data_2TM
#

_chem_comp.id                                   2TM
_chem_comp.name                                 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H18 N3 O13 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        CMPcPP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-01-30
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       481.184
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    2TM
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       4OIO
_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
2TM  "O5'"  "O5'"  O  0  1  N  N  N  -4.777  -3.346  84.515   0.148  -1.185  -0.194  "O5'"  2TM   1  
2TM  "C5'"  "C5'"  C  0  1  N  N  N  -3.688  -2.495  84.454   1.261  -1.869   0.386  "C5'"  2TM   2  
2TM  "C4'"  "C4'"  C  0  1  N  N  R  -4.006  -1.285  83.669   2.445  -1.829  -0.583  "C4'"  2TM   3  
2TM  "O4'"  "O4'"  O  0  1  N  N  N  -2.865  -0.832  82.991   2.913  -0.477  -0.727  "O4'"  2TM   4  
2TM  "C3'"  "C3'"  C  0  1  N  N  S  -5.119  -1.477  82.741   3.612  -2.663  -0.019  "C3'"  2TM   5  
2TM  "O3'"  "O3'"  O  0  1  N  N  N  -6.298  -1.014  83.300   3.945  -3.726  -0.914  "O3'"  2TM   6  
2TM  "C2'"  "C2'"  C  0  1  N  N  R  -4.742  -0.751  81.533   4.782  -1.656   0.086  "C2'"  2TM   7  
2TM  "O2'"  "O2'"  O  0  1  N  N  N  -5.359   0.487  81.421   6.012  -2.255  -0.329  "O2'"  2TM   8  
2TM  "C1'"  "C1'"  C  0  1  N  N  R  -3.289  -0.577  81.656   4.344  -0.544  -0.906  "C1'"  2TM   9  
2TM  C5     C5     C  0  1  N  N  N  -1.047  -3.242  80.327   6.431   2.491  -1.081  C5     2TM  10  
2TM  C6     C6     C  0  1  N  N  N  -1.781  -2.425  81.187   5.860   1.309  -1.414  C6     2TM  11  
2TM  N1     N1     N  0  1  N  N  N  -2.526  -1.417  80.694   4.969   0.735  -0.558  N1     2TM  12  
2TM  C2     C2     C  0  1  N  N  N  -2.559  -1.195  79.360   4.659   1.336   0.605  C2     2TM  13  
2TM  N3     N3     N  0  1  N  N  N  -1.858  -1.970  78.511   5.212   2.499   0.947  N3     2TM  14  
2TM  C4     C4     C  0  1  N  N  N  -1.105  -2.986  78.958   6.089   3.092   0.148  C4     2TM  15  
2TM  O3G    O3G    O  0  1  N  N  N  -7.436  -3.176  90.369  -7.047   2.093  -1.782  O3G    2TM  16  
2TM  PG     PG     P  0  1  N  N  N  -8.071  -4.400  89.723  -6.668   1.080  -0.590  PG     2TM  17  
2TM  O1G    O1G    O  0  1  N  N  N  -9.541  -4.455  90.075  -6.886   1.747   0.713  O1G    2TM  18  
2TM  O2G    O2G    O  0  1  N  N  N  -7.394  -5.647  90.244  -7.599  -0.231  -0.684  O2G    2TM  19  
2TM  O3B    O3B    O  0  1  N  N  N  -7.926  -4.304  88.139  -5.122   0.651  -0.721  O3B    2TM  20  
2TM  PB     PB     P  0  1  N  N  N  -7.039  -3.191  87.437  -4.070  -0.056   0.271  PB     2TM  21  
2TM  O1B    O1B    O  0  1  N  N  N  -7.039  -1.877  88.296  -4.618  -1.512   0.686  O1B    2TM  22  
2TM  O2B    O2B    O  0  1  N  N  N  -7.606  -2.888  86.074  -3.902   0.773   1.485  O2B    2TM  23  
2TM  PA     PA     P  0  1  N  N  N  -4.812  -4.489  85.619  -1.271  -1.031   0.551  PA     2TM  24  
2TM  O1A    O1A    O  0  1  N  N  N  -5.844  -5.603  85.175  -1.775  -2.369   0.933  O1A    2TM  25  
2TM  O2A    O2A    O  0  1  N  N  N  -3.447  -5.096  85.746  -1.089  -0.129   1.872  O2A    2TM  26  
2TM  N4     N4     N  0  1  N  N  N  -0.368  -3.796  78.034   6.654   4.293   0.511  N4     2TM  27  
2TM  O2     O2     O  0  1  N  N  N  -3.234  -0.275  78.877   3.859   0.808   1.359  O2     2TM  28  
2TM  C1     C1     C  0  1  N  N  N  -5.321  -3.788  87.230  -2.463  -0.230  -0.572  C1     2TM  29  
2TM  H1     H1     H  0  1  N  N  N  -2.846  -3.021  83.979   1.540  -1.382   1.321  H1     2TM  30  
2TM  H2     H2     H  0  1  N  N  N  -3.406  -2.198  85.475   0.988  -2.905   0.583  H2     2TM  31  
2TM  H3     H3     H  0  1  N  N  N  -4.308  -0.506  84.384   2.143  -2.222  -1.553  H3     2TM  32  
2TM  H4     H4     H  0  1  N  N  N  -5.207  -2.547  82.504   3.357  -3.059   0.964  H4     2TM  33  
2TM  H5     H5     H  0  1  N  N  N  -6.498  -1.517  84.080   4.674  -4.283  -0.609  H5     2TM  34  
2TM  H6     H6     H  0  1  N  N  N  -4.960  -1.371  80.651   4.866  -1.262   1.099  H6     2TM  35  
2TM  H7     H7     H  0  1  N  N  N  -6.298   0.367  81.342   6.326  -2.955   0.259  H7     2TM  36  
2TM  H8     H8     H  0  1  N  N  N  -3.062   0.474  81.422   4.589  -0.825  -1.931  H8     2TM  37  
2TM  H9     H9     H  0  1  N  N  N  -0.448  -4.054  80.713   7.140   2.964  -1.744  H9     2TM  38  
2TM  H10    H10    H  0  1  N  N  N  -1.752  -2.601  82.252   6.109   0.827  -2.348  H10    2TM  39  
2TM  H11    H11    H  0  1  N  N  N  -8.095  -2.699  90.860  -7.966   2.394  -1.766  H11    2TM  40  
2TM  H12    H12    H  0  1  N  N  N  -8.034  -6.197  90.680  -7.507  -0.720  -1.514  H12    2TM  41  
2TM  H13    H13    H  0  1  N  N  N  -7.395  -1.162  87.782  -4.752  -2.110  -0.062  H13    2TM  42  
2TM  H14    H14    H  0  1  N  N  N  -3.490  -6.021  85.533  -0.760   0.763   1.697  H14    2TM  43  
2TM  H15    H15    H  0  1  N  N  N  -0.414  -3.604  77.054   6.411   4.708   1.354  H15    2TM  44  
2TM  H16    H16    H  0  1  N  N  N   0.193  -4.553  78.369   7.295   4.725  -0.075  H16    2TM  45  
2TM  H17    H17    H  0  1  N  N  N  -5.158  -4.569  87.987  -2.586  -0.841  -1.467  H17    2TM  46  
2TM  H18    H18    H  0  1  N  N  N  -4.657  -2.935  87.434  -2.091   0.755  -0.854  H18    2TM  47  
#   #
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
2TM  N4     C4     SING  N  N   1  
2TM  N3     C4     DOUB  N  N   2  
2TM  N3     C2     SING  N  N   3  
2TM  O2     C2     DOUB  N  N   4  
2TM  C4     C5     SING  N  N   5  
2TM  C2     N1     SING  N  N   6  
2TM  C5     C6     DOUB  N  N   7  
2TM  N1     C6     SING  N  N   8  
2TM  N1     "C1'"  SING  N  N   9  
2TM  "O2'"  "C2'"  SING  N  N  10  
2TM  "C2'"  "C1'"  SING  N  N  11  
2TM  "C2'"  "C3'"  SING  N  N  12  
2TM  "C1'"  "O4'"  SING  N  N  13  
2TM  "C3'"  "O3'"  SING  N  N  14  
2TM  "C3'"  "C4'"  SING  N  N  15  
2TM  "O4'"  "C4'"  SING  N  N  16  
2TM  "C4'"  "C5'"  SING  N  N  17  
2TM  "C5'"  "O5'"  SING  N  N  18  
2TM  "O5'"  PA     SING  N  N  19  
2TM  O1A    PA     DOUB  N  N  20  
2TM  PA     O2A    SING  N  N  21  
2TM  PA     C1     SING  N  N  22  
2TM  O2B    PB     DOUB  N  N  23  
2TM  C1     PB     SING  N  N  24  
2TM  PB     O3B    SING  N  N  25  
2TM  PB     O1B    SING  N  N  26  
2TM  O3B    PG     SING  N  N  27  
2TM  PG     O1G    DOUB  N  N  28  
2TM  PG     O2G    SING  N  N  29  
2TM  PG     O3G    SING  N  N  30  
2TM  "C5'"  H1     SING  N  N  31  
2TM  "C5'"  H2     SING  N  N  32  
2TM  "C4'"  H3     SING  N  N  33  
2TM  "C3'"  H4     SING  N  N  34  
2TM  "O3'"  H5     SING  N  N  35  
2TM  "C2'"  H6     SING  N  N  36  
2TM  "O2'"  H7     SING  N  N  37  
2TM  "C1'"  H8     SING  N  N  38  
2TM  C5     H9     SING  N  N  39  
2TM  C6     H10    SING  N  N  40  
2TM  O3G    H11    SING  N  N  41  
2TM  O2G    H12    SING  N  N  42  
2TM  O1B    H13    SING  N  N  43  
2TM  O2A    H14    SING  N  N  44  
2TM  N4     H15    SING  N  N  45  
2TM  N4     H16    SING  N  N  46  
2TM  C1     H17    SING  N  N  47  
2TM  C1     H18    SING  N  N  48  
#   #
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
2TM  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O"  
2TM  InChI             InChI                 1.03   "InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1"  
2TM  InChIKey          InChI                 1.03   STGUOVSTMBLHFT-ZOQUXTDFSA-N  
2TM  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O"  
2TM  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"  
2TM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O"  
2TM  SMILES            "OpenEye OEToolkits"  1.7.6  "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)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
2TM  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine"  
2TM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2TM  "Create component"  2014-01-30  RCSB  
2TM  "Initial release"   2014-05-07  RCSB  
2TM  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     2TM
_pdbx_chem_comp_synonyms.name        CMPcPP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
