data_VMI # _chem_comp.id VMI _chem_comp.name "[(S)-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]-butoxy-phosphinic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H32 N4 O11 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2023-03-20 _chem_comp.pdbx_modified_date 2023-10-19 _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 605.453 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VMI _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 8OGH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag VMI C5 C1 C 0 1 N N S 9.132 -3.857 14.486 -2.898 -0.587 1.001 C5 VMI 1 N N N VMI C4 C2 C 0 1 N N N 8.767 -6.739 11.679 -5.808 -3.045 -0.720 C4 VMI 2 N N N VMI C6 C3 C 0 1 N N N 7.672 -3.843 14.928 -2.740 -1.449 2.255 C6 VMI 3 N N N VMI N3 N1 N 0 1 Y N N 11.349 1.297 13.970 -4.824 3.731 -0.202 N3 VMI 4 N N N VMI C2 C4 C 0 1 N N N 7.988 -9.062 11.056 -7.926 -4.363 -0.862 C2 VMI 5 N N N VMI S1 S1 S 0 1 Y N N 9.549 -3.614 17.229 -0.368 -0.941 -0.271 S1 VMI 6 N N N VMI C7 C5 C 0 1 Y N N 10.029 -3.409 15.598 -1.552 -0.053 0.586 C7 VMI 7 N N N VMI C1 C6 C 0 1 N N N 7.446 -10.297 11.730 -9.145 -4.857 -0.079 C1 VMI 8 N N N VMI C8 C7 C 0 1 Y N N 11.119 -3.160 17.761 0.706 0.456 -0.252 C8 VMI 9 N N N VMI C9 C8 C 0 1 N N N 11.423 -3.158 19.231 2.086 0.521 -0.853 C9 VMI 10 N N N VMI O2 O1 O 0 1 N N N 10.970 -5.538 13.491 -3.858 -0.739 -1.523 O2 VMI 11 N N N VMI O3 O2 O 0 1 N N N 9.175 -6.504 15.005 -2.542 -2.749 -0.752 O3 VMI 12 N N N VMI O4 O3 O 0 1 N N N 9.228 -3.007 13.350 -3.778 0.503 1.280 O4 VMI 13 N N N VMI C10 C9 C 0 1 N N N 10.306 -2.538 20.010 3.118 0.092 0.192 C10 VMI 14 N N N VMI C11 C10 C 0 1 Y N N 11.940 -2.843 16.734 0.080 1.447 0.390 C11 VMI 15 N N N VMI C12 C11 C 0 1 N N N 13.392 -2.503 16.852 0.702 2.804 0.598 C12 VMI 16 N N N VMI C13 C12 C 0 1 N N N 11.930 -2.445 14.245 -1.947 2.115 1.547 C13 VMI 17 N N N VMI C14 C13 C 0 1 Y N N 12.166 -0.953 14.154 -2.758 2.918 0.563 C14 VMI 18 N N N VMI C15 C14 C 0 1 Y N N 13.439 -0.424 14.126 -2.148 3.576 -0.487 C15 VMI 19 N N N VMI C16 C15 C 0 1 Y N N 12.618 1.699 13.961 -4.201 4.343 -1.188 C16 VMI 20 N N N VMI C17 C16 C 0 1 N N N 12.873 3.166 13.862 -5.005 5.147 -2.177 C17 VMI 21 N N N VMI C18 C17 C 0 1 Y N N 11.116 -0.019 14.057 -4.146 3.013 0.688 C18 VMI 22 N N N VMI C3 C18 C 0 1 N N N 7.723 -7.810 11.843 -7.027 -3.539 0.062 C3 VMI 23 N N N VMI N1 N2 N 1 1 Y N N 11.292 -2.873 15.498 -1.126 1.141 0.824 N1 VMI 24 N N N VMI N2 N3 N 0 1 Y N N 13.674 0.888 14.031 -2.893 4.272 -1.334 N2 VMI 25 N N N VMI N4 N4 N 0 1 N N N 9.836 -0.406 14.053 -4.805 2.372 1.724 N4 VMI 26 N N N VMI O1 O4 O 0 1 N N N 8.571 -5.725 12.684 -4.968 -2.276 0.143 O1 VMI 27 N N N VMI O10 O5 O 0 1 N N N 7.927 -5.130 21.657 9.039 -0.723 0.880 O10 VMI 28 N N N VMI O11 O6 O 0 1 N N N 9.170 -4.654 23.737 8.454 -2.342 -0.966 O11 VMI 29 N N N VMI O5 O7 O 0 1 N N N 10.705 -2.449 21.387 4.427 0.154 -0.379 O5 VMI 30 N N N VMI O6 O8 O 0 1 N N N 9.316 -0.450 21.988 5.624 -1.598 0.989 O6 VMI 31 N N N VMI O7 O9 O 0 1 N N N 10.299 -1.958 23.792 5.968 0.815 1.647 O7 VMI 32 N N N VMI O8 O10 O 0 1 N N N 8.422 -2.777 22.283 7.031 -0.171 -0.546 O8 VMI 33 N N N VMI O9 O11 O 0 1 N N N 6.759 -4.067 23.574 9.476 0.023 -1.492 O9 VMI 34 N N N VMI P1 P1 P 0 1 N N N 9.538 -5.530 13.926 -3.593 -1.599 -0.348 P1 VMI 35 N N N VMI P2 P2 P 0 1 N N N 9.689 -1.811 22.444 5.760 -0.230 0.440 P2 VMI 36 N N N VMI P3 P3 P 0 1 N N N 8.053 -4.242 22.842 8.512 -0.801 -0.501 P3 VMI 37 N N N VMI H1 H1 H 0 1 N N N 9.768 -7.181 11.793 -5.251 -3.901 -1.102 H1 VMI 38 N N N VMI H2 H2 H 0 1 N N N 8.677 -6.288 10.680 -6.139 -2.425 -1.553 H2 VMI 39 N N N VMI H3 H3 H 0 1 N N N 7.549 -4.490 15.809 -2.423 -0.823 3.089 H3 VMI 40 N N N VMI H4 H4 H 0 1 N N N 7.376 -2.815 15.184 -3.694 -1.919 2.496 H4 VMI 41 N N N VMI H5 H5 H 0 1 N N N 7.038 -4.213 14.109 -1.991 -2.220 2.074 H5 VMI 42 N N N VMI H6 H6 H 0 1 N N N 9.075 -9.177 10.932 -7.369 -5.218 -1.244 H6 VMI 43 N N N VMI H7 H7 H 0 1 N N N 7.515 -8.964 10.068 -8.257 -3.743 -1.695 H7 VMI 44 N N N VMI H8 H8 H 0 1 N N N 7.668 -11.180 11.112 -8.815 -5.477 0.754 H8 VMI 45 N N N VMI H9 H9 H 0 1 N N N 7.917 -10.413 12.717 -9.703 -4.002 0.303 H9 VMI 46 N N N VMI H10 H10 H 0 1 N N N 6.357 -10.200 11.853 -9.786 -5.444 -0.738 H10 VMI 47 N N N VMI H11 H11 H 0 1 N N N 11.566 -4.195 19.570 2.140 -0.147 -1.713 H11 VMI 48 N N N VMI H12 H12 H 0 1 N N N 12.345 -2.585 19.407 2.295 1.542 -1.173 H12 VMI 49 N N N VMI H13 H13 H 0 1 N N N 9.946 -6.999 15.258 -2.321 -3.352 -0.028 H13 VMI 50 N N N VMI H14 H14 H 0 1 N N N 9.021 -2.115 13.603 -4.066 0.988 0.494 H14 VMI 51 N N N VMI H15 H15 H 0 1 N N N 10.095 -1.532 19.619 3.065 0.760 1.051 H15 VMI 52 N N N VMI H16 H16 H 0 1 N N N 9.404 -3.161 19.925 2.909 -0.929 0.511 H16 VMI 53 N N N VMI H17 H17 H 0 1 N N N 13.505 -1.417 16.989 0.535 3.420 -0.286 H17 VMI 54 N N N VMI H18 H18 H 0 1 N N N 13.822 -3.029 17.717 0.248 3.283 1.465 H18 VMI 55 N N N VMI H19 H19 H 0 1 N N N 13.917 -2.813 15.936 1.773 2.691 0.764 H19 VMI 56 N N N VMI H20 H20 H 0 1 N N N 11.283 -2.745 13.407 -1.301 2.784 2.116 H20 VMI 57 N N N VMI H21 H21 H 0 1 N N N 12.901 -2.955 14.159 -2.618 1.591 2.228 H21 VMI 58 N N N VMI H22 H22 H 0 1 N N N 14.281 -1.098 14.183 -1.077 3.525 -0.616 H22 VMI 59 N N N VMI H23 H23 H 0 1 N N N 11.914 3.703 13.810 -5.088 6.176 -1.827 H23 VMI 60 N N N VMI H24 H24 H 0 1 N N N 13.433 3.501 14.747 -4.509 5.132 -3.147 H24 VMI 61 N N N VMI H25 H25 H 0 1 N N N 13.460 3.376 12.956 -6.002 4.715 -2.272 H25 VMI 62 N N N VMI H26 H26 H 0 1 N N N 6.755 -7.399 11.520 -6.697 -4.160 0.896 H26 VMI 63 N N N VMI H27 H27 H 0 1 N N N 7.670 -8.078 12.908 -7.585 -2.684 0.445 H27 VMI 64 N N N VMI H28 H28 H 0 1 N N N 9.245 0.397 13.982 -5.771 2.295 1.711 H28 VMI 65 N N N VMI H29 H29 H 0 1 N N N 9.673 -1.010 13.273 -4.299 1.999 2.464 H29 VMI 66 N N N VMI H30 H30 H 0 1 N N N 9.600 -5.420 23.376 8.117 -2.469 -1.864 H30 VMI 67 N N N VMI H31 H31 H 0 1 N N N 10.371 -1.104 24.203 6.064 1.733 1.360 H31 VMI 68 N N N VMI H32 H32 H 0 1 N N N 6.078 -4.566 23.138 10.387 -0.302 -1.515 H32 VMI 69 N N N # 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 VMI C2 C1 SING N N 1 VMI C2 C3 SING N N 2 VMI C4 C3 SING N N 3 VMI C4 O1 SING N N 4 VMI O1 P1 SING N N 5 VMI O4 C5 SING N N 6 VMI O2 P1 DOUB N N 7 VMI C17 C16 SING N N 8 VMI P1 C5 SING N N 9 VMI P1 O3 SING N N 10 VMI C16 N3 DOUB Y N 11 VMI C16 N2 SING Y N 12 VMI N3 C18 SING Y N 13 VMI N2 C15 DOUB Y N 14 VMI N4 C18 SING N N 15 VMI C18 C14 DOUB Y N 16 VMI C15 C14 SING Y N 17 VMI C14 C13 SING N N 18 VMI C13 N1 SING N N 19 VMI C5 C6 SING N N 20 VMI C5 C7 SING N N 21 VMI N1 C7 DOUB Y N 22 VMI N1 C11 SING Y N 23 VMI C7 S1 SING Y N 24 VMI C11 C12 SING N N 25 VMI C11 C8 DOUB Y N 26 VMI S1 C8 SING Y N 27 VMI C8 C9 SING N N 28 VMI C9 C10 SING N N 29 VMI C10 O5 SING N N 30 VMI O5 P2 SING N N 31 VMI O10 P3 DOUB N N 32 VMI O6 P2 DOUB N N 33 VMI O8 P2 SING N N 34 VMI O8 P3 SING N N 35 VMI P2 O7 SING N N 36 VMI P3 O9 SING N N 37 VMI P3 O11 SING N N 38 VMI C4 H1 SING N N 39 VMI C4 H2 SING N N 40 VMI C6 H3 SING N N 41 VMI C6 H4 SING N N 42 VMI C6 H5 SING N N 43 VMI C2 H6 SING N N 44 VMI C2 H7 SING N N 45 VMI C1 H8 SING N N 46 VMI C1 H9 SING N N 47 VMI C1 H10 SING N N 48 VMI C9 H11 SING N N 49 VMI C9 H12 SING N N 50 VMI O3 H13 SING N N 51 VMI O4 H14 SING N N 52 VMI C10 H15 SING N N 53 VMI C10 H16 SING N N 54 VMI C12 H17 SING N N 55 VMI C12 H18 SING N N 56 VMI C12 H19 SING N N 57 VMI C13 H20 SING N N 58 VMI C13 H21 SING N N 59 VMI C15 H22 SING N N 60 VMI C17 H23 SING N N 61 VMI C17 H24 SING N N 62 VMI C17 H25 SING N N 63 VMI C3 H26 SING N N 64 VMI C3 H27 SING N N 65 VMI N4 H28 SING N N 66 VMI N4 H29 SING N N 67 VMI O11 H30 SING N N 68 VMI O7 H31 SING N N 69 VMI O9 H32 SING N N 70 # 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 VMI InChI InChI 1.06 "InChI=1S/C18H31N4O11P3S/c1-5-6-8-31-34(24,25)18(4,23)17-22(11-14-10-20-13(3)21-16(14)19)12(2)15(37-17)7-9-32-36(29,30)33-35(26,27)28/h10,23H,5-9,11H2,1-4H3,(H5-,19,20,21,24,25,26,27,28,29,30)/p+1/t18-/m0/s1" VMI InChIKey InChI 1.06 KQPODQFTFSEDTF-SFHVURJKSA-O VMI SMILES_CANONICAL CACTVS 3.385 "CCCCO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N" VMI SMILES CACTVS 3.385 "CCCCO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N" VMI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCOP(=O)([C@@](C)(c1[n+](c(c(s1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O" VMI SMILES "OpenEye OEToolkits" 2.0.7 "CCCCOP(=O)(C(C)(c1[n+](c(c(s1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O" # _pdbx_chem_comp_identifier.comp_id VMI _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(1~{S})-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]-butoxy-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 VMI "Create component" 2023-03-20 PDBE VMI "Initial release" 2023-05-10 RCSB VMI "Modify charge" 2023-10-19 PDBE #