![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 72R3K
Calculation Name: 2QDO-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2QDO
Chain ID: A
UniProt ID: A7LBW5
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 | 53 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -243207.455608 |
---|---|
FMO2-HF: Nuclear repulsion | 220479.174475 |
FMO2-HF: Total energy | -22728.281133 |
FMO2-MP2: Total energy | -22791.00873 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F030994/ligand_interaction/ligand_F030994.png)
Ligand Interaction
![ligand interaction](./Kdata/F030994/ligand_interaction/ligand_interaction_F030994.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:10:VAL)
Summations of interaction energy for
fragment #1(A:10:VAL)
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. |
-2.971 | 0.639 | -0.029 | -1.892 | -1.687 | -0.004 |
Interaction energy analysis for fragmet #1(A:10:VAL)
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 | 12 | LEU | 0 | -0.011 | 0.001 | 3.862 | -1.499 | 2.111 | -0.029 | -1.892 | -1.687 | -0.004 |
4 | A | 13 | SER | 0 | -0.032 | -0.032 | 5.544 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 14 | PHE | 0 | 0.031 | 0.013 | 7.239 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 15 | GLU | -1 | -0.838 | -0.908 | 10.188 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 16 | GLN | 0 | -0.003 | -0.002 | 5.268 | -0.289 | -0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 17 | GLU | -1 | -0.795 | -0.891 | 10.234 | -0.818 | -0.818 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 18 | PHE | 0 | -0.031 | -0.008 | 12.051 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 19 | GLN | 0 | -0.030 | -0.029 | 11.475 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 20 | MET | 0 | -0.034 | -0.003 | 11.606 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 21 | ARG | 1 | 0.752 | 0.838 | 14.035 | 0.551 | 0.551 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 22 | VAL | 0 | 0.032 | 0.023 | 17.623 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 23 | MET | 0 | -0.046 | -0.018 | 15.129 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 24 | GLU | -1 | -0.815 | -0.889 | 16.451 | -0.426 | -0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 25 | GLU | -1 | -0.921 | -0.959 | 19.817 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 26 | GLN | 0 | -0.033 | -0.002 | 20.337 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 27 | VAL | 0 | 0.006 | -0.029 | 19.486 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 28 | SER | 0 | -0.135 | -0.068 | 22.641 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 29 | ALA | 0 | -0.008 | -0.011 | 25.442 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 30 | MET | 0 | -0.070 | 0.017 | 21.817 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 31 | SER | 0 | -0.006 | -0.004 | 26.770 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 32 | LEU | 0 | 0.015 | -0.011 | 27.637 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 33 | GLN | 0 | -0.007 | -0.019 | 27.662 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 34 | GLU | -1 | -0.813 | -0.901 | 25.302 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 35 | ALA | 0 | 0.055 | 0.020 | 23.376 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 36 | ARG | 1 | 0.898 | 0.951 | 22.761 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 37 | GLU | -1 | -0.857 | -0.906 | 23.385 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 38 | LEU | 0 | 0.048 | 0.018 | 20.189 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 39 | LEU | 0 | 0.023 | 0.023 | 18.520 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 40 | LEU | 0 | 0.000 | 0.001 | 18.908 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 41 | GLN | 0 | -0.082 | -0.056 | 19.774 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 42 | ALA | 0 | 0.031 | 0.017 | 15.099 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 43 | SER | 0 | -0.029 | -0.024 | 14.937 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 44 | ARG | 1 | 0.949 | 0.973 | 16.157 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 45 | LEU | 0 | 0.023 | -0.009 | 12.858 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 46 | LEU | 0 | 0.015 | 0.014 | 10.143 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 47 | MET | 0 | 0.016 | 0.006 | 11.983 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 48 | MET | 0 | -0.051 | -0.022 | 14.244 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 49 | LYS | 1 | 0.943 | 0.975 | 8.368 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 50 | ASP | -1 | -0.775 | -0.858 | 9.762 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 51 | ASN | 0 | 0.003 | -0.006 | 10.991 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 52 | VAL | 0 | -0.007 | 0.006 | 9.919 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 53 | ILE | 0 | 0.034 | 0.019 | 5.610 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 54 | ARG | 1 | 0.799 | 0.871 | 9.498 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 55 | SER | 0 | -0.060 | -0.020 | 12.891 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 56 | LEU | 0 | 0.009 | -0.014 | 8.802 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 57 | VAL | 0 | 0.027 | 0.012 | 9.139 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 58 | LYS | 1 | 0.908 | 0.959 | 11.530 | -0.204 | -0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 59 | ARG | 1 | 0.953 | 0.960 | 14.794 | -0.459 | -0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 60 | ALA | 0 | -0.004 | 0.021 | 11.926 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 61 | ALA | 0 | 0.019 | 0.016 | 14.063 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 62 | ARG | 1 | 0.899 | 0.964 | 16.909 | -0.242 | -0.242 | 0.000 | 0.000 | 0.000 | 0.000 |