FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-04-05
All entries: 36946
Number of unique PDB entries: 7781
FMODB ID: R92G8
Calculation Name: 1A02-J-Xray372
Preferred Name: Transcription factor AP1
Target Type: PROTEIN COMPLEX
Ligand Name:
ligand 3-letter code:
PDB ID: 1A02
Chain ID: J
ChEMBL ID: CHEMBL2111421
UniProt ID: P01100
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 52 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -212644.434819 |
|---|---|
| FMO2-HF: Nuclear repulsion | 191220.075251 |
| FMO2-HF: Total energy | -21424.359568 |
| FMO2-MP2: Total energy | -21486.417074 |
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(J:267:ARG)
Summations of interaction energy for
fragment #1(J:267:ARG)
| 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. |
| 209.533 | 213.735 | 2.925 | -2.41 | -4.717 | -0.003 |
Interaction energy analysis for fragmet #1(J:267:ARG)
| 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 | J | 269 | ARG | 1 | 1.026 | 1.009 | 3.016 | 38.317 | 40.856 | 0.073 | -1.024 | -1.589 | 0.001 |
| 4 | J | 270 | MET | 0 | 0.003 | 0.005 | 2.323 | 3.323 | 4.467 | 2.850 | -1.240 | -2.753 | -0.004 |
| 5 | J | 271 | ARG | 1 | 1.007 | 0.997 | 3.922 | 27.859 | 28.378 | 0.002 | -0.146 | -0.375 | 0.000 |
| 6 | J | 272 | ASN | 0 | 0.003 | 0.001 | 5.816 | 3.402 | 3.402 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | J | 273 | ARG | 1 | 1.024 | 1.020 | 6.737 | 34.620 | 34.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | J | 274 | ILE | 0 | 0.022 | 0.005 | 6.903 | 2.311 | 2.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | J | 275 | ALA | 0 | -0.010 | 0.011 | 9.843 | 1.923 | 1.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | J | 276 | ALA | 0 | 0.057 | 0.018 | 11.789 | 1.574 | 1.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | J | 277 | SER | 0 | -0.029 | -0.010 | 12.435 | 1.583 | 1.583 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | J | 278 | LYS | 1 | 0.975 | 0.980 | 13.445 | 18.419 | 18.419 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | J | 279 | SER | 0 | -0.038 | -0.025 | 15.669 | 1.247 | 1.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | J | 280 | ARG | 1 | 0.987 | 0.992 | 14.684 | 18.645 | 18.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | J | 281 | LYS | 1 | 1.028 | 1.020 | 18.346 | 14.682 | 14.682 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | J | 282 | ARG | 1 | 0.955 | 0.968 | 18.620 | 13.982 | 13.982 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | J | 283 | LYS | 1 | 0.958 | 0.977 | 21.678 | 12.773 | 12.773 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | J | 284 | LEU | 0 | 0.036 | 0.024 | 22.934 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | J | 285 | GLU | -1 | -0.829 | -0.883 | 24.327 | -10.726 | -10.726 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | J | 286 | ARG | 1 | 0.941 | 0.971 | 25.907 | 10.259 | 10.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | J | 287 | ILE | 0 | 0.011 | 0.002 | 27.860 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | J | 288 | ALA | 0 | 0.050 | 0.032 | 29.109 | 0.313 | 0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | J | 289 | ARG | 1 | 0.888 | 0.918 | 26.693 | 10.616 | 10.616 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | J | 290 | LEU | 0 | -0.061 | -0.039 | 31.698 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | J | 291 | GLU | -1 | -0.842 | -0.908 | 33.809 | -8.317 | -8.317 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | J | 292 | GLU | -1 | -0.939 | -0.971 | 32.640 | -8.765 | -8.765 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | J | 293 | LYS | 1 | 0.942 | 0.978 | 35.236 | 8.380 | 8.380 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | J | 294 | VAL | 0 | 0.000 | -0.008 | 37.691 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | J | 295 | LYS | 1 | 0.844 | 0.922 | 37.137 | 8.266 | 8.266 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | J | 296 | THR | 0 | 0.047 | 0.010 | 39.735 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | J | 297 | LEU | 0 | 0.007 | 0.013 | 40.530 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | J | 298 | LYS | 1 | 0.941 | 0.974 | 43.469 | 7.120 | 7.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | J | 299 | ALA | 0 | 0.014 | 0.018 | 45.529 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | J | 300 | GLN | 0 | 0.049 | 0.012 | 43.802 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | J | 301 | ASN | 0 | 0.007 | -0.007 | 47.101 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | J | 302 | SER | 0 | 0.001 | 0.019 | 49.633 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | J | 303 | GLU | -1 | -0.917 | -0.964 | 50.041 | -5.923 | -5.923 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | J | 304 | LEU | 0 | -0.021 | -0.017 | 49.336 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | J | 305 | ALA | 0 | -0.016 | 0.000 | 53.246 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | J | 306 | SER | 0 | -0.033 | -0.012 | 55.458 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | J | 307 | THR | 0 | -0.001 | -0.002 | 55.472 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | J | 308 | ALA | 0 | -0.023 | -0.014 | 56.958 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | J | 309 | ASN | 0 | 0.027 | -0.002 | 58.765 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | J | 310 | MET | 0 | 0.019 | 0.040 | 61.084 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | J | 311 | LEU | 0 | 0.008 | -0.016 | 59.488 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | J | 312 | ARG | 1 | 0.865 | 0.935 | 59.832 | 5.088 | 5.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | J | 313 | GLU | -1 | -0.944 | -0.968 | 64.570 | -4.609 | -4.609 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | J | 314 | GLN | 0 | 0.017 | -0.009 | 65.024 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | J | 315 | VAL | 0 | 0.005 | 0.004 | 65.509 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | J | 316 | ALA | 0 | -0.028 | -0.006 | 68.488 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | J | 317 | GLN | 0 | -0.067 | -0.024 | 70.788 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | J | 318 | LEU | 0 | -0.074 | -0.019 | 69.467 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |