![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 9GV82
Calculation Name: 3R3P-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3R3P
Chain ID: A
UniProt ID: A7KV39
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -760908.007745 |
---|---|
FMO2-HF: Nuclear repulsion | 721357.703102 |
FMO2-HF: Total energy | -39550.304644 |
FMO2-MP2: Total energy | -39668.42973 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021281/ligand_interaction/ligand_F021281.png)
Ligand Interaction
![ligand interaction](./Kdata/F021281/ligand_interaction/ligand_interaction_F021281.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:167:THR)
Summations of interaction energy for
fragment #1(A:167:THR)
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. |
-13.933 | -10.628 | 9.647 | -4.724 | -8.227 | 0.03 |
Interaction energy analysis for fragmet #1(A:167:THR)
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 | 169 | PRO | 0 | 0.059 | 0.005 | 3.414 | -0.254 | 1.514 | 0.010 | -0.922 | -0.856 | 0.000 |
4 | A | 170 | GLU | -1 | -0.849 | -0.912 | 6.153 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 171 | ARG | 1 | 0.778 | 0.879 | 2.039 | -11.975 | -12.784 | 8.890 | -2.841 | -5.241 | 0.029 |
6 | A | 172 | ARG | 1 | 0.954 | 0.972 | 2.975 | -4.490 | -2.322 | 0.749 | -0.953 | -1.964 | 0.001 |
7 | A | 173 | VAL | 0 | 0.026 | 0.021 | 5.047 | -0.044 | -0.002 | -0.001 | -0.002 | -0.038 | 0.000 |
8 | A | 174 | LYS | 1 | 0.797 | 0.868 | 7.358 | -0.563 | -0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 175 | GLU | -1 | -0.827 | -0.904 | 4.610 | 2.281 | 2.417 | -0.001 | -0.006 | -0.128 | 0.000 |
10 | A | 176 | ILE | 0 | 0.001 | 0.002 | 8.406 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 177 | LEU | 0 | -0.032 | -0.024 | 10.723 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 178 | ASP | -1 | -0.766 | -0.841 | 11.085 | 0.534 | 0.534 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 179 | GLU | -1 | -0.896 | -0.938 | 11.729 | 0.645 | 0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 180 | MET | 0 | -0.103 | -0.043 | 14.297 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 181 | ASP | -1 | -0.927 | -0.949 | 16.666 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 182 | ILE | 0 | -0.057 | -0.012 | 16.456 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 183 | VAL | 0 | 0.012 | -0.004 | 16.380 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 184 | TYR | 0 | -0.030 | -0.035 | 12.727 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 185 | PHE | 0 | -0.069 | -0.031 | 17.304 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 186 | THR | 0 | 0.024 | -0.002 | 11.489 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 187 | HIS | 0 | -0.097 | -0.062 | 10.400 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 188 | HIS | 0 | 0.027 | 0.036 | 15.545 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 189 | VAL | 0 | -0.005 | -0.008 | 19.196 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 190 | VAL | 0 | 0.008 | 0.003 | 22.171 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 191 | GLU | -1 | -0.811 | -0.880 | 24.734 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 192 | GLY | 0 | 0.001 | 0.006 | 26.554 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 193 | TRP | 0 | -0.088 | -0.059 | 22.866 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 194 | ASN | 0 | 0.029 | 0.015 | 18.064 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 195 | VAL | 0 | -0.042 | -0.022 | 17.615 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 196 | ALA | 0 | 0.018 | 0.018 | 12.044 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 197 | PHE | 0 | 0.041 | 0.013 | 9.111 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 198 | TYR | 0 | -0.008 | 0.014 | 15.120 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 199 | LEU | 0 | 0.047 | 0.011 | 16.337 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 200 | GLY | 0 | 0.031 | 0.028 | 20.088 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 201 | LYS | 1 | 0.941 | 0.952 | 23.799 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 202 | LYS | 1 | 0.896 | 0.963 | 25.633 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 203 | LEU | 0 | 0.023 | 0.016 | 22.108 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 204 | ALA | 0 | -0.023 | -0.018 | 18.901 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 205 | ILE | 0 | 0.021 | 0.019 | 13.432 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 206 | GLU | -1 | -0.833 | -0.904 | 14.911 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 207 | VAL | 0 | -0.001 | 0.002 | 9.343 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 208 | ASN | 0 | 0.001 | 0.004 | 12.509 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 209 | GLY | 0 | 0.117 | 0.060 | 12.833 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 210 | VAL | 0 | -0.005 | 0.019 | 14.673 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 211 | TYR | 0 | -0.099 | -0.064 | 15.503 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 212 | TRP | 0 | 0.083 | 0.055 | 10.471 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 213 | ALA | 0 | 0.020 | 0.005 | 11.665 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 214 | SER | 0 | 0.012 | 0.006 | 12.106 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 215 | LYS | 1 | 0.809 | 0.910 | 14.404 | 0.300 | 0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 216 | GLN | 0 | 0.011 | -0.001 | 15.950 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 217 | LYS | 1 | 0.940 | 0.970 | 19.527 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 218 | ASN | 0 | 0.022 | 0.003 | 21.058 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 219 | VAL | 0 | 0.112 | 0.053 | 23.934 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 220 | ASN | 0 | -0.004 | 0.000 | 25.293 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 221 | LYS | 1 | 0.920 | 0.971 | 24.253 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 222 | ASP | -1 | -0.861 | -0.931 | 21.229 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 223 | LYS | 1 | 0.958 | 0.972 | 23.526 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 224 | ARG | 1 | 0.820 | 0.882 | 26.424 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 225 | LYS | 1 | 0.902 | 0.951 | 18.790 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 226 | LEU | 0 | 0.029 | 0.016 | 21.087 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 227 | SER | 0 | -0.066 | -0.036 | 25.020 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 228 | GLU | -1 | -0.766 | -0.860 | 28.151 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 229 | LEU | 0 | 0.018 | 0.017 | 22.890 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 230 | HIS | 0 | 0.033 | 0.018 | 27.058 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 231 | SER | 0 | -0.057 | -0.030 | 28.583 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 232 | LYS | 1 | 0.836 | 0.911 | 29.751 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 233 | GLY | 0 | -0.016 | -0.016 | 30.536 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 234 | TYR | 0 | -0.080 | -0.064 | 24.615 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 235 | ARG | 1 | 0.823 | 0.922 | 24.549 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 236 | VAL | 0 | 0.025 | -0.001 | 19.502 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 237 | LEU | 0 | 0.021 | 0.033 | 16.565 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 238 | THR | 0 | -0.031 | -0.026 | 16.457 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 239 | ILE | 0 | -0.016 | 0.002 | 11.649 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 240 | GLU | -1 | -0.879 | -0.956 | 13.196 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 241 | ASP | -1 | -0.891 | -0.981 | 9.558 | -0.247 | -0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 242 | ASP | -1 | -0.886 | -0.948 | 9.957 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 243 | GLU | -1 | -0.817 | -0.894 | 12.533 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 244 | LEU | 0 | -0.088 | -0.037 | 6.499 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 245 | ASN | 0 | -0.095 | -0.043 | 9.386 | 0.290 | 0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 246 | ASP | -1 | -0.792 | -0.879 | 11.400 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 247 | ILE | 0 | 0.016 | -0.006 | 9.058 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 248 | ASP | -1 | -0.914 | -0.946 | 12.119 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 249 | LYS | 1 | 0.837 | 0.904 | 15.721 | -0.299 | -0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 250 | VAL | 0 | 0.030 | 0.027 | 11.055 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 251 | LYS | 1 | 0.881 | 0.924 | 11.795 | -0.697 | -0.697 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 252 | GLN | 0 | 0.058 | 0.039 | 15.077 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 253 | GLN | 0 | -0.092 | -0.071 | 16.851 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 254 | ILE | 0 | 0.043 | 0.011 | 12.741 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 255 | GLN | 0 | -0.012 | 0.004 | 17.209 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 256 | LYS | 1 | 0.888 | 0.927 | 19.803 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 257 | PHE | 0 | -0.024 | 0.013 | 18.925 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 258 | TRP | 0 | 0.080 | 0.035 | 19.796 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 259 | VAL | 0 | 0.016 | 0.003 | 21.844 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 260 | THR | 0 | -0.066 | -0.060 | 24.870 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 261 | HIS | 0 | -0.080 | -0.040 | 24.706 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 262 | ILE | 0 | -0.051 | -0.016 | 23.823 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 263 | SER | 0 | -0.049 | -0.007 | 26.503 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |