![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: K3LQ3
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 | 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 | 53 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -299892.897754 |
---|---|
FMO2-HF: Nuclear repulsion | 275439.705569 |
FMO2-HF: Total energy | -24453.192185 |
FMO2-MP2: Total energy | -24516.961052 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021373/ligand_interaction/ligand_F021373.png)
Ligand Interaction
![ligand interaction](./Kdata/F021373/ligand_interaction/ligand_interaction_F021373.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. |
-34.189 | -26.97 | 8.264 | -2.7 | -12.781 | -0.018 |
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 | 0.145 | 0.075 | 3.865 | -1.650 | -0.385 | -0.011 | -0.530 | -0.724 | 0.002 |
4 | C | 24 | ILE | 0 | -0.093 | -0.036 | 6.110 | 0.588 | 0.588 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | C | 25 | CYS | 0 | -0.128 | -0.047 | 8.190 | -1.061 | -1.061 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | C | 26 | PRO | 0 | 0.003 | 0.006 | 10.910 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 27 | LEU | 0 | 0.019 | 0.000 | 14.470 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 28 | ILE | 0 | -0.018 | 0.008 | 15.810 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 29 | TYR | 0 | 0.004 | -0.001 | 16.438 | -0.180 | -0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 30 | ALA | 0 | 0.001 | -0.015 | 16.405 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 31 | PRO | 0 | -0.056 | -0.019 | 15.342 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 32 | VAL | 0 | -0.008 | 0.003 | 11.412 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 33 | CYS | 0 | -0.074 | 0.001 | 12.976 | -0.326 | -0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 34 | VAL | 0 | -0.007 | -0.003 | 8.212 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 35 | GLU | -1 | -0.901 | -0.956 | 11.335 | -0.661 | -0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 36 | ASP | -1 | -0.845 | -0.929 | 8.999 | -1.514 | -1.514 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 37 | SER | 0 | 0.015 | -0.014 | 9.674 | 0.392 | 0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 38 | ASN | 0 | -0.136 | -0.064 | 11.431 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 39 | GLN | 0 | -0.026 | -0.004 | 13.691 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 40 | ASP | -1 | -0.902 | -0.926 | 13.479 | -0.816 | -0.816 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 41 | PHE | 0 | -0.006 | -0.026 | 13.035 | -0.211 | -0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 42 | TYR | 0 | -0.017 | -0.010 | 10.681 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 43 | LEU | 0 | 0.007 | 0.001 | 12.259 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 44 | PHE | 0 | 0.046 | 0.022 | 7.352 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 45 | VAL | 0 | 0.011 | -0.017 | 12.022 | 0.314 | 0.314 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 46 | ASN | 0 | 0.001 | -0.008 | 11.456 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 47 | GLU | -1 | -0.863 | -0.942 | 10.183 | -2.541 | -2.541 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 49 | GLU | -1 | -0.788 | -0.911 | 6.804 | -5.783 | -5.783 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 50 | VAL | 0 | -0.016 | 0.014 | 5.491 | -1.488 | -1.488 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 51 | ARG | 1 | 0.962 | 0.969 | 3.994 | -1.488 | -0.868 | 0.013 | -0.256 | -0.376 | -0.001 |
31 | C | 52 | LYS | 1 | 0.831 | 0.928 | 2.067 | -8.267 | -6.821 | 4.648 | -2.493 | -3.601 | -0.032 |
32 | C | 53 | CYS | 0 | -0.014 | -0.006 | 2.747 | -4.549 | -0.645 | 0.983 | -2.316 | -2.570 | -0.014 |
35 | C | 57 | ALA | 0 | -0.015 | -0.009 | 3.847 | 0.620 | 2.766 | 0.006 | -0.820 | -1.333 | 0.001 |
36 | C | 58 | GLY | 0 | -0.017 | 0.012 | 2.521 | -4.490 | -2.573 | 2.258 | -1.969 | -2.206 | 0.022 |
37 | C | 59 | PHE | 0 | -0.029 | -0.010 | 2.830 | -1.803 | -4.874 | 0.381 | 4.009 | -1.319 | 0.007 |
38 | C | 60 | VAL | 0 | 0.012 | -0.004 | 3.270 | -1.156 | -2.297 | -0.016 | 1.661 | -0.504 | -0.003 |
39 | C | 61 | TYR | 0 | -0.009 | -0.004 | 3.765 | -0.657 | -0.524 | 0.002 | 0.014 | -0.148 | 0.000 |
40 | C | 62 | THR | 0 | 0.019 | 0.006 | 7.609 | 0.395 | 0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 63 | PHE | 0 | -0.003 | -0.004 | 9.871 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | C | 64 | VAL | 0 | 0.006 | 0.010 | 12.547 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | C | 65 | PRO | 0 | 0.010 | -0.002 | 15.882 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | C | 66 | ARG | 1 | 0.992 | 0.973 | 18.097 | 1.066 | 1.066 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | C | 67 | GLU | -1 | -0.932 | -0.972 | 19.110 | -0.786 | -0.786 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | C | 68 | MET | 0 | -0.023 | 0.006 | 17.669 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | C | 70 | LYS | 1 | 0.978 | 0.993 | 18.274 | 1.034 | 1.034 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | C | 71 | ALA | 0 | 0.013 | -0.011 | 19.333 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | C | 72 | THR | 0 | -0.051 | -0.022 | 20.009 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | C | 73 | THR | 0 | -0.008 | -0.009 | 15.224 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | C | 74 | SER | 0 | -0.045 | -0.016 | 13.092 | 0.237 | 0.237 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | C | 75 | LEU | 0 | -0.004 | -0.003 | 11.776 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | C | 77 | PRO | 0 | 0.009 | 0.028 | 7.772 | 0.448 | 0.448 | 0.000 | 0.000 | 0.000 | 0.000 |