FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-04-23
All entries: 37539
Number of unique PDB entries: 7791
FMODB ID: 89K8Y
Calculation Name: 3PMK-N-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3PMK
Chain ID: N
UniProt ID: B7UCZ3
Base Structure: X-ray
Registration Date: 2023-09-23
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
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 | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -94340.621264 |
|---|---|
| FMO2-HF: Nuclear repulsion | 82189.914225 |
| FMO2-HF: Total energy | -12150.707038 |
| FMO2-MP2: Total energy | -12186.740672 |
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(N:6:LYS)
Summations of interaction energy for
fragment #1(N:6: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. |
| 3.581 | 5.376 | -0.005 | -0.832 | -0.958 | 0 |
Interaction energy analysis for fragmet #1(N:6: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 | N | 8 | ARG | 1 | 0.902 | 0.948 | 3.812 | 31.718 | 33.513 | -0.005 | -0.832 | -0.958 | 0.000 |
| 4 | N | 9 | GLU | -1 | -0.736 | -0.859 | 5.888 | -22.365 | -22.365 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | N | 10 | TYR | 0 | -0.034 | -0.020 | 8.239 | 0.459 | 0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | N | 11 | LEU | 0 | 0.092 | 0.033 | 11.838 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | N | 12 | LYS | 1 | 0.819 | 0.900 | 10.745 | 22.619 | 22.619 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | N | 13 | SER | 0 | -0.005 | 0.004 | 16.483 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | N | 14 | TYR | 0 | -0.015 | 0.003 | 18.340 | 1.019 | 1.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | N | 15 | SER | 0 | 0.005 | 0.006 | 19.133 | -0.364 | -0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | N | 16 | ARG | 1 | 0.813 | 0.891 | 21.229 | 10.628 | 10.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | N | 17 | LEU | 0 | 0.014 | 0.005 | 17.045 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | N | 18 | ASP | -1 | -0.892 | -0.952 | 19.117 | -13.826 | -13.826 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | N | 19 | GLN | 0 | -0.001 | -0.012 | 21.464 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | N | 20 | ALA | 0 | -0.010 | 0.010 | 23.654 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | N | 21 | VAL | 0 | -0.006 | -0.015 | 20.308 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | N | 22 | GLY | 0 | 0.016 | 0.016 | 23.664 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | N | 23 | GLU | -1 | -0.778 | -0.881 | 26.030 | -9.827 | -9.827 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | N | 24 | ILE | 0 | -0.067 | -0.039 | 24.536 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | N | 25 | ASP | -1 | -0.925 | -0.962 | 26.027 | -10.395 | -10.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | N | 26 | GLU | -1 | -0.928 | -0.956 | 27.906 | -8.742 | -8.742 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | N | 27 | ILE | 0 | -0.048 | -0.028 | 31.219 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | N | 28 | GLU | -1 | -0.874 | -0.923 | 27.739 | -9.719 | -9.719 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | N | 29 | ALA | 0 | -0.011 | -0.004 | 30.799 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | N | 30 | GLN | 0 | -0.075 | -0.041 | 32.745 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | N | 31 | ARG | 1 | 0.805 | 0.907 | 30.482 | 9.591 | 9.591 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | N | 32 | ALA | 0 | 0.033 | 0.028 | 33.524 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | N | 33 | GLU | -1 | -0.945 | -0.967 | 35.180 | -7.558 | -7.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | N | 34 | LYS | 1 | 0.862 | 0.916 | 36.731 | 7.787 | 7.787 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | N | 35 | SER | 0 | 0.009 | 0.018 | 39.936 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |