data_I2T
# 
_chem_comp.id                                    I2T 
_chem_comp.name                                  "(2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N3 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-02-09 
_chem_comp.pdbx_modified_date                    2022-08-22 
_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                        439.312 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I2T 
_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        7QIZ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
I2T "O5'"  O1  O 0 1 N N N 292.317 241.415 237.063 3.751  0.693  0.649  "O5'"  I2T 1  
I2T "C5'"  C1  C 0 1 N N N 291.993 242.692 236.532 3.248  0.127  -0.563 "C5'"  I2T 2  
I2T "C4'"  C2  C 0 1 N N R 291.597 243.654 237.623 2.724  -1.284 -0.289 "C4'"  I2T 3  
I2T "O4'"  O2  O 0 1 N N N 290.402 243.172 238.290 1.565  -1.237 0.571  "O4'"  I2T 4  
I2T "C3'"  C3  C 0 1 N N S 292.605 243.841 238.747 2.183  -1.928 -1.590 "C3'"  I2T 5  
I2T "O3'"  O3  O 0 1 N N N 293.618 244.775 238.413 3.234  -2.567 -2.318 "O3'"  I2T 6  
I2T "C2'"  C4  C 0 1 N N R 291.728 244.290 239.909 1.178  -2.970 -1.043 "C2'"  I2T 7  
I2T "O2'"  O4  O 0 1 N N N 291.405 245.669 239.805 1.778  -4.266 -0.991 "O2'"  I2T 8  
I2T "C1'"  C5  C 0 1 N N S 290.461 243.470 239.668 0.848  -2.468 0.376  "C1'"  I2T 9  
I2T C5     C6  C 0 1 N N N 290.396 242.196 240.451 -0.634 -2.224 0.502  C5     I2T 10 
I2T C6     C7  C 0 1 N N N 290.500 240.977 239.885 -1.377 -2.953 1.361  C6     I2T 11 
I2T N1     N1  N 0 1 N N N 290.390 239.811 240.585 -2.721 -2.718 1.463  N1     I2T 12 
I2T C2     C8  C 0 1 N N N 290.162 239.802 241.942 -3.309 -1.767 0.715  C2     I2T 13 
I2T N3     N2  N 0 1 N N N 290.055 241.042 242.548 -2.592 -1.025 -0.150 N3     I2T 14 
I2T C4     C9  C 0 1 N N N 290.164 242.266 241.889 -1.264 -1.222 -0.275 C4     I2T 15 
I2T C34    C10 C 0 1 N N N 288.929 241.240 246.749 -4.025 3.684  -0.239 C34    I2T 16 
I2T CN1    C11 C 0 1 N N N 290.506 238.522 239.908 -3.527 -3.510 2.395  CN1    I2T 17 
I2T N34    N3  N 0 1 N N N 286.755 242.194 246.073 -3.158 2.649  -2.259 N34    I2T 18 
I2T O2     O5  O 0 1 N N N 290.058 238.763 242.567 -4.505 -1.575 0.821  O2     I2T 19 
I2T O4     O6  O 0 1 N N N 290.077 243.314 242.516 -0.614 -0.547 -1.053 O4     I2T 20 
I2T OP1    O7  O 0 1 N N N 290.572 239.863 236.230 5.478  2.295  -0.257 OP1    I2T 21 
I2T OP2    O8  O 0 1 N N N 292.935 239.027 236.731 3.242  3.260  0.405  OP2    I2T 22 
I2T P      P1  P 0 1 N N N 292.033 240.087 236.232 4.383  2.171  0.730  P      I2T 23 
I2T C31    C12 C 0 1 N N N 289.780 241.074 243.990 -3.256 0.004  -0.953 C31    I2T 24 
I2T C32    C13 C 0 1 N N N 288.447 241.733 244.319 -3.239 1.333  -0.195 C32    I2T 25 
I2T C33    C14 C 0 1 N N S 287.855 241.281 245.656 -3.933 2.408  -1.034 C33    I2T 26 
I2T O36    O9  O 0 1 N N N 289.162 242.299 247.369 -4.989 3.831  0.685  O36    I2T 27 
I2T O35    O10 O 0 1 N N N 289.496 240.137 246.945 -3.233 4.575  -0.432 O35    I2T 28 
I2T OP3    O11 O 0 1 N Y N 292.471 240.470 234.734 4.962  2.427  2.211  OP3    I2T 29 
I2T "H5'"  H1  H 0 1 N N N 292.870 243.093 236.002 2.438  0.748  -0.945 "H5'"  I2T 30 
I2T "H5''" H2  H 0 0 N N N 291.155 242.585 235.827 4.049  0.080  -1.302 "H5''" I2T 31 
I2T "H4'"  H3  H 0 1 N N N 291.393 244.636 237.170 3.505  -1.903 0.153  "H4'"  I2T 32 
I2T "H3'"  H4  H 0 1 N N N 293.050 242.866 238.993 1.678  -1.188 -2.210 "H3'"  I2T 33 
I2T H1     H5  H 0 1 N N N 294.223 244.860 239.140 2.945  -2.986 -3.141 H1     I2T 34 
I2T "H2'"  H6  H 0 1 N N N 292.187 244.033 240.875 0.278  -2.992 -1.658 "H2'"  I2T 35 
I2T "HO2'" H7  H 0 0 N N N 290.859 245.923 240.540 2.057  -4.605 -1.852 "HO2'" I2T 36 
I2T "H1'"  H8  H 0 1 N N N 289.597 244.092 239.946 1.168  -3.204 1.113  "H1'"  I2T 37 
I2T H6     H9  H 0 1 N N N 290.680 240.920 238.822 -0.913 -3.719 1.965  H6     I2T 38 
I2T H12    H10 H 0 1 N N N 290.389 237.710 240.641 -3.551 -3.016 3.366  H12    I2T 39 
I2T H10    H11 H 0 1 N N N 289.722 238.439 239.141 -4.543 -3.602 2.010  H10    I2T 40 
I2T H11    H12 H 0 1 N N N 291.494 238.446 239.431 -3.089 -4.502 2.503  H11    I2T 41 
I2T H13    H13 H 0 1 N N N 286.379 241.886 246.947 -3.629 3.308  -2.861 H13    I2T 42 
I2T H15    H14 H 0 1 N N N 287.112 243.123 246.173 -2.224 2.962  -2.040 H15    I2T 43 
I2T H2     H16 H 0 1 N N N 292.421 238.278 237.009 2.491  3.237  1.014  H2     I2T 44 
I2T H18    H17 H 0 1 N N N 289.765 240.041 244.369 -2.731 0.120  -1.901 H18    I2T 45 
I2T H19    H18 H 0 1 N N N 290.583 241.636 244.489 -4.288 -0.293 -1.143 H19    I2T 46 
I2T H21    H19 H 0 1 N N N 288.597 242.822 244.355 -3.764 1.217  0.753  H21    I2T 47 
I2T H20    H20 H 0 1 N N N 287.731 241.488 243.521 -2.208 1.629  -0.005 H20    I2T 48 
I2T H22    H21 H 0 1 N N N 287.449 240.266 245.531 -4.935 2.071  -1.299 H22    I2T 49 
I2T H3     H22 H 0 1 N N N 289.839 242.144 248.018 -5.008 4.667  1.170  H3     I2T 50 
I2T H4     H23 H 0 1 N N N 291.706 240.471 234.170 5.359  3.300  2.332  H4     I2T 51 
# 
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 
I2T OP1   P      DOUB N N 1  
I2T P     OP2    SING N N 2  
I2T P     "O5'"  SING N N 3  
I2T "C5'" "O5'"  SING N N 4  
I2T "C5'" "C4'"  SING N N 5  
I2T "C4'" "O4'"  SING N N 6  
I2T "C4'" "C3'"  SING N N 7  
I2T "O4'" "C1'"  SING N N 8  
I2T "O3'" "C3'"  SING N N 9  
I2T "C3'" "C2'"  SING N N 10 
I2T "C1'" "C2'"  SING N N 11 
I2T "C1'" C5     SING N N 12 
I2T "O2'" "C2'"  SING N N 13 
I2T C6    C5     DOUB N N 14 
I2T C6    N1     SING N N 15 
I2T CN1   N1     SING N N 16 
I2T C5    C4     SING N N 17 
I2T N1    C2     SING N N 18 
I2T C4    O4     DOUB N N 19 
I2T C4    N3     SING N N 20 
I2T C2    N3     SING N N 21 
I2T C2    O2     DOUB N N 22 
I2T N3    C31    SING N N 23 
I2T C31   C32    SING N N 24 
I2T C32   C33    SING N N 25 
I2T C33   N34    SING N N 26 
I2T C33   C34    SING N N 27 
I2T C34   O35    DOUB N N 28 
I2T C34   O36    SING N N 29 
I2T P     OP3    SING N N 30 
I2T "C5'" "H5'"  SING N N 31 
I2T "C5'" "H5''" SING N N 32 
I2T "C4'" "H4'"  SING N N 33 
I2T "C3'" "H3'"  SING N N 34 
I2T "O3'" H1     SING N N 35 
I2T "C2'" "H2'"  SING N N 36 
I2T "O2'" "HO2'" SING N N 37 
I2T "C1'" "H1'"  SING N N 38 
I2T C6    H6     SING N N 39 
I2T CN1   H12    SING N N 40 
I2T CN1   H10    SING N N 41 
I2T CN1   H11    SING N N 42 
I2T N34   H13    SING N N 43 
I2T N34   H15    SING N N 44 
I2T OP2   H2     SING N N 45 
I2T C31   H18    SING N N 46 
I2T C31   H19    SING N N 47 
I2T C32   H21    SING N N 48 
I2T C32   H20    SING N N 49 
I2T C33   H22    SING N N 50 
I2T O36   H3     SING N N 51 
I2T OP3   H4     SING N N 52 
# 
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 
I2T InChI            InChI                1.06  "InChI=1S/C14H22N3O11P/c1-16-4-6(12(20)17(14(16)23)3-2-7(15)13(21)22)11-10(19)9(18)8(28-11)5-27-29(24,25)26/h4,7-11,18-19H,2-3,5,15H2,1H3,(H,21,22)(H2,24,25,26)/t7-,8+,9+,10+,11-/m0/s1" 
I2T InChIKey         InChI                1.06  BVRIEBGMUPJSJF-LXUNUROVSA-N                                                                                                                                                               
I2T SMILES_CANONICAL CACTVS               3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N(CC[C@H](N)C(O)=O)C1=O"                                                                                                        
I2T SMILES           CACTVS               3.385 "CN1C=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N(CC[CH](N)C(O)=O)C1=O"                                                                                                               
I2T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=O)N(C1=O)CC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                       
I2T SMILES           "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           I2T 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic 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 
I2T "Create component"  2022-02-09 PDBE 
I2T "Initial release"   2022-06-15 RCSB 
I2T "Modify descriptor" 2022-08-22 RCSB 
# 
