![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: VRM41
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 | 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 | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -509983.031951 |
---|---|
FMO2-HF: Nuclear repulsion | 478878.860946 |
FMO2-HF: Total energy | -31104.171005 |
FMO2-MP2: Total energy | -31196.854521 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022789/ligand_interaction/ligand_F022789.png)
Ligand Interaction
![ligand interaction](./Kdata/F022789/ligand_interaction/ligand_interaction_F022789.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. |
73.161 | 74.711 | 0.005 | -0.689 | -0.866 | 0.002 |
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 | 0.921 | 0.934 | 3.802 | 43.922 | 45.472 | 0.005 | -0.689 | -0.866 | 0.002 |
4 | A | 5 | ARG | 1 | 0.960 | 0.981 | 6.594 | 23.531 | 23.531 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | VAL | 0 | -0.024 | 0.004 | 9.403 | -1.000 | -1.000 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | GLN | 0 | 0.048 | 0.020 | 11.997 | 0.900 | 0.900 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | ALA | 0 | -0.026 | -0.009 | 15.719 | -0.729 | -0.729 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | LYS | 1 | 0.841 | 0.908 | 18.006 | 12.565 | 12.565 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | ILE | 0 | -0.028 | -0.005 | 20.198 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | GLU | -1 | -0.829 | -0.908 | 24.042 | -10.684 | -10.684 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | MET | 0 | -0.047 | -0.017 | 27.837 | -0.206 | -0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.819 | -0.911 | 30.443 | -8.764 | -8.764 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | PHE | 0 | 0.008 | -0.004 | 32.290 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | PRO | 0 | -0.020 | -0.015 | 37.162 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | SER | 0 | 0.017 | -0.002 | 40.738 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | GLU | -1 | -0.778 | -0.885 | 40.422 | -7.996 | -7.996 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ASP | -1 | -0.858 | -0.923 | 40.497 | -7.095 | -7.095 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | VAL | 0 | -0.049 | -0.019 | 38.465 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ALA | 0 | -0.005 | 0.006 | 36.182 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | LYS | 1 | 0.870 | 0.934 | 36.194 | 7.650 | 7.650 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | VAL | 0 | 0.055 | 0.037 | 37.402 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | VAL | 0 | 0.000 | 0.000 | 32.845 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | -0.021 | -0.011 | 31.211 | -0.372 | -0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLU | -1 | -0.891 | -0.968 | 33.232 | -8.055 | -8.055 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | ALA | 0 | -0.004 | 0.010 | 35.209 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | VAL | 0 | -0.007 | -0.010 | 28.664 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LEU | 0 | -0.052 | -0.019 | 30.285 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | TYR | 0 | 0.045 | 0.025 | 31.660 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | GLU | -1 | -0.843 | -0.916 | 29.484 | -9.460 | -9.460 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | HIS | 0 | -0.006 | -0.006 | 25.746 | -0.625 | -0.625 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | LEU | 0 | -0.027 | -0.016 | 27.856 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | SER | 0 | -0.049 | -0.021 | 30.570 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | VAL | 0 | -0.059 | -0.017 | 25.261 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | PRO | 0 | 0.022 | 0.002 | 25.369 | -0.485 | -0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | TYR | 0 | -0.046 | -0.026 | 21.995 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | ARG | 1 | 0.891 | 0.949 | 20.972 | 11.582 | 11.582 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | ARG | 1 | 0.948 | 0.982 | 15.988 | 13.926 | 13.926 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | SER | 0 | -0.016 | 0.000 | 14.792 | -0.506 | -0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | GLU | -1 | -0.839 | -0.903 | 17.208 | -15.468 | -15.468 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | ILE | 0 | -0.003 | -0.009 | 19.497 | -0.490 | -0.490 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | ASP | -1 | -0.846 | -0.897 | 22.351 | -10.762 | -10.762 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | PHE | 0 | -0.009 | -0.013 | 25.369 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | LYS | 1 | 0.843 | 0.908 | 27.276 | 10.749 | 10.749 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | 0.029 | 0.006 | 30.775 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | GLU | -1 | -0.926 | -0.941 | 33.630 | -8.989 | -8.989 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | GLY | 0 | 0.008 | -0.005 | 36.645 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | LYS | 1 | 0.867 | 0.911 | 37.321 | 8.105 | 8.105 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | LYS | 1 | 0.841 | 0.907 | 31.144 | 9.828 | 9.828 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ILE | 0 | -0.020 | 0.013 | 29.309 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | ILE | 0 | -0.036 | -0.017 | 27.477 | -0.281 | -0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LEU | 0 | 0.015 | 0.009 | 22.919 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | ASP | -1 | -0.768 | -0.861 | 22.196 | -13.160 | -13.160 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ILE | 0 | -0.013 | -0.017 | 17.085 | 0.132 | 0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LYS | 1 | 0.836 | 0.884 | 15.398 | 16.027 | 16.027 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | ALA | 0 | -0.027 | -0.011 | 12.369 | 0.741 | 0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | THR | 0 | 0.030 | -0.009 | 9.180 | -0.561 | -0.561 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ASP | -1 | -0.841 | -0.898 | 6.180 | -26.641 | -26.641 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | SER | 0 | 0.026 | -0.010 | 6.193 | 2.036 | 2.036 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | SER | 0 | -0.046 | -0.024 | 8.414 | 1.926 | 1.926 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ALA | 0 | 0.016 | 0.011 | 10.135 | 1.451 | 1.451 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | LEU | 0 | 0.024 | 0.022 | 11.722 | 0.941 | 0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ARG | 1 | 0.943 | 0.968 | 10.773 | 20.398 | 20.398 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLY | 0 | -0.001 | 0.006 | 14.266 | 0.890 | 0.890 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | THR | 0 | 0.027 | -0.008 | 16.293 | 0.973 | 0.973 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | VAL | 0 | 0.010 | 0.005 | 17.411 | 0.685 | 0.685 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASN | 0 | -0.052 | -0.037 | 17.431 | 1.066 | 1.066 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | SER | 0 | -0.018 | 0.015 | 20.394 | 0.568 | 0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | TYR | 0 | 0.064 | 0.027 | 21.664 | 0.480 | 0.480 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | LEU | 0 | 0.003 | 0.004 | 21.702 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ARG | 1 | 0.825 | 0.908 | 22.456 | 11.989 | 11.989 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.029 | 0.010 | 23.903 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | ILE | 0 | 0.035 | 0.003 | 26.470 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | LYS | 1 | 0.857 | 0.936 | 26.968 | 10.527 | 10.527 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | ALA | 0 | 0.056 | 0.029 | 30.601 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | -0.004 | 0.006 | 32.435 | 0.264 | 0.264 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | ILE | 0 | -0.034 | -0.024 | 32.950 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | ASP | -1 | -0.919 | -0.970 | 33.375 | -8.550 | -8.550 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | -0.065 | -0.022 | 36.613 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ILE | 0 | -0.054 | -0.010 | 38.067 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |