FMODB ID: 39KJL
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 | 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 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -948081.040025 |
---|---|
FMO2-HF: Nuclear repulsion | 903134.477937 |
FMO2-HF: Total energy | -44946.562088 |
FMO2-MP2: Total energy | -45080.850505 |
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. |
-12.551 | -3.379 | 7.906 | -5.134 | -11.946 | -0.032 |
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 | 0.851 | 0.920 | 3.792 | -5.398 | -2.111 | -0.028 | -1.667 | -1.592 | -0.005 |
4 | A | 197 | GLY | 0 | 0.006 | 0.016 | 4.585 | 0.984 | 1.129 | -0.001 | -0.008 | -0.136 | 0.000 |
5 | A | 198 | LYS | 1 | 0.795 | 0.901 | 6.411 | -0.435 | -0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 199 | ILE | 0 | -0.045 | -0.025 | 3.131 | -0.167 | 0.304 | 0.094 | -0.098 | -0.467 | 0.000 |
7 | A | 200 | THR | 0 | 0.016 | 0.006 | 7.205 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 201 | TYR | 0 | -0.016 | -0.023 | 3.998 | -0.199 | 0.007 | 0.000 | -0.023 | -0.184 | 0.000 |
9 | A | 202 | GLN | 0 | 0.044 | 0.032 | 10.575 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 203 | VAL | 0 | -0.068 | -0.043 | 12.101 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 204 | TRP | 0 | 0.031 | 0.013 | 14.715 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 205 | GLY | 0 | 0.023 | 0.008 | 16.913 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 206 | ILE | 0 | -0.010 | -0.006 | 19.154 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 207 | ARG | 1 | 0.785 | 0.894 | 21.860 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 208 | VAL | 0 | 0.015 | 0.014 | 24.903 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 209 | ARG | 1 | 0.810 | 0.891 | 28.171 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 210 | ASN | 0 | -0.001 | -0.004 | 31.534 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 211 | GLY | 0 | 0.017 | 0.014 | 33.753 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 212 | GLN | 0 | -0.019 | -0.001 | 30.922 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 213 | PHE | 0 | 0.013 | 0.003 | 25.185 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 214 | VAL | 0 | 0.018 | 0.011 | 26.446 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 215 | THR | 0 | 0.051 | 0.017 | 22.128 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 216 | SER | 0 | 0.019 | 0.021 | 20.541 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 217 | SER | 0 | -0.081 | -0.023 | 21.941 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 235 | VAL | 0 | -0.026 | -0.022 | 23.468 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 236 | LEU | 0 | 0.004 | 0.006 | 18.124 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 237 | SER | 0 | 0.007 | 0.021 | 17.583 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 238 | PHE | 0 | 0.000 | 0.002 | 14.501 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 239 | ILE | 0 | -0.010 | -0.004 | 9.913 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 240 | THR | 0 | -0.008 | -0.009 | 9.521 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 241 | ALA | 0 | 0.023 | 0.013 | 5.506 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 242 | ASN | 0 | -0.035 | -0.032 | 7.404 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 243 | PHE | 0 | 0.025 | -0.009 | 2.594 | -4.596 | -1.730 | 3.758 | -1.915 | -4.708 | -0.026 |
34 | A | 244 | ASN | 0 | -0.022 | 0.001 | 5.380 | 0.230 | 0.207 | -0.001 | -0.002 | 0.026 | 0.000 |
35 | A | 245 | SER | 0 | -0.037 | -0.035 | 8.617 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 246 | ASN | 0 | -0.066 | -0.026 | 6.750 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 247 | THR | 0 | 0.006 | 0.010 | 8.683 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 248 | LEU | 0 | 0.004 | -0.015 | 7.951 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 249 | ALA | 0 | -0.030 | -0.008 | 10.842 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 250 | GLY | 0 | 0.008 | -0.020 | 12.909 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 251 | LYS | 1 | 0.827 | 0.920 | 15.300 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 252 | ILE | 0 | -0.005 | 0.001 | 16.094 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 253 | LEU | 0 | 0.015 | 0.003 | 18.972 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 254 | GLY | 0 | 0.059 | 0.013 | 22.324 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 255 | ASN | 0 | -0.048 | -0.038 | 25.366 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 256 | SER | 0 | -0.022 | -0.035 | 28.496 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 257 | ASP | -1 | -0.880 | -0.897 | 29.917 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 258 | TYR | 0 | -0.030 | -0.041 | 20.928 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 259 | GLY | 0 | 0.027 | 0.021 | 27.112 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 260 | PRO | 0 | -0.008 | -0.026 | 27.188 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 261 | ASP | -1 | -0.757 | -0.856 | 22.962 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 262 | VAL | 0 | -0.040 | 0.005 | 19.143 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 263 | ASP | -1 | -0.877 | -0.925 | 19.613 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 264 | ILE | 0 | 0.032 | 0.009 | 14.206 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 265 | GLN | 0 | -0.026 | -0.027 | 16.650 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 266 | ASN | 0 | -0.028 | -0.018 | 15.982 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 267 | ALA | 0 | 0.020 | 0.034 | 12.882 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 268 | THR | 0 | 0.029 | 0.008 | 11.393 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 269 | ILE | 0 | -0.059 | -0.023 | 4.835 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 270 | THR | 0 | -0.015 | -0.021 | 7.096 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 271 | GLY | 0 | 0.064 | 0.043 | 4.235 | 0.131 | 0.257 | 0.000 | -0.024 | -0.102 | 0.000 |
62 | A | 272 | PRO | 0 | -0.034 | -0.018 | 2.342 | -2.172 | -0.877 | 1.530 | -1.156 | -1.669 | 0.000 |
63 | A | 273 | THR | 0 | -0.042 | -0.028 | 3.425 | 0.586 | 0.102 | 0.009 | 0.702 | -0.228 | 0.000 |
64 | A | 274 | PHE | 0 | 0.044 | 0.007 | 6.318 | -0.291 | -0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 275 | SER | 0 | -0.011 | 0.003 | 8.619 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 276 | GLY | 0 | 0.040 | 0.016 | 12.448 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 277 | ASP | -1 | -0.804 | -0.872 | 15.713 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 278 | ALA | 0 | 0.002 | 0.007 | 18.035 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 279 | THR | 0 | -0.031 | -0.019 | 19.975 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 280 | SER | 0 | 0.018 | -0.012 | 22.869 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 281 | GLY | 0 | 0.024 | 0.009 | 25.303 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 282 | GLY | 0 | -0.019 | 0.000 | 28.601 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 283 | LYS | 1 | 0.788 | 0.882 | 27.400 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 284 | SER | 0 | 0.035 | 0.007 | 24.372 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 285 | GLY | 0 | 0.014 | -0.003 | 22.368 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 286 | LYS | 1 | 0.801 | 0.892 | 18.702 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 287 | LEU | 0 | -0.010 | -0.002 | 12.850 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 288 | GLU | -1 | -0.836 | -0.921 | 12.795 | -0.272 | -0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 289 | GLY | 0 | 0.014 | 0.001 | 10.054 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 290 | LYS | 1 | 0.840 | 0.929 | 5.198 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 291 | PHE | 0 | 0.042 | 0.027 | 2.304 | -1.465 | -0.847 | 2.539 | -0.857 | -2.300 | -0.001 |
82 | A | 292 | PHE | 0 | 0.009 | 0.003 | 3.980 | -0.024 | 0.320 | 0.006 | -0.047 | -0.304 | 0.000 |
83 | A | 302 | GLU | -1 | -0.923 | -0.960 | 9.465 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 303 | VAL | 0 | -0.035 | -0.018 | 3.860 | -0.129 | 0.054 | 0.001 | -0.023 | -0.160 | 0.000 |
85 | A | 304 | SER | 0 | 0.049 | 0.019 | 6.359 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 305 | ILE | 0 | -0.051 | -0.013 | 5.885 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 306 | GLY | 0 | 0.031 | 0.006 | 8.127 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 307 | GLY | 0 | -0.001 | -0.001 | 10.060 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 308 | LYS | 1 | 0.838 | 0.927 | 12.677 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 309 | ILE | 0 | 0.003 | -0.007 | 15.760 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 310 | THR | 0 | -0.037 | -0.019 | 18.386 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 311 | PHE | 0 | 0.014 | -0.004 | 21.607 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 312 | ASP | -1 | -0.839 | -0.919 | 24.798 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 313 | GLY | 0 | -0.008 | 0.011 | 27.396 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 314 | ASP | -1 | -0.844 | -0.904 | 28.596 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 315 | ARG | 1 | 0.858 | 0.908 | 24.226 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 316 | SER | 0 | -0.050 | -0.026 | 27.516 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 317 | LEU | 0 | 0.014 | 0.001 | 25.623 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 318 | ASP | -1 | -0.753 | -0.834 | 22.844 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 319 | THR | 0 | -0.061 | -0.030 | 19.037 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 320 | VAL | 0 | 0.022 | 0.013 | 16.641 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 321 | PHE | 0 | -0.014 | -0.013 | 11.699 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 322 | GLY | 0 | 0.039 | 0.015 | 12.466 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 323 | GLY | 0 | 0.007 | 0.006 | 11.519 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 324 | VAL | 0 | 0.017 | 0.011 | 9.635 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 325 | SER | 0 | -0.033 | -0.032 | 7.029 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 326 | TYR | 0 | -0.007 | 0.008 | 9.122 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 327 | GLU | -1 | -0.762 | -0.858 | 11.093 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 328 | LYS | 1 | 0.868 | 0.918 | 6.584 | -0.578 | -0.578 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 329 | LYS | 1 | 0.827 | 0.903 | 8.685 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 330 | LEU | 0 | 0.028 | 0.016 | 4.606 | -0.168 | -0.030 | -0.001 | -0.016 | -0.122 | 0.000 |
112 | A | 331 | ASP | -1 | -0.807 | -0.904 | 7.630 | 1.544 | 1.544 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 332 | ASP | -1 | -0.808 | -0.878 | 9.784 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 333 | THR | 0 | -0.002 | -0.001 | 10.270 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 334 | SER | 0 | -0.057 | -0.031 | 12.757 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 335 | GLN | 0 | 0.072 | 0.017 | 11.920 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 336 | ASP | -1 | -0.817 | -0.877 | 13.455 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 337 | THR | 0 | 0.026 | 0.008 | 11.510 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 338 | ASN | 0 | -0.037 | -0.016 | 13.324 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 339 | HIS | 0 | 0.027 | 0.032 | 13.677 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 340 | LEU | 0 | -0.017 | -0.001 | 10.432 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 341 | THR | 0 | 0.029 | 0.013 | 14.440 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |