![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 52Z1Z
Calculation Name: 4ME7-E-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4ME7
Chain ID: E
UniProt ID: P96621
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 78 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -388049.986388 |
---|---|
FMO2-HF: Nuclear repulsion | 355223.955552 |
FMO2-HF: Total energy | -32826.030836 |
FMO2-MP2: Total energy | -32917.509146 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024291/ligand_interaction/ligand_F024291.png)
Ligand Interaction
![ligand interaction](./Kdata/F024291/ligand_interaction/ligand_interaction_F024291.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(E:6:ALA)
Summations of interaction energy for
fragment #1(E:6:ALA)
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. |
-5.132 | -2.145 | -0.025 | -1.526 | -1.437 | -0.001 |
Interaction energy analysis for fragmet #1(E:6:ALA)
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 | E | 8 | THR | 0 | 0.004 | 0.006 | 3.429 | -3.188 | -0.570 | -0.025 | -1.430 | -1.163 | -0.001 |
4 | E | 9 | GLU | -1 | -0.866 | -0.911 | 3.800 | -0.635 | -0.375 | 0.001 | -0.092 | -0.170 | 0.000 |
5 | E | 10 | MET | 0 | -0.004 | -0.004 | 6.171 | 0.276 | 0.276 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 11 | LYS | 1 | 0.869 | 0.917 | 9.162 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 12 | ILE | 0 | 0.006 | 0.004 | 11.396 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 13 | SER | 0 | 0.019 | 0.002 | 14.205 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 14 | LEU | 0 | -0.014 | 0.000 | 14.267 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 15 | PRO | 0 | 0.034 | 0.010 | 18.107 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 16 | GLU | -1 | -0.902 | -0.949 | 20.975 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 17 | ASN | 0 | 0.017 | 0.001 | 22.637 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 18 | LEU | 0 | 0.028 | 0.022 | 18.543 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 19 | VAL | 0 | -0.016 | -0.011 | 16.327 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 20 | ALA | 0 | 0.051 | 0.031 | 18.578 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 21 | GLU | -1 | -0.937 | -0.967 | 21.338 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 22 | LEU | 0 | -0.054 | -0.029 | 13.396 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 23 | ASP | -1 | -0.759 | -0.859 | 16.647 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 24 | GLY | 0 | 0.016 | 0.021 | 18.335 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 25 | VAL | 0 | -0.059 | -0.037 | 17.075 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 26 | ALA | 0 | 0.001 | 0.007 | 15.405 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 27 | MET | 0 | 0.008 | 0.002 | 16.916 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 28 | ARG | 1 | 0.866 | 0.931 | 19.957 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 29 | GLU | -1 | -0.854 | -0.926 | 17.480 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 30 | LYS | 1 | 0.854 | 0.940 | 18.090 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 31 | ARG | 1 | 0.806 | 0.905 | 12.628 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 32 | SER | 0 | 0.016 | -0.004 | 9.916 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 33 | ARG | 1 | 0.872 | 0.882 | 11.216 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 34 | ASN | 0 | -0.019 | -0.008 | 4.689 | -0.225 | -0.116 | -0.001 | -0.004 | -0.104 | 0.000 |
30 | E | 35 | GLU | -1 | -0.754 | -0.868 | 7.213 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 36 | LEU | 0 | 0.047 | 0.027 | 8.107 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 37 | ILE | 0 | 0.011 | 0.008 | 9.089 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 38 | SER | 0 | 0.008 | 0.010 | 4.998 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 39 | GLN | 0 | 0.000 | -0.002 | 7.513 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | E | 40 | ALA | 0 | 0.026 | 0.014 | 10.581 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | E | 41 | VAL | 0 | 0.006 | -0.002 | 9.764 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | E | 42 | ARG | 1 | 0.923 | 0.963 | 5.942 | -1.577 | -1.577 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 43 | ALA | 0 | 0.028 | 0.031 | 11.510 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | E | 44 | TYR | 0 | 0.041 | 0.024 | 14.888 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 45 | VAL | 0 | 0.033 | 0.007 | 12.864 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 46 | SER | 0 | -0.002 | 0.001 | 14.360 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 47 | GLU | -1 | -0.821 | -0.873 | 16.662 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 48 | ARG | 1 | 0.870 | 0.929 | 18.867 | -0.292 | -0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 49 | THR | 0 | 0.006 | -0.012 | 17.292 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 50 | THR | 0 | -0.036 | -0.025 | 19.917 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 51 | ARG | 1 | 0.844 | 0.883 | 22.104 | -0.223 | -0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 52 | HIS | 0 | 0.008 | 0.020 | 22.804 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 53 | ASN | 0 | 0.062 | 0.013 | 21.205 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 54 | ARG | 1 | 0.897 | 0.941 | 24.788 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 55 | ASP | -1 | -0.787 | -0.849 | 27.961 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 56 | LEU | 0 | 0.007 | 0.001 | 25.667 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 57 | MET | 0 | -0.002 | 0.011 | 28.349 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 58 | ARG | 1 | 0.840 | 0.903 | 30.843 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 59 | ARG | 1 | 0.867 | 0.925 | 31.727 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 60 | GLY | 0 | 0.082 | 0.043 | 33.135 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 61 | TYR | 0 | -0.009 | -0.019 | 33.001 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 62 | MET | 0 | -0.052 | -0.024 | 36.830 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 63 | GLU | -1 | -0.943 | -0.972 | 36.032 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 64 | MET | 0 | -0.013 | -0.005 | 37.249 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 65 | ALA | 0 | 0.014 | 0.024 | 40.081 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 66 | LYS | 1 | 0.964 | 0.973 | 42.558 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 67 | ILE | 0 | 0.008 | 0.002 | 41.528 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 68 | ASN | 0 | 0.000 | -0.012 | 40.031 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 69 | LEU | 0 | 0.037 | 0.023 | 43.709 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 70 | ASN | 0 | -0.071 | -0.016 | 46.984 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 71 | ILE | 0 | 0.034 | 0.004 | 42.988 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 72 | SER | 0 | -0.041 | 0.000 | 45.973 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 73 | SER | 0 | -0.008 | -0.030 | 47.778 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 74 | GLU | -1 | -0.968 | -0.986 | 50.362 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 75 | ALA | 0 | -0.004 | -0.003 | 48.976 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | E | 76 | HIS | 0 | -0.061 | -0.030 | 50.999 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | E | 77 | PHE | 0 | -0.012 | -0.010 | 52.360 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | E | 78 | ALA | 0 | -0.009 | -0.008 | 51.989 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | E | 79 | GLU | -1 | -0.919 | -0.947 | 47.839 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | E | 80 | CYS | 0 | -0.042 | -0.024 | 51.650 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | E | 81 | GLU | -1 | -0.967 | -0.977 | 55.036 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | E | 82 | ALA | 0 | -0.055 | -0.023 | 52.192 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 83 | GLU | -1 | -1.023 | -0.997 | 52.756 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |