![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 391ZL
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 | 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 | 121 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -988191.536301 |
---|---|
FMO2-HF: Nuclear repulsion | 938954.740057 |
FMO2-HF: Total energy | -49236.796244 |
FMO2-MP2: Total energy | -49379.225056 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029938/ligand_interaction/ligand_F029938.png)
Ligand Interaction
![ligand interaction](./Kdata/F029938/ligand_interaction/ligand_interaction_F029938.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. |
-16.487 | -17.057 | 7.095 | -2.576 | -3.95 | 0.017 |
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 | 0.859 | 0.916 | 2.119 | -13.304 | -13.874 | 7.095 | -2.576 | -3.950 | 0.017 |
4 | A | 7 | VAL | 0 | 0.024 | 0.022 | 6.336 | -0.351 | -0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | VAL | 0 | -0.001 | -0.004 | 9.125 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 9 | PRO | 0 | -0.025 | -0.019 | 11.618 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | GLU | -1 | -0.770 | -0.835 | 15.330 | -0.256 | -0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | LEU | 0 | -0.013 | -0.024 | 17.818 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | TYR | 0 | 0.014 | 0.012 | 21.039 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | CYS | 0 | -0.094 | -0.041 | 23.845 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | PHE | 0 | -0.019 | -0.026 | 26.659 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | ASP | -1 | -0.843 | -0.922 | 29.979 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | ILE | 0 | 0.079 | 0.035 | 23.931 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | ASN | 0 | 0.032 | 0.021 | 26.988 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | VAL | 0 | -0.049 | -0.005 | 29.013 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | SER | 0 | -0.027 | -0.023 | 25.156 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | GLN | 0 | -0.010 | -0.012 | 23.504 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | SER | 0 | -0.001 | -0.017 | 24.692 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | PHE | 0 | -0.058 | -0.014 | 24.885 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | PHE | 0 | 0.026 | -0.006 | 19.068 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | VAL | 0 | -0.013 | 0.010 | 22.084 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | ASP | -1 | -0.925 | -0.965 | 23.673 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | VAL | 0 | -0.125 | -0.059 | 26.632 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | LEU | 0 | -0.103 | -0.055 | 21.611 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | GLY | 0 | 0.003 | 0.019 | 21.827 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | PHE | 0 | -0.045 | -0.031 | 15.935 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | GLU | -1 | -0.936 | -0.968 | 17.472 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | VAL | 0 | -0.019 | -0.016 | 17.533 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | LYS | 1 | 0.801 | 0.897 | 10.039 | 0.684 | 0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | TYR | 0 | -0.064 | -0.043 | 13.789 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | GLU | -1 | -0.857 | -0.929 | 18.896 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | ARG | 1 | 0.790 | 0.875 | 18.092 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | PRO | 0 | 0.023 | 0.001 | 23.236 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | ASP | -1 | -0.976 | -0.974 | 26.650 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | GLU | -1 | -0.847 | -0.893 | 22.669 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | GLU | -1 | -0.951 | -0.977 | 25.777 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | PHE | 0 | 0.039 | 0.032 | 16.434 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | VAL | 0 | -0.010 | -0.023 | 20.138 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | TYR | 0 | -0.067 | -0.048 | 10.040 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | LEU | 0 | 0.008 | -0.006 | 16.068 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | THR | 0 | -0.024 | -0.042 | 11.488 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | LEU | 0 | 0.023 | 0.020 | 13.620 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | ASP | -1 | -0.936 | -0.972 | 13.639 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | GLY | 0 | -0.052 | -0.023 | 9.683 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | VAL | 0 | -0.077 | -0.028 | 8.586 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | ASP | -1 | -0.738 | -0.835 | 9.584 | -0.717 | -0.717 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | VAL | 0 | -0.028 | -0.009 | 11.658 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | MET | 0 | -0.030 | -0.004 | 13.528 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | LEU | 0 | -0.024 | -0.012 | 16.962 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | GLU | -1 | -0.845 | -0.930 | 20.759 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | GLY | 0 | 0.005 | 0.012 | 23.193 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | ILE | 0 | -0.061 | -0.023 | 26.907 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 67 | LEU | 0 | -0.032 | -0.020 | 30.062 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 68 | GLU | -1 | -0.971 | -0.994 | 32.720 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 69 | PHE | 0 | -0.044 | 0.015 | 29.614 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 70 | PRO | 0 | -0.028 | -0.010 | 28.446 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 71 | LEU | 0 | 0.014 | -0.012 | 26.968 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 72 | GLY | 0 | 0.011 | -0.010 | 24.269 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 73 | SER | 0 | -0.007 | 0.003 | 24.397 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 74 | GLY | 0 | 0.015 | 0.000 | 25.160 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 75 | VAL | 0 | -0.015 | 0.005 | 19.356 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 76 | ASN | 0 | -0.026 | -0.023 | 17.703 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 77 | PHE | 0 | -0.023 | -0.016 | 15.153 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 78 | GLN | 0 | 0.032 | 0.036 | 9.919 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 79 | TRP | 0 | -0.019 | -0.025 | 10.205 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 80 | ASP | -1 | -0.797 | -0.890 | 6.159 | -1.670 | -1.670 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 81 | VAL | 0 | -0.068 | -0.037 | 8.570 | 0.519 | 0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 82 | ILE | 0 | -0.014 | -0.016 | 6.484 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 83 | ASP | -1 | -0.919 | -0.964 | 9.041 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 84 | ILE | 0 | 0.033 | 0.015 | 12.771 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 85 | GLU | -1 | -0.850 | -0.916 | 14.520 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 86 | PRO | 0 | -0.001 | -0.007 | 15.655 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 87 | LEU | 0 | 0.041 | 0.037 | 14.362 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 88 | TYR | 0 | 0.044 | 0.025 | 17.742 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | GLN | 0 | -0.050 | -0.038 | 20.158 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | ARG | 1 | 0.996 | 1.009 | 19.145 | -0.216 | -0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | VAL | 0 | 0.000 | 0.004 | 20.239 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | ASN | 0 | -0.058 | -0.047 | 22.978 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | GLU | -1 | -0.980 | -0.980 | 25.480 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | SER | 0 | -0.134 | -0.075 | 24.496 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | ALA | 0 | -0.034 | -0.025 | 25.921 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | 0.070 | 0.040 | 26.735 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ASP | -1 | -0.954 | -0.973 | 28.130 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 98 | SER | 0 | -0.044 | -0.019 | 25.268 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | -0.063 | -0.025 | 23.559 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | TYR | 0 | -0.021 | -0.011 | 23.740 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | LEU | 0 | -0.015 | -0.007 | 20.973 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | ALA | 0 | 0.003 | -0.001 | 22.561 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | LEU | 0 | -0.031 | -0.020 | 17.918 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.845 | -0.897 | 19.519 | -0.269 | -0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 105 | SER | 0 | -0.036 | -0.041 | 18.294 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 106 | LYS | 1 | 0.834 | 0.918 | 17.425 | 0.353 | 0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 107 | SER | 0 | 0.000 | -0.035 | 17.126 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 108 | TYR | 0 | 0.044 | 0.030 | 16.956 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 109 | GLN | 0 | -0.053 | -0.039 | 19.062 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 110 | CYS | 0 | -0.026 | -0.015 | 16.262 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 111 | GLY | 0 | 0.016 | 0.025 | 18.833 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 112 | ASP | -1 | -0.908 | -0.949 | 21.554 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 113 | SER | 0 | -0.047 | -0.026 | 18.394 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 114 | ILE | 0 | -0.029 | -0.019 | 19.011 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 115 | ALA | 0 | 0.010 | 0.021 | 14.169 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 116 | THR | 0 | 0.010 | -0.006 | 14.800 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 117 | GLN | 0 | -0.008 | 0.001 | 10.797 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 118 | LYS | 1 | 0.856 | 0.935 | 13.861 | 0.440 | 0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 119 | GLN | 0 | 0.006 | -0.005 | 14.169 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 120 | PHE | 0 | 0.039 | 0.019 | 16.347 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 121 | MET | 0 | -0.007 | 0.003 | 18.039 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 122 | VAL | 0 | -0.016 | 0.003 | 20.291 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 123 | GLN | 0 | 0.004 | 0.014 | 21.806 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 124 | THR | 0 | -0.049 | -0.045 | 21.545 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 125 | PRO | 0 | 0.017 | -0.014 | 24.412 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 126 | ASP | -1 | -0.871 | -0.921 | 25.095 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 127 | GLY | 0 | -0.015 | -0.019 | 26.706 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 128 | TYR | 0 | -0.013 | 0.011 | 21.484 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 129 | LEU | 0 | 0.035 | 0.021 | 21.713 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 130 | PHE | 0 | -0.029 | -0.014 | 15.720 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 131 | ARG | 1 | 0.892 | 0.921 | 15.651 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 132 | PHE | 0 | -0.014 | 0.004 | 13.512 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 133 | CYS | 0 | -0.013 | -0.013 | 11.067 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 134 | GLN | 0 | 0.029 | 0.003 | 9.016 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 135 | ASP | -1 | -0.913 | -0.943 | 8.420 | -1.605 | -1.605 | 0.000 | 0.000 | 0.000 | 0.000 |