![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VR751
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 | OptH |
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 | -507599.490814 |
---|---|
FMO2-HF: Nuclear repulsion | 469838.579294 |
FMO2-HF: Total energy | -37760.911519 |
FMO2-MP2: Total energy | -37872.42493 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022869/ligand_interaction/ligand_F022869.png)
Ligand Interaction
![ligand interaction](./Kdata/F022869/ligand_interaction/ligand_interaction_F022869.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. |
1.018 | 2.643 | -0.021 | -0.727 | -0.877 | -0.001 |
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 | 0.000 | 0.005 | 3.871 | -0.204 | 1.421 | -0.021 | -0.727 | -0.877 | -0.001 |
4 | A | 8 | ALA | 0 | 0.034 | 0.021 | 6.554 | 1.547 | 1.547 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | ILE | 0 | -0.036 | -0.019 | 9.225 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | ASP | -1 | -0.922 | -0.955 | 12.756 | -15.099 | -15.099 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | SER | 0 | -0.028 | -0.017 | 15.124 | 1.014 | 1.014 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | TYR | 0 | -0.052 | -0.027 | 17.530 | -0.814 | -0.814 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLN | 0 | -0.027 | -0.010 | 19.572 | 0.667 | 0.667 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | GLU | -1 | -0.872 | -0.941 | 23.067 | -11.901 | -11.901 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | ASP | -1 | -0.955 | -0.957 | 25.082 | -9.592 | -9.592 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | PRO | 0 | -0.099 | -0.067 | 27.057 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | SER | 0 | 0.044 | 0.027 | 25.241 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | VAL | 0 | -0.019 | -0.007 | 23.458 | 0.294 | 0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | VAL | 0 | 0.000 | -0.010 | 26.857 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | VAL | 0 | 0.004 | 0.014 | 23.223 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | SER | 0 | -0.021 | -0.008 | 26.564 | 0.265 | 0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | ASN | 0 | -0.022 | -0.021 | 28.334 | -0.417 | -0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | PHE | 0 | 0.020 | 0.018 | 29.873 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | PHE | 0 | 0.053 | 0.022 | 32.327 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LYS | 1 | 0.963 | 0.958 | 25.766 | 11.540 | 11.540 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | GLY | 0 | 0.033 | 0.014 | 30.171 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | VAL | 0 | -0.028 | 0.010 | 31.068 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | ARG | 1 | 0.928 | 0.953 | 30.566 | 9.319 | 9.319 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | 0.025 | 0.015 | 33.827 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | PRO | 0 | 0.013 | 0.015 | 35.191 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | LYS | 1 | 0.950 | 0.960 | 33.487 | 8.850 | 8.850 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | ASP | -1 | -0.904 | -0.947 | 36.200 | -7.693 | -7.693 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | THR | 0 | -0.036 | -0.015 | 37.351 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | GLU | -1 | -0.939 | -0.951 | 37.415 | -7.484 | -7.484 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | PHE | 0 | -0.048 | -0.030 | 35.233 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | GLN | 0 | 0.015 | 0.006 | 37.520 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | LEU | 0 | -0.007 | 0.004 | 31.907 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | TYR | 0 | 0.012 | -0.002 | 36.101 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LYS | 1 | 0.986 | 0.998 | 34.817 | 8.073 | 8.073 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | LYS | 1 | 0.990 | 0.991 | 36.809 | 7.912 | 7.912 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | ARG | 1 | 0.924 | 0.956 | 38.152 | 6.737 | 6.737 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | LYS | 1 | 0.909 | 0.957 | 33.792 | 8.647 | 8.647 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | GLN | 0 | -0.018 | -0.016 | 39.494 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.868 | -0.927 | 35.137 | -8.550 | -8.550 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | GLN | 0 | 0.013 | 0.001 | 36.969 | 0.358 | 0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | PHE | 0 | 0.007 | -0.011 | 36.399 | -0.194 | -0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | VAL | 0 | 0.052 | 0.024 | 36.178 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | LEU | 0 | -0.050 | -0.019 | 37.430 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | HIS | 1 | 0.838 | 0.896 | 36.866 | 7.671 | 7.671 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | GLY | 0 | -0.012 | -0.011 | 38.837 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | GLU | -1 | -0.839 | -0.930 | 38.281 | -7.516 | -7.516 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | ASN | 0 | 0.001 | -0.004 | 41.653 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | GLU | -1 | -0.860 | -0.932 | 41.593 | -7.041 | -7.041 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | ARG | 1 | 0.909 | 0.964 | 44.797 | 5.769 | 5.769 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | LEU | 0 | -0.068 | -0.036 | 46.388 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | GLU | -1 | -0.858 | -0.921 | 40.393 | -7.387 | -7.387 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | TYR | 0 | -0.056 | -0.032 | 42.670 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | ASP | -1 | -0.800 | -0.875 | 39.749 | -7.526 | -7.526 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | GLY | 0 | 0.030 | 0.007 | 41.644 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | GLU | -1 | -0.946 | -0.951 | 40.944 | -7.403 | -7.403 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | THR | 0 | -0.019 | -0.002 | 41.231 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASP | -1 | -0.832 | -0.917 | 43.269 | -6.485 | -6.485 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.849 | -0.917 | 41.071 | -7.233 | -7.233 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | LEU | 0 | 0.013 | 0.003 | 43.532 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | THR | 0 | 0.016 | 0.003 | 46.696 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | THR | 0 | -0.011 | 0.008 | 41.028 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | LYS | 1 | 0.794 | 0.875 | 41.545 | 7.152 | 7.152 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | THR | 0 | -0.051 | -0.009 | 45.135 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | ASN | 0 | -0.062 | -0.047 | 48.064 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLN | 0 | 0.006 | 0.006 | 46.300 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | TYR | 0 | 0.050 | 0.026 | 46.876 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | MET | 0 | -0.048 | -0.021 | 45.824 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | VAL | 0 | 0.025 | 0.020 | 47.973 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | GLY | 0 | 0.017 | -0.005 | 49.304 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | -0.020 | 0.002 | 49.915 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | TYR | 0 | 0.007 | -0.013 | 53.321 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | ASP | -1 | -0.865 | -0.924 | 56.642 | -5.134 | -5.134 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | LYS | 1 | 0.938 | 0.943 | 58.811 | 4.846 | 4.846 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 79 | GLN | 0 | 0.001 | 0.012 | 62.377 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | SER | 0 | -0.027 | -0.013 | 58.749 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | GLY | 0 | 0.033 | 0.026 | 60.777 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LYS | 1 | 0.924 | 0.967 | 55.374 | 5.380 | 5.380 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 83 | ILE | 0 | -0.001 | -0.010 | 53.095 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | ASN | 0 | -0.023 | 0.007 | 49.185 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | LEU | 0 | -0.010 | -0.016 | 48.594 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | 0.030 | 0.020 | 43.974 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | ARG | 1 | 0.921 | 0.960 | 40.851 | 7.234 | 7.234 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | ALA | 0 | 0.001 | -0.005 | 43.209 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 89 | PRO | 0 | -0.007 | 0.015 | 40.542 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 90 | VAL | 0 | -0.007 | -0.010 | 43.535 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 91 | VAL | 0 | -0.016 | -0.002 | 42.032 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 92 | THR | 0 | -0.036 | -0.013 | 45.228 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 93 | SER | 0 | 0.028 | -0.012 | 45.532 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 94 | LYS | 1 | 0.935 | 0.973 | 45.383 | 6.696 | 6.696 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 95 | ILE | 0 | -0.011 | -0.006 | 46.254 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 96 | VAL | 0 | 0.011 | 0.008 | 45.374 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 97 | SER | 0 | -0.014 | -0.006 | 46.568 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 98 | LYS | 1 | 0.841 | 0.931 | 40.469 | 7.021 | 7.021 | 0.000 | 0.000 | 0.000 | 0.000 |