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: YZZ82
Calculation Name: 5F5S-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5F5S
Chain ID: B
UniProt ID: P55081
Base Structure: X-ray
Registration Date: 2023-06-21
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 | OptAll |
| 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 | 53 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -247548.978595 |
|---|---|
| FMO2-HF: Nuclear repulsion | 224047.487278 |
| FMO2-HF: Total energy | -23501.491317 |
| FMO2-MP2: Total energy | -23570.206295 |
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:270:GLU)
Summations of interaction energy for
fragment #1(B:270:GLU)
| 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. |
| 53.979 | 56.218 | 6.824 | -4.313 | -4.75 | -0.021 |
Interaction energy analysis for fragmet #1(B:270:GLU)
| 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 | 272 | ASP | -1 | -0.932 | -0.965 | 2.047 | 24.346 | 25.731 | 6.822 | -4.104 | -4.103 | -0.021 |
| 4 | B | 273 | GLU | -1 | -0.874 | -0.945 | 3.439 | 23.242 | 23.941 | 0.003 | -0.199 | -0.503 | 0.000 |
| 5 | B | 274 | GLU | -1 | -0.934 | -0.976 | 5.080 | 30.517 | 30.672 | -0.001 | -0.010 | -0.144 | 0.000 |
| 6 | B | 275 | GLU | -1 | -0.820 | -0.887 | 7.426 | 17.513 | 17.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 276 | TYR | 0 | 0.008 | 0.000 | 7.767 | -2.744 | -2.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 277 | GLU | -1 | -0.771 | -0.874 | 9.245 | 16.687 | 16.687 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 278 | ALA | 0 | 0.021 | 0.015 | 11.326 | -1.654 | -1.654 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 279 | TRP | 0 | -0.070 | -0.012 | 12.218 | -1.243 | -1.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 280 | LYS | 1 | 0.853 | 0.904 | 12.412 | -18.569 | -18.569 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 281 | VAL | 0 | -0.028 | -0.010 | 15.277 | -1.102 | -1.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 282 | ARG | 1 | 0.697 | 0.799 | 12.820 | -18.448 | -18.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 283 | GLU | -1 | -0.824 | -0.885 | 17.768 | 11.883 | 11.883 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 284 | LEU | 0 | -0.002 | -0.008 | 18.661 | -0.683 | -0.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 285 | LYS | 1 | 0.893 | 0.948 | 20.855 | -13.390 | -13.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 286 | ARG | 1 | 0.837 | 0.915 | 18.839 | -13.046 | -13.046 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 287 | ILE | 0 | 0.051 | 0.017 | 21.805 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 288 | LYS | 1 | 0.761 | 0.870 | 25.161 | -9.866 | -9.866 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 289 | ARG | 1 | 0.894 | 0.940 | 27.201 | -10.055 | -10.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 290 | ASP | -1 | -0.839 | -0.913 | 26.994 | 9.588 | 9.588 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 291 | ARG | 1 | 0.815 | 0.906 | 29.317 | -9.113 | -9.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 292 | GLU | -1 | -0.786 | -0.878 | 31.029 | 8.831 | 8.831 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 293 | ASP | -1 | -0.862 | -0.938 | 33.066 | 8.178 | 8.178 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 294 | ARG | 1 | 0.809 | 0.893 | 33.249 | -8.284 | -8.284 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 295 | GLU | -1 | -0.833 | -0.914 | 34.022 | 8.103 | 8.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 296 | ALA | 0 | -0.034 | -0.012 | 37.019 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 297 | LEU | 0 | 0.004 | 0.000 | 38.583 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 298 | GLU | -1 | -0.838 | -0.919 | 37.409 | 7.475 | 7.475 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 299 | LYS | 1 | 0.951 | 0.980 | 40.832 | -6.823 | -6.823 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 300 | GLU | -1 | -0.889 | -0.935 | 43.100 | 6.533 | 6.533 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 301 | LYS | 1 | 0.850 | 0.919 | 42.787 | -6.808 | -6.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 302 | ALA | 0 | 0.022 | 0.016 | 44.735 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 303 | GLU | -1 | -0.852 | -0.905 | 46.569 | 5.667 | 5.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 304 | ILE | 0 | 0.001 | -0.004 | 47.706 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 305 | GLU | -1 | -0.845 | -0.913 | 48.257 | 5.744 | 5.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 306 | ARG | 1 | 0.840 | 0.911 | 50.726 | -5.756 | -5.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 307 | MET | 0 | -0.025 | -0.017 | 52.573 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 308 | ARG | 1 | 0.856 | 0.929 | 50.344 | -5.839 | -5.839 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 309 | ASN | 0 | 0.032 | 0.010 | 52.450 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 310 | LEU | 0 | 0.032 | 0.025 | 56.382 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 311 | THR | 0 | 0.002 | -0.008 | 58.628 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 312 | GLU | -1 | -0.929 | -0.968 | 58.056 | 5.008 | 5.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 313 | GLU | -1 | -0.991 | -0.994 | 58.517 | 5.044 | 5.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 314 | GLU | -1 | -0.914 | -0.964 | 62.099 | 4.708 | 4.708 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 315 | ARG | 1 | 0.918 | 0.965 | 64.147 | -4.582 | -4.582 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 316 | ARG | 1 | 0.837 | 0.908 | 59.070 | -5.038 | -5.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 317 | ALA | 0 | 0.008 | 0.020 | 66.379 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 318 | GLU | -1 | -0.859 | -0.929 | 68.226 | 4.344 | 4.344 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 319 | LEU | 0 | -0.024 | -0.025 | 68.792 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 320 | ARG | 1 | 0.838 | 0.914 | 67.041 | -4.463 | -4.463 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 321 | ALA | 0 | -0.021 | 0.007 | 72.309 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 322 | ASN | 0 | -0.087 | -0.034 | 73.390 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |