![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 9GK62
Calculation Name: 2I15-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2I15
Chain ID: A
UniProt ID: P75364
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 122 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -910417.180881 |
---|---|
FMO2-HF: Nuclear repulsion | 860339.145337 |
FMO2-HF: Total energy | -50078.035544 |
FMO2-MP2: Total energy | -50223.153518 |
3D Structure
Ligand structure
![ligand structure](./data_download/9GK62/ligand_interaction/9GK62_ligand.png)
Ligand Interaction
![ligand interaction](./data_download/9GK62/ligand_interaction/9GK62_ligand_interaction.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:1:MET)
Summations of interaction energy for
fragment #1(A:1: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. |
-4.741 | 0.667 | 2.264 | -2.438 | -5.236 | -0.001 |
Interaction energy analysis for fragmet #1(A:1: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 | 3 | PRO | 0 | 0.056 | 0.011 | 3.020 | -1.721 | 1.567 | 0.184 | -1.601 | -1.871 | 0.000 |
4 | A | 4 | GLN | 0 | 0.044 | 0.027 | 4.676 | 0.514 | 0.716 | -0.001 | -0.010 | -0.190 | 0.000 |
5 | A | 5 | LEU | 0 | 0.012 | 0.011 | 3.643 | -0.343 | 0.166 | 0.009 | -0.081 | -0.437 | 0.000 |
6 | A | 6 | LEU | 0 | 0.019 | 0.007 | 2.807 | -0.845 | 0.398 | 2.046 | -0.874 | -2.416 | -0.001 |
7 | A | 7 | ALA | 0 | 0.009 | 0.002 | 4.302 | -0.638 | -0.659 | 0.026 | 0.151 | -0.158 | 0.000 |
8 | A | 8 | LEU | 0 | 0.010 | 0.016 | 7.730 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.903 | 0.936 | 4.363 | -1.836 | -1.649 | 0.000 | -0.023 | -0.164 | 0.000 |
10 | A | 10 | GLN | 0 | 0.003 | 0.006 | 7.755 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | PHE | 0 | 0.000 | 0.020 | 9.095 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | VAL | 0 | 0.047 | 0.014 | 11.008 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLN | 0 | -0.061 | -0.029 | 8.960 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | THR | 0 | -0.008 | -0.029 | 12.335 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.872 | -0.933 | 14.672 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PHE | 0 | -0.020 | -0.006 | 15.285 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLU | -1 | -0.896 | -0.942 | 13.463 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LYS | 1 | 0.761 | 0.886 | 17.634 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.016 | 0.001 | 20.515 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASP | -1 | -0.800 | -0.884 | 22.602 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.037 | 0.019 | 20.176 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLU | -1 | -0.822 | -0.868 | 23.268 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | THR | 0 | -0.035 | -0.049 | 26.596 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | PHE | 0 | -0.017 | -0.010 | 18.936 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ARG | 1 | 0.846 | 0.891 | 23.248 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLN | 0 | 0.006 | -0.008 | 24.232 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | ASN | 0 | 0.036 | 0.022 | 26.221 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | PHE | 0 | 0.019 | 0.024 | 19.677 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ASN | 0 | -0.014 | -0.016 | 24.255 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ARG | 1 | 0.896 | 0.941 | 26.685 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | CYS | 0 | -0.037 | -0.013 | 25.318 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | LEU | 0 | 0.031 | 0.013 | 22.308 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.987 | -0.986 | 26.386 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | ARG | 1 | 0.825 | 0.915 | 30.133 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLU | -1 | -0.842 | -0.924 | 25.328 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | GLN | 0 | -0.131 | -0.082 | 26.452 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | SER | 0 | -0.005 | 0.000 | 29.803 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | THR | 0 | -0.111 | -0.054 | 31.438 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | LEU | 0 | -0.004 | -0.011 | 33.788 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.019 | 0.003 | 36.077 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ILE | 0 | 0.086 | 0.040 | 31.485 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | TYR | 0 | -0.060 | -0.027 | 34.297 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLU | -1 | -0.960 | -0.982 | 36.704 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASP | -1 | -0.897 | -0.930 | 32.105 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ASP | -1 | -1.024 | -1.016 | 29.115 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASP | -1 | -0.758 | -0.879 | 27.986 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | TYR | 0 | -0.176 | -0.129 | 27.277 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASP | -1 | -0.931 | -0.948 | 22.472 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | ASP | -1 | -0.823 | -0.911 | 21.898 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | GLN | 0 | -0.032 | -0.029 | 20.463 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | SER | 0 | 0.064 | 0.013 | 22.331 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | PHE | 0 | -0.081 | -0.047 | 24.361 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | PHE | 0 | 0.010 | -0.005 | 25.800 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | 0.084 | 0.070 | 27.071 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.866 | 0.933 | 28.680 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | PRO | 0 | -0.071 | -0.034 | 30.030 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | MET | 0 | 0.100 | 0.064 | 30.500 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | LEU | 0 | -0.010 | 0.009 | 33.075 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | SER | 0 | -0.053 | -0.039 | 34.909 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ASP | -1 | -0.919 | -0.970 | 35.730 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | 0.022 | 0.016 | 36.870 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | PHE | 0 | -0.019 | -0.004 | 38.556 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | PHE | 0 | -0.045 | -0.027 | 40.087 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ILE | 0 | 0.031 | 0.015 | 38.977 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | SER | 0 | -0.009 | 0.001 | 42.260 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | SER | 0 | -0.043 | -0.027 | 43.959 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | GLU | -1 | -0.871 | -0.952 | 46.255 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | VAL | 0 | -0.006 | -0.005 | 45.297 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | VAL | 0 | 0.002 | 0.009 | 47.708 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | LYS | 1 | 0.762 | 0.904 | 50.269 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | GLN | 0 | 0.008 | 0.013 | 52.674 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | LEU | 0 | -0.076 | -0.073 | 55.194 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ASP | -1 | -0.868 | -0.926 | 55.230 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LEU | 0 | -0.064 | -0.025 | 58.140 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 82 | PRO | 0 | -0.014 | -0.031 | 61.805 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 83 | LYS | 1 | 0.931 | 0.986 | 61.077 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 84 | GLY | 0 | 0.137 | 0.080 | 58.661 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 85 | ASP | -1 | -0.918 | -0.950 | 58.723 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 86 | VAL | 0 | 0.065 | 0.029 | 56.249 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 87 | LYS | 1 | 0.838 | 0.940 | 55.677 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 88 | SER | 0 | 0.017 | -0.018 | 55.122 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 89 | CYS | 0 | -0.014 | 0.019 | 53.074 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 90 | CYS | 0 | -0.051 | -0.038 | 51.223 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 91 | GLN | 0 | -0.071 | -0.054 | 50.356 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 92 | SER | 0 | 0.030 | 0.002 | 49.832 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 93 | PHE | 0 | -0.029 | -0.005 | 44.138 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 94 | TYR | 0 | -0.014 | -0.025 | 45.575 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 95 | GLU | -1 | -0.878 | -0.933 | 45.511 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 96 | ALA | 0 | 0.011 | 0.014 | 43.391 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 97 | LEU | 0 | -0.005 | 0.009 | 40.408 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 98 | THR | 0 | -0.048 | -0.028 | 41.402 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 99 | LEU | 0 | 0.049 | 0.032 | 35.679 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 100 | PHE | 0 | 0.109 | 0.040 | 34.189 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 101 | ILE | 0 | -0.028 | -0.019 | 38.142 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 102 | SER | 0 | 0.009 | 0.000 | 39.737 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 103 | ALA | 0 | 0.049 | 0.043 | 34.687 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 104 | LEU | 0 | -0.033 | -0.002 | 36.297 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 105 | ALA | 0 | -0.047 | -0.019 | 38.077 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 106 | ILE | 0 | 0.025 | 0.008 | 34.608 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 107 | THR | 0 | -0.030 | -0.025 | 33.063 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 108 | LYS | 1 | 0.838 | 0.924 | 35.297 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 109 | GLY | 0 | 0.007 | 0.012 | 37.778 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 110 | VAL | 0 | -0.083 | -0.039 | 39.191 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 111 | ASP | -1 | -0.817 | -0.908 | 42.209 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 112 | VAL | 0 | 0.031 | 0.022 | 40.418 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 113 | GLY | 0 | 0.054 | 0.010 | 43.752 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 114 | ARG | 1 | 0.848 | 0.922 | 47.374 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 115 | TYR | 0 | 0.039 | 0.024 | 42.192 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 116 | HIS | 0 | 0.060 | 0.036 | 43.099 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 117 | GLN | 0 | 0.022 | 0.006 | 47.538 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 118 | GLN | 0 | -0.069 | -0.041 | 48.147 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 119 | LEU | 0 | 0.002 | 0.016 | 46.557 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 120 | GLY | 0 | 0.077 | 0.030 | 49.428 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 121 | LYS | 1 | 0.899 | 0.939 | 52.363 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 122 | ARG | 1 | 0.877 | 0.949 | 48.982 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 123 | PHE | 0 | 0.056 | 0.022 | 48.704 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 124 | GLY | 0 | -0.056 | -0.018 | 53.902 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 125 | VAL | 0 | 0.003 | -0.007 | 50.438 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 126 | LEU | 0 | 0.003 | 0.004 | 53.822 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 127 | THR | 0 | 0.000 | -0.004 | 49.539 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 128 | VAL | 0 | 0.005 | 0.000 | 46.660 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 129 | TYR | 0 | -0.004 | 0.019 | 43.977 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |