FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-05-02
All entries: 37386
Number of unique PDB entries: 7781
FMODB ID: 52Z8Z
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 | 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 | 31 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -122984.969961 |
|---|---|
| FMO2-HF: Nuclear repulsion | 108303.188239 |
| FMO2-HF: Total energy | -14681.781722 |
| FMO2-MP2: Total energy | -14719.099752 |
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. |
| -6.991 | -5.858 | 3.446 | -1.911 | -2.668 | 0.011 |
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 | -0.035 | 0.011 | 3.838 | -3.259 | -1.581 | -0.011 | -0.896 | -0.771 | 0.004 |
| 4 | H | 8 | GLU | -1 | -0.865 | -0.936 | 6.713 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | H | 9 | PRO | 0 | -0.012 | -0.008 | 10.478 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | H | 10 | GLY | 0 | 0.036 | 0.037 | 12.314 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | H | 11 | THR | 0 | -0.039 | -0.036 | 15.086 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | H | 12 | THR | 0 | -0.038 | -0.033 | 14.392 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | H | 13 | PHE | 0 | 0.061 | 0.035 | 7.659 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | H | 14 | LYS | 1 | 0.898 | 0.923 | 12.710 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | H | 15 | ASP | -1 | -0.754 | -0.839 | 7.579 | -1.421 | -1.421 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | H | 16 | LYS | 1 | 0.850 | 0.885 | 7.046 | 1.278 | 1.278 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | H | 17 | CYS | 0 | -0.122 | -0.059 | 11.818 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | H | 18 | ASN | 0 | -0.001 | 0.012 | 12.201 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | H | 19 | THR | 0 | -0.007 | 0.003 | 13.120 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | H | 20 | CYS | 0 | -0.046 | -0.015 | 9.396 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | H | 21 | ARG | 1 | 1.001 | 0.989 | 11.688 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | H | 23 | GLY | 0 | 0.050 | 0.044 | 10.722 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | H | 24 | SER | 0 | 0.022 | 0.009 | 12.737 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | H | 25 | ASP | -1 | -0.857 | -0.919 | 9.070 | 0.494 | 0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | H | 26 | GLY | 0 | 0.048 | 0.013 | 9.052 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | H | 27 | LYS | 1 | 0.795 | 0.887 | 1.818 | -5.044 | -5.597 | 3.458 | -0.996 | -1.909 | 0.007 |
| 23 | H | 28 | SER | 0 | -0.006 | 0.015 | 4.671 | -0.216 | -0.208 | -0.001 | -0.019 | 0.012 | 0.000 |
| 24 | H | 29 | ALA | 0 | 0.064 | 0.012 | 6.839 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | H | 30 | PHE | 0 | -0.039 | -0.008 | 8.266 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | H | 32 | THR | 0 | -0.027 | -0.028 | 11.900 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | H | 33 | ARG | 1 | 0.951 | 0.964 | 13.530 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | H | 34 | LYS | 1 | 0.972 | 0.998 | 15.347 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | H | 35 | LEU | 0 | 0.043 | 0.029 | 15.057 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | H | 37 | TYR | 0 | 0.082 | 0.028 | 15.786 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | H | 38 | GLN | 0 | 0.031 | 0.032 | 14.243 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |