![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QYKJY
Calculation Name: 5UA4-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5UA4
Chain ID: B
UniProt ID: P42485
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.
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 | 32 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -101937.5177 |
---|---|
FMO2-HF: Nuclear repulsion | 89277.909338 |
FMO2-HF: Total energy | -12659.608362 |
FMO2-MP2: Total energy | -12696.409482 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026614/ligand_interaction/ligand_F026614.png)
Ligand Interaction
![ligand interaction](./Kdata/F026614/ligand_interaction/ligand_interaction_F026614.png)
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(B:26:SER)
Summations of interaction energy for
fragment #1(B:26: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. |
-0.717 | 1.574 | 3.741 | -2.768 | -3.263 | -0.006 |
Interaction energy analysis for fragmet #1(B:26: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 | B | 28 | GLU | -1 | -0.842 | -0.926 | 2.936 | -4.425 | -2.298 | 0.047 | -0.905 | -1.269 | 0.000 |
4 | B | 29 | ALA | 0 | -0.047 | -0.029 | 2.256 | 0.747 | 0.128 | 3.685 | -1.511 | -1.555 | -0.006 |
5 | B | 30 | VAL | 0 | 0.012 | 0.001 | 3.709 | 0.357 | 1.140 | 0.009 | -0.352 | -0.439 | 0.000 |
6 | B | 31 | ILE | 0 | 0.031 | 0.021 | 5.722 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 32 | ARG | 1 | 0.944 | 0.960 | 6.813 | 1.495 | 1.495 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 33 | ASP | -1 | -0.937 | -0.963 | 7.649 | -0.397 | -0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 34 | ILE | 0 | 0.016 | 0.009 | 9.387 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 35 | ALA | 0 | 0.016 | 0.002 | 11.283 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 36 | ARG | 1 | 0.874 | 0.948 | 11.920 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 37 | HIS | 0 | 0.031 | 0.003 | 12.763 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 38 | LEU | 0 | 0.007 | 0.001 | 15.500 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 39 | ALA | 0 | 0.018 | 0.027 | 16.742 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 40 | ARG | 1 | 0.935 | 0.971 | 15.973 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 41 | ILE | 0 | -0.028 | -0.015 | 19.295 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 42 | GLY | 0 | 0.033 | 0.020 | 21.219 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 43 | ASP | -1 | -0.863 | -0.937 | 21.669 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 44 | ARG | 1 | 0.828 | 0.902 | 21.612 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 45 | MET | 0 | -0.064 | -0.023 | 25.738 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 46 | GLU | -1 | -0.932 | -0.962 | 26.699 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 47 | TYR | 0 | -0.009 | 0.018 | 25.680 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 48 | GLY | 0 | 0.011 | 0.005 | 29.865 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 49 | ILE | 0 | -0.086 | -0.050 | 25.574 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 50 | ARG | 1 | 0.953 | 0.985 | 28.981 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 51 | PRO | 0 | 0.002 | -0.009 | 28.455 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 52 | GLY | 0 | 0.011 | 0.002 | 28.463 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 53 | LEU | 0 | -0.031 | -0.018 | 28.347 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 54 | VAL | 0 | 0.005 | 0.006 | 31.953 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 55 | ASP | -1 | -0.901 | -0.939 | 35.391 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 56 | SER | 0 | -0.059 | -0.037 | 37.536 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 57 | LEU | 0 | -0.010 | 0.003 | 41.231 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |