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: 25N8R
Calculation Name: 4D2H-E-Xray549
Preferred Name:
Target Type:
Ligand Name: sulfate ion
Ligand 3-letter code: SO4
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4D2H
Chain ID: E
UniProt ID: Q99708
Base Structure: X-ray
Registration Date: 2025-10-12
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -107727.668961 |
|---|---|
| FMO2-HF: Nuclear repulsion | 94996.950261 |
| FMO2-HF: Total energy | -12730.718699 |
| FMO2-MP2: Total energy | -12767.856768 |
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(E:19:ASP)
Summations of interaction energy for
fragment #1(E:19:ASP)
| 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. |
| 16.763 | 20.363 | 0.063 | -1.237 | -2.426 | 0.001 |
Interaction energy analysis for fragmet #1(E:19:ASP)
| 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 | E | 21 | LYS | 1 | 1.021 | 1.003 | 3.872 | 8.485 | 10.363 | -0.007 | -0.770 | -1.101 | 0.001 |
| 4 | E | 22 | ASP | -1 | -0.814 | -0.871 | 3.123 | -3.290 | -2.254 | 0.053 | -0.292 | -0.797 | 0.000 |
| 5 | E | 23 | LEU | 0 | 0.027 | 0.009 | 3.460 | 2.721 | 3.407 | 0.017 | -0.175 | -0.528 | 0.000 |
| 6 | E | 24 | TRP | 0 | -0.015 | -0.002 | 6.015 | 1.598 | 1.598 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | E | 25 | THR | 0 | -0.011 | -0.020 | 8.029 | 1.257 | 1.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | E | 26 | LYS | 1 | 0.876 | 0.915 | 6.133 | 4.057 | 4.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | E | 27 | LEU | 0 | -0.002 | 0.008 | 10.081 | 0.619 | 0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | E | 28 | LYS | 1 | 0.832 | 0.904 | 12.051 | 2.258 | 2.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | E | 29 | GLU | -1 | -0.865 | -0.951 | 12.993 | -2.147 | -2.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | E | 30 | CYS | 0 | -0.101 | -0.041 | 14.041 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | E | 31 | HIS | 0 | 0.063 | 0.033 | 15.837 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | E | 32 | ASP | -1 | -0.821 | -0.897 | 17.788 | -1.491 | -1.491 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | E | 33 | ARG | 1 | 0.906 | 0.948 | 14.056 | 1.567 | 1.567 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | E | 34 | GLU | -1 | -0.942 | -0.953 | 20.067 | -0.604 | -0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | E | 35 | VAL | 0 | 0.018 | -0.002 | 21.920 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | E | 36 | GLN | 0 | -0.026 | -0.009 | 23.316 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | E | 37 | GLY | 0 | 0.019 | 0.002 | 24.408 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | E | 38 | LEU | 0 | -0.018 | -0.009 | 25.503 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | E | 39 | GLN | 0 | 0.035 | 0.014 | 27.843 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | E | 40 | VAL | 0 | -0.020 | 0.004 | 28.765 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | E | 41 | LYS | 1 | 0.934 | 0.966 | 29.546 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | E | 42 | VAL | 0 | 0.008 | 0.002 | 32.137 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | E | 43 | THR | 0 | -0.058 | -0.043 | 33.164 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | E | 44 | LYS | 1 | 0.920 | 0.962 | 32.543 | 0.350 | 0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | E | 45 | LEU | 0 | 0.031 | 0.010 | 35.526 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | E | 46 | LYS | 1 | 0.896 | 0.961 | 36.641 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | E | 47 | GLN | 0 | -0.109 | -0.040 | 40.012 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | E | 48 | GLU | -2 | -1.867 | -1.926 | 38.352 | -0.457 | -0.457 | 0.000 | 0.000 | 0.000 | 0.000 |