data_NMD # _chem_comp.id NMD _chem_comp.name "N-NAPHTHALEN-1-YLMETHYL-2'-[3,5-DIMETHOXYBENZAMIDO]-2'-DEOXY-ADENOSINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H30 N6 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-02-21 _chem_comp.pdbx_modified_date 2011-06-04 _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 570.596 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NMD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1I32 _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 NMD "C5'" C5* C 0 1 N N N 46.755 47.928 28.786 -5.814 0.792 2.670 "C5'" NMD 1 NMD "C4'" C4* C 0 1 N N R 47.554 48.842 29.728 -4.630 -0.176 2.644 "C4'" NMD 2 NMD "O4'" O4* O 0 1 N N N 48.215 48.132 30.776 -4.151 -0.332 1.298 "O4'" NMD 3 NMD "C3'" C3* C 0 1 N N S 48.641 49.630 29.022 -3.469 0.393 3.481 "C3'" NMD 4 NMD "O3'" O3* O 0 1 N N N 48.845 50.908 29.617 -3.143 -0.489 4.556 "O3'" NMD 5 NMD "C2'" C2* C 0 1 N N R 49.835 48.680 29.129 -2.291 0.486 2.480 "C2'" NMD 6 NMD "N2'" N2* N 0 1 N N N 51.124 49.338 29.062 -1.036 0.064 3.109 "N2'" NMD 7 NMD "C1'" C1* C 0 1 N N R 49.606 47.985 30.477 -2.721 -0.513 1.377 "C1'" NMD 8 NMD N9A N9A N 0 1 Y N N 50.013 46.578 30.557 -2.087 -0.182 0.099 N9A NMD 9 NMD C8A C8A C 0 1 Y N N 50.230 45.678 29.542 -2.548 0.710 -0.822 C8A NMD 10 NMD N7A N7A N 0 1 Y N N 50.589 44.481 29.947 -1.739 0.757 -1.839 N7A NMD 11 NMD C5A C5A C 0 1 Y N N 50.613 44.586 31.328 -0.710 -0.099 -1.637 C5A NMD 12 NMD C6A C6A C 0 1 Y N N 50.919 43.664 32.382 0.431 -0.463 -2.370 C6A NMD 13 NMD N6A N6A N 0 1 N N N 51.282 42.374 32.217 0.692 0.107 -3.604 N6A NMD 14 NMD N1A N1A N 0 1 Y N N 50.838 44.119 33.666 1.255 -1.368 -1.852 N1A NMD 15 NMD C2A C2A C 0 1 Y N N 50.482 45.397 33.899 1.015 -1.917 -0.675 C2A NMD 16 NMD N3A N3A N 0 1 Y N N 50.178 46.342 32.996 -0.041 -1.607 0.046 N3A NMD 17 NMD C4A C4A C 0 1 Y N N 50.260 45.876 31.724 -0.918 -0.708 -0.388 C4A NMD 18 NMD C11 C11 C 0 1 N N N 51.444 41.661 30.947 1.888 -0.284 -4.354 C11 NMD 19 NMD C1 C1 C 0 1 Y N N 52.873 41.342 30.539 1.881 0.393 -5.700 C1 NMD 20 NMD C9 C9 C 0 1 Y N N 53.173 40.730 29.266 1.054 -0.088 -6.729 C9 NMD 21 NMD C8 C8 C 0 1 Y N N 52.164 40.383 28.309 0.211 -1.195 -6.530 C8 NMD 22 NMD C7 C7 C 0 1 Y N N 52.500 39.779 27.060 -0.580 -1.629 -7.548 C7 NMD 23 NMD C6 C6 C 0 1 Y N N 53.859 39.511 26.741 -0.572 -0.990 -8.787 C6 NMD 24 NMD C2 C2 C 0 1 Y N N 53.939 41.656 31.436 2.680 1.471 -5.927 C2 NMD 25 NMD C10 C10 C 0 1 Y N N 54.557 40.452 28.927 1.058 0.565 -7.987 C10 NMD 26 NMD C5 C5 C 0 1 Y N N 54.880 39.849 27.675 0.226 0.087 -9.014 C5 NMD 27 NMD C3 C3 C 0 1 Y N N 55.289 41.381 31.098 2.688 2.110 -7.165 C3 NMD 28 NMD C4 C4 C 0 1 Y N N 55.593 40.781 29.847 1.896 1.676 -8.183 C4 NMD 29 NMD C7B C7B C 0 1 N N N 52.110 49.055 28.189 -0.217 0.981 3.660 C7B NMD 30 NMD O7B O7B O 0 1 N N N 51.981 48.190 27.313 -0.518 2.158 3.635 O7B NMD 31 NMD C6B C6B C 0 1 Y N N 53.368 49.826 28.332 1.048 0.555 4.294 C6B NMD 32 NMD C5B C5B C 0 1 Y N N 53.446 50.806 29.360 1.399 -0.794 4.318 C5B NMD 33 NMD C4B C4B C 0 1 Y N N 54.621 51.578 29.550 2.583 -1.190 4.918 C4B NMD 34 NMD O2M O2M O 0 1 N N N 54.623 52.507 30.571 2.923 -2.505 4.946 O2M NMD 35 NMD C2M C2M C 0 1 N N N 53.666 53.572 30.567 4.183 -2.592 5.616 C2M NMD 36 NMD C3B C3B C 0 1 Y N N 55.740 51.346 28.685 3.426 -0.244 5.484 C3B NMD 37 NMD C1B C1B C 0 1 Y N N 54.484 49.601 27.471 1.898 1.503 4.865 C1B NMD 38 NMD C2B C2B C 0 1 Y N N 55.682 50.357 27.641 3.083 1.099 5.458 C2B NMD 39 NMD O1M O1M O 0 1 N N N 56.729 50.094 26.785 3.912 2.022 6.014 O1M NMD 40 NMD C1M C1M C 0 1 N N N 57.778 49.235 27.240 5.034 1.307 6.536 C1M NMD 41 NMD "O5'" O5* O 0 1 N N N 45.732 48.671 28.126 -6.886 0.256 1.892 "O5'" NMD 42 NMD "H5'1" 1H5* H 0 0 N N N 47.416 47.396 28.062 -6.147 0.933 3.698 "H5'1" NMD 43 NMD "H5'2" 2H5* H 0 0 N N N 46.345 47.038 29.318 -5.507 1.751 2.253 "H5'2" NMD 44 NMD "H4'" H4* H 0 1 N N N 46.770 49.521 30.137 -4.935 -1.143 3.044 "H4'" NMD 45 NMD "H3'" H3* H 0 1 N N N 48.411 49.899 27.964 -3.723 1.381 3.864 "H3'" NMD 46 NMD "HO3'" *HO3 H 0 0 N N N 49.525 51.401 29.174 -3.910 -0.507 5.145 "HO3'" NMD 47 NMD "H2'" H2* H 0 1 N N N 49.880 47.975 28.265 -2.202 1.495 2.077 "H2'" NMD 48 NMD "HN2'" *HN2 H 0 0 N N N 51.366 50.090 29.706 -0.796 -0.874 3.128 "HN2'" NMD 49 NMD "H1'" H1* H 0 1 N N N 50.270 48.475 31.226 -2.479 -1.535 1.671 "H1'" NMD 50 NMD H8A H8A H 0 1 N N N 50.122 45.902 28.467 -3.452 1.293 -0.722 H8A NMD 51 NMD H6A H6A H 0 1 N N N 50.625 41.822 32.769 0.083 0.766 -3.972 H6A NMD 52 NMD H2A H2A H 0 1 N N N 50.433 45.707 34.956 1.710 -2.648 -0.291 H2A NMD 53 NMD H111 1H11 H 0 0 N N N 50.836 40.726 30.957 2.778 0.014 -3.801 H111 NMD 54 NMD H112 2H11 H 0 0 N N N 50.933 42.222 30.130 1.892 -1.366 -4.492 H112 NMD 55 NMD H8 H8 H 0 1 N N N 51.104 40.585 28.539 0.194 -1.700 -5.576 H8 NMD 56 NMD H7 H7 H 0 1 N N N 51.706 39.518 26.339 -1.223 -2.483 -7.394 H7 NMD 57 NMD H6 H6 H 0 1 N N N 54.119 39.044 25.776 -1.210 -1.355 -9.578 H6 NMD 58 NMD H2 H2 H 0 1 N N N 53.714 42.120 32.410 3.318 1.836 -5.136 H2 NMD 59 NMD H5 H5 H 0 1 N N N 55.934 39.641 27.425 0.221 0.573 -9.978 H5 NMD 60 NMD H3 H3 H 0 1 N N N 56.098 41.632 31.804 3.331 2.964 -7.319 H3 NMD 61 NMD H4 H4 H 0 1 N N N 56.643 40.568 29.587 1.912 2.181 -9.137 H4 NMD 62 NMD H5B H5B H 0 1 N N N 52.579 50.970 30.022 0.744 -1.531 3.878 H5B NMD 63 NMD H2M1 1H2M H 0 0 N N N 53.667 54.322 31.391 4.498 -3.634 5.663 H2M1 NMD 64 NMD H2M2 2H2M H 0 0 N N N 53.744 54.113 29.595 4.926 -2.012 5.069 H2M2 NMD 65 NMD H2M3 3H2M H 0 0 N N N 52.645 53.129 30.493 4.085 -2.196 6.626 H2M3 NMD 66 NMD H3B H3B H 0 1 N N N 56.660 51.937 28.824 4.350 -0.555 5.948 H3B NMD 67 NMD H1B H1B H 0 1 N N N 54.420 48.841 26.673 1.633 2.549 4.845 H1B NMD 68 NMD H1M1 1H1M H 0 0 N N N 58.625 49.022 26.547 5.730 2.009 6.995 H1M1 NMD 69 NMD H1M2 2H1M H 0 0 N N N 58.184 49.633 28.198 4.693 0.592 7.285 H1M2 NMD 70 NMD H1M3 3H1M H 0 0 N N N 57.335 48.269 27.580 5.535 0.775 5.727 H1M3 NMD 71 NMD "HO5'" *HO5 H 0 0 N N N 45.238 48.105 27.543 -7.610 0.896 1.934 "HO5'" NMD 72 # 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 NMD "C5'" "C4'" SING N N 1 NMD "C5'" "O5'" SING N N 2 NMD "C5'" "H5'1" SING N N 3 NMD "C5'" "H5'2" SING N N 4 NMD "C4'" "O4'" SING N N 5 NMD "C4'" "C3'" SING N N 6 NMD "C4'" "H4'" SING N N 7 NMD "O4'" "C1'" SING N N 8 NMD "C3'" "O3'" SING N N 9 NMD "C3'" "C2'" SING N N 10 NMD "C3'" "H3'" SING N N 11 NMD "O3'" "HO3'" SING N N 12 NMD "C2'" "N2'" SING N N 13 NMD "C2'" "C1'" SING N N 14 NMD "C2'" "H2'" SING N N 15 NMD "N2'" C7B SING N N 16 NMD "N2'" "HN2'" SING N N 17 NMD "C1'" N9A SING N N 18 NMD "C1'" "H1'" SING N N 19 NMD N9A C8A SING Y N 20 NMD N9A C4A SING Y N 21 NMD C8A N7A DOUB Y N 22 NMD C8A H8A SING N N 23 NMD N7A C5A SING Y N 24 NMD C5A C6A DOUB Y N 25 NMD C5A C4A SING Y N 26 NMD C6A N6A SING N N 27 NMD C6A N1A SING Y N 28 NMD N6A C11 SING N N 29 NMD N6A H6A SING N N 30 NMD N1A C2A DOUB Y N 31 NMD C2A N3A SING Y N 32 NMD C2A H2A SING N N 33 NMD N3A C4A DOUB Y N 34 NMD C11 C1 SING N N 35 NMD C11 H111 SING N N 36 NMD C11 H112 SING N N 37 NMD C1 C9 DOUB Y N 38 NMD C1 C2 SING Y N 39 NMD C9 C8 SING Y N 40 NMD C9 C10 SING Y N 41 NMD C8 C7 DOUB Y N 42 NMD C8 H8 SING N N 43 NMD C7 C6 SING Y N 44 NMD C7 H7 SING N N 45 NMD C6 C5 DOUB Y N 46 NMD C6 H6 SING N N 47 NMD C2 C3 DOUB Y N 48 NMD C2 H2 SING N N 49 NMD C10 C5 SING Y N 50 NMD C10 C4 DOUB Y N 51 NMD C5 H5 SING N N 52 NMD C3 C4 SING Y N 53 NMD C3 H3 SING N N 54 NMD C4 H4 SING N N 55 NMD C7B O7B DOUB N N 56 NMD C7B C6B SING N N 57 NMD C6B C5B DOUB Y N 58 NMD C6B C1B SING Y N 59 NMD C5B C4B SING Y N 60 NMD C5B H5B SING N N 61 NMD C4B O2M SING N N 62 NMD C4B C3B DOUB Y N 63 NMD O2M C2M SING N N 64 NMD C2M H2M1 SING N N 65 NMD C2M H2M2 SING N N 66 NMD C2M H2M3 SING N N 67 NMD C3B C2B SING Y N 68 NMD C3B H3B SING N N 69 NMD C1B C2B DOUB Y N 70 NMD C1B H1B SING N N 71 NMD C2B O1M SING N N 72 NMD O1M C1M SING N N 73 NMD C1M H1M1 SING N N 74 NMD C1M H1M2 SING N N 75 NMD C1M H1M3 SING N N 76 NMD "O5'" "HO5'" SING N N 77 # 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 NMD SMILES ACDLabs 10.04 "O=C(c1cc(OC)cc(OC)c1)NC6C(O)C(OC6n3cnc2c(ncnc23)NCc5c4ccccc4ccc5)CO" NMD SMILES_CANONICAL CACTVS 3.341 "COc1cc(OC)cc(c1)C(=O)N[C@@H]2[C@H](O)[C@@H](CO)O[C@H]2n3cnc4c(NCc5cccc6ccccc56)ncnc34" NMD SMILES CACTVS 3.341 "COc1cc(OC)cc(c1)C(=O)N[CH]2[CH](O)[CH](CO)O[CH]2n3cnc4c(NCc5cccc6ccccc56)ncnc34" NMD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1)OC)C(=O)N[C@@H]2[C@@H]([C@H](O[C@H]2n3cnc4c3ncnc4NCc5cccc6c5cccc6)CO)O" NMD SMILES "OpenEye OEToolkits" 1.5.0 "COc1cc(cc(c1)OC)C(=O)NC2C(C(OC2n3cnc4c3ncnc4NCc5cccc6c5cccc6)CO)O" NMD InChI InChI 1.03 "InChI=1S/C30H30N6O6/c1-40-20-10-19(11-21(12-20)41-2)29(39)35-24-26(38)23(14-37)42-30(24)36-16-34-25-27(32-15-33-28(25)36)31-13-18-8-5-7-17-6-3-4-9-22(17)18/h3-12,15-16,23-24,26,30,37-38H,13-14H2,1-2H3,(H,35,39)(H,31,32,33)/t23-,24-,26-,30-/m1/s1" NMD InChIKey InChI 1.03 OARVXDFNTLYMCJ-JVUUKAHWSA-N # 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 NMD "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-2'-{[(3,5-dimethoxyphenyl)carbonyl]amino}-N-(naphthalen-1-ylmethyl)adenosine" NMD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(2R,3R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-2-[6-(naphthalen-1-ylmethylamino)purin-9-yl]oxolan-3-yl]-3,5-dimethoxy-benzamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NMD "Create component" 2001-02-21 RCSB NMD "Modify descriptor" 2011-06-04 RCSB #