![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YY632
Calculation Name: 3NFG-A-Xray320
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3NFG
Chain ID: A
UniProt ID: Q6FNZ9
Base Structure: X-ray
Registration Date: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 96 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -510792.170219 |
---|---|
FMO2-HF: Nuclear repulsion | 472860.324001 |
FMO2-HF: Total energy | -37931.846218 |
FMO2-MP2: Total energy | -38043.892793 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016339/ligand_interaction/ligand_F016339.png)
Ligand Interaction
![ligand interaction](./Kdata/F016339/ligand_interaction/ligand_interaction_F016339.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:ACE )
Summations of interaction energy for
fragment #1(A:4:ACE )
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. |
0.859 | 1.83 | -0.006 | -0.447 | -0.518 | -0.001 |
Interaction energy analysis for fragmet #1(A:4:ACE )
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 | SER | 0 | -0.001 | 0.013 | 3.825 | 0.737 | 1.708 | -0.006 | -0.447 | -0.518 | -0.001 |
4 | A | 7 | ILE | 0 | 0.005 | 0.008 | 6.465 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 8 | ALA | 0 | 0.032 | 0.020 | 9.845 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 9 | ILE | 0 | -0.035 | -0.019 | 11.511 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 10 | ASP | -1 | -0.923 | -0.955 | 15.138 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 11 | SER | 0 | -0.028 | -0.017 | 17.420 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 12 | TYR | 0 | -0.051 | -0.027 | 20.266 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 13 | GLN | 0 | -0.027 | -0.010 | 22.120 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 14 | GLU | -1 | -0.872 | -0.941 | 25.815 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 15 | ASP | -1 | -0.955 | -0.957 | 27.696 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 16 | PRO | 0 | -0.100 | -0.067 | 30.349 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 17 | SER | 0 | 0.045 | 0.028 | 29.084 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 18 | VAL | 0 | -0.019 | -0.007 | 28.224 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 19 | VAL | 0 | 0.001 | -0.010 | 31.455 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 20 | VAL | 0 | 0.002 | 0.013 | 28.413 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 21 | SER | 0 | -0.022 | -0.009 | 31.843 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 22 | ASN | 0 | -0.021 | -0.020 | 33.743 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 23 | PHE | 0 | 0.020 | 0.018 | 35.397 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 24 | PHE | 0 | 0.053 | 0.022 | 38.225 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 25 | LYS | 1 | 0.963 | 0.959 | 32.190 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 26 | GLY | 0 | 0.032 | 0.014 | 36.576 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 27 | VAL | 0 | -0.029 | 0.011 | 37.137 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 28 | ARG | 1 | 0.930 | 0.953 | 37.168 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 29 | VAL | 0 | 0.024 | 0.014 | 39.728 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 30 | PRO | 0 | 0.014 | 0.015 | 41.112 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 31 | LYS | 1 | 0.950 | 0.961 | 39.124 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 32 | ASP | -1 | -0.904 | -0.947 | 41.963 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 33 | THR | 0 | -0.036 | -0.015 | 43.033 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 34 | GLU | -1 | -0.939 | -0.951 | 42.908 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 35 | PHE | 0 | -0.048 | -0.031 | 40.642 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 36 | GLN | 0 | 0.015 | 0.006 | 42.413 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 37 | LEU | 0 | -0.007 | 0.004 | 36.143 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 38 | TYR | 0 | 0.012 | -0.002 | 40.571 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 39 | LYS | 1 | 0.986 | 0.997 | 38.155 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 40 | LYS | 1 | 0.990 | 0.991 | 40.417 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 41 | ARG | 1 | 0.923 | 0.956 | 41.334 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 42 | LYS | 1 | 0.910 | 0.958 | 36.397 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 43 | GLN | 0 | -0.018 | -0.016 | 42.291 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 44 | ASP | -1 | -0.869 | -0.928 | 37.248 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 45 | GLN | 0 | 0.010 | 0.001 | 38.877 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 46 | PHE | 0 | 0.008 | -0.011 | 37.906 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 47 | VAL | 0 | 0.056 | 0.025 | 37.200 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 48 | LEU | 0 | -0.051 | -0.020 | 38.385 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 49 | HIS | 1 | 0.837 | 0.896 | 37.285 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 50 | GLY | 0 | -0.015 | -0.013 | 39.326 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 51 | GLU | -1 | -0.847 | -0.938 | 38.437 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 52 | ASN | 0 | -0.002 | -0.006 | 41.809 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 53 | GLU | -1 | -0.863 | -0.935 | 41.313 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 54 | ARG | 1 | 0.913 | 0.967 | 44.583 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 55 | LEU | 0 | -0.073 | -0.039 | 46.428 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 56 | GLU | -1 | -0.851 | -0.919 | 40.642 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 57 | TYR | 0 | -0.058 | -0.033 | 43.089 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 58 | ASP | -1 | -0.798 | -0.873 | 40.462 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 59 | GLY | 0 | 0.028 | 0.006 | 42.508 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 60 | GLU | -1 | -0.944 | -0.950 | 42.074 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 61 | THR | 0 | -0.020 | -0.001 | 42.806 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 62 | ASP | -1 | -0.833 | -0.918 | 44.716 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 63 | GLU | -1 | -0.850 | -0.918 | 43.314 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 64 | LEU | 0 | 0.015 | 0.004 | 45.596 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 65 | THR | 0 | 0.016 | 0.003 | 48.985 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 66 | THR | 0 | -0.011 | 0.009 | 43.237 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 67 | LYS | 1 | 0.795 | 0.876 | 44.331 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 68 | THR | 0 | -0.052 | -0.009 | 47.722 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 69 | ASN | 0 | -0.064 | -0.048 | 50.343 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 70 | GLN | 0 | 0.008 | 0.006 | 48.480 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 71 | TYR | 0 | 0.048 | 0.025 | 48.756 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 72 | MET | 0 | -0.048 | -0.021 | 48.046 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 73 | VAL | 0 | 0.028 | 0.020 | 49.479 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 74 | GLY | 0 | 0.016 | -0.005 | 51.011 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 75 | LEU | 0 | -0.020 | 0.001 | 51.358 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 76 | TYR | 0 | 0.007 | -0.013 | 54.919 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 77 | ASP | -1 | -0.865 | -0.924 | 58.359 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 78 | LYS | 1 | 0.937 | 0.943 | 60.531 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 79 | GLN | 0 | 0.001 | 0.012 | 64.077 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 80 | SER | 0 | -0.028 | -0.014 | 60.678 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 81 | GLY | 0 | 0.034 | 0.027 | 62.816 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 82 | LYS | 1 | 0.923 | 0.967 | 57.444 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 83 | ILE | 0 | 0.000 | -0.009 | 55.030 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 84 | ASN | 0 | -0.023 | 0.007 | 51.020 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 85 | LEU | 0 | -0.011 | -0.016 | 50.713 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 86 | TYR | 0 | 0.029 | 0.019 | 45.668 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 87 | ARG | 1 | 0.921 | 0.961 | 43.072 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 88 | ALA | 0 | 0.005 | -0.002 | 44.915 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 89 | PRO | 0 | -0.010 | 0.014 | 41.992 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 90 | VAL | 0 | -0.007 | -0.010 | 45.072 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 91 | VAL | 0 | -0.015 | -0.002 | 43.157 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 92 | THR | 0 | -0.038 | -0.013 | 46.400 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 93 | SER | 0 | 0.030 | -0.011 | 46.379 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 94 | LYS | 1 | 0.932 | 0.972 | 46.374 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 95 | ILE | 0 | -0.009 | -0.005 | 46.923 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 96 | VAL | 0 | 0.013 | 0.009 | 45.903 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 97 | SER | 0 | -0.039 | -0.022 | 46.917 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 98 | LYS | 1 | 0.898 | 0.959 | 40.369 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 99 | NME | 0 | -0.025 | -0.002 | 45.798 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |