![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 53VGZ
Calculation Name: 4GI3-C-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4GI3
Chain ID: C
UniProt ID: P85064
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 | 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 | 53 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -300979.527884 |
---|---|
FMO2-HF: Nuclear repulsion | 276526.045245 |
FMO2-HF: Total energy | -24453.482638 |
FMO2-MP2: Total energy | -24517.283363 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021371/ligand_interaction/ligand_F021371.png)
Ligand Interaction
![ligand interaction](./Kdata/F021371/ligand_interaction/ligand_interaction_F021371.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(C:21:CYS)
Summations of interaction energy for
fragment #1(C:21:CYS)
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. |
-37.175 | -28.684 | 9.512 | -4.277 | -13.727 | -0.03 |
Interaction energy analysis for fragmet #1(C:21:CYS)
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 | 23 | SER | 0 | 0.054 | 0.013 | 3.839 | -0.787 | 0.627 | -0.006 | -0.558 | -0.850 | 0.002 |
4 | C | 24 | ILE | 0 | -0.087 | -0.042 | 5.210 | 0.960 | 1.094 | -0.002 | -0.008 | -0.124 | 0.000 |
5 | C | 25 | CYS | 0 | -0.051 | -0.009 | 8.131 | -1.099 | -1.099 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 26 | PRO | 0 | 0.007 | 0.001 | 10.385 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 27 | LEU | 0 | 0.019 | 0.014 | 14.199 | -0.188 | -0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 28 | ILE | 0 | -0.020 | -0.004 | 15.602 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 29 | TYR | 0 | 0.019 | 0.009 | 16.375 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 30 | ALA | 0 | -0.002 | -0.009 | 16.236 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 31 | PRO | 0 | -0.016 | 0.008 | 15.332 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 32 | VAL | 0 | 0.015 | 0.006 | 11.676 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 33 | CYS | 0 | -0.069 | 0.003 | 13.247 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 34 | VAL | 0 | -0.012 | -0.014 | 8.468 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 35 | GLU | -1 | -0.834 | -0.904 | 11.550 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 36 | ASP | -1 | -0.804 | -0.917 | 9.057 | -1.447 | -1.447 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 37 | SER | 0 | -0.013 | -0.010 | 9.524 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 38 | ASN | 0 | -0.124 | -0.069 | 11.348 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 39 | GLN | 0 | -0.094 | -0.056 | 13.774 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 40 | ASP | -1 | -0.847 | -0.877 | 13.486 | -0.857 | -0.857 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 41 | PHE | 0 | -0.027 | -0.023 | 13.509 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 42 | TYR | 0 | -0.083 | -0.068 | 10.941 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 43 | LEU | 0 | 0.023 | 0.005 | 12.459 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 44 | PHE | 0 | 0.034 | 0.018 | 7.376 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 45 | VAL | 0 | 0.021 | -0.013 | 12.119 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 46 | ASN | 0 | -0.034 | -0.031 | 11.713 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 47 | GLU | -1 | -0.763 | -0.875 | 9.933 | -2.944 | -2.944 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 49 | GLU | -1 | -0.773 | -0.895 | 6.590 | -6.224 | -6.224 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 50 | VAL | 0 | -0.030 | 0.012 | 5.588 | -1.389 | -1.389 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 51 | ARG | 1 | 0.853 | 0.902 | 3.891 | -1.610 | -0.979 | 0.018 | -0.277 | -0.373 | -0.002 |
31 | C | 52 | LYS | 1 | 0.772 | 0.900 | 2.052 | -8.493 | -6.869 | 4.789 | -2.581 | -3.833 | -0.032 |
32 | C | 53 | CYS | 0 | -0.011 | 0.008 | 2.548 | -4.161 | -0.952 | 2.471 | -2.414 | -3.267 | -0.021 |
35 | C | 57 | ALA | 0 | -0.023 | -0.011 | 3.552 | -0.764 | 1.355 | 0.038 | -0.606 | -1.552 | 0.002 |
36 | C | 58 | GLY | 0 | -0.012 | 0.011 | 2.520 | -4.658 | -2.719 | 2.051 | -1.822 | -2.167 | 0.020 |
37 | C | 59 | PHE | 0 | -0.030 | -0.013 | 2.939 | -2.319 | -4.642 | 0.137 | 3.244 | -1.057 | 0.004 |
38 | C | 60 | VAL | 0 | 0.020 | 0.008 | 3.421 | -3.299 | -3.689 | 0.010 | 0.714 | -0.333 | -0.003 |
39 | C | 61 | TYR | 0 | -0.020 | -0.014 | 3.631 | -0.555 | -0.421 | 0.006 | 0.031 | -0.171 | 0.000 |
40 | C | 62 | THR | 0 | 0.011 | 0.004 | 7.763 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 63 | PHE | 0 | -0.012 | -0.009 | 9.195 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 64 | VAL | 0 | 0.002 | 0.009 | 12.296 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 65 | PRO | 0 | 0.019 | -0.001 | 15.739 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 66 | ARG | 1 | 0.914 | 0.954 | 18.131 | 1.104 | 1.104 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 67 | GLU | -1 | -0.896 | -0.968 | 19.145 | -0.849 | -0.849 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 68 | MET | 0 | -0.037 | -0.005 | 17.638 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 70 | LYS | 1 | 0.973 | 0.985 | 18.307 | 1.042 | 1.042 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 71 | ALA | 0 | 0.011 | -0.002 | 19.365 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 72 | THR | 0 | -0.039 | -0.019 | 20.125 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 73 | THR | 0 | -0.005 | 0.000 | 15.635 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 74 | SER | 0 | -0.051 | -0.027 | 13.352 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 75 | LEU | 0 | -0.014 | -0.012 | 11.697 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 77 | PRO | 0 | -0.014 | 0.014 | 7.659 | 0.965 | 0.965 | 0.000 | 0.000 | 0.000 | 0.000 |