data_HN1
# 
_chem_comp.id                                    HN1 
_chem_comp.name                                  "(6S,8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-6-[(1S)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C19 H30 N5 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-08-12 
_chem_comp.pdbx_modified_date                    2012-02-10 
_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                        503.443 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     HN1 
_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        3T5H 
_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 
HN1 C      C      C 0 1 N N N -17.164 32.769 10.953 -5.088 -2.267 0.303  C      HN1 1  
HN1 P      P      P 0 1 N N N -6.274  36.888 14.824 7.495  0.549  -0.353 P      HN1 2  
HN1 C1     C1     C 0 1 N N R -15.907 32.069 11.052 -4.072 -3.302 -0.185 C1     HN1 3  
HN1 N1     N1     N 0 1 N N N -14.756 32.727 11.797 -2.736 -2.698 -0.129 N1     HN1 4  
HN1 C2     C2     C 0 1 N N N -14.932 34.011 12.329 -2.563 -1.421 -0.617 C2     HN1 5  
HN1 N2     N2     N 0 1 N N N -16.067 34.656 12.194 -3.583 -0.646 -0.814 N2     HN1 6  
HN1 C3     C3     C 0 1 N N S -17.205 34.271 11.361 -4.959 -0.980 -0.501 C3     HN1 7  
HN1 N3     N3     N 0 1 N N N -14.009 34.703 13.007 -1.294 -0.927 -0.887 N3     HN1 8  
HN1 C4     C4     C 0 1 Y N N -12.817 34.042 13.164 -0.253 -1.473 -0.162 C4     HN1 9  
HN1 C5     C5     C 0 1 Y N N -12.480 32.785 12.701 -0.421 -2.704 0.488  C5     HN1 10 
HN1 C6     C6     C 0 1 N N N -13.488 32.039 11.957 -1.709 -3.401 0.413  C6     HN1 11 
HN1 O6     O6     O 0 1 N N N -13.326 30.907 11.485 -1.849 -4.542 0.813  O6     HN1 12 
HN1 C7     C7     C 0 1 N N S -18.509 34.665 12.128 -5.575 0.167  0.302  C7     HN1 13 
HN1 N7     N7     N 0 1 Y N N -11.159 32.482 13.077 0.737  -2.998 1.098  N7     HN1 14 
HN1 C8     C8     C 0 1 Y N N -10.771 33.551 13.736 1.591  -2.035 0.874  C8     HN1 15 
HN1 C9     C9     C 0 1 N N N -19.735 34.760 11.177 -5.454 1.469  -0.493 C9     HN1 16 
HN1 N9     N9     N 0 1 Y N N -11.727 34.530 13.820 1.004  -1.072 0.097  N9     HN1 17 
HN1 "C1'"  "C1'"  C 0 1 N N R -11.645 35.846 14.476 1.631  0.167  -0.368 "C1'"  HN1 18 
HN1 C10    C10    C 0 1 N N N -20.880 35.693 11.652 -6.179 2.591  0.252  C10    HN1 19 
HN1 O10    O10    O 0 1 N N N -18.311 35.959 12.771 -4.884 0.303  1.546  O10    HN1 20 
HN1 C11    C11    C 0 1 N N N -21.576 35.200 12.945 -6.057 3.893  -0.543 C11    HN1 21 
HN1 O11    O11    O 0 1 N N N -15.496 31.755 9.728  -4.375 -3.677 -1.530 O11    HN1 22 
HN1 C12    C12    C 0 1 N N N -23.095 34.997 12.765 -6.782 5.015  0.203  C12    HN1 23 
HN1 C13    C13    C 0 1 N N N -23.755 34.263 13.944 -6.661 6.317  -0.592 C13    HN1 24 
HN1 OP1    O1P    O 0 1 N N N -5.754  38.228 15.204 7.706  -0.462 0.706  OP1    HN1 25 
HN1 "C2'"  "C2'"  C 0 1 N N N -11.623 35.790 16.003 1.289  1.321  0.594  "C2'"  HN1 26 
HN1 OP3    OP3    O 0 1 N Y N -5.556  35.659 15.264 8.140  0.025  -1.732 OP3    HN1 27 
HN1 "C3'"  "C3'"  C 0 1 N N S -10.536 36.781 16.391 2.667  1.829  1.083  "C3'"  HN1 28 
HN1 "O3'"  "O3'"  O 0 1 N N N -10.966 37.792 17.302 2.691  3.257  1.146  "O3'"  HN1 29 
HN1 "C4'"  "C4'"  C 0 1 N N R -10.123 37.421 15.072 3.617  1.309  -0.026 "C4'"  HN1 30 
HN1 "O4'"  "O4'"  O 0 1 N N N -10.423 36.430 14.078 3.061  0.021  -0.369 "O4'"  HN1 31 
HN1 "C5'"  "C5'"  C 0 1 N N N -8.681  37.850 15.003 5.042  1.160  0.511  "C5'"  HN1 32 
HN1 "O5'"  "O5'"  O 0 1 N N N -7.800  36.775 15.304 5.917  0.792  -0.557 "O5'"  HN1 33 
HN1 OP2    O2P    O 0 1 N N N -6.290  36.561 13.135 8.200  1.932  0.076  OP2    HN1 34 
HN1 H      H      H 0 1 N N N -17.469 32.721 9.897  -6.095 -2.666 0.186  H      HN1 35 
HN1 HA     HA     H 0 1 N N N -17.870 32.244 11.613 -4.907 -2.053 1.357  HA     HN1 36 
HN1 H31    H31    H 0 1 N N N -16.125 31.199 11.689 -4.105 -4.181 0.458  H31    HN1 37 
HN1 H3     H3     H 0 1 N N N -17.170 34.810 10.403 -5.514 -1.092 -1.433 H3     HN1 38 
HN1 HN3    HN3    H 0 1 N N N -14.174 35.621 13.368 -1.145 -0.235 -1.550 HN3    HN1 39 
HN1 H7     H7     H 0 1 N N N -18.713 33.881 12.872 -6.627 -0.046 0.492  H7     HN1 40 
HN1 H8     H8     H 0 1 N N N -9.788  33.649 14.172 2.605  -2.004 1.244  H8     HN1 41 
HN1 H9     H9     H 0 1 N N N -19.375 35.144 10.211 -4.401 1.729  -0.607 H9     HN1 42 
HN1 H9A    H9A    H 0 1 N N N -20.154 33.748 11.075 -5.903 1.337  -1.477 H9A    HN1 43 
HN1 "H1'"  "H1'"  H 0 1 N N N -12.543 36.409 14.180 1.281  0.406  -1.372 "H1'"  HN1 44 
HN1 H10    H10    H 0 1 N N N -20.454 36.688 11.849 -7.231 2.331  0.366  H10    HN1 45 
HN1 H10A   H10A   H 0 0 N N N -21.635 35.745 10.854 -5.729 2.723  1.236  H10A   HN1 46 
HN1 HO10   HO10   H 0 0 N N N -19.100 36.205 13.239 -3.941 0.493  1.453  HO10   HN1 47 
HN1 H11    H11    H 0 1 N N N -21.129 34.237 13.234 -5.005 4.152  -0.656 H11    HN1 48 
HN1 H11A   H11A   H 0 0 N N N -21.417 35.951 13.733 -6.507 3.760  -1.527 H11A   HN1 49 
HN1 H16    H16    H 0 1 N N N -14.634 31.356 9.750  -3.769 -4.332 -1.902 H16    HN1 50 
HN1 H12    H12    H 0 1 N N N -23.565 35.987 12.670 -7.835 4.755  0.316  H12    HN1 51 
HN1 H12A   H12A   H 0 0 N N N -23.257 34.401 11.855 -6.333 5.147  1.187  H12A   HN1 52 
HN1 H13    H13    H 0 1 N N N -24.832 34.153 13.751 -7.178 7.116  -0.061 H13    HN1 53 
HN1 H13A   H13A   H 0 0 N N N -23.299 33.268 14.058 -5.609 6.576  -0.706 H13A   HN1 54 
HN1 H13B   H13B   H 0 0 N N N -23.605 34.843 14.867 -7.111 6.184  -1.576 H13B   HN1 55 
HN1 HOP3   HOP3   H 0 0 N Y N -4.793  35.903 15.774 9.091  -0.143 -1.683 HOP3   HN1 56 
HN1 "H2'"  "H2'"  H 0 1 N N N -12.596 36.076 16.428 0.755  2.112  0.068  "H2'"  HN1 57 
HN1 "H2'A" "H2'A" H 0 0 N N N -11.389 34.777 16.363 0.698  0.954  1.434  "H2'A" HN1 58 
HN1 "H3'"  "H3'"  H 0 1 N N N -9.723  36.260 16.918 2.922  1.395  2.049  "H3'"  HN1 59 
HN1 "HO3'" "HO3'" H 0 0 N Y N -10.239 38.372 17.499 2.048  3.634  1.763  "HO3'" HN1 60 
HN1 "H4'"  "H4'"  H 0 1 N N N -10.669 38.365 14.926 3.601  1.975  -0.889 "H4'"  HN1 61 
HN1 "H5'"  "H5'"  H 0 1 N N N -8.467  38.209 13.985 5.369  2.107  0.939  "H5'"  HN1 62 
HN1 "H5'A" "H5'A" H 0 0 N N N -8.517  38.657 15.732 5.061  0.387  1.279  "H5'A" HN1 63 
HN1 HOP2   HO2P   H 0 0 N N N -5.951  37.313 12.663 8.102  2.642  -0.573 HOP2   HN1 64 
# 
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 
HN1 C     C1     SING N N 1  
HN1 C     C3     SING N N 2  
HN1 P     OP1    DOUB N N 3  
HN1 P     OP3    SING N N 4  
HN1 P     "O5'"  SING N N 5  
HN1 C1    N1     SING N N 6  
HN1 N1    C6     SING N N 7  
HN1 N1    C2     SING N N 8  
HN1 C2    N3     SING N N 9  
HN1 N2    C2     DOUB N N 10 
HN1 C3    N2     SING N N 11 
HN1 C3    C7     SING N N 12 
HN1 N3    C4     SING N N 13 
HN1 C4    N9     SING Y N 14 
HN1 C5    C4     DOUB Y N 15 
HN1 C5    N7     SING Y N 16 
HN1 C6    C5     SING N N 17 
HN1 O6    C6     DOUB N N 18 
HN1 C7    O10    SING N N 19 
HN1 N7    C8     DOUB Y N 20 
HN1 C8    N9     SING Y N 21 
HN1 C9    C7     SING N N 22 
HN1 C9    C10    SING N N 23 
HN1 N9    "C1'"  SING N N 24 
HN1 "C1'" "C2'"  SING N N 25 
HN1 C10   C11    SING N N 26 
HN1 O11   C1     SING N N 27 
HN1 C12   C11    SING N N 28 
HN1 C12   C13    SING N N 29 
HN1 "C2'" "C3'"  SING N N 30 
HN1 "C3'" "O3'"  SING N N 31 
HN1 "C4'" "C3'"  SING N N 32 
HN1 "O4'" "C1'"  SING N N 33 
HN1 "O4'" "C4'"  SING N N 34 
HN1 "C5'" "C4'"  SING N N 35 
HN1 "C5'" "O5'"  SING N N 36 
HN1 P     OP2    SING N N 37 
HN1 C     H      SING N N 38 
HN1 C     HA     SING N N 39 
HN1 C1    H31    SING N N 40 
HN1 C3    H3     SING N N 41 
HN1 N3    HN3    SING N N 42 
HN1 C7    H7     SING N N 43 
HN1 C8    H8     SING N N 44 
HN1 C9    H9     SING N N 45 
HN1 C9    H9A    SING N N 46 
HN1 "C1'" "H1'"  SING N N 47 
HN1 C10   H10    SING N N 48 
HN1 C10   H10A   SING N N 49 
HN1 O10   HO10   SING N N 50 
HN1 C11   H11    SING N N 51 
HN1 C11   H11A   SING N N 52 
HN1 O11   H16    SING N N 53 
HN1 C12   H12    SING N N 54 
HN1 C12   H12A   SING N N 55 
HN1 C13   H13    SING N N 56 
HN1 C13   H13A   SING N N 57 
HN1 C13   H13B   SING N N 58 
HN1 OP3   HOP3   SING N N 59 
HN1 "C2'" "H2'"  SING N N 60 
HN1 "C2'" "H2'A" SING N N 61 
HN1 "C3'" "H3'"  SING N N 62 
HN1 "O3'" "HO3'" SING N N 63 
HN1 "C4'" "H4'"  SING N N 64 
HN1 "C5'" "H5'"  SING N N 65 
HN1 "C5'" "H5'A" SING N N 66 
HN1 OP2   HOP2   SING N N 67 
# 
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 
HN1 SMILES           ACDLabs              12.01 "O=P(O)(O)OCC4OC(n1cnc3c1NC2=NC(C(O)CCCCC)CC(O)N2C3=O)CC4O"                                                                                                                                                   
HN1 InChI            InChI                1.03  "InChI=1S/C19H30N5O9P/c1-2-3-4-5-11(25)10-6-14(27)24-18(28)16-17(22-19(24)21-10)23(9-20-16)15-7-12(26)13(33-15)8-32-34(29,30)31/h9-15,25-27H,2-8H2,1H3,(H,21,22)(H2,29,30,31)/t10-,11-,12-,13+,14+,15+/m0/s1" 
HN1 InChIKey         InChI                1.03  OOIOCUIVTIOESO-PKCACUDHSA-N                                                                                                                                                                                   
HN1 SMILES_CANONICAL CACTVS               3.370 "CCCCC[C@H](O)[C@@H]1C[C@@H](O)N2C(=O)c3ncn([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)c3NC2=N1"                                                                                                                  
HN1 SMILES           CACTVS               3.370 "CCCCC[CH](O)[CH]1C[CH](O)N2C(=O)c3ncn([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)c3NC2=N1"                                                                                                                           
HN1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CCCCC[C@@H]([C@@H]1C[C@H](N2C(=O)c3c(n(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)NC2=N1)O)O"                                                                                                                  
HN1 SMILES           "OpenEye OEToolkits" 1.7.2 "CCCCCC(C1CC(N2C(=O)c3c(n(cn3)C4CC(C(O4)COP(=O)(O)O)O)NC2=N1)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 
HN1 "SYSTEMATIC NAME" ACDLabs              12.01 "(6S,8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-6-[(1S)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one"                        
HN1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-3-oxidanyl-5-[(6S,8R)-8-oxidanyl-6-[(1S)-1-oxidanylhexyl]-10-oxidanylidene-4,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl]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 
HN1 "Create component"              2011-08-12 RCSB 
HN1 "Modify model coordinates code" 2011-08-25 RCSB 
# 
