![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: GQM21
Calculation Name: 1WMI-B-Xray315
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 62 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -280932.057232 |
---|---|
FMO2-HF: Nuclear repulsion | 255115.847099 |
FMO2-HF: Total energy | -25816.210133 |
FMO2-MP2: Total energy | -25890.615157 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015876/ligand_interaction/ligand_F015876.png)
Ligand Interaction
![ligand interaction](./Kdata/F015876/ligand_interaction/ligand_interaction_F015876.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:6:ACE )
Summations of interaction energy for
fragment #1(B:6:ACE )
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. |
1.144 | 1.425 | 2.66 | -1.371 | -1.571 | -0.004 |
Interaction energy analysis for fragmet #1(B:6:ACE )
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 | 8 | ASP | -1 | -0.932 | -0.957 | 3.831 | 0.155 | 1.149 | -0.006 | -0.407 | -0.582 | -0.001 |
4 | B | 9 | VAL | 0 | 0.024 | 0.003 | 3.718 | 0.100 | 0.327 | 0.006 | -0.057 | -0.176 | 0.000 |
5 | B | 10 | LEU | 0 | -0.006 | -0.001 | 2.318 | 0.867 | -0.073 | 2.660 | -0.907 | -0.813 | -0.003 |
6 | B | 11 | LYS | 1 | 1.007 | 1.011 | 6.065 | 0.879 | 0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 12 | GLU | -1 | -0.889 | -0.954 | 8.186 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 13 | LEU | 0 | -0.015 | -0.011 | 7.815 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 14 | GLU | -1 | -0.925 | -0.958 | 10.042 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 15 | ARG | 1 | 0.905 | 0.967 | 12.030 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 16 | LEU | 0 | 0.002 | -0.016 | 12.728 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 17 | LYS | 1 | 0.954 | 0.991 | 14.536 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 18 | VAL | 0 | 0.029 | 0.018 | 16.293 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 19 | GLU | -1 | -0.953 | -0.985 | 18.092 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 20 | ILE | 0 | -0.042 | -0.025 | 18.298 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 21 | GLN | 0 | 0.021 | 0.008 | 19.450 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 22 | ARG | 1 | 0.973 | 0.982 | 22.339 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 23 | LEU | 0 | -0.030 | -0.018 | 23.620 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 24 | GLU | -1 | -0.922 | -0.965 | 24.337 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 25 | ALA | 0 | 0.001 | -0.008 | 26.757 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 26 | MET | 0 | -0.059 | -0.031 | 28.020 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 27 | LEU | 0 | -0.114 | -0.043 | 29.571 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 28 | MET | 0 | -0.064 | -0.001 | 29.761 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 29 | PRO | 0 | -0.048 | -0.027 | 33.591 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 30 | GLU | -1 | -0.932 | -0.964 | 36.764 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 31 | GLU | -1 | -1.011 | -1.019 | 38.090 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 32 | ARG | 1 | 0.826 | 0.929 | 39.518 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 33 | ASP | -1 | -0.814 | -0.895 | 41.320 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 34 | GLU | -1 | -1.052 | -1.040 | 44.085 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 35 | ASP | -1 | -0.952 | -1.000 | 44.766 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 36 | ILE | 0 | -0.036 | 0.023 | 40.130 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 37 | THR | 0 | -0.013 | 0.000 | 44.255 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 38 | GLU | -1 | -0.963 | -1.004 | 43.801 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 39 | GLU | -1 | -0.900 | -0.971 | 43.701 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 40 | GLU | -1 | -0.834 | -0.914 | 41.820 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 41 | ILE | 0 | 0.021 | 0.013 | 38.879 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 42 | ALA | 0 | -0.066 | -0.037 | 39.344 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 43 | GLU | -1 | -0.954 | -0.976 | 40.128 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 44 | LEU | 0 | 0.057 | 0.036 | 36.867 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 45 | LEU | 0 | -0.110 | -0.052 | 34.552 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 46 | GLU | -1 | -1.038 | -1.020 | 35.446 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 47 | LEU | 0 | 0.058 | 0.018 | 35.773 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 48 | ALA | 0 | -0.047 | -0.013 | 31.781 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 49 | ARG | 1 | 0.848 | 0.917 | 31.334 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 50 | ASP | -1 | -0.877 | -0.912 | 32.958 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 51 | GLU | -1 | -0.919 | -0.978 | 28.192 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 52 | ASH | 0 | -0.180 | -0.145 | 31.447 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 53 | PRO | 0 | 0.006 | -0.019 | 30.584 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 54 | GLU | -1 | -0.942 | -0.904 | 32.313 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 55 | ASN | 0 | -0.006 | -0.002 | 34.969 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 56 | TRP | 0 | -0.119 | -0.044 | 30.048 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 57 | ILE | 0 | -0.005 | -0.008 | 29.400 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 58 | ASP | -1 | -0.960 | -0.958 | 24.431 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 59 | ALA | 0 | -0.009 | -0.027 | 25.364 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 60 | GLU | -1 | -0.977 | -1.004 | 21.064 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 61 | GLU | -1 | -0.976 | -0.965 | 24.527 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 62 | LEU | 0 | -0.056 | -0.024 | 27.359 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 63 | PRO | 0 | -0.053 | -0.039 | 29.173 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 64 | GLU | -1 | -0.937 | -0.975 | 28.924 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 65 | PRO | 0 | -0.142 | -0.078 | 31.206 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 66 | GLU | -1 | -0.973 | -0.973 | 34.216 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 67 | ASP | -2 | -1.919 | -1.941 | 35.923 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |