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: Y92M2
Calculation Name: 2JOT-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2JOT
Chain ID: A
UniProt ID: P68425
Base Structure: SolutionNMR
Registration Date: 2025-10-04
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 | 52 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -282566.480144 |
|---|---|
| FMO2-HF: Nuclear repulsion | 259414.184273 |
| FMO2-HF: Total energy | -23152.295871 |
| FMO2-MP2: Total energy | -23214.360921 |
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:ILE)
Summations of interaction energy for
fragment #1(A:1:ILE)
| 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. |
| 125.935 | 133.555 | 7.564 | -5.375 | -9.809 | -0.02 |
Interaction energy analysis for fragmet #1(A:1:ILE)
| 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 | THR | 0 | 0.063 | 0.024 | 3.720 | 3.071 | 5.786 | -0.021 | -1.320 | -1.375 | -0.002 |
| 4 | A | 4 | CYS | 0 | -0.103 | -0.069 | 2.465 | -9.855 | -9.457 | 7.255 | -2.140 | -5.512 | -0.004 |
| 5 | A | 5 | ARG | 1 | 0.935 | 0.973 | 2.993 | 57.232 | 58.243 | 0.026 | -0.348 | -0.689 | 0.001 |
| 25 | A | 25 | ARG | 1 | 0.950 | 0.957 | 4.030 | 19.037 | 19.257 | 0.001 | -0.055 | -0.166 | 0.000 |
| 26 | A | 26 | THR | 0 | 0.007 | 0.024 | 5.294 | 0.103 | 0.165 | -0.001 | 0.000 | -0.060 | 0.000 |
| 49 | A | 51 | ARG | 1 | 0.888 | 0.940 | 3.635 | 41.786 | 42.129 | 0.005 | -0.076 | -0.273 | 0.000 |
| 50 | A | 53 | ALA | 0 | 0.014 | 0.028 | 3.513 | -1.608 | -1.191 | 0.006 | -0.097 | -0.326 | -0.001 |
| 52 | A | 55 | ALA | -1 | -0.916 | -0.936 | 2.900 | -61.307 | -58.853 | 0.293 | -1.339 | -1.408 | -0.014 |
| 6 | A | 6 | LEU | 0 | -0.007 | 0.015 | 7.089 | 3.160 | 3.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.038 | 0.009 | 9.900 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | SER | 0 | -0.063 | -0.052 | 11.960 | 0.745 | 0.745 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.828 | -0.906 | 14.026 | -14.074 | -14.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | ARG | 1 | 0.889 | 0.927 | 17.777 | 13.005 | 13.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | 0.000 | -0.004 | 20.256 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ARG | 1 | 0.948 | 0.957 | 22.759 | 10.425 | 10.425 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | CYS | 0 | -0.070 | -0.030 | 21.619 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LYS | 1 | 0.973 | 0.991 | 28.199 | 9.282 | 9.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | 0.023 | 0.030 | 26.765 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | SER | 0 | 0.011 | -0.014 | 25.995 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PHE | 0 | 0.050 | 0.036 | 23.625 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLU | -1 | -0.920 | -0.953 | 21.591 | -12.448 | -12.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ARG | 1 | 0.875 | 0.946 | 17.467 | 13.671 | 13.671 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | TRP | 0 | 0.025 | -0.001 | 13.816 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | TYR | 0 | -0.025 | -0.003 | 11.247 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PHE | 0 | -0.006 | 0.011 | 6.231 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ASN | 0 | 0.020 | 0.018 | 8.298 | 1.500 | 1.500 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | GLY | 0 | 0.036 | 0.015 | 6.200 | 1.071 | 1.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | CYS | 0 | -0.046 | -0.013 | 8.546 | -3.412 | -3.412 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ALA | 0 | 0.021 | 0.024 | 10.617 | 1.010 | 1.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | LYS | 1 | 0.971 | 0.978 | 13.520 | 13.392 | 13.392 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | PHE | 0 | 0.002 | 0.009 | 15.898 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ILE | 0 | 0.006 | 0.018 | 19.487 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | TYR | 0 | -0.033 | -0.033 | 18.252 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | GLY | 0 | 0.034 | 0.018 | 21.251 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | GLY | 0 | -0.013 | -0.016 | 21.257 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 36 | GLY | 0 | 0.118 | 0.059 | 19.344 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 37 | GLY | 0 | -0.016 | -0.013 | 15.429 | -0.304 | -0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | ASN | 0 | 0.063 | 0.029 | 11.925 | -0.736 | -0.736 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | GLY | 0 | 0.023 | 0.007 | 9.568 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ASN | 0 | -0.007 | 0.020 | 7.985 | 0.492 | 0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | LYS | 1 | 0.867 | 0.945 | 9.368 | 18.627 | 18.627 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | PHE | 0 | 0.037 | 0.001 | 8.538 | -0.370 | -0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | PRO | 0 | 0.003 | -0.005 | 13.494 | 0.802 | 0.802 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | THR | 0 | 0.064 | 0.018 | 15.318 | 0.323 | 0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | GLN | 0 | 0.013 | -0.005 | 12.756 | -1.468 | -1.468 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 46 | GLU | -1 | -0.900 | -0.936 | 11.984 | -18.195 | -18.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 47 | ALA | 0 | 0.015 | 0.013 | 11.174 | -1.322 | -1.322 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 49 | MET | 0 | 0.044 | -0.003 | 7.275 | -3.825 | -3.825 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 50 | LYS | 1 | 0.947 | 0.975 | 7.365 | 20.616 | 20.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 54 | LYS | 1 | 0.906 | 0.963 | 5.927 | 24.538 | 24.538 | 0.000 | 0.000 | 0.000 | 0.000 |