![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LZ2L9
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 | OptH |
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 | -444183.280976 |
---|---|
FMO2-HF: Nuclear repulsion | 416009.146396 |
FMO2-HF: Total energy | -28174.13458 |
FMO2-MP2: Total energy | -28256.967829 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031017/ligand_interaction/ligand_F031017.png)
Ligand Interaction
![ligand interaction](./Kdata/F031017/ligand_interaction/ligand_interaction_F031017.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. |
-1.23 | 0.236 | -0.016 | -0.661 | -0.79 | 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 | -0.795 | -0.884 | 3.799 | 1.755 | 3.117 | -0.015 | -0.624 | -0.724 | 0.000 |
4 | A | 31 | PHE | 0 | -0.082 | -0.032 | 6.297 | 0.387 | 0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 32 | ARG | 1 | 0.959 | 0.982 | 8.840 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 33 | VAL | 0 | 0.040 | 0.006 | 11.978 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 34 | GLY | 0 | 0.017 | 0.005 | 15.570 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 35 | GLU | -1 | -0.833 | -0.906 | 9.587 | 0.987 | 0.987 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 36 | ARG | 1 | 0.786 | 0.880 | 13.676 | -0.370 | -0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 37 | VAL | 0 | -0.032 | -0.025 | 11.268 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 38 | TRP | 0 | 0.011 | -0.011 | 13.230 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 39 | VAL | 0 | 0.026 | 0.013 | 14.286 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 40 | ASN | 0 | 0.039 | 0.003 | 15.721 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 41 | GLY | 0 | -0.007 | -0.004 | 17.672 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 42 | ASN | 0 | -0.010 | 0.011 | 17.014 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 43 | LYS | 1 | 0.961 | 0.984 | 18.610 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 44 | PRO | 0 | 0.005 | 0.009 | 17.920 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 45 | GLY | 0 | 0.085 | 0.042 | 17.559 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 46 | PHE | 0 | -0.010 | -0.003 | 16.784 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 47 | ILE | 0 | -0.033 | -0.008 | 11.828 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 48 | GLN | 0 | 0.010 | -0.001 | 16.401 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 49 | PHE | 0 | -0.011 | -0.007 | 18.098 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 50 | LEU | 0 | 0.001 | -0.001 | 12.410 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 51 | GLY | 0 | 0.046 | 0.038 | 16.160 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 52 | GLU | -1 | -0.965 | -0.977 | 17.472 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 53 | THR | 0 | -0.059 | -0.037 | 20.307 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 54 | GLN | 0 | 0.065 | 0.011 | 23.299 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 55 | PHE | 0 | -0.027 | -0.003 | 22.271 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 56 | ALA | 0 | -0.009 | -0.008 | 23.321 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 57 | PRO | 0 | 0.072 | 0.051 | 22.649 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 58 | GLY | 0 | 0.032 | 0.021 | 18.694 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 59 | GLN | 0 | 0.057 | 0.022 | 13.921 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 60 | TRP | 0 | -0.060 | -0.029 | 16.352 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 61 | ALA | 0 | 0.037 | 0.017 | 14.143 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 62 | GLY | 0 | -0.019 | -0.009 | 16.229 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 63 | ILE | 0 | -0.038 | -0.028 | 15.676 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 64 | VAL | 0 | 0.022 | 0.015 | 19.260 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 65 | LEU | 0 | -0.037 | -0.053 | 20.321 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 66 | ASP | -1 | -0.781 | -0.865 | 21.828 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 67 | GLU | -1 | -0.916 | -0.961 | 24.020 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 68 | PRO | 0 | -0.046 | -0.013 | 26.300 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 69 | ILE | 0 | -0.032 | -0.028 | 23.806 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 70 | GLY | 0 | -0.023 | -0.028 | 25.611 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 71 | LYS | 1 | 0.902 | 0.923 | 26.035 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 72 | ASN | 0 | -0.001 | 0.013 | 25.054 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 73 | ASP | -1 | -0.714 | -0.804 | 27.857 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 74 | GLY | 0 | 0.047 | 0.014 | 25.419 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 75 | SER | 0 | -0.076 | -0.078 | 26.398 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 76 | VAL | 0 | -0.018 | -0.019 | 26.149 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 77 | ALA | 0 | -0.002 | -0.003 | 29.248 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 78 | GLY | 0 | 0.026 | 0.016 | 32.599 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 79 | VAL | 0 | -0.015 | 0.012 | 28.233 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 80 | ARG | 1 | 0.813 | 0.872 | 28.129 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 81 | TYR | 0 | -0.018 | 0.008 | 23.101 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 82 | PHE | 0 | 0.005 | 0.005 | 22.403 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 83 | GLN | 0 | 0.000 | 0.001 | 24.974 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 84 | CYS | 0 | -0.082 | -0.015 | 25.675 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 85 | GLU | -1 | -0.818 | -0.919 | 27.810 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 86 | PRO | 0 | 0.054 | 0.006 | 29.053 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 87 | LEU | 0 | 0.020 | 0.020 | 29.788 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 88 | LYS | 1 | 0.892 | 0.969 | 25.779 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 89 | GLY | 0 | 0.064 | 0.059 | 23.914 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 90 | ILE | 0 | -0.058 | -0.008 | 19.547 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 91 | PHE | 0 | 0.021 | 0.016 | 20.122 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 92 | THR | 0 | -0.025 | -0.015 | 15.711 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 93 | ARG | 1 | 0.858 | 0.923 | 15.276 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 94 | PRO | 0 | 0.080 | 0.026 | 10.840 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 95 | SER | 0 | 0.010 | 0.009 | 10.704 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 96 | LYS | 1 | 0.884 | 0.946 | 11.770 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 97 | MET | 0 | 0.007 | 0.018 | 11.126 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 98 | THR | 0 | 0.000 | 0.015 | 9.406 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 99 | ARG | 1 | 0.831 | 0.882 | 4.442 | -3.547 | -3.443 | -0.001 | -0.037 | -0.066 | 0.000 |
73 | A | 100 | LYS | 1 | 0.871 | 0.939 | 9.756 | -0.486 | -0.486 | 0.000 | 0.000 | 0.000 | 0.000 |