![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LJ4L9
Calculation Name: 1WMI-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1WMI
Chain ID: B
UniProt ID: O73966
Base Structure: X-ray
Registration Date: 2023-06-20
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 | OptHSide |
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 | 61 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -278318.175286 |
---|---|
FMO2-HF: Nuclear repulsion | 252651.908434 |
FMO2-HF: Total energy | -25666.266851 |
FMO2-MP2: Total energy | -25740.156806 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021622/ligand_interaction/ligand_F021622.png)
Ligand Interaction
![ligand interaction](./Kdata/F021622/ligand_interaction/ligand_interaction_F021622.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(B:7:GLY)
Summations of interaction energy for
fragment #1(B:7:GLY)
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. |
-2.813 | 0.381 | 1.873 | -1.926 | -3.142 | 0.011 |
Interaction energy analysis for fragmet #1(B:7:GLY)
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 | B | 9 | VAL | 0 | 0.021 | 0.004 | 2.974 | -0.023 | 1.749 | 0.043 | -0.776 | -1.039 | 0.001 |
4 | B | 10 | LEU | 0 | 0.011 | -0.002 | 2.640 | -2.822 | -1.785 | 1.830 | -0.981 | -1.886 | 0.010 |
5 | B | 11 | LYS | 1 | 0.987 | 0.999 | 3.947 | -0.105 | 0.280 | 0.000 | -0.169 | -0.217 | 0.000 |
6 | B | 12 | GLU | -1 | -0.880 | -0.945 | 5.626 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 13 | LEU | 0 | -0.022 | -0.015 | 7.651 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 14 | GLU | -1 | -0.828 | -0.901 | 8.056 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 15 | ARG | 1 | 0.844 | 0.928 | 9.553 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 16 | LEU | 0 | -0.010 | -0.019 | 11.540 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 17 | LYS | 1 | 0.841 | 0.914 | 12.321 | -0.271 | -0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 18 | VAL | 0 | 0.033 | 0.020 | 13.519 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 19 | GLU | -1 | -0.878 | -0.936 | 15.739 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 20 | ILE | 0 | -0.037 | -0.025 | 16.832 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 21 | GLN | 0 | 0.023 | 0.013 | 17.204 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 22 | ARG | 1 | 0.945 | 0.972 | 19.706 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 23 | LEU | 0 | -0.045 | -0.020 | 21.732 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 24 | GLU | -1 | -0.913 | -0.967 | 22.599 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 25 | ALA | 0 | 0.015 | 0.013 | 24.446 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 26 | MET | 0 | -0.058 | -0.031 | 25.765 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 27 | LEU | 0 | -0.112 | -0.040 | 27.745 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 28 | MET | 0 | -0.038 | -0.004 | 27.846 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 29 | PRO | 0 | -0.043 | -0.022 | 31.286 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 30 | GLU | -1 | -0.864 | -0.916 | 33.829 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 31 | GLU | -1 | -1.007 | -1.016 | 35.265 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 32 | ARG | 1 | 0.778 | 0.883 | 36.624 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 33 | ASP | -1 | -0.841 | -0.902 | 38.450 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 34 | GLU | -1 | -1.030 | -1.029 | 41.326 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 35 | ASP | -1 | -0.957 | -0.998 | 42.055 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 36 | ILE | 0 | -0.051 | 0.013 | 36.915 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 37 | THR | 0 | -0.039 | -0.048 | 41.072 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 38 | GLU | -1 | -0.969 | -1.007 | 40.275 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 39 | GLU | -1 | -0.866 | -0.916 | 40.028 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 40 | GLU | -1 | -0.849 | -0.927 | 38.234 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 41 | ILE | 0 | 0.018 | 0.009 | 35.228 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 42 | ALA | 0 | -0.065 | -0.032 | 35.588 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 43 | GLU | -1 | -0.958 | -0.978 | 36.165 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 44 | LEU | 0 | 0.079 | 0.043 | 33.136 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 45 | LEU | 0 | -0.097 | -0.047 | 30.628 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 46 | GLU | -1 | -1.042 | -1.023 | 31.388 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 47 | LEU | 0 | 0.047 | 0.018 | 31.338 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 48 | ALA | 0 | -0.038 | -0.012 | 27.852 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 49 | ARG | 1 | 0.826 | 0.907 | 27.217 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 50 | ASP | -1 | -0.837 | -0.899 | 28.795 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 51 | GLU | -1 | -0.963 | -0.981 | 24.042 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 52 | ASH | 0 | -0.146 | -0.111 | 27.219 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 53 | PRO | 0 | 0.011 | -0.015 | 26.390 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 54 | GLU | -1 | -0.956 | -0.921 | 28.207 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 55 | ASN | 0 | -0.054 | -0.038 | 30.838 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 56 | TRP | 0 | -0.100 | -0.040 | 26.109 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 57 | ILE | 0 | -0.016 | -0.011 | 25.998 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 58 | ASP | -1 | -0.928 | -0.946 | 20.599 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 59 | ALA | 0 | -0.016 | -0.029 | 22.432 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 60 | GLU | -1 | -0.974 | -1.001 | 18.393 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 61 | GLU | -1 | -0.982 | -0.979 | 21.881 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 62 | LEU | 0 | -0.050 | -0.012 | 24.653 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 63 | PRO | 0 | -0.041 | -0.034 | 26.952 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 64 | GLU | -1 | -0.915 | -0.965 | 27.157 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 65 | PRO | 0 | -0.116 | -0.048 | 29.584 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 66 | GLU | -1 | -0.901 | -0.928 | 32.814 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 67 | ASP | -1 | -1.055 | -1.035 | 35.424 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |