data_DNR
# 
_chem_comp.id                                    DNR 
_chem_comp.name                                  
;2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H15 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2002-04-04 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        308.205 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     DNR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1LAQ 
_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 
DNR P      P    P 0 1 N N N -0.684 -7.446 15.813 -3.968 -1.665 3.118  P      DNR 1  
DNR OP1    O1P  O 0 1 N N N 0.421  -7.036 14.917 -4.406 -2.599 4.208  OP1    DNR 2  
DNR OP2    O2P  O 0 1 N N N -1.407 -8.711 15.556 -3.912 -2.311 1.636  OP2    DNR 3  
DNR "O5'"  O5*  O 0 1 N N N -1.767 -6.248 15.855 -2.493 -1.028 3.315  "O5'"  DNR 4  
DNR "C5'"  C5*  C 0 1 N N N -2.936 -6.352 16.678 -2.005 -0.136 2.327  "C5'"  DNR 5  
DNR "C4'"  C4*  C 0 1 N N R -3.852 -5.142 16.542 -0.611 0.328  2.728  "C4'"  DNR 6  
DNR "O4'"  O4*  O 0 1 N N N -3.125 -3.913 16.795 0.247  -0.829 2.764  "O4'"  DNR 7  
DNR "C1'"  C1*  C 0 1 N N R -3.181 -3.066 15.625 1.157  -0.778 1.657  "C1'"  DNR 8  
DNR N1     N1   N 0 1 N N N -1.853 -2.469 15.339 1.164  -2.047 0.989  N1     DNR 9  
DNR C6     C6   C 0 1 N N N -0.754 -3.262 15.217 -0.015 -2.783 0.959  C6     DNR 10 
DNR C2     C2   C 0 1 N N N -1.760 -1.079 15.249 2.335  -2.532 0.381  C2     DNR 11 
DNR O2     O2   O 0 1 N N N -2.767 -0.382 15.363 3.425  -1.977 0.342  O2     DNR 12 
DNR N3     N3   N 1 1 N N N -0.527 -0.524 15.041 2.203  -3.824 -0.257 N3     DNR 13 
DNR C4     C4   C 0 1 N N N 0.561  -1.305 14.927 1.089  -4.548 -0.301 C4     DNR 14 
DNR N4     N4   N 0 1 N N N 1.753  -0.747 14.733 0.968  -5.729 -0.886 N4     DNR 15 
DNR C5     C5   C 0 1 N N N 0.463  -2.728 15.014 -0.107 -3.974 0.362  C5     DNR 16 
DNR "C2'"  C2*  C 0 1 N N N -3.671 -3.939 14.490 0.710  0.360  0.754  "C2'"  DNR 17 
DNR "C3'"  C3*  C 0 1 N N S -4.447 -5.040 15.147 0.008  1.286  1.720  "C3'"  DNR 18 
DNR "O3'"  O3*  O 0 1 N N N -5.846 -4.728 15.206 0.965  2.121  2.368  "O3'"  DNR 19 
DNR OP3    O3P  O 0 1 N Y N ?      ?      ?      -4.901 -0.360 2.920  OP3    DNR 20 
DNR HOP2   2HOP H 0 0 N N N -2.116 -8.974 16.130 -4.684 -2.823 1.313  HOP2   DNR 21 
DNR "H5'"  1H5* H 0 1 N N N -2.630 -6.429 17.716 -1.971 -0.654 1.366  "H5'"  DNR 22 
DNR "H5''" 2H5* H 0 0 N N N -3.489 -7.251 16.403 -2.683 0.718  2.254  "H5''" DNR 23 
DNR "H4'"  H4*  H 0 1 N N N -4.660 -5.225 17.266 -0.644 0.753  3.736  "H4'"  DNR 24 
DNR "H1'"  H1*  H 0 1 N N N -3.901 -2.280 15.793 2.163  -0.604 2.054  "H1'"  DNR 25 
DNR H6     H6   H 0 1 N N N -0.864 -4.341 15.274 -0.871 -2.335 1.453  H6     DNR 26 
DNR HN3    HN3  H 0 1 N N N -0.421 0.491  15.056 3.017  -4.226 -0.715 HN3    DNR 27 
DNR H41    H41  H 0 1 N N N 1.833  0.257  14.671 0.511  -5.815 -1.789 H41    DNR 28 
DNR H42    H42  H 0 1 N N N 2.576  -1.326 14.649 1.332  -6.567 -0.439 H42    DNR 29 
DNR H5     H5   H 0 1 N N N 1.346  -3.360 14.919 -1.040 -4.526 0.354  H5     DNR 30 
DNR "H2'"  1H2* H 0 1 N N N -2.839 -4.348 13.921 -0.003 -0.001 0.003  "H2'"  DNR 31 
DNR "H2''" 2H2* H 0 0 N N N -4.322 -3.365 13.847 1.556  0.818  0.232  "H2''" DNR 32 
DNR "H3'"  H3*  H 0 1 N N N -4.291 -5.978 14.608 -0.722 1.941  1.236  "H3'"  DNR 33 
DNR "HO3'" H3T  H 0 0 N Y N -6.217 -4.664 14.334 0.743  3.042  2.146  "HO3'" DNR 34 
DNR HOP3   3HOP H 0 0 N N N -0.709 -0.263 0.574  -5.874 -0.475 2.871  HOP3   DNR 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 
DNR P     OP1    DOUB N N 1  
DNR P     OP2    SING N N 2  
DNR P     "O5'"  SING N N 3  
DNR P     OP3    SING N N 4  
DNR OP2   HOP2   SING N N 5  
DNR "O5'" "C5'"  SING N N 6  
DNR "C5'" "C4'"  SING N N 7  
DNR "C5'" "H5'"  SING N N 8  
DNR "C5'" "H5''" SING N N 9  
DNR "C4'" "O4'"  SING N N 10 
DNR "C4'" "C3'"  SING N N 11 
DNR "C4'" "H4'"  SING N N 12 
DNR "O4'" "C1'"  SING N N 13 
DNR "C1'" N1     SING N N 14 
DNR "C1'" "C2'"  SING N N 15 
DNR "C1'" "H1'"  SING N N 16 
DNR N1    C6     SING N N 17 
DNR N1    C2     SING N N 18 
DNR C6    C5     DOUB N N 19 
DNR C6    H6     SING N N 20 
DNR C2    O2     DOUB N N 21 
DNR C2    N3     SING N N 22 
DNR N3    C4     DOUB N N 23 
DNR N3    HN3    SING N N 24 
DNR C4    N4     SING N N 25 
DNR C4    C5     SING N N 26 
DNR N4    H41    SING N N 27 
DNR N4    H42    SING N N 28 
DNR C5    H5     SING N N 29 
DNR "C2'" "C3'"  SING N N 30 
DNR "C2'" "H2'"  SING N N 31 
DNR "C2'" "H2''" SING N N 32 
DNR "C3'" "O3'"  SING N N 33 
DNR "C3'" "H3'"  SING N N 34 
DNR "O3'" "HO3'" SING N N 35 
DNR OP3   HOP3   SING 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 
DNR SMILES           ACDLabs              10.04 "O=C1[NH+]=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O"                                                                                                      
DNR SMILES_CANONICAL CACTVS               3.341 "NC1=[NH+]C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                                     
DNR SMILES           CACTVS               3.341 "NC1=[NH+]C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                         
DNR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O"                                                                                         
DNR SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O"                                                                                                      
DNR InChI            InChI                1.03  "InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/p+1/t5-,6+,8+/m0/s1" 
DNR InChIKey         InChI                1.03  NCMVOABPESMRCP-SHYZEUOFSA-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 
DNR "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5'-cytidylic acid
;
DNR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-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 
DNR "Create component"  2002-04-04 RCSB 
DNR "Modify descriptor" 2011-06-04 RCSB 
# 
