data_C2L
# 
_chem_comp.id                                    C2L 
_chem_comp.name                                  
;5-METHYL-3'-O-METHOXYETHYL CYTIDINE 5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H22 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-10-29 
_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                        395.302 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     C2L 
_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        ? 
_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 
C2L OP3    O3P  O 0 1 N Y N ?      ?       ?      1.198  0.588  -4.548 OP3    C2L 1  
C2L P      P    P 0 1 N N N 9.194  -7.166  11.808 2.787  0.324  -4.407 P      C2L 2  
C2L OP1    O1P  O 0 1 N N N 9.354  -8.268  12.783 3.659  1.172  -5.286 OP1    C2L 3  
C2L OP2    O2P  O 0 1 N N N 10.384 -6.400  11.367 2.921  -1.270 -4.647 OP2    C2L 4  
C2L "O5'"  O5*  O 0 1 N N N 8.481  -7.741  10.486 3.063  0.476  -2.819 "O5'"  C2L 5  
C2L "C5'"  C5*  C 0 1 N N N 7.425  -8.675  10.568 2.282  -0.292 -1.921 "C5'"  C2L 6  
C2L "C4'"  C4*  C 0 1 N N R 6.661  -8.731  9.246  2.725  0.023  -0.498 "C4'"  C2L 7  
C2L "O4'"  O4*  O 0 1 N N N 6.013  -7.497  8.989  2.470  1.422  -0.246 "O4'"  C2L 8  
C2L "C3'"  C3*  C 0 1 N N S 7.515  -9.005  8.011  1.940  -0.742 0.560  "C3'"  C2L 9  
C2L "O3'"  O3*  O 0 1 N N N 7.899  -10.370 7.891  2.742  -0.809 1.739  "O3'"  C2L 10 
C2L "C2'"  C2*  C 0 1 N N R 6.556  -8.525  6.922  0.748  0.163  0.786  "C2'"  C2L 11 
C2L "O2'"  O2*  O 0 1 N N N 5.561  -9.520  6.688  0.137  -0.058 2.041  "O2'"  C2L 12 
C2L "C1'"  C1*  C 0 1 N N R 5.907  -7.315  7.581  1.373  1.543  0.675  "C1'"  C2L 13 
C2L N1     N1   N 0 1 N N N 6.445  -6.016  7.117  0.452  2.524  0.177  N1     C2L 14 
C2L C2     C2   C 0 1 N N N 5.823  -5.340  6.063  -0.308 3.346  1.042  C2     C2L 15 
C2L O2     O2   O 0 1 N N N 4.829  -5.801  5.509  -0.204 3.247  2.266  O2     C2L 16 
C2L N3     N3   N 0 1 N N N 6.340  -4.145  5.653  -1.176 4.269  0.491  N3     C2L 17 
C2L C4     C4   C 0 1 N N N 7.419  -3.614  6.243  -1.306 4.396  -0.806 C4     C2L 18 
C2L N4     N4   N 0 1 N N N 7.854  -2.437  5.783  -2.189 5.336  -1.292 N4     C2L 19 
C2L C5     C5   C 0 1 N N N 8.070  -4.303  7.335  -0.522 3.547  -1.759 C5     C2L 20 
C2L C6     C6   C 0 1 N N N 7.543  -5.490  7.719  0.307  2.665  -1.195 C6     C2L 21 
C2L "CA'"  CA*  C 0 1 N N N 8.728  -10.614 6.765  3.867  -1.652 1.551  "CA'"  C2L 22 
C2L "CB'"  CB*  C 0 1 N N N 9.142  -12.085 6.734  4.693  -1.667 2.823  "CB'"  C2L 23 
C2L "OC'"  OC*  O 0 1 N N N 9.998  -12.362 7.830  5.141  -0.346 3.101  "OC'"  C2L 24 
C2L "CD'"  CD*  C 0 1 N N N 10.417 -13.714 7.854  5.904  -0.296 4.298  "CD'"  C2L 25 
C2L C7     C7   C 0 1 N N N 9.289  -3.768  8.048  -0.687 3.708  -3.234 C7     C2L 26 
C2L HOP3   3HOP H 0 0 N N N -0.103 0.707   -0.626 0.799  0.616  -5.443 HOP3   C2L 27 
C2L HOP2   2HOP H 0 0 N N N 10.910 -6.810  12.043 2.886  -1.617 -5.563 HOP2   C2L 28 
C2L "H5'"  1H5* H 0 1 N N N 7.832  -9.660  10.800 1.229  -0.035 -2.051 "H5'"  C2L 29 
C2L "H5''" 2H5* H 0 0 N N N 6.735  -8.378  11.358 2.428  -1.352 -2.133 "H5''" C2L 30 
C2L "H4'"  H4*  H 0 1 N N N 5.896  -9.507  9.319  3.804  -0.139 -0.410 "H4'"  C2L 31 
C2L "H3'"  H3*  H 0 1 N N N 8.396  -8.365  8.018  1.675  -1.764 0.277  "H3'"  C2L 32 
C2L "H2'"  H2*  H 0 1 N N N 7.118  -8.221  6.044  -0.000 0.004  -0.000 "H2'"  C2L 33 
C2L "HO2'" 2HO* H 0 0 N N N 4.965  -9.222  6.011  -0.494 0.669  2.185  "HO2'" C2L 34 
C2L "H1'"  H1*  H 0 1 N N N 4.865  -7.263  7.353  1.754  1.910  1.633  "H1'"  C2L 35 
C2L H41    1H4  H 0 1 N N N 7.359  -1.996  5.014  -2.573 5.189  -2.193 H41    C2L 36 
C2L H42    2H4  H 0 1 N N N 8.663  -1.997  6.193  -2.398 6.116  -0.718 H42    C2L 37 
C2L H6     H6   H 0 1 N N N 7.947  -6.089  8.507  0.921  2.002  -1.796 H6     C2L 38 
C2L "HA'1" 1HA* H 0 0 N N N 9.620  -9.989  6.812  3.504  -2.655 1.304  "HA'1" C2L 39 
C2L "HA'2" 2HA* H 0 0 N N N 8.181  -10.391 5.849  4.455  -1.258 0.717  "HA'2" C2L 40 
C2L "HB'1" 1HB* H 0 0 N N N 8.250  -12.711 6.779  5.572  -2.309 2.715  "HB'1" C2L 41 
C2L "HB'2" 2HB* H 0 0 N N N 9.672  -12.279 5.800  4.088  -2.009 3.668  "HB'2" C2L 42 
C2L "HD'1" 1HD* H 0 0 N N N 9.552  -14.374 7.933  5.249  -0.053 5.138  "HD'1" C2L 43 
C2L "HD'2" 2HD* H 0 0 N N N 11.062 -13.871 8.719  6.686  0.461  4.201  "HD'2" C2L 44 
C2L "HD'3" 3HD* H 0 0 N N N 10.976 -13.949 6.948  6.363  -1.273 4.468  "HD'3" C2L 45 
C2L H71    1H7  H 0 1 N N N 9.572  -4.521  8.785  -0.306 2.826  -3.748 H71    C2L 46 
C2L H72    2H7  H 0 1 N N N 9.042  -2.827  8.577  -0.139 4.587  -3.575 H72    C2L 47 
C2L H73    3H7  H 0 1 N N N 10.095 -3.618  7.336  -1.742 3.837  -3.477 H73    C2L 48 
# 
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 
C2L OP3   P      SING N N 1  
C2L OP3   HOP3   SING N N 2  
C2L P     OP1    DOUB N N 3  
C2L P     OP2    SING N N 4  
C2L P     "O5'"  SING N N 5  
C2L OP2   HOP2   SING N N 6  
C2L "O5'" "C5'"  SING N N 7  
C2L "C5'" "C4'"  SING N N 8  
C2L "C5'" "H5'"  SING N N 9  
C2L "C5'" "H5''" SING N N 10 
C2L "C4'" "O4'"  SING N N 11 
C2L "C4'" "C3'"  SING N N 12 
C2L "C4'" "H4'"  SING N N 13 
C2L "O4'" "C1'"  SING N N 14 
C2L "C3'" "O3'"  SING N N 15 
C2L "C3'" "C2'"  SING N N 16 
C2L "C3'" "H3'"  SING N N 17 
C2L "O3'" "CA'"  SING N N 18 
C2L "C2'" "O2'"  SING N N 19 
C2L "C2'" "C1'"  SING N N 20 
C2L "C2'" "H2'"  SING N N 21 
C2L "O2'" "HO2'" SING N N 22 
C2L "C1'" N1     SING N N 23 
C2L "C1'" "H1'"  SING N N 24 
C2L N1    C2     SING N N 25 
C2L N1    C6     SING N N 26 
C2L C2    O2     DOUB N N 27 
C2L C2    N3     SING N N 28 
C2L N3    C4     DOUB N N 29 
C2L C4    N4     SING N N 30 
C2L C4    C5     SING N N 31 
C2L N4    H41    SING N N 32 
C2L N4    H42    SING N N 33 
C2L C5    C6     DOUB N N 34 
C2L C5    C7     SING N N 35 
C2L C6    H6     SING N N 36 
C2L "CA'" "CB'"  SING N N 37 
C2L "CA'" "HA'1" SING N N 38 
C2L "CA'" "HA'2" SING N N 39 
C2L "CB'" "OC'"  SING N N 40 
C2L "CB'" "HB'1" SING N N 41 
C2L "CB'" "HB'2" SING N N 42 
C2L "OC'" "CD'"  SING N N 43 
C2L "CD'" "HD'1" SING N N 44 
C2L "CD'" "HD'2" SING N N 45 
C2L "CD'" "HD'3" SING N N 46 
C2L C7    H71    SING N N 47 
C2L C7    H72    SING N N 48 
C2L C7    H73    SING N N 49 
# 
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 
C2L SMILES           ACDLabs              10.04 "O=C1N=C(N)C(=CN1C2OC(C(OCCOC)C2O)COP(=O)(O)O)C"                                                                                                                                             
C2L InChI            InChI                1.02b "InChI=1/C13H22N3O9P/c1-7-5-16(13(18)15-11(7)14)12-9(17)10(23-4-3-22-2)8(25-12)6-24-26(19,20)21/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1/f/h19-20H,14H2" 
C2L InChIKey         InChI                1.02b DVYXLKQTQMTZSH-DUEBWFQZDO                                                                                                                                                                    
C2L SMILES_CANONICAL CACTVS               3.341 "COCCO[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C)C(=NC2=O)N"                                                                                                                        
C2L SMILES           CACTVS               3.341 "COCCO[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C)C(=NC2=O)N"                                                                                                                               
C2L SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)OCCOC)O"                                                                                                                         
C2L SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)OCCOC)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 
C2L "SYSTEMATIC NAME" ACDLabs              10.04 
;3'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate)
;
C2L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-4-hydroxy-3-(2-methoxyethoxy)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
