![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: LJMZ9
Calculation Name: 3NFG-H-Xray317
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3NFG
Chain ID: H
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 | 121 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -846711.433391 |
---|---|
FMO2-HF: Nuclear repulsion | 799959.365517 |
FMO2-HF: Total energy | -46752.067875 |
FMO2-MP2: Total energy | -46889.448978 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016071/ligand_interaction/ligand_F016071.png)
Ligand Interaction
![ligand interaction](./Kdata/F016071/ligand_interaction/ligand_interaction_F016071.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(H:23:ACE )
Summations of interaction energy for
fragment #1(H:23: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. |
1.446 | 2.396 | -0.007 | -0.461 | -0.482 | 0 |
Interaction energy analysis for fragmet #1(H:23: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 | H | 25 | TYR | 0 | -0.018 | -0.003 | 3.812 | 0.834 | 1.784 | -0.007 | -0.461 | -0.482 | 0.000 |
4 | H | 26 | GLN | 0 | 0.018 | 0.004 | 7.097 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | H | 27 | PRO | 0 | -0.038 | -0.004 | 9.574 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | H | 28 | PRO | 0 | 0.016 | 0.014 | 13.322 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | H | 29 | SER | 0 | 0.004 | -0.002 | 15.923 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | H | 30 | ASP | -1 | -0.899 | -0.947 | 17.013 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | H | 31 | TYR | 0 | -0.022 | -0.001 | 17.423 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | H | 32 | LYS | 1 | 0.963 | 0.975 | 17.482 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | H | 33 | GLN | 0 | -0.044 | -0.029 | 15.463 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | H | 34 | CYS | 0 | 0.003 | 0.007 | 18.344 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | H | 35 | LYS | 1 | 0.998 | 0.982 | 16.929 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | H | 36 | HIS | 0 | -0.054 | -0.023 | 21.691 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | H | 37 | LEU | 0 | 0.014 | 0.019 | 22.029 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | H | 38 | LYS | 1 | 0.914 | 0.952 | 25.990 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | H | 39 | SER | 0 | 0.005 | 0.001 | 29.113 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | H | 40 | PHE | 0 | 0.066 | 0.027 | 30.519 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | H | 41 | PRO | 0 | 0.033 | 0.026 | 32.247 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | H | 42 | VAL | 0 | 0.008 | -0.010 | 30.060 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | H | 43 | SER | 0 | -0.054 | -0.043 | 33.147 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | H | 44 | GLU | -1 | -0.899 | -0.952 | 36.356 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | H | 45 | LEU | 0 | -0.018 | 0.004 | 32.502 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | H | 46 | LYS | 1 | 0.819 | 0.914 | 32.317 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | H | 47 | GLY | 0 | 0.033 | 0.010 | 37.974 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | H | 48 | ASP | -1 | -0.921 | -0.950 | 41.714 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | H | 49 | ASN | 0 | -0.027 | -0.020 | 44.232 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | H | 50 | LYS | 1 | 0.886 | 0.958 | 40.712 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | H | 51 | GLU | -1 | -0.717 | -0.837 | 41.389 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | H | 52 | LEU | 0 | -0.113 | -0.044 | 33.389 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | H | 53 | TRP | 0 | 0.007 | -0.025 | 38.053 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | H | 54 | LEU | 0 | -0.029 | -0.009 | 33.024 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | H | 55 | MET | 0 | -0.009 | 0.004 | 36.493 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | H | 56 | LYS | 1 | 0.951 | 0.993 | 35.679 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | H | 57 | VAL | 0 | 0.031 | 0.004 | 37.616 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | H | 58 | PRO | 0 | -0.021 | -0.003 | 38.580 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | H | 59 | ALA | 0 | 0.017 | -0.003 | 36.930 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | H | 60 | ASN | 0 | -0.086 | -0.052 | 38.713 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | H | 61 | ILE | 0 | -0.007 | 0.010 | 41.797 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | H | 62 | ASP | -1 | -0.818 | -0.889 | 41.399 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | H | 63 | ILE | 0 | 0.020 | -0.014 | 39.837 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | H | 64 | SER | 0 | -0.073 | -0.047 | 41.072 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | H | 65 | GLN | 0 | -0.051 | -0.025 | 42.848 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | H | 66 | LEU | 0 | -0.041 | -0.003 | 44.605 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | H | 67 | LYS | 1 | 0.918 | 0.955 | 46.490 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | H | 68 | SER | 0 | -0.016 | -0.015 | 48.778 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | H | 69 | LEU | 0 | 0.043 | 0.023 | 43.378 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | H | 70 | PRO | 0 | -0.020 | -0.002 | 48.079 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | H | 71 | LEU | 0 | -0.008 | -0.012 | 44.607 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | H | 72 | ASP | -1 | -0.873 | -0.938 | 49.301 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | H | 73 | THR | 0 | -0.028 | -0.033 | 48.121 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | H | 74 | ASP | -1 | -0.908 | -0.939 | 48.805 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | H | 75 | ALA | 0 | -0.035 | -0.002 | 51.164 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | H | 76 | THR | 0 | -0.037 | -0.018 | 47.290 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | H | 77 | VAL | 0 | 0.012 | -0.005 | 47.845 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | H | 78 | SER | 0 | 0.012 | 0.007 | 49.987 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | H | 79 | THR | 0 | -0.050 | -0.031 | 51.014 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | H | 80 | VAL | 0 | 0.018 | 0.012 | 47.800 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | H | 81 | GLU | -1 | -0.951 | -0.978 | 51.030 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | H | 82 | LEU | 0 | -0.009 | 0.011 | 46.071 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | H | 83 | GLY | 0 | -0.013 | -0.010 | 50.225 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | H | 84 | SER | 0 | -0.040 | -0.024 | 50.977 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | H | 85 | LYS | 1 | 0.992 | 0.990 | 49.120 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | H | 86 | ASN | 0 | 0.041 | 0.017 | 51.438 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | H | 87 | PHE | 0 | -0.025 | -0.007 | 46.516 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | H | 88 | ASN | 0 | 0.011 | 0.000 | 47.921 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | H | 89 | VAL | 0 | 0.017 | 0.004 | 45.617 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | H | 90 | LEU | 0 | 0.020 | 0.012 | 43.017 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | H | 91 | GLN | 0 | 0.003 | 0.010 | 43.461 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | H | 92 | ASN | 0 | 0.019 | -0.012 | 39.886 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | H | 93 | THR | 0 | 0.051 | 0.028 | 39.542 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | H | 94 | SER | 0 | -0.013 | 0.020 | 42.064 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | H | 95 | THR | 0 | -0.024 | -0.016 | 43.829 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | H | 96 | GLN | 0 | -0.003 | -0.018 | 44.144 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | H | 97 | GLU | -1 | -0.977 | -0.978 | 41.439 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | H | 98 | GLY | 0 | -0.004 | -0.008 | 38.960 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | H | 99 | SER | 0 | 0.014 | 0.018 | 39.621 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | H | 100 | ASP | -1 | -0.876 | -0.916 | 34.888 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | H | 101 | ASN | 0 | -0.024 | -0.029 | 34.167 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | H | 102 | THR | 0 | -0.062 | -0.044 | 31.965 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | H | 103 | ASN | 0 | 0.000 | 0.005 | 28.817 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | H | 104 | LEU | 0 | -0.060 | -0.023 | 27.712 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | H | 105 | SER | 0 | 0.041 | 0.018 | 25.409 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | H | 106 | LEU | 0 | 0.020 | 0.018 | 26.684 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | H | 107 | LEU | 0 | -0.021 | -0.016 | 21.148 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | H | 108 | ILE | 0 | 0.018 | 0.007 | 24.993 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | H | 109 | PRO | 0 | 0.029 | 0.011 | 23.766 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | H | 110 | SER | 0 | -0.058 | -0.021 | 22.166 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | H | 111 | GLU | -1 | -0.873 | -0.971 | 24.222 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | H | 112 | LYS | 1 | 0.878 | 0.949 | 21.919 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | H | 113 | LYS | 1 | 0.997 | 1.002 | 17.843 | 0.259 | 0.259 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | H | 114 | LYS | 1 | 0.998 | 1.008 | 21.382 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | H | 115 | GLU | -1 | -0.902 | -0.954 | 16.189 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | H | 116 | THR | 0 | -0.039 | -0.015 | 16.254 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | H | 117 | LEU | 0 | 0.027 | 0.001 | 19.016 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | H | 118 | LYS | 1 | 0.916 | 0.960 | 19.803 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | H | 119 | VAL | 0 | 0.065 | 0.035 | 22.179 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | H | 120 | ALA | 0 | -0.012 | 0.008 | 24.684 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | H | 121 | THR | 0 | 0.021 | 0.016 | 26.481 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | H | 122 | SER | 0 | -0.033 | -0.032 | 29.147 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | H | 123 | LYS | 1 | 0.931 | 0.947 | 31.242 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | H | 124 | ASP | -1 | -0.853 | -0.909 | 32.170 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | H | 125 | ASN | 0 | -0.046 | -0.028 | 27.244 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | H | 126 | LYS | 1 | 0.965 | 0.988 | 29.961 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | H | 127 | SER | 0 | -0.002 | -0.014 | 28.174 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | H | 128 | VAL | 0 | -0.029 | -0.016 | 30.391 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | H | 129 | TYR | 0 | 0.027 | 0.029 | 31.509 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | H | 130 | PHE | 0 | -0.034 | -0.026 | 31.402 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | H | 131 | ASP | -1 | -0.828 | -0.901 | 36.022 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | H | 132 | ARG | 1 | 0.809 | 0.902 | 39.647 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | H | 133 | VAL | 0 | -0.022 | -0.022 | 36.919 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | H | 134 | PHE | 0 | 0.008 | -0.005 | 39.365 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | H | 135 | THR | 0 | -0.033 | -0.026 | 39.260 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | H | 136 | ILE | 0 | -0.018 | 0.004 | 41.443 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | H | 137 | SER | 0 | 0.021 | -0.007 | 42.443 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | H | 138 | GLU | -1 | -0.874 | -0.935 | 44.446 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | H | 139 | THR | 0 | 0.011 | 0.008 | 46.818 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | H | 140 | ALA | 0 | 0.010 | -0.002 | 49.658 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | H | 141 | ARG | 1 | 0.886 | 0.947 | 48.295 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | H | 142 | ILE | 0 | -0.040 | -0.015 | 50.319 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | H | 143 | PRO | -1 | -0.930 | -0.952 | 48.218 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |