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: 4991N
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 | 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 | 53 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -246819.504761 |
|---|---|
| FMO2-HF: Nuclear repulsion | 223319.048158 |
| FMO2-HF: Total energy | -23500.456604 |
| FMO2-MP2: Total energy | -23569.192347 |
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. |
| 58.097 | 64.484 | 0.199 | -3.004 | -3.582 | -0.004 |
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 | -0.964 | -0.971 | 2.973 | 28.237 | 33.523 | 0.189 | -2.680 | -2.795 | -0.004 |
| 4 | B | 273 | GLU | -1 | -0.863 | -0.933 | 3.258 | 23.734 | 24.675 | 0.011 | -0.314 | -0.639 | 0.000 |
| 5 | B | 274 | GLU | -1 | -0.939 | -0.991 | 4.651 | 26.882 | 27.042 | -0.001 | -0.010 | -0.148 | 0.000 |
| 6 | B | 275 | GLU | -1 | -0.970 | -0.972 | 6.981 | 19.659 | 19.659 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 276 | TYR | 0 | -0.010 | -0.015 | 7.506 | -2.900 | -2.900 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 277 | GLU | -1 | -0.913 | -0.962 | 8.886 | 17.564 | 17.564 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 278 | ALA | 0 | -0.021 | -0.018 | 10.957 | -1.736 | -1.736 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 279 | TRP | 0 | -0.081 | -0.043 | 12.175 | -1.309 | -1.309 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 280 | LYS | 1 | 0.974 | 0.991 | 12.210 | -18.418 | -18.418 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 281 | VAL | 0 | -0.006 | 0.012 | 15.087 | -1.112 | -1.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 282 | ARG | 1 | 0.912 | 0.952 | 13.746 | -17.363 | -17.363 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 283 | GLU | -1 | -0.801 | -0.877 | 17.825 | 11.844 | 11.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 284 | LEU | 0 | 0.004 | 0.004 | 18.418 | -0.645 | -0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 285 | LYS | 1 | 0.875 | 0.943 | 20.579 | -13.282 | -13.282 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 286 | ARG | 1 | 0.840 | 0.889 | 18.400 | -13.286 | -13.286 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 287 | ILE | 0 | 0.039 | 0.029 | 21.815 | -0.419 | -0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 288 | LYS | 1 | 0.899 | 0.951 | 25.163 | -10.065 | -10.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 289 | ARG | 1 | 0.884 | 0.939 | 26.525 | -10.193 | -10.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 290 | ASP | -1 | -0.819 | -0.902 | 27.342 | 9.580 | 9.580 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 291 | ARG | 1 | 0.870 | 0.938 | 28.871 | -9.239 | -9.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 292 | GLU | -1 | -0.873 | -0.945 | 30.876 | 8.661 | 8.661 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 293 | ASP | -1 | -0.893 | -0.943 | 32.754 | 8.293 | 8.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 294 | ARG | 1 | 0.873 | 0.935 | 32.671 | -8.430 | -8.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 295 | GLU | -1 | -0.897 | -0.952 | 33.890 | 8.019 | 8.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 296 | ALA | 0 | -0.037 | -0.010 | 36.939 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 297 | LEU | 0 | 0.020 | -0.004 | 38.481 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 298 | GLU | -1 | -0.954 | -0.976 | 36.697 | 7.456 | 7.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 299 | LYS | 1 | 0.953 | 0.974 | 40.696 | -6.850 | -6.850 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 300 | GLU | -1 | -0.952 | -0.970 | 42.950 | 6.523 | 6.523 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 301 | LYS | 1 | 0.921 | 0.949 | 42.788 | -6.788 | -6.788 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 302 | ALA | 0 | 0.027 | 0.023 | 44.794 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 303 | GLU | -1 | -0.930 | -0.957 | 46.551 | 5.676 | 5.676 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 304 | ILE | 0 | -0.020 | -0.022 | 47.808 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 305 | GLU | -1 | -0.945 | -0.985 | 48.545 | 5.838 | 5.838 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 306 | ARG | 1 | 0.942 | 0.991 | 50.670 | -5.719 | -5.719 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 307 | MET | 0 | -0.035 | -0.020 | 52.479 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 308 | ARG | 1 | 0.914 | 0.957 | 50.446 | -5.796 | -5.796 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 309 | ASN | 0 | 0.062 | 0.024 | 52.365 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 310 | LEU | 0 | -0.008 | 0.009 | 56.305 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 311 | THR | 0 | 0.034 | 0.016 | 58.551 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 312 | GLU | -1 | -0.991 | -0.995 | 57.175 | 5.127 | 5.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 313 | GLU | -1 | -1.011 | -1.018 | 58.046 | 5.025 | 5.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 314 | GLU | -1 | -0.894 | -0.959 | 62.060 | 4.729 | 4.729 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 315 | ARG | 1 | 0.996 | 1.014 | 64.114 | -4.628 | -4.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 316 | ARG | 1 | 0.908 | 0.941 | 61.166 | -4.894 | -4.894 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 317 | ALA | 0 | -0.031 | -0.016 | 66.284 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 318 | GLU | -1 | -0.913 | -0.951 | 68.082 | 4.330 | 4.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 319 | LEU | 0 | -0.061 | -0.027 | 68.568 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 320 | ARG | 1 | 0.864 | 0.933 | 66.563 | -4.508 | -4.508 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 321 | ALA | 0 | -0.030 | 0.006 | 72.225 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 322 | ASN | 0 | -0.056 | -0.022 | 73.583 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |