data_RBD
# 
_chem_comp.id                                    RBD 
_chem_comp.name                                  "(R,R)-N6,N6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-01-07 
_chem_comp.pdbx_modified_date                    2014-05-23 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        419.327 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     RBD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2MHX 
_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 
RBD P      P      P 0 1 N N N 5.883  -6.485 20.015 -6.057 1.692  -0.509 P      RBD 1  
RBD O1P    O1P    O 0 1 N N N 6.417  -7.762 20.553 -4.878 2.915  -0.238 O1P    RBD 2  
RBD O2P    O2P    O 0 1 N N N 6.686  -5.751 19.006 -6.639 1.898  1.097  O2P    RBD 3  
RBD "O5'"  "O5'"  O 0 1 N N N 4.417  -6.763 19.390 -4.806 0.557  -0.831 "O5'"  RBD 4  
RBD "C5'"  "C5'"  C 0 1 N N N 3.381  -7.378 20.151 -4.345 -0.144 0.325  "C5'"  RBD 5  
RBD "C4'"  "C4'"  C 0 1 N N R 2.014  -7.347 19.444 -3.322 -1.202 -0.094 "C4'"  RBD 6  
RBD "O4'"  "O4'"  O 0 1 N N N 1.626  -5.992 19.220 -2.108 -0.577 -0.564 "O4'"  RBD 7  
RBD "C1'"  "C1'"  C 0 1 N N R 1.525  -5.776 17.821 -1.061 -1.555 -0.451 "C1'"  RBD 8  
RBD N9     N9     N 0 1 Y N N 2.061  -4.440 17.472 0.203  -0.895 -0.115 N9     RBD 9  
RBD C8     C8     C 0 1 Y N N 3.328  -4.084 17.071 0.344  0.315  0.497  C8     RBD 10 
RBD N7     N7     N 0 1 Y N N 3.443  -2.842 16.689 1.606  0.595  0.642  N7     RBD 11 
RBD C5     C5     C 0 1 Y N N 2.154  -2.333 16.878 2.354  -0.414 0.134  C5     RBD 12 
RBD C6     C6     C 0 1 Y N N 1.550  -1.081 16.630 3.732  -0.659 0.013  C6     RBD 13 
RBD N6     N6     N 0 1 N N N 2.172  -0.064 16.014 4.658  0.259  0.479  N6     RBD 14 
RBD CA     CA     C 0 1 N N N 2.833  1.035  16.721 6.045  -0.217 0.242  CA     RBD 15 
RBD CB     CB     C 0 1 N N R 3.802  1.575  15.663 6.909  1.062  0.292  CB     RBD 16 
RBD OB     OB     O 0 1 N N N 5.002  2.131  16.193 7.958  0.990  -0.676 OB     RBD 17 
RBD CG     CG     C 0 1 N N R 4.088  0.327  14.810 5.941  2.213  -0.052 CG     RBD 18 
RBD OG     OG     O 0 1 N N N 4.635  0.641  13.533 5.862  3.136  1.036  OG     RBD 19 
RBD CD     CD     C 0 1 N N N 2.693  -0.253 14.657 4.574  1.533  -0.280 CD     RBD 20 
RBD N1     N1     N 0 1 Y N N 0.257  -0.893 16.954 4.127  -1.792 -0.559 N1     RBD 21 
RBD C2     C2     C 0 1 Y N N -0.428 -1.913 17.458 3.251  -2.673 -1.006 C2     RBD 22 
RBD N3     N3     N 0 1 Y N N -0.005 -3.148 17.691 1.951  -2.486 -0.915 N3     RBD 23 
RBD C4     C4     C 0 1 Y N N 1.313  -3.291 17.384 1.462  -1.385 -0.353 C4     RBD 24 
RBD "C3'"  "C3'"  C 0 1 N N S 2.008  -8.088 18.096 -2.856 -2.027 1.133  "C3'"  RBD 25 
RBD "C2'"  "C2'"  C 0 1 N N N 2.238  -6.939 17.122 -1.463 -2.528 0.675  "C2'"  RBD 26 
RBD "O3'"  "O3'"  O 0 1 N N N 0.750  -8.715 17.886 -3.741 -3.122 1.377  "O3'"  RBD 27 
RBD H1     H1     H 0 1 N N N 5.805  -8.121 21.185 -4.514 3.297  -1.048 H1     RBD 28 
RBD H3     H3     H 0 1 N N N 7.552  -5.578 19.355 -7.378 1.316  1.324  H3     RBD 29 
RBD "H5'2" "H5'2" H 0 0 N N N 3.657  -8.427 20.335 -3.879 0.559  1.015  "H5'2" RBD 30 
RBD "H5'1" "H5'1" H 0 0 N N N 3.291  -6.849 21.111 -5.189 -0.629 0.816  "H5'1" RBD 31 
RBD "H4'"  "H4'"  H 0 1 N N N 1.280  -7.834 20.103 -3.739 -1.855 -0.860 "H4'"  RBD 32 
RBD "H1'"  "H1'"  H 0 1 N N N 0.465  -5.810 17.527 -0.958 -2.098 -1.390 "H1'"  RBD 33 
RBD H8     H8     H 0 1 N N N 4.158  -4.775 17.072 -0.472 0.947  0.814  H8     RBD 34 
RBD HA2    HA2    H 0 1 N N N 3.374  0.670  17.606 6.348  -0.911 1.026  HA2    RBD 35 
RBD HA1    HA1    H 0 1 N N N 2.108  1.804  17.026 6.122  -0.692 -0.736 HA1    RBD 36 
RBD HB     HB     H 0 1 N N N 3.276  2.316  15.043 7.324  1.199  1.290  HB     RBD 37 
RBD HOB    HOB    H 0 1 N N N 4.793  2.898  16.713 8.572  0.256  -0.536 HOB    RBD 38 
RBD HG     HG     H 0 1 N N N 4.731  -0.370 15.367 6.266  2.723  -0.958 HG     RBD 39 
RBD HOG    HOG    H 0 1 N N N 5.507  1.003  13.642 5.268  3.882  0.877  HOG    RBD 40 
RBD HD1    HD1    H 0 1 N N N 2.102  0.303  13.914 4.421  1.334  -1.341 HD1    RBD 41 
RBD HD2    HD2    H 0 1 N N N 2.724  -1.317 14.379 3.769  2.156  0.111  HD2    RBD 42 
RBD H2     H2     H 0 1 N N N -1.459 -1.711 17.710 3.614  -3.581 -1.464 H2     RBD 43 
RBD "H3'"  "H3'"  H 0 1 N N N 2.841  -8.805 18.050 -2.769 -1.395 2.017  "H3'"  RBD 44 
RBD "H2'1" "H2'1" H 0 0 N N N 1.788  -7.151 16.141 -1.534 -3.546 0.292  "H2'1" RBD 45 
RBD "H2'2" "H2'2" H 0 0 N N N 3.311  -6.731 16.996 -0.748 -2.477 1.496  "H2'2" RBD 46 
RBD H4     H4     H 0 1 N N N 0.641  -9.424 18.509 -3.492 -3.668 2.135  H4     RBD 47 
RBD O3P    O3P    O 0 1 N Y N ?      ?      ?      -7.236 0.470  -0.780 O3P    RBD 48 
RBD H5     H5     H 0 1 N N N ?      ?      ?      -6.629 2.487  -1.605 H5     RBD 49 
RBD H6     H6     H 0 1 N N N ?      ?      ?      -8.149 0.773  -0.676 H6     RBD 50 
# 
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 
RBD OG    CG     SING N N 1  
RBD CD    CG     SING N N 2  
RBD CD    N6     SING N N 3  
RBD CG    CB     SING N N 4  
RBD CB    OB     SING N N 5  
RBD CB    CA     SING N N 6  
RBD N6    C6     SING N N 7  
RBD N6    CA     SING N N 8  
RBD C6    C5     DOUB Y N 9  
RBD C6    N1     SING Y N 10 
RBD N7    C5     SING Y N 11 
RBD N7    C8     DOUB Y N 12 
RBD C5    C4     SING Y N 13 
RBD N1    C2     DOUB Y N 14 
RBD C8    N9     SING Y N 15 
RBD "C2'" "C1'"  SING N N 16 
RBD "C2'" "C3'"  SING N N 17 
RBD C4    N9     SING Y N 18 
RBD C4    N3     DOUB Y N 19 
RBD C2    N3     SING Y N 20 
RBD N9    "C1'"  SING N N 21 
RBD "C1'" "O4'"  SING N N 22 
RBD "O3'" "C3'"  SING N N 23 
RBD "C3'" "C4'"  SING N N 24 
RBD O2P   P      SING N N 25 
RBD "O4'" "C4'"  SING N N 26 
RBD "O5'" P      SING N N 27 
RBD "O5'" "C5'"  SING N N 28 
RBD "C4'" "C5'"  SING N N 29 
RBD P     O1P    SING N N 30 
RBD O1P   H1     SING N N 31 
RBD O2P   H3     SING N N 32 
RBD "C5'" "H5'2" SING N N 33 
RBD "C5'" "H5'1" SING N N 34 
RBD "C4'" "H4'"  SING N N 35 
RBD "C1'" "H1'"  SING N N 36 
RBD C8    H8     SING N N 37 
RBD CA    HA2    SING N N 38 
RBD CA    HA1    SING N N 39 
RBD CB    HB     SING N N 40 
RBD OB    HOB    SING N N 41 
RBD CG    HG     SING N N 42 
RBD OG    HOG    SING N N 43 
RBD CD    HD1    SING N N 44 
RBD CD    HD2    SING N N 45 
RBD C2    H2     SING N N 46 
RBD "C3'" "H3'"  SING N N 47 
RBD "C2'" "H2'1" SING N N 48 
RBD "C2'" "H2'2" SING N N 49 
RBD "O3'" H4     SING N N 50 
RBD P     O3P    SING N N 51 
RBD P     H5     SING N N 52 
RBD O3P   H6     SING N N 53 
# 
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 
RBD SMILES           ACDLabs              12.01 "n3c1c(ncnc1N2CC(O)C(O)C2)n(c3)C4OC(C(O)C4)COP(O)(O)O"                                                                                                      
RBD InChI            InChI                1.03  "InChI=1S/C14H22N5O8P/c20-7-1-11(27-10(7)4-26-28(23,24)25)19-6-17-12-13(15-5-16-14(12)19)18-2-8(21)9(22)3-18/h5-11,20-25,28H,1-4H2/t7-,8+,9+,10+,11+/m0/s1" 
RBD InChIKey         InChI                1.03  AFIPVZHEZSDVQA-VPJKUYQRSA-N                                                                                                                                 
RBD SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[C@@H](O)[C@H](O)C4"                                                                                
RBD SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[CH](O)[CH](O)C4"                                                                                        
RBD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3C[C@H]([C@@H](C3)O)O)ncn2[C@H]4C[C@@H]([C@H](O4)COP(O)(O)O)O"                                                                                
RBD SMILES           "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3CC(C(C3)O)O)ncn2C4CC(C(O4)COP(O)(O)O)O"                                                                                                      
# 
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 
RBD "SYSTEMATIC NAME" ACDLabs              12.01 "(3R,4R)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol (non-preferred name)" 
RBD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(3R,4R)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol"                                   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
RBD "Create component" 2014-01-07 RCSB 
RBD "Initial release"  2014-05-28 RCSB 
# 
