![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6N18Z
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 | 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 | 119 |
LigandCharge | CYM=-1 |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -870376.904709 |
---|---|
FMO2-HF: Nuclear repulsion | 824771.099541 |
FMO2-HF: Total energy | -45605.805168 |
FMO2-MP2: Total energy | -45739.678794 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F030012/ligand_interaction/ligand_F030012.png)
Ligand Interaction
![ligand interaction](./Kdata/F030012/ligand_interaction/ligand_interaction_F030012.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. |
-2.922 | 0.04 | 0.671 | -1.317 | -2.314 | -0.001 |
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 | -0.036 | -0.017 | 2.388 | 0.707 | 2.684 | 0.665 | -0.875 | -1.766 | -0.002 |
4 | A | 22 | LEU | 0 | -0.004 | 0.011 | 4.830 | -0.089 | -0.077 | -0.001 | -0.006 | -0.004 | 0.000 |
5 | A | 23 | ARG | 1 | 0.910 | 0.963 | 3.360 | 1.221 | 1.889 | 0.007 | -0.290 | -0.385 | 0.002 |
6 | A | 24 | PHE | 0 | 0.035 | -0.001 | 9.773 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 25 | ALA | 0 | -0.009 | 0.001 | 13.522 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 26 | LYS | 1 | 0.835 | 0.916 | 15.928 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 27 | LEU | 0 | -0.041 | -0.025 | 19.612 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 28 | THR | 0 | -0.015 | -0.019 | 22.034 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 29 | GLU | -1 | -0.879 | -0.946 | 23.784 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 30 | ASN | 0 | -0.049 | -0.029 | 25.866 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 31 | ALA | 0 | 0.008 | 0.019 | 21.586 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 32 | LEU | 0 | -0.029 | -0.014 | 22.623 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 33 | GLU | -1 | -0.827 | -0.913 | 17.915 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 34 | PRO | 0 | -0.032 | -0.015 | 15.970 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 35 | VAL | 0 | -0.016 | 0.006 | 16.967 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 36 | ARG | 1 | 0.912 | 0.947 | 17.248 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 37 | GLY | 0 | 0.044 | 0.038 | 19.969 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 38 | SER | 0 | -0.028 | -0.032 | 22.685 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 39 | ALA | 0 | 0.042 | 0.017 | 21.701 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 40 | LYS | 1 | 0.958 | 0.962 | 21.195 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 41 | ALA | 0 | -0.019 | 0.023 | 21.292 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 42 | ALA | 0 | 0.055 | 0.029 | 19.660 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 43 | GLY | 0 | 0.043 | 0.029 | 17.236 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 44 | VAL | 0 | -0.074 | -0.029 | 15.668 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 45 | ASP | -1 | -0.840 | -0.941 | 18.466 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 46 | LEU | 0 | -0.012 | -0.010 | 18.558 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 47 | ARG | 1 | 0.882 | 0.920 | 22.058 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 48 | SER | 0 | -0.034 | -0.008 | 24.719 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 49 | ALA | 0 | 0.069 | 0.041 | 25.608 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 50 | TYR | 0 | -0.028 | -0.023 | 27.379 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 51 | ASH | 0 | -0.095 | -0.073 | 31.143 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 52 | VAL | 0 | -0.014 | -0.014 | 32.127 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 53 | VAL | 0 | 0.031 | 0.031 | 35.186 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 54 | VAL | 0 | -0.038 | -0.024 | 35.492 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 55 | PRO | 0 | 0.038 | 0.017 | 38.301 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 56 | ALA | 0 | 0.039 | 0.016 | 41.435 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 57 | ARG | 1 | 0.789 | 0.895 | 43.262 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 58 | GLY | 0 | 0.025 | 0.033 | 41.009 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 59 | LYS | 1 | 0.938 | 0.959 | 35.656 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 60 | ALA | 0 | 0.007 | 0.010 | 34.724 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 61 | ILE | 0 | -0.028 | -0.007 | 27.493 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 62 | VAL | 0 | 0.012 | 0.005 | 28.650 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 63 | LYS | 1 | 0.853 | 0.916 | 24.451 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 64 | THR | 0 | 0.033 | -0.006 | 21.796 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 65 | ASP | -1 | -0.753 | -0.841 | 23.221 | -0.181 | -0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 66 | LEU | 0 | -0.025 | 0.009 | 17.768 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 67 | GLN | 0 | -0.045 | -0.017 | 16.011 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 68 | VAL | 0 | -0.021 | -0.028 | 12.534 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 69 | GLN | 0 | -0.039 | -0.013 | 6.526 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 70 | VAL | 0 | -0.027 | -0.018 | 9.102 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 71 | PRO | 0 | 0.006 | 0.003 | 5.528 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 72 | GLU | -1 | -0.820 | -0.890 | 3.770 | -5.893 | -5.588 | 0.000 | -0.146 | -0.159 | -0.001 |
55 | A | 73 | GLY | 0 | 0.014 | 0.017 | 6.909 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 74 | SER | 0 | -0.139 | -0.086 | 9.306 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 75 | TYR | 0 | 0.035 | 0.008 | 11.180 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 76 | GLY | 0 | 0.000 | 0.005 | 14.230 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 77 | ARG | 1 | 0.819 | 0.883 | 15.492 | 0.404 | 0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 78 | VAL | 0 | -0.010 | -0.003 | 19.166 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 79 | ALA | 0 | 0.009 | -0.005 | 21.495 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 80 | PRO | 0 | 0.069 | 0.029 | 24.090 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 81 | ARG | 1 | 0.864 | 0.945 | 25.748 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 89 | PHE | 0 | 0.018 | 0.004 | 37.290 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 90 | ILE | 0 | -0.033 | -0.025 | 34.366 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 91 | ASP | -1 | -0.929 | -0.947 | 33.531 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 92 | VAL | 0 | 0.011 | -0.003 | 27.816 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 93 | GLY | 0 | 0.048 | 0.032 | 29.284 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 94 | ALA | 0 | -0.029 | -0.026 | 25.848 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 95 | GLY | 0 | -0.001 | -0.005 | 23.263 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 96 | VAL | 0 | -0.042 | -0.020 | 18.256 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 97 | VAL | 0 | -0.046 | -0.009 | 15.273 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 98 | ASP | -1 | -0.788 | -0.916 | 14.069 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 99 | GLU | -1 | -0.815 | -0.915 | 9.402 | -1.342 | -1.342 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 100 | ASP | -1 | -0.867 | -0.914 | 11.458 | -0.545 | -0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 101 | TYR | 0 | -0.066 | -0.021 | 14.243 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 102 | ARG | 1 | 0.852 | 0.896 | 11.390 | 0.626 | 0.626 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 103 | GLY | 0 | 0.012 | 0.024 | 17.321 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 104 | ASN | 0 | -0.005 | -0.015 | 19.203 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 105 | LEU | 0 | 0.018 | 0.013 | 17.020 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 106 | GLY | 0 | 0.042 | 0.016 | 21.155 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 107 | VAL | 0 | -0.035 | 0.001 | 24.394 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 108 | VAL | 0 | -0.018 | -0.001 | 27.092 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 109 | LEU | 0 | -0.014 | 0.005 | 30.448 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 110 | PHE | 0 | 0.004 | -0.023 | 32.447 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 111 | ASN | 0 | -0.016 | -0.011 | 36.443 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 112 | HIS | 0 | -0.021 | -0.010 | 37.763 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 113 | SER | 0 | -0.037 | -0.022 | 42.042 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 114 | ASP | -1 | -0.846 | -0.943 | 44.344 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 115 | VAL | 0 | -0.019 | -0.002 | 44.830 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 116 | ASP | -1 | -0.849 | -0.908 | 42.363 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 117 | PHE | 0 | -0.021 | -0.017 | 34.849 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 118 | GLU | -1 | -0.812 | -0.870 | 37.601 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 119 | VAL | 0 | -0.026 | -0.010 | 31.147 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 120 | LYS | 1 | 0.880 | 0.929 | 33.616 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 121 | HIS | 0 | -0.029 | -0.017 | 27.769 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 122 | GLY | 0 | 0.036 | 0.001 | 27.569 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 123 | ASP | -1 | -0.865 | -0.910 | 28.093 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 124 | ARG | 1 | 0.818 | 0.896 | 25.366 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 125 | ILE | 0 | 0.010 | -0.002 | 25.511 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 126 | ALA | 0 | -0.001 | 0.004 | 23.842 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 127 | GLN | 0 | -0.045 | -0.024 | 21.064 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 128 | PHE | 0 | 0.035 | 0.023 | 13.619 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 129 | ILE | 0 | -0.017 | -0.017 | 17.197 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 130 | CYS | 0 | 0.008 | 0.012 | 12.207 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 131 | GLU | -1 | -0.826 | -0.879 | 14.226 | -0.295 | -0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 132 | ARG | 1 | 0.806 | 0.855 | 6.140 | 1.752 | 1.752 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 133 | ILE | 0 | 0.020 | 0.023 | 13.707 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 134 | PHE | 0 | -0.016 | -0.011 | 14.771 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 135 | TYR | 0 | 0.014 | -0.005 | 15.529 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 136 | PRO | 0 | -0.022 | 0.006 | 19.417 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 137 | GLN | 0 | 0.010 | 0.000 | 21.615 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 138 | LEU | 0 | 0.002 | 0.000 | 24.577 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 139 | VAL | 0 | -0.004 | -0.006 | 27.529 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 140 | MET | 0 | 0.001 | 0.010 | 31.151 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 141 | VAL | 0 | -0.008 | -0.012 | 33.769 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 142 | ASP | -1 | -0.841 | -0.905 | 36.466 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 143 | LYS | 1 | 0.855 | 0.906 | 39.174 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 144 | LEU | 0 | -0.004 | 0.012 | 33.604 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |