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: VRV61
Calculation Name: 1BH0-A-Xray372
Preferred Name: Glucagon
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1BH0
Chain ID: A
ChEMBL ID: CHEMBL5736
UniProt ID: P01275
Base Structure: X-ray
Registration Date: 2023-03-13
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 | 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 | 29 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -95867.811212 |
|---|---|
| FMO2-HF: Nuclear repulsion | 83715.230663 |
| FMO2-HF: Total energy | -12152.58055 |
| FMO2-MP2: Total energy | -12188.014732 |
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(A:1:HIS)
Summations of interaction energy for
fragment #1(A:1:HIS)
| 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. |
| -5.963 | -14.795 | 13.964 | 2.482 | -7.616 | 0.003 |
Interaction energy analysis for fragmet #1(A:1:HIS)
| 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 | A | 3 | GLN | 0 | 0.051 | 0.016 | 2.372 | -3.015 | -5.872 | 6.280 | 1.207 | -4.630 | -0.008 |
| 4 | A | 4 | GLY | 0 | -0.019 | -0.020 | 2.294 | -3.509 | -4.299 | 7.647 | -4.396 | -2.462 | 0.011 |
| 5 | A | 5 | THR | 0 | -0.073 | -0.037 | 3.173 | 1.050 | -4.135 | 0.037 | 5.671 | -0.524 | 0.000 |
| 6 | A | 6 | PHE | 0 | 0.095 | 0.015 | 6.890 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | THR | 0 | 0.033 | 0.028 | 10.542 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | SER | 0 | -0.061 | 0.004 | 9.468 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.948 | -1.013 | 11.252 | 1.338 | 1.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | TYR | 0 | 0.051 | 0.025 | 13.406 | -0.243 | -0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | -0.004 | -0.004 | 16.144 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LYS | 1 | 0.978 | 0.993 | 16.010 | -0.744 | -0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | TYR | 0 | 0.026 | 0.022 | 20.379 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | LEU | 0 | -0.029 | -0.010 | 21.556 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ASP | -1 | -0.774 | -0.909 | 21.817 | 0.303 | 0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | SER | 0 | -0.094 | -0.031 | 24.158 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LYS | 1 | 0.914 | 0.953 | 25.970 | -0.329 | -0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | LYS | 1 | 0.847 | 0.922 | 26.983 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ALA | 0 | 0.008 | 0.020 | 28.679 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLN | 0 | 0.067 | 0.011 | 30.394 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLU | -1 | -0.883 | -0.952 | 31.486 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | PHE | 0 | 0.036 | 0.019 | 33.209 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | VAL | 0 | 0.039 | 0.036 | 34.867 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | GLN | 0 | -0.018 | -0.008 | 35.927 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | TRP | 0 | -0.071 | -0.038 | 37.336 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LEU | 0 | -0.097 | -0.017 | 37.409 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | MET | 0 | -0.080 | -0.076 | 39.894 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ASN | 0 | -0.014 | 0.014 | 40.899 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | THR | 0 | -0.007 | 0.014 | 42.617 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |