data_VMI
# 
_chem_comp.id                                    VMI 
_chem_comp.name                                  "[(1~{S})-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-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                    0 
_chem_comp.pdbx_initial_date                     2023-03-20 
_chem_comp.pdbx_modified_date                    2023-05-05 
_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   Y 
_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 
VMI C5  C1  C 0 1 N N S 9.132  -3.857  14.486 ? ? ? C5  VMI 1  
VMI C4  C2  C 0 1 N N N 8.767  -6.739  11.679 ? ? ? C4  VMI 2  
VMI C6  C3  C 0 1 N N N 7.672  -3.843  14.928 ? ? ? C6  VMI 3  
VMI N3  N1  N 0 1 Y N N 11.349 1.297   13.970 ? ? ? N3  VMI 4  
VMI C2  C4  C 0 1 N N N 7.988  -9.062  11.056 ? ? ? C2  VMI 5  
VMI S1  S1  S 0 1 Y N N 9.549  -3.614  17.229 ? ? ? S1  VMI 6  
VMI C7  C5  C 0 1 Y N N 10.029 -3.409  15.598 ? ? ? C7  VMI 7  
VMI C1  C6  C 0 1 N N N 7.446  -10.297 11.730 ? ? ? C1  VMI 8  
VMI C8  C7  C 0 1 Y N N 11.119 -3.160  17.761 ? ? ? C8  VMI 9  
VMI C9  C8  C 0 1 N N N 11.423 -3.158  19.231 ? ? ? C9  VMI 10 
VMI O2  O1  O 0 1 N N N 10.970 -5.538  13.491 ? ? ? O2  VMI 11 
VMI O3  O2  O 0 1 N N N 9.175  -6.504  15.005 ? ? ? O3  VMI 12 
VMI O4  O3  O 0 1 N N N 9.228  -3.007  13.350 ? ? ? O4  VMI 13 
VMI C10 C9  C 0 1 N N N 10.306 -2.538  20.010 ? ? ? C10 VMI 14 
VMI C11 C10 C 0 1 Y N N 11.940 -2.843  16.734 ? ? ? C11 VMI 15 
VMI C12 C11 C 0 1 N N N 13.392 -2.503  16.852 ? ? ? C12 VMI 16 
VMI C13 C12 C 0 1 N N N 11.930 -2.445  14.245 ? ? ? C13 VMI 17 
VMI C14 C13 C 0 1 Y N N 12.166 -0.953  14.154 ? ? ? C14 VMI 18 
VMI C15 C14 C 0 1 Y N N 13.439 -0.424  14.126 ? ? ? C15 VMI 19 
VMI C16 C15 C 0 1 Y N N 12.618 1.699   13.961 ? ? ? C16 VMI 20 
VMI C17 C16 C 0 1 N N N 12.873 3.166   13.862 ? ? ? C17 VMI 21 
VMI C18 C17 C 0 1 Y N N 11.116 -0.019  14.057 ? ? ? C18 VMI 22 
VMI C3  C18 C 0 1 N N N 7.723  -7.810  11.843 ? ? ? C3  VMI 23 
VMI N1  N2  N 4 1 Y N N 11.292 -2.873  15.498 ? ? ? N1  VMI 24 
VMI N2  N3  N 0 1 Y N N 13.674 0.888   14.031 ? ? ? N2  VMI 25 
VMI N4  N4  N 0 1 N N N 9.836  -0.406  14.053 ? ? ? N4  VMI 26 
VMI O1  O4  O 0 1 N N N 8.571  -5.725  12.684 ? ? ? O1  VMI 27 
VMI O10 O5  O 0 1 N N N 7.927  -5.130  21.657 ? ? ? O10 VMI 28 
VMI O11 O6  O 0 1 N N N 9.170  -4.654  23.737 ? ? ? O11 VMI 29 
VMI O5  O7  O 0 1 N N N 10.705 -2.449  21.387 ? ? ? O5  VMI 30 
VMI O6  O8  O 0 1 N N N 9.316  -0.450  21.988 ? ? ? O6  VMI 31 
VMI O7  O9  O 0 1 N N N 10.299 -1.958  23.792 ? ? ? O7  VMI 32 
VMI O8  O10 O 0 1 N N N 8.422  -2.777  22.283 ? ? ? O8  VMI 33 
VMI O9  O11 O 0 1 N N N 6.759  -4.067  23.574 ? ? ? O9  VMI 34 
VMI P1  P1  P 0 1 N N N 9.538  -5.530  13.926 ? ? ? P1  VMI 35 
VMI P2  P2  P 0 1 N N N 9.689  -1.811  22.444 ? ? ? P2  VMI 36 
VMI P3  P3  P 0 1 N N N 8.053  -4.242  22.842 ? ? ? P3  VMI 37 
VMI H1  H1  H 0 1 N N N 9.768  -7.181  11.793 ? ? ? H1  VMI 38 
VMI H2  H2  H 0 1 N N N 8.677  -6.288  10.680 ? ? ? H2  VMI 39 
VMI H3  H3  H 0 1 N N N 7.549  -4.490  15.809 ? ? ? H3  VMI 40 
VMI H4  H4  H 0 1 N N N 7.376  -2.815  15.184 ? ? ? H4  VMI 41 
VMI H5  H5  H 0 1 N N N 7.038  -4.213  14.109 ? ? ? H5  VMI 42 
VMI H6  H6  H 0 1 N N N 9.075  -9.177  10.932 ? ? ? H6  VMI 43 
VMI H7  H7  H 0 1 N N N 7.515  -8.964  10.068 ? ? ? H7  VMI 44 
VMI H8  H8  H 0 1 N N N 7.668  -11.180 11.112 ? ? ? H8  VMI 45 
VMI H9  H9  H 0 1 N N N 7.917  -10.413 12.717 ? ? ? H9  VMI 46 
VMI H10 H10 H 0 1 N N N 6.357  -10.200 11.853 ? ? ? H10 VMI 47 
VMI H11 H11 H 0 1 N N N 11.566 -4.195  19.570 ? ? ? H11 VMI 48 
VMI H12 H12 H 0 1 N N N 12.345 -2.585  19.407 ? ? ? H12 VMI 49 
VMI H13 H13 H 0 1 N N N 9.946  -6.999  15.258 ? ? ? H13 VMI 50 
VMI H14 H14 H 0 1 N N N 9.021  -2.115  13.603 ? ? ? H14 VMI 51 
VMI H15 H15 H 0 1 N N N 10.095 -1.532  19.619 ? ? ? H15 VMI 52 
VMI H16 H16 H 0 1 N N N 9.404  -3.161  19.925 ? ? ? H16 VMI 53 
VMI H17 H17 H 0 1 N N N 13.693 -2.539  17.909 ? ? ? H17 VMI 54 
VMI H18 H18 H 0 1 N N N 13.986 -3.229  16.277 ? ? ? H18 VMI 55 
VMI H19 H19 H 0 1 N N N 13.565 -1.492  16.456 ? ? ? H19 VMI 56 
VMI H20 H20 H 0 1 N N N 11.283 -2.745  13.407 ? ? ? H20 VMI 57 
VMI H21 H21 H 0 1 N N N 12.901 -2.955  14.159 ? ? ? H21 VMI 58 
VMI H22 H22 H 0 1 N N N 14.281 -1.098  14.183 ? ? ? H22 VMI 59 
VMI H23 H23 H 0 1 N N N 11.914 3.703   13.810 ? ? ? H23 VMI 60 
VMI H24 H24 H 0 1 N N N 13.433 3.501   14.747 ? ? ? H24 VMI 61 
VMI H25 H25 H 0 1 N N N 13.460 3.376   12.956 ? ? ? H25 VMI 62 
VMI H26 H26 H 0 1 N N N 6.755  -7.399  11.520 ? ? ? H26 VMI 63 
VMI H27 H27 H 0 1 N N N 7.670  -8.078  12.908 ? ? ? H27 VMI 64 
VMI H28 H28 H 0 1 N N N 9.245  0.397   13.982 ? ? ? H28 VMI 65 
VMI H29 H29 H 0 1 N N N 9.673  -1.010  13.273 ? ? ? H29 VMI 66 
VMI H30 H30 H 0 1 N N N 9.600  -5.420  23.376 ? ? ? H30 VMI 67 
VMI H31 H31 H 0 1 N N N 10.371 -1.104  24.203 ? ? ? H31 VMI 68 
VMI H32 H32 H 0 1 N N N 6.078  -4.566  23.138 ? ? ? H32 VMI 69 
# 
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/C18H32N4O11P3S/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,(H,24,25)(H,29,30)(H2,19,20,21)(H2,26,27,28)/t18-/m0/s1" 
VMI InChIKey         InChI                1.06  POFXPCWZRLCYSJ-SFHVURJKSA-N                                                                                                                                                                                           
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-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 
# 
