data_CDM
# 
_chem_comp.id                                    CDM 
_chem_comp.name                                  4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H25 N3 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-05-22 
_chem_comp.pdbx_modified_date                    2008-10-14 
_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                        521.308 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CDM 
_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        1INI 
_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 
CDM N1     N1   N 0 1 N N N 48.972 -15.320 32.129 -0.822 -0.498 -5.725 N1     CDM 1  
CDM C2     C2   C 0 1 N N N 47.711 -15.455 32.800 -1.530 0.567  -5.309 C2     CDM 2  
CDM N3     N3   N 0 1 N N N 47.604 -16.211 33.929 -2.757 0.801  -5.771 N3     CDM 3  
CDM C4     C4   C 0 1 N N N 48.759 -16.883 34.469 -3.318 -0.020 -6.649 C4     CDM 4  
CDM C5     C5   C 0 1 N N N 50.037 -16.794 33.854 -2.605 -1.149 -7.101 C5     CDM 5  
CDM C6     C6   C 0 1 N N N 50.086 -16.008 32.703 -1.356 -1.370 -6.626 C6     CDM 6  
CDM O2     O2   O 0 1 N N N 46.649 -14.916 32.422 -1.036 1.337  -4.502 O2     CDM 7  
CDM N4     N4   N 0 1 N N N 48.591 -17.609 35.589 -4.588 0.228  -7.115 N4     CDM 8  
CDM "C1'"  C1*  C 0 1 N N R 49.134 -14.495 30.891 0.527  -0.726 -5.203 "C1'"  CDM 9  
CDM "C2'"  C2*  C 0 1 N N R 50.055 -13.319 31.132 1.426  0.512  -5.447 "C2'"  CDM 10 
CDM "O2'"  O2*  O 0 1 N N N 49.351 -12.350 31.855 2.025  0.459  -6.744 "O2'"  CDM 11 
CDM "C3'"  C3*  C 0 1 N N S 50.529 -12.941 29.743 2.499  0.358  -4.337 "C3'"  CDM 12 
CDM "C4'"  C4*  C 0 1 N N R 50.336 -14.252 28.943 1.831  -0.561 -3.297 "C4'"  CDM 13 
CDM "O4'"  O4*  O 0 1 N N N 49.735 -15.210 29.845 0.502  -0.846 -3.764 "O4'"  CDM 14 
CDM "O3'"  O3*  O 0 1 N N N 49.677 -11.980 29.080 3.681  -0.246 -4.864 "O3'"  CDM 15 
CDM "C5'"  C5*  C 0 1 N N N 51.739 -14.679 28.527 1.765  0.147  -1.942 "C5'"  CDM 16 
CDM "O5'"  O5*  O 0 1 N N N 52.433 -15.082 29.674 1.138  -0.709 -0.986 "O5'"  CDM 17 
CDM PA     PA   P 0 1 N N R 54.056 -15.077 29.828 1.102  0.095  0.407  PA     CDM 18 
CDM O1A    O1A  O 0 1 N N N 54.488 -13.616 29.398 2.484  0.423  0.822  O1A    CDM 19 
CDM O2A    O2A  O 0 1 N N N 54.346 -15.458 31.470 0.261  1.454  0.220  O2A    CDM 20 
CDM O3A    O3A  O 0 1 N N N 54.497 -16.134 28.879 0.405  -0.816 1.535  O3A    CDM 21 
CDM PB     PB   P 0 1 N N S 54.585 -17.612 28.672 0.403  0.045  2.895  PB     CDM 22 
CDM O1B    O1B  O 0 1 N N N 53.337 -18.265 29.179 -0.426 1.405  2.667  O1B    CDM 23 
CDM O2B    O2B  O 0 1 N N N 55.839 -18.087 29.434 1.796  0.374  3.272  O2B    CDM 24 
CDM O3B    O3B  O 0 1 N N N 54.687 -18.200 27.300 -0.283 -0.810 4.073  O3B    CDM 25 
CDM C1M    C1M  C 0 1 N N N 53.636 -17.827 26.427 -0.254 0.003  5.246  C1M    CDM 26 
CDM C2M    C2M  C 0 1 N N R 54.008 -18.440 25.091 -0.896 -0.755 6.410  C2M    CDM 27 
CDM O2M    O2M  O 0 1 N N N 53.969 -19.941 25.302 -0.169 -1.961 6.650  O2M    CDM 28 
CDM C3M    C3M  C 0 1 N N S 53.045 -18.056 23.911 -0.865 0.117  7.666  C3M    CDM 29 
CDM C4M    C4M  C 0 1 N N N 53.514 -18.842 22.709 -1.507 -0.641 8.830  C4M    CDM 30 
CDM C5M    C5M  C 0 1 N N N 51.561 -18.347 24.271 0.584  0.456  8.017  C5M    CDM 31 
CDM O3M    O3M  O 0 1 N N N 53.182 -16.597 23.532 -1.592 1.323  7.426  O3M    CDM 32 
CDM O4M    O4M  O 0 1 N N N 54.967 -18.442 22.335 -1.478 0.173  10.003 O4M    CDM 33 
CDM H5     H5   H 0 1 N N N 50.934 -17.302 34.245 -3.048 -1.827 -7.816 H5     CDM 34 
CDM H6     H6   H 0 1 N N N 51.071 -15.925 32.214 -0.790 -2.228 -6.957 H6     CDM 35 
CDM H41    1H4  H 0 1 N N N 49.408 -18.084 35.971 -5.076 1.006  -6.802 H41    CDM 36 
CDM H42    2H4  H 0 1 N N N 47.844 -18.288 35.440 -4.995 -0.373 -7.758 H42    CDM 37 
CDM "H1'"  H1*  H 0 1 N N N 48.099 -14.178 30.622 0.967  -1.615 -5.655 "H1'"  CDM 38 
CDM "H2'"  H2*  H 0 1 N N N 50.955 -13.504 31.762 0.861  1.434  -5.319 "H2'"  CDM 39 
CDM "HO'2" 2HO* H 0 0 N N N 49.929 -11.611 32.006 2.569  1.254  -6.833 "HO'2" CDM 40 
CDM "H3'"  H3*  H 0 1 N N N 51.555 -12.509 29.802 2.732  1.327  -3.895 "H3'"  CDM 41 
CDM "H4'"  H4*  H 0 1 N N N 49.683 -14.153 28.044 2.398  -1.487 -3.203 "H4'"  CDM 42 
CDM H3T    H3T  H 0 1 N N N 49.974 -11.743 28.209 4.018  0.346  -5.549 H3T    CDM 43 
CDM "H5'1" 1H5* H 0 0 N N N 51.732 -15.461 27.732 1.187  1.066  -2.041 "H5'1" CDM 44 
CDM "H5'2" 2H5* H 0 0 N N N 52.277 -13.887 27.955 2.774  0.387  -1.608 "H5'2" CDM 45 
CDM HO2A   HO2A H 0 0 N N N 55.291 -15.455 31.559 -0.630 1.196  -0.049 HO2A   CDM 46 
CDM HO1B   HO1B H 0 0 N N N 53.392 -19.204 29.047 -1.325 1.147  2.423  HO1B   CDM 47 
CDM H1M1   1H1M H 0 0 N N N 52.621 -18.113 26.790 -0.809 0.924  5.063  H1M1   CDM 48 
CDM H1M2   2H1M H 0 0 N N N 53.449 -16.728 26.385 0.778  0.245  5.496  H1M2   CDM 49 
CDM H2M1   1H2M H 0 0 N N N 55.008 -18.053 24.786 -1.929 -0.996 6.160  H2M1   CDM 50 
CDM H2M2   2H2M H 0 0 N N N 54.202 -20.325 24.464 0.737  -1.703 6.867  H2M2   CDM 51 
CDM H4M1   1H4M H 0 0 N N N 53.413 -19.941 22.866 -2.540 -0.883 8.580  H4M1   CDM 52 
CDM H4M2   2H4M H 0 0 N N N 52.817 -18.734 21.844 -0.952 -1.562 9.013  H4M2   CDM 53 
CDM H5M1   1H5M H 0 0 N N N 50.877 -18.074 23.433 1.139  -0.463 8.200  H5M1   CDM 54 
CDM H5M2   2H5M H 0 0 N N N 51.417 -19.406 24.586 1.041  0.997  7.188  H5M2   CDM 55 
CDM H5M3   3H5M H 0 0 N N N 51.264 -17.842 25.220 0.606  1.078  8.912  H5M3   CDM 56 
CDM H3M    H3M  H 0 1 N N N 52.599 -16.364 22.818 -2.499 1.065  7.210  H3M    CDM 57 
CDM H4M    H4M  H 0 1 N N N 55.261 -18.936 21.579 -1.891 -0.341 10.711 H4M    CDM 58 
# 
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 
CDM N1    C2     SING N N 1  
CDM N1    C6     SING N N 2  
CDM N1    "C1'"  SING N N 3  
CDM C2    N3     SING N N 4  
CDM C2    O2     DOUB N N 5  
CDM N3    C4     DOUB N N 6  
CDM C4    C5     SING N N 7  
CDM C4    N4     SING N N 8  
CDM C5    C6     DOUB N N 9  
CDM C5    H5     SING N N 10 
CDM C6    H6     SING N N 11 
CDM N4    H41    SING N N 12 
CDM N4    H42    SING N N 13 
CDM "C1'" "C2'"  SING N N 14 
CDM "C1'" "O4'"  SING N N 15 
CDM "C1'" "H1'"  SING N N 16 
CDM "C2'" "O2'"  SING N N 17 
CDM "C2'" "C3'"  SING N N 18 
CDM "C2'" "H2'"  SING N N 19 
CDM "O2'" "HO'2" SING N N 20 
CDM "C3'" "C4'"  SING N N 21 
CDM "C3'" "O3'"  SING N N 22 
CDM "C3'" "H3'"  SING N N 23 
CDM "C4'" "O4'"  SING N N 24 
CDM "C4'" "C5'"  SING N N 25 
CDM "C4'" "H4'"  SING N N 26 
CDM "O3'" H3T    SING N N 27 
CDM "C5'" "O5'"  SING N N 28 
CDM "C5'" "H5'1" SING N N 29 
CDM "C5'" "H5'2" SING N N 30 
CDM "O5'" PA     SING N N 31 
CDM PA    O1A    DOUB N N 32 
CDM PA    O2A    SING N N 33 
CDM PA    O3A    SING N N 34 
CDM O2A   HO2A   SING N N 35 
CDM O3A   PB     SING N N 36 
CDM PB    O1B    SING N N 37 
CDM PB    O2B    DOUB N N 38 
CDM PB    O3B    SING N N 39 
CDM O1B   HO1B   SING N N 40 
CDM O3B   C1M    SING N N 41 
CDM C1M   C2M    SING N N 42 
CDM C1M   H1M1   SING N N 43 
CDM C1M   H1M2   SING N N 44 
CDM C2M   O2M    SING N N 45 
CDM C2M   C3M    SING N N 46 
CDM C2M   H2M1   SING N N 47 
CDM O2M   H2M2   SING N N 48 
CDM C3M   C4M    SING N N 49 
CDM C3M   C5M    SING N N 50 
CDM C3M   O3M    SING N N 51 
CDM C4M   O4M    SING N N 52 
CDM C4M   H4M1   SING N N 53 
CDM C4M   H4M2   SING N N 54 
CDM C5M   H5M1   SING N N 55 
CDM C5M   H5M2   SING N N 56 
CDM C5M   H5M3   SING N N 57 
CDM O3M   H3M    SING N N 58 
CDM O4M   H4M    SING N N 59 
# 
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 
CDM SMILES           ACDLabs              10.04 O=P(O)(OCC(O)C(O)(C)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O 
CDM InChI            InChI                1.02b 
InChI=1/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1/f/h24,26H,15H2 
CDM InChIKey         InChI                1.02b YFAUKWZNPVBCFF-BFXDQDSFDK 
CDM SMILES_CANONICAL CACTVS               3.341 C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N 
CDM SMILES           CACTVS               3.341 C[C](O)(CO)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N 
CDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O 
CDM SMILES           "OpenEye OEToolkits" 1.5.0 CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)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 
CDM "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphoryl]oxy}phosphoryl]cytidine"                                                      
CDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3S)-2,3,4-trihydroxy-3-methyl-butoxy]phosphoryl] hydrogen phosphate" 
# 
