![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 5345Z
Calculation Name: 3FX7-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FX7
Chain ID: A
UniProt ID: O24902
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 | 84 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -549109.232685 |
---|---|
FMO2-HF: Nuclear repulsion | 513332.430594 |
FMO2-HF: Total energy | -35776.802091 |
FMO2-MP2: Total energy | -35882.755179 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020951/ligand_interaction/ligand_F020951.png)
Ligand Interaction
![ligand interaction](./Kdata/F020951/ligand_interaction/ligand_interaction_F020951.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:GLN)
Summations of interaction energy for
fragment #1(A:5:GLN)
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. |
-5.559 | -2.942 | 0.093 | -1.038 | -1.671 | 0.004 |
Interaction energy analysis for fragmet #1(A:5:GLN)
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 | ASP | -1 | -0.815 | -0.890 | 3.782 | -2.924 | -1.262 | -0.003 | -0.709 | -0.949 | 0.002 |
4 | A | 8 | THR | 0 | -0.008 | -0.056 | 6.046 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | GLH | 0 | -0.062 | -0.053 | 8.102 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | GLU | -1 | -0.967 | -0.984 | 8.144 | -1.263 | -1.263 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | VAL | 0 | -0.011 | -0.021 | 7.954 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | ARG | 1 | 0.799 | 0.854 | 11.064 | -0.705 | -0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLU | -1 | -0.859 | -0.893 | 13.528 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | PHE | 0 | -0.038 | -0.010 | 13.220 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | VAL | 0 | -0.015 | -0.012 | 13.522 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | GLY | 0 | 0.031 | 0.021 | 16.222 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | HIS | 0 | -0.030 | -0.015 | 18.351 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | LEU | 0 | -0.006 | 0.000 | 17.276 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | GLU | -1 | -0.791 | -0.894 | 19.918 | 0.596 | 0.596 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | ARG | 1 | 0.869 | 0.932 | 22.205 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | PHE | 0 | -0.032 | -0.015 | 22.784 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | LYS | 1 | 0.824 | 0.900 | 21.855 | -0.505 | -0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | GLU | -1 | -0.918 | -0.947 | 25.884 | 0.271 | 0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | LEU | 0 | -0.022 | -0.014 | 27.995 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LEU | 0 | 0.000 | -0.001 | 26.978 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | ARG | 1 | 0.832 | 0.906 | 28.144 | -0.330 | -0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | GLU | -1 | -0.878 | -0.930 | 31.867 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | GLU | -1 | -0.899 | -0.962 | 33.097 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | -0.036 | -0.016 | 33.638 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | ASN | 0 | -0.021 | -0.014 | 35.627 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | SER | 0 | -0.030 | -0.001 | 37.772 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | LEU | 0 | 0.013 | 0.004 | 37.923 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | SER | 0 | 0.009 | -0.012 | 39.508 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | ASN | 0 | -0.031 | -0.017 | 41.325 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | HIS | 0 | -0.005 | 0.002 | 43.390 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | PHE | 0 | -0.027 | -0.014 | 43.910 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | HIS | 0 | -0.083 | -0.051 | 43.685 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | ASN | 0 | 0.025 | 0.020 | 47.367 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LEU | 0 | -0.033 | 0.009 | 48.620 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | GLU | -1 | -0.874 | -0.951 | 50.700 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | SER | 0 | -0.068 | -0.027 | 54.283 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | TRP | 0 | -0.055 | -0.020 | 46.647 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | ARG | 1 | 0.923 | 0.933 | 52.099 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.823 | -0.898 | 52.340 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | ALA | 0 | 0.075 | 0.026 | 52.258 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | ARG | 1 | 0.924 | 0.959 | 49.157 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | ARG | 1 | 0.915 | 0.980 | 47.814 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | ASP | -1 | -0.878 | -0.946 | 47.387 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | LYS | 1 | 0.772 | 0.869 | 43.840 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | PHE | 0 | 0.005 | -0.011 | 40.737 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | SER | 0 | 0.033 | 0.011 | 42.491 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | GLU | -1 | -0.795 | -0.869 | 42.235 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | VAL | 0 | -0.042 | -0.003 | 38.320 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | LEU | 0 | 0.000 | 0.002 | 37.864 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | ASP | -1 | -0.846 | -0.926 | 37.599 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | ASN | 0 | -0.026 | -0.026 | 35.875 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | LEU | 0 | -0.010 | 0.017 | 32.223 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | LYS | 1 | 0.874 | 0.934 | 32.656 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | SER | 0 | -0.041 | -0.020 | 32.827 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | THR | 0 | 0.035 | 0.005 | 28.666 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | PHE | 0 | -0.039 | -0.035 | 28.480 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASN | 0 | -0.023 | -0.008 | 27.996 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.910 | -0.947 | 27.160 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | PHE | 0 | -0.005 | -0.009 | 21.108 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | ASP | -1 | -0.799 | -0.869 | 23.286 | 0.447 | 0.447 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | GLU | -1 | -0.946 | -0.968 | 23.747 | 0.502 | 0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | ALA | 0 | 0.040 | 0.021 | 20.720 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | ALA | 0 | -0.020 | -0.026 | 19.209 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | GLN | 0 | 0.019 | 0.010 | 18.973 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLU | -1 | -0.919 | -0.953 | 18.707 | 0.851 | 0.851 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | GLN | 0 | -0.042 | -0.023 | 13.749 | 0.328 | 0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | ILE | 0 | -0.014 | -0.006 | 14.578 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | ALA | 0 | -0.032 | -0.014 | 15.675 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | TRP | 0 | 0.018 | 0.009 | 7.515 | 0.312 | 0.312 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | 0.016 | -0.008 | 9.818 | 0.370 | 0.370 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | LYS | 1 | 0.816 | 0.894 | 11.221 | -0.522 | -0.522 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | GLU | -1 | -0.835 | -0.902 | 13.056 | 1.214 | 1.214 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | ARG | 1 | 0.900 | 0.965 | 4.051 | -7.442 | -7.279 | 0.000 | -0.024 | -0.139 | 0.000 |
75 | A | 79 | ILE | 0 | 0.004 | -0.010 | 8.143 | 0.606 | 0.606 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | ARG | 1 | 0.825 | 0.909 | 9.539 | -1.246 | -1.246 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | VAL | 0 | 0.015 | 0.014 | 7.923 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LEU | 0 | -0.036 | -0.024 | 3.558 | 0.024 | 0.816 | 0.096 | -0.305 | -0.583 | 0.002 |
79 | A | 83 | GLU | -1 | -0.737 | -0.816 | 6.997 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | GLU | -1 | -0.950 | -0.982 | 9.255 | 0.892 | 0.892 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | ASP | -1 | -0.948 | -0.973 | 6.824 | 1.210 | 1.210 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | -0.064 | -0.030 | 5.732 | -0.608 | -0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | LEU | 0 | -0.090 | -0.046 | 8.558 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | GLU | -1 | -1.079 | -1.018 | 11.605 | 0.408 | 0.408 | 0.000 | 0.000 | 0.000 | 0.000 |