data_EDC
#

_chem_comp.id                                   EDC
_chem_comp.name                                 "N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H14 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_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                       331.219
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    EDC
_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       3UBY
_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
EDC  OP3     OP3     O  0  1  N  Y  N   3.262   1.316  35.492  -4.900   2.099  -1.289  OP3     EDC   1  
EDC  P       P       P  0  1  N  N  N   2.260   1.465  34.267  -4.513   1.125  -0.067  P       EDC   2  
EDC  N1      N1      N  0  1  N  N  N   0.733  -0.643  30.679   2.019  -0.380  -0.095  N1      EDC   3  
EDC  C2      C2      C  0  1  N  N  N   0.949  -0.198  29.354   3.100  -0.163  -0.864  C2      EDC   4  
EDC  O2      O2      O  0  1  N  N  N   1.642  -0.892  28.572   3.114  -0.586  -2.003  O2      EDC   5  
EDC  N3      N3      N  0  1  Y  N  N   0.427   0.971  28.931   4.165   0.511  -0.399  N3      EDC   6  
EDC  C4      C4      C  0  1  Y  N  N  -0.316   1.735  29.755   4.164   0.996   0.887  C4      EDC   7  
EDC  N4      N4      N  0  1  Y  N  N  -0.711   2.830  29.087   5.308   1.611   1.096  N4      EDC   8  
EDC  C5      C5      C  0  1  N  N  N  -0.554   1.323  31.066   2.987   0.759   1.727  C5      EDC   9  
EDC  C6      C6      C  0  1  N  N  N  -0.016   0.115  31.504   1.950   0.081   1.198  C6      EDC  10  
EDC  C7      C7      C  0  1  Y  N  N  -0.217   2.768  27.834   6.056   1.543  -0.015  C7      EDC  11  
EDC  C8      C8      C  0  1  Y  N  N   0.497   1.591  27.744   5.369   0.867  -0.956  C8      EDC  12  
EDC  "C1'"   "C1'"   C  0  1  N  N  R   1.297  -1.931  31.130   0.884  -1.122  -0.651  "C1'"   EDC  13  
EDC  "C2'"   "C2'"   C  0  1  N  N  N   2.814  -1.931  31.308   0.703  -2.450   0.110  "C2'"   EDC  14  
EDC  "C3'"   "C3'"   C  0  1  N  N  S   3.024  -2.598  32.654  -0.739  -2.372   0.669  "C3'"   EDC  15  
EDC  "O3'"   "O3'"   O  0  1  N  N  N   3.234  -3.995  32.416  -1.402  -3.632   0.545  "O3'"   EDC  16  
EDC  "C4'"   "C4'"   C  0  1  N  N  R   1.715  -2.407  33.406  -1.390  -1.312  -0.256  "C4'"   EDC  17  
EDC  "O4'"   "O4'"   O  0  1  N  N  N   0.719  -2.322  32.386  -0.325  -0.363  -0.482  "O4'"   EDC  18  
EDC  "C5'"   "C5'"   C  0  1  N  N  N   1.700  -1.153  34.294  -2.572  -0.639   0.444  "C5'"   EDC  19  
EDC  "O5'"   "O5'"   O  0  1  N  N  N   2.262  -0.025  33.620  -3.224   0.247  -0.468  "O5'"   EDC  20  
EDC  OP1     OP1     O  0  1  N  N  N   2.960   2.350  33.256  -4.204   1.936   1.131  OP1     EDC  21  
EDC  OP2     OP2     O  0  1  N  N  N   0.856   1.768  34.726  -5.751   0.146   0.252  OP2     EDC  22  
EDC  HOP3    HOP3    H  0  0  N  Y  N   4.056   1.807  35.314  -5.669   2.658  -1.118  HOP3    EDC  23  
EDC  H5      H5      H  0  1  N  N  N  -1.147   1.932  31.732   2.949   1.124   2.743  H5      EDC  24  
EDC  H6      H6      H  0  1  N  N  N  -0.201  -0.217  32.515   1.066  -0.104   1.791  H6      EDC  25  
EDC  H7      H7      H  0  1  N  N  N  -0.354   3.499  27.051   7.044   1.962  -0.135  H7      EDC  26  
EDC  H8      H8      H  0  1  N  N  N   1.021   1.232  26.870   5.703   0.645  -1.959  H8      EDC  27  
EDC  "H1'"   "H1'"   H  0  1  N  N  N   1.052  -2.695  30.377   1.054  -1.321  -1.709  "H1'"   EDC  28  
EDC  "H2'"   "H2'"   H  0  1  N  N  N   3.302  -2.505  30.507   0.803  -3.296  -0.570  "H2'"   EDC  29  
EDC  "H2''"  "H2''"  H  0  0  N  N  N   3.207  -0.904  31.315   1.424  -2.525   0.924  "H2''"  EDC  30  
EDC  "H3'"   "H3'"   H  0  1  N  N  N   3.861  -2.136  33.197  -0.737  -2.035   1.705  "H3'"   EDC  31  
EDC  "HO3'"  "HO3'"  H  0  0  N  Y  N   3.369  -4.441  33.244  -0.977  -4.350   1.036  "HO3'"  EDC  32  
EDC  "H4'"   "H4'"   H  0  1  N  N  N   1.536  -3.289  34.038  -1.708  -1.765  -1.195  "H4'"   EDC  33  
EDC  "H5'"   "H5'"   H  0  1  N  N  N   0.660  -0.923  34.569  -3.277  -1.400   0.778  "H5'"   EDC  34  
EDC  "H5''"  "H5''"  H  0  0  N  N  N   2.285  -1.353  35.204  -2.211  -0.075   1.304  "H5''"  EDC  35  
EDC  HOP2    HOP2    H  0  0  N  N  N   0.542   2.551  34.289  -6.008  -0.417  -0.491  HOP2    EDC  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
EDC  P      OP3     SING  N  N   1  
EDC  OP3    HOP3    SING  N  N   2  
EDC  OP1    P       DOUB  N  N   3  
EDC  "O5'"  P       SING  N  N   4  
EDC  P      OP2     SING  N  N   5  
EDC  C2     N1      SING  N  N   6  
EDC  N1     "C1'"   SING  N  N   7  
EDC  N1     C6      SING  N  N   8  
EDC  O2     C2      DOUB  N  N   9  
EDC  N3     C2      SING  N  N  10  
EDC  C8     N3      SING  Y  N  11  
EDC  N3     C4      SING  Y  N  12  
EDC  N4     C4      DOUB  Y  N  13  
EDC  C4     C5      SING  N  N  14  
EDC  C7     N4      SING  Y  N  15  
EDC  C5     C6      DOUB  N  N  16  
EDC  C5     H5      SING  N  N  17  
EDC  C6     H6      SING  N  N  18  
EDC  C8     C7      DOUB  Y  N  19  
EDC  C7     H7      SING  N  N  20  
EDC  C8     H8      SING  N  N  21  
EDC  "C1'"  "C2'"   SING  N  N  22  
EDC  "C1'"  "O4'"   SING  N  N  23  
EDC  "C1'"  "H1'"   SING  N  N  24  
EDC  "C2'"  "C3'"   SING  N  N  25  
EDC  "C2'"  "H2'"   SING  N  N  26  
EDC  "C2'"  "H2''"  SING  N  N  27  
EDC  "O3'"  "C3'"   SING  N  N  28  
EDC  "C3'"  "C4'"   SING  N  N  29  
EDC  "C3'"  "H3'"   SING  N  N  30  
EDC  "O3'"  "HO3'"  SING  N  N  31  
EDC  "O4'"  "C4'"   SING  N  N  32  
EDC  "C4'"  "C5'"   SING  N  N  33  
EDC  "C4'"  "H4'"   SING  N  N  34  
EDC  "O5'"  "C5'"   SING  N  N  35  
EDC  "C5'"  "H5'"   SING  N  N  36  
EDC  "C5'"  "H5''"  SING  N  N  37  
EDC  OP2    HOP2    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
EDC  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC3OC(N2C(=O)n1c(ncc1)C=C2)CC3O"  
EDC  InChI             InChI                 1.03   "InChI=1S/C11H14N3O7P/c15-7-5-10(21-8(7)6-20-22(17,18)19)14-3-1-9-12-2-4-13(9)11(14)16/h1-4,7-8,10,15H,5-6H2,(H2,17,18,19)/t7-,8+,10+/m0/s1"  
EDC  InChIKey          InChI                 1.03   GFTHJCBXWZWVBW-QXFUBDJGSA-N  
EDC  SMILES_CANONICAL  CACTVS                3.370  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=Cc3nccn3C2=O"  
EDC  SMILES            CACTVS                3.370  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=Cc3nccn3C2=O"  
EDC  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "c1cn2c(n1)C=CN(C2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O"  
EDC  SMILES            "OpenEye OEToolkits"  1.7.6  "c1cn2c(n1)C=CN(C2=O)C3CC(C(O3)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
EDC  "SYSTEMATIC NAME"  ACDLabs               12.01  "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one"  
EDC  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,5R)-3-oxidanyl-5-(5-oxidanylideneimidazo[1,2-c]pyrimidin-6-yl)oxolan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EDC  "Create component"    1999-07-08  RCSB  
EDC  "Modify descriptor"   2011-06-04  RCSB  
EDC  "Other modification"  2011-12-19  RCSB  
EDC  "Other modification"  2012-01-09  RCSB  
EDC  "Modify synonyms"     2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     EDC
_pdbx_chem_comp_synonyms.name        "6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
