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: R5Q38
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 | OptH |
| 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 | -75323.185376 |
|---|---|
| FMO2-HF: Nuclear repulsion | 65429.834442 |
| FMO2-HF: Total energy | -9893.350934 |
| FMO2-MP2: Total energy | -9923.0757 |
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. |
| -19.281 | -15.675 | 0.003 | -1.431 | -2.178 | -0.001 |
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 | 0.878 | 0.944 | 3.704 | -3.668 | -1.416 | -0.018 | -1.092 | -1.142 | -0.002 |
| 4 | B | 1947 | LYS | 1 | 0.951 | 0.971 | 3.324 | -9.643 | -8.717 | 0.022 | -0.229 | -0.719 | 0.001 |
| 5 | B | 1948 | GLU | -1 | -0.777 | -0.894 | 4.091 | -4.608 | -4.239 | 0.000 | -0.110 | -0.259 | 0.000 |
| 6 | B | 1949 | LEU | 0 | 0.022 | 0.015 | 6.287 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 1950 | ILE | 0 | -0.013 | -0.009 | 8.219 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 1951 | GLU | -1 | -0.954 | -0.975 | 5.138 | -1.208 | -1.149 | -0.001 | 0.000 | -0.058 | 0.000 |
| 9 | B | 1952 | SER | 0 | -0.059 | -0.028 | 9.329 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 1953 | ALA | 0 | 0.052 | 0.014 | 11.389 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 1954 | ARG | 1 | 0.932 | 0.990 | 11.138 | -0.608 | -0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 1955 | LYS | 1 | 0.951 | 0.991 | 10.664 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 1956 | VAL | 0 | -0.018 | -0.003 | 15.283 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 1957 | SER | 0 | -0.026 | -0.018 | 17.261 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 1958 | GLU | -1 | -0.824 | -0.938 | 15.640 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 1959 | LYS | 1 | 0.941 | 0.973 | 17.580 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 1960 | VAL | 0 | 0.002 | 0.010 | 21.489 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 1961 | SER | 0 | -0.045 | -0.028 | 22.414 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 1962 | HIS | 0 | 0.015 | -0.004 | 22.124 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 1963 | VAL | 0 | 0.003 | -0.002 | 25.776 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 1964 | LEU | 0 | -0.072 | -0.025 | 26.400 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 1965 | ALA | 0 | 0.032 | 0.026 | 28.368 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 1966 | ALA | 0 | -0.003 | -0.004 | 30.110 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 1967 | LEU | 0 | -0.051 | -0.026 | 32.754 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 1968 | GLN | 0 | -0.010 | 0.002 | 31.798 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 1969 | ALA | 0 | -0.022 | 0.004 | 36.236 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |