data_2DM # _chem_comp.id 2DM _chem_comp.name "2-HYDROXY-3-(PYREN-1-YLMETHOXY)PROPYL DIHYDROGEN PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C20 H19 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-02-09 _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 386.335 _chem_comp.one_letter_code N _chem_comp.three_letter_code 2DM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1S88 _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 2DM P P P 0 1 N N N -6.921 3.687 19.275 5.494 -4.860 -5.192 P 2DM 1 2DM OP1 O1P O 0 1 N N N -7.692 2.655 18.546 6.306 -6.101 -4.958 OP1 2DM 2 2DM OP2 O2P O 0 1 N N N -7.613 4.906 19.745 6.214 -3.723 -6.089 OP2 2DM 3 2DM "O1'" "O1'" O 0 1 N N N -6.205 2.993 20.553 5.047 -4.071 -3.855 "O1'" 2DM 4 2DM "O3'" O3* O 0 1 N N N -4.768 4.072 23.533 5.192 -1.977 -1.974 "O3'" 2DM 5 2DM "C1'" "C1'" C 0 1 N N N -5.016 3.527 21.123 4.274 -2.884 -3.999 "C1'" 2DM 6 2DM "C2'" "C2'" C 0 1 N N S -4.695 3.042 22.547 3.961 -2.300 -2.626 "C2'" 2DM 7 2DM "C3'" "C3'" C 0 1 N N N -5.439 1.762 22.974 3.139 -1.023 -2.738 "C3'" 2DM 8 2DM "O4'" "O4'" O 0 1 N N N -5.020 0.563 22.312 2.855 -0.541 -1.431 "O4'" 2DM 9 2DM "C4'" "C4'" C 0 1 N N N -3.619 0.284 22.216 2.104 0.664 -1.471 "C4'" 2DM 10 2DM C1 C1 C 0 1 Y N N -3.314 -1.159 21.856 1.835 1.122 -0.071 C1 2DM 11 2DM C2 C2 C 0 1 Y N N -4.360 -2.099 21.768 0.670 0.663 0.540 C2 2DM 12 2DM C11 C11 C 0 1 Y N N -1.972 -1.585 21.694 2.710 1.978 0.614 C11 2DM 13 2DM C15 C15 C 0 1 Y N N -1.703 -2.952 21.450 2.398 2.374 1.935 C15 2DM 14 2DM C3 C3 C 0 1 Y N N -4.081 -3.458 21.572 0.361 1.052 1.843 C3 2DM 15 2DM C12 C12 C 0 1 Y N N -2.754 -3.888 21.414 1.215 1.908 2.553 C12 2DM 16 2DM C16 C16 C 0 1 Y N N -0.381 -3.395 21.253 3.272 3.239 2.640 C16 2DM 17 2DM C5 C5 C 0 1 Y N N -1.169 -5.697 20.926 1.783 3.163 4.558 C5 2DM 18 2DM C4 C4 C 0 1 Y N N -2.492 -5.254 21.211 0.922 2.311 3.863 C4 2DM 19 2DM C10 C10 C 0 1 Y N N -0.890 -0.677 21.761 3.887 2.451 0.017 C10 2DM 20 2DM C14 C14 C 0 1 Y N N 0.689 -2.480 21.334 4.456 3.706 2.022 C14 2DM 21 2DM C9 C9 C 0 1 Y N N 0.430 -1.124 21.580 4.748 3.303 0.712 C9 2DM 22 2DM C8 C8 C 0 1 Y N N 2.013 -2.923 21.179 5.310 4.561 2.733 C8 2DM 23 2DM C7 C7 C 0 1 Y N N 2.259 -4.270 20.877 5.001 4.950 4.035 C7 2DM 24 2DM C6 C6 C 0 1 Y N N 1.191 -5.156 20.697 3.835 4.492 4.646 C6 2DM 25 2DM C13 C13 C 0 1 Y N N -0.127 -4.750 20.952 2.960 3.635 3.961 C13 2DM 26 2DM OP3 O3P O 0 1 N Y N ? ? ? 4.087 -5.098 -5.952 OP3 2DM 27 2DM HOP2 2HOP H 0 0 N N N -7.118 5.568 20.213 6.633 -3.982 -6.937 HOP2 2DM 28 2DM "HO3'" H3T H 0 0 N Y N -4.570 3.773 24.413 4.953 -1.557 -1.135 "HO3'" 2DM 29 2DM "H1'1" "H1'1" H 0 0 N N N -5.059 4.611 21.155 4.844 -2.181 -4.615 "H1'1" 2DM 30 2DM "H1'2" "H1'2" H 0 0 N N N -4.185 3.254 20.472 3.357 -3.156 -4.531 "H1'2" 2DM 31 2DM "H2'" "H2'" H 0 1 N N N -3.634 2.824 22.514 3.451 -3.033 -1.991 "H2'" 2DM 32 2DM "H3'1" "H3'1" H 0 0 N N N -6.499 1.910 22.782 2.185 -1.209 -3.243 "H3'1" 2DM 33 2DM "H3'2" "H3'2" H 0 0 N N N -5.390 1.641 24.054 3.691 -0.244 -3.274 "H3'2" 2DM 34 2DM "H4'1" "H4'1" H 0 0 N N N -3.168 0.949 21.479 1.168 0.481 -2.013 "H4'1" 2DM 35 2DM "H4'2" "H4'2" H 0 0 N N N -3.101 0.420 23.156 2.670 1.419 -2.027 "H4'2" 2DM 36 2DM H2 H2 H 0 1 N N N -5.392 -1.793 21.853 -0.008 -0.000 0.009 H2 2DM 37 2DM H3 H3 H 0 1 N N N -4.899 -4.163 21.526 -0.555 0.681 2.298 H3 2DM 38 2DM H5 H5 H 0 1 N N N -0.873 -6.733 20.696 1.522 3.455 5.573 H5 2DM 39 2DM H4 H4 H 0 1 N N N -3.377 -5.877 21.295 0.018 1.964 4.359 H4 2DM 40 2DM H10 H10 H 0 1 N N N -1.044 0.377 21.942 4.162 2.169 -0.996 H10 2DM 41 2DM H9 H9 H 0 1 N N N 1.255 -0.427 21.604 5.653 3.649 0.217 H9 2DM 42 2DM H8 H8 H 0 1 N N N 2.841 -2.236 21.283 6.226 4.933 2.278 H8 2DM 43 2DM H7 H7 H 0 1 N N N 3.260 -4.650 20.783 5.670 5.613 4.576 H7 2DM 44 2DM H6 H6 H 0 1 N N N 1.410 -6.168 20.398 3.616 4.810 5.663 H6 2DM 45 2DM HOP3 3HOP H 0 0 N N N 0.495 0.662 0.468 4.073 -5.648 -6.764 HOP3 2DM 46 # 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 2DM P OP1 DOUB N N 1 2DM P OP2 SING N N 2 2DM P "O1'" SING N N 3 2DM P OP3 SING N N 4 2DM OP2 HOP2 SING N N 5 2DM "O1'" "C1'" SING N N 6 2DM "O3'" "C2'" SING N N 7 2DM "O3'" "HO3'" SING N N 8 2DM "C1'" "C2'" SING N N 9 2DM "C1'" "H1'1" SING N N 10 2DM "C1'" "H1'2" SING N N 11 2DM "C2'" "C3'" SING N N 12 2DM "C2'" "H2'" SING N N 13 2DM "C3'" "O4'" SING N N 14 2DM "C3'" "H3'1" SING N N 15 2DM "C3'" "H3'2" SING N N 16 2DM "O4'" "C4'" SING N N 17 2DM "C4'" C1 SING N N 18 2DM "C4'" "H4'1" SING N N 19 2DM "C4'" "H4'2" SING N N 20 2DM C1 C2 DOUB Y N 21 2DM C1 C11 SING Y N 22 2DM C2 C3 SING Y N 23 2DM C2 H2 SING N N 24 2DM C11 C15 DOUB Y N 25 2DM C11 C10 SING Y N 26 2DM C15 C12 SING Y N 27 2DM C15 C16 SING Y N 28 2DM C3 C12 DOUB Y N 29 2DM C3 H3 SING N N 30 2DM C12 C4 SING Y N 31 2DM C16 C14 DOUB Y N 32 2DM C16 C13 SING Y N 33 2DM C5 C4 DOUB Y N 34 2DM C5 C13 SING Y N 35 2DM C5 H5 SING N N 36 2DM C4 H4 SING N N 37 2DM C10 C9 DOUB Y N 38 2DM C10 H10 SING N N 39 2DM C14 C9 SING Y N 40 2DM C14 C8 SING Y N 41 2DM C9 H9 SING N N 42 2DM C8 C7 DOUB Y N 43 2DM C8 H8 SING N N 44 2DM C7 C6 SING Y N 45 2DM C7 H7 SING N N 46 2DM C6 C13 DOUB Y N 47 2DM C6 H6 SING N N 48 2DM OP3 HOP3 SING N N 49 # 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 2DM SMILES ACDLabs 10.04 "O=P(O)(O)OCC(O)COCc4ccc2ccc1cccc3c1c2c4cc3" 2DM SMILES_CANONICAL CACTVS 3.341 "O[C@@H](COCc1ccc2ccc3cccc4ccc1c2c34)CO[P](O)(O)=O" 2DM SMILES CACTVS 3.341 "O[CH](COCc1ccc2ccc3cccc4ccc1c2c34)CO[P](O)(O)=O" 2DM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)COC[C@@H](COP(=O)(O)O)O" 2DM SMILES "OpenEye OEToolkits" 1.5.0 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)COCC(COP(=O)(O)O)O" 2DM InChI InChI 1.03 "InChI=1S/C20H19O6P/c21-17(12-26-27(22,23)24)11-25-10-16-7-6-15-5-4-13-2-1-3-14-8-9-18(16)20(15)19(13)14/h1-9,17,21H,10-12H2,(H2,22,23,24)/t17-/m0/s1" 2DM InChIKey InChI 1.03 JJGYAQIYOOQCJK-KRWDZBQOSA-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 2DM "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-hydroxy-3-(pyren-1-ylmethoxy)propyl dihydrogen phosphate" 2DM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S)-2-hydroxy-3-(pyren-1-ylmethoxy)propyl] 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 2DM "Create component" 2004-02-09 RCSB 2DM "Modify descriptor" 2011-06-04 RCSB #