data_A5M
# 
_chem_comp.id                                    A5M 
_chem_comp.name                                  "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 N4 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-03-10 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        322.212 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     A5M 
_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        1YRM 
_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 
A5M P      P    P 0 1 N N N -9.460  29.698 52.637 0.446  -1.873 4.859  P      A5M 1  
A5M OP1    O1P  O 0 1 N N N -10.659 30.137 53.398 -0.107 -2.073 6.241  OP1    A5M 2  
A5M OP2    O2P  O 0 1 N N N -8.106  30.004 53.165 1.980  -1.366 4.795  OP2    A5M 3  
A5M "O5'"  O5*  O 0 1 N N N -9.589  28.125 52.453 -0.353 -0.795 3.953  "O5'"  A5M 4  
A5M "C5'"  C5*  C 0 1 N N N -10.740 27.578 51.827 0.105  -0.548 2.636  "C5'"  A5M 5  
A5M "C4'"  C4*  C 0 1 N N R -10.457 26.178 51.370 -0.801 0.494  1.992  "C4'"  A5M 6  
A5M "O4'"  O4*  O 0 1 N N N -9.420  26.202 50.352 -0.692 1.715  2.752  "O4'"  A5M 7  
A5M "C1'"  C1*  C 0 1 N N R -8.634  25.027 50.446 0.057  2.684  1.996  "C1'"  A5M 8  
A5M N1     N1   N 0 1 N N N -7.231  25.429 50.636 1.073  3.249  2.838  N1     A5M 9  
A5M C6     C6   C 0 1 N N N -6.917  26.645 51.173 1.662  2.445  3.803  C6     A5M 10 
A5M C2     C2   C 0 1 N N N -6.212  24.537 50.257 1.490  4.598  2.712  C2     A5M 11 
A5M O2     O2   O 0 1 N N N -6.529  23.446 49.753 0.988  5.340  1.866  O2     A5M 12 
A5M N3     N3   N 0 1 N N N -4.915  24.890 50.444 2.476  5.076  3.559  N3     A5M 13 
A5M C4     C4   C 0 1 N N N -4.620  26.081 50.974 3.021  4.304  4.463  C4     A5M 14 
A5M N4     N4   N 0 1 N N N -3.328  26.394 51.139 3.999  4.798  5.294  N4     A5M 15 
A5M C5     C5   C 0 1 N N N -5.639  27.010 51.358 2.612  2.885  4.626  C5     A5M 16 
A5M "C2'"  C2*  C 0 1 N N R -9.212  24.196 51.597 0.629  1.952  0.788  "C2'"  A5M 17 
A5M "N2'"  N2*  N 0 1 N N N -10.205 23.259 51.046 0.826  2.817  -0.363 "N2'"  A5M 18 
A5M "C3'"  C3*  C 0 1 N N S -9.870  25.282 52.440 -0.394 0.849  0.567  "C3'"  A5M 19 
A5M "O3'"  O3*  O 0 1 N N N ?       ?      ?      -1.541 1.334  -0.132 "O3'"  A5M 20 
A5M OP3    O3P  O 0 1 N Y N ?       ?      ?      0.451  -3.195 3.928  OP3    A5M 21 
A5M HOP2   2HOP H 0 0 N N N -7.339  29.723 52.678 2.656  -1.831 5.333  HOP2   A5M 22 
A5M "H5'"  1H5* H 0 1 N N N -11.638 27.629 52.485 1.131  -0.178 2.676  "H5'"  A5M 23 
A5M "H5''" 2H5* H 0 0 N N N -11.110 28.222 50.995 0.072  -1.477 2.064  "H5''" A5M 24 
A5M "H4'"  H4*  H 0 1 N N N -11.446 25.789 51.032 -1.841 0.157  2.052  "H4'"  A5M 25 
A5M "H1'"  H1*  H 0 1 N N N -8.658  24.394 49.527 -0.632 3.489  1.718  "H1'"  A5M 26 
A5M H6     H6   H 0 1 N N N -7.714  27.349 51.464 1.304  1.422  3.854  H6     A5M 27 
A5M H41    1H4  H 0 1 N N N -3.102  27.302 51.543 4.342  5.712  5.119  H41    A5M 28 
A5M H42    2H4  H 0 1 N N N -2.843  26.296 50.246 4.319  4.219  6.032  H42    A5M 29 
A5M H5     H5   H 0 1 N N N -5.440  28.003 51.794 3.075  2.263  5.380  H5     A5M 30 
A5M "H2'"  H2*  H 0 1 N N N -8.482  23.577 52.169 1.591  1.494  1.051  "H2'"  A5M 31 
A5M "H'1N" 1NH* H 0 0 N N N -10.589 22.706 51.811 1.265  3.705  -0.221 "H'1N" A5M 32 
A5M "H'2N" 2NH* H 0 0 N N N -9.823  22.679 50.298 0.344  2.598  -1.212 "H'2N" A5M 33 
A5M "H3'"  H3*  H 0 1 N N N -9.975  25.556 53.515 -0.000 -0.001 0.002  "H3'"  A5M 34 
A5M "HO3'" H3T  H 0 0 N Y N 0.368   -0.562 0.671  -1.289 1.389  -1.066 "HO3'" A5M 35 
A5M HOP3   3HOP H 0 0 N N N 0.766   -0.280 -0.486 0.804  -4.033 4.296  HOP3   A5M 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 
A5M P     OP1    DOUB N N 1  
A5M P     OP2    SING N N 2  
A5M P     "O5'"  SING N N 3  
A5M P     OP3    SING N N 4  
A5M OP2   HOP2   SING N N 5  
A5M "O5'" "C5'"  SING N N 6  
A5M "C5'" "C4'"  SING N N 7  
A5M "C5'" "H5'"  SING N N 8  
A5M "C5'" "H5''" SING N N 9  
A5M "C4'" "O4'"  SING N N 10 
A5M "C4'" "C3'"  SING N N 11 
A5M "C4'" "H4'"  SING N N 12 
A5M "O4'" "C1'"  SING N N 13 
A5M "C1'" N1     SING N N 14 
A5M "C1'" "C2'"  SING N N 15 
A5M "C1'" "H1'"  SING N N 16 
A5M N1    C6     SING N N 17 
A5M N1    C2     SING N N 18 
A5M C6    C5     DOUB N N 19 
A5M C6    H6     SING N N 20 
A5M C2    O2     DOUB N N 21 
A5M C2    N3     SING N N 22 
A5M N3    C4     DOUB N N 23 
A5M C4    N4     SING N N 24 
A5M C4    C5     SING N N 25 
A5M N4    H41    SING N N 26 
A5M N4    H42    SING N N 27 
A5M C5    H5     SING N N 28 
A5M "C2'" "N2'"  SING N N 29 
A5M "C2'" "C3'"  SING N N 30 
A5M "C2'" "H2'"  SING N N 31 
A5M "N2'" "H'1N" SING N N 32 
A5M "N2'" "H'2N" SING N N 33 
A5M "C3'" "O3'"  SING N N 34 
A5M "C3'" "H3'"  SING N N 35 
A5M "O3'" "HO3'" SING N N 36 
A5M OP3   HOP3   SING N N 37 
# 
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 
A5M SMILES           ACDLabs              10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2N)COP(=O)(O)O"                                                                                                                          
A5M InChI            InChI                1.02b "InChI=1/C9H15N4O7P/c10-5-1-2-13(9(15)12-5)8-6(11)7(14)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,14H,3,11H2,(H2,10,12,15)(H2,16,17,18)/t4-,6-,7?,8-/m1/s1/f/h16-17H,10H2" 
A5M InChIKey         InChI                1.02b HGDDYYFPFZSUMP-KCFFXKEFDY                                                                                                                                          
A5M SMILES_CANONICAL CACTVS               3.341 "N[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N"                                                                                                      
A5M SMILES           CACTVS               3.341 "N[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N"                                                                                                            
A5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)N"                                                                                                    
A5M SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)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 
A5M "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-amino-2'-deoxycytidine 5'-(dihydrogen phosphate)
;
A5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-4-amino-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
