data_5HC
# 
_chem_comp.id                                    5HC 
_chem_comp.name                                  
;2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-08-22 
_chem_comp.pdbx_modified_date                    2013-01-11 
_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                        337.223 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5HC 
_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        4GLC 
_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 
5HC P      P     P 0 1 N N N -12.034 5.599  -19.575 -4.516 1.030  -0.276 P     5HC 1  
5HC OP1    OP1   O 0 1 N N N -13.504 5.422  -19.477 -5.616 0.094  0.048  OP1   5HC 2  
5HC OP2    OP2   O 0 1 N N N -11.289 6.307  -18.501 -4.258 2.009  0.975  OP2   5HC 3  
5HC "O5'"  "O5'" O 0 1 N N N -11.381 4.165  -19.775 -3.176 0.194  -0.590 "O5'" 5HC 4  
5HC "C5'"  "C5'" C 0 1 N N N -12.022 3.221  -20.643 -2.621 -0.757 0.319  "C5'" 5HC 5  
5HC "C4'"  "C4'" C 0 1 N N R -11.100 2.054  -20.896 -1.355 -1.365 -0.288 "C4'" 5HC 6  
5HC "O4'"  "O4'" O 0 1 N N N -9.797  2.476  -21.343 -0.299 -0.382 -0.338 "O4'" 5HC 7  
5HC "C3'"  "C3'" C 0 1 N N S -10.855 1.230  -19.635 -0.807 -2.487 0.623  "C3'" 5HC 8  
5HC "O3'"  "O3'" O 0 1 N N N -11.810 0.167  -19.574 -1.218 -3.768 0.141  "O3'" 5HC 9  
5HC "C2'"  "C2'" C 0 1 N N N -9.442  0.743  -19.755 0.727  -2.336 0.521  "C2'" 5HC 10 
5HC "C1'"  "C1'" C 0 1 N N R -8.788  1.626  -20.790 0.924  -1.142 -0.439 "C1'" 5HC 11 
5HC N1     N1    N 0 1 N N N -7.749  2.536  -20.273 2.066  -0.329 -0.013 N1    5HC 12 
5HC C2     C2    C 0 1 N N N -6.417  2.142  -20.350 2.050  0.269  1.192  C2    5HC 13 
5HC O2     O2    O 0 1 N N N -6.154  1.046  -20.846 1.081  0.128  1.919  O2    5HC 14 
5HC N3     N3    N 0 1 N N N -5.449  2.970  -19.880 3.075  1.013  1.604  N3    5HC 15 
5HC C4     C4    C 0 1 N N N -5.769  4.144  -19.352 4.141  1.184  0.834  C4    5HC 16 
5HC N4     N4    N 0 1 N N N -4.780  4.930  -18.900 5.194  1.954  1.271  N4    5HC 17 
5HC C5     C5    C 0 1 N N N -7.127  4.577  -19.259 4.190  0.570  -0.435 C5    5HC 18 
5HC C5M    C5M   C 0 1 N N N -7.456  5.904  -18.663 5.391  0.751  -1.326 C5M   5HC 19 
5HC O5     O5    O 0 1 N N N -6.932  6.095  -17.352 5.192  0.032  -2.546 O5    5HC 20 
5HC C6     C6    C 0 1 N N N -8.069  3.750  -19.728 3.142  -0.187 -0.837 C6    5HC 21 
5HC OP3    OP3   O 0 1 N Y N -11.730 6.385  -20.943 -4.919 1.904  -1.567 O1    5HC 22 
5HC HOP2   H1    H 0 0 N N N -11.895 6.584  -17.824 -3.548 2.650  0.833  H1    5HC 23 
5HC "H5'"  H2    H 0 1 N N N -12.264 3.709  -21.599 -2.372 -0.261 1.257  H2    5HC 24 
5HC "H5''" H3    H 0 0 N N N -12.947 2.860  -20.171 -3.349 -1.546 0.509  H3    5HC 25 
5HC H4     H4    H 0 1 N N N -11.557 1.402  -21.655 -1.563 -1.754 -1.285 H4    5HC 26 
5HC "H3'"  H5    H 0 1 N N N -10.946 1.882  -18.754 -1.140 -2.341 1.650  H5    5HC 27 
5HC "HO3'" H6    H 0 0 N Y N -11.661 -0.349 -18.790 -0.901 -4.509 0.676  H6    5HC 28 
5HC "H2'"  H7    H 0 1 N N N -9.425  -0.307 -20.082 1.155  -2.115 1.499  H7    5HC 29 
5HC "H2''" H8    H 0 0 N N N -8.922  0.835  -18.790 1.173  -3.240 0.106  H8    5HC 30 
5HC "H1'"  H9    H 0 1 N N N -8.357  0.992  -21.579 1.070  -1.494 -1.460 H9    5HC 31 
5HC HN41   H10   H 0 0 N N N -3.830  4.626  -18.966 5.158  2.374  2.144  H10   5HC 32 
5HC HN42   H11   H 0 0 N N N -4.993  5.820  -18.497 5.973  2.077  0.705  H11   5HC 33 
5HC H5M2   H12   H 0 0 N N N -7.047  6.688  -19.317 5.525  1.810  -1.546 H12   5HC 34 
5HC H5M1   H13   H 0 0 N N N -8.551  6.000  -18.616 6.279  0.369  -0.821 H13   5HC 35 
5HC HO5    H14   H 0 1 N N N -7.178  6.956  -17.035 5.928  0.104  -3.169 H14   5HC 36 
5HC H6     H15   H 0 1 N N N -9.106  4.048  -19.675 3.158  -0.671 -1.803 H15   5HC 37 
5HC HOP3   H16   H 0 0 N N N -12.547 6.567  -21.393 -5.719 2.434  -1.449 H16   5HC 38 
# 
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 
5HC "O4'" "C4'"  SING N N 1  
5HC "O4'" "C1'"  SING N N 2  
5HC "C4'" "C5'"  SING N N 3  
5HC "C4'" "C3'"  SING N N 4  
5HC O2    C2     DOUB N N 5  
5HC "C1'" N1     SING N N 6  
5HC "C1'" "C2'"  SING N N 7  
5HC "C5'" "O5'"  SING N N 8  
5HC C2    N1     SING N N 9  
5HC C2    N3     SING N N 10 
5HC N1    C6     SING N N 11 
5HC N3    C4     DOUB N N 12 
5HC "O5'" P      SING N N 13 
5HC "C2'" "C3'"  SING N N 14 
5HC C6    C5     DOUB N N 15 
5HC "C3'" "O3'"  SING N N 16 
5HC P     OP1    DOUB N N 17 
5HC P     OP2    SING N N 18 
5HC C4    C5     SING N N 19 
5HC C4    N4     SING N N 20 
5HC C5    C5M    SING N N 21 
5HC C5M   O5     SING N N 22 
5HC P     OP3    SING N N 23 
5HC OP2   HOP2   SING N N 24 
5HC "C5'" "H5'"  SING N N 25 
5HC "C5'" "H5''" SING N N 26 
5HC "C4'" H4     SING N N 27 
5HC "C3'" "H3'"  SING N N 28 
5HC "O3'" "HO3'" SING N N 29 
5HC "C2'" "H2'"  SING N N 30 
5HC "C2'" "H2''" SING N N 31 
5HC "C1'" "H1'"  SING N N 32 
5HC N4    HN41   SING N N 33 
5HC N4    HN42   SING N N 34 
5HC C5M   H5M2   SING N N 35 
5HC C5M   H5M1   SING N N 36 
5HC O5    HO5    SING N N 37 
5HC C6    H6     SING N N 38 
5HC OP3   HOP3   SING N N 39 
# 
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 
5HC SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)CC2O"                                                                                                          
5HC InChI            InChI                1.03  "InChI=1S/C10H16N3O8P/c11-9-5(3-14)2-13(10(16)12-9)8-1-6(15)7(21-8)4-20-22(17,18)19/h2,6-8,14-15H,1,3-4H2,(H2,11,12,16)(H2,17,18,19)/t6-,7+,8+/m0/s1" 
5HC InChIKey         InChI                1.03  BTIWPBKNTZFNRI-XLPZGREQSA-N                                                                                                                           
5HC SMILES_CANONICAL CACTVS               3.370 "NC1=NC(=O)N(C=C1CO)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                                           
5HC SMILES           CACTVS               3.370 "NC1=NC(=O)N(C=C1CO)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                               
5HC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)COP(=O)(O)O)O"                                                                                             
5HC SMILES           "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=C(C(=NC2=O)N)CO)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 
5HC "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
;
5HC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-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 
5HC "Create component" 2012-08-22 RCSB 
5HC "Initial release"  2013-01-11 RCSB 
# 
