data_8CP
# 
_chem_comp.id                                    8CP 
_chem_comp.name                                  "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H17 N4 O12 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-01-19 
_chem_comp.pdbx_modified_date                    2017-07-21 
_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                        466.172 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8CP 
_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        5UGP 
_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 
8CP N1    N1  N 0 1 N N N 6.770  7.972 10.405 5.069  -0.636 0.674  N1    8CP 1  
8CP C2    C1  C 0 1 N N N 7.612  8.317 9.332  5.251  -0.771 -0.653 C2    8CP 2  
8CP N3    N2  N 0 1 N N N 8.931  8.319 9.510  6.022  -1.738 -1.146 N3    8CP 3  
8CP C4    C2  C 0 1 N N N 9.473  7.981 10.683 6.633  -2.595 -0.339 C4    8CP 4  
8CP C5    C3  C 0 1 N N N 8.650  7.634 11.789 6.464  -2.481 1.056  C5    8CP 5  
8CP C6    C4  C 0 1 N N N 7.299  7.590 11.573 5.676  -1.493 1.542  C6    8CP 6  
8CP O2    O1  O 0 1 N N N 7.102  8.621 8.256  4.700  0.005  -1.416 O2    8CP 7  
8CP N4    N3  N 0 1 N N N 10.804 7.974 10.852 7.428  -3.590 -0.860 N4    8CP 8  
8CP "C1'" C5  C 0 1 N N R 5.362  7.914 10.083 4.219  0.441  1.187  "C1'" 8CP 9  
8CP "C2'" C6  C 0 1 N N N 4.973  6.524 9.656  4.797  1.818  0.790  "C2'" 8CP 10 
8CP "C3'" C7  C 0 1 N N S 4.471  5.806 10.907 3.548  2.676  0.488  "C3'" 8CP 11 
8CP "C4'" C8  C 0 1 N N R 3.744  6.966 11.589 2.364  1.717  0.738  "C4'" 8CP 12 
8CP "O4'" O2  O 0 1 N N N 4.592  8.127 11.264 2.917  0.394  0.563  "O4'" 8CP 13 
8CP "O3'" O3  O 0 1 N N N 3.599  4.734 10.546 3.483  3.794  1.376  "O3'" 8CP 14 
8CP "C5'" C9  C 0 1 N N N 3.552  6.809 13.088 1.251  1.968  -0.282 "C5'" 8CP 15 
8CP "O5'" O4  O 0 1 N N N 4.816  6.649 13.661 0.121  1.154  0.036  "O5'" 8CP 16 
8CP PA    P1  P 0 1 N N N 5.074  5.498 14.787 -1.237 1.161  -0.830 PA    8CP 17 
8CP O1A   O5  O 0 1 N N N 6.430  5.702 15.412 -1.752 2.545  -0.928 O1A   8CP 18 
8CP O2A   O6  O 0 1 N N N 3.954  5.538 15.803 -0.934 0.595  -2.306 O2A   8CP 19 
8CP O3A   O7  O 0 1 N N N 5.073  4.086 13.975 -2.336 0.229  -0.112 O3A   8CP 20 
8CP PB    P2  P 0 1 N N N 3.919  3.021 13.784 -3.928 0.052  -0.272 PB    8CP 21 
8CP O1B   O8  O 0 1 N N N 2.604  3.456 14.231 -4.658 1.452  0.041  O1B   8CP 22 
8CP O2B   O9  O 0 1 N N N 3.845  2.607 12.329 -4.241 -0.369 -1.656 O2B   8CP 23 
8CP PG    P3  P 0 1 N N N 4.135  1.525 16.298 -6.137 -1.336 0.672  PG    8CP 24 
8CP O1G   O10 O 0 1 N N N 3.172  0.467 16.539 -6.826 -0.060 0.968  O1G   8CP 25 
8CP O2G   O11 O 0 1 N N N 5.483  1.173 16.976 -6.618 -2.461 1.719  O2G   8CP 26 
8CP O3G   O12 O 0 1 N N N 3.642  2.888 16.804 -6.497 -1.806 -0.825 O3G   8CP 27 
8CP N3B   N4  N 0 1 N N N 4.372  1.653 14.640 -4.473 -1.119 0.807  N3B   8CP 28 
8CP H1    H1  H 0 1 N N N 9.073  7.414 12.758 6.955  -3.171 1.726  H1    8CP 29 
8CP H2    H2  H 0 1 N N N 6.648  7.240 12.360 5.530  -1.385 2.607  H2    8CP 30 
8CP H3    H3  H 0 1 N N N 11.406 8.224 10.093 7.542  -3.667 -1.821 H3    8CP 31 
8CP H4    H4  H 0 1 N N N 11.194 7.719 11.737 7.873  -4.215 -0.268 H4    8CP 32 
8CP H5    H5  H 0 1 N N N 5.104  8.640 9.298  4.124  0.365  2.270  H5    8CP 33 
8CP H6    H6  H 0 1 N N N 4.176  6.569 8.899  5.364  2.246  1.617  H6    8CP 34 
8CP H7    H7  H 0 1 N N N 5.845  5.997 9.240  5.423  1.728  -0.098 H7    8CP 35 
8CP H8    H8  H 0 1 N N N 5.316  5.463 11.523 3.557  3.011  -0.549 H8    8CP 36 
8CP H9    H9  H 0 1 N N N 2.758  7.090 11.117 1.983  1.840  1.752  H9    8CP 37 
8CP H10   H10 H 0 1 N N N 3.699  4.021 11.166 4.234  4.398  1.304  H10   8CP 38 
8CP H11   H11 H 0 1 N N N 3.064  7.705 13.500 0.962  3.018  -0.253 H11   8CP 39 
8CP H12   H12 H 0 1 N N N 2.931  5.925 13.296 1.610  1.717  -1.280 H12   8CP 40 
8CP H13   H13 H 0 1 N N N 4.316  5.688 16.668 -0.593 -0.309 -2.319 H13   8CP 41 
8CP H14   H14 H 0 1 N N N 1.986  3.386 13.513 -4.496 1.789  0.933  H14   8CP 42 
8CP H15   H15 H 0 1 N N N 5.408  0.333 17.414 -7.569 -2.638 1.696  H15   8CP 43 
8CP H16   H16 H 0 1 N N N 2.780  2.790 17.190 -6.079 -2.637 -1.087 H16   8CP 44 
8CP H17   H17 H 0 1 N N N 3.879  0.887 14.226 -3.983 -1.991 0.673  H17   8CP 45 
# 
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 
8CP O2    C2    DOUB N N 1  
8CP C2    N3    SING N N 2  
8CP C2    N1    SING N N 3  
8CP N3    C4    DOUB N N 4  
8CP "C2'" "C1'" SING N N 5  
8CP "C2'" "C3'" SING N N 6  
8CP "C1'" N1    SING N N 7  
8CP "C1'" "O4'" SING N N 8  
8CP N1    C6    SING N N 9  
8CP "O3'" "C3'" SING N N 10 
8CP C4    N4    SING N N 11 
8CP C4    C5    SING N N 12 
8CP "C3'" "C4'" SING N N 13 
8CP "O4'" "C4'" SING N N 14 
8CP C6    C5    DOUB N N 15 
8CP "C4'" "C5'" SING N N 16 
8CP O2B   PB    DOUB N N 17 
8CP "C5'" "O5'" SING N N 18 
8CP "O5'" PA    SING N N 19 
8CP PB    O3A   SING N N 20 
8CP PB    O1B   SING N N 21 
8CP PB    N3B   SING N N 22 
8CP O3A   PA    SING N N 23 
8CP N3B   PG    SING N N 24 
8CP PA    O1A   DOUB N N 25 
8CP PA    O2A   SING N N 26 
8CP PG    O1G   DOUB N N 27 
8CP PG    O3G   SING N N 28 
8CP PG    O2G   SING N N 29 
8CP C5    H1    SING N N 30 
8CP C6    H2    SING N N 31 
8CP N4    H3    SING N N 32 
8CP N4    H4    SING N N 33 
8CP "C1'" H5    SING N N 34 
8CP "C2'" H6    SING N N 35 
8CP "C2'" H7    SING N N 36 
8CP "C3'" H8    SING N N 37 
8CP "C4'" H9    SING N N 38 
8CP "O3'" H10   SING N N 39 
8CP "C5'" H11   SING N N 40 
8CP "C5'" H12   SING N N 41 
8CP O2A   H13   SING N N 42 
8CP O1B   H14   SING N N 43 
8CP O2G   H15   SING N N 44 
8CP O3G   H16   SING N N 45 
8CP N3B   H17   SING N N 46 
# 
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 
8CP SMILES           ACDLabs              12.01 "N1(C=CC(=NC1=O)N)C2OC(C(C2)O)COP(=O)(O)OP(O)(NP(=O)(O)O)=O"                                                                                                                              
8CP InChI            InChI                1.03  "InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-28(21,22)25-27(19,20)12-26(16,17)18/h1-2,5-6,8,14H,3-4H2,(H,21,22)(H2,10,11,15)(H4,12,16,17,18,19,20)/t5-,6+,8+/m0/s1" 
8CP InChIKey         InChI                1.03  ICHPBSCTWPZUQK-SHYZEUOFSA-N                                                                                                                                                               
8CP SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2"                                                                                                           
8CP SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2"                                                                                                               
8CP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O"                                                                                                                   
8CP SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(NP(=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 
8CP "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine"                                                                            
8CP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic 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 
8CP "Create component" 2017-01-19 RCSB 
8CP "Initial release"  2017-07-26 RCSB 
# 
