![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: JL4Q9
Calculation Name: 5EE2-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5EE2
Chain ID: A
UniProt ID: A0A0H4
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -949241.629923 |
---|---|
FMO2-HF: Nuclear repulsion | 904295.300579 |
FMO2-HF: Total energy | -44946.329344 |
FMO2-MP2: Total energy | -45080.663032 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F026484/ligand_interaction/ligand_F026484.png)
Ligand Interaction
![ligand interaction](./Kdata/F026484/ligand_interaction/ligand_interaction_F026484.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:194:LEU)
Summations of interaction energy for
fragment #1(A:194:LEU)
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. |
-13.027 | -5.454 | 7.851 | -4.464 | -10.96 | -0.033 |
Interaction energy analysis for fragmet #1(A:194:LEU)
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 | 196 | LYS | 1 | 0.890 | 0.955 | 3.592 | -3.259 | -0.913 | -0.017 | -1.086 | -1.243 | -0.001 |
4 | A | 197 | GLY | 0 | 0.015 | 0.016 | 4.410 | -0.029 | 0.099 | -0.001 | -0.016 | -0.112 | 0.000 |
5 | A | 198 | LYS | 1 | 0.796 | 0.912 | 6.804 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 199 | ILE | 0 | -0.046 | -0.024 | 3.197 | 0.060 | 0.483 | 0.054 | -0.085 | -0.393 | 0.000 |
7 | A | 200 | THR | 0 | 0.031 | 0.022 | 6.893 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 201 | TYR | 0 | -0.003 | -0.012 | 4.087 | -0.279 | -0.067 | 0.000 | -0.020 | -0.192 | 0.000 |
9 | A | 202 | GLN | 0 | 0.032 | 0.017 | 10.392 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 203 | VAL | 0 | -0.038 | -0.029 | 12.312 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 204 | TRP | 0 | 0.019 | 0.012 | 14.944 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 205 | GLY | 0 | 0.011 | 0.001 | 17.164 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 206 | ILE | 0 | 0.001 | 0.000 | 19.208 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 207 | ARG | 1 | 0.778 | 0.897 | 21.799 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 208 | VAL | 0 | 0.021 | 0.016 | 24.712 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 209 | ARG | 1 | 0.831 | 0.897 | 27.883 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 210 | ASN | 0 | -0.001 | -0.006 | 31.144 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 211 | GLY | 0 | 0.006 | 0.004 | 32.712 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 212 | GLN | 0 | 0.011 | 0.018 | 30.642 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 213 | PHE | 0 | 0.001 | -0.004 | 24.904 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 214 | VAL | 0 | 0.011 | 0.012 | 26.319 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 215 | THR | 0 | 0.061 | 0.019 | 22.257 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 216 | SER | 0 | -0.015 | 0.002 | 20.754 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 217 | SER | 0 | -0.051 | -0.014 | 21.637 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 235 | VAL | 0 | -0.031 | -0.025 | 23.243 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 236 | LEU | 0 | -0.002 | 0.008 | 18.210 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 237 | SER | 0 | 0.028 | 0.032 | 17.695 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 238 | PHE | 0 | -0.004 | 0.000 | 14.156 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 239 | ILE | 0 | -0.005 | -0.005 | 10.119 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 240 | THR | 0 | -0.011 | 0.000 | 9.617 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 241 | ALA | 0 | 0.015 | 0.006 | 5.576 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 242 | ASN | 0 | -0.048 | -0.046 | 7.079 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 243 | PHE | 0 | 0.024 | -0.019 | 2.748 | -5.066 | -2.195 | 3.748 | -2.005 | -4.615 | -0.029 |
34 | A | 244 | ASN | 0 | -0.018 | -0.002 | 5.522 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 245 | SER | 0 | -0.043 | -0.034 | 8.925 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 246 | ASN | 0 | -0.067 | -0.029 | 6.877 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 247 | THR | 0 | 0.021 | 0.017 | 8.674 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 248 | LEU | 0 | 0.006 | -0.011 | 7.809 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 249 | ALA | 0 | -0.031 | -0.012 | 10.987 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 250 | GLY | 0 | 0.011 | -0.007 | 13.325 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 251 | LYS | 1 | 0.860 | 0.937 | 15.598 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 252 | ILE | 0 | -0.037 | -0.013 | 16.290 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 253 | LEU | 0 | 0.027 | 0.014 | 19.293 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 254 | GLY | 0 | 0.042 | 0.012 | 22.656 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 255 | ASN | 0 | -0.028 | -0.021 | 25.287 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 256 | SER | 0 | -0.008 | -0.006 | 28.705 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 257 | ASP | -1 | -0.906 | -0.938 | 29.949 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 258 | TYR | 0 | -0.047 | -0.047 | 20.761 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 259 | GLY | 0 | 0.015 | 0.008 | 26.915 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 260 | PRO | 0 | -0.016 | -0.029 | 26.689 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 261 | ASP | -1 | -0.739 | -0.842 | 23.358 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 262 | VAL | 0 | -0.065 | -0.018 | 19.018 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 263 | ASP | -1 | -0.879 | -0.926 | 19.623 | -0.298 | -0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 264 | ILE | 0 | 0.021 | 0.000 | 13.933 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 265 | GLN | 0 | -0.011 | -0.012 | 16.676 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 266 | ASN | 0 | -0.051 | -0.021 | 15.739 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 267 | ALA | 0 | 0.025 | 0.022 | 12.287 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 268 | THR | 0 | -0.010 | -0.017 | 11.574 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 269 | ILE | 0 | -0.027 | -0.003 | 4.853 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 270 | THR | 0 | 0.009 | -0.003 | 7.561 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 271 | GLY | 0 | 0.036 | 0.028 | 4.547 | 0.186 | 0.279 | -0.001 | -0.013 | -0.078 | 0.000 |
62 | A | 272 | PRO | 0 | -0.034 | -0.020 | 2.426 | -1.823 | -0.795 | 0.805 | -0.639 | -1.194 | 0.001 |
63 | A | 273 | THR | 0 | -0.030 | -0.017 | 3.332 | 0.494 | 0.257 | 0.010 | 0.425 | -0.197 | 0.000 |
64 | A | 274 | PHE | 0 | 0.042 | 0.005 | 6.348 | -0.320 | -0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 275 | SER | 0 | -0.013 | 0.000 | 8.579 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 276 | GLY | 0 | 0.049 | 0.024 | 12.317 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 277 | ASP | -1 | -0.813 | -0.872 | 15.414 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 278 | ALA | 0 | -0.002 | 0.005 | 17.699 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 279 | THR | 0 | -0.005 | -0.002 | 19.551 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 280 | SER | 0 | 0.003 | -0.022 | 22.595 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 281 | GLY | 0 | 0.036 | 0.017 | 24.813 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 282 | GLY | 0 | -0.022 | -0.008 | 28.025 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 283 | LYS | 1 | 0.853 | 0.945 | 26.908 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 284 | SER | 0 | 0.044 | 0.010 | 23.962 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 285 | GLY | 0 | -0.004 | -0.008 | 21.441 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 286 | LYS | 1 | 0.816 | 0.886 | 18.804 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 287 | LEU | 0 | -0.014 | -0.014 | 12.299 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 288 | GLU | -1 | -0.849 | -0.927 | 12.749 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 289 | GLY | 0 | 0.015 | 0.003 | 10.117 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 290 | LYS | 1 | 0.828 | 0.929 | 5.477 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 291 | PHE | 0 | 0.047 | 0.025 | 2.373 | -1.367 | -1.182 | 3.251 | -0.976 | -2.459 | -0.004 |
82 | A | 292 | PHE | 0 | 0.011 | 0.000 | 4.056 | 0.009 | 0.294 | 0.003 | -0.025 | -0.262 | 0.000 |
83 | A | 302 | GLU | -1 | -0.963 | -0.988 | 9.617 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 303 | VAL | 0 | -0.033 | -0.016 | 3.902 | -0.061 | 0.090 | 0.000 | -0.020 | -0.132 | 0.000 |
85 | A | 304 | SER | 0 | 0.054 | 0.016 | 6.333 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 305 | ILE | 0 | -0.047 | -0.004 | 5.967 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 306 | GLY | 0 | 0.027 | 0.006 | 7.932 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 307 | GLY | 0 | -0.003 | -0.005 | 10.055 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 308 | LYS | 1 | 0.831 | 0.925 | 12.630 | 0.310 | 0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 309 | ILE | 0 | -0.004 | -0.009 | 15.819 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 310 | THR | 0 | -0.024 | 0.001 | 18.325 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 311 | PHE | 0 | 0.008 | -0.006 | 21.435 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 312 | ASP | -1 | -0.854 | -0.930 | 24.598 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 313 | GLY | 0 | -0.015 | 0.000 | 27.185 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 314 | ASP | -1 | -0.880 | -0.936 | 28.304 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 315 | ARG | 1 | 0.912 | 0.948 | 24.311 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 316 | SER | 0 | -0.060 | -0.029 | 26.848 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 317 | LEU | 0 | 0.009 | 0.008 | 25.201 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 318 | ASP | -1 | -0.750 | -0.856 | 22.590 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 319 | THR | 0 | -0.077 | -0.038 | 18.697 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 320 | VAL | 0 | 0.015 | 0.008 | 16.178 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 321 | PHE | 0 | -0.009 | -0.012 | 11.308 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 322 | GLY | 0 | 0.040 | 0.014 | 12.460 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 323 | GLY | 0 | 0.026 | 0.007 | 11.709 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 324 | VAL | 0 | 0.010 | 0.012 | 9.781 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 325 | SER | 0 | -0.058 | -0.031 | 7.350 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 326 | TYR | 0 | -0.015 | -0.013 | 9.356 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 327 | GLU | -1 | -0.787 | -0.894 | 11.002 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 328 | LYS | 1 | 0.931 | 0.971 | 5.543 | -0.889 | -0.889 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 329 | LYS | 1 | 0.834 | 0.905 | 8.910 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 330 | LEU | 0 | 0.015 | 0.012 | 4.576 | -0.173 | -0.085 | -0.001 | -0.004 | -0.083 | 0.000 |
112 | A | 331 | ASP | -1 | -0.815 | -0.921 | 7.432 | 0.845 | 0.845 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 332 | ASP | -1 | -0.839 | -0.893 | 9.973 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 333 | THR | 0 | 0.018 | 0.013 | 10.116 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 334 | SER | 0 | -0.067 | -0.041 | 12.678 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 335 | GLN | 0 | 0.068 | 0.021 | 12.316 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 336 | ASP | -1 | -0.820 | -0.884 | 13.420 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 337 | THR | 0 | 0.019 | 0.006 | 11.372 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 338 | ASN | 0 | -0.014 | 0.000 | 13.410 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 339 | HIS | 0 | 0.020 | 0.022 | 13.643 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 340 | LEU | 0 | -0.025 | -0.010 | 10.404 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 341 | THR | 0 | 0.011 | 0.008 | 14.346 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |