data_ABM # _chem_comp.id ABM _chem_comp.name "METHYL PHOSPHONIC ACID ADENOSINE ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N5 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-12-16 _chem_comp.pdbx_modified_date 2021-03-01 _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 345.248 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ABM _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 1DKU _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 ABM P P P 0 1 N N S 27.599 50.279 49.750 -0.998 -0.075 4.699 P ABM 1 ABM CM CM C 0 1 N N N 29.108 49.287 49.619 -2.263 -1.174 5.417 CM ABM 2 ABM O2P O2P O 0 1 N N N 27.850 51.490 48.808 0.077 0.150 5.689 O2P ABM 3 ABM O3P O3P O 0 1 N N N 27.425 50.533 51.247 -1.671 1.333 4.307 O3P ABM 4 ABM "O5'" O5* O 0 1 N N N 26.445 49.271 49.202 -0.379 -0.760 3.380 "O5'" ABM 5 ABM "C5'" C5* C 0 1 N N N 25.249 49.714 48.448 0.600 0.144 2.866 "C5'" ABM 6 ABM "C4'" C4* C 0 1 N N R 24.893 48.793 47.239 1.230 -0.449 1.605 "C4'" ABM 7 ABM "O4'" O4* O 0 1 N N N 24.399 47.467 47.661 0.224 -0.630 0.594 "O4'" ABM 8 ABM "C3'" C3* C 0 1 N N S 23.819 49.413 46.279 2.284 0.522 1.038 "C3'" ABM 9 ABM "O3'" O3* O 0 1 N N N 24.328 49.418 44.920 3.574 -0.091 1.004 "O3'" ABM 10 ABM "C2'" C2* C 0 1 N N R 22.611 48.468 46.339 1.786 0.820 -0.400 "C2'" ABM 11 ABM "O2'" O2* O 0 1 N N N 22.046 48.269 45.004 2.878 0.849 -1.320 "O2'" ABM 12 ABM "C1'" C1* C 0 1 N N R 23.134 47.148 46.982 0.859 -0.390 -0.679 "C1'" ABM 13 ABM N9 N9 N 0 1 Y N N 22.174 46.573 47.983 -0.138 -0.056 -1.698 N9 ABM 14 ABM C8 C8 C 0 1 Y N N 20.935 47.026 48.375 -1.340 0.549 -1.481 C8 ABM 15 ABM N7 N7 N 0 1 Y N N 20.270 46.194 49.155 -1.975 0.694 -2.608 N7 ABM 16 ABM C5 C5 C 0 1 Y N N 21.110 45.089 49.208 -1.222 0.194 -3.617 C5 ABM 17 ABM C6 C6 C 0 1 Y N N 21.054 43.880 49.948 -1.385 0.077 -5.008 C6 ABM 18 ABM N6 N6 N 0 1 N N N 20.066 43.565 50.771 -2.533 0.540 -5.627 N6 ABM 19 ABM N1 N1 N 0 1 Y N N 21.950 42.938 49.634 -0.411 -0.486 -5.714 N1 ABM 20 ABM C2 C2 C 0 1 Y N N 22.967 43.278 48.819 0.687 -0.931 -5.132 C2 ABM 21 ABM N3 N3 N 0 1 Y N N 23.284 44.490 48.305 0.883 -0.843 -3.833 N3 ABM 22 ABM C4 C4 C 0 1 Y N N 22.279 45.345 48.526 -0.032 -0.289 -3.046 C4 ABM 23 ABM HM1 HM1 H 0 1 N N N 28.928 48.418 50.294 -2.682 -0.711 6.310 HM1 ABM 24 ABM HM2 HM2 H 0 1 N N N 29.378 49.004 48.574 -3.056 -1.341 4.688 HM2 ABM 25 ABM HM3 HM3 H 0 1 N N N 30.044 49.850 49.840 -1.807 -2.128 5.683 HM3 ABM 26 ABM HOP3 3HOP H 0 0 N N N 26.633 51.053 51.315 -2.366 1.141 3.661 HOP3 ABM 27 ABM "H5'1" 1H5* H 0 0 N N N 24.373 49.825 49.129 0.124 1.094 2.622 "H5'1" ABM 28 ABM "H5'2" 2H5* H 0 0 N N N 25.362 50.772 48.116 1.373 0.307 3.617 "H5'2" ABM 29 ABM "H4'" H4* H 0 1 N N N 25.858 48.686 46.692 1.697 -1.405 1.839 "H4'" ABM 30 ABM "H3'" H3* H 0 1 N N N 23.561 50.456 46.574 2.313 1.438 1.629 "H3'" ABM 31 ABM "HO3'" *HO3 H 0 0 N N N 23.677 49.793 44.338 4.173 0.541 0.586 "HO3'" ABM 32 ABM "H2'" H2* H 0 1 N N N 21.776 48.884 46.949 1.225 1.754 -0.433 "H2'" ABM 33 ABM "HO2'" *HO2 H 0 0 N N N 21.298 47.684 45.041 3.414 1.622 -1.094 "HO2'" ABM 34 ABM "H1'" H1* H 0 1 N N N 23.262 46.384 46.179 1.443 -1.258 -0.986 "H1'" ABM 35 ABM H8 H8 H 0 1 N N N 20.501 47.996 48.081 -1.712 0.861 -0.516 H8 ABM 36 ABM HN61 1HN6 H 0 0 N N N 20.025 42.695 51.303 -2.634 0.454 -6.588 HN61 ABM 37 ABM HN62 2HN6 H 0 0 N N N 19.198 43.631 50.238 -3.236 0.950 -5.101 HN62 ABM 38 ABM H2 H2 H 0 1 N N N 23.633 42.447 48.532 1.453 -1.383 -5.744 H2 ABM 39 # # 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 ABM P CM SING N N 1 ABM P O2P DOUB N N 2 ABM P O3P SING N N 3 ABM P "O5'" SING N N 4 ABM CM HM1 SING N N 5 ABM CM HM2 SING N N 6 ABM CM HM3 SING N N 7 ABM O3P HOP3 SING N N 8 ABM "O5'" "C5'" SING N N 9 ABM "C5'" "C4'" SING N N 10 ABM "C5'" "H5'1" SING N N 11 ABM "C5'" "H5'2" SING N N 12 ABM "C4'" "O4'" SING N N 13 ABM "C4'" "C3'" SING N N 14 ABM "C4'" "H4'" SING N N 15 ABM "O4'" "C1'" SING N N 16 ABM "C3'" "O3'" SING N N 17 ABM "C3'" "C2'" SING N N 18 ABM "C3'" "H3'" SING N N 19 ABM "O3'" "HO3'" SING N N 20 ABM "C2'" "O2'" SING N N 21 ABM "C2'" "C1'" SING N N 22 ABM "C2'" "H2'" SING N N 23 ABM "O2'" "HO2'" SING N N 24 ABM "C1'" N9 SING N N 25 ABM "C1'" "H1'" SING N N 26 ABM N9 C8 SING Y N 27 ABM N9 C4 SING Y N 28 ABM C8 N7 DOUB Y N 29 ABM C8 H8 SING N N 30 ABM N7 C5 SING Y N 31 ABM C5 C6 SING Y N 32 ABM C5 C4 DOUB Y N 33 ABM C6 N6 SING N N 34 ABM C6 N1 DOUB Y N 35 ABM N6 HN61 SING N N 36 ABM N6 HN62 SING N N 37 ABM N1 C2 SING Y N 38 ABM C2 N3 DOUB Y N 39 ABM C2 H2 SING N N 40 ABM N3 C4 SING Y 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 ABM SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C" ABM SMILES_CANONICAL CACTVS 3.341 "C[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" ABM SMILES CACTVS 3.341 "C[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" ABM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" ABM SMILES "OpenEye OEToolkits" 1.5.0 "CP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" ABM InChI InChI 1.03 "InChI=1S/C11H16N5O6P/c1-23(19,20)21-2-5-7(17)8(18)11(22-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1" ABM InChIKey InChI 1.03 PXSSQXBLDTZHLF-IOSLPCCCSA-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 ABM "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine" ABM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-methyl-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ABM "Create component" 1999-12-16 RCSB ABM "Modify descriptor" 2011-06-04 RCSB ABM "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id ABM _pdbx_chem_comp_synonyms.name "ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##