![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 14Z7Z
Calculation Name: 3NFG-A-Xray372
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: 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 | 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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -508989.163749 |
---|---|
FMO2-HF: Nuclear repulsion | 471227.591026 |
FMO2-HF: Total energy | -37761.572723 |
FMO2-MP2: Total energy | -37873.115644 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022868/ligand_interaction/ligand_F022868.png)
Ligand Interaction
![ligand interaction](./Kdata/F022868/ligand_interaction/ligand_interaction_F022868.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:5:ARG)
Summations of interaction energy for
fragment #1(A:5:ARG)
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. |
0.632 | 2.68 | -0.022 | -1 | -1.027 | 0.002 |
Interaction energy analysis for fragmet #1(A:5:ARG)
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 | 7 | ILE | 0 | -0.008 | 0.005 | 3.871 | -0.538 | 1.510 | -0.022 | -1.000 | -1.027 | 0.002 |
4 | A | 8 | ALA | 0 | 0.025 | 0.017 | 6.593 | 1.517 | 1.517 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | ILE | 0 | -0.027 | -0.015 | 9.265 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | ASP | -1 | -0.894 | -0.934 | 12.797 | -15.142 | -15.142 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | SER | 0 | -0.030 | -0.030 | 15.161 | 0.953 | 0.953 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | TYR | 0 | -0.106 | -0.076 | 17.473 | -0.890 | -0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLN | 0 | -0.020 | -0.004 | 19.507 | 0.552 | 0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | GLU | -1 | -0.862 | -0.904 | 22.765 | -12.139 | -12.139 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | ASP | -1 | -0.927 | -0.952 | 24.670 | -9.615 | -9.615 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | PRO | 0 | -0.110 | -0.074 | 26.664 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | SER | 0 | 0.034 | 0.019 | 25.243 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | VAL | 0 | -0.017 | 0.001 | 23.079 | 0.308 | 0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | VAL | 0 | -0.001 | -0.010 | 26.519 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | VAL | 0 | 0.004 | 0.014 | 22.766 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | SER | 0 | -0.025 | -0.014 | 26.103 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | ASN | 0 | -0.011 | -0.017 | 27.782 | -0.493 | -0.493 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | PHE | 0 | 0.016 | 0.018 | 29.357 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | PHE | 0 | 0.050 | 0.024 | 31.762 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LYS | 1 | 0.967 | 0.963 | 25.777 | 11.579 | 11.579 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | GLY | 0 | 0.034 | 0.012 | 29.664 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | VAL | 0 | -0.021 | 0.013 | 30.517 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | ARG | 1 | 0.908 | 0.946 | 30.174 | 9.419 | 9.419 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | 0.033 | 0.019 | 33.425 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | PRO | 0 | 0.011 | 0.015 | 34.873 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | LYS | 1 | 0.948 | 0.968 | 33.867 | 8.815 | 8.815 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | ASP | -1 | -0.895 | -0.946 | 36.057 | -7.801 | -7.801 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | THR | 0 | -0.046 | -0.029 | 37.045 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | GLU | -1 | -0.934 | -0.946 | 37.177 | -7.563 | -7.563 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | PHE | 0 | -0.050 | -0.035 | 35.187 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | GLN | 0 | 0.014 | 0.006 | 37.201 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | LEU | 0 | -0.007 | 0.005 | 31.571 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | TYR | 0 | 0.013 | -0.001 | 35.666 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LYS | 1 | 0.986 | 0.994 | 33.865 | 8.407 | 8.407 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | LYS | 1 | 0.988 | 0.992 | 36.219 | 8.017 | 8.017 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | ARG | 1 | 0.924 | 0.957 | 37.559 | 6.831 | 6.831 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | LYS | 1 | 0.859 | 0.916 | 33.230 | 8.855 | 8.855 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | GLN | 0 | -0.043 | -0.026 | 39.063 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.821 | -0.888 | 35.027 | -8.653 | -8.653 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | GLN | 0 | 0.031 | 0.012 | 36.874 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | PHE | 0 | -0.002 | -0.018 | 36.376 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | VAL | 0 | 0.040 | 0.016 | 35.973 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | LEU | 0 | -0.049 | -0.018 | 37.216 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | HIS | 1 | 0.837 | 0.880 | 36.626 | 7.785 | 7.785 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | GLY | 0 | -0.016 | -0.011 | 38.482 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | GLU | -1 | -0.793 | -0.887 | 37.741 | -7.695 | -7.695 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | ASN | 0 | -0.016 | -0.007 | 41.268 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | GLU | -1 | -0.807 | -0.896 | 41.324 | -7.126 | -7.126 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | ARG | 1 | 0.890 | 0.952 | 44.372 | 5.847 | 5.847 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | LEU | 0 | -0.061 | -0.036 | 45.998 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | GLU | -1 | -0.829 | -0.916 | 40.171 | -7.460 | -7.460 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | TYR | 0 | -0.046 | -0.030 | 42.419 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | ASP | -1 | -0.801 | -0.877 | 39.540 | -7.689 | -7.689 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | GLY | 0 | 0.018 | 0.002 | 41.502 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | GLU | -1 | -0.877 | -0.912 | 40.949 | -7.380 | -7.380 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | THR | 0 | 0.012 | 0.014 | 41.192 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASP | -1 | -0.770 | -0.865 | 43.269 | -6.585 | -6.585 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.811 | -0.882 | 41.315 | -7.325 | -7.325 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | LEU | 0 | 0.037 | 0.014 | 43.615 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | THR | 0 | -0.006 | -0.044 | 46.711 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | THR | 0 | -0.073 | -0.024 | 40.789 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | LYS | 1 | 0.756 | 0.853 | 41.886 | 7.206 | 7.206 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | THR | 0 | -0.049 | -0.004 | 44.948 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | ASN | 0 | -0.057 | -0.042 | 47.867 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLN | 0 | 0.024 | 0.014 | 45.640 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | TYR | 0 | 0.059 | 0.033 | 46.699 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | MET | 0 | -0.044 | -0.020 | 45.773 | -0.184 | -0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | VAL | 0 | 0.028 | 0.022 | 47.951 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | GLY | 0 | 0.020 | -0.005 | 49.347 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | -0.022 | 0.002 | 49.916 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | TYR | 0 | 0.006 | -0.013 | 53.364 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | ASP | -1 | -0.802 | -0.862 | 56.684 | -5.159 | -5.159 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | LYS | 1 | 0.944 | 0.945 | 58.853 | 4.906 | 4.906 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 79 | GLN | 0 | -0.009 | 0.011 | 62.396 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | SER | 0 | -0.063 | -0.065 | 58.754 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | GLY | 0 | 0.004 | 0.007 | 60.819 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LYS | 1 | 0.932 | 0.975 | 55.416 | 5.396 | 5.396 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 83 | ILE | 0 | 0.002 | -0.012 | 53.052 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | ASN | 0 | -0.034 | 0.003 | 49.268 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | LEU | 0 | -0.004 | -0.012 | 48.550 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | 0.034 | 0.018 | 44.125 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | ARG | 1 | 0.889 | 0.937 | 40.408 | 7.366 | 7.366 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | ALA | 0 | 0.000 | 0.000 | 43.252 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 89 | PRO | 0 | -0.002 | 0.017 | 40.598 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 90 | VAL | 0 | -0.011 | -0.008 | 43.535 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 91 | VAL | 0 | -0.015 | -0.003 | 41.896 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 92 | THR | 0 | -0.032 | -0.005 | 45.137 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 93 | SER | 0 | 0.017 | -0.020 | 45.534 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 94 | LYS | 1 | 0.849 | 0.923 | 44.027 | 7.000 | 7.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 95 | ILE | 0 | -0.012 | -0.005 | 46.100 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 96 | VAL | 0 | 0.009 | 0.007 | 45.349 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 97 | SER | 0 | -0.020 | -0.010 | 46.393 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 98 | LYS | 1 | 0.776 | 0.892 | 39.899 | 7.165 | 7.165 | 0.000 | 0.000 | 0.000 | 0.000 |