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: 34QKL
Calculation Name: 4YCU-C-Xray549
Preferred Name:
Target Type:
Ligand Name: cladosporin
Ligand 3-letter code: KRS
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 4YCU
Chain ID: C
UniProt ID: Q13155
Base Structure: X-ray
Registration Date: 2025-10-12
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 | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | ac.sh, 23 2024 Oct |
| Water | No |
| Procedure | Manual calculation |
| Remarks |
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. 23 (BINDS Ver. 1) / 20230922 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -79394.212934 |
|---|---|
| FMO2-HF: Nuclear repulsion | 66724.153058 |
| FMO2-HF: Total energy | -12670.059876 |
| FMO2-MP2: Total energy | -12704.93396 |
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(C:2:PRO)
Summations of interaction energy for
fragment #1(C:2:PRO)
| 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. |
| 22.829 | 24.974 | 0.076 | -1.105 | -1.116 | -0.006 |
Interaction energy analysis for fragmet #1(C:2:PRO)
| 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 | C | 4 | TYR | 0 | 0.030 | 0.020 | 3.105 | -6.262 | -4.117 | 0.076 | -1.105 | -1.116 | -0.006 |
| 4 | C | 5 | GLN | 0 | -0.012 | -0.009 | 5.749 | 3.763 | 3.763 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | C | 6 | VAL | 0 | 0.036 | 0.015 | 7.309 | 2.112 | 2.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | C | 7 | LYS | 1 | 0.860 | 0.944 | 10.685 | 18.171 | 18.171 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | C | 8 | PRO | 0 | 0.036 | 0.007 | 12.811 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | C | 9 | TYR | 0 | 0.052 | 0.017 | 15.182 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | C | 10 | HIS | 0 | 0.020 | 0.029 | 17.389 | 0.803 | 0.803 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | C | 11 | GLY | 0 | 0.053 | 0.037 | 18.926 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | C | 12 | GLY | 0 | -0.057 | -0.050 | 16.235 | -0.779 | -0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | C | 13 | GLY | 0 | 0.000 | 0.005 | 17.219 | -0.436 | -0.436 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | C | 14 | ALA | 0 | 0.029 | 0.006 | 20.101 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | C | 15 | PRO | 0 | -0.017 | -0.012 | 20.239 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | C | 16 | LEU | 0 | 0.017 | 0.015 | 21.709 | 0.430 | 0.430 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | C | 17 | ARG | 1 | 0.925 | 0.957 | 24.246 | 10.665 | 10.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | C | 18 | VAL | 0 | 0.016 | 0.014 | 27.752 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | C | 19 | GLU | -1 | -0.908 | -0.944 | 30.527 | -8.529 | -8.529 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | C | 20 | LEU | 0 | -0.033 | -0.023 | 32.622 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | C | 21 | PRO | 0 | 0.006 | -0.003 | 36.193 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | C | 22 | THR | 0 | -0.007 | 0.004 | 39.395 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | C | 23 | CYS | 0 | -0.031 | -0.021 | 41.786 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | C | 24 | MET | 0 | 0.001 | 0.016 | 45.109 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | C | 25 | TYR | 0 | 0.009 | 0.003 | 46.323 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | C | 26 | ARG | 1 | 0.950 | 0.963 | 47.966 | 6.066 | 6.066 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | C | 27 | LEU | 0 | 0.029 | 0.020 | 50.837 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | C | 28 | PRO | 0 | 0.013 | 0.004 | 53.478 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | C | 29 | ASN | 0 | 0.020 | -0.002 | 56.013 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | C | 30 | VAL | 0 | 0.004 | -0.007 | 59.701 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | C | 31 | HIS | 0 | -0.052 | -0.024 | 61.571 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | C | 32 | GLY | -1 | -0.957 | -0.951 | 61.090 | -5.057 | -5.057 | 0.000 | 0.000 | 0.000 | 0.000 |