![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZVNGN
Calculation Name: 4FI5-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4FI5
Chain ID: A
UniProt ID: P05133
Base Structure: X-ray
Registration Date: 2023-09-22
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 | 71 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -406394.676754 |
---|---|
FMO2-HF: Nuclear repulsion | 377439.229219 |
FMO2-HF: Total energy | -28955.447535 |
FMO2-MP2: Total energy | -29039.788699 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033991/ligand_interaction/ligand_F033991.png)
Ligand Interaction
![ligand interaction](./Kdata/F033991/ligand_interaction/ligand_interaction_F033991.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:0:SER)
Summations of interaction energy for
fragment #1(A:0:SER)
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. |
-0.757 | 0.693 | -0.017 | -0.644 | -0.788 | 0.002 |
Interaction energy analysis for fragmet #1(A:0:SER)
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 | 2 | THR | 0 | 0.025 | -0.023 | 3.842 | 2.411 | 3.757 | -0.016 | -0.626 | -0.703 | 0.002 |
4 | A | 3 | MET | 0 | 0.028 | 0.012 | 6.749 | 0.404 | 0.404 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | GLU | -1 | -0.878 | -0.946 | 9.521 | 0.550 | 0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | GLU | -1 | -0.875 | -0.917 | 6.563 | -1.196 | -1.196 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | LEU | 0 | 0.010 | 0.024 | 7.263 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLN | 0 | 0.016 | -0.007 | 9.102 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ARG | 1 | 0.899 | 0.952 | 10.788 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | GLU | -1 | -0.781 | -0.871 | 9.499 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | ILE | 0 | -0.011 | -0.002 | 12.097 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | ASN | 0 | 0.013 | 0.006 | 14.174 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | ALA | 0 | -0.008 | 0.002 | 14.962 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | HIS | 0 | -0.046 | -0.038 | 12.652 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | GLU | -1 | -0.789 | -0.893 | 17.148 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | GLY | 0 | 0.014 | 0.009 | 19.876 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | GLN | 0 | -0.040 | -0.032 | 15.798 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | LEU | 0 | 0.005 | 0.019 | 21.155 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | VAL | 0 | -0.004 | 0.001 | 22.760 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | -0.044 | -0.026 | 23.481 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ALA | 0 | -0.001 | -0.007 | 23.760 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | ARG | 1 | 0.942 | 0.960 | 24.493 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | GLN | 0 | -0.009 | 0.003 | 28.466 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | LYS | 1 | 0.919 | 0.955 | 25.861 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | VAL | 0 | 0.013 | 0.017 | 28.805 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ARG | 1 | 0.917 | 0.966 | 31.103 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | ASP | -1 | -0.858 | -0.917 | 33.948 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | ALA | 0 | -0.029 | -0.013 | 33.260 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLU | -1 | -0.847 | -0.937 | 34.948 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | LYS | 1 | 0.913 | 0.955 | 37.317 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | GLN | 0 | -0.046 | -0.012 | 37.909 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | TYR | 0 | -0.007 | -0.011 | 38.309 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.956 | -0.979 | 40.252 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | LYS | 1 | 0.788 | 0.902 | 42.344 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ASP | -1 | -0.960 | -0.995 | 43.387 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | PRO | 0 | 0.013 | 0.034 | 42.322 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | ASP | -1 | -0.778 | -0.902 | 41.371 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLU | -1 | -0.815 | -0.905 | 40.143 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | LEU | 0 | -0.049 | -0.024 | 37.204 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | -0.010 | -0.004 | 36.547 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | LYS | 1 | 0.847 | 0.915 | 36.612 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | ARG | 1 | 0.846 | 0.916 | 31.491 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | THR | 0 | -0.039 | -0.023 | 32.210 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LEU | 0 | -0.005 | 0.003 | 31.617 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | THR | 0 | 0.038 | 0.022 | 30.893 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ASP | -1 | -0.839 | -0.907 | 28.122 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | ARG | 1 | 0.843 | 0.917 | 27.023 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | GLU | -1 | -0.854 | -0.938 | 27.106 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | GLY | 0 | 0.016 | 0.012 | 25.884 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | VAL | 0 | -0.036 | -0.018 | 22.126 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | ALA | 0 | 0.026 | 0.015 | 22.096 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | VAL | 0 | -0.018 | -0.002 | 22.805 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | SER | 0 | -0.044 | -0.030 | 19.163 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ILE | 0 | 0.006 | -0.007 | 18.051 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLN | 0 | -0.009 | -0.009 | 18.068 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | 0.030 | 0.022 | 18.253 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | LYS | 1 | 0.861 | 0.929 | 9.927 | -0.174 | -0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | ILE | 0 | -0.025 | -0.023 | 13.748 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.880 | -0.936 | 15.014 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.842 | -0.901 | 10.714 | 1.021 | 1.021 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | LEU | 0 | -0.047 | -0.014 | 9.065 | 0.187 | 0.187 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | LYS | 1 | 0.866 | 0.905 | 11.088 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ARG | 1 | 0.885 | 0.953 | 12.866 | -0.623 | -0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | GLN | 0 | -0.021 | -0.030 | 6.589 | 0.633 | 0.633 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | LEU | 0 | -0.020 | -0.016 | 9.911 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | ALA | 0 | -0.003 | -0.008 | 11.258 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | ASP | -1 | -0.880 | -0.943 | 11.261 | 1.001 | 1.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | ARG | 1 | 0.784 | 0.895 | 4.610 | -4.962 | -4.858 | -0.001 | -0.018 | -0.085 | 0.000 |
69 | A | 68 | ILE | 0 | -0.051 | -0.014 | 11.215 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | ALA | 0 | -0.028 | -0.005 | 14.549 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | THR | 0 | -0.075 | -0.043 | 10.622 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |