![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YY412
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 | OptAll |
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 | -551058.765641 |
---|---|
FMO2-HF: Nuclear repulsion | 515281.774119 |
FMO2-HF: Total energy | -35776.991522 |
FMO2-MP2: Total energy | -35882.8799 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020950/ligand_interaction/ligand_F020950.png)
Ligand Interaction
![ligand interaction](./Kdata/F020950/ligand_interaction/ligand_interaction_F020950.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. |
-6.633 | -3.519 | 0.624 | -1.328 | -2.409 | 0.007 |
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 | -0.801 | -0.891 | 3.868 | -2.228 | -0.828 | 0.000 | -0.586 | -0.814 | 0.002 |
4 | A | 8 | THR | 0 | -0.015 | -0.047 | 5.850 | 0.692 | 0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 9 | GLH | 0 | -0.067 | -0.060 | 7.937 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 10 | GLU | -1 | -0.981 | -0.994 | 8.055 | -1.362 | -1.362 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 11 | VAL | 0 | 0.003 | -0.016 | 7.923 | 0.178 | 0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 12 | ARG | 1 | 0.793 | 0.859 | 11.075 | -0.674 | -0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 13 | GLU | -1 | -0.850 | -0.890 | 13.495 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 14 | PHE | 0 | -0.043 | -0.013 | 13.027 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 15 | VAL | 0 | 0.003 | -0.004 | 13.456 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 16 | GLY | 0 | 0.031 | 0.021 | 16.096 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 17 | HIS | 0 | -0.032 | -0.016 | 18.322 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 18 | LEU | 0 | -0.002 | 0.000 | 16.925 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 19 | GLU | -1 | -0.794 | -0.891 | 19.658 | 0.642 | 0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 20 | ARG | 1 | 0.830 | 0.893 | 21.919 | -0.234 | -0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 21 | PHE | 0 | -0.026 | -0.014 | 22.584 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 22 | LYS | 1 | 0.823 | 0.900 | 21.575 | -0.542 | -0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 23 | GLU | -1 | -0.938 | -0.952 | 25.533 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 24 | LEU | 0 | 0.006 | 0.007 | 27.847 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 25 | LEU | 0 | -0.005 | -0.002 | 26.563 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 26 | ARG | 1 | 0.847 | 0.908 | 27.377 | -0.357 | -0.357 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 27 | GLU | -1 | -0.831 | -0.901 | 31.562 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 28 | GLU | -1 | -0.872 | -0.951 | 33.071 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 29 | VAL | 0 | -0.045 | -0.013 | 33.345 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 30 | ASN | 0 | -0.048 | -0.035 | 35.074 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 31 | SER | 0 | -0.030 | 0.010 | 37.458 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 32 | LEU | 0 | 0.010 | -0.002 | 37.465 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 33 | SER | 0 | 0.018 | -0.002 | 39.151 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 34 | ASN | 0 | -0.061 | -0.038 | 40.949 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 35 | HIS | 0 | -0.009 | 0.005 | 43.112 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 36 | PHE | 0 | -0.013 | -0.008 | 43.363 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 37 | HIS | 0 | -0.034 | -0.027 | 43.285 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 38 | ASN | 0 | 0.032 | 0.015 | 46.840 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 39 | LEU | 0 | -0.021 | 0.008 | 48.121 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 40 | GLU | -1 | -0.814 | -0.897 | 50.264 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 41 | SER | 0 | -0.061 | -0.035 | 53.825 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 42 | TRP | 0 | -0.063 | -0.026 | 46.322 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 43 | ARG | 1 | 0.838 | 0.883 | 52.084 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 44 | ASP | -1 | -0.808 | -0.899 | 52.801 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 45 | ALA | 0 | 0.073 | 0.031 | 51.776 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 46 | ARG | 1 | 0.894 | 0.945 | 48.768 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 47 | ARG | 1 | 0.907 | 0.979 | 47.363 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 48 | ASP | -1 | -0.883 | -0.950 | 46.994 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 49 | LYS | 1 | 0.767 | 0.868 | 43.655 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 50 | PHE | 0 | 0.002 | -0.009 | 40.908 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 51 | SER | 0 | 0.007 | 0.003 | 42.181 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 52 | GLU | -1 | -0.799 | -0.875 | 41.627 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 53 | VAL | 0 | -0.025 | 0.003 | 37.991 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 54 | LEU | 0 | 0.000 | 0.008 | 37.509 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 55 | ASP | -1 | -0.802 | -0.904 | 37.323 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 56 | ASN | 0 | -0.029 | -0.026 | 35.644 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 57 | LEU | 0 | -0.020 | 0.014 | 32.155 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 58 | LYS | 1 | 0.823 | 0.902 | 32.540 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 59 | SER | 0 | -0.054 | -0.016 | 32.638 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 60 | THR | 0 | 0.046 | 0.007 | 28.594 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 61 | PHE | 0 | -0.035 | -0.030 | 28.193 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 62 | ASN | 0 | -0.028 | -0.013 | 27.869 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 63 | GLU | -1 | -0.910 | -0.957 | 27.128 | 0.322 | 0.322 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 64 | PHE | 0 | -0.023 | -0.012 | 20.975 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 65 | ASP | -1 | -0.798 | -0.869 | 23.069 | 0.476 | 0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 66 | GLU | -1 | -0.934 | -0.968 | 23.537 | 0.528 | 0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 67 | ALA | 0 | 0.050 | 0.027 | 20.708 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 68 | ALA | 0 | -0.008 | -0.016 | 18.867 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 69 | GLN | 0 | 0.013 | 0.009 | 18.641 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 70 | GLU | -1 | -0.926 | -0.959 | 18.189 | 0.932 | 0.932 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 71 | GLN | 0 | -0.043 | -0.019 | 13.741 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 72 | ILE | 0 | -0.015 | -0.007 | 14.093 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 73 | ALA | 0 | -0.022 | -0.006 | 15.283 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 74 | TRP | 0 | 0.013 | -0.002 | 7.132 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 75 | LEU | 0 | 0.008 | -0.004 | 9.342 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 76 | LYS | 1 | 0.823 | 0.900 | 10.697 | -0.552 | -0.552 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 77 | GLU | -1 | -0.845 | -0.902 | 12.610 | 1.291 | 1.291 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 78 | ARG | 1 | 0.897 | 0.963 | 3.271 | -9.588 | -9.020 | 0.043 | -0.200 | -0.410 | 0.001 |
75 | A | 79 | ILE | 0 | 0.000 | -0.010 | 7.540 | 0.792 | 0.792 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 80 | ARG | 1 | 0.815 | 0.897 | 9.144 | -1.323 | -1.323 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 81 | VAL | 0 | 0.030 | 0.018 | 7.716 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 82 | LEU | 0 | -0.041 | -0.026 | 2.801 | 0.051 | 1.197 | 0.581 | -0.542 | -1.185 | 0.004 |
79 | A | 83 | GLU | -1 | -0.750 | -0.818 | 6.663 | 0.209 | 0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 84 | GLU | -1 | -0.936 | -0.982 | 9.112 | 0.987 | 0.987 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 85 | ASP | -1 | -0.941 | -0.966 | 6.349 | 1.080 | 1.080 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 86 | TYR | 0 | -0.052 | -0.017 | 6.031 | -0.632 | -0.632 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 87 | LEU | 0 | -0.083 | -0.034 | 8.344 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 88 | GLU | -1 | -1.090 | -1.040 | 11.272 | 0.345 | 0.345 | 0.000 | 0.000 | 0.000 | 0.000 |