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: LG429
Calculation Name: 6CKF-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 6CKF
Chain ID: A
UniProt ID: A0A330
Base Structure: SolutionNMR
Registration Date: 2025-10-04
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 |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 33 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -133209.785151 |
|---|---|
| FMO2-HF: Nuclear repulsion | 118418.268023 |
| FMO2-HF: Total energy | -14791.517128 |
| FMO2-MP2: Total energy | -14829.313358 |
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:ALA)
Summations of interaction energy for
fragment #1(A:1:ALA)
| 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. |
| 75.861 | 77.334 | -0.022 | -0.683 | -0.768 | 0 |
Interaction energy analysis for fragmet #1(A:1:ALA)
| 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 | LYS | 1 | 1.034 | 1.009 | 3.826 | 28.400 | 29.873 | -0.022 | -0.683 | -0.768 | 0.000 |
| 4 | A | 4 | ASP | -1 | -0.922 | -0.946 | 6.894 | -25.890 | -25.890 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | VAL | 0 | -0.066 | -0.053 | 10.591 | 1.337 | 1.337 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | PHE | 0 | -0.002 | -0.004 | 13.006 | 1.702 | 1.702 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | PRO | 0 | 0.074 | 0.045 | 15.465 | -0.777 | -0.777 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ALA | 0 | 0.121 | 0.035 | 16.680 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ALA | 0 | -0.026 | -0.014 | 17.867 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | THR | 0 | 0.035 | 0.016 | 20.103 | 0.476 | 0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | CYS | 0 | -0.041 | -0.015 | 11.402 | -1.607 | -1.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ARG | 1 | 0.969 | 0.986 | 18.167 | 14.288 | 14.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | HIS | 0 | 0.022 | 0.025 | 20.030 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | ALA | 0 | 0.028 | 0.010 | 19.278 | 0.299 | 0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LYS | 1 | 0.833 | 0.895 | 14.820 | 19.743 | 19.743 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | SER | 0 | -0.014 | 0.001 | 19.806 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | VAL | 0 | -0.011 | -0.003 | 23.346 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | GLY | 0 | 0.041 | 0.038 | 21.608 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ASN | 0 | 0.014 | -0.014 | 21.734 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | CYS | 0 | -0.163 | -0.076 | 12.063 | 1.201 | 1.201 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | SER | 0 | 0.044 | 0.010 | 17.021 | -1.288 | -1.288 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | SER | 0 | 0.004 | 0.020 | 19.270 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | GLU | -1 | -0.832 | -0.941 | 16.639 | -16.955 | -16.955 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LYS | 1 | 0.958 | 0.987 | 16.457 | 12.998 | 12.998 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | TYR | 0 | -0.030 | -0.015 | 17.082 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LYS | 1 | 0.946 | 0.983 | 12.582 | 21.033 | 21.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | ARG | 1 | 0.896 | 0.946 | 11.924 | 16.820 | 16.820 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ASN | 0 | 0.017 | 0.013 | 11.279 | -2.386 | -2.386 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 30 | ALA | 0 | 0.046 | 0.026 | 7.350 | 0.822 | 0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 31 | ILE | 0 | 0.078 | 0.039 | 6.008 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 32 | THR | 0 | -0.001 | 0.006 | 8.788 | 2.473 | 2.473 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 34 | GLY | 0 | -0.010 | -0.014 | 9.139 | 1.385 | 1.385 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 35 | ALA | 0 | -0.054 | -0.007 | 9.321 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |