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: QYV9Y
Calculation Name: 2WZR-4-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2WZR
Chain ID: 4
UniProt ID: Q6PMU1
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 46 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -140132.232669 |
|---|---|
| FMO2-HF: Nuclear repulsion | 122188.792232 |
| FMO2-HF: Total energy | -17943.440436 |
| FMO2-MP2: Total energy | -17994.553636 |
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(4:15:SER)
Summations of interaction energy for
fragment #1(4:15:SER)
| 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. |
| -0.495 | 1.927 | -0.025 | -1.23 | -1.166 | 0.006 |
Interaction energy analysis for fragmet #1(4:15:SER)
| 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 | 4 | 17 | ASN | 0 | -0.016 | -0.015 | 3.797 | -1.049 | 1.244 | -0.023 | -1.200 | -1.069 | 0.006 |
| 4 | 4 | 18 | THR | 0 | -0.002 | 0.000 | 4.093 | 1.141 | 1.264 | -0.001 | -0.019 | -0.103 | 0.000 |
| 5 | 4 | 19 | GLY | 0 | 0.024 | 0.003 | 4.428 | -1.588 | -1.582 | -0.001 | -0.011 | 0.006 | 0.000 |
| 6 | 4 | 20 | SER | 0 | -0.018 | 0.000 | 6.761 | 0.519 | 0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | 4 | 21 | ILE | 0 | -0.003 | -0.006 | 9.130 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | 4 | 22 | ILE | 0 | -0.021 | 0.003 | 10.657 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | 4 | 23 | ASN | 0 | 0.010 | -0.008 | 10.073 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | 4 | 24 | ASN | 0 | -0.005 | -0.011 | 8.922 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | 4 | 25 | TYR | 0 | -0.005 | 0.012 | 11.517 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | 4 | 26 | TYR | 0 | 0.023 | 0.023 | 14.168 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | 4 | 27 | MET | 0 | 0.011 | -0.003 | 13.677 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | 4 | 28 | GLN | 0 | 0.063 | 0.012 | 10.390 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | 4 | 29 | GLN | 0 | 0.022 | 0.008 | 12.774 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | 4 | 30 | TYR | 0 | -0.053 | -0.013 | 15.181 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | 4 | 31 | GLN | 0 | -0.041 | -0.011 | 10.131 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | 4 | 32 | ASN | 0 | -0.028 | -0.016 | 8.432 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | 4 | 33 | SER | 0 | 0.027 | 0.022 | 11.998 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | 4 | 34 | MET | 0 | -0.030 | -0.020 | 12.047 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | 4 | 35 | ASP | -1 | -0.879 | -0.928 | 10.439 | 0.376 | 0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | 4 | 36 | THR | 0 | -0.079 | -0.049 | 13.737 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | 4 | 37 | GLN | 0 | -0.006 | -0.009 | 13.782 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | 4 | 38 | LEU | 0 | 0.011 | 0.008 | 18.248 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | 4 | 39 | GLY | 0 | -0.018 | 0.001 | 21.430 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | 4 | 65 | ASN | 0 | -0.029 | -0.037 | 12.607 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | 4 | 66 | ASP | -1 | -0.831 | -0.909 | 11.426 | 1.160 | 1.160 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | 4 | 67 | TRP | 0 | -0.021 | -0.020 | 13.681 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | 4 | 68 | PHE | 0 | 0.093 | 0.017 | 15.411 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | 4 | 69 | SER | 0 | 0.017 | 0.057 | 13.579 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | 4 | 70 | LYS | 1 | 0.947 | 0.962 | 15.643 | -0.817 | -0.817 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | 4 | 71 | LEU | 0 | -0.016 | -0.004 | 18.643 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | 4 | 72 | ALA | 0 | -0.003 | 0.016 | 18.212 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | 4 | 73 | GLN | 0 | -0.018 | -0.022 | 17.489 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 35 | 4 | 74 | SER | 0 | -0.110 | -0.071 | 20.798 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
| 36 | 4 | 75 | ALA | 0 | -0.006 | 0.016 | 23.662 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 37 | 4 | 76 | PHE | 0 | -0.005 | 0.001 | 25.653 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 38 | 4 | 77 | SER | 0 | 0.008 | -0.005 | 27.166 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 39 | 4 | 78 | GLY | 0 | -0.018 | 0.000 | 29.328 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 40 | 4 | 79 | LEU | 0 | 0.004 | -0.004 | 32.832 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 41 | 4 | 80 | VAL | 0 | -0.009 | 0.001 | 36.272 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 42 | 4 | 81 | GLY | 0 | 0.002 | 0.003 | 38.496 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 43 | 4 | 82 | ALA | 0 | -0.014 | -0.008 | 41.293 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 44 | 4 | 83 | LEU | 0 | 0.029 | 0.010 | 39.562 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 45 | 4 | 84 | LEU | 0 | -0.020 | -0.017 | 43.011 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 46 | 4 | 85 | ALA | 0 | -0.001 | 0.014 | 43.696 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |