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                    2008-10-14 
_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 InChI            InChI                1.02b 
InChI=1/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/f/h31,35H 
NMD InChIKey         InChI                1.02b OARVXDFNTLYMCJ-JIVAOKARDK 
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 
# 
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 
# 
