![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YZ712
Calculation Name: 2EBB-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2EBB
Chain ID: A
UniProt ID: Q5KYG7
Base Structure: X-ray
Registration Date: 2023-06-26
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 | OptAll |
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 | 96 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -767081.371608 |
---|---|
FMO2-HF: Nuclear repulsion | 727431.072363 |
FMO2-HF: Total energy | -39650.299246 |
FMO2-MP2: Total energy | -39767.882832 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F027750/ligand_interaction/ligand_F027750.png)
Ligand Interaction
![ligand interaction](./Kdata/F027750/ligand_interaction/ligand_interaction_F027750.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(A:3:MET)
Summations of interaction energy for
fragment #1(A:3:MET)
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. |
-13.454 | -8.857 | 1.256 | -2.194 | -3.659 | -0.017 |
Interaction energy analysis for fragmet #1(A:3:MET)
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 | 5 | LEU | 0 | -0.044 | -0.004 | 2.523 | -7.265 | -3.901 | 1.245 | -1.935 | -2.673 | -0.017 |
4 | A | 6 | THR | 0 | -0.033 | -0.052 | 4.198 | 1.369 | 1.627 | -0.001 | -0.020 | -0.237 | 0.000 |
5 | A | 7 | GLU | -1 | -0.893 | -0.947 | 5.909 | -0.577 | -0.577 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | GLU | -1 | -0.829 | -0.926 | 9.467 | -1.499 | -1.499 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | GLU | -1 | -0.841 | -0.894 | 4.935 | -5.868 | -5.806 | -0.001 | -0.002 | -0.059 | 0.000 |
8 | A | 10 | VAL | 0 | -0.018 | -0.011 | 8.471 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | GLN | 0 | -0.058 | -0.036 | 10.622 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | ALA | 0 | 0.011 | 0.011 | 12.144 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | LEU | 0 | -0.022 | -0.009 | 8.902 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | LEU | 0 | -0.021 | -0.022 | 13.206 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | GLU | -1 | -0.914 | -0.925 | 15.771 | -0.582 | -0.582 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | LYS | 1 | 0.782 | 0.883 | 15.637 | 0.911 | 0.911 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | ALA | 0 | 0.011 | -0.004 | 16.469 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | ASP | -1 | -0.825 | -0.899 | 18.567 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | GLY | 0 | -0.063 | -0.033 | 21.826 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | TRP | 0 | -0.011 | -0.002 | 17.377 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | LYS | 1 | 0.871 | 0.934 | 19.027 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | LEU | 0 | 0.046 | 0.027 | 13.977 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | ALA | 0 | -0.004 | -0.004 | 17.287 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | ASP | -1 | -0.813 | -0.901 | 17.287 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | GLU | -1 | -0.821 | -0.891 | 15.368 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | ARG | 1 | 0.786 | 0.879 | 12.255 | -0.185 | -0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | TRP | 0 | 0.014 | 0.020 | 12.633 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | ILE | 0 | 0.005 | 0.023 | 13.037 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | VAL | 0 | -0.022 | -0.025 | 15.863 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | LYS | 1 | 0.832 | 0.906 | 19.245 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | LYS | 1 | 0.869 | 0.923 | 21.778 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | TYR | 0 | 0.011 | -0.018 | 20.925 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ARG | 1 | 0.963 | 0.986 | 26.974 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | PHE | 0 | 0.032 | 0.026 | 27.329 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLN | 0 | 0.067 | 0.022 | 33.007 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | ASP | -1 | -0.790 | -0.902 | 35.673 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | TYR | 0 | -0.017 | -0.007 | 33.444 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | LEU | 0 | 0.021 | 0.008 | 33.554 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 39 | GLN | 0 | -0.016 | -0.012 | 32.374 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | GLY | 0 | 0.043 | 0.031 | 29.731 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | ILE | 0 | -0.006 | -0.012 | 28.692 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | GLU | -1 | -0.748 | -0.827 | 28.867 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | PHE | 0 | -0.016 | -0.016 | 22.812 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | VAL | 0 | 0.006 | -0.003 | 24.492 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | ARG | 1 | 0.863 | 0.905 | 24.090 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | ARG | 1 | 0.859 | 0.910 | 24.490 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | ILE | 0 | 0.034 | 0.017 | 20.008 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | ALA | 0 | -0.004 | 0.027 | 19.506 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | ALA | 0 | -0.003 | 0.003 | 20.099 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | ILE | 0 | -0.016 | -0.010 | 16.766 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | SER | 0 | -0.003 | -0.022 | 15.665 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | GLU | -1 | -0.882 | -0.916 | 15.637 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | ASN | 0 | -0.016 | -0.003 | 16.631 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | ALA | 0 | -0.046 | -0.026 | 12.478 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | ASN | 0 | -0.099 | -0.044 | 12.102 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | HIS | 0 | -0.073 | -0.047 | 8.400 | 0.335 | 0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | HIS | 0 | -0.034 | -0.033 | 12.719 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | PRO | 0 | -0.012 | 0.009 | 15.233 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | PHE | 0 | -0.019 | -0.005 | 16.522 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | ILE | 0 | 0.015 | -0.015 | 19.421 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | SER | 0 | 0.005 | 0.006 | 22.565 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | ILE | 0 | -0.014 | -0.020 | 26.116 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | ASP | -1 | -0.883 | -0.925 | 29.274 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | TYR | 0 | 0.067 | 0.014 | 31.603 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LYS | 1 | 0.834 | 0.917 | 32.629 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | LEU | 0 | -0.077 | -0.041 | 29.155 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | ILE | 0 | 0.030 | 0.036 | 24.781 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | THR | 0 | -0.037 | -0.012 | 23.504 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | VAL | 0 | 0.017 | 0.012 | 18.392 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | LYS | 1 | 0.839 | 0.900 | 17.597 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | LEU | 0 | 0.002 | 0.012 | 12.399 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | SER | 0 | 0.028 | -0.018 | 10.824 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | SER | 0 | 0.007 | 0.016 | 6.683 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | TRP | 0 | 0.052 | 0.012 | 8.563 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | ARG | 1 | 0.932 | 0.970 | 7.791 | -1.600 | -1.600 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | ALA | 0 | 0.016 | 0.009 | 4.669 | 0.128 | 0.246 | -0.001 | -0.020 | -0.097 | 0.000 |
75 | A | 77 | LYS | 1 | 0.891 | 0.945 | 6.460 | -2.474 | -2.474 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | GLY | 0 | 0.025 | 0.006 | 9.047 | -0.362 | -0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | LEU | 0 | -0.003 | 0.020 | 8.264 | 0.419 | 0.419 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | THR | 0 | -0.009 | -0.025 | 3.418 | -1.139 | -0.547 | 0.015 | -0.202 | -0.406 | 0.000 |
79 | A | 81 | LYS | 1 | 0.892 | 0.911 | 4.653 | 1.558 | 1.761 | -0.001 | -0.015 | -0.187 | 0.000 |
80 | A | 82 | LEU | 0 | 0.054 | 0.030 | 5.842 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | ASP | -1 | -0.731 | -0.834 | 7.817 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | PHE | 0 | 0.057 | 0.002 | 9.564 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | ASP | -1 | -0.853 | -0.889 | 10.079 | -0.941 | -0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | LEU | 0 | 0.022 | 0.003 | 11.327 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | ALA | 0 | 0.010 | 0.008 | 13.692 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LYS | 1 | 0.909 | 0.947 | 15.399 | 0.644 | 0.644 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLN | 0 | 0.006 | 0.005 | 14.837 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | TYR | 0 | -0.002 | -0.029 | 15.927 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | ASP | -1 | -0.803 | -0.870 | 19.709 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | GLU | -1 | -0.826 | -0.898 | 21.084 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | VAL | 0 | -0.036 | -0.017 | 22.078 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | TYR | 0 | -0.022 | -0.034 | 23.992 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | ASN | 0 | -0.032 | 0.002 | 24.797 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | GLN | 0 | -0.009 | -0.013 | 26.542 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 97 | MET | 0 | -0.099 | -0.025 | 28.473 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 98 | LYS | 1 | 0.784 | 0.893 | 27.680 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |