FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: JL499
Calculation Name: 1EAI-C-Xray372
Preferred Name: Elastase 1
Target Type: SINGLE PROTEIN
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1EAI
Chain ID: C
ChEMBL ID: CHEMBL3517
UniProt ID: P00772
Base Structure: X-ray
Registration Date: 2023-06-22
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 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 56 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -297552.750542 |
|---|---|
| FMO2-HF: Nuclear repulsion | 270915.341025 |
| FMO2-HF: Total energy | -26637.409517 |
| FMO2-MP2: Total energy | -26702.848095 |
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(C:1:GLY)
Summations of interaction energy for
fragment #1(C:1:GLY)
| 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. |
| -8.068 | -10.14 | 20.861 | -12.501 | -6.285 | -0.053 |
Interaction energy analysis for fragmet #1(C:1:GLY)
| 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 | C | 3 | GLU | -1 | -0.962 | -0.994 | 3.799 | 0.060 | 1.540 | -0.017 | -0.836 | -0.627 | 0.005 |
| 4 | C | 4 | SER | 0 | -0.021 | -0.003 | 6.307 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 5 | CYS | 0 | -0.006 | 0.049 | 3.127 | -2.118 | -0.711 | 0.447 | -0.731 | -1.123 | 0.004 |
| 6 | C | 6 | GLY | 0 | 0.055 | 0.027 | 5.272 | -0.798 | -0.789 | -0.001 | -0.001 | -0.006 | 0.000 |
| 7 | C | 7 | PRO | 0 | -0.032 | -0.055 | 5.149 | -0.055 | -0.056 | -0.001 | 0.001 | 0.002 | 0.000 |
| 8 | C | 8 | ASN | 0 | -0.048 | -0.040 | 6.052 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 9 | GLU | -1 | -0.807 | -0.877 | 4.431 | 1.260 | 1.439 | -0.001 | -0.086 | -0.092 | 0.000 |
| 10 | C | 10 | VAL | 0 | -0.036 | -0.036 | 2.021 | -6.095 | -6.594 | 6.257 | -3.214 | -2.545 | -0.028 |
| 11 | C | 11 | TRP | 0 | -0.019 | -0.028 | 1.462 | 1.260 | -3.347 | 14.148 | -7.848 | -1.692 | -0.033 |
| 12 | C | 12 | THR | 0 | -0.005 | 0.013 | 3.384 | -0.616 | -0.656 | 0.029 | 0.214 | -0.202 | -0.001 |
| 13 | C | 13 | GLU | -1 | -0.861 | -0.949 | 6.986 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 14 | CYS | 0 | -0.109 | -0.049 | 10.304 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 15 | THR | 0 | 0.018 | 0.010 | 10.649 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 16 | GLY | 0 | 0.015 | 0.003 | 11.942 | -0.104 | -0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 17 | CYS | 0 | -0.051 | -0.026 | 14.575 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 18 | GLU | -1 | -0.762 | -0.891 | 11.221 | 0.599 | 0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 19 | MET | 0 | 0.002 | 0.001 | 15.176 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 20 | LYS | 1 | 0.977 | 0.987 | 16.584 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 21 | CYS | 0 | -0.089 | -0.030 | 18.816 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 22 | GLY | 0 | 0.011 | -0.002 | 20.400 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 23 | PRO | 0 | -0.062 | -0.046 | 21.034 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 24 | ASP | -1 | -0.845 | -0.886 | 23.206 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 25 | GLU | -1 | -0.968 | -0.997 | 23.783 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 26 | ASN | 0 | -0.049 | -0.024 | 24.854 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 27 | THR | 0 | -0.027 | -0.003 | 23.401 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 28 | PRO | 0 | 0.024 | 0.004 | 23.940 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 30 | PRO | 0 | -0.030 | -0.023 | 21.580 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 31 | LEU | 0 | 0.045 | 0.019 | 20.723 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 32 | MET | 0 | -0.030 | -0.005 | 20.239 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | C | 34 | ARG | 1 | 0.903 | 0.964 | 14.866 | -0.330 | -0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | C | 35 | ARG | 1 | 0.949 | 0.956 | 14.156 | -0.269 | -0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | C | 36 | PRO | 0 | 0.054 | 0.031 | 9.860 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | C | 37 | SER | 0 | -0.070 | -0.018 | 8.376 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | C | 39 | GLU | -1 | -0.849 | -0.933 | 5.772 | 0.346 | 0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | C | 40 | CYS | 0 | -0.047 | 0.013 | 6.537 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | C | 41 | SER | 0 | 0.022 | -0.015 | 9.023 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | C | 42 | PRO | 0 | -0.007 | -0.012 | 11.126 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | C | 43 | GLY | 0 | 0.022 | 0.021 | 14.000 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | C | 44 | ARG | 1 | 0.906 | 0.959 | 7.733 | -0.665 | -0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | C | 45 | GLY | 0 | 0.015 | 0.015 | 12.084 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | C | 46 | MET | 0 | -0.041 | -0.007 | 9.058 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | C | 47 | ARG | 1 | 0.912 | 0.945 | 12.684 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | C | 48 | ARG | 1 | 0.829 | 0.910 | 9.363 | -0.625 | -0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | C | 49 | THR | 0 | -0.007 | -0.011 | 15.062 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | C | 50 | ASN | 0 | -0.083 | -0.070 | 17.631 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | C | 51 | ASP | -1 | -0.839 | -0.917 | 17.712 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | C | 52 | GLY | 0 | -0.005 | -0.001 | 15.678 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 50 | C | 53 | LYS | 1 | 0.955 | 0.998 | 12.365 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 51 | C | 55 | ILE | 0 | 0.009 | 0.011 | 11.075 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 52 | C | 56 | PRO | 0 | 0.105 | 0.038 | 12.810 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 53 | C | 57 | ALA | 0 | 0.038 | 0.012 | 14.463 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 54 | C | 58 | SER | 0 | -0.049 | -0.017 | 17.467 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 55 | C | 59 | GLN | 0 | -0.024 | -0.015 | 17.362 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 56 | C | 61 | PRO | 0 | 0.002 | 0.005 | 20.978 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |