
FMODB ID: YVGK2
Calculation Name: 3C8P-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3C8P
Chain ID: A
UniProt ID: P83554
Base Structure: X-ray
Registration Date: 2023-09-23
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
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 | 43 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -201297.706142 |
---|---|
FMO2-HF: Nuclear repulsion | 182677.782208 |
FMO2-HF: Total energy | -18619.923934 |
FMO2-MP2: Total energy | -18669.049067 |
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(A:1:LYS)
Summations of interaction energy for
fragment #1(A:1:LYS)
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. |
55.229 | 67.34 | 15.516 | -11.971 | -15.656 | -0.106 |
Interaction energy analysis for fragmet #1(A:1:LYS)
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 | 3 | CYS | 0 | -0.044 | -0.003 | 2.816 | -15.736 | -10.556 | 2.042 | -2.149 | -5.073 | -0.012 |
4 | A | 4 | CYS | 0 | -0.114 | -0.047 | 4.605 | 3.637 | 3.729 | -0.002 | -0.012 | -0.078 | 0.000 |
5 | A | 5 | PRO | 0 | 0.086 | 0.046 | 8.174 | -1.479 | -1.479 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | SER | 0 | 0.032 | 0.013 | 11.492 | 0.630 | 0.630 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | THR | 0 | 0.039 | 0.002 | 11.940 | -1.826 | -1.826 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | THR | 0 | 0.058 | 0.035 | 13.222 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | GLY | 0 | 0.060 | 0.040 | 12.362 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ARG | 1 | 0.822 | 0.885 | 4.790 | 37.158 | 37.229 | -0.001 | -0.001 | -0.069 | 0.000 |
11 | A | 11 | ASN | 0 | 0.023 | -0.002 | 10.737 | -0.964 | -0.964 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ILE | 0 | 0.029 | 0.027 | 13.984 | 0.484 | 0.484 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | TYR | 0 | -0.024 | -0.018 | 6.063 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | ASN | 0 | 0.013 | -0.023 | 9.494 | -1.043 | -1.043 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | THR | 0 | 0.049 | 0.034 | 11.775 | 0.843 | 0.843 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | CYS | 0 | 0.005 | 0.008 | 10.661 | 1.086 | 1.086 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | ARG | 1 | 0.867 | 0.926 | 8.535 | 20.772 | 20.772 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | LEU | 0 | -0.010 | 0.004 | 12.484 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | THR | 0 | -0.036 | -0.021 | 15.588 | 0.749 | 0.749 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.032 | 0.035 | 15.687 | 0.588 | 0.588 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | SER | 0 | -0.007 | 0.001 | 14.935 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | SER | 0 | 0.029 | 0.007 | 12.048 | -1.182 | -1.182 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ARG | 1 | 0.996 | 0.973 | 5.106 | 23.372 | 23.372 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | GLU | -1 | -0.882 | -0.934 | 9.121 | -17.013 | -17.013 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | THR | 0 | 0.009 | 0.003 | 10.802 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | ALA | 0 | -0.043 | -0.019 | 8.730 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LYS | 1 | 0.950 | 0.976 | 10.800 | 14.543 | 14.543 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | LEU | 0 | 0.024 | 0.021 | 14.154 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | SER | 0 | -0.048 | -0.032 | 11.403 | -0.415 | -0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | GLY | 0 | 0.026 | 0.023 | 13.038 | -0.373 | -0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | LYS | 1 | 0.957 | 0.983 | 7.355 | 23.341 | 23.341 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ILE | 0 | -0.016 | -0.016 | 3.336 | -4.879 | -4.266 | 0.041 | -0.253 | -0.401 | 0.001 |
33 | A | 35 | ILE | 0 | 0.016 | -0.003 | 2.649 | 3.287 | 4.672 | 0.089 | -0.499 | -0.976 | 0.000 |
34 | A | 36 | SER | 0 | 0.042 | 0.032 | 1.899 | -14.537 | -16.566 | 9.319 | -4.203 | -3.087 | -0.044 |
35 | A | 37 | ALA | 0 | 0.017 | 0.009 | 3.244 | 4.663 | 5.208 | 0.020 | -0.161 | -0.405 | 0.001 |
36 | A | 38 | SER | 0 | 0.048 | 0.024 | 2.785 | -10.860 | -8.289 | 0.785 | -1.350 | -2.006 | -0.012 |
37 | A | 39 | THR | 0 | -0.051 | -0.040 | 2.111 | -30.612 | -27.078 | 3.223 | -3.317 | -3.439 | -0.040 |
38 | A | 41 | PRO | 0 | 0.072 | 0.039 | 4.283 | 2.622 | 2.771 | 0.000 | -0.026 | -0.122 | 0.000 |
39 | A | 42 | SER | 0 | 0.047 | 0.005 | 7.992 | -0.772 | -0.772 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | ASN | 0 | 0.040 | 0.024 | 10.633 | -0.898 | -0.898 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | TYR | 0 | -0.080 | -0.046 | 7.717 | 2.145 | 2.145 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | PRO | 0 | 0.056 | 0.036 | 6.907 | -5.102 | -5.102 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | LYS | 1 | 0.963 | 1.000 | 6.144 | 22.203 | 22.203 | 0.000 | 0.000 | 0.000 | 0.000 |