![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7J8YK
Calculation Name: 3R3P-A-Xray313
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 99 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -765769.787341 |
---|---|
FMO2-HF: Nuclear repulsion | 726049.443374 |
FMO2-HF: Total energy | -39720.343967 |
FMO2-MP2: Total energy | -39839.033979 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015728/ligand_interaction/ligand_F015728.png)
Ligand Interaction
![ligand interaction](./Kdata/F015728/ligand_interaction/ligand_interaction_F015728.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:166:ACE )
Summations of interaction energy for
fragment #1(A:166:ACE )
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. |
3.448 | 7.995 | 2.761 | -3.373 | -3.935 | -0.019 |
Interaction energy analysis for fragmet #1(A:166:ACE )
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 | 168 | THR | 0 | 0.038 | 0.028 | 3.835 | 0.482 | 1.327 | -0.006 | -0.397 | -0.443 | 0.000 |
4 | A | 169 | PRO | 0 | 0.098 | 0.026 | 5.020 | 0.347 | 0.416 | 0.000 | -0.003 | -0.065 | 0.000 |
5 | A | 170 | GLU | -1 | -0.820 | -0.897 | 7.179 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 171 | ARG | 1 | 0.906 | 0.968 | 2.380 | 0.190 | 0.743 | 1.714 | -0.885 | -1.381 | 0.000 |
7 | A | 172 | ARG | 1 | 0.950 | 0.962 | 2.734 | -0.176 | 0.544 | 0.291 | -0.350 | -0.661 | -0.002 |
8 | A | 173 | VAL | 0 | 0.027 | 0.018 | 4.614 | -0.201 | -0.167 | 0.000 | -0.010 | -0.025 | 0.000 |
9 | A | 174 | LYS | 1 | 0.859 | 0.924 | 6.706 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 175 | GLU | -1 | -0.929 | -0.967 | 2.814 | 2.549 | 4.875 | 0.762 | -1.728 | -1.360 | -0.017 |
11 | A | 176 | ILE | 0 | 0.010 | 0.011 | 6.883 | -0.207 | -0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 177 | LEU | 0 | -0.034 | -0.023 | 9.609 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 178 | ASP | -1 | -0.756 | -0.866 | 9.870 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 179 | GLU | -1 | -0.985 | -0.979 | 9.018 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 180 | MET | 0 | -0.131 | -0.064 | 12.532 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 181 | ASP | -1 | -0.937 | -0.958 | 14.693 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 182 | ILE | 0 | -0.058 | -0.020 | 15.154 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 183 | VAL | 0 | 0.016 | -0.001 | 15.101 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 184 | TYR | 0 | -0.105 | -0.080 | 11.431 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 185 | PHE | 0 | -0.072 | -0.022 | 16.801 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 186 | THR | 0 | 0.026 | -0.008 | 12.362 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 187 | HIS | 0 | -0.081 | -0.046 | 12.364 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 188 | HIS | 0 | 0.013 | 0.022 | 16.717 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 189 | VAL | 0 | 0.018 | -0.002 | 19.911 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 190 | VAL | 0 | -0.022 | -0.019 | 22.931 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 191 | GLU | -1 | -0.866 | -0.936 | 25.282 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 192 | GLY | 0 | -0.030 | -0.010 | 27.778 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 193 | TRP | 0 | -0.060 | -0.036 | 24.109 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 194 | ASN | 0 | 0.013 | 0.010 | 19.636 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 195 | VAL | 0 | -0.011 | -0.005 | 18.509 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 196 | ALA | 0 | 0.034 | 0.034 | 12.834 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 197 | PHE | 0 | 0.040 | 0.020 | 9.314 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 198 | TYR | 0 | -0.020 | -0.004 | 15.355 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 199 | LEU | 0 | 0.065 | 0.017 | 15.964 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 200 | GLY | 0 | 0.015 | 0.021 | 19.662 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 201 | LYS | 1 | 0.936 | 0.947 | 23.374 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 202 | LYS | 1 | 0.925 | 0.979 | 25.548 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 203 | LEU | 0 | 0.029 | 0.032 | 21.488 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 204 | ALA | 0 | -0.011 | -0.011 | 19.351 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 205 | ILE | 0 | 0.023 | 0.017 | 13.789 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 206 | GLU | -1 | -0.844 | -0.944 | 15.886 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 207 | VAL | 0 | -0.025 | 0.004 | 10.589 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 208 | ASN | 0 | -0.023 | -0.012 | 13.804 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 209 | GLY | 0 | 0.090 | 0.043 | 14.314 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 210 | VAL | 0 | 0.021 | 0.014 | 16.348 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 211 | TYR | 0 | -0.093 | -0.069 | 17.547 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 212 | TRP | 0 | 0.094 | 0.050 | 14.865 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 213 | ALA | 0 | 0.021 | 0.013 | 16.755 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 214 | SER | 0 | -0.019 | -0.008 | 17.403 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 215 | LYS | 1 | 0.883 | 0.975 | 18.390 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 216 | GLN | 0 | 0.013 | 0.001 | 19.970 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 217 | LYS | 1 | 0.920 | 0.955 | 23.519 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 218 | ASN | 0 | 0.050 | 0.005 | 24.860 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 219 | VAL | 0 | 0.083 | 0.050 | 26.597 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 220 | ASN | 0 | 0.024 | 0.007 | 27.705 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 221 | LYS | 1 | 0.921 | 0.968 | 26.528 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 222 | ASP | -1 | -0.830 | -0.915 | 22.656 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 223 | LYS | 1 | 0.948 | 0.973 | 25.290 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 224 | ARG | 1 | 0.915 | 0.958 | 28.031 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 225 | LYS | 1 | 0.899 | 0.963 | 20.275 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 226 | LEU | 0 | 0.034 | 0.015 | 22.627 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 227 | SER | 0 | -0.087 | -0.042 | 26.535 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 228 | GLU | -1 | -0.856 | -0.941 | 29.666 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 229 | LEU | 0 | 0.023 | 0.034 | 23.988 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 230 | HIS | 0 | 0.025 | 0.019 | 28.088 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 231 | SER | 0 | -0.109 | -0.068 | 29.367 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 232 | LYS | 1 | 0.935 | 0.969 | 30.415 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 233 | GLY | 0 | -0.037 | -0.023 | 30.810 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 234 | TYR | 0 | -0.106 | -0.060 | 24.794 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 235 | ARG | 1 | 0.890 | 0.959 | 24.683 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 236 | VAL | 0 | 0.015 | -0.004 | 20.333 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 237 | LEU | 0 | 0.000 | 0.015 | 16.810 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 238 | THR | 0 | -0.027 | -0.025 | 17.421 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 239 | ILE | 0 | -0.028 | -0.010 | 11.795 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 240 | GLU | -1 | -0.886 | -0.945 | 14.048 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 241 | ASP | -1 | -0.896 | -0.973 | 11.029 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 242 | ASP | -1 | -0.906 | -0.962 | 10.759 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 243 | GLU | -1 | -0.897 | -0.956 | 12.707 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 244 | LEU | 0 | -0.052 | -0.025 | 6.945 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 245 | ASN | 0 | -0.116 | -0.047 | 8.835 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 246 | ASP | -1 | -0.865 | -0.937 | 10.618 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 247 | ILE | 0 | 0.021 | -0.005 | 7.480 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 248 | ASP | -1 | -0.930 | -0.957 | 10.763 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 249 | LYS | 1 | 0.966 | 0.999 | 14.142 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 250 | VAL | 0 | 0.016 | 0.005 | 10.945 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 251 | LYS | 1 | 0.990 | 0.989 | 10.471 | -0.542 | -0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 252 | GLN | 0 | 0.043 | 0.036 | 14.012 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 253 | GLN | 0 | -0.095 | -0.057 | 16.375 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 254 | ILE | 0 | 0.052 | 0.016 | 12.359 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 255 | GLN | 0 | 0.008 | 0.018 | 16.702 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 256 | LYS | 1 | 0.901 | 0.946 | 18.893 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 257 | PHE | 0 | -0.024 | 0.018 | 19.288 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 258 | TRP | 0 | 0.090 | 0.034 | 19.192 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 259 | VAL | 0 | 0.016 | -0.003 | 21.274 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 260 | THR | 0 | -0.080 | -0.071 | 24.088 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 261 | HIS | 0 | -0.041 | -0.019 | 24.260 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 262 | ILE | 0 | -0.047 | -0.014 | 23.417 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 263 | SER | 0 | -0.083 | -0.029 | 25.842 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 264 | NME | 0 | -0.010 | 0.010 | 28.506 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |