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: 24Z9R
Calculation Name: 2JWG-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2JWG
Chain ID: A
UniProt ID: P26329
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 | 44 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -208061.558173 |
|---|---|
| FMO2-HF: Nuclear repulsion | 189138.075656 |
| FMO2-HF: Total energy | -18923.482517 |
| FMO2-MP2: Total energy | -18975.498624 |
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:382:GLY)
Summations of interaction energy for
fragment #1(A:382:GLY)
| 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. |
| -94.7 | -92.967 | 16.986 | -10.951 | -7.77 | -0.138 |
Interaction energy analysis for fragmet #1(A:382:GLY)
| 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 | 384 | SER | 0 | 0.076 | 0.022 | 3.763 | -0.450 | 0.520 | -0.002 | -0.393 | -0.575 | 0.001 |
| 7 | A | 388 | GLU | -1 | -0.843 | -0.909 | 1.837 | -143.307 | -142.572 | 16.990 | -10.557 | -7.169 | -0.139 |
| 8 | A | 389 | CYS | 0 | 0.035 | 0.048 | 5.356 | 1.749 | 1.777 | -0.002 | -0.001 | -0.026 | 0.000 |
| 4 | A | 385 | PRO | 0 | 0.041 | 0.012 | 5.205 | -2.579 | -2.579 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 386 | GLU | -1 | -0.920 | -0.947 | 6.188 | -24.642 | -24.642 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 387 | ALA | 0 | -0.012 | -0.007 | 5.785 | 1.721 | 1.721 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 390 | ASN | 0 | 0.013 | -0.018 | 9.128 | 3.264 | 3.264 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 391 | LYS | 1 | 0.898 | 0.960 | 4.825 | 54.113 | 54.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 392 | ILE | 0 | 0.016 | 0.018 | 8.482 | 1.201 | 1.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 393 | THR | 0 | -0.121 | -0.066 | 11.474 | 1.885 | 1.885 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 394 | GLU | -1 | -0.844 | -0.924 | 14.828 | -15.766 | -15.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 395 | GLU | -1 | -0.895 | -0.962 | 16.358 | -14.727 | -14.727 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 396 | PRO | 0 | 0.007 | -0.002 | 18.294 | -0.417 | -0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 397 | LYS | 1 | 1.000 | 0.994 | 13.729 | 19.167 | 19.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 398 | CYS | 0 | -0.034 | 0.009 | 12.823 | -1.054 | -1.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 399 | SER | 0 | -0.053 | -0.032 | 14.590 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 400 | GLU | -1 | -0.965 | -0.965 | 15.992 | -16.305 | -16.305 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 401 | GLU | -1 | -0.942 | -0.964 | 9.576 | -31.014 | -31.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 402 | LYS | 1 | 0.931 | 0.969 | 9.576 | 24.037 | 24.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 403 | ILE | 0 | -0.060 | -0.032 | 8.811 | -2.688 | -2.688 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 405 | SER | 0 | 0.054 | 0.025 | 12.032 | 2.101 | 2.101 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 406 | TRP | 0 | 0.031 | 0.026 | 15.677 | -0.929 | -0.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 407 | HIS | 1 | 0.788 | 0.901 | 17.915 | 16.132 | 16.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 408 | LYS | 1 | 0.974 | 0.970 | 19.976 | 12.326 | 12.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 409 | GLU | -1 | -0.884 | -0.922 | 23.102 | -11.269 | -11.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 410 | VAL | 0 | -0.025 | -0.015 | 20.158 | -0.648 | -0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 411 | LYS | 1 | 0.912 | 0.957 | 23.410 | 13.050 | 13.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 412 | ALA | 0 | 0.025 | 0.003 | 22.946 | -0.649 | -0.649 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 413 | GLY | 0 | 0.024 | 0.013 | 21.046 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 414 | GLU | -1 | -0.867 | -0.919 | 18.981 | -14.829 | -14.829 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 415 | LYS | 1 | 0.906 | 0.944 | 13.981 | 18.805 | 18.805 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 416 | ASN | 0 | 0.011 | 0.024 | 16.884 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 418 | GLN | 0 | 0.014 | -0.010 | 12.330 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 419 | PHE | 0 | 0.057 | 0.008 | 10.156 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 420 | ASN | 0 | -0.024 | -0.033 | 12.095 | 1.820 | 1.820 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 421 | SER | 0 | 0.024 | 0.013 | 13.271 | 1.357 | 1.357 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 422 | THR | 0 | 0.024 | -0.003 | 14.642 | -0.456 | -0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 423 | LYS | 1 | 0.910 | 0.967 | 17.204 | 16.370 | 16.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 424 | ALA | 0 | -0.027 | -0.009 | 14.709 | 0.508 | 0.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 425 | SER | 0 | -0.029 | -0.024 | 16.698 | 0.591 | 0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 426 | LYS | 1 | 0.884 | 0.948 | 16.288 | 15.918 | 15.918 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 427 | SER | -1 | -0.859 | -0.923 | 14.975 | -18.836 | -18.836 | 0.000 | 0.000 | 0.000 | 0.000 |