data_D3N
# 
_chem_comp.id                                    D3N 
_chem_comp.name                                  "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H17 N2 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-11-02 
_chem_comp.pdbx_modified_date                    2013-06-07 
_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                        380.289 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D3N 
_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        4HQI 
_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 
D3N O1P   O1P   O 0 1 N N N 9.151  11.502 5.034  -6.295 -0.278 0.125  O1P   D3N 1  
D3N P     P     P 0 1 N N N 10.467 10.803 4.830  -4.990 -1.154 0.474  P     D3N 2  
D3N O2P   O2P   O 0 1 N N N 11.529 11.563 4.178  -4.745 -2.129 -0.612 O2P   D3N 3  
D3N "O5'" "O5'" O 0 1 N N N 10.132 9.407  4.099  -3.714 -0.183 0.621  "O5'" D3N 4  
D3N "C5'" "C5'" C 0 1 N N N 9.339  9.445  2.962  -3.183 0.574  -0.468 "C5'" D3N 5  
D3N "C4'" "C4'" C 0 1 N N R 9.661  8.312  2.011  -1.979 1.386  0.014  "C4'" D3N 6  
D3N "O4'" "O4'" O 0 1 N N N 8.863  7.224  2.387  -0.891 0.511  0.382  "O4'" D3N 7  
D3N "C3'" "C3'" C 0 1 N N S 9.320  8.677  0.601  -1.390 2.229  -1.145 "C3'" D3N 8  
D3N "O3'" "O3'" O 0 1 N N N 10.640 8.976  -0.003 -2.065 3.483  -1.258 "O3'" D3N 9  
D3N "C2'" "C2'" C 0 1 N N N 8.658  7.422  0.042  0.076  2.429  -0.687 "C2'" D3N 10 
D3N "C1'" "C1'" C 0 1 N N R 8.417  6.534  1.230  0.313  1.294  0.327  "C1'" D3N 11 
D3N N1    N1    N 0 1 N N N 7.078  6.124  1.580  1.431  0.457  -0.115 N1    D3N 12 
D3N C2    C2    C 0 1 N N N 6.110  7.057  1.685  1.299  -0.310 -1.214 C2    D3N 13 
D3N O2    O2    O 0 1 N N N 6.297  8.251  1.417  0.245  -0.290 -1.820 O2    D3N 14 
D3N N3    N3    N 0 1 N N N 4.887  6.635  2.099  2.293  -1.098 -1.667 N3    D3N 15 
D3N C4    C4    C 0 1 Y N N 4.594  5.301  2.451  3.514  -1.147 -0.999 C4    D3N 16 
D3N C5    C5    C 0 1 Y N N 5.607  4.371  2.331  3.685  -0.356 0.155  C5    D3N 17 
D3N C6    C6    C 0 1 Y N N 6.891  4.763  1.888  2.627  0.463  0.600  C6    D3N 18 
D3N C7    C7    C 0 1 Y N N 7.850  3.823  1.781  2.804  1.236  1.724  C7    D3N 19 
D3N C8    C8    C 0 1 Y N N 7.548  2.482  2.091  4.017  1.213  2.411  C8    D3N 20 
D3N C9    C9    C 0 1 Y N N 6.313  2.075  2.503  5.055  0.433  1.996  C9    D3N 21 
D3N C10   C10   C 0 1 Y N N 5.329  3.022  2.649  4.909  -0.380 0.859  C10   D3N 22 
D3N C11   C11   C 0 1 Y N N 4.040  2.682  3.115  5.947  -1.202 0.389  C11   D3N 23 
D3N C12   C12   C 0 1 Y N N 3.039  3.617  3.226  5.759  -1.959 -0.730 C12   D3N 24 
D3N C13   C13   C 0 1 Y N N 3.306  4.953  2.885  4.554  -1.940 -1.428 C13   D3N 25 
D3N H1    H1    H 0 1 N N N 9.205  12.386 4.690  -6.515 0.383  0.796  H1    D3N 26 
D3N H3    H3    H 0 1 N N N 9.505  10.401 2.445  -2.870 -0.103 -1.263 H3    D3N 27 
D3N H4    H4    H 0 1 N N N 8.283  9.368  3.262  -3.949 1.251  -0.847 H4    D3N 28 
D3N H5    H5    H 0 1 N N N 10.730 8.064  2.083  -2.259 2.024  0.853  H5    D3N 29 
D3N H6    H6    H 0 1 N N N 8.641  9.541  0.556  -1.432 1.680  -2.086 H6    D3N 30 
D3N H7    H7    H 0 1 N N N 10.996 9.766  0.387  -1.732 4.046  -1.970 H7    D3N 31 
D3N H8    H8    H 0 1 N N N 7.706  7.675  -0.449 0.756  2.334  -1.533 H8    D3N 32 
D3N H9    H9    H 0 1 N N N 9.323  6.926  -0.681 0.196  3.401  -0.207 H9    D3N 33 
D3N H10   H10   H 0 1 N N N 9.032  5.631  1.100  0.531  1.714  1.309  H10   D3N 34 
D3N H11   H11   H 0 1 N N N 4.151  7.310  2.158  2.157  -1.635 -2.463 H11   D3N 35 
D3N H12   H12   H 0 1 N N N 8.844  4.096  1.460  2.000  1.864  2.077  H12   D3N 36 
D3N H13   H13   H 0 1 N N N 8.330  1.743  1.998  4.137  1.827  3.291  H13   D3N 37 
D3N H14   H14   H 0 1 N N N 6.114  1.034  2.709  5.985  0.433  2.545  H14   D3N 38 
D3N H15   H15   H 0 1 N N N 3.835  1.658  3.392  6.891  -1.235 0.912  H15   D3N 39 
D3N H16   H16   H 0 1 N N N 2.058  3.328  3.572  6.564  -2.587 -1.083 H16   D3N 40 
D3N H17   H17   H 0 1 N N N 2.531  5.702  2.956  4.435  -2.550 -2.311 H17   D3N 41 
D3N OP3   OP3   O 0 1 N Y N ?      ?      ?      -5.227 -1.942 1.859  OP3   D3N 42 
D3N H2    H2    H 0 1 N Y N ?      ?      ?      -5.981 -2.547 1.842  H2    D3N 43 
# 
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 
D3N "O3'" "C3'" SING N N 1  
D3N "C2'" "C3'" SING N N 2  
D3N "C2'" "C1'" SING N N 3  
D3N "C3'" "C4'" SING N N 4  
D3N "C1'" N1    SING N N 5  
D3N "C1'" "O4'" SING N N 6  
D3N O2    C2    DOUB N N 7  
D3N N1    C2    SING N N 8  
D3N N1    C6    SING N N 9  
D3N C2    N3    SING N N 10 
D3N C7    C6    DOUB Y N 11 
D3N C7    C8    SING Y N 12 
D3N C6    C5    SING Y N 13 
D3N "C4'" "O4'" SING N N 14 
D3N "C4'" "C5'" SING N N 15 
D3N C8    C9    DOUB Y N 16 
D3N N3    C4    SING N N 17 
D3N C5    C4    DOUB Y N 18 
D3N C5    C10   SING Y N 19 
D3N C4    C13   SING Y N 20 
D3N C9    C10   SING Y N 21 
D3N C10   C11   DOUB Y N 22 
D3N C13   C12   DOUB Y N 23 
D3N "C5'" "O5'" SING N N 24 
D3N C11   C12   SING Y N 25 
D3N "O5'" P     SING N N 26 
D3N O2P   P     DOUB N N 27 
D3N P     O1P   SING N N 28 
D3N O1P   H1    SING N N 29 
D3N "C5'" H3    SING N N 30 
D3N "C5'" H4    SING N N 31 
D3N "C4'" H5    SING N N 32 
D3N "C3'" H6    SING N N 33 
D3N "O3'" H7    SING N N 34 
D3N "C2'" H8    SING N N 35 
D3N "C2'" H9    SING N N 36 
D3N "C1'" H10   SING N N 37 
D3N N3    H11   SING N N 38 
D3N C7    H12   SING N N 39 
D3N C8    H13   SING N N 40 
D3N C9    H14   SING N N 41 
D3N C11   H15   SING N N 42 
D3N C12   H16   SING N N 43 
D3N C13   H17   SING N N 44 
D3N P     OP3   SING N N 45 
D3N OP3   H2    SING N N 46 
# 
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 
D3N SMILES           ACDLabs              12.01 "O=P(O)(O)OCC4OC(N1C(=O)Nc3c2c1cccc2ccc3)CC4O"                                                                                                                         
D3N InChI            InChI                1.03  "InChI=1S/C16H17N2O7P/c19-12-7-14(25-13(12)8-24-26(21,22)23)18-11-6-2-4-9-3-1-5-10(15(9)11)17-16(18)20/h1-6,12-14,19H,7-8H2,(H,17,20)(H2,21,22,23)/t12-,13+,14+/m0/s1" 
D3N InChIKey         InChI                1.03  SQPAXPCPGSJUFJ-BFHYXJOUSA-N                                                                                                                                            
D3N SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34"                                                                                                         
D3N SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34"                                                                                                              
D3N SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc2cccc3c2c(c1)NC(=O)N3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O"                                                                                                        
D3N SMILES           "OpenEye OEToolkits" 1.7.6 "c1cc2cccc3c2c(c1)NC(=O)N3C4CC(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 
D3N "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one"                      
D3N "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-(2-oxidanylidene-3H-perimidin-1-yl)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 
D3N "Create component" 2012-11-02 RCSB 
D3N "Initial release"  2013-06-12 RCSB 
# 
