FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: YZ6M2
Calculation Name: 4DJZ-H-Xray372
Preferred Name: Mannan-binding lectin serine protease 1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 4DJZ
Chain ID: H
ChEMBL ID: CHEMBL4295768
UniProt ID: P48740
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 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 | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -122811.530222 |
|---|---|
| FMO2-HF: Nuclear repulsion | 108129.57625 |
| FMO2-HF: Total energy | -14681.953973 |
| FMO2-MP2: Total energy | -14719.267545 |
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(H:5:VAL)
Summations of interaction energy for
fragment #1(H:5:VAL)
| 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. |
| -3.692 | -1.057 | 0.507 | -1.434 | -1.709 | 0.007 |
Interaction energy analysis for fragmet #1(H:5:VAL)
| 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 | H | 7 | CYS | 0 | -0.062 | -0.008 | 3.898 | -1.965 | -0.350 | -0.017 | -0.830 | -0.768 | 0.003 |
| 4 | H | 8 | GLU | -1 | -0.842 | -0.930 | 6.868 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | H | 9 | PRO | 0 | -0.028 | -0.013 | 10.632 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | H | 10 | GLY | 0 | 0.046 | 0.039 | 12.722 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | H | 11 | THR | 0 | -0.057 | -0.044 | 14.802 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | H | 12 | THR | 0 | -0.026 | -0.024 | 14.490 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | H | 13 | PHE | 0 | 0.048 | 0.027 | 7.708 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | H | 14 | LYS | 1 | 0.895 | 0.923 | 12.030 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | H | 15 | ASP | -1 | -0.748 | -0.842 | 7.618 | -0.854 | -0.854 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | H | 16 | LYS | 1 | 0.869 | 0.903 | 6.981 | 0.753 | 0.753 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | H | 17 | CYS | 0 | -0.100 | -0.054 | 11.731 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | H | 18 | ASN | 0 | 0.006 | 0.025 | 12.198 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | H | 19 | THR | 0 | -0.010 | 0.001 | 13.474 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | H | 20 | CYS | 0 | -0.046 | -0.014 | 9.764 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | H | 21 | ARG | 1 | 0.981 | 0.983 | 12.043 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | H | 23 | GLY | 0 | 0.037 | 0.044 | 10.765 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | H | 24 | SER | 0 | 0.035 | 0.014 | 12.770 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | H | 25 | ASP | -1 | -0.831 | -0.895 | 9.506 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | H | 26 | GLY | 0 | 0.062 | 0.025 | 9.340 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | H | 27 | LYS | 1 | 0.752 | 0.863 | 2.234 | -2.423 | -1.401 | 0.525 | -0.597 | -0.951 | 0.004 |
| 23 | H | 28 | SER | 0 | -0.009 | -0.006 | 5.052 | -0.288 | -0.290 | -0.001 | -0.007 | 0.010 | 0.000 |
| 24 | H | 29 | ALA | 0 | 0.039 | 0.001 | 6.684 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | H | 30 | PHE | 0 | -0.023 | -0.002 | 8.405 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | H | 32 | THR | 0 | -0.028 | -0.031 | 12.288 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | H | 33 | ARG | 1 | 0.957 | 0.965 | 13.562 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | H | 34 | LYS | 1 | 0.917 | 0.965 | 15.395 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | H | 35 | LEU | 0 | 0.051 | 0.037 | 14.940 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | H | 37 | TYR | 0 | 0.064 | 0.024 | 15.532 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | H | 38 | GLN | 0 | 0.043 | 0.038 | 13.579 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |