![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 179RZ
Calculation Name: 6EHR-F-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 6EHR
Chain ID: F
UniProt ID: Q6IAA8
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 | 110 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -886769.212886 |
---|---|
FMO2-HF: Nuclear repulsion | 842022.488677 |
FMO2-HF: Total energy | -44746.724209 |
FMO2-MP2: Total energy | -44875.008781 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F027528/ligand_interaction/ligand_F027528.png)
Ligand Interaction
![ligand interaction](./Kdata/F027528/ligand_interaction/ligand_interaction_F027528.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(F:182:GLY)
Summations of interaction energy for
fragment #1(F:182:GLY)
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. |
1.082 | 3.92 | 0.08 | -1.096 | -1.822 | 0.001 |
Interaction energy analysis for fragmet #1(F:182:GLY)
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 | F | 184 | VAL | 0 | 0.015 | 0.013 | 3.239 | -0.578 | 1.129 | 0.019 | -0.778 | -0.948 | 0.001 |
4 | F | 185 | GLN | 0 | 0.040 | 0.016 | 3.945 | 0.647 | 0.951 | 0.000 | -0.066 | -0.239 | 0.000 |
5 | F | 186 | GLN | 0 | -0.030 | -0.006 | 2.975 | 0.443 | 1.270 | 0.061 | -0.252 | -0.635 | 0.000 |
6 | F | 187 | LEU | 0 | 0.010 | -0.004 | 5.597 | 0.465 | 0.465 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | F | 188 | GLU | -1 | -0.810 | -0.902 | 8.037 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | F | 189 | MET | 0 | -0.018 | -0.004 | 8.971 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | F | 190 | ASN | 0 | -0.048 | -0.028 | 9.027 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | F | 191 | LEU | 0 | 0.039 | 0.020 | 11.456 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | F | 192 | ARG | 1 | 0.977 | 1.003 | 13.526 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | F | 193 | ASN | 0 | -0.082 | -0.042 | 14.372 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | F | 194 | PHE | 0 | -0.006 | -0.013 | 15.542 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | F | 195 | ALA | 0 | 0.026 | 0.011 | 17.419 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | F | 196 | GLN | 0 | -0.006 | -0.010 | 18.623 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | F | 197 | ILE | 0 | -0.052 | -0.012 | 19.955 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | F | 198 | ILE | 0 | -0.061 | -0.022 | 21.696 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | F | 199 | GLU | -1 | -0.884 | -0.951 | 24.285 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | F | 200 | ALA | 0 | -0.035 | -0.032 | 22.368 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | F | 201 | ASP | -1 | -0.978 | -0.974 | 22.864 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | F | 202 | GLU | -1 | -0.893 | -0.957 | 21.210 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | F | 203 | VAL | 0 | -0.035 | -0.019 | 17.288 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | F | 204 | LEU | 0 | -0.026 | -0.005 | 17.664 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | F | 205 | LEU | 0 | 0.010 | 0.003 | 12.106 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | F | 206 | PHE | 0 | -0.040 | -0.010 | 15.287 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | F | 207 | GLU | -1 | -0.780 | -0.842 | 15.276 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | F | 208 | ARG | 1 | 0.942 | 0.954 | 16.778 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | F | 209 | ALA | 0 | -0.077 | -0.026 | 18.823 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | F | 210 | THR | 0 | -0.079 | -0.104 | 19.115 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | F | 211 | PHE | 0 | 0.029 | 0.002 | 19.848 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | F | 212 | LEU | 0 | 0.055 | 0.071 | 15.367 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | F | 213 | VAL | 0 | -0.010 | -0.013 | 15.955 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | F | 214 | ILE | 0 | -0.040 | -0.005 | 10.210 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | F | 215 | SER | 0 | -0.037 | -0.021 | 10.291 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | F | 216 | HIS | 0 | -0.019 | -0.031 | 12.348 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | F | 217 | TYR | 0 | 0.035 | 0.022 | 14.559 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | F | 218 | GLN | 0 | 0.029 | 0.008 | 17.152 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | F | 219 | CYS | 0 | -0.017 | 0.015 | 20.314 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | F | 228 | PHE | 0 | 0.035 | 0.016 | 17.977 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | F | 229 | GLU | -1 | -0.832 | -0.929 | 22.093 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | F | 230 | LYS | 1 | 0.927 | 0.959 | 23.308 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | F | 231 | ILE | 0 | 0.019 | -0.002 | 23.467 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | F | 232 | SER | 0 | 0.012 | -0.028 | 21.215 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | F | 233 | ASN | 0 | 0.012 | -0.015 | 23.781 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | F | 234 | ILE | 0 | -0.018 | 0.005 | 26.828 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | F | 235 | ILE | 0 | 0.036 | 0.032 | 23.955 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | F | 236 | LYS | 1 | 0.922 | 0.976 | 23.502 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | F | 237 | GLN | 0 | -0.008 | -0.010 | 27.193 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | F | 238 | PHE | 0 | 0.035 | 0.032 | 30.514 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | F | 239 | LYS | 1 | 1.009 | 1.008 | 24.565 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | F | 240 | LEU | 0 | -0.005 | 0.020 | 30.012 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | F | 241 | SER | 0 | -0.063 | -0.055 | 31.967 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | F | 242 | CYS | 0 | -0.056 | -0.034 | 32.761 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | F | 243 | SER | 0 | -0.048 | -0.046 | 31.590 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | F | 244 | LYS | 1 | 0.887 | 0.961 | 34.113 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | F | 245 | LEU | 0 | -0.030 | 0.003 | 37.375 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | F | 246 | ALA | 0 | 0.029 | 0.012 | 37.320 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | F | 247 | ALA | 0 | 0.000 | -0.007 | 35.433 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | F | 248 | SER | 0 | -0.031 | -0.011 | 30.010 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | F | 249 | PHE | 0 | -0.008 | -0.009 | 26.324 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | F | 250 | GLN | 0 | 0.005 | 0.006 | 27.647 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | F | 251 | SER | 0 | 0.030 | 0.010 | 26.684 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | F | 252 | MET | 0 | -0.050 | -0.024 | 28.466 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | F | 253 | GLU | -1 | -0.776 | -0.860 | 29.006 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | F | 254 | VAL | 0 | -0.055 | -0.009 | 30.943 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | F | 255 | ARG | 1 | 0.899 | 0.957 | 32.022 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | F | 256 | ASN | 0 | -0.014 | 0.001 | 34.629 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | F | 257 | SER | 0 | 0.012 | -0.013 | 36.632 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | F | 258 | ASN | 0 | -0.044 | -0.022 | 35.583 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | F | 259 | PHE | 0 | 0.035 | 0.011 | 29.680 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | F | 260 | ALA | 0 | 0.025 | 0.021 | 30.520 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | F | 261 | ALA | 0 | 0.007 | 0.021 | 27.491 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | F | 262 | PHE | 0 | -0.019 | -0.010 | 25.850 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | F | 263 | ILE | 0 | -0.003 | -0.009 | 23.853 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | F | 264 | ASP | -1 | -0.838 | -0.925 | 23.456 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | F | 265 | ILE | 0 | -0.018 | -0.010 | 21.373 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | F | 266 | PHE | 0 | -0.009 | 0.019 | 15.202 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | F | 267 | THR | 0 | 0.078 | 0.080 | 14.539 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | F | 268 | SER | 0 | 0.011 | 0.002 | 16.592 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | F | 269 | ASN | 0 | -0.053 | -0.035 | 13.101 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | F | 270 | THR | 0 | -0.009 | -0.053 | 13.472 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | F | 271 | TYR | 0 | -0.027 | -0.014 | 16.864 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | F | 272 | VAL | 0 | 0.003 | 0.019 | 17.989 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | F | 273 | MET | 0 | -0.015 | -0.011 | 19.786 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | F | 274 | VAL | 0 | 0.013 | 0.015 | 21.295 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | F | 275 | VAL | 0 | 0.011 | -0.002 | 23.255 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | F | 276 | MET | 0 | -0.024 | -0.011 | 25.446 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | F | 277 | SER | 0 | 0.037 | 0.004 | 28.023 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | F | 278 | ASP | -1 | -0.786 | -0.823 | 30.013 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | F | 279 | PRO | 0 | -0.053 | -0.038 | 32.118 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | F | 280 | SER | 0 | -0.109 | -0.112 | 34.044 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | F | 281 | ILE | 0 | 0.041 | 0.032 | 29.829 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | F | 282 | PRO | 0 | -0.017 | -0.018 | 33.487 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | F | 283 | SER | 0 | 0.020 | -0.038 | 31.947 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | F | 284 | ALA | 0 | -0.007 | 0.000 | 31.061 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | F | 285 | ALA | 0 | 0.013 | 0.012 | 30.416 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | F | 286 | THR | 0 | 0.054 | 0.023 | 26.050 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | F | 287 | LEU | 0 | -0.004 | -0.006 | 26.205 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | F | 288 | ILE | 0 | -0.025 | -0.010 | 26.820 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | F | 289 | ASN | 0 | 0.034 | 0.023 | 23.526 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | F | 290 | ILE | 0 | 0.018 | 0.015 | 22.052 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | F | 291 | ARG | 1 | 0.910 | 0.952 | 21.951 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | F | 292 | ASN | 0 | -0.019 | -0.023 | 22.822 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | F | 293 | ALA | 0 | 0.024 | 0.017 | 18.038 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | F | 294 | ARG | 1 | 0.866 | 0.937 | 17.550 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | F | 295 | LYS | 1 | 0.929 | 0.954 | 18.076 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | F | 296 | HIS | 0 | -0.013 | 0.014 | 13.366 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | F | 297 | PHE | 0 | -0.011 | -0.029 | 12.246 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | F | 298 | GLU | -1 | -1.007 | -0.986 | 13.011 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | F | 299 | LYS | 1 | 0.900 | 0.967 | 8.552 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |