![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QYL2Y
Calculation Name: 5V8Z-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5V8Z
Chain ID: A
UniProt ID: E2RA18
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 | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -704748.605315 |
---|---|
FMO2-HF: Nuclear repulsion | 666406.040738 |
FMO2-HF: Total energy | -38342.564576 |
FMO2-MP2: Total energy | -38454.62204 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F027494/ligand_interaction/ligand_F027494.png)
Ligand Interaction
![ligand interaction](./Kdata/F027494/ligand_interaction/ligand_interaction_F027494.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:157:SER)
Summations of interaction energy for
fragment #1(A:157:SER)
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. |
-10.331 | -5.452 | 0.472 | -2.316 | -3.034 | 0.014 |
Interaction energy analysis for fragmet #1(A:157:SER)
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 | 159 | PRO | 0 | 0.095 | 0.056 | 2.677 | -1.281 | 1.570 | 0.334 | -1.380 | -1.805 | 0.005 |
4 | A | 160 | VAL | 0 | 0.024 | 0.017 | 5.603 | 0.355 | 0.355 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 161 | TYR | 0 | -0.001 | -0.034 | 6.620 | 0.327 | 0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 162 | ASP | -1 | -0.825 | -0.874 | 4.439 | -1.907 | -1.737 | -0.001 | -0.018 | -0.152 | 0.000 |
7 | A | 163 | ALA | 0 | -0.034 | -0.011 | 7.554 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 164 | LEU | 0 | 0.021 | 0.008 | 10.593 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 165 | ALA | 0 | -0.004 | 0.010 | 10.315 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 166 | GLY | 0 | 0.031 | 0.010 | 11.768 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 167 | GLU | -1 | -0.961 | -0.999 | 13.650 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 168 | PHE | 0 | -0.013 | -0.012 | 15.253 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 169 | ILE | 0 | -0.013 | -0.021 | 15.582 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 170 | ARG | 1 | 0.886 | 0.957 | 14.814 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 171 | ALA | 0 | -0.022 | 0.019 | 19.760 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 172 | SER | 0 | 0.005 | -0.005 | 21.727 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 173 | GLY | 0 | 0.029 | 0.013 | 25.169 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 174 | VAL | 0 | 0.040 | 0.002 | 24.807 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 175 | GLU | -1 | -0.919 | -0.960 | 24.771 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 176 | ALA | 0 | 0.019 | 0.014 | 23.201 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 177 | ARG | 1 | 0.801 | 0.876 | 20.413 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 178 | GLN | 0 | 0.036 | 0.023 | 19.961 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 179 | ALA | 0 | -0.005 | -0.002 | 21.359 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 180 | LEU | 0 | 0.024 | 0.020 | 16.565 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 181 | LEU | 0 | 0.005 | 0.000 | 16.444 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 182 | LYS | 1 | 0.797 | 0.897 | 17.237 | 0.210 | 0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 183 | GLN | 0 | 0.068 | 0.029 | 15.863 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 184 | GLY | 0 | 0.043 | 0.005 | 13.492 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 185 | GLN | 0 | -0.014 | -0.003 | 13.825 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 186 | ASP | -1 | -0.824 | -0.900 | 16.266 | -0.272 | -0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 187 | ASN | 0 | -0.064 | -0.045 | 12.006 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 188 | LEU | 0 | 0.038 | 0.023 | 11.507 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 189 | SER | 0 | -0.087 | -0.041 | 13.457 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 190 | SER | 0 | -0.001 | 0.008 | 12.172 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 191 | VAL | 0 | -0.049 | -0.006 | 8.461 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 192 | LYS | 1 | 0.965 | 0.987 | 7.172 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 193 | GLU | -1 | -0.833 | -0.929 | 10.676 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 194 | THR | 0 | -0.007 | -0.009 | 10.103 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 195 | GLN | 0 | -0.083 | -0.057 | 3.425 | -2.939 | -2.255 | 0.026 | -0.397 | -0.312 | 0.004 |
40 | A | 196 | LYS | 1 | 0.973 | 0.988 | 7.566 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 197 | LYS | 1 | 1.035 | 1.024 | 9.027 | -0.492 | -0.492 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 198 | TRP | 0 | -0.053 | -0.027 | 4.892 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 199 | ALA | 0 | 0.059 | 0.031 | 6.985 | -0.285 | -0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 200 | GLU | -1 | -0.904 | -0.961 | 8.223 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 201 | GLN | 0 | -0.044 | -0.015 | 8.454 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 202 | TYR | 0 | -0.054 | -0.080 | 4.700 | -0.432 | -0.344 | -0.001 | -0.006 | -0.080 | 0.000 |
47 | A | 203 | LEU | 0 | 0.028 | 0.021 | 10.080 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 204 | LYS | 1 | 0.916 | 0.957 | 13.153 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 205 | ILE | 0 | -0.035 | -0.011 | 10.516 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 206 | MET | 0 | -0.004 | 0.007 | 12.653 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 207 | GLY | 0 | 0.033 | 0.017 | 16.098 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 208 | LYS | 1 | 0.941 | 0.972 | 17.627 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 209 | ILE | 0 | -0.052 | -0.009 | 15.899 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 210 | LEU | 0 | -0.053 | -0.022 | 19.767 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 211 | ASP | -1 | -0.934 | -0.949 | 22.112 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 212 | GLN | 0 | -0.087 | -0.065 | 22.358 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 213 | GLY | 0 | 0.031 | 0.026 | 23.128 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 214 | GLU | -1 | -0.846 | -0.916 | 21.545 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 215 | ASP | -1 | -0.888 | -0.935 | 20.977 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 216 | PHE | 0 | -0.016 | -0.006 | 15.717 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 217 | PRO | 0 | 0.047 | 0.014 | 15.031 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 218 | ALA | 0 | 0.052 | 0.029 | 16.686 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 219 | SER | 0 | -0.041 | -0.016 | 18.974 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 220 | GLU | -1 | -0.788 | -0.892 | 15.295 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 221 | MET | 0 | -0.016 | -0.023 | 13.796 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 222 | THR | 0 | -0.009 | 0.008 | 16.248 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 223 | ARG | 1 | 0.781 | 0.880 | 16.995 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 224 | ILE | 0 | -0.022 | -0.022 | 13.623 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 225 | ALA | 0 | 0.059 | 0.034 | 16.594 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 226 | ARG | 1 | 0.995 | 0.998 | 17.418 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 227 | LEU | 0 | -0.084 | -0.044 | 18.664 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 228 | ILE | 0 | 0.008 | -0.003 | 13.718 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 229 | GLU | -1 | -0.935 | -0.956 | 17.911 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 230 | LYS | 1 | 0.905 | 0.934 | 20.619 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 231 | ASN | 0 | 0.009 | 0.015 | 20.558 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 232 | LYS | 1 | 0.906 | 0.962 | 21.627 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 233 | MET | 0 | -0.046 | -0.014 | 18.146 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 234 | SER | 0 | 0.048 | 0.028 | 19.192 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 235 | ASP | -1 | -0.803 | -0.909 | 17.370 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 236 | GLY | 0 | 0.022 | 0.011 | 14.979 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 237 | LYS | 1 | 0.871 | 0.917 | 14.031 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 238 | LYS | 1 | 0.950 | 0.974 | 14.425 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 239 | GLU | -1 | -0.923 | -0.947 | 10.569 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 240 | GLU | -1 | -0.904 | -0.946 | 9.785 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 241 | LEU | 0 | -0.028 | -0.022 | 10.163 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 242 | GLN | 0 | 0.045 | 0.021 | 9.234 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 243 | LYS | 1 | 0.906 | 0.948 | 2.981 | -5.423 | -4.456 | 0.114 | -0.485 | -0.597 | 0.005 |
88 | A | 244 | SER | 0 | -0.005 | -0.011 | 6.691 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 245 | LEU | 0 | -0.026 | 0.005 | 9.070 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 246 | ASN | 0 | 0.004 | -0.004 | 4.009 | 0.174 | 0.293 | 0.000 | -0.030 | -0.088 | 0.000 |
91 | A | 247 | ILE | 0 | -0.022 | 0.006 | 4.937 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 248 | LEU | 0 | 0.006 | -0.001 | 7.004 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 249 | THR | 0 | -0.056 | -0.026 | 8.866 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 250 | ALA | 0 | 0.006 | 0.017 | 7.832 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 251 | PHE | 0 | -0.053 | -0.031 | 9.938 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 252 | GLN | 0 | -0.028 | -0.015 | 13.109 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 253 | LYS | 1 | 0.978 | 0.996 | 15.492 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |