FMODB ID: 52JVZ
Calculation Name: 1YO5-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1YO5
Chain ID: C
UniProt ID: O95238
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 | 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 | 88 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -708172.683545 |
---|---|
FMO2-HF: Nuclear repulsion | 671609.059329 |
FMO2-HF: Total energy | -36563.624217 |
FMO2-MP2: Total energy | -36673.800049 |
3D Structure
Ligand structure
Ligand Interaction
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(C:247:GLN)
Summations of interaction energy for
fragment #1(C:247:GLN)
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. |
-23.679 | -22.526 | 9.166 | -5.155 | -5.164 | 0.045 |
Interaction energy analysis for fragmet #1(C:247:GLN)
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 | C | 249 | ILE | 0 | 0.027 | 0.026 | 2.828 | -0.565 | 2.192 | 0.384 | -1.455 | -1.686 | -0.002 |
4 | C | 250 | HIS | 0 | 0.030 | 0.003 | 1.828 | -15.650 | -17.254 | 8.782 | -3.700 | -3.478 | 0.047 |
5 | C | 251 | LEU | 0 | 0.011 | 0.000 | 6.249 | -0.887 | -0.887 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 252 | TRP | 0 | 0.030 | -0.006 | 6.766 | -1.078 | -1.078 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 253 | GLN | 0 | 0.030 | 0.032 | 5.210 | -0.553 | -0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 254 | PHE | 0 | 0.036 | 0.009 | 9.456 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 255 | LEU | 0 | 0.013 | -0.003 | 11.029 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 256 | LYS | 1 | 0.900 | 0.956 | 12.967 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 257 | GLU | -1 | -0.796 | -0.852 | 12.291 | -0.993 | -0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 258 | LEU | 0 | -0.021 | -0.015 | 14.345 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 259 | LEU | 0 | -0.009 | 0.000 | 17.145 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 260 | LEU | 0 | -0.031 | 0.003 | 16.283 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 261 | LYS | 1 | 0.869 | 0.927 | 16.039 | 0.677 | 0.677 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 262 | PRO | 0 | 0.047 | 0.015 | 20.867 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 263 | HIS | 0 | 0.072 | 0.042 | 23.757 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 264 | SER | 0 | 0.046 | 0.030 | 21.438 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 265 | TYR | 0 | -0.005 | -0.016 | 17.356 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 266 | GLY | 0 | 0.022 | 0.017 | 22.564 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 267 | ARG | 1 | 0.852 | 0.923 | 25.104 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 268 | PHE | 0 | 0.011 | 0.002 | 22.140 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 269 | ILE | 0 | -0.034 | -0.023 | 18.164 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 270 | ARG | 1 | 0.883 | 0.936 | 22.240 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 271 | TRP | 0 | -0.004 | -0.026 | 18.807 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 272 | LEU | 0 | -0.048 | -0.021 | 24.459 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 273 | ASN | 0 | 0.057 | 0.027 | 26.147 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 274 | LYS | 1 | 0.971 | 0.983 | 21.903 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 275 | GLU | -1 | -0.780 | -0.853 | 23.399 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 276 | LYS | 1 | 0.860 | 0.917 | 24.451 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 277 | GLY | 0 | 0.059 | 0.032 | 20.937 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 278 | ILE | 0 | 0.001 | -0.006 | 20.957 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 279 | PHE | 0 | -0.011 | -0.013 | 17.740 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 280 | LYS | 1 | 0.892 | 0.924 | 22.936 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 281 | ILE | 0 | -0.044 | -0.012 | 19.018 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 282 | GLU | -1 | -0.752 | -0.858 | 23.147 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 283 | ASP | -1 | -0.797 | -0.887 | 24.487 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 284 | SER | 0 | -0.014 | -0.025 | 22.497 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 285 | ALA | 0 | 0.035 | 0.026 | 22.023 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 286 | GLN | 0 | 0.052 | 0.028 | 22.056 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 287 | VAL | 0 | -0.019 | -0.008 | 17.458 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 288 | ALA | 0 | -0.025 | -0.015 | 17.342 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 289 | ARG | 1 | 0.967 | 0.981 | 17.648 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 290 | LEU | 0 | -0.004 | 0.000 | 16.844 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 291 | TRP | 0 | 0.008 | -0.005 | 8.309 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 292 | GLY | 0 | 0.020 | -0.003 | 13.216 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 293 | ILE | 0 | 0.004 | 0.003 | 15.008 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 294 | ARG | 1 | 0.809 | 0.893 | 9.949 | 1.040 | 1.040 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 295 | LYS | 1 | 0.810 | 0.908 | 6.831 | -0.617 | -0.617 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 296 | ASN | 0 | 0.033 | 0.024 | 11.119 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 297 | ARG | 1 | 0.895 | 0.952 | 11.775 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 298 | PRO | 0 | 0.080 | 0.028 | 15.467 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 299 | ALA | 0 | 0.045 | 0.040 | 19.059 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 300 | MET | 0 | -0.090 | -0.032 | 14.391 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 301 | ASN | 0 | 0.024 | -0.024 | 18.731 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 302 | TYR | 0 | 0.096 | 0.040 | 19.554 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 303 | ASP | -1 | -0.800 | -0.865 | 20.616 | 0.342 | 0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 304 | LYS | 1 | 0.924 | 0.962 | 17.610 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 305 | LEU | 0 | 0.024 | 0.028 | 15.230 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 306 | SER | 0 | -0.014 | -0.022 | 16.324 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 307 | ARG | 1 | 0.867 | 0.919 | 17.537 | -0.837 | -0.837 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 308 | SER | 0 | -0.012 | -0.012 | 12.838 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 309 | ILE | 0 | -0.010 | -0.006 | 14.053 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | C | 310 | ARG | 1 | 0.918 | 0.959 | 15.765 | -0.512 | -0.512 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | C | 311 | GLN | 0 | 0.009 | 0.021 | 13.337 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | C | 312 | TYR | 0 | -0.003 | -0.015 | 8.497 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | C | 313 | TYR | 0 | 0.054 | 0.029 | 14.155 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | C | 314 | LYS | 1 | 0.990 | 0.993 | 16.624 | -0.972 | -0.972 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | C | 315 | LYS | 1 | 0.916 | 0.965 | 10.581 | -2.154 | -2.154 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | C | 316 | GLY | 0 | 0.072 | 0.057 | 14.535 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | C | 317 | ILE | 0 | -0.018 | -0.010 | 10.089 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | C | 318 | ILE | 0 | -0.051 | -0.033 | 13.775 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | C | 319 | ARG | 1 | 0.805 | 0.868 | 16.662 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | C | 320 | LYS | 1 | 0.843 | 0.916 | 20.241 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | C | 321 | PRO | 0 | 0.014 | 0.012 | 23.632 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | C | 322 | ASP | -1 | -0.778 | -0.871 | 26.036 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | C | 323 | ILE | 0 | 0.036 | 0.039 | 29.005 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | C | 324 | SER | 0 | -0.001 | 0.000 | 27.976 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | C | 325 | GLN | 0 | 0.042 | 0.011 | 27.757 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | C | 326 | ARG | 1 | 0.974 | 0.975 | 27.103 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | C | 327 | LEU | 0 | -0.018 | -0.012 | 24.330 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | C | 328 | VAL | 0 | 0.034 | 0.030 | 23.792 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | C | 329 | TYR | 0 | -0.082 | -0.049 | 19.917 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | C | 330 | GLN | 0 | 0.057 | 0.032 | 20.739 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | C | 331 | PHE | 0 | -0.046 | -0.029 | 14.180 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | C | 332 | VAL | 0 | -0.014 | -0.001 | 17.175 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | C | 333 | HIS | 0 | 0.068 | 0.059 | 15.111 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | C | 334 | PRO | 0 | 0.005 | -0.007 | 16.368 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |