FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-09-03
All entries: 45600
Number of unique PDB entries: 8613
FMODB ID: G87L1
Calculation Name: 1DFS-A-Other547
Preferred Name:
Target Type:
Ligand Name: cadmium ion
Ligand 3-letter code: CD
Ligand of Interest (LOI):
PDB ID: 1DFS
Chain ID: A
UniProt ID: P02802
Base Structure: SolutionNMR
Registration Date: 2025-09-02
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 | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -88676.442775 |
|---|---|
| FMO2-HF: Nuclear repulsion | 75068.719526 |
| FMO2-HF: Total energy | -13607.723249 |
| FMO2-MP2: Total energy | -13636.367223 |
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(A:1:LYS)
Summations of interaction energy for
fragment #1(A:1:LYS)
| 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. |
| 17.77 | 19.445 | 0.002 | -0.766 | -0.911 | -0.003 |
Interaction energy analysis for fragmet #1(A:1:LYS)
| 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 | A | 3 | CYS | 0 | 0.005 | 0.018 | 3.903 | 0.897 | 2.247 | -0.010 | -0.682 | -0.658 | -0.002 |
| 9 | A | 9 | VAL | 0 | -0.031 | -0.026 | 3.570 | -4.464 | -4.139 | 0.012 | -0.084 | -0.253 | -0.001 |
| 4 | A | 4 | CYS | 0 | 0.011 | -0.001 | 5.900 | 2.531 | 2.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | 0.004 | -0.001 | 7.142 | -5.622 | -5.622 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | CYS | 0 | -0.019 | 0.005 | 8.963 | 2.105 | 2.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | CYS | 0 | -0.012 | -0.005 | 10.175 | 3.670 | 3.670 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | PRO | 0 | 0.060 | 0.038 | 8.956 | -5.181 | -5.181 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | -0.018 | -0.007 | 6.240 | -1.446 | -1.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | CYS | 0 | -0.056 | -0.013 | 8.673 | 5.798 | 5.798 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | SER | 0 | 0.085 | 0.029 | 11.467 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | LYS | 1 | 0.961 | 0.977 | 14.822 | 29.080 | 29.080 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | CYS | 0 | -0.045 | -0.035 | 11.063 | 1.574 | 1.574 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | 0.012 | 0.022 | 10.979 | -3.454 | -3.454 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLN | 0 | 0.002 | 0.002 | 11.089 | -0.681 | -0.681 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | GLY | 0 | 0.033 | 0.016 | 13.042 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | CYS | 0 | -0.046 | -0.013 | 11.087 | 0.802 | 0.802 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | VAL | 0 | 0.059 | 0.018 | 13.254 | 1.959 | 1.959 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | CYS | 0 | -0.048 | -0.029 | 13.008 | 2.139 | 2.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | LYS | 1 | 1.006 | 0.990 | 15.386 | 25.482 | 25.482 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLY | 0 | 0.033 | 0.032 | 17.132 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ALA | 0 | -0.009 | -0.009 | 11.946 | -0.699 | -0.699 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ALA | 0 | -0.012 | -0.020 | 11.364 | -3.099 | -3.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ASP | -1 | -0.893 | -0.923 | 12.371 | -34.054 | -34.054 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LYS | 1 | 0.986 | 0.986 | 15.081 | 26.989 | 26.989 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | CYS | 0 | -0.066 | -0.040 | 15.599 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | THR | 0 | 0.017 | 0.004 | 18.221 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | CYS | 0 | -0.014 | -0.017 | 17.412 | 0.607 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | CYS | 0 | -0.101 | -0.050 | 14.877 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ALA | -1 | -0.860 | -0.902 | 18.089 | -27.284 | -27.284 | 0.000 | 0.000 | 0.000 | 0.000 |