FMODB ID: 2NLYR
Calculation Name: 2B26-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2B26
Chain ID: C
UniProt ID: P11146
Base Structure: X-ray
Registration Date: 2023-09-22
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 | 122 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -915100.555794 |
---|---|
FMO2-HF: Nuclear repulsion | 867944.338506 |
FMO2-HF: Total energy | -47156.217289 |
FMO2-MP2: Total energy | -47296.72356 |
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:190:LEU)
Summations of interaction energy for
fragment #1(C:190:LEU)
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. |
-11.842 | -1.464 | 8.641 | -5.751 | -13.268 | -0.006 |
Interaction energy analysis for fragmet #1(C:190:LEU)
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 | 192 | ASP | -1 | -0.852 | -0.905 | 2.571 | -1.809 | 0.793 | 0.160 | -1.170 | -1.591 | 0.003 |
4 | C | 193 | LEU | 0 | -0.033 | -0.020 | 2.362 | 0.102 | 0.959 | 2.602 | -1.114 | -2.344 | -0.003 |
5 | C | 194 | PHE | 0 | -0.001 | 0.000 | 4.418 | 0.391 | 0.681 | -0.001 | -0.048 | -0.242 | 0.000 |
6 | C | 195 | VAL | 0 | -0.004 | -0.009 | 5.554 | 0.543 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 196 | GLY | 0 | -0.016 | 0.004 | 8.154 | 0.281 | 0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 197 | LYS | 1 | 0.816 | 0.885 | 5.979 | 0.984 | 0.984 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 198 | LYS | 1 | 0.881 | 0.934 | 8.332 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 199 | LYS | 1 | 0.901 | 0.939 | 7.725 | -0.563 | -0.563 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 200 | SER | 0 | 0.056 | 0.038 | 10.684 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 201 | PHE | 0 | 0.003 | 0.011 | 12.581 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 218 | ASP | -1 | -0.845 | -0.921 | 15.711 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 219 | ILE | 0 | 0.007 | 0.000 | 12.590 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 220 | GLN | 0 | -0.037 | -0.024 | 12.480 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 221 | LEU | 0 | -0.004 | 0.003 | 6.929 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 222 | LYS | 1 | 0.975 | 0.995 | 10.960 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 223 | PRO | 0 | 0.025 | 0.006 | 9.195 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 224 | GLY | 0 | 0.073 | 0.056 | 8.260 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 225 | TRP | 0 | -0.052 | -0.033 | 8.167 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 226 | LYS | 1 | 0.926 | 0.956 | 6.245 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 227 | ALA | 0 | -0.042 | -0.011 | 6.932 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 228 | GLY | 0 | 0.042 | 0.033 | 8.650 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 229 | THR | 0 | -0.030 | -0.002 | 11.495 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 252 | VAL | 0 | 0.016 | -0.009 | 12.891 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 253 | ILE | 0 | -0.048 | -0.004 | 7.776 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 254 | GLN | 0 | 0.064 | 0.010 | 8.026 | -0.230 | -0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 255 | GLU | -1 | -0.800 | -0.885 | 2.574 | -2.267 | -0.660 | 0.296 | -0.584 | -1.319 | -0.003 |
29 | C | 256 | LYS | 1 | 0.936 | 0.974 | 3.467 | -6.060 | -4.951 | 0.048 | -0.380 | -0.778 | 0.002 |
30 | C | 257 | SER | 0 | 0.031 | 0.008 | 2.724 | -2.493 | -1.051 | 0.461 | -0.709 | -1.194 | -0.009 |
31 | C | 258 | HIS | 0 | 0.008 | -0.009 | 2.296 | -0.640 | 0.897 | 1.668 | -0.910 | -2.295 | 0.001 |
32 | C | 259 | PRO | 0 | -0.018 | -0.007 | 4.283 | -0.226 | -0.133 | 0.000 | -0.023 | -0.070 | 0.000 |
33 | C | 260 | ASN | 0 | -0.016 | -0.005 | 6.284 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 261 | PHE | 0 | -0.010 | -0.003 | 3.093 | -0.497 | 0.006 | 0.045 | -0.087 | -0.461 | 0.000 |
35 | C | 262 | LYS | 1 | 0.826 | 0.900 | 4.291 | 0.190 | 0.465 | 0.000 | -0.031 | -0.244 | 0.000 |
36 | C | 263 | ARG | 1 | 0.805 | 0.876 | 3.363 | 0.375 | 0.980 | 0.015 | -0.115 | -0.505 | 0.000 |
37 | C | 264 | ASP | -1 | -0.826 | -0.907 | 5.408 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 265 | GLY | 0 | 0.009 | 0.011 | 8.826 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 266 | ASP | -1 | -0.832 | -0.938 | 7.570 | -0.504 | -0.504 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 267 | ASP | -1 | -0.772 | -0.856 | 8.906 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 268 | LEU | 0 | -0.035 | -0.022 | 3.821 | -0.315 | -0.082 | 0.003 | -0.036 | -0.200 | 0.000 |
42 | C | 269 | ILE | 0 | -0.020 | 0.000 | 7.590 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 270 | TYR | 0 | 0.022 | -0.002 | 7.366 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 271 | THR | 0 | -0.038 | -0.012 | 9.507 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 272 | LEU | 0 | 0.039 | 0.022 | 12.272 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 273 | PRO | 0 | 0.004 | 0.014 | 14.452 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 274 | LEU | 0 | -0.041 | -0.016 | 17.310 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 275 | SER | 0 | 0.028 | -0.011 | 20.997 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 276 | PHE | 0 | 0.059 | 0.011 | 24.318 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 277 | LYS | 1 | 0.985 | 0.990 | 27.203 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 278 | GLU | -1 | -0.765 | -0.861 | 23.340 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 279 | SER | 0 | -0.017 | -0.012 | 24.975 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 280 | LEU | 0 | -0.044 | -0.016 | 25.841 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | C | 281 | LEU | 0 | 0.009 | -0.002 | 29.372 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | C | 282 | GLY | 0 | -0.003 | 0.017 | 26.355 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | C | 283 | PHE | 0 | -0.035 | -0.038 | 20.351 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | C | 284 | SER | 0 | -0.015 | -0.022 | 23.274 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | C | 285 | LYS | 1 | 0.858 | 0.926 | 18.538 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | C | 286 | THR | 0 | -0.031 | -0.027 | 17.274 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | C | 287 | ILE | 0 | -0.014 | 0.019 | 10.870 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | C | 288 | GLN | 0 | 0.024 | 0.010 | 10.339 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | C | 289 | THR | 0 | 0.016 | -0.025 | 10.079 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | C | 290 | ILE | 0 | 0.007 | 0.000 | 3.137 | -0.497 | -0.069 | 0.046 | -0.106 | -0.368 | 0.000 |
64 | C | 291 | ASP | -1 | -0.842 | -0.878 | 7.106 | -1.046 | -1.046 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | C | 292 | GLY | 0 | -0.013 | 0.004 | 9.927 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | C | 293 | ARG | 1 | 0.929 | 0.963 | 11.272 | 0.521 | 0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | C | 294 | THR | 0 | 0.040 | 0.030 | 13.830 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | C | 295 | LEU | 0 | -0.010 | -0.006 | 13.920 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | C | 296 | PRO | 0 | 0.007 | 0.004 | 16.692 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | C | 297 | LEU | 0 | -0.010 | -0.013 | 14.867 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | C | 298 | SER | 0 | 0.009 | 0.005 | 19.553 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | C | 299 | ARG | 1 | 0.806 | 0.899 | 22.131 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | C | 300 | VAL | 0 | 0.027 | 0.020 | 25.481 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | C | 301 | GLN | 0 | 0.044 | 0.015 | 28.019 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | C | 302 | PRO | 0 | 0.070 | 0.054 | 27.456 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | C | 303 | VAL | 0 | -0.062 | -0.012 | 22.030 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | C | 304 | GLN | 0 | 0.052 | 0.020 | 25.089 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | C | 305 | PRO | 0 | 0.010 | -0.010 | 22.908 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | C | 306 | SER | 0 | 0.001 | 0.008 | 19.671 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | C | 307 | GLN | 0 | 0.003 | 0.020 | 19.601 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | C | 308 | THR | 0 | -0.001 | -0.022 | 16.180 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | C | 309 | SER | 0 | -0.027 | 0.005 | 17.287 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | C | 310 | THR | 0 | -0.016 | -0.009 | 15.886 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | C | 311 | TYR | 0 | 0.007 | -0.001 | 14.496 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | C | 312 | PRO | 0 | 0.069 | 0.019 | 14.442 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | C | 313 | GLY | 0 | 0.039 | 0.035 | 14.385 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | C | 314 | GLN | 0 | -0.091 | -0.059 | 11.858 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | C | 315 | GLY | 0 | 0.008 | 0.025 | 8.217 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | C | 316 | MET | 0 | -0.031 | -0.016 | 2.464 | 0.227 | -0.976 | 3.298 | -0.438 | -1.657 | 0.003 |
90 | C | 317 | PRO | 0 | -0.018 | -0.013 | 7.342 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | C | 318 | THR | 0 | 0.026 | -0.006 | 10.129 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | C | 319 | PRO | 0 | -0.012 | -0.025 | 11.285 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | C | 320 | LYS | 1 | 0.831 | 0.941 | 13.343 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | C | 321 | ASN | 0 | -0.007 | -0.033 | 15.707 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | C | 322 | PRO | 0 | 0.053 | 0.040 | 12.618 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | C | 323 | SER | 0 | -0.028 | 0.002 | 14.170 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | C | 324 | GLN | 0 | 0.018 | 0.007 | 15.680 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | C | 325 | ARG | 1 | 0.761 | 0.881 | 9.417 | 0.702 | 0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | C | 326 | GLY | 0 | 0.096 | 0.066 | 11.223 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | C | 327 | ASN | 0 | -0.084 | -0.073 | 12.088 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | C | 328 | LEU | 0 | 0.007 | 0.013 | 8.976 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | C | 329 | ILE | 0 | -0.025 | -0.020 | 11.211 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | C | 330 | VAL | 0 | 0.026 | 0.019 | 12.005 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | C | 331 | LYS | 1 | 0.967 | 0.978 | 13.343 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | C | 332 | TYR | 0 | 0.007 | -0.017 | 15.082 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | C | 333 | LYS | 1 | 0.874 | 0.952 | 16.039 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | C | 334 | VAL | 0 | 0.020 | 0.006 | 17.964 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | C | 335 | ASP | -1 | -0.928 | -0.953 | 21.623 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | C | 336 | TYR | 0 | 0.010 | -0.013 | 23.310 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | C | 337 | PRO | 0 | -0.024 | -0.015 | 26.798 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | C | 338 | ILE | 0 | 0.040 | 0.032 | 28.708 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | C | 339 | SER | 0 | -0.003 | -0.002 | 30.599 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | C | 340 | LEU | 0 | -0.026 | -0.011 | 33.706 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | C | 341 | ASN | 0 | 0.066 | 0.029 | 36.357 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | C | 342 | ASP | -1 | -0.781 | -0.904 | 38.815 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | C | 343 | ALA | 0 | -0.017 | 0.014 | 40.687 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | C | 344 | GLN | 0 | 0.048 | 0.013 | 33.670 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | C | 345 | LYS | 1 | 0.824 | 0.914 | 38.637 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | C | 346 | ARG | 1 | 0.883 | 0.915 | 40.720 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | C | 347 | ALA | 0 | -0.006 | -0.002 | 39.806 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | C | 348 | ILE | 0 | -0.062 | -0.016 | 35.846 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | C | 349 | ASP | -1 | -0.952 | -0.957 | 39.283 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |