![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Z6GYN
Calculation Name: 4JVU-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4JVU
Chain ID: A
UniProt ID: P01872
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 | 113 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -839590.370059 |
---|---|
FMO2-HF: Nuclear repulsion | 795732.836148 |
FMO2-HF: Total energy | -43857.53391 |
FMO2-MP2: Total energy | -43985.020847 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F028036/ligand_interaction/ligand_F028036.png)
Ligand Interaction
![ligand interaction](./Kdata/F028036/ligand_interaction/ligand_interaction_F028036.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:224:GLY)
Summations of interaction energy for
fragment #1(A:224:GLY)
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. |
0.705 | 2.212 | -0.009 | -0.772 | -0.726 | 0.003 |
Interaction energy analysis for fragmet #1(A:224:GLY)
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 | 226 | PRO | 0 | -0.014 | 0.007 | 3.868 | 0.489 | 1.996 | -0.009 | -0.772 | -0.726 | 0.003 |
4 | A | 227 | ALA | 0 | 0.005 | -0.005 | 6.484 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 228 | VAL | 0 | 0.003 | -0.008 | 9.455 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 229 | ALA | 0 | -0.007 | 0.000 | 12.539 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 230 | GLU | -1 | -0.765 | -0.852 | 13.511 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 231 | MET | 0 | -0.070 | -0.028 | 16.515 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 232 | ASN | 0 | 0.071 | 0.024 | 18.930 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 233 | PRO | 0 | -0.042 | 0.000 | 20.487 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 234 | ASN | 0 | 0.001 | 0.013 | 22.535 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 235 | VAL | 0 | 0.002 | -0.015 | 25.165 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 236 | ASN | 0 | -0.031 | -0.015 | 27.481 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 237 | VAL | 0 | 0.012 | -0.012 | 29.969 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 238 | PHE | 0 | -0.031 | -0.001 | 30.912 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 239 | VAL | 0 | 0.020 | -0.001 | 35.298 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 240 | PRO | 0 | -0.006 | 0.018 | 38.405 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 241 | PRO | 0 | 0.026 | 0.013 | 41.325 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 242 | ARG | 1 | 0.951 | 0.959 | 44.457 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 243 | ASP | -1 | -0.884 | -0.941 | 47.553 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 244 | GLY | 0 | 0.001 | 0.015 | 44.100 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 245 | PHE | 0 | -0.019 | -0.008 | 42.830 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 246 | SER | 0 | -0.059 | -0.023 | 43.721 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 247 | GLY | 0 | 0.048 | 0.017 | 45.888 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 248 | PRO | 0 | 0.024 | -0.005 | 47.152 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 249 | ALA | 0 | 0.009 | 0.022 | 48.593 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 250 | PRO | 0 | -0.027 | -0.010 | 46.889 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 251 | ARG | 1 | 0.852 | 0.890 | 46.646 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 252 | LYS | 1 | 0.935 | 0.961 | 41.299 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 253 | SER | 0 | 0.015 | -0.005 | 40.841 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 254 | LYS | 1 | 0.945 | 0.966 | 34.407 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 255 | LEU | 0 | 0.000 | 0.031 | 34.536 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 256 | ILE | 0 | -0.001 | -0.003 | 30.475 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 257 | CYS | 0 | -0.056 | -0.002 | 28.114 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 258 | GLU | -1 | -0.833 | -0.901 | 26.259 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 259 | ALA | 0 | 0.017 | 0.014 | 22.549 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 260 | THR | 0 | -0.011 | -0.024 | 22.621 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 261 | ASN | 0 | 0.004 | -0.009 | 21.820 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 262 | PHE | 0 | 0.028 | 0.040 | 16.536 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 263 | THR | 0 | -0.014 | -0.039 | 14.157 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 264 | PRO | 0 | 0.047 | 0.025 | 10.470 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 265 | LYS | 1 | 0.883 | 0.959 | 11.302 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 266 | PRO | 0 | -0.028 | -0.019 | 10.257 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 267 | ILE | 0 | -0.009 | 0.006 | 13.212 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 268 | THR | 0 | 0.008 | 0.015 | 17.011 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 269 | VAL | 0 | 0.021 | 0.005 | 19.862 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 270 | SER | 0 | -0.041 | -0.021 | 23.418 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 271 | TRP | 0 | 0.029 | 0.012 | 26.699 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 272 | LEU | 0 | -0.015 | -0.008 | 30.447 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 273 | LYS | 1 | 0.839 | 0.902 | 33.430 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 274 | ASP | -1 | -0.803 | -0.899 | 37.177 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 275 | GLY | 0 | -0.018 | -0.011 | 36.017 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 276 | LYS | 1 | 0.855 | 0.926 | 35.991 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 277 | LEU | 0 | 0.035 | 0.013 | 28.967 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 278 | VAL | 0 | -0.033 | -0.013 | 32.115 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 279 | GLU | -1 | -0.900 | -0.955 | 30.599 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 280 | SER | 0 | -0.034 | -0.014 | 31.101 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 281 | GLY | 0 | 0.041 | 0.013 | 32.725 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 282 | PHE | 0 | -0.019 | -0.003 | 26.201 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 283 | THR | 0 | -0.029 | -0.011 | 26.858 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 284 | THR | 0 | -0.031 | -0.024 | 22.300 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 285 | ASP | -1 | -0.877 | -0.926 | 23.330 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 286 | PRO | 0 | -0.011 | -0.023 | 18.526 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 287 | VAL | 0 | -0.002 | 0.008 | 16.045 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 288 | THR | 0 | 0.009 | 0.004 | 16.704 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 289 | ILE | 0 | -0.013 | -0.007 | 14.130 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 290 | GLU | -1 | -0.766 | -0.845 | 17.870 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 291 | ASN | 0 | -0.046 | -0.058 | 19.060 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 292 | LYS | 1 | 0.880 | 0.924 | 21.626 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 293 | GLY | 0 | 0.025 | 0.027 | 22.917 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 294 | SER | 0 | 0.021 | 0.016 | 22.243 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 295 | THR | 0 | -0.048 | -0.028 | 19.219 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 296 | PRO | 0 | 0.016 | 0.027 | 16.874 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 297 | GLN | 0 | 0.037 | 0.009 | 14.014 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 298 | THR | 0 | -0.015 | -0.013 | 15.379 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 299 | TYR | 0 | -0.054 | -0.045 | 11.997 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 300 | LYS | 1 | 0.854 | 0.920 | 17.973 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 301 | VAL | 0 | -0.039 | -0.019 | 19.880 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 302 | ILE | 0 | 0.034 | 0.030 | 21.768 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 303 | SER | 0 | 0.042 | 0.019 | 24.787 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 304 | THR | 0 | 0.026 | 0.012 | 27.086 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 305 | LEU | 0 | 0.003 | 0.011 | 30.616 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 306 | THR | 0 | -0.050 | -0.034 | 33.098 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 307 | ILE | 0 | -0.027 | -0.007 | 36.483 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 308 | SER | 0 | -0.009 | -0.026 | 39.355 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 309 | GLU | -1 | -0.753 | -0.857 | 43.032 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 310 | ILE | 0 | 0.014 | 0.005 | 45.863 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 311 | ASP | -1 | -0.806 | -0.867 | 42.586 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 312 | TRP | 0 | 0.022 | 0.008 | 39.568 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 313 | LEU | 0 | 0.011 | 0.014 | 44.304 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 314 | ASN | 0 | -0.099 | -0.048 | 47.117 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 315 | LEU | 0 | -0.030 | -0.020 | 45.780 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 316 | ASN | 0 | -0.004 | 0.024 | 41.720 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 317 | VAL | 0 | 0.001 | 0.000 | 38.222 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 318 | TYR | 0 | 0.020 | 0.005 | 35.745 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 319 | THR | 0 | -0.030 | -0.036 | 31.287 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 321 | ARG | 1 | 0.857 | 0.891 | 24.874 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 322 | VAL | 0 | 0.026 | 0.005 | 22.133 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 323 | ASP | -1 | -0.798 | -0.853 | 20.997 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 324 | HIS | 0 | -0.010 | -0.024 | 15.587 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 325 | ARG | 1 | 0.835 | 0.867 | 12.531 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 326 | GLY | 0 | -0.004 | 0.013 | 16.560 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 327 | LEU | 0 | -0.039 | -0.001 | 19.541 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 328 | THR | 0 | -0.008 | -0.031 | 22.156 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 329 | PHE | 0 | -0.025 | -0.012 | 21.772 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 330 | LEU | 0 | 0.005 | -0.004 | 26.588 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 331 | LYS | 1 | 0.903 | 0.957 | 29.724 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 332 | ASN | 0 | 0.037 | 0.032 | 32.129 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 333 | VAL | 0 | -0.030 | -0.021 | 35.466 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 334 | SER | 0 | 0.041 | 0.008 | 37.994 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 335 | SER | 0 | -0.006 | -0.016 | 41.496 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 336 | THR | 0 | -0.017 | 0.003 | 44.679 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 337 | CYS | 0 | -0.001 | 0.010 | 45.490 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |