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: ZZJ7N
Calculation Name: 5B83-E-Xray547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5B83
Chain ID: E
UniProt ID: Q96CV9
Base Structure: X-ray
Registration Date: 2025-10-05
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 | 50 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -200777.599346 |
|---|---|
| FMO2-HF: Nuclear repulsion | 179569.613797 |
| FMO2-HF: Total energy | -21207.985549 |
| FMO2-MP2: Total energy | -21268.084766 |
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:453:LYS)
Summations of interaction energy for
fragment #1(A:453:LYS)
| 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. |
| -324.638 | -319.479 | 9.47 | -6.73 | -7.899 | -0.077 |
Interaction energy analysis for fragmet #1(A:453:LYS)
| 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 | 455 | GLU | -1 | -0.889 | -0.946 | 2.201 | -135.939 | -131.069 | 9.468 | -6.546 | -7.792 | -0.076 |
| 4 | A | 456 | GLU | -1 | -0.857 | -0.934 | 4.084 | -97.101 | -96.812 | 0.002 | -0.184 | -0.107 | -0.001 |
| 5 | A | 457 | ASP | -1 | -0.885 | -0.941 | 7.060 | -56.114 | -56.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 458 | LEU | 0 | -0.083 | -0.051 | 6.079 | 6.362 | 6.362 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 459 | GLU | -1 | -0.918 | -0.944 | 9.162 | -46.748 | -46.748 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 460 | THR | 0 | 0.025 | 0.003 | 11.310 | 4.749 | 4.749 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 461 | MET | 0 | -0.018 | 0.004 | 11.303 | 3.849 | 3.849 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 462 | THR | 0 | -0.051 | -0.032 | 14.139 | 2.327 | 2.327 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 463 | ILE | 0 | 0.011 | 0.003 | 16.358 | 2.122 | 2.122 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 464 | LEU | 0 | -0.009 | -0.005 | 16.132 | 1.739 | 1.739 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 465 | ARG | 1 | 0.914 | 0.961 | 15.339 | 34.982 | 34.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 466 | ALA | 0 | 0.081 | 0.046 | 20.352 | 1.262 | 1.262 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 467 | GLN | 0 | -0.021 | -0.009 | 22.259 | 2.044 | 2.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 468 | MET | 0 | -0.027 | -0.008 | 23.228 | 0.855 | 0.855 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 469 | GLU | -1 | -0.929 | -0.981 | 23.282 | -24.959 | -24.959 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 470 | VAL | 0 | -0.006 | 0.003 | 26.456 | 0.986 | 0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 471 | TYR | 0 | 0.020 | 0.006 | 26.437 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 472 | CYS | 0 | -0.073 | -0.025 | 28.812 | 0.964 | 0.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 473 | SER | 0 | 0.010 | -0.001 | 30.635 | 0.859 | 0.859 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 474 | ASP | -1 | -0.870 | -0.945 | 32.124 | -18.555 | -18.555 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 475 | PHE | 0 | -0.054 | -0.023 | 33.690 | 0.776 | 0.776 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 476 | HIS | 0 | -0.010 | -0.014 | 33.194 | 0.976 | 0.976 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 477 | ALA | 0 | -0.011 | 0.003 | 36.881 | 0.562 | 0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 478 | GLU | -1 | -0.895 | -0.945 | 38.333 | -14.912 | -14.912 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 479 | ARG | 1 | 0.858 | 0.938 | 39.508 | 16.152 | 16.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 480 | ALA | 0 | 0.058 | 0.024 | 41.174 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 481 | ALA | 0 | -0.036 | -0.013 | 42.852 | 0.432 | 0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 482 | ARG | 1 | 0.948 | 0.962 | 43.229 | 14.584 | 14.584 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 483 | GLU | -1 | -0.938 | -0.988 | 44.097 | -14.118 | -14.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 484 | LYS | 1 | 0.937 | 0.977 | 44.917 | 14.207 | 14.207 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 485 | ILE | 0 | 0.060 | 0.040 | 48.370 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 486 | HIS | 0 | -0.060 | -0.018 | 49.938 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 487 | GLU | -1 | -0.828 | -0.899 | 51.680 | -11.219 | -11.219 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 488 | GLU | -1 | -0.898 | -0.955 | 52.418 | -11.901 | -11.901 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 489 | LYS | 1 | 0.821 | 0.920 | 54.224 | 11.934 | 11.934 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 490 | GLU | -1 | -0.939 | -0.989 | 54.658 | -11.416 | -11.416 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 491 | GLN | 0 | -0.054 | -0.040 | 57.201 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 492 | LEU | 0 | -0.005 | -0.001 | 59.085 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 493 | ALA | 0 | -0.022 | -0.011 | 60.213 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 494 | LEU | 0 | -0.005 | -0.001 | 61.970 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 495 | GLN | 0 | 0.000 | -0.002 | 63.841 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 496 | LEU | 0 | -0.017 | -0.009 | 64.632 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 497 | ALA | 0 | -0.023 | -0.023 | 66.108 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 498 | VAL | 0 | -0.086 | -0.042 | 67.866 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 499 | LEU | 0 | -0.004 | 0.001 | 69.770 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 500 | LEU | 0 | -0.052 | -0.018 | 68.629 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 501 | LYS | 1 | 0.853 | 0.927 | 71.900 | 8.931 | 8.931 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 502 | GLU | -2 | -1.858 | -1.910 | 75.009 | -16.600 | -16.600 | 0.000 | 0.000 | 0.000 | 0.000 |