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: ZVY2N
Calculation Name: 5B83-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 5B83
Chain ID: B
UniProt ID: Q96CV9
Base Structure: X-ray
Registration Date: 2023-09-20
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 59 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -251612.625717 |
|---|---|
| FMO2-HF: Nuclear repulsion | 226236.303535 |
| FMO2-HF: Total energy | -25376.322182 |
| FMO2-MP2: Total energy | -25446.894793 |
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(B:443:GLN)
Summations of interaction energy for
fragment #1(B:443:GLN)
| 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. |
| -2.564 | -1.28 | -0.015 | -0.499 | -0.77 | 0 |
Interaction energy analysis for fragmet #1(B:443:GLN)
| 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 | B | 445 | ASP | -1 | -0.836 | -0.930 | 3.845 | -4.090 | -2.806 | -0.015 | -0.499 | -0.770 | 0.000 |
| 4 | B | 446 | GLU | -1 | -0.881 | -0.956 | 6.509 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 447 | MET | 0 | -0.011 | 0.006 | 8.225 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 448 | LYS | 1 | 0.983 | 0.997 | 9.994 | 1.127 | 1.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 449 | GLN | 0 | 0.000 | 0.015 | 12.103 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 450 | THR | 0 | -0.019 | -0.029 | 12.556 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 451 | ILE | 0 | -0.028 | -0.012 | 12.964 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 452 | ALA | 0 | 0.019 | 0.014 | 15.968 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 453 | LYS | 1 | 0.769 | 0.874 | 17.559 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 454 | GLN | 0 | 0.012 | 0.004 | 17.976 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 455 | GLU | -1 | -0.936 | -0.977 | 18.938 | -0.344 | -0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 456 | GLU | -1 | -0.846 | -0.910 | 22.067 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 457 | ASP | -1 | -0.845 | -0.909 | 23.344 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 458 | LEU | 0 | -0.071 | -0.043 | 22.798 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 459 | GLU | -1 | -0.932 | -0.960 | 26.031 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 460 | THR | 0 | 0.028 | 0.005 | 27.769 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 461 | MET | 0 | -0.025 | 0.001 | 28.355 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 462 | THR | 0 | -0.104 | -0.055 | 30.277 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 463 | ILE | 0 | 0.054 | 0.029 | 32.456 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 464 | LEU | 0 | -0.008 | -0.008 | 32.074 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 465 | ARG | 1 | 0.903 | 0.950 | 32.299 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 466 | ALA | 0 | 0.039 | 0.022 | 36.626 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 467 | GLN | 0 | -0.004 | -0.007 | 38.094 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 468 | MET | 0 | -0.044 | -0.020 | 39.200 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 469 | GLU | -1 | -0.945 | -0.988 | 39.684 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 470 | VAL | 0 | 0.008 | 0.013 | 42.695 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 471 | TYR | 0 | 0.021 | 0.003 | 41.833 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 472 | CYS | 0 | -0.088 | -0.029 | 45.215 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 473 | SER | 0 | 0.006 | -0.015 | 46.970 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 474 | ASP | -1 | -0.897 | -0.940 | 48.342 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 475 | PHE | 0 | 0.000 | 0.004 | 49.899 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 476 | HIS | 0 | -0.018 | -0.006 | 49.799 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 477 | ALA | 0 | 0.006 | 0.009 | 53.290 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 478 | GLU | -1 | -0.899 | -0.948 | 54.390 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 479 | ARG | 1 | 0.798 | 0.895 | 55.758 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 480 | ALA | 0 | 0.011 | 0.004 | 57.580 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 481 | ALA | 0 | 0.017 | 0.019 | 59.023 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 482 | ARG | 1 | 0.958 | 0.966 | 59.225 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 483 | GLU | -1 | -0.912 | -0.964 | 60.576 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 484 | LYS | 1 | 0.859 | 0.920 | 63.448 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 485 | ILE | 0 | 0.031 | 0.015 | 64.354 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 486 | HIS | 0 | 0.004 | -0.003 | 65.946 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 487 | GLU | -1 | -0.904 | -0.949 | 67.720 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 488 | GLU | -1 | -0.852 | -0.919 | 68.948 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 489 | LYS | 1 | 0.800 | 0.890 | 69.667 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 490 | GLU | -1 | -0.877 | -0.936 | 71.229 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 491 | GLN | 0 | -0.049 | -0.024 | 73.643 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 492 | LEU | 0 | -0.018 | -0.008 | 74.556 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 493 | ALA | 0 | 0.014 | 0.013 | 75.984 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 494 | LEU | 0 | 0.010 | 0.015 | 77.902 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 495 | GLN | 0 | -0.037 | -0.026 | 79.885 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | B | 496 | LEU | 0 | -0.015 | -0.008 | 79.408 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | B | 497 | ALA | 0 | 0.010 | 0.004 | 81.665 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | B | 498 | VAL | 0 | -0.060 | -0.041 | 83.542 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | B | 499 | LEU | 0 | -0.051 | -0.012 | 85.477 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | B | 500 | LEU | 0 | -0.018 | -0.002 | 87.873 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | B | 501 | LYS | 1 | 0.935 | 0.983 | 87.059 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |