FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: XR118
Calculation Name: 3E8Y-X-Xray13
Preferred Name:
Target Type:
Ligand Name: sulfate ion
ligand 3-letter code: SO4
PDB ID: 3E8Y
Chain ID: X
UniProt ID: P83407
Base Structure: X-ray
Registration Date: 2017-12-04
Reference:
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE. |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20181213 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | CL-=-1,SO4=-2 |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -113753.020033 |
|---|---|
| FMO2-HF: Nuclear repulsion | 99230.051881 |
| FMO2-HF: Total energy | -14522.968152 |
| FMO2-MP2: Total energy | -14556.545321 |
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(X:1:ACE)
Summations of interaction energy for
fragment #1(X:1:ACE)
| 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. |
| 1.729 | 2.324 | -0.01 | -0.282 | -0.303 | 0.001 |
Interaction energy analysis for fragmet #1(X:1:ACE)
| 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 | X | 22 | CYS | 0 | -0.087 | -0.014 | 3.848 | 1.540 | 2.120 | -0.009 | -0.274 | -0.297 | 0.001 |
| 4 | X | 4 | TYR | 0 | 0.119 | 0.057 | 4.504 | -0.135 | -0.120 | -0.001 | -0.008 | -0.006 | 0.000 |
| 5 | X | 5 | SER | 0 | 0.034 | -0.008 | 9.264 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | X | 6 | SER | 0 | 0.020 | 0.007 | 12.946 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | X | 7 | ASP | -1 | -0.817 | -0.906 | 9.713 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | X | 27 | CYS | 0 | -0.136 | -0.072 | 9.750 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | X | 9 | ARG | 1 | 0.906 | 0.951 | 12.367 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | X | 10 | VAL | 0 | 0.054 | 0.030 | 15.232 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | X | 11 | LYS | 1 | 0.961 | 0.979 | 8.514 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | X | 29 | CYS | 0 | 0.000 | -0.003 | 14.810 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | X | 13 | VAL | 0 | 0.036 | 0.024 | 16.958 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | X | 14 | ALA | 0 | -0.046 | -0.016 | 17.692 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | X | 15 | MET | 0 | -0.093 | -0.049 | 15.531 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | X | 16 | GLY | 0 | 0.046 | 0.039 | 19.938 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | X | 17 | PHE | 0 | -0.078 | -0.030 | 18.396 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | X | 18 | SER | 0 | 0.015 | -0.018 | 21.805 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | X | 19 | SER | 0 | -0.026 | -0.029 | 19.698 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | X | 20 | GLY | 0 | 0.041 | 0.014 | 16.222 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | X | 21 | LYS | 1 | 0.870 | 0.940 | 15.251 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | X | 23 | ILE | 0 | 0.038 | 0.010 | 12.315 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | X | 24 | ASN | 0 | 0.013 | 0.000 | 12.356 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | X | 25 | SER | 0 | 0.009 | -0.017 | 7.008 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | X | 26 | LYS | 1 | 0.881 | 0.957 | 7.424 | 0.369 | 0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | X | 28 | LYS | 1 | 0.939 | 0.973 | 11.214 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | X | 30 | TYR | 0 | -0.071 | -0.032 | 17.398 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | X | 31 | LYS | 0 | 0.216 | 0.131 | 21.003 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | X | 101 | CL- | -1 | -0.876 | -0.927 | 10.787 | -0.896 | -0.896 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | X | 102 | SO4 | -2 | -1.994 | -1.996 | 28.252 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |