FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 3NMML
Calculation Name: 1L2Y-A-MD57-77800ps
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-13
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 10 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -24566.305089 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19964.05946 |
| FMO2-HF: Total energy | -4602.24563 |
| FMO2-MP2: Total energy | -4615.709772 |
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(:1:GLN )
Summations of interaction energy for
fragment #1(:1:GLN )
| 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. |
| -90.208 | -88.139 | 23.317 | -11.691 | -13.696 | -0.114 |
Interaction energy analysis for fragmet #1(:1:GLN )
| 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 | 3 | GLN | 0 | 0.018 | 0.006 | 3.374 | -0.428 | 1.188 | 0.025 | -0.770 | -0.871 | -0.002 | |
| 4 | 4 | GLN | 0 | 0.084 | 0.051 | 6.204 | 3.015 | 3.015 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.006 | -0.034 | 6.005 | -4.489 | -4.489 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.011 | 0.032 | 3.357 | 0.605 | 1.073 | 0.019 | -0.098 | -0.390 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.018 | 0.003 | 2.474 | -14.978 | -12.129 | 2.410 | -2.182 | -3.077 | -0.027 | |
| 8 | 8 | GLN | 0 | 0.025 | 0.003 | 1.795 | -46.000 | -48.237 | 20.824 | -9.438 | -9.149 | -0.084 | |
| 9 | 9 | GLN | 0 | -0.018 | -0.015 | 3.031 | 0.823 | 0.196 | 0.039 | 0.797 | -0.209 | -0.001 | |
| 10 | 10 | GLN | -1 | -0.891 | -0.912 | 6.232 | -28.756 | -28.756 | 0.000 | 0.000 | 0.000 | 0.000 |