![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 53MZZ
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 | 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 | 79 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -508319.468379 |
---|---|
FMO2-HF: Nuclear repulsion | 477217.397471 |
FMO2-HF: Total energy | -31102.070908 |
FMO2-MP2: Total energy | -31194.921283 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F022791/ligand_interaction/ligand_F022791.png)
Ligand Interaction
![ligand interaction](./Kdata/F022791/ligand_interaction/ligand_interaction_F022791.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. |
87.902 | 87.894 | 4.045 | -1.02 | -3.018 | 0.006 |
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 | 0.930 | 0.963 | 2.050 | 57.876 | 57.868 | 4.045 | -1.020 | -3.018 | 0.006 |
4 | A | 5 | ARG | 1 | 0.994 | 1.015 | 6.371 | 21.562 | 21.562 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 6 | VAL | 0 | -0.034 | -0.008 | 9.003 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | GLN | 0 | -0.009 | -0.019 | 11.796 | 1.317 | 1.317 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | ALA | 0 | 0.006 | 0.018 | 15.584 | -0.395 | -0.395 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | LYS | 1 | 0.982 | 0.990 | 17.990 | 12.179 | 12.179 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | ILE | 0 | -0.047 | -0.021 | 20.729 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | GLU | -1 | -0.822 | -0.881 | 24.247 | -10.161 | -10.161 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | MET | 0 | -0.064 | -0.027 | 27.941 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.808 | -0.924 | 30.356 | -8.820 | -8.820 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | PHE | 0 | -0.039 | -0.026 | 31.620 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | PRO | 0 | -0.010 | -0.007 | 36.835 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | SER | 0 | 0.052 | 0.023 | 40.630 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | GLU | -1 | -0.770 | -0.900 | 40.201 | -7.521 | -7.521 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ASP | -1 | -0.932 | -0.954 | 40.471 | -6.931 | -6.931 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | VAL | 0 | -0.089 | -0.065 | 38.604 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ALA | 0 | -0.045 | 0.011 | 36.136 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | LYS | 1 | 0.954 | 0.967 | 36.353 | 7.326 | 7.326 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | VAL | 0 | 0.014 | 0.024 | 37.620 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | VAL | 0 | -0.004 | 0.006 | 32.713 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | -0.017 | -0.019 | 31.536 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | GLU | -1 | -0.931 | -0.986 | 33.219 | -7.735 | -7.735 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | ALA | 0 | -0.003 | 0.014 | 35.164 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | VAL | 0 | -0.016 | -0.012 | 28.627 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | LEU | 0 | -0.003 | 0.006 | 29.931 | -0.327 | -0.327 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | TYR | 0 | 0.063 | 0.023 | 31.395 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | GLU | -1 | -0.916 | -0.955 | 29.635 | -9.241 | -9.241 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | HIS | 0 | -0.050 | -0.025 | 25.605 | -0.695 | -0.695 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | LEU | 0 | -0.038 | -0.027 | 27.905 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | SER | 0 | -0.058 | -0.026 | 30.600 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | VAL | 0 | -0.037 | -0.012 | 25.004 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | PRO | 0 | -0.013 | -0.001 | 25.656 | -0.424 | -0.424 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | TYR | 0 | -0.040 | -0.016 | 21.988 | -0.239 | -0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | ARG | 1 | 0.981 | 1.006 | 21.229 | 11.000 | 11.000 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | ARG | 1 | 0.929 | 0.979 | 15.788 | 13.914 | 13.914 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | SER | 0 | 0.075 | 0.006 | 14.515 | -0.698 | -0.698 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | GLU | -1 | -0.990 | -0.998 | 16.960 | -14.178 | -14.178 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | ILE | 0 | -0.045 | -0.037 | 19.014 | -0.232 | -0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | ASP | -1 | -0.891 | -0.935 | 22.217 | -10.353 | -10.353 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | PHE | 0 | -0.007 | -0.024 | 25.334 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | LYS | 1 | 0.939 | 0.966 | 27.232 | 10.122 | 10.122 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | 0.022 | 0.045 | 30.606 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | GLU | -1 | -0.944 | -0.971 | 33.592 | -8.479 | -8.479 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | GLY | 0 | -0.010 | 0.004 | 36.110 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | LYS | 1 | 0.987 | 0.960 | 37.401 | 7.847 | 7.847 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | LYS | 1 | 0.822 | 0.905 | 31.385 | 9.470 | 9.470 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | ILE | 0 | -0.024 | 0.001 | 29.137 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | ILE | 0 | -0.050 | -0.027 | 26.853 | -0.271 | -0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LEU | 0 | -0.041 | -0.009 | 22.706 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | ASP | -1 | -0.787 | -0.881 | 21.998 | -12.390 | -12.390 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ILE | 0 | -0.040 | -0.041 | 17.248 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | LYS | 1 | 0.908 | 0.945 | 12.622 | 17.813 | 17.813 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | ALA | 0 | -0.026 | -0.011 | 11.469 | 0.481 | 0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | THR | 0 | 0.013 | -0.005 | 9.032 | -0.654 | -0.654 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | ASP | -1 | -0.825 | -0.929 | 5.954 | -25.938 | -25.938 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | SER | 0 | 0.036 | -0.008 | 5.339 | 1.614 | 1.614 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | SER | 0 | -0.039 | -0.030 | 8.107 | 1.662 | 1.662 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | ALA | 0 | -0.091 | 0.000 | 9.862 | 1.368 | 1.368 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | LEU | 0 | 0.043 | 0.016 | 11.761 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | ARG | 1 | 1.019 | 1.016 | 12.148 | 19.040 | 19.040 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLY | 0 | -0.009 | -0.008 | 14.466 | 0.815 | 0.815 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | THR | 0 | 0.027 | 0.004 | 16.362 | 1.028 | 1.028 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | VAL | 0 | 0.042 | 0.017 | 17.476 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | ASN | 0 | -0.097 | -0.048 | 18.543 | 0.857 | 0.857 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | SER | 0 | -0.014 | -0.003 | 20.262 | 0.423 | 0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | TYR | 0 | 0.032 | 0.000 | 21.904 | 0.346 | 0.346 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | LEU | 0 | 0.050 | 0.029 | 22.064 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ARG | 1 | 0.868 | 0.939 | 23.749 | 11.614 | 11.614 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | TRP | 0 | 0.055 | 0.043 | 25.769 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | ILE | 0 | 0.058 | 0.021 | 27.618 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | LYS | 1 | 0.896 | 0.950 | 27.535 | 10.232 | 10.232 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | ALA | 0 | -0.036 | -0.024 | 30.410 | 0.230 | 0.230 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | ALA | 0 | 0.018 | 0.019 | 32.145 | 0.242 | 0.242 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | ILE | 0 | -0.055 | -0.029 | 32.666 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | ASP | -1 | -0.915 | -0.966 | 34.210 | -8.255 | -8.255 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | VAL | 0 | -0.085 | -0.018 | 36.763 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ILE | 0 | -0.041 | -0.013 | 38.481 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |