![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YY322
Calculation Name: 3ENC-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3ENC
Chain ID: A
UniProt ID: Q8TZI1
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 | 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 | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -509227.337952 |
---|---|
FMO2-HF: Nuclear repulsion | 478124.063326 |
FMO2-HF: Total energy | -31103.274626 |
FMO2-MP2: Total energy | -31196.052097 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022790/ligand_interaction/ligand_F022790.png)
Ligand Interaction
![ligand interaction](./Kdata/F022790/ligand_interaction/ligand_interaction_F022790.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:2:LYS)
Summations of interaction energy for
fragment #1(A:2:LYS)
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. |
72.242 | 74.371 | 0.259 | -0.969 | -1.42 | 0.005 |
Interaction energy analysis for fragmet #1(A:2:LYS)
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 | 4 | LYS | 1 | 0.908 | 0.931 | 2.470 | 44.319 | 46.448 | 0.259 | -0.969 | -1.420 | 0.005 |
4 | A | 5 | ARG | 1 | 0.979 | 1.008 | 6.380 | 22.075 | 22.075 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | VAL | 0 | -0.001 | -0.003 | 9.013 | -0.627 | -0.627 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | GLN | 0 | 0.014 | 0.005 | 11.796 | 0.994 | 0.994 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | ALA | 0 | -0.004 | 0.012 | 15.584 | -0.404 | -0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | LYS | 1 | 0.872 | 0.923 | 17.943 | 12.225 | 12.225 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | ILE | 0 | -0.049 | -0.028 | 20.430 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | GLU | -1 | -0.809 | -0.882 | 24.202 | -10.330 | -10.330 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | MET | 0 | -0.044 | -0.022 | 27.811 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.817 | -0.912 | 30.314 | -8.664 | -8.664 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | PHE | 0 | 0.003 | -0.003 | 31.927 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | PRO | 0 | -0.009 | -0.010 | 36.794 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | SER | 0 | 0.058 | 0.028 | 40.590 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | GLU | -1 | -0.733 | -0.870 | 40.164 | -7.669 | -7.669 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ASP | -1 | -0.932 | -0.954 | 40.430 | -6.965 | -6.965 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | VAL | 0 | -0.092 | -0.071 | 38.794 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ALA | 0 | -0.055 | 0.012 | 36.112 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | LYS | 1 | 0.913 | 0.941 | 36.313 | 7.388 | 7.388 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | VAL | 0 | 0.014 | 0.021 | 37.616 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | VAL | 0 | 0.010 | 0.010 | 32.659 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | -0.014 | -0.016 | 31.014 | -0.325 | -0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLU | -1 | -0.927 | -0.988 | 33.219 | -7.780 | -7.780 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | ALA | 0 | -0.007 | 0.013 | 35.164 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | VAL | 0 | -0.021 | -0.018 | 28.702 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LEU | 0 | -0.024 | 0.004 | 29.931 | -0.331 | -0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | TYR | 0 | 0.067 | 0.024 | 31.395 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | GLU | -1 | -0.921 | -0.951 | 29.714 | -9.081 | -9.081 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | HIS | 0 | -0.018 | -0.008 | 25.472 | -0.712 | -0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | LEU | 0 | -0.034 | -0.021 | 27.905 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | SER | 0 | -0.063 | -0.030 | 30.600 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | VAL | 0 | -0.037 | -0.012 | 25.532 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | PRO | 0 | 0.001 | 0.007 | 25.656 | -0.421 | -0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | TYR | 0 | -0.040 | -0.015 | 22.019 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | ARG | 1 | 0.923 | 0.965 | 21.229 | 11.205 | 11.205 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | ARG | 1 | 0.943 | 0.993 | 15.887 | 13.672 | 13.672 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | SER | 0 | 0.074 | 0.017 | 14.538 | -0.432 | -0.432 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | GLU | -1 | -0.885 | -0.934 | 16.954 | -14.999 | -14.999 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | ILE | 0 | -0.029 | -0.020 | 19.012 | -0.293 | -0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | ASP | -1 | -0.837 | -0.895 | 22.216 | -10.404 | -10.404 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | PHE | 0 | -0.008 | -0.016 | 25.334 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | LYS | 1 | 0.864 | 0.916 | 27.232 | 10.322 | 10.322 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | 0.017 | 0.044 | 30.606 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | GLU | -1 | -0.952 | -0.974 | 33.592 | -8.711 | -8.711 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | GLY | 0 | 0.017 | 0.011 | 36.067 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | LYS | 1 | 0.915 | 0.914 | 37.369 | 8.180 | 8.180 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | LYS | 1 | 0.831 | 0.912 | 31.101 | 9.562 | 9.562 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ILE | 0 | -0.025 | -0.001 | 29.302 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | ILE | 0 | -0.040 | -0.026 | 26.936 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LEU | 0 | 0.004 | 0.005 | 22.743 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | ASP | -1 | -0.766 | -0.843 | 21.983 | -12.690 | -12.690 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ILE | 0 | -0.042 | -0.040 | 17.066 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LYS | 1 | 0.832 | 0.874 | 14.727 | 15.622 | 15.622 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | ALA | 0 | -0.037 | -0.009 | 11.749 | 0.574 | 0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | THR | 0 | 0.019 | 0.004 | 9.447 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ASP | -1 | -0.794 | -0.914 | 6.020 | -25.202 | -25.202 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | SER | 0 | -0.004 | -0.015 | 6.151 | 1.096 | 1.096 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | SER | 0 | -0.004 | -0.021 | 8.070 | 1.730 | 1.730 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ALA | 0 | -0.093 | 0.001 | 9.853 | 1.277 | 1.277 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | LEU | 0 | 0.065 | 0.024 | 11.776 | 0.909 | 0.909 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ARG | 1 | 0.969 | 0.991 | 11.487 | 19.484 | 19.484 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLY | 0 | 0.008 | 0.005 | 14.438 | 0.814 | 0.814 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | THR | 0 | 0.001 | -0.016 | 16.334 | 0.992 | 0.992 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | VAL | 0 | 0.033 | 0.011 | 17.443 | 0.604 | 0.604 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASN | 0 | -0.090 | -0.046 | 17.900 | 0.984 | 0.984 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | SER | 0 | -0.015 | -0.002 | 20.232 | 0.536 | 0.536 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | TYR | 0 | 0.046 | 0.002 | 21.891 | 0.449 | 0.449 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | LEU | 0 | 0.051 | 0.028 | 21.833 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ARG | 1 | 0.875 | 0.941 | 23.434 | 11.623 | 11.623 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.060 | 0.037 | 25.266 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | ILE | 0 | 0.043 | 0.015 | 26.635 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | LYS | 1 | 0.893 | 0.953 | 27.585 | 10.184 | 10.184 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | ALA | 0 | -0.013 | -0.013 | 30.384 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | 0.006 | 0.013 | 32.121 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | ILE | 0 | -0.039 | -0.027 | 32.787 | 0.191 | 0.191 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | ASP | -1 | -0.921 | -0.973 | 33.793 | -8.356 | -8.356 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | -0.071 | -0.015 | 36.736 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ILE | 0 | -0.036 | -0.007 | 37.607 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |