FMODB ID: N9ZNQ
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 | 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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -948809.943997 |
---|---|
FMO2-HF: Nuclear repulsion | 903864.171311 |
FMO2-HF: Total energy | -44945.772686 |
FMO2-MP2: Total energy | -45080.111438 |
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: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. |
-12.101 | -4.94 | 8.04 | -4.326 | -10.876 | -0.029 |
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 | 0.955 | 0.992 | 3.577 | -3.347 | -0.964 | -0.015 | -1.108 | -1.260 | -0.002 |
4 | A | 197 | GLY | 0 | 0.011 | 0.014 | 4.395 | 0.027 | 0.147 | -0.001 | -0.016 | -0.103 | 0.000 |
5 | A | 198 | LYS | 1 | 0.801 | 0.907 | 6.790 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 199 | ILE | 0 | -0.057 | -0.032 | 3.256 | 0.025 | 0.438 | 0.052 | -0.083 | -0.382 | 0.000 |
7 | A | 200 | THR | 0 | 0.032 | 0.023 | 7.012 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 201 | TYR | 0 | -0.005 | -0.014 | 3.439 | 0.065 | 0.351 | 0.004 | -0.046 | -0.244 | 0.000 |
9 | A | 202 | GLN | 0 | 0.021 | 0.013 | 10.220 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 203 | VAL | 0 | -0.025 | -0.020 | 12.062 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 204 | TRP | 0 | 0.017 | 0.011 | 14.673 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 205 | GLY | 0 | 0.010 | -0.004 | 17.262 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 206 | ILE | 0 | -0.001 | 0.001 | 19.242 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 207 | ARG | 1 | 0.776 | 0.884 | 21.865 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 208 | VAL | 0 | 0.023 | 0.016 | 24.692 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 209 | ARG | 1 | 0.845 | 0.906 | 27.905 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 210 | ASN | 0 | -0.008 | -0.008 | 31.125 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 211 | GLY | 0 | 0.006 | 0.002 | 32.727 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 212 | GLN | 0 | 0.013 | 0.018 | 30.667 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 213 | PHE | 0 | 0.006 | -0.003 | 24.902 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 214 | VAL | 0 | 0.004 | 0.012 | 26.383 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 215 | THR | 0 | 0.056 | 0.015 | 22.477 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 216 | SER | 0 | 0.008 | 0.020 | 20.737 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 217 | SER | 0 | -0.065 | -0.026 | 21.739 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 235 | VAL | 0 | -0.025 | -0.020 | 23.156 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 236 | LEU | 0 | -0.009 | 0.002 | 17.905 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 237 | SER | 0 | 0.033 | 0.034 | 17.543 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 238 | PHE | 0 | 0.002 | 0.004 | 14.035 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 239 | ILE | 0 | -0.006 | -0.006 | 9.722 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 240 | THR | 0 | -0.014 | -0.034 | 9.591 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 241 | ALA | 0 | 0.011 | 0.005 | 5.554 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 242 | ASN | 0 | -0.045 | -0.051 | 7.227 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 243 | PHE | 0 | 0.000 | -0.029 | 2.709 | -4.137 | -1.778 | 3.728 | -1.760 | -4.327 | -0.024 |
34 | A | 244 | ASN | 0 | -0.016 | 0.001 | 5.516 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 245 | SER | 0 | -0.049 | -0.047 | 8.935 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 246 | ASN | 0 | -0.042 | -0.015 | 6.910 | -0.317 | -0.317 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 247 | THR | 0 | 0.015 | 0.013 | 8.703 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 248 | LEU | 0 | 0.004 | -0.012 | 8.058 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 249 | ALA | 0 | -0.033 | -0.014 | 11.104 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 250 | GLY | 0 | 0.008 | -0.009 | 13.225 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 251 | LYS | 1 | 0.955 | 0.993 | 15.454 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 252 | ILE | 0 | -0.030 | -0.008 | 16.384 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 253 | LEU | 0 | 0.024 | 0.011 | 19.157 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 254 | GLY | 0 | 0.047 | 0.019 | 22.407 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 255 | ASN | 0 | -0.022 | -0.012 | 25.148 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 256 | SER | 0 | 0.013 | 0.000 | 28.484 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 257 | ASP | -1 | -0.922 | -0.941 | 29.798 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 258 | TYR | 0 | -0.072 | -0.065 | 20.637 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 259 | GLY | 0 | 0.013 | 0.012 | 26.956 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 260 | PRO | 0 | -0.023 | -0.029 | 26.686 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 261 | ASP | -1 | -0.803 | -0.889 | 23.272 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 262 | VAL | 0 | -0.064 | -0.031 | 18.975 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 263 | ASP | -1 | -0.908 | -0.954 | 19.743 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 264 | ILE | 0 | 0.023 | 0.005 | 14.016 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 265 | GLN | 0 | 0.002 | 0.000 | 16.813 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 266 | ASN | 0 | -0.050 | -0.016 | 15.767 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 267 | ALA | 0 | 0.032 | 0.024 | 12.274 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 268 | THR | 0 | -0.022 | -0.021 | 11.585 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 269 | ILE | 0 | -0.015 | 0.004 | 4.897 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 270 | THR | 0 | -0.001 | -0.009 | 7.463 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 271 | GLY | 0 | 0.032 | 0.030 | 4.562 | 0.155 | 0.250 | -0.001 | -0.013 | -0.081 | 0.000 |
62 | A | 272 | PRO | 0 | -0.027 | -0.017 | 2.481 | -1.821 | -0.727 | 0.899 | -0.697 | -1.295 | 0.001 |
63 | A | 273 | THR | 0 | -0.038 | -0.022 | 3.344 | 0.408 | 0.115 | 0.014 | 0.483 | -0.204 | 0.000 |
64 | A | 274 | PHE | 0 | 0.035 | 0.001 | 6.222 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 275 | SER | 0 | -0.020 | -0.005 | 8.521 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 276 | GLY | 0 | 0.054 | 0.027 | 12.270 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 277 | ASP | -1 | -0.874 | -0.917 | 15.416 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 278 | ALA | 0 | -0.012 | -0.009 | 17.759 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 279 | THR | 0 | -0.010 | -0.006 | 19.604 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 280 | SER | 0 | 0.009 | -0.006 | 22.677 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 281 | GLY | 0 | 0.051 | 0.023 | 24.878 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 282 | GLY | 0 | -0.026 | -0.010 | 28.104 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 283 | LYS | 1 | 0.912 | 0.972 | 26.950 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 284 | SER | 0 | 0.043 | 0.011 | 23.960 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 285 | GLY | 0 | -0.011 | -0.010 | 21.432 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 286 | LYS | 1 | 0.894 | 0.949 | 18.778 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 287 | LEU | 0 | -0.005 | -0.010 | 12.330 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 288 | GLU | -1 | -0.916 | -0.968 | 12.637 | -0.334 | -0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 289 | GLY | 0 | 0.013 | 0.001 | 10.038 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 290 | LYS | 1 | 0.873 | 0.956 | 5.944 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 291 | PHE | 0 | 0.051 | 0.020 | 2.369 | -1.358 | -1.232 | 3.356 | -1.011 | -2.471 | -0.004 |
82 | A | 292 | PHE | 0 | -0.016 | -0.014 | 3.997 | -0.091 | 0.264 | 0.005 | -0.052 | -0.309 | 0.000 |
83 | A | 302 | GLU | -1 | -0.963 | -0.990 | 9.635 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 303 | VAL | 0 | -0.039 | -0.022 | 3.931 | -0.072 | 0.083 | 0.000 | -0.020 | -0.135 | 0.000 |
85 | A | 304 | SER | 0 | 0.031 | 0.006 | 6.131 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 305 | ILE | 0 | -0.023 | 0.009 | 5.907 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 306 | GLY | 0 | 0.023 | 0.004 | 8.026 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 307 | GLY | 0 | -0.003 | -0.004 | 9.973 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 308 | LYS | 1 | 0.889 | 0.963 | 12.552 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 309 | ILE | 0 | -0.004 | -0.007 | 15.751 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 310 | THR | 0 | -0.005 | 0.013 | 18.280 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 311 | PHE | 0 | 0.010 | -0.008 | 21.446 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 312 | ASP | -1 | -0.902 | -0.966 | 24.555 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 313 | GLY | 0 | -0.054 | -0.019 | 27.114 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 314 | ASP | -1 | -0.883 | -0.939 | 28.273 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 315 | ARG | 1 | 0.916 | 0.942 | 24.671 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 316 | SER | 0 | -0.059 | -0.023 | 26.787 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 317 | LEU | 0 | 0.003 | 0.003 | 25.107 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 318 | ASP | -1 | -0.754 | -0.843 | 22.549 | -0.191 | -0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 319 | THR | 0 | -0.075 | -0.035 | 18.720 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 320 | VAL | 0 | 0.010 | 0.006 | 16.139 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 321 | PHE | 0 | -0.004 | -0.012 | 11.352 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 322 | GLY | 0 | 0.037 | 0.012 | 12.536 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 323 | GLY | 0 | 0.027 | 0.007 | 11.647 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 324 | VAL | 0 | 0.018 | 0.020 | 9.711 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 325 | SER | 0 | -0.057 | -0.030 | 7.405 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 326 | TYR | 0 | -0.024 | -0.017 | 9.401 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 327 | GLU | -1 | -0.820 | -0.881 | 11.017 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 328 | LYS | 1 | 0.941 | 0.969 | 5.269 | -0.996 | -0.996 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 329 | LYS | 1 | 0.936 | 0.969 | 8.886 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 330 | LEU | 0 | 0.012 | 0.007 | 4.648 | -0.120 | -0.052 | -0.001 | -0.003 | -0.065 | 0.000 |
112 | A | 331 | ASP | -1 | -0.853 | -0.932 | 7.426 | 0.836 | 0.836 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 332 | ASP | -1 | -0.866 | -0.877 | 9.932 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 333 | THR | 0 | 0.015 | 0.010 | 10.101 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 334 | SER | 0 | -0.059 | -0.071 | 12.662 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 335 | GLN | 0 | 0.066 | 0.022 | 12.300 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 336 | ASP | -1 | -0.822 | -0.881 | 13.401 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 337 | THR | 0 | 0.015 | 0.008 | 11.511 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 338 | ASN | 0 | 0.005 | 0.008 | 13.513 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 339 | HIS | 0 | 0.023 | 0.062 | 13.703 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 340 | LEU | 0 | -0.035 | -0.015 | 10.387 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 341 | THR | 0 | -0.051 | -0.055 | 14.476 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |