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: Z685N
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 | 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 | 52 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -212725.52059 |
|---|---|
| FMO2-HF: Nuclear repulsion | 191301.514349 |
| FMO2-HF: Total energy | -21424.006241 |
| FMO2-MP2: Total energy | -21486.130844 |
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. |
| 218.371 | 222.792 | 4.95 | -3.182 | -6.19 | -0.007 |
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 | 1.025 | 1.008 | 2.730 | 41.648 | 44.759 | 0.298 | -1.269 | -2.140 | -0.001 |
| 4 | J | 270 | MET | 0 | 0.011 | 0.007 | 2.244 | 3.731 | 4.495 | 4.646 | -1.777 | -3.634 | -0.006 |
| 5 | J | 271 | ARG | 1 | 1.007 | 0.999 | 3.885 | 28.936 | 29.482 | 0.006 | -0.136 | -0.416 | 0.000 |
| 6 | J | 272 | ASN | 0 | 0.006 | -0.002 | 5.749 | 4.034 | 4.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | J | 273 | ARG | 1 | 1.008 | 1.016 | 6.305 | 36.336 | 36.336 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | J | 274 | ILE | 0 | 0.017 | 0.000 | 6.921 | 2.499 | 2.499 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | J | 275 | ALA | 0 | -0.013 | 0.010 | 9.786 | 2.005 | 2.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | J | 276 | ALA | 0 | 0.063 | 0.020 | 11.724 | 1.622 | 1.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | J | 277 | SER | 0 | -0.043 | -0.009 | 12.275 | 1.667 | 1.667 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | J | 278 | LYS | 1 | 0.986 | 0.981 | 13.244 | 18.983 | 18.983 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | J | 279 | SER | 0 | -0.021 | -0.018 | 15.610 | 1.283 | 1.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | J | 280 | ARG | 1 | 0.984 | 0.988 | 14.524 | 18.844 | 18.844 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | J | 281 | LYS | 1 | 1.017 | 1.016 | 18.188 | 15.466 | 15.466 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | J | 282 | ARG | 1 | 0.946 | 0.967 | 18.065 | 14.288 | 14.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | J | 283 | LYS | 1 | 0.952 | 0.970 | 21.618 | 12.780 | 12.780 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | J | 284 | LEU | 0 | 0.038 | 0.026 | 22.619 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | J | 285 | GLU | -1 | -0.884 | -0.931 | 24.272 | -10.808 | -10.808 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | J | 286 | ARG | 1 | 0.926 | 0.967 | 25.845 | 10.373 | 10.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | J | 287 | ILE | 0 | 0.005 | -0.001 | 27.800 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | J | 288 | ALA | 0 | 0.057 | 0.041 | 29.056 | 0.304 | 0.304 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | J | 289 | ARG | 1 | 0.955 | 0.969 | 26.788 | 10.683 | 10.683 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | J | 290 | LEU | 0 | -0.068 | -0.045 | 31.692 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | J | 291 | GLU | -1 | -0.908 | -0.941 | 33.602 | -8.825 | -8.825 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | J | 292 | GLU | -1 | -0.925 | -0.972 | 32.342 | -8.929 | -8.929 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | J | 293 | LYS | 1 | 0.945 | 0.981 | 35.510 | 8.428 | 8.428 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | J | 294 | VAL | 0 | 0.002 | -0.008 | 37.629 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | J | 295 | LYS | 1 | 0.917 | 0.961 | 38.075 | 8.137 | 8.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | J | 296 | THR | 0 | 0.059 | 0.018 | 39.850 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | J | 297 | LEU | 0 | 0.001 | 0.008 | 40.727 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | J | 298 | LYS | 1 | 0.944 | 0.977 | 43.361 | 7.164 | 7.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | J | 299 | ALA | 0 | 0.009 | 0.016 | 45.469 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | J | 300 | GLN | 0 | 0.038 | 0.006 | 44.077 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | J | 301 | ASN | 0 | 0.013 | -0.004 | 47.607 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | J | 302 | SER | 0 | -0.011 | 0.012 | 49.570 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | J | 303 | GLU | -1 | -0.913 | -0.963 | 50.524 | -5.909 | -5.909 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | J | 304 | LEU | 0 | -0.023 | -0.018 | 49.167 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | J | 305 | ALA | 0 | -0.015 | -0.002 | 53.241 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | J | 306 | SER | 0 | -0.013 | -0.001 | 55.394 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | J | 307 | THR | 0 | 0.009 | 0.003 | 55.594 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | J | 308 | ALA | 0 | -0.026 | -0.015 | 56.998 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | J | 309 | ASN | 0 | -0.015 | -0.031 | 58.760 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | J | 310 | MET | 0 | 0.024 | 0.042 | 61.081 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | J | 311 | LEU | 0 | -0.016 | -0.027 | 59.417 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | J | 312 | ARG | 1 | 0.905 | 0.956 | 59.737 | 5.123 | 5.123 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | J | 313 | GLU | -1 | -0.937 | -0.961 | 64.564 | -4.640 | -4.640 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | J | 314 | GLN | 0 | 0.000 | -0.009 | 65.493 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | J | 315 | VAL | 0 | -0.003 | 0.001 | 65.576 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | J | 316 | ALA | 0 | -0.031 | -0.010 | 68.481 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | J | 317 | GLN | 0 | -0.067 | -0.026 | 70.782 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | J | 318 | LEU | 0 | -0.048 | -0.008 | 70.305 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |