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: NN6VQ
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 | OptAll |
| 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 | -94652.883946 |
|---|---|
| FMO2-HF: Nuclear repulsion | 82502.082584 |
| FMO2-HF: Total energy | -12150.801362 |
| FMO2-MP2: Total energy | -12186.823809 |
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. |
| 3.259 | 4.927 | -0.008 | -0.823 | -0.837 | 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 | 0.907 | 0.947 | 3.879 | 30.711 | 32.379 | -0.008 | -0.823 | -0.837 | 0.001 |
| 4 | N | 9 | GLU | -1 | -0.747 | -0.852 | 6.295 | -22.087 | -22.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | N | 10 | TYR | 0 | -0.002 | -0.006 | 8.123 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | N | 11 | LEU | 0 | 0.072 | 0.023 | 11.865 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | N | 12 | LYS | 1 | 0.803 | 0.889 | 10.978 | 22.395 | 22.395 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | N | 13 | SER | 0 | 0.019 | 0.016 | 16.524 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | N | 14 | TYR | 0 | -0.003 | 0.008 | 18.035 | 0.977 | 0.977 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | N | 15 | SER | 0 | -0.034 | -0.024 | 19.868 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | N | 16 | ARG | 1 | 0.843 | 0.902 | 21.473 | 10.856 | 10.856 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | N | 17 | LEU | 0 | 0.021 | 0.016 | 16.887 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | N | 18 | ASP | -1 | -0.903 | -0.951 | 18.855 | -13.710 | -13.710 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | N | 19 | GLN | 0 | 0.006 | -0.001 | 21.294 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | N | 20 | ALA | 0 | 0.017 | 0.017 | 23.666 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | N | 21 | VAL | 0 | -0.020 | -0.022 | 20.119 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | N | 22 | GLY | 0 | 0.020 | 0.024 | 23.488 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | N | 23 | GLU | -1 | -0.801 | -0.893 | 26.007 | -9.930 | -9.930 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | N | 24 | ILE | 0 | -0.060 | -0.033 | 24.718 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | N | 25 | ASP | -1 | -0.932 | -0.959 | 25.757 | -10.379 | -10.379 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | N | 26 | GLU | -1 | -0.932 | -0.966 | 27.717 | -8.734 | -8.734 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | N | 27 | ILE | 0 | -0.051 | -0.032 | 31.021 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | N | 28 | GLU | -1 | -0.869 | -0.915 | 27.895 | -9.713 | -9.713 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | N | 29 | ALA | 0 | -0.005 | -0.008 | 30.793 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | N | 30 | GLN | 0 | -0.091 | -0.049 | 32.718 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | N | 31 | ARG | 1 | 0.832 | 0.911 | 30.722 | 9.562 | 9.562 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | N | 32 | ALA | 0 | 0.021 | 0.024 | 33.246 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | N | 33 | GLU | -1 | -0.937 | -0.956 | 34.860 | -7.566 | -7.566 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | N | 34 | LYS | 1 | 0.851 | 0.904 | 36.695 | 7.814 | 7.814 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | N | 35 | SER | 0 | -0.010 | 0.011 | 39.691 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |