![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2JV8R
Calculation Name: 3ECY-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3ECY
Chain ID: A
UniProt ID: Q9V3I1
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 | 119 |
LigandCharge | CYM=-1 |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -869144.23801 |
---|---|
FMO2-HF: Nuclear repulsion | 823539.34308 |
FMO2-HF: Total energy | -45604.89493 |
FMO2-MP2: Total energy | -45738.797099 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F030013/ligand_interaction/ligand_F030013.png)
Ligand Interaction
![ligand interaction](./Kdata/F030013/ligand_interaction/ligand_interaction_F030013.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:19:THR)
Summations of interaction energy for
fragment #1(A:19: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. |
-2.507 | -0.565 | 1.683 | -1.059 | -2.565 | -0.004 |
Interaction energy analysis for fragmet #1(A:19: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 | 21 | VAL | 0 | -0.031 | -0.018 | 2.276 | 0.707 | 2.260 | 1.685 | -1.004 | -2.234 | -0.004 |
4 | A | 22 | LEU | 0 | -0.002 | 0.011 | 5.073 | -0.109 | -0.075 | -0.001 | -0.005 | -0.027 | 0.000 |
5 | A | 23 | ARG | 1 | 0.931 | 0.969 | 3.621 | 2.638 | 2.863 | 0.000 | -0.039 | -0.186 | 0.000 |
6 | A | 24 | PHE | 0 | 0.037 | 0.004 | 9.769 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 25 | ALA | 0 | -0.015 | -0.003 | 13.503 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 26 | LYS | 1 | 0.931 | 0.973 | 15.868 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 27 | LEU | 0 | -0.034 | -0.023 | 19.599 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 28 | THR | 0 | -0.016 | -0.014 | 21.878 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 29 | GLU | -1 | -0.898 | -0.957 | 23.821 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 30 | ASN | 0 | -0.030 | -0.013 | 25.807 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 31 | ALA | 0 | -0.011 | 0.012 | 21.592 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 32 | LEU | 0 | -0.057 | -0.044 | 22.633 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 33 | GLU | -1 | -0.915 | -0.955 | 17.755 | -0.299 | -0.299 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 34 | PRO | 0 | 0.004 | 0.000 | 16.482 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 35 | VAL | 0 | -0.035 | 0.001 | 16.767 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 36 | ARG | 1 | 0.916 | 0.964 | 16.972 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 37 | GLY | 0 | 0.046 | 0.041 | 19.646 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 38 | SER | 0 | -0.041 | -0.040 | 22.308 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 39 | ALA | 0 | 0.046 | 0.017 | 21.299 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 40 | LYS | 1 | 0.942 | 0.956 | 21.085 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 41 | ALA | 0 | -0.030 | 0.013 | 20.983 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 42 | ALA | 0 | 0.050 | 0.017 | 19.662 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 43 | GLY | 0 | 0.033 | 0.025 | 17.269 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 44 | VAL | 0 | -0.057 | -0.018 | 15.471 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 45 | ASP | -1 | -0.859 | -0.961 | 18.435 | -0.269 | -0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 46 | LEU | 0 | -0.004 | -0.015 | 18.473 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 47 | ARG | 1 | 0.877 | 0.919 | 22.133 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 48 | SER | 0 | -0.042 | -0.013 | 24.760 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 49 | ALA | 0 | 0.076 | 0.041 | 25.667 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 50 | TYR | 0 | -0.045 | -0.046 | 27.397 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 51 | ASH | 0 | -0.133 | -0.121 | 31.134 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 52 | VAL | 0 | -0.006 | -0.009 | 32.068 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 53 | VAL | 0 | 0.034 | 0.032 | 35.104 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 54 | VAL | 0 | -0.038 | -0.024 | 35.256 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 55 | PRO | 0 | 0.036 | 0.016 | 38.207 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 56 | ALA | 0 | 0.060 | 0.033 | 41.421 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 57 | ARG | 1 | 0.839 | 0.925 | 43.314 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 58 | GLY | 0 | 0.018 | 0.028 | 41.105 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 59 | LYS | 1 | 0.946 | 0.964 | 35.857 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 60 | ALA | 0 | 0.005 | 0.006 | 34.677 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 61 | ILE | 0 | -0.035 | -0.009 | 27.919 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 62 | VAL | 0 | 0.018 | 0.008 | 28.415 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 63 | LYS | 1 | 0.886 | 0.941 | 24.928 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 64 | THR | 0 | 0.038 | 0.001 | 21.616 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 65 | ASP | -1 | -0.738 | -0.832 | 23.174 | -0.251 | -0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 66 | LEU | 0 | -0.035 | 0.002 | 17.718 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 67 | GLN | 0 | -0.051 | -0.030 | 16.205 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 68 | VAL | 0 | -0.014 | -0.024 | 12.622 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 69 | GLN | 0 | -0.022 | 0.002 | 7.182 | 0.553 | 0.553 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 70 | VAL | 0 | -0.026 | -0.013 | 9.148 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 71 | PRO | 0 | 0.013 | 0.007 | 5.822 | -0.177 | -0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 72 | GLU | -1 | -0.857 | -0.911 | 4.706 | -6.262 | -6.132 | -0.001 | -0.011 | -0.118 | 0.000 |
55 | A | 73 | GLY | 0 | -0.024 | -0.020 | 7.014 | 0.140 | 0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 74 | SER | 0 | -0.145 | -0.086 | 9.397 | 0.362 | 0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 75 | TYR | 0 | 0.034 | 0.009 | 11.082 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 76 | GLY | 0 | 0.007 | 0.003 | 14.336 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 77 | ARG | 1 | 0.910 | 0.960 | 15.768 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 78 | VAL | 0 | -0.013 | -0.002 | 19.404 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 79 | ALA | 0 | -0.001 | -0.012 | 21.592 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 80 | PRO | 0 | 0.075 | 0.029 | 24.116 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 81 | ARG | 1 | 0.863 | 0.941 | 25.912 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | PHE | 0 | 0.000 | -0.021 | 37.883 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ILE | 0 | -0.018 | -0.001 | 34.258 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | ASP | -1 | -0.911 | -0.939 | 33.791 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | VAL | 0 | 0.002 | -0.006 | 27.768 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | 0.048 | 0.025 | 29.506 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ALA | 0 | -0.032 | -0.027 | 26.099 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | GLY | 0 | -0.001 | -0.002 | 23.626 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | VAL | 0 | -0.040 | -0.019 | 18.514 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | VAL | 0 | -0.055 | -0.015 | 15.401 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | ASP | -1 | -0.786 | -0.914 | 14.628 | -0.832 | -0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | GLU | -1 | -0.807 | -0.907 | 10.319 | -1.775 | -1.775 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | ASP | -1 | -0.870 | -0.906 | 12.238 | -0.951 | -0.951 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | TYR | 0 | -0.069 | -0.031 | 15.068 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 102 | ARG | 1 | 0.875 | 0.912 | 11.790 | 0.981 | 0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 103 | GLY | 0 | -0.010 | 0.015 | 17.728 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 104 | ASN | 0 | -0.014 | -0.008 | 19.375 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 105 | LEU | 0 | 0.048 | 0.018 | 17.221 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 106 | GLY | 0 | 0.025 | 0.002 | 21.199 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 107 | VAL | 0 | -0.034 | 0.005 | 24.498 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 108 | VAL | 0 | -0.019 | -0.009 | 27.159 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 109 | LEU | 0 | -0.014 | 0.006 | 30.420 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 110 | PHE | 0 | -0.006 | -0.022 | 32.640 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 111 | ASN | 0 | -0.019 | -0.013 | 36.533 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 112 | HIS | 0 | -0.006 | -0.002 | 38.262 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 113 | SER | 0 | -0.047 | -0.025 | 42.090 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 114 | ASP | -1 | -0.876 | -0.962 | 44.295 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 115 | VAL | 0 | -0.030 | -0.009 | 44.685 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 116 | ASP | -1 | -0.859 | -0.922 | 42.229 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 117 | PHE | 0 | -0.034 | -0.025 | 34.955 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 118 | GLU | -1 | -0.805 | -0.842 | 37.301 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 119 | VAL | 0 | -0.034 | -0.013 | 31.124 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 120 | LYS | 1 | 0.905 | 0.954 | 33.726 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 121 | HIS | 0 | -0.015 | -0.005 | 27.853 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 122 | GLY | 0 | 0.032 | -0.002 | 27.578 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 123 | ASP | -1 | -0.861 | -0.917 | 28.060 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 124 | ARG | 1 | 0.858 | 0.928 | 25.264 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 125 | ILE | 0 | 0.010 | 0.006 | 25.381 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 126 | ALA | 0 | 0.000 | 0.000 | 23.728 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 127 | GLN | 0 | -0.012 | -0.009 | 20.961 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 128 | PHE | 0 | 0.005 | 0.017 | 13.759 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 129 | ILE | 0 | -0.024 | -0.021 | 17.217 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 130 | CYS | 0 | 0.002 | 0.008 | 12.211 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 131 | GLU | -1 | -0.898 | -0.949 | 14.125 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 132 | ARG | 1 | 0.895 | 0.932 | 6.002 | 1.649 | 1.649 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 133 | ILE | 0 | 0.016 | 0.026 | 13.571 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 134 | PHE | 0 | -0.023 | -0.021 | 14.634 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 135 | TYR | 0 | 0.022 | 0.003 | 15.547 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 136 | PRO | 0 | -0.028 | 0.005 | 19.279 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 137 | GLN | 0 | 0.013 | -0.003 | 21.466 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 138 | LEU | 0 | 0.001 | 0.002 | 24.433 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 139 | VAL | 0 | 0.002 | 0.000 | 27.387 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 140 | MET | 0 | -0.005 | 0.002 | 31.005 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 141 | VAL | 0 | -0.011 | -0.015 | 33.626 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 142 | ASP | -1 | -0.841 | -0.903 | 36.312 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 143 | LYS | 1 | 0.862 | 0.915 | 39.003 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 144 | LEU | 0 | -0.008 | 0.005 | 33.482 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |