FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: 49R8N
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 | 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 | 31 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -122853.75059 |
|---|---|
| FMO2-HF: Nuclear repulsion | 108172.053455 |
| FMO2-HF: Total energy | -14681.697135 |
| FMO2-MP2: Total energy | -14719.006853 |
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. |
| -3.454 | -3.074 | 4.486 | -2.089 | -2.775 | 0.009 |
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 | -0.024 | 0.015 | 3.838 | -2.732 | -1.152 | -0.009 | -0.804 | -0.766 | 0.004 |
| 4 | H | 8 | GLU | -1 | -0.882 | -0.932 | 6.706 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | H | 9 | PRO | 0 | 0.000 | -0.010 | 10.473 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | H | 10 | GLY | 0 | 0.036 | 0.036 | 12.314 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | H | 11 | THR | 0 | -0.042 | -0.038 | 15.072 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | H | 12 | THR | 0 | -0.038 | -0.031 | 14.301 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | H | 13 | PHE | 0 | 0.054 | 0.035 | 7.498 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | H | 14 | LYS | 1 | 0.900 | 0.926 | 12.685 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | H | 15 | ASP | -1 | -0.754 | -0.847 | 7.173 | -1.267 | -1.267 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | H | 16 | LYS | 1 | 0.848 | 0.894 | 7.025 | 1.087 | 1.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | H | 17 | CYS | 0 | -0.122 | -0.054 | 11.740 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | H | 18 | ASN | 0 | -0.004 | 0.003 | 12.055 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | H | 19 | THR | 0 | 0.000 | 0.007 | 12.951 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | H | 20 | CYS | 0 | -0.041 | -0.013 | 9.436 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | H | 21 | ARG | 1 | 1.011 | 0.992 | 11.612 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | H | 23 | GLY | 0 | 0.013 | 0.029 | 10.564 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | H | 24 | SER | 0 | 0.028 | 0.007 | 12.577 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | H | 25 | ASP | -1 | -0.881 | -0.935 | 9.259 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | H | 26 | GLY | 0 | 0.051 | 0.015 | 8.890 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | H | 27 | LYS | 1 | 0.801 | 0.891 | 1.769 | -1.485 | -2.694 | 4.496 | -1.268 | -2.018 | 0.005 |
| 23 | H | 28 | SER | 0 | 0.008 | 0.020 | 4.723 | -0.551 | -0.542 | -0.001 | -0.017 | 0.009 | 0.000 |
| 24 | H | 29 | ALA | 0 | 0.076 | 0.015 | 6.725 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | H | 30 | PHE | 0 | -0.036 | -0.004 | 8.149 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | H | 32 | THR | 0 | -0.023 | -0.023 | 11.869 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | H | 33 | ARG | 1 | 0.954 | 0.963 | 13.431 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | H | 34 | LYS | 1 | 0.975 | 0.998 | 15.376 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | H | 35 | LEU | 0 | 0.047 | 0.031 | 14.851 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | H | 37 | TYR | 0 | 0.092 | 0.031 | 15.679 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | H | 38 | GLN | 0 | -0.002 | 0.017 | 14.262 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |