![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LZKG9
Calculation Name: 2RK9-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2RK9
Chain ID: A
UniProt ID: A3UM69
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 | 121 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -989512.971519 |
---|---|
FMO2-HF: Nuclear repulsion | 940276.039259 |
FMO2-HF: Total energy | -49236.932259 |
FMO2-MP2: Total energy | -49379.35078 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029937/ligand_interaction/ligand_F029937.png)
Ligand Interaction
![ligand interaction](./Kdata/F029937/ligand_interaction/ligand_interaction_F029937.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:4:THR)
Summations of interaction energy for
fragment #1(A:4:THR)
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. |
-18.544 | -23.918 | 13.514 | -3.895 | -4.245 | 0.023 |
Interaction energy analysis for fragmet #1(A:4:THR)
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 | 6 | ARG | 1 | 0.860 | 0.907 | 1.934 | -17.174 | -22.548 | 13.514 | -3.895 | -4.245 | 0.023 |
4 | A | 7 | VAL | 0 | 0.010 | 0.015 | 6.497 | -0.335 | -0.335 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | VAL | 0 | 0.003 | 0.005 | 9.234 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 9 | PRO | 0 | -0.029 | -0.020 | 11.848 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | GLU | -1 | -0.763 | -0.831 | 15.658 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | LEU | 0 | -0.020 | -0.014 | 18.000 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | TYR | 0 | 0.027 | 0.021 | 21.323 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | CYS | 0 | -0.090 | -0.043 | 23.949 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | PHE | 0 | -0.037 | -0.037 | 26.843 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | ASP | -1 | -0.814 | -0.898 | 29.795 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | ILE | 0 | 0.072 | 0.053 | 23.628 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | ASN | 0 | 0.002 | 0.004 | 26.728 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | VAL | 0 | -0.041 | -0.008 | 28.633 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | SER | 0 | -0.022 | -0.026 | 25.277 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | GLN | 0 | -0.013 | -0.016 | 23.346 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | SER | 0 | -0.013 | -0.023 | 24.669 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | PHE | 0 | -0.061 | -0.027 | 25.224 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | PHE | 0 | 0.020 | -0.010 | 19.019 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | VAL | 0 | -0.011 | 0.009 | 22.133 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | ASP | -1 | -0.925 | -0.967 | 23.649 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | VAL | 0 | -0.130 | -0.063 | 26.296 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | LEU | 0 | -0.082 | -0.035 | 21.953 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | GLY | 0 | 0.002 | 0.013 | 21.657 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | PHE | 0 | -0.051 | -0.028 | 15.891 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | GLU | -1 | -0.940 | -0.966 | 17.045 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | VAL | 0 | -0.002 | -0.013 | 17.248 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | LYS | 1 | 0.793 | 0.887 | 9.658 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | TYR | 0 | -0.061 | -0.037 | 13.686 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | GLU | -1 | -0.835 | -0.917 | 18.441 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | ARG | 1 | 0.750 | 0.849 | 18.819 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | PRO | 0 | 0.033 | 0.010 | 23.409 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | ASP | -1 | -0.967 | -0.974 | 26.526 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | GLU | -1 | -0.865 | -0.904 | 23.267 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | GLU | -1 | -0.947 | -0.974 | 25.953 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | PHE | 0 | 0.029 | 0.032 | 16.428 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | VAL | 0 | -0.001 | -0.017 | 20.263 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | TYR | 0 | -0.052 | -0.040 | 9.960 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | LEU | 0 | -0.012 | -0.015 | 15.952 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | THR | 0 | -0.023 | -0.039 | 11.306 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | LEU | 0 | 0.026 | 0.028 | 13.822 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | ASP | -1 | -0.928 | -0.966 | 13.674 | 0.526 | 0.526 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | GLY | 0 | -0.036 | -0.015 | 9.744 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | VAL | 0 | -0.096 | -0.048 | 8.905 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | ASP | -1 | -0.759 | -0.837 | 9.371 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | VAL | 0 | -0.042 | -0.019 | 11.467 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | MET | 0 | -0.013 | 0.000 | 13.478 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | LEU | 0 | -0.017 | -0.010 | 16.907 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | GLU | -1 | -0.838 | -0.926 | 20.712 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | GLY | 0 | 0.064 | 0.032 | 23.021 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | ILE | 0 | -0.100 | -0.040 | 26.836 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 67 | LEU | 0 | -0.018 | -0.011 | 29.921 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 68 | GLU | -1 | -0.982 | -0.999 | 32.834 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 69 | PHE | 0 | -0.037 | 0.006 | 29.699 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 70 | PRO | 0 | -0.046 | -0.010 | 28.237 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 71 | LEU | 0 | 0.014 | -0.018 | 27.082 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 72 | GLY | 0 | 0.008 | -0.005 | 24.325 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 73 | SER | 0 | -0.020 | -0.012 | 24.663 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 74 | GLY | 0 | 0.028 | 0.014 | 25.666 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 75 | VAL | 0 | -0.031 | -0.002 | 19.759 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 76 | ASN | 0 | -0.043 | -0.032 | 18.142 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 77 | PHE | 0 | -0.018 | -0.013 | 15.128 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 78 | GLN | 0 | 0.006 | 0.010 | 9.584 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 79 | TRP | 0 | -0.007 | -0.016 | 10.146 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 80 | ASP | -1 | -0.789 | -0.876 | 6.465 | -1.068 | -1.068 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 81 | VAL | 0 | -0.073 | -0.043 | 8.402 | 0.422 | 0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 82 | ILE | 0 | -0.013 | -0.019 | 6.146 | -0.311 | -0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 83 | ASP | -1 | -0.895 | -0.950 | 8.782 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 84 | ILE | 0 | 0.012 | 0.011 | 12.468 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 85 | GLU | -1 | -0.833 | -0.896 | 14.281 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 86 | PRO | 0 | 0.008 | -0.016 | 15.704 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 87 | LEU | 0 | 0.014 | 0.025 | 13.956 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 88 | TYR | 0 | 0.045 | 0.024 | 17.283 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | GLN | 0 | -0.071 | -0.041 | 19.825 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | ARG | 1 | 1.009 | 1.007 | 18.739 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | VAL | 0 | -0.001 | 0.011 | 20.255 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | ASN | 0 | -0.051 | -0.049 | 22.942 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | GLU | -1 | -0.985 | -0.992 | 24.662 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | SER | 0 | -0.133 | -0.076 | 24.630 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | ALA | 0 | -0.021 | -0.011 | 25.584 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | 0.059 | 0.036 | 26.828 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ASP | -1 | -0.937 | -0.966 | 27.713 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 98 | SER | 0 | -0.044 | -0.021 | 25.200 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | -0.068 | -0.032 | 23.347 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | TYR | 0 | 0.007 | 0.008 | 23.619 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | LEU | 0 | -0.026 | -0.012 | 21.264 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | ALA | 0 | 0.021 | 0.009 | 22.410 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | LEU | 0 | -0.048 | -0.022 | 17.440 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.823 | -0.889 | 19.126 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 105 | SER | 0 | -0.007 | -0.038 | 18.140 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 106 | LYS | 1 | 0.846 | 0.929 | 17.252 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 107 | SER | 0 | -0.003 | -0.010 | 17.050 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 108 | TYR | 0 | 0.031 | 0.022 | 16.975 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 109 | GLN | 0 | -0.045 | -0.028 | 18.951 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 110 | CYS | 0 | -0.022 | -0.018 | 16.413 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 111 | GLY | 0 | 0.014 | 0.025 | 18.985 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 112 | ASP | -1 | -0.908 | -0.951 | 21.831 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 113 | SER | 0 | -0.047 | -0.024 | 18.495 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 114 | ILE | 0 | -0.020 | -0.011 | 18.808 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 115 | ALA | 0 | 0.010 | 0.019 | 14.201 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 116 | THR | 0 | -0.002 | -0.032 | 14.407 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 117 | GLN | 0 | -0.022 | 0.005 | 10.597 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 118 | LYS | 1 | 0.871 | 0.946 | 13.619 | 0.472 | 0.472 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 119 | GLN | 0 | 0.006 | 0.000 | 13.798 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 120 | PHE | 0 | 0.019 | 0.012 | 16.000 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 121 | MET | 0 | -0.011 | -0.001 | 17.787 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 122 | VAL | 0 | -0.042 | -0.016 | 20.110 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 123 | GLN | 0 | 0.009 | 0.015 | 21.897 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 124 | THR | 0 | -0.051 | -0.049 | 21.853 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 125 | PRO | 0 | -0.001 | -0.021 | 24.662 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 126 | ASP | -1 | -0.823 | -0.894 | 25.345 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 127 | GLY | 0 | -0.012 | -0.014 | 26.861 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 128 | TYR | 0 | -0.012 | 0.010 | 21.752 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 129 | LEU | 0 | 0.020 | 0.014 | 21.810 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 130 | PHE | 0 | -0.012 | -0.002 | 15.862 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 131 | ARG | 1 | 0.879 | 0.901 | 15.489 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 132 | PHE | 0 | 0.026 | 0.027 | 13.454 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 133 | CYS | 0 | -0.022 | -0.020 | 10.936 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 134 | GLN | 0 | 0.000 | -0.014 | 8.988 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 135 | ASP | -1 | -0.929 | -0.969 | 8.047 | -1.380 | -1.380 | 0.000 | 0.000 | 0.000 | 0.000 |