FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: G5R31
Calculation Name: 1W0T-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1W0T
Chain ID: A
UniProt ID: P54274
Base Structure: X-ray
Registration Date: 2023-09-23
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
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. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -316731.029927 |
|---|---|
| FMO2-HF: Nuclear repulsion | 294107.108451 |
| FMO2-HF: Total energy | -22623.921476 |
| FMO2-MP2: Total energy | -22690.388245 |
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:379:LYS)
Summations of interaction energy for
fragment #1(A:379: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. |
| 93.746 | 94.998 | 4.243 | -2.124 | -3.371 | -0.021 |
Interaction energy analysis for fragmet #1(A:379: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 | 381 | GLN | 0 | -0.003 | -0.010 | 2.529 | -23.598 | -22.524 | 4.244 | -2.105 | -3.214 | -0.021 |
| 4 | A | 382 | ALA | 0 | 0.020 | 0.022 | 4.594 | 8.425 | 8.603 | -0.001 | -0.019 | -0.157 | 0.000 |
| 5 | A | 383 | TRP | 0 | 0.012 | -0.017 | 6.956 | -0.968 | -0.968 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 384 | LEU | 0 | 0.040 | 0.044 | 8.624 | 0.677 | 0.677 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 385 | TRP | 0 | 0.078 | 0.033 | 11.372 | 1.875 | 1.875 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 386 | GLU | -1 | -0.836 | -0.929 | 13.974 | -21.019 | -21.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 387 | GLU | -1 | -0.789 | -0.890 | 10.023 | -28.180 | -28.180 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 388 | ASP | -1 | -0.759 | -0.878 | 14.641 | -20.092 | -20.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 389 | LYS | 1 | 0.923 | 0.972 | 16.636 | 15.050 | 15.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 390 | ASN | 0 | 0.004 | 0.005 | 17.439 | 1.928 | 1.928 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 391 | LEU | 0 | 0.007 | 0.017 | 16.908 | 0.807 | 0.807 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 392 | ARG | 1 | 0.988 | 0.984 | 19.468 | 15.983 | 15.983 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 393 | SER | 0 | -0.111 | -0.062 | 22.257 | 0.899 | 0.899 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 394 | GLY | 0 | 0.027 | 0.001 | 22.557 | 0.585 | 0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 395 | VAL | 0 | -0.017 | -0.020 | 22.650 | 0.480 | 0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 396 | ARG | 1 | 0.900 | 0.971 | 25.234 | 12.333 | 12.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 397 | LYS | 1 | 0.944 | 0.988 | 27.349 | 11.265 | 11.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 398 | TYR | 0 | -0.009 | -0.016 | 25.601 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 399 | GLY | 0 | 0.061 | 0.046 | 27.960 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 400 | GLU | -1 | -0.846 | -0.953 | 25.319 | -12.475 | -12.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 401 | GLY | 0 | 0.012 | -0.004 | 24.403 | 0.340 | 0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 402 | ASN | 0 | -0.042 | -0.007 | 24.840 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 403 | TRP | 0 | 0.028 | 0.005 | 19.364 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 404 | SER | 0 | 0.041 | 0.004 | 20.111 | -0.724 | -0.724 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 405 | LYS | 1 | 1.009 | 1.013 | 21.174 | 10.831 | 10.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 406 | ILE | 0 | -0.019 | 0.025 | 19.866 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 407 | LEU | 0 | -0.033 | -0.036 | 14.942 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 408 | LEU | 0 | -0.008 | -0.002 | 18.690 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 409 | HIS | 0 | -0.063 | -0.031 | 21.188 | 0.700 | 0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 410 | TYR | 0 | -0.023 | 0.005 | 19.729 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 411 | LYS | 1 | 0.961 | 0.988 | 13.479 | 21.083 | 21.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 412 | PHE | 0 | 0.022 | -0.001 | 13.578 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 413 | ASN | 0 | -0.049 | -0.038 | 8.546 | 1.509 | 1.509 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 414 | ASN | 0 | -0.023 | 0.000 | 6.648 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 415 | ARG | 1 | 0.846 | 0.898 | 7.969 | 30.565 | 30.565 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 416 | THR | 0 | 0.088 | 0.027 | 10.982 | 1.345 | 1.345 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 417 | SER | 0 | 0.057 | 0.016 | 13.380 | -0.479 | -0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 418 | VAL | 0 | 0.046 | 0.016 | 14.406 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 419 | MET | 0 | 0.004 | 0.027 | 8.202 | -0.514 | -0.514 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 420 | LEU | 0 | 0.012 | 0.015 | 13.413 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 421 | LYS | 1 | 0.880 | 0.946 | 16.216 | 16.596 | 16.596 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 422 | ASP | -1 | -0.842 | -0.919 | 14.472 | -17.784 | -17.784 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 423 | ARG | 1 | 0.824 | 0.919 | 13.443 | 21.838 | 21.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 424 | TRP | 0 | 0.054 | 0.024 | 15.995 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 425 | ARG | 1 | 0.918 | 0.962 | 17.364 | 16.333 | 16.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 426 | THR | 0 | -0.088 | -0.063 | 15.544 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 427 | MET | 0 | -0.005 | -0.014 | 17.488 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | A | 428 | LYS | 1 | 0.883 | 0.953 | 19.437 | 12.852 | 12.852 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | A | 429 | LYS | 1 | 0.880 | 0.967 | 19.870 | 15.385 | 15.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | A | 430 | LEU | 0 | 0.018 | 0.012 | 16.914 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |