![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 946Y2
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 | 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 | 73 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -443711.067902 |
---|---|
FMO2-HF: Nuclear repulsion | 415536.722916 |
FMO2-HF: Total energy | -28174.344986 |
FMO2-MP2: Total energy | -28257.140887 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031016/ligand_interaction/ligand_F031016.png)
Ligand Interaction
![ligand interaction](./Kdata/F031016/ligand_interaction/ligand_interaction_F031016.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. |
-0.328 | 1.037 | -0.016 | -0.609 | -0.74 | 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 | -0.838 | -0.901 | 3.799 | 1.935 | 3.257 | -0.015 | -0.600 | -0.707 | 0.000 |
4 | A | 31 | PHE | 0 | -0.046 | -0.021 | 6.310 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 32 | ARG | 1 | 0.962 | 0.988 | 8.828 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 33 | VAL | 0 | 0.033 | 0.000 | 11.992 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 34 | GLY | 0 | 0.024 | 0.011 | 15.584 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 35 | GLU | -1 | -0.824 | -0.895 | 9.635 | 1.007 | 1.007 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 36 | ARG | 1 | 0.762 | 0.862 | 13.676 | -0.365 | -0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 37 | VAL | 0 | -0.028 | -0.024 | 11.186 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 38 | TRP | 0 | 0.037 | -0.004 | 13.230 | -0.151 | -0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 39 | VAL | 0 | 0.035 | 0.018 | 14.280 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 40 | ASN | 0 | 0.034 | 0.001 | 15.686 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 41 | GLY | 0 | 0.016 | 0.010 | 17.669 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 42 | ASN | 0 | 0.008 | 0.015 | 17.488 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 43 | LYS | 1 | 0.923 | 0.967 | 18.602 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 44 | PRO | 0 | 0.011 | 0.015 | 17.921 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 45 | GLY | 0 | 0.072 | 0.036 | 17.561 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 46 | PHE | 0 | -0.012 | -0.007 | 16.780 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 47 | ILE | 0 | -0.036 | -0.008 | 11.894 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 48 | GLN | 0 | 0.005 | -0.004 | 16.414 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 49 | PHE | 0 | -0.007 | -0.004 | 18.101 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 50 | LEU | 0 | 0.001 | 0.001 | 12.409 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 51 | GLY | 0 | 0.047 | 0.038 | 16.172 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 52 | GLU | -1 | -0.951 | -0.972 | 17.483 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 53 | THR | 0 | -0.058 | -0.039 | 20.317 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 54 | GLN | 0 | 0.052 | 0.009 | 23.309 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 55 | PHE | 0 | -0.019 | 0.003 | 22.317 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 56 | ALA | 0 | 0.000 | -0.003 | 23.349 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 57 | PRO | 0 | 0.074 | 0.049 | 22.585 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 58 | GLY | 0 | 0.032 | 0.029 | 18.699 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 59 | GLN | 0 | 0.042 | 0.017 | 13.904 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 60 | TRP | 0 | -0.066 | -0.031 | 16.360 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 61 | ALA | 0 | 0.038 | 0.016 | 14.139 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 62 | GLY | 0 | -0.012 | -0.006 | 16.239 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 63 | ILE | 0 | -0.043 | -0.032 | 15.686 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 64 | VAL | 0 | 0.039 | 0.019 | 19.271 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 65 | LEU | 0 | -0.036 | -0.047 | 20.259 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 66 | ASP | -1 | -0.749 | -0.846 | 22.005 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 67 | GLU | -1 | -0.912 | -0.960 | 24.020 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 68 | PRO | 0 | -0.049 | -0.013 | 26.300 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 69 | ILE | 0 | -0.030 | -0.029 | 24.094 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 70 | GLY | 0 | -0.028 | -0.026 | 25.622 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 71 | LYS | 1 | 0.906 | 0.922 | 26.158 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 72 | ASN | 0 | -0.005 | 0.008 | 25.040 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 73 | ASP | -1 | -0.729 | -0.829 | 27.868 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 74 | GLY | 0 | 0.055 | 0.020 | 25.428 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 75 | SER | 0 | -0.070 | -0.062 | 26.410 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 76 | VAL | 0 | -0.010 | -0.016 | 26.071 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 77 | ALA | 0 | -0.004 | -0.005 | 29.258 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 78 | GLY | 0 | 0.031 | 0.019 | 32.609 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 79 | VAL | 0 | -0.017 | 0.011 | 28.387 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 80 | ARG | 1 | 0.824 | 0.889 | 28.004 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 81 | TYR | 0 | -0.027 | 0.001 | 23.132 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 82 | PHE | 0 | -0.002 | 0.003 | 22.363 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 83 | GLN | 0 | -0.011 | -0.007 | 24.987 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 84 | CYS | 0 | -0.065 | -0.008 | 25.665 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 85 | GLU | -1 | -0.772 | -0.874 | 27.822 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 86 | PRO | 0 | 0.052 | 0.002 | 29.064 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 87 | LEU | 0 | 0.021 | 0.022 | 29.786 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 88 | LYS | 1 | 0.842 | 0.926 | 25.770 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 89 | GLY | 0 | 0.057 | 0.055 | 23.924 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 90 | ILE | 0 | -0.061 | -0.012 | 20.064 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 91 | PHE | 0 | 0.023 | 0.016 | 20.127 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 92 | THR | 0 | -0.026 | -0.016 | 15.709 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 93 | ARG | 1 | 0.856 | 0.913 | 15.187 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 94 | PRO | 0 | 0.074 | 0.023 | 10.839 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 95 | SER | 0 | 0.013 | 0.010 | 10.708 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 96 | LYS | 1 | 0.878 | 0.945 | 11.773 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 97 | MET | 0 | -0.004 | 0.013 | 11.020 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 98 | THR | 0 | -0.002 | 0.010 | 9.400 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 99 | ARG | 1 | 0.820 | 0.867 | 4.843 | -2.822 | -2.779 | -0.001 | -0.009 | -0.033 | 0.000 |
73 | A | 100 | LYS | 1 | 0.844 | 0.931 | 9.745 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |