data_8NI
# 
_chem_comp.id                                    8NI 
_chem_comp.name                                  "N-[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H16 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-09-22 
_chem_comp.pdbx_modified_date                    2022-07-29 
_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                        365.237 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8NI 
_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        7S9Q 
_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 
8NI C5    C1  C 0 1 N N S 13.638 9.828  2.108  3.629  0.037  -0.502 C5    8NI 1  
8NI C4    C2  C 0 1 N N N 14.966 9.509  2.209  2.407  0.452  0.296  C4    8NI 2  
8NI N2    N1  N 0 1 N N N 15.096 8.107  5.577  3.103  -1.060 3.417  N2    8NI 3  
8NI N7    N2  N 0 1 N N N 13.038 10.440 0.931  3.176  -0.714 -1.675 N7    8NI 4  
8NI C8    C3  C 0 1 N N N 12.096 9.708  0.100  3.946  -0.766 -2.780 C8    8NI 5  
8NI "C1'" C4  C 0 1 N N R 15.647 10.318 -0.095 0.265  1.592  0.540  "C1'" 8NI 6  
8NI C2    C5  C 0 1 N N N 14.591 8.712  4.358  3.283  -0.696 2.110  C2    8NI 7  
8NI "C2'" C6  C 0 1 N N N 16.749 11.260 -0.528 -0.205 3.002  0.133  "C2'" 8NI 8  
8NI "C3'" C7  C 0 1 N N S 16.709 11.102 -2.005 -1.670 2.797  -0.324 "C3'" 8NI 9  
8NI "C4'" C8  C 0 1 N N R 16.209 9.722  -2.274 -2.040 1.459  0.365  "C4'" 8NI 10 
8NI "C5'" C9  C 0 1 N N N 17.365 8.787  -2.593 -3.173 0.760  -0.389 "C5'" 8NI 11 
8NI C6    C10 C 0 1 N N N 12.816 9.576  3.156  4.649  -0.811 0.237  C6    8NI 12 
8NI N1    N3  N 0 1 N N N 13.287 9.031  4.258  4.383  -1.112 1.508  N1    8NI 13 
8NI N3    N4  N 0 1 N N N 15.418 8.959  3.324  2.333  0.049  1.545  N3    8NI 14 
8NI N9    N5  N 0 1 N N N 15.952 9.731  1.161  1.433  1.207  -0.256 N9    8NI 15 
8NI "O3'" O1  O 0 1 N N N 15.734 11.992 -2.529 -2.504 3.859  0.143  "O3'" 8NI 16 
8NI "O4'" O2  O 0 1 N N N 15.542 9.288  -1.097 -0.821 0.686  0.285  "O4'" 8NI 17 
8NI "O5'" O3  O 0 1 N N N 18.261 8.767  -1.522 -3.574 -0.409 0.329  "O5'" 8NI 18 
8NI O6    O4  O 0 1 N N N 11.666 9.850  3.087  5.664  -1.198 -0.307 O6    8NI 19 
8NI O8    O5  O 0 1 N N N 11.619 10.231 -0.852 5.014  -0.192 -2.803 O8    8NI 20 
8NI OP1   O6  O 0 1 N N N 20.181 7.587  -0.015 -5.983 -0.609 -0.394 OP1   8NI 21 
8NI OP2   O7  O 0 1 N N N 18.282 6.085  -1.184 -4.302 -2.090 -1.556 OP2   8NI 22 
8NI P     P1  P 0 1 N N N 19.210 7.438  -1.339 -4.746 -1.390 -0.176 P     8NI 23 
8NI H1    H1  H 0 1 N N N 13.427 8.829  1.699  4.128  0.939  -0.854 H1    8NI 24 
8NI H2    H2  H 0 1 N N N 16.065 7.870  5.654  3.771  -1.603 3.865  H2    8NI 25 
8NI H3    H3  H 0 1 N N N 14.475 7.927  6.340  2.309  -0.775 3.895  H3    8NI 26 
8NI H4    H4  H 0 1 N N N 13.278 11.380 0.690  2.321  -1.173 -1.657 H4    8NI 27 
8NI H5    H5  H 0 1 N N N 11.831 8.691  0.349  3.611  -1.319 -3.645 H5    8NI 28 
8NI H6    H6  H 0 1 N N N 14.702 10.878 -0.033 0.518  1.578  1.600  H6    8NI 29 
8NI H7    H7  H 0 1 N N N 17.723 10.955 -0.117 -0.163 3.680  0.986  H7    8NI 30 
8NI H8    H8  H 0 1 N N N 16.533 12.296 -0.229 0.402  3.385  -0.687 H8    8NI 31 
8NI H9    H9  H 0 1 N N N 17.702 11.260 -2.451 -1.730 2.705  -1.408 H9    8NI 32 
8NI H10   H10 H 0 1 N N N 15.515 9.742  -3.127 -2.318 1.627  1.406  H10   8NI 33 
8NI H11   H11 H 0 1 N N N 16.978 7.772  -2.765 -4.021 1.438  -0.481 H11   8NI 34 
8NI H12   H12 H 0 1 N N N 17.883 9.140  -3.497 -2.827 0.474  -1.382 H12   8NI 35 
8NI H13   H13 H 0 1 N N N 16.897 9.454  1.336  1.507  1.495  -1.179 H13   8NI 36 
8NI H14   H14 H 0 1 N Y N 16.011 12.889 -2.380 -2.253 4.731  -0.192 H14   8NI 37 
8NI H16   H16 H 0 1 N N N 18.486 5.653  -0.363 -3.496 -2.620 -1.487 H16   8NI 38 
8NI OP3   O8  O 0 1 N Y N 20.040 7.351  -2.717 -5.016 -2.522 0.937  O1    8NI 39 
8NI H15   H15 H 0 1 N N N 20.970 7.401  -2.531 -5.711 -3.150 0.699  H15   8NI 40 
# 
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 
8NI "C5'" "C4'" SING N N 1  
8NI "C5'" "O5'" SING N N 2  
8NI "O3'" "C3'" SING N N 3  
8NI "C4'" "C3'" SING N N 4  
8NI "C4'" "O4'" SING N N 5  
8NI "C3'" "C2'" SING N N 6  
8NI "O5'" P     SING N N 7  
8NI P     OP2   SING N N 8  
8NI P     OP1   DOUB N N 9  
8NI "O4'" "C1'" SING N N 10 
8NI O8    C8    DOUB N N 11 
8NI "C2'" "C1'" SING N N 12 
8NI "C1'" N9    SING N N 13 
8NI C8    N7    SING N N 14 
8NI N7    C5    SING N N 15 
8NI N9    C4    SING N N 16 
8NI C5    C4    SING N N 17 
8NI C5    C6    SING N N 18 
8NI C4    N3    DOUB N N 19 
8NI O6    C6    DOUB N N 20 
8NI C6    N1    SING N N 21 
8NI N3    C2    SING N N 22 
8NI N1    C2    DOUB N N 23 
8NI C2    N2    SING N N 24 
8NI C5    H1    SING N N 25 
8NI N2    H2    SING N N 26 
8NI N2    H3    SING N N 27 
8NI N7    H4    SING N N 28 
8NI C8    H5    SING N N 29 
8NI "C1'" H6    SING N N 30 
8NI "C2'" H7    SING N N 31 
8NI "C2'" H8    SING N N 32 
8NI "C3'" H9    SING N N 33 
8NI "C4'" H10   SING N N 34 
8NI "C5'" H11   SING N N 35 
8NI "C5'" H12   SING N N 36 
8NI N9    H13   SING N N 37 
8NI "O3'" H14   SING N N 38 
8NI OP2   H16   SING N N 39 
8NI P     OP3   SING N N 40 
8NI OP3   H15   SING N N 41 
# 
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 
8NI SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(NC2=NC(N)=NC(=O)C2NC=O)CC1O"                                                                                                                           
8NI InChI            InChI                1.03  "InChI=1S/C10H16N5O8P/c11-10-14-8(7(12-3-16)9(18)15-10)13-6-1-4(17)5(23-6)2-22-24(19,20)21/h3-7,17H,1-2H2,(H,12,16)(H2,19,20,21)(H3,11,13,14,15,18)/t4-,5+,6+,7-/m0/s1" 
8NI InChIKey         InChI                1.03  WCQYTGCUHURFQH-WNJXEPBRSA-N                                                                                                                                             
8NI SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)[C@@H](NC=O)C(=N1)N[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"                                                                                                   
8NI SMILES           CACTVS               3.385 "NC1=NC(=O)[CH](NC=O)C(=N1)N[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"                                                                                                         
8NI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1NC2=NC(=NC(=O)C2NC=O)N)COP(=O)(O)O)O"                                                                                                            
8NI SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1NC2=NC(=NC(=O)C2NC=O)N)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 
8NI "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine"                        
8NI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-[(2-azanyl-5-formamido-6-oxidanylidene-5~{H}-pyrimidin-4-yl)amino]-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 
8NI "Create component" 2021-09-22 RCSB 
8NI "Initial release"  2022-08-03 RCSB 
# 
