![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: N1VYQ
Calculation Name: 3ENC-A-Xray320
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: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 81 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -512303.893708 |
---|---|
FMO2-HF: Nuclear repulsion | 481030.900284 |
FMO2-HF: Total energy | -31272.993424 |
FMO2-MP2: Total energy | -31366.374568 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F016314/ligand_interaction/ligand_F016314.png)
Ligand Interaction
![ligand interaction](./Kdata/F016314/ligand_interaction/ligand_interaction_F016314.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:1:ACE )
Summations of interaction energy for
fragment #1(A:1:ACE )
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. |
1.933 | 2.897 | -0.005 | -0.451 | -0.507 | 0 |
Interaction energy analysis for fragmet #1(A:1:ACE )
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 | 3 | ALA | 0 | -0.007 | 0.010 | 3.764 | 0.802 | 1.766 | -0.005 | -0.451 | -0.507 | 0.000 |
4 | A | 4 | LYS | 1 | 0.936 | 0.968 | 5.688 | 1.513 | 1.513 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | ARG | 1 | 0.996 | 1.016 | 8.789 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | -0.039 | -0.010 | 9.459 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | GLN | 0 | -0.006 | -0.017 | 12.495 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | ALA | 0 | 0.004 | 0.017 | 16.024 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | LYS | 1 | 0.984 | 0.991 | 18.025 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ILE | 0 | -0.047 | -0.022 | 20.335 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLU | -1 | -0.821 | -0.881 | 24.110 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | MET | 0 | -0.065 | -0.028 | 27.562 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | GLU | -1 | -0.808 | -0.923 | 30.089 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | PHE | 0 | -0.037 | -0.025 | 30.964 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | PRO | 0 | -0.010 | -0.007 | 36.413 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | SER | 0 | 0.050 | 0.022 | 40.191 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLU | -1 | -0.767 | -0.899 | 39.675 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | ASP | -1 | -0.934 | -0.953 | 39.776 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | VAL | 0 | -0.089 | -0.066 | 37.868 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ALA | 0 | -0.044 | 0.011 | 35.551 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | LYS | 1 | 0.954 | 0.966 | 35.520 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | VAL | 0 | 0.014 | 0.025 | 36.644 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | VAL | 0 | -0.005 | 0.005 | 31.724 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | TYR | 0 | -0.019 | -0.020 | 30.816 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | GLU | -1 | -0.927 | -0.985 | 32.147 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | ALA | 0 | -0.005 | 0.013 | 33.820 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | VAL | 0 | -0.016 | -0.012 | 27.412 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | LEU | 0 | -0.001 | 0.007 | 28.587 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | TYR | 0 | 0.061 | 0.023 | 30.083 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | GLU | -1 | -0.918 | -0.956 | 27.940 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | HIS | 0 | -0.042 | -0.021 | 24.295 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | LEU | 0 | -0.043 | -0.028 | 26.519 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | SER | 0 | -0.058 | -0.025 | 29.226 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | -0.040 | -0.013 | 23.404 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | PRO | 0 | -0.011 | 0.000 | 24.065 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | TYR | 0 | -0.039 | -0.016 | 20.294 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | ARG | 1 | 0.978 | 1.006 | 19.683 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.928 | 0.977 | 13.862 | -0.147 | -0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | SER | 0 | 0.071 | 0.001 | 13.494 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLU | -1 | -0.988 | -0.994 | 15.906 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ILE | 0 | -0.041 | -0.035 | 18.548 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | ASP | -1 | -0.890 | -0.935 | 21.617 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | PHE | 0 | -0.012 | -0.025 | 25.021 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | LYS | 1 | 0.942 | 0.968 | 26.613 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LEU | 0 | 0.021 | 0.044 | 30.115 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | GLU | -1 | -0.943 | -0.970 | 33.085 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | GLY | 0 | -0.010 | 0.004 | 35.830 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | LYS | 1 | 0.987 | 0.959 | 37.057 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LYS | 1 | 0.823 | 0.906 | 31.685 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | ILE | 0 | -0.027 | 0.000 | 28.478 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ILE | 0 | -0.049 | -0.027 | 26.675 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | LEU | 0 | -0.040 | -0.008 | 21.881 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ASP | -1 | -0.786 | -0.880 | 21.832 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | ILE | 0 | -0.040 | -0.041 | 16.537 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.906 | 0.945 | 13.795 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ALA | 0 | -0.026 | -0.012 | 10.665 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | THR | 0 | 0.010 | -0.005 | 8.193 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | ASP | -1 | -0.820 | -0.926 | 5.287 | 0.442 | 0.442 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | SER | 0 | 0.036 | -0.011 | 5.035 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | SER | 0 | -0.044 | -0.032 | 7.117 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ALA | 0 | -0.088 | 0.002 | 8.393 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | LEU | 0 | 0.046 | 0.017 | 10.349 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 1.019 | 1.017 | 10.529 | -0.555 | -0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | GLY | 0 | -0.009 | -0.008 | 12.935 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | THR | 0 | 0.017 | -0.004 | 14.835 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | VAL | 0 | 0.047 | 0.019 | 16.276 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ASN | 0 | -0.098 | -0.047 | 17.350 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | SER | 0 | -0.012 | -0.006 | 18.667 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | TYR | 0 | 0.041 | 0.007 | 20.328 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | LEU | 0 | 0.053 | 0.029 | 21.342 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ARG | 1 | 0.862 | 0.936 | 21.888 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | TRP | 0 | 0.056 | 0.044 | 23.978 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ILE | 0 | 0.052 | 0.018 | 26.346 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | LYS | 1 | 0.900 | 0.951 | 26.302 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ALA | 0 | -0.037 | -0.024 | 29.013 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ALA | 0 | 0.015 | 0.017 | 30.785 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | ILE | 0 | -0.056 | -0.031 | 31.763 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ASP | -1 | -0.913 | -0.964 | 32.778 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | VAL | 0 | -0.087 | -0.022 | 35.437 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | ILE | 0 | 0.013 | 0.002 | 37.506 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | NME | 0 | -0.052 | -0.012 | 39.497 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |