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: 3MGGL
Calculation Name: 2YSB-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2YSB
Chain ID: A
UniProt ID: Q8VEB2
Base Structure: SolutionNMR
Registration Date: 2025-10-05
Reference: Sci Data 11, 1164 (2024).
DOI: https://doi.org/10.1038/s41597-024-03999-2
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptAll |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Homology Modeling |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE. |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 49 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -212550.550805 |
|---|---|
| FMO2-HF: Nuclear repulsion | 193720.107119 |
| FMO2-HF: Total energy | -18830.443686 |
| FMO2-MP2: Total energy | -18885.415844 |
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:GLY)
Summations of interaction energy for
fragment #1(A:1:GLY)
| 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. |
| -42.033 | -41.074 | 0.005 | -0.491 | -0.472 | -0.002 |
Interaction energy analysis for fragmet #1(A:1:GLY)
| 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 | SER | 0 | -0.032 | -0.021 | 3.546 | -7.217 | -6.258 | 0.005 | -0.491 | -0.472 | -0.002 |
| 4 | A | 4 | GLY | 0 | 0.042 | 0.013 | 5.647 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | -0.010 | -0.003 | 7.550 | 3.648 | 3.648 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | -0.037 | -0.012 | 9.809 | 3.062 | 3.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | GLY | 0 | 0.018 | 0.002 | 11.153 | 2.321 | 2.321 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLU | -1 | -0.940 | -0.967 | 9.543 | -33.155 | -33.155 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.972 | -0.987 | 12.580 | -17.364 | -17.364 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | LEU | 0 | 0.044 | 0.039 | 15.210 | 0.926 | 0.926 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | PRO | 0 | 0.010 | 0.009 | 17.736 | 0.511 | 0.511 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | LEU | 0 | -0.009 | -0.007 | 21.301 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | PRO | 0 | 0.033 | 0.025 | 23.536 | 0.313 | 0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | PRO | 0 | 0.020 | -0.001 | 26.848 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | 0.065 | 0.028 | 30.148 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | TRP | 0 | 0.001 | -0.002 | 24.976 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | -0.015 | 0.004 | 26.767 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | VAL | 0 | -0.046 | -0.020 | 20.730 | -0.259 | -0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ASP | -1 | -0.839 | -0.908 | 24.085 | -11.824 | -11.824 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | TRP | 0 | 0.025 | -0.005 | 18.235 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | THR | 0 | -0.036 | -0.017 | 23.398 | 0.587 | 0.587 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | MET | 0 | 0.024 | -0.008 | 24.308 | -0.348 | -0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ARG | 1 | 0.915 | 0.957 | 23.169 | 11.409 | 11.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | GLY | 0 | 0.052 | 0.039 | 20.472 | -0.408 | -0.408 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.868 | 0.948 | 19.166 | 13.766 | 13.766 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | LYS | 1 | 0.927 | 0.979 | 16.551 | 19.283 | 19.283 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | TYR | 0 | -0.035 | -0.030 | 20.220 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | TYR | 0 | 0.054 | 0.019 | 17.179 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | ILE | 0 | -0.019 | -0.015 | 24.072 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | ASP | -1 | -0.771 | -0.851 | 27.893 | -10.614 | -10.614 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | HIS | 0 | -0.042 | -0.041 | 29.749 | 0.538 | 0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ASN | 0 | -0.085 | -0.041 | 31.136 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | THR | 0 | -0.064 | -0.062 | 31.246 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | ASN | 0 | -0.029 | -0.004 | 33.715 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | THR | 0 | -0.005 | -0.002 | 30.653 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | A | 36 | THR | 0 | -0.015 | -0.010 | 27.332 | -0.231 | -0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 37 | HIS | 1 | 0.896 | 0.957 | 23.812 | 11.995 | 11.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 38 | TRP | 0 | 0.009 | 0.000 | 20.667 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 39 | SER | 0 | 0.027 | 0.015 | 18.473 | -0.538 | -0.538 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 40 | HIS | 0 | 0.041 | 0.005 | 18.045 | 0.935 | 0.935 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 41 | PRO | 0 | -0.011 | -0.007 | 19.819 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 42 | LEU | 0 | -0.026 | -0.019 | 19.912 | 0.347 | 0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 43 | GLU | -1 | -0.913 | -0.950 | 13.989 | -21.505 | -21.505 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 44 | SER | 0 | -0.068 | -0.037 | 18.019 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 45 | GLY | 0 | -0.011 | 0.001 | 20.611 | 0.636 | 0.636 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | A | 46 | PRO | 0 | 0.014 | 0.008 | 21.136 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 47 | A | 47 | SER | 0 | -0.073 | -0.045 | 23.644 | 0.424 | 0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 48 | SER | 0 | -0.041 | -0.014 | 25.893 | 0.528 | 0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 49 | GLY | -1 | -0.943 | -0.953 | 26.976 | -11.172 | -11.172 | 0.000 | 0.000 | 0.000 | 0.000 |