data_D5M
# 
_chem_comp.id                                    D5M 
_chem_comp.name                                  "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H14 N5 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-05-03 
_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                        331.222 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     D5M 
_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        1Z1C 
_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 
D5M "O5'"  O5*  O 0 1 N N N -51.464 14.039 60.113 2.211  -1.232 -3.468 "O5'"  D5M 1  
D5M "C5'"  C5*  C 0 1 N N N -51.078 14.680 58.895 1.348  -1.500 -2.377 "C5'"  D5M 2  
D5M "C4'"  C4*  C 0 1 N N R -49.647 14.357 58.531 2.156  -1.432 -1.088 "C4'"  D5M 3  
D5M "O4'"  O4*  O 0 1 N N N -49.503 12.918 58.415 2.678  -0.093 -0.958 "O4'"  D5M 4  
D5M "C3'"  C3*  C 0 1 N N S -49.179 14.929 57.190 1.309  -1.697 0.152  "C3'"  D5M 5  
D5M "O3'"  O3*  O 0 1 N N N -47.747 15.116 57.200 2.127  -2.250 1.180  "O3'"  D5M 6  
D5M "C2'"  C2*  C 0 1 N N N -49.481 13.795 56.223 0.878  -0.312 0.578  "C2'"  D5M 7  
D5M "C1'"  C1*  C 0 1 N N R -49.156 12.570 57.073 2.101  0.516  0.211  "C1'"  D5M 8  
D5M N9     N9   N 0 1 Y N N -49.877 11.341 56.724 1.818  1.923  -0.049 N9     D5M 9  
D5M C8     C8   C 0 1 Y N N -51.158 11.208 56.223 1.432  2.463  -1.249 C8     D5M 10 
D5M N7     N7   N 0 1 Y N N -51.538 9.960  56.060 1.250  3.765  -1.175 N7     D5M 11 
D5M C5     C5   C 0 1 Y N N -50.433 9.217  56.470 1.530  4.086  0.130  C5     D5M 12 
D5M C6     C6   C 0 1 Y N N -50.200 7.826  56.554 1.519  5.292  0.822  C6     D5M 13 
D5M N6     N6   N 0 1 N N N -51.110 6.903  56.229 1.171  6.489  0.173  N6     D5M 14 
D5M N1     N1   N 0 1 Y N N -48.985 7.418  56.997 1.849  5.300  2.136  N1     D5M 15 
D5M C2     C2   C 0 1 Y N N -48.075 8.350  57.338 2.176  4.115  2.707  C2     D5M 16 
D5M N3     N3   N 0 1 Y N N -48.178 9.681  57.314 2.223  2.888  2.144  N3     D5M 17 
D5M C4     C4   C 0 1 Y N N -49.397 10.056 56.866 1.886  2.954  0.847  C4     D5M 18 
D5M P      P    P 0 1 N N N ?       ?      ?      1.592  -1.245 -4.964 P      D5M 19 
D5M O1P    O1P  O 0 1 N N N ?       ?      ?      2.575  -0.951 -6.059 O1P    D5M 20 
D5M O3P    O3P  O 0 1 N N N ?       ?      ?      0.339  -0.227 -4.868 O3P    D5M 21 
D5M O2P    O2P  O 0 1 N N N ?       ?      ?      0.886  -2.697 -5.051 O2P    D5M 22 
D5M "H5'1" 1H5* H 0 0 N N N -51.737 14.332 58.086 0.551  -0.756 -2.359 "H5'1" D5M 23 
D5M "H5'2" 2H5* H 0 0 N N N -51.164 15.768 59.033 0.917  -2.495 -2.497 "H5'2" D5M 24 
D5M "H4'"  H4*  H 0 1 N N N -49.041 14.809 59.330 3.008  -2.117 -1.157 "H4'"  D5M 25 
D5M H1     H1   H 0 1 N N N -49.653 15.892 56.950 0.475  -2.383 -0.018 H1     D5M 26 
D5M "H3'"  H3*  H 0 1 N N N -47.426 15.157 56.307 2.928  -1.706 1.218  "H3'"  D5M 27 
D5M "H2'1" 1H2* H 0 0 N N N -50.529 13.802 55.889 0.008  0.008  -0.009 "H2'1" D5M 28 
D5M "H2'2" 2H2* H 0 0 N N N -48.910 13.848 55.284 0.635  -0.225 1.641  "H2'2" D5M 29 
D5M "H1'"  H1*  H 0 1 N N N -48.093 12.336 56.911 2.853  0.503  1.007  "H1'"  D5M 30 
D5M H8     H8   H 0 1 N N N -51.789 12.052 55.987 1.301  1.859  -2.137 H8     D5M 31 
D5M HN61   1HN6 H 0 0 N N N -51.337 6.986  55.259 0.205  6.745  0.096  HN61   D5M 32 
D5M HN62   2HN6 H 0 0 N N N -50.739 5.992  56.408 1.883  7.025  -0.286 HN62   D5M 33 
D5M H2     H2   H 0 1 N N N -47.125 7.966  57.680 2.435  4.159  3.759  H2     D5M 34 
D5M H3P    H3P  H 0 1 N N N ?       ?      ?      -0.163 -0.014 -5.684 H3P    D5M 35 
D5M H2P    H2P  H 0 1 N N N ?       ?      ?      0.508  -2.990 -5.907 H2P    D5M 36 
# 
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 
D5M "O5'" "C5'"  SING N N 1  
D5M "O5'" P      SING N N 2  
D5M "C5'" "C4'"  SING N N 3  
D5M "C5'" "H5'1" SING N N 4  
D5M "C5'" "H5'2" SING N N 5  
D5M "C4'" "O4'"  SING N N 6  
D5M "C4'" "C3'"  SING N N 7  
D5M "C4'" "H4'"  SING N N 8  
D5M "O4'" "C1'"  SING N N 9  
D5M "C3'" "O3'"  SING N N 10 
D5M "C3'" "C2'"  SING N N 11 
D5M "C3'" H1     SING N N 12 
D5M "O3'" "H3'"  SING N N 13 
D5M "C2'" "C1'"  SING N N 14 
D5M "C2'" "H2'1" SING N N 15 
D5M "C2'" "H2'2" SING N N 16 
D5M "C1'" N9     SING N N 17 
D5M "C1'" "H1'"  SING N N 18 
D5M N9    C8     SING Y N 19 
D5M N9    C4     SING Y N 20 
D5M C8    N7     DOUB Y N 21 
D5M C8    H8     SING N N 22 
D5M N7    C5     SING Y N 23 
D5M C5    C6     SING Y N 24 
D5M C5    C4     DOUB Y N 25 
D5M C6    N6     SING N N 26 
D5M C6    N1     DOUB Y N 27 
D5M N6    HN61   SING N N 28 
D5M N6    HN62   SING N N 29 
D5M N1    C2     SING Y N 30 
D5M C2    N3     DOUB Y N 31 
D5M C2    H2     SING N N 32 
D5M N3    C4     SING Y N 33 
D5M P     O1P    DOUB N N 34 
D5M P     O3P    SING N N 35 
D5M P     O2P    SING N N 36 
D5M O3P   H3P    SING N N 37 
D5M O2P   H2P    SING N N 38 
# 
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 
D5M SMILES           ACDLabs              10.04 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O"                                                                                                          
D5M SMILES_CANONICAL CACTVS               3.341 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3"                                                                                         
D5M SMILES           CACTVS               3.341 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3"                                                                                             
D5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N"                                                                                       
D5M SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N"                                                                                                    
D5M InChI            InChI                1.03  "InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1" 
D5M InChIKey         InChI                1.03  KHWCHTKSEGGWEX-RRKCRQDMSA-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 
D5M "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5'-adenylic acid
;
D5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(6-aminopurin-9-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 
D5M "Create component"  2005-05-03 RCSB 
D5M "Modify descriptor" 2011-06-04 RCSB 
# 
