data_93D
# 
_chem_comp.id                                    93D 
_chem_comp.name                                  "(1R)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H15 N4 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-03-31 
_chem_comp.pdbx_modified_date                    2018-03-02 
_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                        306.212 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     93D 
_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        5VBS 
_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 
93D P     P1  P 0 1 N N N 28.755 -6.311 21.467 4.206  0.883  0.146  P     93D 1  
93D OP2   O1  O 0 1 N Y N 29.584 -6.000 22.661 4.742  1.582  1.493  OP2   93D 2  
93D "O5'" O2  O 0 1 N N N 27.424 -5.506 21.757 2.840  0.090  0.460  "O5'" 93D 3  
93D "C5'" C1  C 0 1 N N N 27.548 -4.080 21.847 2.171  -0.722 -0.507 "C5'" 93D 4  
93D "C4'" C2  C 0 1 N N R 26.246 -3.473 21.405 0.912  -1.327 0.117  "C4'" 93D 5  
93D "C3'" C3  C 0 1 N N S 25.078 -4.298 21.937 0.240  -2.307 -0.870 "C3'" 93D 6  
93D "O3'" O3  O 0 1 N N N 24.191 -3.419 22.630 0.602  -3.655 -0.562 "O3'" 93D 7  
93D "C2'" C4  C 0 1 N N N 24.544 -4.961 20.675 -1.273 -2.088 -0.645 "C2'" 93D 8  
93D "C1'" C5  C 0 1 N N R 24.783 -3.878 19.645 -1.336 -1.002 0.451  "C1'" 93D 9  
93D "O4'" O4  O 0 1 N N N 26.106 -3.462 19.955 -0.077 -0.301 0.349  "O4'" 93D 10 
93D C1    C6  C 0 1 Y N N 24.752 -4.341 18.241 -2.483 -0.060 0.191  C1    93D 11 
93D C6    C7  C 0 1 Y N N 25.209 -5.538 17.838 -2.297 1.094  -0.545 C6    93D 12 
93D N5    N1  N 0 1 Y N N 25.172 -5.977 16.413 -3.326 1.901  -0.757 N5    93D 13 
93D C4    C8  C 0 1 Y N N 24.568 -4.941 15.509 -4.526 1.615  -0.273 C4    93D 14 
93D N3    N2  N 0 1 Y N N 24.132 -3.768 15.992 -4.746 0.520  0.438  N3    93D 15 
93D C2    C9  C 0 1 Y N N 24.238 -3.518 17.309 -3.760 -0.337 0.684  C2    93D 16 
93D N2    N3  N 0 1 N N N 23.766 -2.300 17.710 -3.993 -1.482 1.427  N2    93D 17 
93D N4    N4  N 0 1 N N N 24.453 -5.172 14.160 -5.574 2.487  -0.511 N4    93D 18 
93D OP3   O5  O 0 1 N Y N 28.518 -7.729 21.061 3.927  2.010  -0.970 OP3   93D 19 
93D HOP2  H1  H 0 0 N Y N 29.633 -5.058 22.776 5.563  2.079  1.378  HOP2  93D 20 
93D H2    H2  H 0 1 N N N 28.362 -3.734 21.194 1.893  -0.110 -1.365 H2    93D 21 
93D H3    H3  H 0 1 N N N 27.762 -3.789 22.886 2.836  -1.522 -0.832 H3    93D 22 
93D H4    H4  H 0 1 N N N 26.170 -2.448 21.798 1.159  -1.836 1.049  H4    93D 23 
93D H5    H5  H 0 1 N N N 25.463 -5.072 22.617 0.515  -2.064 -1.896 H5    93D 24 
93D H6    H6  H 0 1 N N N 24.628 -3.066 23.396 0.208  -4.313 -1.151 H6    93D 25 
93D H7    H7  H 0 1 N N N 23.474 -5.199 20.768 -1.747 -1.735 -1.561 H7    93D 26 
93D H8    H8  H 0 1 N N N 25.104 -5.877 20.434 -1.745 -3.009 -0.301 H8    93D 27 
93D H9    H9  H 0 1 N N N 24.064 -3.058 19.792 -1.436 -1.460 1.435  H9    93D 28 
93D H10   H10 H 0 1 N N N 25.620 -6.210 18.576 -1.323 1.336  -0.944 H10   93D 29 
93D H11   H11 H 0 1 N N N 23.415 -1.801 16.918 -4.881 -1.664 1.773  H11   93D 30 
93D H12   H12 H 0 1 N N N 23.030 -2.430 18.374 -3.268 -2.103 1.603  H12   93D 31 
93D H13   H13 H 0 1 N N N 24.035 -4.377 13.720 -6.457 2.292  -0.158 H13   93D 32 
93D H14   H14 H 0 1 N N N 25.360 -5.330 13.770 -5.426 3.293  -1.030 H14   93D 33 
93D HOP3  H15 H 0 0 N Y N 29.351 -8.157 20.902 3.269  2.668  -0.708 HOP3  93D 34 
93D OP1   OP1 O 0 1 N N N ?      ?      ?      5.224  -0.067 -0.355 OP1   93D 35 
# 
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 
93D N4    C4    SING N N 1  
93D C4    N3    DOUB Y N 2  
93D C4    N5    SING Y N 3  
93D N3    C2    SING Y N 4  
93D N5    C6    DOUB Y N 5  
93D C2    N2    SING N N 6  
93D C2    C1    DOUB Y N 7  
93D C6    C1    SING Y N 8  
93D C1    "C1'" SING N N 9  
93D "C1'" "O4'" SING N N 10 
93D "C1'" "C2'" SING N N 11 
93D "O4'" "C4'" SING N N 12 
93D "C2'" "C3'" SING N N 13 
93D OP3   P     SING N N 14 
93D "C4'" "C5'" SING N N 15 
93D "C4'" "C3'" SING N N 16 
93D P     "O5'" SING N N 17 
93D P     OP2   SING N N 18 
93D "O5'" "C5'" SING N N 19 
93D "C3'" "O3'" SING N N 20 
93D OP2   HOP2  SING N N 21 
93D "C5'" H2    SING N N 22 
93D "C5'" H3    SING N N 23 
93D "C4'" H4    SING N N 24 
93D "C3'" H5    SING N N 25 
93D "O3'" H6    SING N N 26 
93D "C2'" H7    SING N N 27 
93D "C2'" H8    SING N N 28 
93D "C1'" H9    SING N N 29 
93D C6    H10   SING N N 30 
93D N2    H11   SING N N 31 
93D N2    H12   SING N N 32 
93D N4    H13   SING N N 33 
93D N4    H14   SING N N 34 
93D OP3   HOP3  SING N N 35 
93D P     OP1   DOUB N N 36 
# 
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 
93D SMILES           ACDLabs              12.01 "P(OCC1C(O)CC(O1)c2cnc(nc2N)N)(O)(=O)O"                                                                                                      
93D InChI            InChI                1.03  "InChI=1S/C9H15N4O6P/c10-8-4(2-12-9(11)13-8)6-1-5(14)7(19-6)3-18-20(15,16)17/h2,5-7,14H,1,3H2,(H2,15,16,17)(H4,10,11,12,13)/t5-,6+,7+/m0/s1" 
93D InChIKey         InChI                1.03  MXGZIYVRSFKADT-RRKCRQDMSA-N                                                                                                                  
93D SMILES_CANONICAL CACTVS               3.385 "Nc1ncc([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)c(N)n1"                                                                                       
93D SMILES           CACTVS               3.385 "Nc1ncc([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)c(N)n1"                                                                                           
93D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(n1)N)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                       
93D SMILES           "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(n1)N)N)C2CC(C(O2)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 
93D "SYSTEMATIC NAME" ACDLabs              12.01 "(1R)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol"                   
93D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,4-bis(azanyl)pyrimidin-5-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
93D "Create component" 2017-03-31 RCSB 
93D "Initial release"  2018-03-07 RCSB 
# 
