data_XC5
# 
_chem_comp.id                                    XC5 
_chem_comp.name                                  "2'-deoxy-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 O12 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-03-06 
_chem_comp.pdbx_modified_date                    2017-05-05 
_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                        465.184 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XC5 
_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        5V1P 
_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 
XC5 PA    P1  P 0 1 N N N 55.950 6.099 14.952 1.177  -1.074 -0.507 PA    XC5 1  
XC5 O1A   O1  O 0 1 N N N 54.700 6.177 15.952 1.014  -0.300 -1.910 O1A   XC5 2  
XC5 O2A   O2  O 0 1 N N N 57.148 6.586 15.659 1.700  -2.437 -0.753 O2A   XC5 3  
XC5 C3A   C1  C 0 1 N N N 56.322 4.397 14.450 2.340  -0.161 0.559  C3A   XC5 4  
XC5 PB    P2  P 0 1 N N N 54.901 3.375 13.958 3.962  -0.049 -0.266 PB    XC5 5  
XC5 O1B   O3  O 0 1 N N N 54.989 3.035 12.507 3.812  0.662  -1.555 O1B   XC5 6  
XC5 O2B   O4  O 0 1 N N N 53.504 4.043 14.302 4.530  -1.532 -0.534 O2B   XC5 7  
XC5 O3B   O5  O 0 1 N N N 55.029 2.019 14.781 4.989  0.757  0.676  O3B   XC5 8  
XC5 PG    P3  P 0 1 N N N 54.950 1.881 16.365 6.534  1.187  0.534  PG    XC5 9  
XC5 O1G   O6  O 0 1 N N N 54.499 3.210 16.844 7.137  1.510  1.992  O1G   XC5 10 
XC5 O2G   O7  O 0 1 N N N 53.936 0.702 16.732 7.300  0.080  -0.082 O2G   XC5 11 
XC5 O3G   O8  O 0 1 N N N 56.397 1.555 16.951 6.644  2.498  -0.395 O3G   XC5 12 
XC5 N1    N1  N 0 1 N N N 57.598 8.283 10.392 -5.242 0.574  0.647  N1    XC5 13 
XC5 C2    C2  C 0 1 N N N 58.444 8.679 9.417  -5.299 0.898  -0.658 C2    XC5 14 
XC5 N3    N2  N 0 1 N N N 59.780 8.715 9.614  -6.021 1.935  -1.077 N3    XC5 15 
XC5 C4    C3  C 0 1 N N N 60.298 8.359 10.787 -6.705 2.677  -0.216 C4    XC5 16 
XC5 C5    C4  C 0 1 N N N 59.441 7.955 11.824 -6.667 2.363  1.158  C5    XC5 17 
XC5 C6    C5  C 0 1 N N N 58.094 7.919 11.602 -5.927 1.306  1.569  C6    XC5 18 
XC5 O2    O9  O 0 1 N N N 57.962 8.988 8.338  -4.679 0.231  -1.469 O2    XC5 19 
XC5 N4    N3  N 0 1 N N N 61.654 8.386 10.994 -7.448 3.746  -0.661 N4    XC5 20 
XC5 "C1'" C6  C 0 1 N N R 56.145 8.256 10.118 -4.443 -0.576 1.078  "C1'" XC5 21 
XC5 "C2'" C7  C 0 1 N N N 55.751 6.852 9.649  -4.981 -1.875 0.438  "C2'" XC5 22 
XC5 "C3'" C8  C 0 1 N N S 55.299 6.185 10.970 -3.710 -2.698 0.133  "C3'" XC5 23 
XC5 "C4'" C9  C 0 1 N N R 54.526 7.379 11.597 -2.554 -1.800 0.625  "C4'" XC5 24 
XC5 "O4'" O10 O 0 1 N N N 55.415 8.490 11.322 -3.089 -0.459 0.591  "O4'" XC5 25 
XC5 "O5'" O11 O 0 1 N N N 55.658 6.929 13.666 -0.255 -1.172 0.221  "O5'" XC5 26 
XC5 "C5'" C10 C 0 1 N N N 54.369 7.197 13.112 -1.351 -1.918 -0.313 "C5'" XC5 27 
XC5 "O3'" O12 O 0 1 N N N 54.474 5.035 10.690 -3.727 -3.932 0.854  "O3'" XC5 28 
XC5 H1    H1  H 0 1 N N N 54.986 6.519 16.791 0.675  0.601  -1.824 H1    XC5 29 
XC5 H2    H2  H 0 1 N N N 56.817 3.898 15.296 1.955  0.843  0.740  H2    XC5 30 
XC5 H3    H3  H 0 1 N N N 57.014 4.443 13.596 2.451  -0.684 1.508  H3    XC5 31 
XC5 H4    H4  H 0 1 N N N 52.978 4.103 13.513 4.654  -2.057 0.269  H4    XC5 32 
XC5 H5    H5  H 0 1 N N N 53.667 3.119 17.294 8.066  1.777  1.983  H5    XC5 33 
XC5 H6    H6  H 0 1 N N N 56.375 0.721 17.405 6.164  3.264  -0.051 H6    XC5 34 
XC5 H7    H7  H 0 1 N N N 59.843 7.676 12.787 -7.219 2.957  1.872  H7    XC5 35 
XC5 H8    H8  H 0 1 N N N 57.425 7.601 12.388 -5.882 1.046  2.616  H8    XC5 36 
XC5 H9    H9  H 0 1 N N N 62.266 8.676 10.258 -7.472 3.960  -1.607 H9    XC5 37 
XC5 H10   H10 H 0 1 N N N 62.030 8.116 11.880 -7.947 4.287  -0.029 H10   XC5 38 
XC5 H11   H11 H 0 1 N N N 55.885 8.993 9.344  -4.450 -0.656 2.165  H11   XC5 39 
XC5 H12   H12 H 0 1 N N N 54.929 6.891 8.919  -5.623 -2.409 1.138  H12   XC5 40 
XC5 H13   H13 H 0 1 N N N 56.608 6.323 9.207  -5.521 -1.652 -0.483 H13   XC5 41 
XC5 H14   H14 H 0 1 N N N 56.171 5.926 11.588 -3.621 -2.882 -0.938 H14   XC5 42 
XC5 H15   H15 H 0 1 N N N 53.546 7.502 11.113 -2.269 -2.070 1.642  H15   XC5 43 
XC5 H16   H16 H 0 1 N N N 53.956 8.115 13.556 -1.065 -2.965 -0.408 H16   XC5 44 
XC5 H17   H17 H 0 1 N N N 53.693 6.354 13.318 -1.615 -1.523 -1.294 H17   XC5 45 
XC5 H18   H18 H 0 1 N N N 54.659 4.350 11.322 -4.469 -4.510 0.627  H18   XC5 46 
# 
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 
XC5 O2    C2    DOUB N N 1  
XC5 C2    N3    SING N N 2  
XC5 C2    N1    SING N N 3  
XC5 N3    C4    DOUB N N 4  
XC5 "C2'" "C1'" SING N N 5  
XC5 "C2'" "C3'" SING N N 6  
XC5 "C1'" N1    SING N N 7  
XC5 "C1'" "O4'" SING N N 8  
XC5 N1    C6    SING N N 9  
XC5 "O3'" "C3'" SING N N 10 
XC5 C4    N4    SING N N 11 
XC5 C4    C5    SING N N 12 
XC5 "C3'" "C4'" SING N N 13 
XC5 "O4'" "C4'" SING N N 14 
XC5 "C4'" "C5'" SING N N 15 
XC5 C6    C5    DOUB N N 16 
XC5 O1B   PB    DOUB N N 17 
XC5 "C5'" "O5'" SING N N 18 
XC5 "O5'" PA    SING N N 19 
XC5 PB    O2B   SING N N 20 
XC5 PB    C3A   SING N N 21 
XC5 PB    O3B   SING N N 22 
XC5 C3A   PA    SING N N 23 
XC5 O3B   PG    SING N N 24 
XC5 PA    O2A   DOUB N N 25 
XC5 PA    O1A   SING N N 26 
XC5 PG    O2G   DOUB N N 27 
XC5 PG    O1G   SING N N 28 
XC5 PG    O3G   SING N N 29 
XC5 O1A   H1    SING N N 30 
XC5 C3A   H2    SING N N 31 
XC5 C3A   H3    SING N N 32 
XC5 O2B   H4    SING N N 33 
XC5 O1G   H5    SING N N 34 
XC5 O3G   H6    SING N N 35 
XC5 C5    H7    SING N N 36 
XC5 C6    H8    SING N N 37 
XC5 N4    H9    SING N N 38 
XC5 N4    H10   SING N N 39 
XC5 "C1'" H11   SING N N 40 
XC5 "C2'" H12   SING N N 41 
XC5 "C2'" H13   SING N N 42 
XC5 "C3'" H14   SING N N 43 
XC5 "C4'" H15   SING N N 44 
XC5 "C5'" H16   SING N N 45 
XC5 "C5'" H17   SING N N 46 
XC5 "O3'" H18   SING N N 47 
# 
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 
XC5 SMILES           ACDLabs              12.01 "P(=O)(O)(CP(O)(OP(=O)(O)O)=O)OCC2C(CC(N1C=CC(=NC1=O)N)O2)O"                                                                                                                               
XC5 InChI            InChI                1.03  "InChI=1S/C10H18N3O12P3/c11-8-1-2-13(10(15)12-8)9-3-6(14)7(24-9)4-23-26(16,17)5-27(18,19)25-28(20,21)22/h1-2,6-7,9,14H,3-5H2,(H,16,17)(H,18,19)(H2,11,12,15)(H2,20,21,22)/t6-,7+,9+/m0/s1" 
XC5 InChIKey         InChI                1.03  YSCOIIOUWFAHFY-LKEWCRSYSA-N                                                                                                                                                                
XC5 SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                            
XC5 SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                                
XC5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                    
XC5 SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=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 
XC5 "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine"                                                                
XC5 "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(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 
XC5 "Create component" 2017-03-06 RCSB 
XC5 "Initial release"  2017-05-10 RCSB 
# 
