![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: JL5Y9
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 | 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 | 121 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -988086.115866 |
---|---|
FMO2-HF: Nuclear repulsion | 938849.86044 |
FMO2-HF: Total energy | -49236.255426 |
FMO2-MP2: Total energy | -49378.689385 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F029939/ligand_interaction/ligand_F029939.png)
Ligand Interaction
![ligand interaction](./Kdata/F029939/ligand_interaction/ligand_interaction_F029939.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. |
-12.365 | -11.072 | 3.937 | -1.997 | -3.231 | 0.01 |
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 | 0.886 | 0.941 | 2.349 | -9.418 | -8.125 | 3.937 | -1.997 | -3.231 | 0.010 |
4 | A | 7 | VAL | 0 | 0.021 | 0.021 | 6.336 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | VAL | 0 | 0.000 | -0.004 | 9.179 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 9 | PRO | 0 | -0.040 | -0.029 | 11.622 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | GLU | -1 | -0.842 | -0.910 | 15.336 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | LEU | 0 | -0.035 | -0.035 | 17.817 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | TYR | 0 | 0.004 | 0.009 | 21.041 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | CYS | 0 | -0.087 | -0.043 | 23.854 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | PHE | 0 | -0.021 | -0.022 | 26.659 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | ASP | -1 | -0.862 | -0.933 | 29.992 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | ILE | 0 | 0.096 | 0.037 | 23.986 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | ASN | 0 | 0.040 | 0.018 | 26.983 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | VAL | 0 | -0.051 | -0.001 | 29.009 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | SER | 0 | -0.014 | -0.019 | 25.043 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | GLN | 0 | 0.031 | 0.016 | 23.397 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | SER | 0 | 0.001 | -0.009 | 24.691 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | PHE | 0 | -0.047 | -0.009 | 24.890 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | PHE | 0 | 0.024 | -0.010 | 19.247 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | VAL | 0 | -0.014 | 0.012 | 22.178 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | ASP | -1 | -0.932 | -0.967 | 23.674 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | VAL | 0 | -0.127 | -0.057 | 26.633 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | LEU | 0 | -0.102 | -0.057 | 21.574 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | GLY | 0 | 0.001 | 0.018 | 21.839 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | PHE | 0 | -0.046 | -0.031 | 16.296 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | GLU | -1 | -0.932 | -0.968 | 17.520 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | VAL | 0 | -0.020 | -0.013 | 17.526 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | LYS | 1 | 0.879 | 0.945 | 10.719 | 0.690 | 0.690 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | TYR | 0 | -0.067 | -0.046 | 13.441 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | GLU | -1 | -0.878 | -0.947 | 18.857 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | ARG | 1 | 0.843 | 0.921 | 17.388 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | PRO | 0 | 0.018 | -0.002 | 23.213 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | ASP | -1 | -0.976 | -0.989 | 26.622 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | GLU | -1 | -0.887 | -0.921 | 22.760 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | GLU | -1 | -0.951 | -0.969 | 25.772 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | PHE | 0 | 0.010 | 0.017 | 16.504 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | VAL | 0 | -0.001 | -0.016 | 20.051 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | TYR | 0 | -0.071 | -0.060 | 9.967 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | LEU | 0 | 0.002 | -0.012 | 16.045 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | THR | 0 | -0.031 | -0.044 | 11.448 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | LEU | 0 | 0.030 | 0.024 | 13.616 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | ASP | -1 | -0.943 | -0.975 | 13.651 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | GLY | 0 | -0.063 | -0.029 | 9.689 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | VAL | 0 | -0.084 | -0.031 | 8.593 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | ASP | -1 | -0.791 | -0.865 | 9.429 | -0.606 | -0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | VAL | 0 | -0.036 | -0.012 | 11.660 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | MET | 0 | -0.042 | -0.008 | 13.467 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | LEU | 0 | -0.031 | -0.016 | 16.942 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | GLU | -1 | -0.843 | -0.928 | 20.754 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | GLY | 0 | -0.008 | 0.007 | 23.184 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | ILE | 0 | -0.042 | -0.015 | 26.900 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 67 | LEU | 0 | -0.059 | -0.052 | 30.230 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 68 | GLU | -1 | -0.944 | -0.962 | 32.767 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 69 | PHE | 0 | -0.034 | 0.022 | 29.732 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 70 | PRO | 0 | -0.038 | -0.016 | 28.480 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 71 | LEU | 0 | 0.026 | -0.008 | 26.911 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 72 | GLY | 0 | 0.004 | -0.013 | 24.269 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 73 | SER | 0 | -0.007 | 0.001 | 24.407 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 74 | GLY | 0 | 0.018 | 0.003 | 25.165 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 75 | VAL | 0 | 0.001 | 0.014 | 19.281 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 76 | ASN | 0 | -0.027 | -0.010 | 17.787 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 77 | PHE | 0 | -0.024 | -0.019 | 15.135 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 78 | GLN | 0 | 0.039 | 0.035 | 10.226 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 79 | TRP | 0 | -0.018 | -0.024 | 10.520 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 80 | ASP | -1 | -0.810 | -0.893 | 6.132 | -1.673 | -1.673 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 81 | VAL | 0 | -0.070 | -0.040 | 8.589 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 82 | ILE | 0 | -0.016 | -0.023 | 6.267 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 83 | ASP | -1 | -0.928 | -0.974 | 8.700 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 84 | ILE | 0 | 0.029 | 0.018 | 12.380 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 85 | GLU | -1 | -0.879 | -0.934 | 14.125 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 86 | PRO | 0 | -0.016 | -0.017 | 15.306 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 87 | LEU | 0 | 0.046 | 0.043 | 14.535 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 88 | TYR | 0 | 0.057 | 0.026 | 17.440 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | GLN | 0 | -0.060 | -0.037 | 19.772 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | ARG | 1 | 0.987 | 1.006 | 19.429 | -0.208 | -0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | VAL | 0 | -0.007 | -0.001 | 20.282 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | ASN | 0 | -0.066 | -0.057 | 22.981 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | GLU | -1 | -0.976 | -0.982 | 25.279 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | SER | 0 | -0.133 | -0.070 | 24.498 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | ALA | 0 | -0.031 | -0.025 | 25.906 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | 0.075 | 0.041 | 26.741 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ASP | -1 | -0.957 | -0.975 | 28.006 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 98 | SER | 0 | -0.053 | -0.023 | 25.200 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | -0.046 | -0.020 | 23.636 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | TYR | 0 | -0.033 | -0.015 | 23.807 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | LEU | 0 | -0.022 | -0.008 | 20.831 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | ALA | 0 | 0.008 | -0.001 | 22.652 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | LEU | 0 | -0.032 | -0.017 | 17.665 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.931 | -0.957 | 19.696 | -0.249 | -0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 105 | SER | 0 | -0.038 | -0.035 | 18.371 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 106 | LYS | 1 | 0.987 | 1.008 | 17.526 | 0.357 | 0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 107 | SER | 0 | 0.006 | 0.006 | 17.184 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 108 | TYR | 0 | 0.045 | 0.034 | 16.878 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 109 | GLN | 0 | -0.052 | -0.035 | 19.088 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 110 | CYS | 0 | -0.029 | -0.015 | 16.242 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 111 | GLY | 0 | 0.019 | 0.023 | 18.775 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 112 | ASP | -1 | -0.913 | -0.951 | 21.472 | -0.443 | -0.443 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 113 | SER | 0 | -0.042 | -0.022 | 18.329 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 114 | ILE | 0 | -0.018 | -0.017 | 18.889 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 115 | ALA | 0 | -0.004 | 0.015 | 14.197 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 116 | THR | 0 | -0.021 | -0.056 | 14.863 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 117 | GLN | 0 | -0.019 | -0.018 | 10.621 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 118 | LYS | 1 | 0.889 | 0.952 | 13.849 | 0.481 | 0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 119 | GLN | 0 | -0.013 | -0.019 | 14.261 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 120 | PHE | 0 | 0.045 | 0.025 | 16.437 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 121 | MET | 0 | -0.006 | 0.002 | 18.126 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 122 | VAL | 0 | -0.013 | 0.003 | 20.326 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 123 | GLN | 0 | 0.010 | 0.016 | 21.806 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 124 | THR | 0 | -0.026 | -0.018 | 21.478 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 125 | PRO | 0 | 0.024 | -0.013 | 24.418 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 126 | ASP | -1 | -0.937 | -0.962 | 25.820 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 127 | GLY | 0 | -0.006 | -0.014 | 26.742 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 128 | TYR | 0 | -0.010 | 0.011 | 21.493 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 129 | LEU | 0 | 0.041 | 0.023 | 21.713 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 130 | PHE | 0 | -0.030 | -0.012 | 15.671 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 131 | ARG | 1 | 0.970 | 0.988 | 15.756 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 132 | PHE | 0 | -0.019 | 0.003 | 13.436 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 133 | CYS | 0 | -0.009 | -0.009 | 10.963 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 134 | GLN | 0 | 0.048 | 0.019 | 8.551 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 135 | ASP | -1 | -0.892 | -0.924 | 8.228 | -1.655 | -1.655 | 0.000 | 0.000 | 0.000 | 0.000 |