FMODB ID: VQL81
Calculation Name: 3EJ9-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3EJ9
Chain ID: C
UniProt ID: Q9EV84
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 | 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 | 63 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -317864.173216 |
---|---|
FMO2-HF: Nuclear repulsion | 292750.131114 |
FMO2-HF: Total energy | -25114.042102 |
FMO2-MP2: Total energy | -25186.033151 |
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(C:1:PRO)
Summations of interaction energy for
fragment #1(C:1: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. |
-14.931 | -7.705 | 11.769 | -6.821 | -12.174 | -0.043 |
Interaction energy analysis for fragmet #1(C:1: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 | C | 3 | ILE | 0 | 0.000 | 0.007 | 2.889 | -0.451 | 1.494 | 0.116 | -0.788 | -1.274 | 0.003 |
4 | C | 4 | SER | 0 | 0.005 | -0.005 | 6.148 | -0.189 | -0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 5 | CYS | 0 | -0.066 | -0.028 | 9.906 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 6 | ASP | -1 | -0.831 | -0.896 | 12.824 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 7 | MET | 0 | -0.052 | -0.039 | 16.302 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 8 | ARG | 1 | 0.891 | 0.944 | 18.997 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 9 | TYR | 0 | 0.053 | 0.027 | 21.838 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 10 | GLY | 0 | 0.022 | 0.000 | 23.658 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 11 | ARG | 1 | 0.855 | 0.945 | 20.020 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 12 | THR | 0 | 0.045 | 0.019 | 22.501 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 13 | ASP | -1 | -0.859 | -0.944 | 20.434 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 14 | GLU | -1 | -0.948 | -0.978 | 19.451 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 15 | GLN | 0 | 0.010 | 0.000 | 19.495 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 16 | LYS | 1 | 0.882 | 0.939 | 16.313 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 17 | ARG | 1 | 0.985 | 0.994 | 14.865 | 0.259 | 0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 18 | ALA | 0 | 0.027 | 0.021 | 15.001 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 19 | LEU | 0 | -0.003 | -0.003 | 12.630 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 20 | SER | 0 | -0.031 | -0.014 | 10.586 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 21 | ALA | 0 | 0.013 | 0.009 | 10.081 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 22 | GLY | 0 | -0.033 | -0.018 | 11.481 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 23 | LEU | 0 | 0.034 | -0.003 | 7.878 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 24 | LEU | 0 | 0.001 | -0.002 | 6.367 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 25 | ARG | 1 | 0.942 | 0.987 | 7.126 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 26 | VAL | 0 | -0.024 | -0.018 | 8.706 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 27 | ILE | 0 | 0.026 | 0.015 | 2.577 | -0.707 | 0.010 | 0.787 | -0.314 | -1.189 | 0.001 |
28 | C | 28 | SER | 0 | -0.059 | -0.043 | 4.702 | -0.091 | 0.052 | -0.001 | -0.011 | -0.131 | 0.000 |
29 | C | 29 | GLU | -1 | -0.957 | -0.972 | 5.800 | -0.285 | -0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 30 | ALA | 0 | -0.067 | -0.026 | 6.690 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 31 | THR | 0 | -0.063 | -0.056 | 2.716 | -1.593 | -0.437 | 0.324 | -0.493 | -0.987 | -0.002 |
32 | C | 32 | GLY | 0 | 0.021 | 0.025 | 5.461 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 33 | GLU | -1 | -0.878 | -0.931 | 2.270 | -3.059 | -2.640 | 2.156 | -0.662 | -1.913 | -0.004 |
34 | C | 34 | PRO | 0 | 0.024 | 0.046 | 4.777 | 0.111 | 0.181 | -0.001 | -0.008 | -0.061 | 0.000 |
35 | C | 35 | ARG | 1 | 0.961 | 0.944 | 4.977 | 0.144 | 0.215 | -0.001 | -0.001 | -0.068 | 0.000 |
36 | C | 36 | GLU | -1 | -0.982 | -0.983 | 6.740 | -1.186 | -1.186 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 37 | ASN | 0 | -0.051 | -0.018 | 3.292 | 0.220 | 0.806 | 0.035 | -0.214 | -0.408 | -0.001 |
38 | C | 38 | ILE | 0 | -0.024 | -0.002 | 2.043 | -10.143 | -8.625 | 8.349 | -4.188 | -5.680 | -0.040 |
39 | C | 39 | PHE | 0 | -0.009 | 0.003 | 3.509 | 1.980 | 2.581 | 0.005 | -0.142 | -0.463 | 0.000 |
40 | C | 40 | PHE | 0 | -0.019 | -0.034 | 5.330 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 41 | VAL | 0 | -0.024 | -0.002 | 7.782 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 42 | ILE | 0 | 0.001 | -0.001 | 11.158 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 43 | ARG | 1 | 0.895 | 0.945 | 11.992 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 44 | GLU | -1 | -0.837 | -0.919 | 16.739 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 45 | GLY | 0 | 0.031 | 0.016 | 20.155 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 46 | SER | 0 | 0.028 | 0.000 | 23.345 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 47 | GLY | 0 | 0.012 | 0.001 | 25.805 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 48 | ILE | 0 | 0.029 | 0.016 | 27.127 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 49 | ASN | 0 | -0.017 | -0.001 | 24.321 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 50 | PHE | 0 | -0.057 | -0.009 | 19.397 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 51 | VAL | 0 | 0.030 | 0.015 | 24.181 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 52 | GLN | 0 | -0.039 | -0.020 | 21.157 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 53 | HIS | 0 | 0.027 | 0.001 | 25.559 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 54 | GLY | 0 | -0.008 | 0.010 | 27.914 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 55 | GLU | -1 | -0.941 | -0.961 | 29.405 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 56 | HIS | 0 | -0.059 | -0.052 | 28.539 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 57 | LEU | 0 | -0.043 | -0.017 | 23.962 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 58 | PRO | 0 | 0.040 | 0.032 | 28.400 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 59 | ASP | -1 | -0.833 | -0.935 | 28.536 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 60 | TYR | 0 | -0.071 | -0.047 | 24.904 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 61 | VAL | 0 | 0.027 | 0.013 | 27.505 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 62 | PRO | 0 | -0.038 | -0.012 | 27.508 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 63 | GLY | 0 | 0.013 | 0.018 | 27.766 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |