FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 8KQRY
Calculation Name: 6OSK-T-Other547
Preferred Name:
Target Type:
Ligand Name: n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6n-dimethyladenosine-5'-monophoshate | 2-methyladenosine-5'-monophosphate | 4n,o2'-methylcytidine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 3-methyluridine-5'-monophoshate | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (3s)-3-(methylsulfanyl)-l-aspartic acid | n-formylmethionine
Ligand 3-letter code: G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMC | OMU | 0TD | FME
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6OSK
Chain ID: T
UniProt ID: P0ADY7
Base Structure: ElectronMicroscopy
Registration Date: 2025-10-06
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 94 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -635518.938238 |
|---|---|
| FMO2-HF: Nuclear repulsion | 598726.553477 |
| FMO2-HF: Total energy | -36792.384762 |
| FMO2-MP2: Total energy | -36900.943076 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
| IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
|---|---|---|---|---|---|
| IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
| 102.596 | 106.104 | 0.985 | -1.541 | -2.951 | -0.011 |
Interaction energy analysis for fragmet #1(A:1:MET)
| frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | A | 3 | ARG | 1 | 0.955 | 0.977 | 2.642 | 23.097 | 25.623 | 0.633 | -1.318 | -1.841 | -0.011 |
| 7 | A | 7 | LEU | 0 | -0.004 | -0.014 | 2.931 | 1.649 | 2.072 | 0.063 | -0.079 | -0.407 | 0.000 |
| 45 | A | 45 | ALA | 0 | 0.008 | 0.006 | 2.865 | -0.537 | -0.161 | 0.291 | -0.139 | -0.528 | 0.000 |
| 46 | A | 46 | ALA | 0 | -0.018 | -0.014 | 4.321 | -0.185 | -0.133 | -0.001 | -0.003 | -0.048 | 0.000 |
| 49 | A | 49 | LYS | 1 | 0.843 | 0.937 | 4.670 | 34.543 | 34.674 | -0.001 | -0.002 | -0.127 | 0.000 |
| 4 | A | 4 | GLU | -1 | -0.802 | -0.925 | 4.959 | -32.731 | -32.731 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | GLU | -1 | -0.807 | -0.900 | 6.470 | -20.362 | -20.362 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | ARG | 1 | 0.831 | 0.921 | 7.320 | 29.153 | 29.153 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LEU | 0 | 0.051 | 0.030 | 7.551 | 1.991 | 1.991 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LYS | 1 | 0.861 | 0.936 | 10.830 | 21.455 | 21.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | VAL | 0 | -0.010 | 0.005 | 9.124 | 1.650 | 1.650 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | LEU | 0 | 0.031 | 0.017 | 11.090 | 1.327 | 1.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ARG | 1 | 0.809 | 0.902 | 13.640 | 16.536 | 16.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | ALA | 0 | 0.032 | 0.014 | 17.411 | 0.466 | 0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | PRO | 0 | 0.149 | 0.082 | 18.587 | -0.444 | -0.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | HIS | 0 | -0.074 | -0.054 | 20.260 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | VAL | 0 | 0.093 | 0.058 | 23.023 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | -0.065 | -0.056 | 26.261 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLU | -1 | -0.805 | -0.882 | 28.306 | -8.507 | -8.507 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | LYS | 1 | 0.955 | 0.978 | 26.246 | 9.992 | 9.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | ALA | 0 | -0.069 | -0.047 | 23.926 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | SER | 0 | 0.074 | 0.031 | 24.513 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | THR | 0 | -0.003 | -0.012 | 26.822 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ALA | 0 | -0.052 | -0.033 | 22.919 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | MET | 0 | 0.041 | 0.026 | 21.128 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | GLU | -1 | -0.909 | -0.960 | 23.359 | -9.206 | -9.206 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LYS | 1 | 0.934 | 0.973 | 26.361 | 9.000 | 9.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | SER | 0 | -0.077 | -0.043 | 23.077 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ASN | 0 | 0.019 | 0.029 | 19.025 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | THR | 0 | -0.043 | -0.024 | 18.436 | -0.830 | -0.830 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ILE | 0 | 0.073 | 0.055 | 14.444 | 0.523 | 0.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | VAL | 0 | -0.075 | -0.042 | 17.824 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | LEU | 0 | 0.043 | 0.020 | 14.026 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | LYS | 1 | 0.813 | 0.908 | 17.997 | 12.455 | 12.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | VAL | 0 | 0.020 | 0.006 | 14.042 | -0.350 | -0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | ALA | 0 | 0.031 | 0.020 | 14.539 | 0.954 | 0.954 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | LYS | 1 | 0.880 | 0.929 | 16.102 | 12.465 | 12.465 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | ASP | -1 | -0.876 | -0.947 | 16.124 | -17.923 | -17.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | ALA | 0 | 0.033 | 0.046 | 11.857 | -1.281 | -1.281 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | THR | 0 | 0.007 | 0.003 | 10.082 | 1.855 | 1.855 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | LYS | 1 | 0.965 | 0.975 | 10.519 | 15.466 | 15.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | ALA | 0 | 0.044 | 0.022 | 7.312 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | GLU | -1 | -0.839 | -0.924 | 5.815 | -31.746 | -31.746 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | ILE | 0 | -0.011 | -0.014 | 7.112 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | LYS | 1 | 0.883 | 0.953 | 6.688 | 22.398 | 22.398 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | VAL | 0 | 0.020 | 0.004 | 7.225 | 0.942 | 0.942 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | GLN | 0 | -0.007 | -0.011 | 5.550 | 1.413 | 1.413 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 50 | LEU | 0 | -0.050 | -0.039 | 7.049 | 0.522 | 0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 51 | PHE | 0 | 0.006 | 0.008 | 10.340 | 1.125 | 1.125 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 52 | GLU | -1 | -0.919 | -0.944 | 10.199 | -18.295 | -18.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | A | 53 | VAL | 0 | 0.061 | 0.050 | 10.789 | 0.776 | 0.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | A | 54 | GLU | -1 | -0.829 | -0.911 | 10.285 | -18.689 | -18.689 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | A | 55 | VAL | 0 | -0.035 | -0.020 | 9.358 | 0.838 | 0.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | A | 56 | GLU | -1 | -0.898 | -0.938 | 11.062 | -15.132 | -15.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | A | 57 | VAL | 0 | -0.020 | -0.021 | 12.614 | -1.142 | -1.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | A | 58 | VAL | 0 | 0.016 | 0.016 | 10.577 | 0.299 | 0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | A | 59 | ASN | 0 | -0.010 | -0.005 | 13.714 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | A | 60 | THR | 0 | 0.002 | -0.014 | 15.043 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | A | 61 | LEU | 0 | -0.003 | 0.009 | 18.037 | 0.357 | 0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | A | 62 | VAL | 0 | 0.022 | 0.004 | 21.051 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 63 | A | 63 | VAL | 0 | 0.008 | 0.016 | 23.021 | 0.566 | 0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 64 | A | 64 | LYS | 1 | 0.902 | 0.941 | 25.805 | 10.789 | 10.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 65 | A | 65 | GLY | 0 | 0.017 | 0.011 | 28.689 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 66 | A | 66 | LYS | 1 | 0.941 | 0.960 | 30.228 | 8.997 | 8.997 | 0.000 | 0.000 | 0.000 | 0.000 |
| 67 | A | 67 | VAL | 0 | 0.045 | 0.025 | 33.672 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 68 | A | 68 | LYS | 1 | 0.911 | 0.952 | 36.428 | 7.982 | 7.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 69 | A | 69 | ARG | 1 | 0.935 | 0.961 | 38.615 | 6.768 | 6.768 | 0.000 | 0.000 | 0.000 | 0.000 |
| 70 | A | 70 | HIS | 0 | 0.013 | 0.022 | 40.201 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 71 | A | 71 | GLY | 0 | 0.078 | 0.037 | 42.180 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 72 | A | 72 | GLN | 0 | 0.048 | 0.008 | 45.982 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 73 | A | 73 | ARG | 1 | 0.961 | 1.001 | 41.992 | 7.058 | 7.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 74 | A | 74 | ILE | 0 | 0.028 | 0.013 | 40.225 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 75 | A | 75 | GLY | 0 | 0.061 | 0.019 | 37.649 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 76 | A | 76 | ARG | 1 | 0.853 | 0.932 | 29.715 | 9.802 | 9.802 | 0.000 | 0.000 | 0.000 | 0.000 |
| 77 | A | 77 | ARG | 1 | 0.946 | 0.976 | 30.544 | 8.810 | 8.810 | 0.000 | 0.000 | 0.000 | 0.000 |
| 78 | A | 78 | SER | 0 | 0.075 | 0.028 | 26.168 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 79 | A | 79 | ASP | -1 | -0.811 | -0.905 | 25.061 | -10.842 | -10.842 | 0.000 | 0.000 | 0.000 | 0.000 |
| 80 | A | 80 | TRP | 0 | -0.012 | -0.011 | 21.759 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
| 81 | A | 81 | LYS | 1 | 0.834 | 0.920 | 15.907 | 17.406 | 17.406 | 0.000 | 0.000 | 0.000 | 0.000 |
| 82 | A | 82 | LYS | 1 | 0.921 | 0.978 | 19.377 | 11.178 | 11.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 83 | A | 83 | ALA | 0 | 0.005 | -0.008 | 15.000 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 84 | A | 84 | TYR | 0 | -0.009 | 0.000 | 17.134 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
| 85 | A | 85 | VAL | 0 | 0.012 | -0.007 | 12.162 | -0.388 | -0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
| 86 | A | 86 | THR | 0 | 0.008 | 0.010 | 15.156 | 0.363 | 0.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 87 | A | 87 | LEU | 0 | 0.009 | 0.008 | 13.792 | -1.262 | -1.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 88 | A | 88 | LYS | 1 | 0.878 | 0.929 | 12.393 | 18.305 | 18.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 89 | A | 89 | GLU | -1 | -0.897 | -0.951 | 16.657 | -11.332 | -11.332 | 0.000 | 0.000 | 0.000 | 0.000 |
| 90 | A | 90 | GLY | 0 | -0.016 | -0.010 | 19.602 | -0.245 | -0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 91 | A | 91 | GLN | 0 | -0.075 | -0.037 | 15.407 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 92 | A | 92 | ASN | 0 | 0.025 | 0.013 | 18.357 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 93 | A | 93 | LEU | 0 | -0.101 | -0.054 | 15.026 | -0.814 | -0.814 | 0.000 | 0.000 | 0.000 | 0.000 |
| 94 | A | 94 | ASP | -2 | -1.860 | -1.916 | 18.945 | -25.228 | -25.228 | 0.000 | 0.000 | 0.000 | 0.000 |