data_5CM
# 
_chem_comp.id                                    5CM 
_chem_comp.name                                  "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_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                        321.224 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     5CM 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1BSU 
_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 
5CM N1     N1   N 0 1 N N N -6.764  4.376  -2.686 -0.347 -0.407 2.286  N1     5CM 1  
5CM C2     C2   C 0 1 N N N -6.371  3.063  -2.997 0.114  0.856  2.277  C2     5CM 2  
5CM N3     N3   N 0 1 N N N -6.060  2.741  -4.275 0.826  1.335  3.296  N3     5CM 3  
5CM C4     C4   C 0 1 N N N -6.146  3.660  -5.224 1.094  0.576  4.351  C4     5CM 4  
5CM C5     C5   C 0 1 N N N -6.585  5.001  -4.944 0.629  -0.754 4.388  C5     5CM 5  
5CM C5A    C5A  C 0 1 N N N -6.653  5.992  -6.052 0.927  -1.635 5.574  C5A    5CM 6  
5CM C6     C6   C 0 1 N N N -6.901  5.303  -3.678 -0.093 -1.226 3.345  C6     5CM 7  
5CM O2     O2   O 0 1 N N N -6.317  2.232  -2.087 -0.124 1.575  1.321  O2     5CM 8  
5CM N4     N4   N 0 1 N N N -5.804  3.305  -6.460 1.831  1.081  5.397  N4     5CM 9  
5CM "C1'"  C1*  C 0 1 N N R -6.948  4.750  -1.277 -1.128 -0.905 1.151  "C1'"  5CM 10 
5CM "C2'"  C2*  C 0 1 N N N -5.910  5.808  -1.036 -2.394 -0.046 0.969  "C2'"  5CM 11 
5CM "C3'"  C3*  C 0 1 N N S -6.658  7.044  -0.587 -2.274 0.504  -0.472 "C3'"  5CM 12 
5CM "C4'"  C4*  C 0 1 N N R -8.122  6.650  -0.467 -1.288 -0.498 -1.122 "C4'"  5CM 13 
5CM "O4'"  O4*  O 0 1 N N N -8.222  5.359  -1.127 -0.358 -0.798 -0.057 "O4'"  5CM 14 
5CM "O3'"  O3*  O 0 1 N N N -5.995  7.611  0.520  -3.540 0.478  -1.135 "O3'"  5CM 15 
5CM "C5'"  C5*  C 0 1 N N N -8.971  7.591  -1.284 -0.566 0.146  -2.307 "C5'"  5CM 16 
5CM "O5'"  O5*  O 0 1 N N N -8.233  8.001  -2.450 0.336  -0.797 -2.887 "O5'"  5CM 17 
5CM P      P    P 0 1 N N N -8.823  9.079  -3.449 1.057  -0.055 -4.120 P      5CM 18 
5CM OP1    O1P  O 0 1 N N N -7.912  9.098  -4.649 1.787  1.131  -3.623 OP1    5CM 19 
5CM OP2    O2P  O 0 1 N N N -9.120  10.362 -2.728 2.093  -1.067 -4.824 OP2    5CM 20 
5CM OP3    O3P  O 0 1 N Y N -10.237 8.438  -3.818 -0.052 0.406  -5.191 OP3    5CM 21 
5CM H5A1   1H5A H 0 0 N N N -6.993  7.031  -5.835 1.516  -1.077 6.302  H5A1   5CM 22 
5CM H5A2   2H5A H 0 0 N N N -5.656  6.039  -6.550 -0.008 -1.956 6.032  H5A2   5CM 23 
5CM H5A3   3H5A H 0 0 N N N -7.286  5.572  -6.867 1.489  -2.509 5.245  H5A3   5CM 24 
5CM H6     H6   H 0 1 N N N -7.274  6.316  -3.452 -0.463 -2.240 3.352  H6     5CM 25 
5CM HN41   1HN4 H 0 0 N N N -5.870  4.013  -7.191 2.155  1.995  5.365  HN41   5CM 26 
5CM HN42   2HN4 H 0 0 N N N -6.344  2.484  -6.736 2.025  0.524  6.167  HN42   5CM 27 
5CM "H1'"  H1*  H 0 1 N N N -6.867  3.876  -0.588 -1.408 -1.945 1.322  "H1'"  5CM 28 
5CM "H2'"  1H2* H 0 1 N N N -5.112  5.491  -0.324 -3.290 -0.659 1.069  "H2'"  5CM 29 
5CM "H2''" 2H2* H 0 0 N N N -5.247  5.986  -1.915 -2.408 0.771  1.690  "H2''" 5CM 30 
5CM "H3'"  H3*  H 0 1 N N N -6.660  7.896  -1.305 -1.859 1.512  -0.470 "H3'"  5CM 31 
5CM "H4'"  H4*  H 0 1 N N N -8.450  6.655  0.598  -1.810 -1.400 -1.438 "H4'"  5CM 32 
5CM "HO3'" *HO3 H 0 0 N Y N -6.464  8.387  0.801  -4.133 1.051  -0.629 "HO3'" 5CM 33 
5CM "H5'"  1H5* H 0 1 N N N -9.962  7.150  -1.543 -1.297 0.456  -3.053 "H5'"  5CM 34 
5CM "H5''" 2H5* H 0 0 N N N -9.336  8.459  -0.686 -0.008 1.017  -1.962 "H5''" 5CM 35 
5CM HOP2   2HOP H 0 0 N N N -9.473  11.008 -3.327 2.502  -0.585 -5.555 HOP2   5CM 36 
5CM HOP3   3HOP H 0 0 N N N -10.590 9.084  -4.417 -0.504 -0.394 -5.489 HOP3   5CM 37 
# 
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 
5CM N1    C2     SING N N 1  
5CM N1    C6     SING N N 2  
5CM N1    "C1'"  SING N N 3  
5CM C2    N3     SING N N 4  
5CM C2    O2     DOUB N N 5  
5CM N3    C4     DOUB N N 6  
5CM C4    C5     SING N N 7  
5CM C4    N4     SING N N 8  
5CM C5    C5A    SING N N 9  
5CM C5    C6     DOUB N N 10 
5CM C5A   H5A1   SING N N 11 
5CM C5A   H5A2   SING N N 12 
5CM C5A   H5A3   SING N N 13 
5CM C6    H6     SING N N 14 
5CM N4    HN41   SING N N 15 
5CM N4    HN42   SING N N 16 
5CM "C1'" "C2'"  SING N N 17 
5CM "C1'" "O4'"  SING N N 18 
5CM "C1'" "H1'"  SING N N 19 
5CM "C2'" "C3'"  SING N N 20 
5CM "C2'" "H2'"  SING N N 21 
5CM "C2'" "H2''" SING N N 22 
5CM "C3'" "C4'"  SING N N 23 
5CM "C3'" "O3'"  SING N N 24 
5CM "C3'" "H3'"  SING N N 25 
5CM "C4'" "O4'"  SING N N 26 
5CM "C4'" "C5'"  SING N N 27 
5CM "C4'" "H4'"  SING N N 28 
5CM "O3'" "HO3'" SING N N 29 
5CM "C5'" "O5'"  SING N N 30 
5CM "C5'" "H5'"  SING N N 31 
5CM "C5'" "H5''" SING N N 32 
5CM "O5'" P      SING N N 33 
5CM P     OP1    DOUB N N 34 
5CM P     OP2    SING N N 35 
5CM P     OP3    SING N N 36 
5CM OP2   HOP2   SING N N 37 
5CM OP3   HOP3   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 
5CM SMILES           ACDLabs              10.04 "O=C1N=C(N)C(=CN1C2OC(C(O)C2)COP(=O)(O)O)C"                                                                                                                     
5CM InChI            InChI                1.02b "InChI=1/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(20-8)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1/f/h16-17H,11H2" 
5CM InChIKey         InChI                1.02b RGDVNLHBCKWZDA-VVAHTBKFDJ                                                                                                                                       
5CM SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                                      
5CM SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1N"                                                                                                          
5CM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                        
5CM SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)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 
5CM "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5-methylcytidine 5'-(dihydrogen phosphate)
;
5CM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
