FMODB ID: YVJK2
Calculation Name: 4EMG-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4EMG
Chain ID: A
UniProt ID: Q9Y7M4
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 71 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -448369.684115 |
---|---|
FMO2-HF: Nuclear repulsion | 419601.163539 |
FMO2-HF: Total energy | -28768.520576 |
FMO2-MP2: Total energy | -28852.836448 |
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:9:GLU)
Summations of interaction energy for
fragment #1(A:9:GLU)
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. |
26.163 | 31.61 | 3.172 | -4.071 | -4.548 | -0.029 |
Interaction energy analysis for fragmet #1(A:9:GLU)
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 | 11 | LEU | 0 | 0.027 | 0.000 | 3.550 | -6.317 | -4.240 | -0.005 | -0.947 | -1.125 | 0.004 |
4 | A | 12 | ASP | -1 | -0.828 | -0.910 | 2.342 | 34.651 | 37.806 | 3.178 | -3.105 | -3.228 | -0.033 |
5 | A | 13 | LEU | 0 | -0.006 | 0.009 | 4.721 | -3.515 | -3.300 | -0.001 | -0.019 | -0.195 | 0.000 |
6 | A | 14 | VAL | 0 | 0.009 | 0.015 | 7.526 | -3.244 | -3.244 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 15 | ARG | 1 | 0.885 | 0.936 | 5.461 | -34.143 | -34.143 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 16 | LEU | 0 | -0.038 | -0.029 | 6.898 | -1.969 | -1.969 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 17 | SER | 0 | -0.034 | -0.027 | 10.305 | -1.760 | -1.760 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 18 | LEU | 0 | -0.034 | -0.013 | 11.873 | -1.493 | -1.493 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 19 | ASP | -1 | -0.900 | -0.964 | 14.545 | 14.594 | 14.594 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 20 | GLU | -1 | -0.922 | -0.946 | 15.743 | 15.890 | 15.890 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 21 | ILE | 0 | -0.072 | -0.042 | 17.999 | -0.346 | -0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 22 | VAL | 0 | -0.005 | -0.001 | 14.798 | 0.567 | 0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 23 | TYR | 0 | -0.037 | -0.020 | 17.496 | -0.751 | -0.751 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 24 | VAL | 0 | 0.013 | -0.008 | 16.834 | 1.162 | 1.162 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 25 | LYS | 1 | 0.830 | 0.934 | 18.225 | -13.755 | -13.755 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 26 | LEU | 0 | 0.020 | -0.007 | 19.303 | 0.567 | 0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 27 | ARG | 1 | 0.870 | 0.910 | 18.831 | -14.609 | -14.609 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 28 | GLY | 0 | -0.043 | -0.009 | 23.468 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 29 | ASP | -1 | -0.919 | -0.956 | 26.403 | 10.451 | 10.451 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 30 | ARG | 1 | 0.896 | 0.933 | 25.466 | -11.011 | -11.011 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 31 | GLU | -1 | -0.833 | -0.901 | 23.174 | 13.249 | 13.249 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 32 | LEU | 0 | 0.005 | 0.000 | 20.985 | -0.600 | -0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 33 | ASN | 0 | -0.016 | 0.000 | 21.885 | 1.081 | 1.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 34 | GLY | 0 | 0.072 | 0.036 | 21.355 | -0.707 | -0.707 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 35 | ARG | 1 | 0.849 | 0.941 | 20.326 | -12.884 | -12.884 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 36 | LEU | 0 | -0.013 | 0.008 | 13.078 | -0.496 | -0.496 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 37 | HIS | 0 | 0.052 | 0.015 | 17.503 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 38 | ALA | 0 | -0.011 | -0.009 | 15.966 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 39 | TYR | 0 | 0.003 | -0.009 | 7.649 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 40 | ASP | -1 | -0.778 | -0.868 | 12.800 | 16.299 | 16.299 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 41 | GLU | -1 | -0.859 | -0.941 | 10.391 | 18.333 | 18.333 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 42 | HIS | 0 | -0.112 | -0.049 | 11.381 | 0.757 | 0.757 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 43 | LEU | 0 | -0.015 | -0.007 | 10.349 | -0.162 | -0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 44 | ASN | 0 | -0.060 | -0.045 | 13.227 | -1.031 | -1.031 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 45 | MET | 0 | -0.015 | -0.003 | 14.856 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 46 | VAL | 0 | -0.017 | -0.003 | 17.234 | -0.897 | -0.897 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 47 | LEU | 0 | -0.015 | -0.008 | 18.073 | 0.548 | 0.548 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 48 | GLY | 0 | 0.012 | -0.005 | 21.249 | -0.661 | -0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 49 | ASP | -1 | -0.935 | -0.964 | 23.987 | 10.887 | 10.887 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 50 | ALA | 0 | -0.001 | 0.004 | 24.337 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 51 | GLU | -1 | -0.811 | -0.891 | 25.703 | 10.273 | 10.273 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 52 | GLU | -1 | -0.825 | -0.894 | 25.900 | 10.918 | 10.918 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 53 | ILE | 0 | -0.054 | -0.042 | 26.355 | -0.525 | -0.525 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 54 | VAL | 0 | -0.002 | 0.007 | 28.105 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 55 | THR | 0 | 0.011 | 0.010 | 28.568 | -0.524 | -0.524 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 70 | THR | 0 | -0.025 | -0.035 | 32.281 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 71 | ILE | 0 | -0.035 | -0.006 | 33.434 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 72 | ARG | 1 | 0.835 | 0.891 | 29.027 | -10.060 | -10.060 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 73 | LYS | 1 | 0.883 | 0.946 | 31.139 | -9.750 | -9.750 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 74 | HIS | 0 | -0.027 | -0.017 | 29.624 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 75 | TYR | 0 | -0.051 | -0.048 | 27.572 | -0.488 | -0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 76 | GLU | -1 | -0.879 | -0.925 | 28.250 | 9.780 | 9.780 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 77 | MET | 0 | -0.013 | -0.001 | 23.547 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 78 | LEU | 0 | -0.032 | -0.004 | 23.741 | -0.376 | -0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 79 | PHE | 0 | -0.003 | 0.012 | 20.249 | 0.493 | 0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 80 | VAL | 0 | -0.012 | -0.014 | 19.255 | -0.442 | -0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 81 | ARG | 1 | 0.864 | 0.911 | 19.416 | -12.043 | -12.043 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 82 | GLY | 0 | 0.099 | 0.042 | 16.410 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 83 | ASP | -1 | -0.814 | -0.890 | 17.020 | 14.052 | 14.052 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 84 | SER | 0 | -0.129 | -0.062 | 18.868 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 85 | VAL | 0 | 0.031 | 0.012 | 15.019 | -0.446 | -0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 86 | ILE | 0 | -0.063 | -0.024 | 16.466 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 87 | LEU | 0 | -0.037 | -0.022 | 14.443 | 1.074 | 1.074 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 88 | ILE | 0 | 0.052 | 0.017 | 11.829 | -0.930 | -0.930 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 89 | ALA | 0 | -0.054 | -0.016 | 12.685 | 1.557 | 1.557 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 90 | PRO | 0 | 0.040 | 0.034 | 11.327 | -1.219 | -1.219 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 91 | PRO | 0 | 0.032 | 0.025 | 14.388 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 92 | ARG | 1 | 0.915 | 0.941 | 15.638 | -15.243 | -15.243 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 93 | ASN | 0 | 0.008 | 0.018 | 15.353 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |