![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 435YN
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 | 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 | 84 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -548420.389139 |
---|---|
FMO2-HF: Nuclear repulsion | 512644.134293 |
FMO2-HF: Total energy | -35776.254845 |
FMO2-MP2: Total energy | -35882.195431 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020952/ligand_interaction/ligand_F020952.png)
Ligand Interaction
![ligand interaction](./Kdata/F020952/ligand_interaction/ligand_interaction_F020952.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. |
-6.2 | -3.835 | 0.039 | -0.934 | -1.47 | 0.003 |
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 | -0.831 | -0.901 | 3.782 | -3.905 | -2.271 | -0.004 | -0.701 | -0.928 | 0.002 |
4 | A | 8 | THR | 0 | -0.012 | -0.053 | 5.997 | 0.723 | 0.723 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | GLH | 0 | -0.051 | -0.049 | 8.108 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | GLU | -1 | -0.963 | -0.977 | 8.262 | -1.054 | -1.054 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | VAL | 0 | -0.008 | -0.021 | 7.988 | 0.268 | 0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | ARG | 1 | 0.805 | 0.881 | 11.064 | -0.478 | -0.478 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLU | -1 | -0.848 | -0.886 | 13.536 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | PHE | 0 | -0.037 | -0.009 | 13.732 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | VAL | 0 | -0.017 | -0.013 | 13.545 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | GLY | 0 | 0.044 | 0.029 | 16.233 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | HIS | 0 | -0.051 | -0.026 | 18.843 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | LEU | 0 | -0.003 | 0.001 | 17.230 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | GLU | -1 | -0.828 | -0.920 | 19.860 | 0.575 | 0.575 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | ARG | 1 | 1.010 | 1.007 | 22.216 | -0.226 | -0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | PHE | 0 | -0.045 | -0.018 | 23.162 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | LYS | 1 | 0.878 | 0.946 | 22.143 | -0.574 | -0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | GLU | -1 | -0.990 | -0.986 | 25.775 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | LEU | 0 | 0.001 | -0.001 | 28.234 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LEU | 0 | 0.013 | 0.004 | 27.497 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | ARG | 1 | 0.884 | 0.952 | 28.421 | -0.376 | -0.376 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | GLU | -1 | -0.960 | -0.977 | 32.006 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | GLU | -1 | -0.916 | -0.969 | 33.482 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | -0.033 | -0.013 | 33.756 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | ASN | 0 | -0.020 | -0.016 | 35.874 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | SER | 0 | -0.021 | 0.004 | 37.993 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | LEU | 0 | 0.026 | 0.009 | 38.619 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | SER | 0 | 0.024 | 0.013 | 39.768 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | ASN | 0 | -0.031 | -0.021 | 41.542 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | HIS | 0 | -0.010 | -0.001 | 43.682 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | PHE | 0 | -0.028 | -0.014 | 44.227 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | HIS | 0 | -0.102 | -0.061 | 43.342 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | ASN | 0 | 0.025 | 0.019 | 47.547 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LEU | 0 | -0.028 | 0.014 | 48.779 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | GLU | -1 | -0.899 | -0.964 | 51.045 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | SER | 0 | -0.076 | -0.044 | 54.592 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | TRP | 0 | -0.037 | -0.007 | 47.160 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | ARG | 1 | 0.928 | 0.948 | 51.818 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.823 | -0.907 | 52.795 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | ALA | 0 | 0.076 | 0.029 | 52.584 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | ARG | 1 | 0.919 | 0.957 | 49.669 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | ARG | 1 | 0.927 | 0.988 | 48.227 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | ASP | -1 | -0.877 | -0.945 | 47.694 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | LYS | 1 | 0.862 | 0.926 | 43.938 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | PHE | 0 | -0.006 | -0.014 | 40.967 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | SER | 0 | 0.025 | 0.003 | 42.806 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | GLU | -1 | -0.864 | -0.916 | 42.407 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | VAL | 0 | -0.062 | -0.022 | 38.713 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | LEU | 0 | -0.001 | -0.008 | 37.933 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | ASP | -1 | -0.903 | -0.947 | 37.769 | 0.204 | 0.204 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | ASN | 0 | 0.000 | -0.011 | 36.007 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | LEU | 0 | -0.028 | -0.001 | 32.340 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | LYS | 1 | 0.919 | 0.944 | 32.808 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | SER | 0 | -0.021 | -0.005 | 32.922 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | THR | 0 | 0.024 | 0.008 | 28.899 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | PHE | 0 | -0.046 | -0.040 | 28.527 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASN | 0 | -0.029 | -0.013 | 28.106 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.920 | -0.948 | 27.207 | 0.423 | 0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | PHE | 0 | -0.003 | -0.008 | 21.019 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | ASP | -1 | -0.862 | -0.928 | 23.411 | 0.533 | 0.533 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | GLU | -1 | -0.944 | -0.968 | 23.884 | 0.611 | 0.611 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | ALA | 0 | 0.037 | 0.019 | 20.760 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | ALA | 0 | -0.027 | -0.026 | 19.365 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | GLN | 0 | 0.016 | -0.007 | 19.046 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLU | -1 | -0.927 | -0.959 | 18.907 | 0.950 | 0.950 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | GLN | 0 | -0.019 | -0.012 | 13.828 | 0.367 | 0.367 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | ILE | 0 | -0.020 | -0.005 | 14.584 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | ALA | 0 | -0.044 | -0.021 | 15.680 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | TRP | 0 | 0.022 | 0.011 | 7.543 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | 0.027 | -0.003 | 9.766 | 0.320 | 0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | LYS | 1 | 0.822 | 0.908 | 11.221 | -0.614 | -0.614 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | GLU | -1 | -0.888 | -0.955 | 13.056 | 1.139 | 1.139 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | ARG | 1 | 0.904 | 0.967 | 4.207 | -6.544 | -6.424 | -0.001 | -0.018 | -0.101 | 0.000 |
75 | A | 79 | ILE | 0 | 0.008 | -0.007 | 8.143 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | ARG | 1 | 0.908 | 0.968 | 9.539 | -1.171 | -1.171 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | VAL | 0 | 0.022 | 0.021 | 7.815 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LEU | 0 | -0.041 | -0.027 | 3.708 | 0.111 | 0.722 | 0.044 | -0.215 | -0.441 | 0.001 |
79 | A | 83 | GLU | -1 | -0.774 | -0.860 | 6.979 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | GLU | -1 | -0.973 | -0.987 | 9.274 | 0.602 | 0.602 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | ASP | -1 | -0.941 | -0.974 | 7.021 | 0.459 | 0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | -0.094 | -0.042 | 5.907 | -0.653 | -0.653 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | LEU | 0 | -0.084 | -0.043 | 8.570 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | GLU | -1 | -1.040 | -0.998 | 12.113 | 0.344 | 0.344 | 0.000 | 0.000 | 0.000 | 0.000 |