![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2294R
Calculation Name: 3FB9-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FB9
Chain ID: A
UniProt ID: A0A0H2
Base Structure: X-ray
Registration Date: 2023-06-19
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 | 89 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -626393.644193 |
---|---|
FMO2-HF: Nuclear repulsion | 590359.35983 |
FMO2-HF: Total energy | -36034.284363 |
FMO2-MP2: Total energy | -36139.266987 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020918/ligand_interaction/ligand_F020918.png)
Ligand Interaction
![ligand interaction](./Kdata/F020918/ligand_interaction/ligand_interaction_F020918.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:0:GLY)
Summations of interaction energy for
fragment #1(A:0: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. |
-0.587 | 0.029 | 0 | -0.276 | -0.34 | 0.001 |
Interaction energy analysis for fragmet #1(A:0: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 | A | 2 | SER | 0 | 0.056 | 0.020 | 3.852 | -0.759 | -0.143 | 0.000 | -0.276 | -0.340 | 0.001 |
4 | A | 3 | ASP | -1 | -0.878 | -0.950 | 6.397 | -0.705 | -0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | ALA | 0 | -0.007 | -0.005 | 9.038 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | PHE | 0 | -0.026 | -0.022 | 7.647 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | THR | 0 | -0.031 | -0.004 | 8.558 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | ASP | -1 | -0.830 | -0.925 | 10.327 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | VAL | 0 | -0.048 | -0.030 | 13.495 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | ALA | 0 | 0.010 | 0.017 | 12.775 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | LYS | 1 | 0.892 | 0.938 | 11.886 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | MET | 0 | 0.004 | 0.003 | 15.321 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | LYS | 1 | 0.792 | 0.889 | 18.250 | 0.253 | 0.253 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | LYS | 1 | 0.874 | 0.919 | 17.849 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | ILE | 0 | 0.046 | 0.031 | 17.675 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | LYS | 1 | 0.847 | 0.926 | 21.033 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | GLU | -1 | -0.871 | -0.920 | 22.067 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | GLU | -1 | -0.819 | -0.883 | 20.560 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | ILE | 0 | 0.006 | 0.000 | 24.684 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | LYS | 1 | 0.939 | 0.973 | 26.962 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ALA | 0 | -0.064 | -0.035 | 27.659 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | HIS | 0 | 0.011 | 0.011 | 28.388 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | GLU | -1 | -0.920 | -0.957 | 30.423 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | GLY | 0 | -0.038 | -0.020 | 33.159 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLN | 0 | -0.063 | -0.028 | 32.368 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | VAL | 0 | 0.020 | 0.007 | 32.488 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | VAL | 0 | -0.007 | -0.001 | 28.194 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | GLU | -1 | -0.841 | -0.904 | 27.669 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | MET | 0 | -0.050 | -0.027 | 25.949 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | THR | 0 | -0.024 | -0.020 | 24.345 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | LEU | 0 | -0.021 | -0.009 | 24.628 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLU | -1 | -0.815 | -0.885 | 18.619 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | ASN | 0 | 0.001 | -0.004 | 21.999 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLY | 0 | 0.002 | 0.016 | 21.472 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ARG | 1 | 0.952 | 0.962 | 20.381 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | LYS | 1 | 0.865 | 0.937 | 22.249 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | ARG | 1 | 0.883 | 0.936 | 18.979 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLN | 0 | 0.030 | 0.005 | 25.960 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | LYS | 1 | 0.913 | 0.948 | 29.026 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | -0.002 | -0.007 | 26.675 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | ARG | 1 | 0.763 | 0.868 | 29.656 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | LEU | 0 | 0.023 | 0.005 | 30.936 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLY | 0 | 0.009 | -0.006 | 32.675 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LYS | 1 | 0.939 | 0.989 | 33.463 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | LEU | 0 | -0.010 | -0.005 | 29.387 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ILE | 0 | -0.055 | -0.029 | 33.257 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | GLU | -1 | -0.837 | -0.894 | 34.712 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | VAL | 0 | 0.007 | 0.004 | 29.882 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | TYR | 0 | -0.036 | -0.030 | 31.592 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | PRO | 0 | -0.014 | -0.011 | 30.030 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | SER | 0 | -0.048 | -0.036 | 28.301 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | LEU | 0 | -0.020 | -0.010 | 28.146 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | PHE | 0 | 0.033 | 0.023 | 25.394 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ILE | 0 | 0.017 | 0.007 | 30.718 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | VAL | 0 | 0.008 | 0.008 | 30.318 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | GLU | -1 | -0.944 | -0.965 | 33.656 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | PHE | 0 | 0.032 | -0.014 | 30.747 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | GLY | 0 | 0.053 | 0.019 | 36.771 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.787 | -0.893 | 39.488 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | VAL | 0 | 0.007 | 0.032 | 35.753 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | GLU | -1 | -0.938 | -0.979 | 38.943 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | GLY | 0 | -0.017 | -0.012 | 38.645 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ASP | -1 | -0.851 | -0.926 | 35.345 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | LYS | 1 | 0.760 | 0.889 | 38.236 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | GLN | 0 | -0.086 | -0.055 | 38.217 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | VAL | 0 | -0.036 | -0.019 | 42.074 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | ASN | 0 | -0.042 | -0.018 | 40.941 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | VAL | 0 | 0.047 | 0.032 | 41.131 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | TYR | 0 | -0.067 | -0.018 | 35.223 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | VAL | 0 | 0.047 | 0.021 | 37.072 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | GLU | -1 | -0.823 | -0.881 | 31.310 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | SER | 0 | -0.014 | 0.000 | 32.322 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | PHE | 0 | -0.006 | -0.007 | 26.782 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | THR | 0 | -0.006 | -0.029 | 25.399 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | TYR | 0 | 0.044 | -0.016 | 22.729 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | SER | 0 | 0.010 | 0.000 | 20.828 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ASP | -1 | -0.788 | -0.833 | 20.544 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | ILE | 0 | 0.016 | 0.013 | 19.861 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | LEU | 0 | -0.019 | -0.009 | 15.328 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | THR | 0 | -0.079 | -0.064 | 15.976 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | GLU | -1 | -0.909 | -0.942 | 14.064 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | LYS | 1 | 0.897 | 0.953 | 18.361 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | ASN | 0 | -0.054 | -0.044 | 21.694 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | LEU | 0 | 0.005 | 0.005 | 18.847 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | ILE | 0 | -0.007 | -0.018 | 21.846 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | HIS | 0 | 0.005 | 0.009 | 22.397 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | TYR | 0 | -0.001 | -0.020 | 22.123 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | LEU | 0 | -0.048 | -0.008 | 26.986 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | ASP | -1 | -0.933 | -0.972 | 29.697 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |