
RBY CX     CX   C 0 1 N N N 12.674 31.563 63.009 -1.905  0.686  0.090  CX     RBY 21 
RBY PB     PB   P 0 1 N N S 13.867 30.267 63.536 -3.489  0.904  -0.786 PB     RBY 22 
RBY O1B    O1B  O 0 1 N N N 14.750 31.498 62.754 -3.289  0.662  -2.233 O1B    RBY 23 
RBY OR5    OR5  O 0 1 N N N 14.204 30.292 64.921 -4.569  -0.142 -0.212 OR5    RBY 24 
RBY CR5    CR5  C 0 1 N N N 13.801 29.618 66.081 -5.878  -0.292 -0.765 CR5    RBY 25 
RBY CR4    CR4  C 0 1 N N S 14.589 30.221 67.090 -6.641  -1.365 0.014  CR4    RBY 26 
RBY OR4    OR4  O 0 1 N N N 15.761 30.538 67.703 -6.955  -0.894 1.343  OR4    RBY 27 
RBY CR3    CR3  C 0 1 N N S 13.517 31.120 67.399 -8.013  -1.633 -0.643 CR3    RBY 28 
RBY OR3    OR3  O 0 1 N N N 12.292 31.380 66.927 -8.437  -0.497 -1.399 OR3    RBY 29 
RBY CR2    CR2  C 0 1 N N R 13.948 32.030 68.412 -8.962  -1.872 0.553  CR2    RBY 30 
RBY OR2    OR2  O 0 1 N N N 13.046 32.231 69.547 -9.516  -3.188 0.497  OR2    RBY 31 
RBY CR1    CR1  C 0 1 N N R 15.406 31.569 68.683 -8.051  -1.720 1.791  CR1    RBY 32 
RBY OR1    OR1  O 0 1 N N N 16.269 32.693 68.471 -8.759  -1.076 2.852  OR1    RBY 33 
RBY O2A    O2A  O 0 1 N N N 11.336 30.234 61.145 -0.482  1.628  -2.007 O2A    RBY 34 
RBY O2B    O2B  O 0 1 N N N 14.005 28.815 62.759 -4.024  2.406  -0.562 O2B    RBY 35 
RBY O1A    O1A  O 0 1 N N N 10.227 31.710 63.094 -1.217  3.372  -0.336 O1A    RBY 36 
RBY "H5'1" 1H5* H 0 0 N N N 10.204 34.209 60.274 2.175   2.155  -1.168 "H5'1" RBY 37 
RBY "H5'2" 2H5* H 0 0 N N N 10.861 33.259 59.147 1.731   3.459  -0.041 "H5'2" RBY 38 
RBY "H4'"  H4*  H 0 1 N N N 11.556 34.716 59.687 2.743   2.110  1.832  "H4'"  RBY 39 
RBY "H3'"  H3*  H 0 1 N N N 14.232 34.063 59.035 4.122   3.477  -0.348 "H3'"  RBY 40 
RBY "HO3'" HO3* H 0 0 N N N 13.408 36.439 58.182 5.518   4.048  1.533  "HO3'" RBY 41 
RBY "H2'"  H2*  H 0 1 N N N 15.747 35.286 60.330 5.464   1.647  -0.954 "H2'"  RBY 42 
RBY "HO2'" HO2* H 0 0 N N N 15.604 37.663 60.219 6.997   2.943  0.399  "HO2'" RBY 43 
RBY "H1'"  H1*  H 0 1 N N N 13.545 37.223 61.416 5.039   0.435  1.836  "H1'"  RBY 44 
RBY H8     H8   H 0 1 N N N 14.632 34.199 63.137 3.762   -1.142 -1.356 H8     RBY 45 
RBY HN61   1HN6 H 0 0 N N N 18.961 37.012 65.563 7.139   -4.540 -1.987 HN61   RBY 46 
RBY HN62   2HN6 H 0 0 N N N 17.958 37.783 66.596 8.621   -4.919 -1.293 HN62   RBY 47 
RBY H2     H2   H 0 1 N N N 16.940 40.419 63.181 9.339   -1.785 1.941  H2     RBY 48 
RBY HX1    1HX  H 0 1 N N N 13.330 32.295 62.515 -1.543  -0.331 -0.061 HX1    RBY 49 
RBY HX2    2HX  H 0 1 N N N 12.120 31.620 63.958 -2.053  0.864  1.156  HX2    RBY 50 
RBY HR51   1HR5 H 0 0 N N N 12.726 29.747 66.273 -6.412  0.655  -0.697 HR51   RBY 51 
RBY HR52   2HR5 H 0 0 N N N 13.942 28.529 66.017 -5.799  -0.590 -1.811 HR52   RBY 52 
RBY HOR3   HOR3 H 0 0 N N N 11.680 31.442 67.651 -9.293  -0.611 -1.834 HOR3   RBY 53 
RBY HR2    HR2  H 0 1 N N N 13.921 33.083 68.094 -9.755  -1.124 0.567  HR2    RBY 54 
RBY HOR2   HOR2 H 0 0 N N N 13.552 32.275 70.350 -10.120 -3.392 1.225  HOR2   RBY 55 
RBY HR1    HR1  H 0 1 N N N 15.504 31.178 69.707 -7.685  -2.694 2.115  HR1    RBY 56 
RBY HOR1   HOR1 H 0 0 N N N 16.460 33.108 69.304 -8.221  -0.910 3.639  HOR1   RBY 57 
RBY HO2B   HO2B H 0 0 N N N 14.031 28.959 61.820 -4.177  2.634  0.365  HO2B   RBY 58 
RBY HO1A   HO1A H 0 0 N N N 10.562 31.741 63.982 -1.371  3.601  0.591  HO1A   RBY 59 
RBY HR3    HR3  H 0 1 N N N 12.992 30.325 66.850 -7.966  -2.519 -1.276 HR3    RBY 60 
RBY HR4    HR4  H 0 1 N N N 15.372 29.453 67.172 -6.058  -2.284 0.064  HR4    RBY 61 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
RBY "O3'" "C3'"  SING N N 1  
RBY "C3'" "C2'"  SING N N 2  
RBY "C3'" "C4'"  SING N N 3  
RBY "O2'" "C2'"  SING N N 4  
RBY "C5'" "C4'"  SING N N 5  
RBY "C5'" "O5'"  SING N N 6  
RBY "C2'" "C1'"  SING N N 7  
RBY "C4'" "O4'"  SING N N 8  
RBY "O5'" PA     SING N N 9  
RBY O2A   PA     DOUB N N 10 
RBY "C1'" "O4'"  SING N N 11 
RBY "C1'" N9     SING N N 12 
RBY PA    CX     SING N N 13 
RBY PA    O1A    SING N N 14 
RBY N9    C4     SING Y N 15 
RBY N9    C8     SING Y N 16 
RBY N3    C4     DOUB Y N 17 
RBY N3    C2     SING Y N 18 
RBY O1B   PB     DOUB N N 19 
RBY O2B   PB     SING N N 20 
RBY C4    C5     SING Y N 21 
RBY CX    PB     SING N N 22 
RBY C8    N7     DOUB Y N 23 
RBY C2    N1     DOUB Y N 24 
RBY PB    OR5    SING N N 25 
RBY C5    N7     SING Y N 26 
RBY C5    C6     DOUB Y N 27 
RBY N1    C6     SING Y N 28 
RBY C6    N6     SING N N 29 
RBY OR5   CR5    SING N N 30 
RBY CR5   CR4    SING N N 31 
RBY OR3   CR3    SING N N 32 
RBY CR4   CR3    SING N N 33 
RBY CR4   OR4    SING N N 34 
RBY CR3   CR2    SING N N 35 
RBY OR4   CR1    SING N N 36 
RBY CR2   CR1    SING N N 37 
RBY CR2   OR2    SING N N 38 
RBY OR1   CR1    SING N N 39 
RBY "C5'" "H5'1" SING N N 40 
RBY "C5'" "H5'2" SING N N 41 
RBY "C4'" "H4'"  SING N N 42 
RBY "C3'" "H3'"  SING N N 43 
RBY "O3'" "HO3'" SING N N 44 
RBY "C2'" "H2'"  SING N N 45 
RBY "O2'" "HO2'" SING N N 46 
RBY "C1'" "H1'"  SING N N 47 
RBY C8    H8     SING N N 48 
RBY N6    HN61   SING N N 49 
RBY N6    HN62   SING N N 50 
RBY C2    H2     SING N N 51 
RBY CX    HX1    SING N N 52 
RBY CX    HX2    SING N N 53 
RBY CR5   HR51   SING N N 54 
RBY CR5   HR52   SING N N 55 
RBY OR3   HOR3   SING N N 56 
RBY CR2   HR2    SING N N 57 
RBY OR2   HOR2   SING N N 58 
RBY CR1   HR1    SING N N 59 
RBY OR1   HOR1   SING N N 60 
RBY O2B   HO2B   SING N N 61 
RBY O1A   HO1A   SING N N 62 
RBY CR3   HR3    SING N N 63 
RBY CR4   HR4    SING N N 64 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
RBY SMILES           ACDLabs              10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC4OC(O)C(O)C4O" 
RBY SMILES_CANONICAL CACTVS               3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H]3O" 
RBY SMILES           CACTVS               3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O" 
RBY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OCC4C([C@H]([C@@H](O4)O)O)O)O)O)O)N" 
RBY SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)O)N" 
RBY InChI            InChI                1.03  
"InChI=1S/C16H25N5O13P2/c17-13-8-14(19-3-18-13)21(4-20-8)15-11(24)9(22)6(33-15)1-31-35(27,28)5-36(29,30)32-2-7-10(23)12(25)16(26)34-7/h3-4,6-7,9-12,15-16,22-26H,1-2,5H2,(H,27,28)(H,29,30)(H2,17,18,19)/t6-,7-,9-,10+,11-,12-,15-,16-/m1/s1" 
RBY InChIKey         InChI                1.03  ZPZRETFSCSWNDT-CAUCCWOKSA-N 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
RBY "SYSTEMATIC NAME" ACDLabs              10.04 
"[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R,5R)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl methanediylbis[hydrogen (S,R)-phosphonate] (non-preferred name)" 
RBY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[hydroxy-[[(4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl]methyl]phosphinic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
RBY "Create component"     2007-07-27 RCSB 
RBY "Modify aromatic_flag" 2011-06-04 RCSB 
RBY "Modify descriptor"    2011-06-04 RCSB 
# 
