FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-05-02
All entries: 37386
Number of unique PDB entries: 7781
FMODB ID: 7221K
Calculation Name: 5F5V-B-Xray372
Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5F5V
Chain ID: B
ChEMBL ID:
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UniProt ID: G0S6R0
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.
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 | 62 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -306392.13047 |
|---|---|
| FMO2-HF: Nuclear repulsion | 280098.062723 |
| FMO2-HF: Total energy | -26294.067747 |
| FMO2-MP2: Total energy | -26372.3445 |
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:217:THR)
Summations of interaction energy for
fragment #1(B:217:THR)
| 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. |
| -1.47 | 0.083 | -0.017 | -0.62 | -0.917 | 0 |
Interaction energy analysis for fragmet #1(B:217:THR)
| 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 | 219 | ASP | -1 | -0.888 | -0.947 | 3.876 | -1.877 | -0.324 | -0.017 | -0.620 | -0.917 | 0.000 |
| 4 | B | 220 | ASP | -1 | -0.931 | -0.955 | 5.874 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 221 | VAL | 0 | -0.079 | -0.043 | 6.137 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 222 | ASP | -1 | -0.864 | -0.936 | 8.969 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 223 | PRO | 0 | 0.046 | 0.018 | 11.818 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 224 | GLU | -1 | -0.951 | -0.965 | 13.273 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 225 | ALA | 0 | -0.001 | 0.003 | 12.458 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 226 | GLU | -1 | -0.714 | -0.822 | 8.411 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 227 | TYR | 0 | 0.031 | 0.025 | 11.819 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 228 | ALA | 0 | -0.009 | -0.009 | 14.972 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 229 | ALA | 0 | 0.010 | 0.004 | 12.567 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 230 | TRP | 0 | -0.043 | -0.032 | 13.375 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 231 | LYS | 1 | 0.937 | 0.976 | 14.811 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 232 | LEU | 0 | -0.012 | -0.005 | 17.558 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 233 | ARG | 1 | 0.749 | 0.829 | 10.521 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 234 | GLU | -1 | -0.819 | -0.877 | 17.393 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 235 | LEU | 0 | -0.009 | -0.015 | 19.525 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 236 | ARG | 1 | 0.938 | 0.967 | 19.629 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 237 | ARG | 1 | 0.801 | 0.869 | 16.469 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 238 | LEU | 0 | 0.077 | 0.040 | 22.272 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 239 | ARG | 1 | 0.910 | 0.968 | 25.075 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 240 | ARG | 1 | 0.887 | 0.925 | 21.793 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 241 | GLU | -1 | -0.826 | -0.884 | 24.680 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 242 | ARG | 1 | 0.832 | 0.879 | 28.383 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 243 | ASP | -1 | -0.912 | -0.954 | 29.738 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 244 | ALA | 0 | -0.042 | -0.026 | 30.794 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 245 | ILE | 0 | -0.008 | -0.006 | 31.468 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 246 | GLU | -1 | -0.823 | -0.890 | 34.474 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 247 | ALA | 0 | -0.051 | -0.017 | 35.545 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 248 | ARG | 1 | 0.845 | 0.887 | 34.254 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | B | 249 | GLU | -1 | -0.928 | -0.956 | 38.419 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | B | 250 | ARG | 1 | 0.954 | 0.959 | 37.560 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | B | 251 | GLU | -1 | -0.817 | -0.865 | 39.093 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | B | 252 | LEU | 0 | -0.004 | -0.012 | 41.105 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | B | 253 | ALA | 0 | -0.019 | 0.001 | 44.211 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | B | 254 | GLU | -1 | -0.903 | -0.962 | 45.978 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | B | 255 | LEU | 0 | 0.036 | 0.017 | 45.407 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | B | 256 | GLU | -1 | -0.866 | -0.898 | 48.272 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | B | 257 | ARG | 1 | 0.895 | 0.930 | 47.598 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | B | 258 | ARG | 1 | 0.796 | 0.891 | 51.380 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | B | 259 | ARG | 1 | 0.828 | 0.893 | 50.039 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | B | 260 | ASN | 0 | -0.111 | -0.078 | 53.657 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | B | 261 | LEU | 0 | -0.024 | 0.024 | 55.530 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | B | 262 | THR | 0 | 0.032 | 0.012 | 58.416 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | B | 263 | GLU | -1 | -0.936 | -0.980 | 59.821 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | B | 264 | GLU | -1 | -0.928 | -0.966 | 61.125 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | B | 265 | GLU | -1 | -0.820 | -0.924 | 59.631 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | B | 266 | ARG | 1 | 0.865 | 0.946 | 56.061 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | B | 267 | ARG | 1 | 0.907 | 0.964 | 57.541 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | B | 268 | ALA | 0 | 0.040 | 0.020 | 59.892 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | B | 269 | GLU | -1 | -0.819 | -0.900 | 52.743 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | B | 270 | ASP | -1 | -0.806 | -0.902 | 54.305 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | B | 271 | GLU | -1 | -0.868 | -0.939 | 56.214 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | B | 272 | ALA | 0 | 0.024 | 0.039 | 56.584 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 57 | B | 273 | HIS | 1 | 0.833 | 0.901 | 52.070 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 58 | B | 274 | LEU | 0 | -0.031 | -0.017 | 53.862 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 59 | B | 275 | ALA | 0 | -0.012 | -0.002 | 56.149 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 60 | B | 276 | LYS | 1 | 0.804 | 0.897 | 53.653 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 61 | B | 277 | GLN | 0 | -0.014 | 0.003 | 50.617 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 62 | B | 278 | LYS | 1 | 0.872 | 0.944 | 54.451 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |