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: G57L1
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 | 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 | 30 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -93829.797032 |
|---|---|
| FMO2-HF: Nuclear repulsion | 81679.323133 |
| FMO2-HF: Total energy | -12150.473899 |
| FMO2-MP2: Total energy | -12186.485565 |
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. |
| 2.021 | 3.642 | -0.013 | -0.764 | -0.843 | 0.001 |
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 | 0.923 | 0.965 | 3.819 | 28.244 | 29.865 | -0.013 | -0.764 | -0.843 | 0.001 |
| 4 | N | 9 | GLU | -1 | -0.884 | -0.933 | 5.874 | -20.684 | -20.684 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | N | 10 | TYR | 0 | -0.041 | -0.043 | 8.227 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | N | 11 | LEU | 0 | 0.091 | 0.037 | 11.824 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | N | 12 | LYS | 1 | 0.939 | 0.966 | 10.286 | 22.648 | 22.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | N | 13 | SER | 0 | -0.004 | 0.001 | 16.468 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | N | 14 | TYR | 0 | -0.012 | 0.010 | 18.202 | 0.935 | 0.935 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | N | 15 | SER | 0 | 0.007 | 0.006 | 19.122 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | N | 16 | ARG | 1 | 0.853 | 0.922 | 21.219 | 10.242 | 10.242 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | N | 17 | LEU | 0 | 0.013 | 0.004 | 17.003 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | N | 18 | ASP | -1 | -0.885 | -0.947 | 18.903 | -13.285 | -13.285 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | N | 19 | GLN | 0 | -0.020 | -0.019 | 21.458 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | N | 20 | ALA | 0 | -0.006 | 0.012 | 23.659 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | N | 21 | VAL | 0 | -0.003 | -0.016 | 20.302 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | N | 22 | GLY | 0 | 0.017 | 0.016 | 23.657 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | N | 23 | GLU | -1 | -0.802 | -0.908 | 26.024 | -9.531 | -9.531 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | N | 24 | ILE | 0 | -0.071 | -0.038 | 24.242 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | N | 25 | ASP | -1 | -0.914 | -0.959 | 26.072 | -10.216 | -10.216 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | N | 26 | GLU | -1 | -0.947 | -0.961 | 27.986 | -8.561 | -8.561 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | N | 27 | ILE | 0 | -0.035 | -0.023 | 31.286 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | N | 28 | GLU | -1 | -0.916 | -0.967 | 27.926 | -9.739 | -9.739 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | N | 29 | ALA | 0 | -0.004 | -0.002 | 30.870 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | N | 30 | GLN | 0 | -0.090 | -0.046 | 32.839 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | N | 31 | ARG | 1 | 0.831 | 0.942 | 30.363 | 9.474 | 9.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | N | 32 | ALA | 0 | 0.021 | 0.022 | 33.624 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | N | 33 | GLU | -1 | -0.964 | -0.974 | 35.272 | -7.570 | -7.570 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | N | 34 | LYS | 1 | 0.915 | 0.936 | 37.219 | 7.648 | 7.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | N | 35 | SER | 0 | -0.003 | 0.015 | 40.048 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |