![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LZ399
Calculation Name: 3C0C-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3C0C
Chain ID: A
UniProt ID: O35964
Base Structure: X-ray
Registration Date: 2023-09-19
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 | 64 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -371986.741648 |
---|---|
FMO2-HF: Nuclear repulsion | 346403.944936 |
FMO2-HF: Total energy | -25582.796712 |
FMO2-MP2: Total energy | -25657.380939 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029217/ligand_interaction/ligand_F029217.png)
Ligand Interaction
![ligand interaction](./Kdata/F029217/ligand_interaction/ligand_interaction_F029217.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:305:PRO)
Summations of interaction energy for
fragment #1(A:305:PRO)
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. |
-3.908 | -2.288 | -0.013 | -0.624 | -0.984 | 0.001 |
Interaction energy analysis for fragmet #1(A:305:PRO)
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 | 307 | ASP | -1 | -0.903 | -0.944 | 3.773 | -3.950 | -2.330 | -0.013 | -0.624 | -0.984 | 0.001 |
4 | A | 308 | GLN | 0 | -0.025 | -0.009 | 6.024 | 0.584 | 0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 309 | PRO | 0 | -0.010 | -0.011 | 8.423 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 310 | SER | 0 | 0.030 | 0.020 | 7.994 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 311 | CYS | 0 | -0.010 | 0.014 | 10.795 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 312 | LYS | 1 | 0.936 | 0.972 | 12.012 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 313 | ALA | 0 | 0.044 | 0.033 | 13.829 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 314 | LEU | 0 | -0.068 | -0.039 | 17.570 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 315 | TYR | 0 | -0.027 | -0.013 | 19.586 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 316 | ASP | -1 | -0.859 | -0.929 | 22.160 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 317 | PHE | 0 | -0.027 | -0.024 | 23.642 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 318 | GLU | -1 | -0.893 | -0.957 | 25.375 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 319 | PRO | 0 | -0.030 | 0.004 | 27.203 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 320 | GLU | -1 | -0.900 | -0.972 | 28.980 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 321 | ASN | 0 | -0.100 | -0.057 | 31.189 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 322 | ASP | -1 | -0.898 | -0.961 | 30.367 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 323 | GLY | 0 | -0.059 | -0.014 | 29.155 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 324 | GLU | -1 | -0.893 | -0.927 | 26.536 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 325 | LEU | 0 | -0.041 | -0.014 | 19.579 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 326 | GLY | 0 | 0.005 | 0.004 | 23.486 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 327 | PHE | 0 | -0.065 | -0.056 | 19.847 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 328 | ARG | 1 | 0.833 | 0.927 | 20.794 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 329 | GLU | -1 | -0.913 | -0.954 | 19.706 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 330 | GLY | 0 | -0.075 | -0.044 | 16.495 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 331 | ASP | -1 | -0.841 | -0.922 | 15.162 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 332 | LEU | 0 | -0.088 | -0.051 | 9.841 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 333 | ILE | 0 | -0.001 | 0.013 | 12.928 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 334 | THR | 0 | -0.032 | -0.023 | 12.592 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 335 | LEU | 0 | -0.021 | -0.013 | 12.991 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 336 | THR | 0 | -0.025 | -0.038 | 14.745 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 337 | ASN | 0 | 0.009 | 0.003 | 17.480 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 338 | GLN | 0 | -0.041 | -0.026 | 19.709 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 339 | ILE | 0 | -0.073 | -0.013 | 21.244 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 340 | ASP | -1 | -0.802 | -0.922 | 24.810 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 341 | GLU | -1 | -0.960 | -0.980 | 24.201 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 342 | ASN | 0 | -0.065 | -0.033 | 24.440 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 343 | TRP | 0 | -0.011 | 0.025 | 24.057 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 344 | TYR | 0 | 0.027 | 0.002 | 17.245 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 345 | GLU | -1 | -0.927 | -0.961 | 20.416 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 346 | GLY | 0 | 0.029 | -0.002 | 17.924 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 347 | MET | 0 | -0.053 | -0.030 | 16.721 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 348 | LEU | 0 | 0.026 | 0.012 | 16.266 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 349 | HIS | 0 | -0.003 | 0.000 | 17.098 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 350 | GLY | 0 | -0.041 | -0.020 | 18.049 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 351 | GLN | 0 | -0.021 | 0.003 | 19.701 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 352 | SER | 0 | 0.005 | -0.017 | 20.628 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 353 | GLY | 0 | 0.057 | 0.037 | 22.229 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 354 | PHE | 0 | -0.033 | -0.026 | 22.411 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 355 | PHE | 0 | 0.014 | 0.009 | 17.557 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 356 | PRO | 0 | 0.046 | 0.030 | 22.928 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 357 | LEU | 0 | -0.006 | -0.023 | 19.900 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 358 | SER | 0 | -0.051 | -0.021 | 20.545 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 359 | TYR | 0 | 0.020 | 0.011 | 21.860 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 360 | VAL | 0 | -0.007 | 0.008 | 16.452 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 361 | GLN | 0 | -0.027 | -0.003 | 13.663 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 362 | VAL | 0 | -0.015 | -0.010 | 11.746 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 363 | LEU | 0 | -0.081 | -0.032 | 7.522 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 364 | VAL | 0 | -0.034 | -0.006 | 5.716 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 365 | PRO | 0 | 0.015 | 0.008 | 8.692 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 366 | LEU | 0 | 0.035 | 0.016 | 11.823 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 367 | PRO | 0 | -0.029 | -0.015 | 14.070 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 368 | GLN | 0 | 0.008 | 0.012 | 15.828 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |