![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 3QVJL
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 | 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 | -759837.281252 |
---|---|
FMO2-HF: Nuclear repulsion | 720287.87985 |
FMO2-HF: Total energy | -39549.401402 |
FMO2-MP2: Total energy | -39667.546478 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021283/ligand_interaction/ligand_F021283.png)
Ligand Interaction
![ligand interaction](./Kdata/F021283/ligand_interaction/ligand_interaction_F021283.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. |
-10.054 | -9.672 | 13.201 | -5.179 | -8.403 | 0.012 |
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 | 0.094 | 0.025 | 3.505 | -2.206 | -0.039 | -0.003 | -1.102 | -1.063 | 0.001 |
4 | A | 170 | GLU | -1 | -0.822 | -0.898 | 5.954 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 171 | ARG | 1 | 0.922 | 0.967 | 1.853 | -10.791 | -14.588 | 12.929 | -3.323 | -5.809 | 0.015 |
6 | A | 172 | ARG | 1 | 0.956 | 0.966 | 2.615 | 4.636 | 6.586 | 0.276 | -0.749 | -1.477 | -0.004 |
7 | A | 173 | VAL | 0 | 0.023 | 0.016 | 4.886 | 0.317 | 0.379 | -0.001 | -0.005 | -0.054 | 0.000 |
8 | A | 174 | LYS | 1 | 0.863 | 0.925 | 7.911 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 175 | GLU | -1 | -0.951 | -0.973 | 5.264 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 176 | ILE | 0 | 0.010 | 0.011 | 8.759 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 177 | LEU | 0 | -0.034 | -0.023 | 10.961 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 178 | ASP | -1 | -0.757 | -0.867 | 11.983 | 0.279 | 0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 179 | GLU | -1 | -0.985 | -0.979 | 11.154 | -0.545 | -0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 180 | MET | 0 | -0.130 | -0.064 | 14.533 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 181 | ASP | -1 | -0.939 | -0.960 | 16.612 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 182 | ILE | 0 | -0.056 | -0.019 | 16.670 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 183 | VAL | 0 | 0.014 | -0.001 | 16.677 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 184 | TYR | 0 | -0.104 | -0.080 | 13.073 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 185 | PHE | 0 | -0.071 | -0.021 | 17.947 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 186 | THR | 0 | 0.024 | -0.008 | 12.179 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 187 | HIS | 0 | -0.077 | -0.044 | 10.910 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 188 | HIS | 0 | 0.012 | 0.021 | 16.088 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 189 | VAL | 0 | 0.016 | -0.003 | 19.684 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 190 | VAL | 0 | -0.016 | -0.017 | 22.678 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 191 | GLU | -1 | -0.871 | -0.938 | 25.111 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 192 | GLY | 0 | -0.029 | -0.010 | 26.883 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 193 | TRP | 0 | -0.062 | -0.036 | 23.235 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 194 | ASN | 0 | 0.015 | 0.010 | 18.335 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 195 | VAL | 0 | -0.014 | -0.006 | 17.902 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 196 | ALA | 0 | 0.037 | 0.034 | 12.399 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 197 | PHE | 0 | 0.041 | 0.020 | 9.680 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 198 | TYR | 0 | -0.024 | -0.005 | 15.584 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 199 | LEU | 0 | 0.065 | 0.018 | 16.632 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 200 | GLY | 0 | 0.017 | 0.022 | 20.418 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 201 | LYS | 1 | 0.935 | 0.946 | 24.117 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 202 | LYS | 1 | 0.926 | 0.979 | 25.773 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 203 | LEU | 0 | 0.029 | 0.031 | 21.872 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 204 | ALA | 0 | -0.012 | -0.011 | 19.467 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 205 | ILE | 0 | 0.025 | 0.018 | 13.706 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 206 | GLU | -1 | -0.846 | -0.944 | 15.172 | -0.270 | -0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 207 | VAL | 0 | -0.021 | 0.006 | 9.715 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 208 | ASN | 0 | -0.024 | -0.011 | 12.605 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 209 | GLY | 0 | 0.089 | 0.043 | 12.679 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 210 | VAL | 0 | 0.023 | 0.014 | 14.615 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 211 | TYR | 0 | -0.094 | -0.070 | 14.492 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 212 | TRP | 0 | 0.094 | 0.052 | 10.270 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 213 | ALA | 0 | 0.022 | 0.012 | 11.448 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 214 | SER | 0 | -0.020 | -0.008 | 12.036 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 215 | LYS | 1 | 0.882 | 0.974 | 13.918 | 0.464 | 0.464 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 216 | GLN | 0 | 0.014 | 0.002 | 15.325 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 217 | LYS | 1 | 0.921 | 0.956 | 18.985 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 218 | ASN | 0 | 0.048 | 0.005 | 20.971 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 219 | VAL | 0 | 0.083 | 0.051 | 23.615 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 220 | ASN | 0 | 0.023 | 0.006 | 25.057 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 221 | LYS | 1 | 0.921 | 0.968 | 23.813 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 222 | ASP | -1 | -0.828 | -0.914 | 20.336 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 223 | LYS | 1 | 0.946 | 0.972 | 23.396 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 224 | ARG | 1 | 0.913 | 0.958 | 26.567 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 225 | LYS | 1 | 0.900 | 0.963 | 19.326 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 226 | LEU | 0 | 0.032 | 0.015 | 21.589 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 227 | SER | 0 | -0.085 | -0.041 | 25.539 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 228 | GLU | -1 | -0.857 | -0.941 | 28.801 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 229 | LEU | 0 | 0.024 | 0.034 | 23.419 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 230 | HIS | 0 | 0.024 | 0.018 | 27.509 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 231 | SER | 0 | -0.109 | -0.068 | 28.818 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 232 | LYS | 1 | 0.935 | 0.969 | 30.075 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 233 | GLY | 0 | -0.037 | -0.023 | 30.692 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 234 | TYR | 0 | -0.105 | -0.059 | 24.754 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 235 | ARG | 1 | 0.890 | 0.959 | 24.708 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 236 | VAL | 0 | 0.013 | -0.005 | 19.778 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 237 | LEU | 0 | 0.002 | 0.016 | 16.754 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 238 | THR | 0 | -0.024 | -0.025 | 16.441 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 239 | ILE | 0 | -0.029 | -0.009 | 11.424 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 240 | GLU | -1 | -0.889 | -0.946 | 12.901 | -0.678 | -0.678 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 241 | ASP | -1 | -0.895 | -0.973 | 9.475 | -1.307 | -1.307 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 242 | ASP | -1 | -0.908 | -0.963 | 9.761 | -1.259 | -1.259 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 243 | GLU | -1 | -0.897 | -0.957 | 12.276 | -0.748 | -0.748 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 244 | LEU | 0 | -0.050 | -0.025 | 6.184 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 245 | ASN | 0 | -0.117 | -0.047 | 9.304 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 246 | ASP | -1 | -0.867 | -0.937 | 10.856 | -0.566 | -0.566 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 247 | ILE | 0 | 0.022 | -0.004 | 8.873 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 248 | ASP | -1 | -0.931 | -0.958 | 11.818 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 249 | LYS | 1 | 0.966 | 1.000 | 15.330 | 0.583 | 0.583 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 250 | VAL | 0 | 0.016 | 0.005 | 11.149 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 251 | LYS | 1 | 0.989 | 0.989 | 12.132 | 0.754 | 0.754 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 252 | GLN | 0 | 0.042 | 0.035 | 15.030 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 253 | GLN | 0 | -0.096 | -0.058 | 16.465 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 254 | ILE | 0 | 0.050 | 0.016 | 12.611 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 255 | GLN | 0 | 0.012 | 0.020 | 17.171 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 256 | LYS | 1 | 0.898 | 0.946 | 19.764 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 257 | PHE | 0 | -0.026 | 0.017 | 19.630 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 258 | TRP | 0 | 0.090 | 0.034 | 19.966 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 259 | VAL | 0 | 0.011 | -0.007 | 21.970 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 260 | THR | 0 | -0.086 | -0.066 | 24.912 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 261 | HIS | 0 | -0.056 | -0.025 | 24.623 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 262 | ILE | 0 | -0.040 | -0.008 | 24.280 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 263 | SER | 0 | -0.070 | -0.016 | 26.683 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |