![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: MV7MZ
Calculation Name: 2QK0-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2QK0
Chain ID: A
UniProt ID: P30622
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 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 | 73 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -443747.547108 |
---|---|
FMO2-HF: Nuclear repulsion | 415573.119452 |
FMO2-HF: Total energy | -28174.427656 |
FMO2-MP2: Total energy | -28257.222568 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031015/ligand_interaction/ligand_F031015.png)
Ligand Interaction
![ligand interaction](./Kdata/F031015/ligand_interaction/ligand_interaction_F031015.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(A:28:GLY)
Summations of interaction energy for
fragment #1(A:28: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. |
-0.029 | 1.358 | -0.013 | -0.658 | -0.716 | 0 |
Interaction energy analysis for fragmet #1(A:28: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 | A | 30 | ASP | -1 | -0.804 | -0.893 | 3.848 | 2.481 | 3.838 | -0.012 | -0.653 | -0.692 | 0.000 |
4 | A | 31 | PHE | 0 | -0.048 | -0.027 | 6.418 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 32 | ARG | 1 | 0.939 | 0.967 | 7.179 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 33 | VAL | 0 | 0.023 | 0.001 | 12.286 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 34 | GLY | 0 | 0.028 | 0.017 | 15.914 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 35 | GLU | -1 | -0.813 | -0.890 | 9.652 | 1.121 | 1.121 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 36 | ARG | 1 | 0.750 | 0.847 | 13.760 | -0.390 | -0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 37 | VAL | 0 | -0.037 | -0.020 | 11.294 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 38 | TRP | 0 | 0.031 | -0.008 | 13.106 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 39 | VAL | 0 | 0.035 | 0.020 | 14.145 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 40 | ASN | 0 | 0.017 | -0.007 | 15.515 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 41 | GLY | 0 | 0.025 | 0.014 | 17.592 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 42 | ASN | 0 | -0.004 | 0.008 | 17.591 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 43 | LYS | 1 | 0.932 | 0.969 | 18.663 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 44 | PRO | 0 | 0.015 | 0.024 | 18.002 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 45 | GLY | 0 | 0.067 | 0.021 | 17.681 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 46 | PHE | 0 | -0.016 | -0.011 | 16.776 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 47 | ILE | 0 | -0.023 | 0.002 | 12.113 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 48 | GLN | 0 | 0.000 | -0.004 | 16.572 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 49 | PHE | 0 | -0.012 | -0.006 | 18.564 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 50 | LEU | 0 | -0.011 | -0.005 | 12.796 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 51 | GLY | 0 | 0.048 | 0.039 | 16.589 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 52 | GLU | -1 | -0.903 | -0.952 | 18.165 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 53 | THR | 0 | -0.037 | -0.032 | 20.627 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 54 | GLN | 0 | 0.029 | 0.003 | 23.775 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 55 | PHE | 0 | -0.009 | 0.007 | 22.781 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 56 | ALA | 0 | -0.001 | -0.009 | 23.992 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 57 | PRO | 0 | 0.063 | 0.048 | 23.357 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 58 | GLY | 0 | 0.052 | 0.049 | 19.550 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 59 | GLN | 0 | 0.010 | -0.012 | 14.544 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 60 | TRP | 0 | -0.092 | -0.040 | 16.855 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 61 | ALA | 0 | 0.040 | 0.017 | 14.258 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 62 | GLY | 0 | -0.017 | -0.009 | 16.386 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 63 | ILE | 0 | -0.043 | -0.031 | 15.942 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 64 | VAL | 0 | 0.051 | 0.028 | 19.608 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 65 | LEU | 0 | -0.017 | -0.022 | 20.388 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 66 | ASP | -1 | -0.737 | -0.840 | 21.871 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 67 | GLU | -1 | -0.886 | -0.951 | 24.095 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 68 | PRO | 0 | -0.049 | -0.011 | 26.576 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 69 | ILE | 0 | -0.034 | -0.027 | 24.446 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 70 | GLY | 0 | -0.021 | -0.015 | 25.840 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 71 | LYS | 1 | 0.897 | 0.922 | 26.338 | -0.129 | -0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 72 | ASN | 0 | 0.015 | 0.017 | 25.600 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 73 | ASP | -1 | -0.739 | -0.826 | 28.417 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 74 | GLY | 0 | 0.063 | 0.022 | 25.549 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 75 | SER | 0 | -0.072 | -0.060 | 26.559 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 76 | VAL | 0 | -0.004 | -0.014 | 26.384 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 77 | ALA | 0 | -0.009 | -0.008 | 29.514 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 78 | GLY | 0 | 0.033 | 0.029 | 32.824 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 79 | VAL | 0 | -0.014 | 0.007 | 28.552 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 80 | ARG | 1 | 0.815 | 0.878 | 28.157 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 81 | TYR | 0 | -0.014 | 0.001 | 23.375 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 82 | PHE | 0 | -0.018 | 0.007 | 22.533 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 83 | GLN | 0 | -0.011 | -0.008 | 25.088 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 84 | CYS | 0 | -0.063 | -0.013 | 25.631 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 85 | GLU | -1 | -0.758 | -0.873 | 27.789 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 86 | PRO | 0 | 0.029 | -0.003 | 29.084 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 87 | LEU | 0 | 0.020 | 0.016 | 30.280 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 88 | LYS | 1 | 0.793 | 0.906 | 25.699 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 89 | GLY | 0 | 0.061 | 0.042 | 24.343 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 90 | ILE | 0 | -0.065 | -0.025 | 20.065 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 91 | PHE | 0 | 0.035 | 0.011 | 20.365 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 92 | THR | 0 | -0.022 | -0.012 | 15.937 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 93 | ARG | 1 | 0.856 | 0.914 | 15.446 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 94 | PRO | 0 | 0.081 | 0.023 | 10.714 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 95 | SER | 0 | -0.002 | 0.007 | 11.123 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 96 | LYS | 1 | 0.887 | 0.947 | 12.130 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 97 | MET | 0 | -0.009 | 0.015 | 11.091 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 98 | THR | 0 | 0.001 | 0.014 | 9.492 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 99 | ARG | 1 | 0.809 | 0.864 | 5.053 | -2.770 | -2.740 | -0.001 | -0.005 | -0.024 | 0.000 |
73 | A | 100 | LYS | 1 | 0.874 | 0.951 | 9.565 | -0.552 | -0.552 | 0.000 | 0.000 | 0.000 | 0.000 |