![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: KGJ33
Calculation Name: 4MBQ-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4MBQ
Chain ID: B
UniProt ID: Q9HZA6
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 50 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -234654.901236 |
---|---|
FMO2-HF: Nuclear repulsion | 215495.576498 |
FMO2-HF: Total energy | -19159.324737 |
FMO2-MP2: Total energy | -19214.99914 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036628/ligand_interaction/ligand_F036628.png)
Ligand Interaction
![ligand interaction](./Kdata/F036628/ligand_interaction/ligand_interaction_F036628.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(B:869:GLY)
Summations of interaction energy for
fragment #1(B:869: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. |
-24.104 | -22.01 | 11.679 | -7.759 | -6.016 | -0.059 |
Interaction energy analysis for fragmet #1(B:869: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 | B | 871 | ASP | -1 | -0.932 | -0.958 | 3.125 | -2.266 | 0.454 | 0.103 | -1.473 | -1.350 | 0.011 |
4 | B | 872 | GLU | -1 | -0.850 | -0.929 | 1.858 | -19.278 | -20.220 | 11.579 | -6.218 | -4.420 | -0.070 |
5 | B | 873 | ALA | 0 | 0.037 | 0.024 | 4.306 | 0.672 | 0.853 | -0.001 | -0.042 | -0.139 | 0.000 |
6 | B | 874 | ALA | 0 | -0.022 | -0.017 | 6.341 | 0.471 | 0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 875 | THR | 0 | -0.008 | -0.002 | 7.435 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 876 | LYS | 1 | 0.792 | 0.866 | 7.016 | 2.122 | 2.122 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 877 | LEU | 0 | -0.006 | 0.003 | 10.208 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 878 | ASP | -1 | -0.861 | -0.925 | 12.178 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 879 | LEU | 0 | -0.041 | -0.016 | 11.577 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 880 | ALA | 0 | 0.021 | 0.012 | 14.234 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 881 | ARG | 1 | 0.776 | 0.856 | 14.642 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 882 | ALA | 0 | 0.020 | 0.017 | 17.620 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 883 | TYR | 0 | -0.033 | -0.016 | 17.568 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 884 | ILE | 0 | -0.017 | -0.004 | 19.561 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 885 | ASP | -1 | -0.949 | -0.962 | 22.231 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 886 | MET | 0 | -0.139 | -0.058 | 20.993 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 887 | GLY | 0 | -0.047 | -0.018 | 25.107 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 888 | ASP | -1 | -0.930 | -0.965 | 22.945 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 889 | SER | 0 | 0.022 | -0.026 | 22.232 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 890 | GLU | -1 | -0.857 | -0.904 | 21.530 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 891 | GLY | 0 | 0.052 | 0.025 | 19.877 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 892 | ALA | 0 | -0.010 | -0.012 | 17.741 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 893 | ARG | 1 | 0.813 | 0.883 | 16.695 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 894 | ASP | -1 | -0.898 | -0.934 | 16.489 | -0.416 | -0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 895 | ILE | 0 | -0.023 | -0.006 | 12.250 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 896 | LEU | 0 | -0.030 | -0.028 | 11.939 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 897 | ASP | -1 | -0.952 | -0.970 | 12.681 | -0.580 | -0.580 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 898 | GLU | -1 | -0.866 | -0.918 | 9.085 | -1.167 | -1.167 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 899 | VAL | 0 | -0.018 | -0.013 | 8.126 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 900 | LEU | 0 | -0.071 | -0.029 | 8.630 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 901 | ALA | 0 | -0.038 | -0.009 | 9.273 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 902 | GLU | -1 | -0.886 | -0.917 | 4.107 | -2.707 | -2.641 | -0.001 | -0.011 | -0.054 | 0.000 |
35 | B | 903 | GLY | 0 | -0.027 | -0.012 | 4.461 | -0.635 | -0.566 | -0.001 | -0.015 | -0.053 | 0.000 |
36 | B | 904 | ASN | 0 | -0.029 | -0.022 | 6.594 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 905 | ASP | -1 | -0.858 | -0.942 | 8.042 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 906 | SER | 0 | -0.054 | -0.036 | 11.502 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 907 | GLN | 0 | -0.002 | -0.013 | 6.676 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 908 | GLN | 0 | 0.040 | 0.031 | 10.070 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 909 | ALA | 0 | -0.059 | -0.034 | 12.102 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 910 | GLU | -1 | -0.798 | -0.888 | 13.664 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 911 | ALA | 0 | 0.026 | 0.010 | 12.635 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 912 | ARG | 1 | 0.892 | 0.935 | 14.197 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 913 | GLU | -1 | -0.824 | -0.891 | 17.539 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 914 | LEU | 0 | 0.001 | -0.003 | 15.841 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 915 | LEU | 0 | -0.029 | -0.018 | 16.473 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 916 | GLU | -1 | -0.996 | -0.996 | 20.074 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 917 | ARG | 1 | 0.764 | 0.885 | 21.417 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 918 | LEU | 0 | -0.099 | -0.040 | 20.576 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |