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: YRN32
Calculation Name: 2D56-A-Other547
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 2D56
Chain ID: A
UniProt ID: P90683
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 | -226253.708006 |
|---|---|
| FMO2-HF: Nuclear repulsion | 204374.523029 |
| FMO2-HF: Total energy | -21879.184977 |
| FMO2-MP2: Total energy | -21934.780504 |
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:ALA)
Summations of interaction energy for
fragment #1(A:1:ALA)
| 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. |
| -32.513 | -25.26 | 1.416 | -4.519 | -4.152 | -0.052 |
Interaction energy analysis for fragmet #1(A:1:ALA)
| 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 | ASP | -1 | -0.876 | -0.930 | 3.906 | -42.525 | -40.971 | -0.017 | -0.747 | -0.791 | -0.001 |
| 34 | A | 34 | THR | 0 | -0.095 | -0.043 | 4.319 | 4.224 | 4.275 | -0.001 | -0.006 | -0.044 | 0.000 |
| 36 | A | 36 | HIS | 0 | -0.001 | -0.005 | 4.734 | -1.927 | -1.809 | -0.001 | -0.019 | -0.098 | 0.000 |
| 46 | A | 49 | ASP | -1 | -0.863 | -0.927 | 2.249 | -96.266 | -91.228 | 1.434 | -3.602 | -2.870 | -0.050 |
| 47 | A | 50 | ARG | 1 | 0.789 | 0.875 | 3.723 | 35.232 | 35.724 | 0.001 | -0.145 | -0.349 | -0.001 |
| 4 | A | 4 | PHE | 0 | 0.075 | 0.038 | 6.573 | 4.731 | 4.731 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | A | 5 | SER | 0 | -0.052 | -0.033 | 8.167 | 4.480 | 4.480 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | SER | 0 | 0.019 | 0.009 | 8.036 | -3.801 | -3.801 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | CYS | 0 | -0.077 | -0.035 | 7.478 | 3.995 | 3.995 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | ALA | 0 | 0.016 | 0.024 | 13.139 | 1.512 | 1.512 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ARG | 1 | 0.917 | 0.943 | 14.000 | 19.756 | 19.756 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | MET | 0 | -0.022 | -0.010 | 17.633 | 0.866 | 0.866 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | ASP | -1 | -0.750 | -0.845 | 18.844 | -15.907 | -15.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | VAL | 0 | -0.035 | -0.022 | 17.879 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | PRO | 0 | 0.051 | 0.010 | 20.996 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLY | 0 | 0.018 | 0.024 | 21.310 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LEU | 0 | 0.006 | -0.005 | 20.286 | -0.593 | -0.593 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | SER | 0 | 0.038 | 0.011 | 15.390 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | LYS | 1 | 0.969 | 0.993 | 16.230 | 14.233 | 14.233 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | VAL | 0 | -0.001 | 0.001 | 17.016 | -0.497 | -0.497 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ALA | 0 | 0.010 | 0.005 | 17.127 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | GLN | 0 | 0.039 | -0.001 | 11.957 | 0.460 | 0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | GLY | 0 | 0.035 | 0.025 | 13.130 | -1.293 | -1.293 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | LEU | 0 | 0.021 | 0.009 | 15.476 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | CYS | 0 | -0.047 | -0.010 | 11.094 | -2.055 | -2.055 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ILE | 0 | -0.039 | -0.003 | 9.453 | -0.949 | -0.949 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | SER | 0 | 0.004 | -0.004 | 11.752 | -0.430 | -0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | SER | 0 | -0.037 | -0.031 | 14.754 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | CYS | 0 | -0.034 | -0.030 | 7.608 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | LYS | 1 | 0.972 | 0.991 | 10.923 | 20.990 | 20.990 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | PHE | 0 | -0.049 | -0.020 | 11.997 | 0.625 | 0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | GLN | 0 | -0.024 | -0.009 | 12.145 | 1.193 | 1.193 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | ASN | 0 | -0.049 | -0.046 | 12.220 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | CYS | 0 | 0.053 | 0.041 | 5.831 | 4.524 | 4.524 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | GLY | 0 | 0.051 | 0.036 | 7.625 | -2.779 | -2.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | A | 35 | GLY | 0 | 0.068 | 0.027 | 6.708 | -2.787 | -2.787 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | A | 38 | GLU | -1 | -0.902 | -0.936 | 7.575 | -32.066 | -32.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | A | 39 | LYS | 1 | 0.844 | 0.909 | 10.214 | 19.251 | 19.251 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | A | 40 | ARG | 1 | 1.014 | 0.997 | 12.174 | 20.751 | 20.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | A | 41 | GLY | 0 | 0.028 | 0.023 | 15.399 | 0.641 | 0.641 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | A | 42 | GLY | 0 | 0.000 | -0.003 | 18.585 | 0.607 | 0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | A | 43 | ARG | 1 | 0.882 | 0.928 | 16.680 | 15.370 | 15.370 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | A | 44 | PRO | 0 | 0.030 | 0.009 | 15.226 | -1.103 | -1.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | A | 45 | THR | 0 | 0.012 | 0.013 | 12.045 | 1.296 | 1.296 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | A | 47 | VAL | 0 | 0.027 | 0.021 | 6.245 | 1.632 | 1.632 | 0.000 | 0.000 | 0.000 | 0.000 |
| 48 | A | 52 | GLY | 0 | 0.022 | 0.018 | 7.924 | -1.964 | -1.964 | 0.000 | 0.000 | 0.000 | 0.000 |
| 49 | A | 53 | ARG | 0 | 0.019 | 0.017 | 8.380 | -2.240 | -2.240 | 0.000 | 0.000 | 0.000 | 0.000 |