FMODB ID: Q13MY
Calculation Name: 4UE9-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4UE9
Chain ID: B
UniProt ID: Q8IH18
Base Structure: X-ray
Registration Date: 2023-06-20
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 | OptHSide |
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 | 39 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -150995.044328 |
---|---|
FMO2-HF: Nuclear repulsion | 134425.73843 |
FMO2-HF: Total energy | -16569.305898 |
FMO2-MP2: Total energy | -16616.99726 |
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(B:6:PRO)
Summations of interaction energy for
fragment #1(B:6: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. |
0.314 | 2.984 | 0.054 | -1.056 | -1.668 | 0.002 |
Interaction energy analysis for fragmet #1(B:6: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 | B | 8 | MET | 0 | 0.009 | 0.016 | 3.136 | -1.349 | 1.321 | 0.054 | -1.056 | -1.668 | 0.002 |
4 | B | 9 | ARG | 1 | 0.920 | 0.965 | 5.480 | 0.979 | 0.979 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 10 | TYR | 0 | 0.041 | 0.021 | 8.342 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 11 | SER | 0 | -0.021 | -0.034 | 11.858 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 12 | LYS | 1 | 1.005 | 0.978 | 15.262 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 13 | VAL | 0 | 0.015 | 0.001 | 18.393 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 14 | ASP | -1 | -0.778 | -0.857 | 14.139 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 15 | LEU | 0 | -0.022 | -0.008 | 13.451 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 16 | LEU | 0 | -0.063 | -0.043 | 16.564 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 17 | ALA | 0 | -0.002 | 0.010 | 18.321 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 18 | LEU | 0 | 0.032 | 0.027 | 14.397 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 19 | ARG | 1 | 0.905 | 0.960 | 18.814 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 20 | TYR | 0 | -0.051 | -0.047 | 21.507 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 21 | GLU | -1 | -0.823 | -0.885 | 18.686 | -0.290 | -0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 22 | GLY | 0 | 0.005 | -0.019 | 22.076 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 23 | LYS | 1 | 0.965 | 0.950 | 17.870 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 24 | SER | 0 | -0.008 | 0.020 | 19.679 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 25 | ARG | 1 | 0.891 | 0.951 | 21.745 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 26 | GLN | 0 | 0.007 | 0.037 | 25.488 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 27 | ARG | 1 | 0.907 | 0.900 | 27.621 | 0.145 | 0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 28 | PRO | 0 | 0.009 | 0.021 | 23.961 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 29 | GLN | 0 | -0.040 | -0.011 | 23.922 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 30 | CYS | 0 | 0.013 | 0.022 | 25.338 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 31 | SER | 0 | 0.017 | 0.001 | 23.862 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 32 | THR | 0 | 0.028 | 0.011 | 21.723 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 33 | ARG | 1 | 0.802 | 0.875 | 23.865 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 34 | LEU | 0 | 0.008 | -0.001 | 25.637 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 35 | GLU | -1 | -0.816 | -0.880 | 27.477 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 36 | LEU | 0 | 0.023 | 0.018 | 31.069 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 37 | GLN | 0 | 0.011 | 0.011 | 29.652 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 38 | THR | 0 | 0.010 | 0.004 | 34.432 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 39 | LEU | 0 | 0.003 | -0.007 | 32.081 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 40 | GLY | 0 | 0.026 | 0.005 | 35.313 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 41 | PHE | 0 | -0.021 | -0.001 | 28.560 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 42 | TRP | 0 | -0.021 | 0.002 | 27.628 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 43 | LYS | 1 | 0.954 | 0.976 | 29.738 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 44 | ILE | 0 | 0.033 | 0.021 | 33.436 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |