FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: YVNN2
Calculation Name: 1ZVB-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1ZVB
Chain ID: A
UniProt ID: P59594
Base Structure: X-ray
Registration Date: 2023-09-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
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 | 34 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -104944.641172 |
|---|---|
| FMO2-HF: Nuclear repulsion | 92419.235605 |
| FMO2-HF: Total energy | -12525.405568 |
| FMO2-MP2: Total energy | -12562.862503 |
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. |
| 1.897 | 5.98 | 0.335 | -1.726 | -2.691 | 0 |
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 | ASN | 0 | 0.073 | 0.021 | 3.374 | -0.755 | 0.853 | 0.003 | -0.670 | -0.941 | 0.001 |
| 4 | A | 4 | THR | 0 | -0.035 | -0.018 | 2.497 | -1.001 | 0.993 | 0.334 | -0.929 | -1.399 | -0.001 |
| 5 | A | 5 | LEU | 0 | 0.066 | 0.051 | 3.745 | 0.805 | 1.182 | -0.001 | -0.121 | -0.255 | 0.000 |
| 6 | A | 6 | VAL | 0 | 0.050 | 0.021 | 5.387 | 0.613 | 0.717 | -0.001 | -0.006 | -0.096 | 0.000 |
| 7 | A | 7 | LYS | 1 | 0.919 | 0.958 | 7.333 | 1.376 | 1.376 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | GLN | 0 | 0.004 | 0.001 | 6.116 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LEU | 0 | 0.004 | 0.001 | 9.320 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | SER | 0 | 0.000 | -0.004 | 11.374 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | SER | 0 | -0.047 | -0.012 | 12.642 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ASN | 0 | 0.030 | 0.005 | 12.301 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | PHE | 0 | 0.008 | -0.004 | 14.448 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | GLY | 0 | 0.013 | 0.023 | 17.068 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | ALA | 0 | -0.010 | -0.001 | 18.191 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ILE | 0 | -0.002 | -0.012 | 18.122 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | SER | 0 | -0.009 | -0.001 | 21.258 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | SER | 0 | -0.014 | -0.002 | 22.838 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | VAL | 0 | 0.015 | 0.002 | 23.592 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | LEU | 0 | 0.005 | -0.004 | 24.628 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ASN | 0 | 0.032 | 0.016 | 27.194 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | ASP | -1 | -0.921 | -0.956 | 28.680 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | ILE | 0 | -0.022 | -0.029 | 28.271 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | LEU | 0 | 0.007 | 0.003 | 30.309 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | SER | 0 | 0.037 | 0.032 | 33.188 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ARG | 1 | 0.803 | 0.898 | 32.265 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | LEU | 0 | -0.011 | 0.005 | 35.211 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | ASP | -1 | -0.847 | -0.920 | 37.281 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | LYS | 1 | 0.844 | 0.909 | 38.001 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | VAL | 0 | 0.020 | 0.017 | 40.136 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLU | -1 | -0.967 | -0.986 | 40.209 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | ALA | 0 | -0.071 | -0.029 | 43.276 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 33 | A | 33 | GLU | -1 | -0.989 | -0.996 | 44.171 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
| 34 | A | 34 | VAL | 0 | -0.098 | -0.031 | 46.040 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |