![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 3Q1NL
Calculation Name: 3NFG-H-Xray372
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: 2023-06-20
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 | OptAll |
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 | 120 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -848132.566014 |
---|---|
FMO2-HF: Nuclear repulsion | 801530.464173 |
FMO2-HF: Total energy | -46602.101842 |
FMO2-MP2: Total energy | -46739.128949 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022023/ligand_interaction/ligand_F022023.png)
Ligand Interaction
![ligand interaction](./Kdata/F022023/ligand_interaction/ligand_interaction_F022023.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:24:GLY)
Summations of interaction energy for
fragment #1(H:24:GLY)
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. |
-0.567 | 1.057 | -0.002 | -0.831 | -0.79 | 0.004 |
Interaction energy analysis for fragmet #1(H:24:GLY)
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 | 26 | GLN | 0 | 0.008 | -0.002 | 3.856 | -0.143 | 1.481 | -0.002 | -0.831 | -0.790 | 0.004 |
4 | H | 27 | PRO | 0 | -0.033 | -0.002 | 6.689 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | H | 28 | PRO | 0 | 0.030 | 0.005 | 10.359 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | H | 29 | SER | 0 | -0.021 | -0.019 | 13.413 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | H | 30 | ASP | -1 | -0.876 | -0.926 | 15.110 | -0.528 | -0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | H | 31 | TYR | 0 | -0.031 | -0.002 | 14.352 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | H | 32 | LYS | 1 | 0.968 | 0.972 | 14.183 | 0.240 | 0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | H | 33 | GLN | 0 | -0.002 | 0.000 | 11.889 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | H | 34 | CYS | 0 | 0.035 | 0.016 | 14.141 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | H | 35 | LYS | 1 | 0.804 | 0.862 | 11.912 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | H | 36 | HIS | 0 | -0.041 | -0.015 | 17.143 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | H | 37 | LEU | 0 | 0.025 | 0.027 | 17.942 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | H | 38 | LYS | 1 | 0.883 | 0.929 | 21.787 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | H | 39 | SER | 0 | 0.024 | 0.018 | 25.349 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | H | 40 | PHE | 0 | 0.073 | 0.023 | 26.888 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | H | 41 | PRO | 0 | 0.061 | 0.042 | 28.573 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | H | 42 | VAL | 0 | -0.022 | -0.029 | 26.280 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | H | 43 | SER | 0 | -0.026 | -0.021 | 29.554 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | H | 44 | GLU | -1 | -0.790 | -0.897 | 32.884 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | H | 45 | LEU | 0 | -0.049 | -0.015 | 28.921 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | H | 46 | LYS | 1 | 0.799 | 0.902 | 29.067 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | H | 47 | GLY | 0 | 0.038 | 0.020 | 34.760 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | H | 48 | ASP | -1 | -0.898 | -0.944 | 38.511 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | H | 49 | ASN | 0 | -0.046 | -0.018 | 41.044 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | H | 50 | LYS | 1 | 0.785 | 0.890 | 37.232 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | H | 51 | GLU | -1 | -0.720 | -0.813 | 37.774 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | H | 52 | LEU | 0 | -0.117 | -0.056 | 29.791 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | H | 53 | TRP | 0 | -0.002 | -0.027 | 34.402 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | H | 54 | LEU | 0 | -0.035 | -0.012 | 29.991 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | H | 55 | MET | 0 | -0.013 | -0.008 | 33.423 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | H | 56 | LYS | 1 | 0.957 | 0.998 | 33.624 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | H | 57 | VAL | 0 | 0.030 | 0.001 | 34.753 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | H | 58 | PRO | 0 | -0.020 | -0.006 | 35.709 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | H | 59 | ALA | 0 | 0.018 | 0.004 | 34.081 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | H | 60 | ASN | 0 | -0.080 | -0.041 | 35.836 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | H | 61 | ILE | 0 | -0.019 | -0.002 | 38.460 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | H | 62 | ASP | -1 | -0.788 | -0.855 | 37.945 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | H | 63 | ILE | 0 | 0.028 | -0.009 | 35.914 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | H | 64 | SER | 0 | -0.071 | -0.043 | 37.183 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | H | 65 | GLN | 0 | -0.006 | -0.023 | 38.984 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | H | 66 | LEU | 0 | -0.030 | 0.006 | 40.656 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | H | 67 | LYS | 1 | 0.825 | 0.894 | 42.674 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | H | 68 | SER | 0 | -0.011 | 0.001 | 44.882 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | H | 69 | LEU | 0 | 0.038 | 0.007 | 39.945 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | H | 70 | PRO | 0 | -0.026 | 0.002 | 44.668 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | H | 71 | LEU | 0 | -0.017 | -0.015 | 41.456 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | H | 72 | ASP | -1 | -0.835 | -0.910 | 45.930 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | H | 73 | THR | 0 | -0.003 | -0.016 | 44.630 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | H | 74 | ASP | -1 | -0.896 | -0.930 | 45.498 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | H | 75 | ALA | 0 | -0.059 | -0.023 | 48.039 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | H | 76 | THR | 0 | 0.000 | -0.007 | 44.526 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | H | 77 | VAL | 0 | -0.022 | -0.017 | 44.913 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | H | 78 | SER | 0 | 0.013 | 0.009 | 46.981 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | H | 79 | THR | 0 | -0.005 | -0.009 | 47.867 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | H | 80 | VAL | 0 | -0.020 | -0.006 | 44.276 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | H | 81 | GLU | -1 | -0.863 | -0.924 | 47.683 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | H | 82 | LEU | 0 | 0.004 | 0.012 | 42.632 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | H | 83 | GLY | 0 | 0.021 | -0.002 | 46.749 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | H | 84 | SER | 0 | -0.051 | -0.033 | 47.645 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | H | 85 | LYS | 1 | 0.937 | 0.977 | 44.814 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | H | 86 | ASN | 0 | -0.021 | -0.011 | 48.047 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | H | 87 | PHE | 0 | -0.016 | -0.007 | 43.397 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | H | 88 | ASN | 0 | 0.030 | 0.006 | 45.466 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | H | 89 | VAL | 0 | 0.008 | -0.003 | 42.651 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | H | 90 | LEU | 0 | 0.021 | 0.020 | 40.569 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | H | 91 | GLN | 0 | 0.009 | -0.002 | 40.717 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | H | 92 | ASN | 0 | 0.044 | 0.013 | 37.283 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | H | 93 | THR | 0 | 0.067 | 0.054 | 36.772 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | H | 94 | SER | 0 | -0.018 | 0.001 | 39.215 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | H | 95 | THR | 0 | -0.067 | -0.035 | 40.610 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | H | 96 | GLN | 0 | 0.003 | -0.006 | 41.338 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | H | 97 | GLU | -1 | -0.960 | -0.982 | 39.480 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | H | 98 | GLY | 0 | -0.013 | -0.003 | 36.434 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | H | 99 | SER | 0 | 0.009 | 0.016 | 37.083 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | H | 100 | ASP | -1 | -0.846 | -0.903 | 32.919 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | H | 101 | ASN | 0 | -0.031 | -0.036 | 31.829 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | H | 102 | THR | 0 | -0.049 | -0.049 | 29.409 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | H | 103 | ASN | 0 | -0.040 | -0.013 | 26.519 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | H | 104 | LEU | 0 | -0.057 | -0.017 | 25.594 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | H | 105 | SER | 0 | 0.018 | 0.002 | 22.982 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | H | 106 | LEU | 0 | 0.030 | 0.031 | 23.803 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | H | 107 | LEU | 0 | -0.018 | -0.014 | 17.844 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | H | 108 | ILE | 0 | 0.010 | 0.007 | 21.673 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | H | 109 | PRO | 0 | 0.020 | 0.006 | 20.150 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | H | 110 | SER | 0 | -0.044 | -0.023 | 17.930 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | H | 111 | GLU | -1 | -0.785 | -0.890 | 20.466 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | H | 112 | LYS | 1 | 0.962 | 0.973 | 19.939 | -0.177 | -0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | H | 113 | LYS | 1 | 0.967 | 0.989 | 13.534 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | H | 114 | LYS | 1 | 0.874 | 0.942 | 17.679 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | H | 115 | GLU | -1 | -0.818 | -0.881 | 12.807 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | H | 116 | THR | 0 | -0.043 | -0.026 | 12.927 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | H | 117 | LEU | 0 | 0.026 | 0.005 | 15.517 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | H | 118 | LYS | 1 | 0.842 | 0.928 | 16.418 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | H | 119 | VAL | 0 | 0.102 | 0.053 | 18.872 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | H | 120 | ALA | 0 | 0.019 | 0.023 | 21.479 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | H | 121 | THR | 0 | 0.004 | 0.000 | 23.841 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | H | 122 | SER | 0 | 0.005 | -0.010 | 26.448 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | H | 123 | LYS | 1 | 0.939 | 0.956 | 28.400 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | H | 124 | ASP | -1 | -0.790 | -0.867 | 30.059 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | H | 125 | ASN | 0 | -0.029 | -0.019 | 25.000 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | H | 126 | LYS | 1 | 0.899 | 0.935 | 27.450 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | H | 127 | SER | 0 | -0.018 | -0.009 | 25.767 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | H | 128 | VAL | 0 | -0.053 | -0.027 | 27.551 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | H | 129 | TYR | 0 | -0.006 | 0.002 | 28.341 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | H | 130 | PHE | 0 | 0.003 | -0.022 | 27.691 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | H | 131 | ASP | -1 | -0.798 | -0.884 | 32.732 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | H | 132 | ARG | 1 | 0.801 | 0.885 | 36.078 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | H | 133 | VAL | 0 | -0.009 | -0.012 | 33.692 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | H | 134 | PHE | 0 | 0.002 | 0.006 | 36.298 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | H | 135 | THR | 0 | -0.047 | -0.036 | 36.785 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | H | 136 | ILE | 0 | -0.001 | 0.009 | 38.534 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | H | 137 | SER | 0 | -0.023 | -0.029 | 39.410 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | H | 138 | GLU | -1 | -0.815 | -0.897 | 41.649 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | H | 139 | THR | 0 | 0.025 | 0.032 | 43.747 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | H | 140 | ALA | 0 | -0.010 | -0.004 | 47.198 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | H | 141 | ARG | 1 | 0.826 | 0.885 | 45.186 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | H | 142 | ILE | 0 | 0.017 | 0.011 | 48.252 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | H | 143 | PRO | 0 | -0.012 | 0.006 | 45.779 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |