FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: Q1K9Y
Calculation Name: 1RKC-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1RKC
Chain ID: B
UniProt ID: P54939
Base Structure: X-ray
Registration Date: 2023-03-13
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 26 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -75121.961619 |
|---|---|
| FMO2-HF: Nuclear repulsion | 65228.2211 |
| FMO2-HF: Total energy | -9893.740519 |
| FMO2-MP2: Total energy | -9923.432171 |
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(B:1944:TYR)
Summations of interaction energy for
fragment #1(B:1944:TYR)
| 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. |
| -18.657 | -14.857 | 0.197 | -1.596 | -2.4 | 0 |
Interaction energy analysis for fragmet #1(B:1944:TYR)
| 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 | B | 1946 | LYS | 1 | 0.920 | 0.965 | 3.763 | -3.746 | -1.443 | -0.017 | -1.128 | -1.158 | -0.002 |
| 4 | B | 1947 | LYS | 1 | 0.950 | 0.977 | 2.728 | -9.900 | -8.750 | 0.215 | -0.375 | -0.989 | 0.002 |
| 5 | B | 1948 | GLU | -1 | -0.767 | -0.883 | 4.342 | -3.979 | -3.632 | -0.001 | -0.093 | -0.253 | 0.000 |
| 6 | B | 1949 | LEU | 0 | 0.046 | 0.055 | 6.313 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 1950 | ILE | 0 | 0.012 | -0.010 | 8.433 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 1951 | GLU | -1 | -0.912 | -0.937 | 6.073 | -0.539 | -0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 1952 | SER | 0 | -0.042 | -0.043 | 9.351 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 1953 | ALA | 0 | 0.033 | 0.012 | 11.413 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 1954 | ARG | 1 | 0.942 | 0.992 | 11.355 | -0.659 | -0.659 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 1955 | LYS | 1 | 0.868 | 0.929 | 9.813 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 1956 | VAL | 0 | -0.006 | -0.001 | 15.303 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 1957 | SER | 0 | -0.040 | -0.030 | 17.201 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 1958 | GLU | -1 | -0.838 | -0.928 | 15.851 | 0.251 | 0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 1959 | LYS | 1 | 0.929 | 0.967 | 17.668 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 1960 | VAL | 0 | 0.003 | 0.008 | 21.508 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 1961 | SER | 0 | -0.052 | -0.037 | 22.510 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 1962 | HIS | 0 | 0.013 | -0.006 | 21.605 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 1963 | VAL | 0 | -0.010 | -0.002 | 25.794 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 1964 | LEU | 0 | -0.060 | -0.018 | 26.679 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 1965 | ALA | 0 | 0.039 | 0.023 | 28.329 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 1966 | ALA | 0 | -0.013 | -0.005 | 30.128 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 1967 | LEU | 0 | -0.047 | -0.024 | 32.925 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 1968 | GLN | 0 | -0.004 | -0.001 | 32.101 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 1969 | ALA | 0 | -0.018 | 0.007 | 36.252 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |