FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: LJ459
Calculation Name: 3K6G-D-Xray372
Preferred Name: Telomeric repeat-binding factor 2-interacting protein 1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 3K6G
Chain ID: D
ChEMBL ID: CHEMBL3751647
UniProt ID: Q9NYB0
Base Structure: X-ray
Registration Date: 2023-06-20
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 | OptHSide |
| 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 | 33 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -109070.869219 |
|---|---|
| FMO2-HF: Nuclear repulsion | 96503.479892 |
| FMO2-HF: Total energy | -12567.389327 |
| FMO2-MP2: Total energy | -12602.816713 |
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(D:282:THR)
Summations of interaction energy for
fragment #1(D:282: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. |
| 0.61 | 2.582 | 0.051 | -0.832 | -1.191 | 0 |
Interaction energy analysis for fragmet #1(D:282: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 | D | 284 | GLY | 0 | 0.052 | 0.034 | 3.367 | -1.139 | 0.783 | 0.052 | -0.830 | -1.144 | 0.000 |
| 4 | D | 285 | MET | 0 | 0.060 | 0.022 | 4.594 | 0.537 | 0.587 | -0.001 | -0.002 | -0.047 | 0.000 |
| 5 | D | 286 | MET | 0 | 0.032 | 0.000 | 7.236 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | D | 287 | THR | 0 | 0.000 | 0.005 | 7.290 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | D | 288 | LEU | 0 | 0.012 | 0.005 | 7.149 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | D | 289 | LYS | 1 | 0.856 | 0.935 | 9.047 | 0.432 | 0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | D | 290 | ALA | 0 | -0.001 | 0.000 | 12.121 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | D | 291 | ALA | 0 | 0.016 | 0.020 | 11.398 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | D | 292 | PHE | 0 | 0.006 | 0.005 | 13.029 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | D | 293 | LYS | 1 | 0.865 | 0.901 | 14.814 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | D | 294 | THR | 0 | -0.069 | -0.040 | 16.601 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | D | 295 | LEU | 0 | -0.036 | -0.024 | 14.381 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | D | 296 | SER | 0 | -0.053 | -0.008 | 18.294 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | D | 297 | GLY | 0 | 0.040 | 0.027 | 20.270 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | D | 298 | ALA | 0 | 0.024 | 0.020 | 22.678 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | D | 299 | GLN | 0 | -0.044 | -0.032 | 23.257 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | D | 300 | ASP | -1 | -0.868 | -0.939 | 24.401 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | D | 301 | SER | 0 | -0.025 | -0.019 | 19.118 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | D | 302 | GLU | -1 | -0.787 | -0.872 | 18.639 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | D | 303 | ALA | 0 | 0.040 | 0.015 | 18.968 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | D | 304 | ALA | 0 | 0.004 | 0.002 | 20.156 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | D | 305 | PHE | 0 | 0.020 | -0.002 | 10.632 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | D | 306 | ALA | 0 | 0.019 | 0.008 | 15.807 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | D | 307 | LYS | 1 | 0.932 | 0.966 | 17.653 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | D | 308 | LEU | 0 | -0.048 | -0.029 | 15.254 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | D | 309 | ASP | -1 | -0.919 | -0.949 | 12.390 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | D | 310 | GLN | 0 | -0.025 | 0.001 | 14.732 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | D | 311 | LYS | 1 | 0.818 | 0.901 | 18.105 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | D | 312 | ASP | -1 | -0.856 | -0.911 | 17.151 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | D | 313 | LEU | 0 | -0.042 | -0.025 | 13.794 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | D | 314 | VAL | 0 | -0.022 | -0.008 | 17.210 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |