FMODB ID: YZKN2
Calculation Name: 3B5N-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3B5N
Chain ID: A
UniProt ID: P40357
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 61 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -237898.519242 |
---|---|
FMO2-HF: Nuclear repulsion | 213970.466464 |
FMO2-HF: Total energy | -23928.052778 |
FMO2-MP2: Total energy | -23997.167989 |
3D Structure
Ligand structure
Ligand Interaction
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:26:GLY)
Summations of interaction energy for
fragment #1(A:26:GLY)
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. |
-1.37 | 1.069 | 0.027 | -1.011 | -1.456 | 0.001 |
Interaction energy analysis for fragmet #1(A:26:GLY)
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 | 28 | ARG | 1 | 1.004 | 1.006 | 3.314 | -1.737 | -0.070 | 0.006 | -0.795 | -0.878 | 0.001 |
4 | A | 29 | THR | 0 | -0.014 | -0.020 | 3.285 | -0.537 | 0.049 | 0.022 | -0.159 | -0.449 | 0.000 |
5 | A | 30 | ALA | 0 | 0.014 | 0.015 | 4.331 | 0.694 | 0.880 | -0.001 | -0.057 | -0.129 | 0.000 |
6 | A | 31 | GLU | -1 | -0.899 | -0.946 | 6.165 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 32 | LEU | 0 | -0.029 | -0.012 | 7.953 | 0.161 | 0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 33 | GLN | 0 | -0.084 | -0.059 | 8.629 | 0.105 | 0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 34 | ALA | 0 | 0.033 | 0.019 | 10.294 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 35 | GLU | -1 | -0.906 | -0.944 | 12.274 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 36 | ILE | 0 | -0.023 | -0.011 | 12.240 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 37 | ASP | -1 | -0.868 | -0.931 | 13.900 | -0.369 | -0.369 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 38 | ASP | -1 | -0.897 | -0.941 | 16.315 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 39 | THR | 0 | -0.089 | -0.054 | 17.864 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 40 | VAL | 0 | -0.025 | -0.022 | 18.753 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 41 | GLY | 0 | -0.003 | 0.006 | 20.636 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 42 | ILE | 0 | 0.025 | 0.011 | 21.876 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 43 | MET | 0 | 0.007 | 0.003 | 23.706 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 44 | ARG | 1 | 0.918 | 0.962 | 23.051 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 45 | ASP | -1 | -0.845 | -0.908 | 26.720 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 46 | ASN | 0 | -0.042 | -0.041 | 27.466 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 47 | ILE | 0 | -0.016 | -0.001 | 28.889 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 48 | ASN | 0 | -0.001 | -0.003 | 30.579 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 49 | LYS | 1 | 0.913 | 0.953 | 30.191 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 50 | VAL | 0 | -0.049 | -0.027 | 33.820 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 51 | ALA | 0 | 0.014 | 0.014 | 35.543 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 52 | GLU | -1 | -0.917 | -0.948 | 37.365 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 53 | ARG | 1 | 0.922 | 0.953 | 38.079 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 54 | GLY | 0 | 0.013 | 0.002 | 39.657 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 55 | GLU | -1 | -0.827 | -0.883 | 41.452 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 56 | ARG | 1 | 0.829 | 0.889 | 43.176 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 57 | LEU | 0 | -0.012 | -0.017 | 42.158 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 58 | THR | 0 | 0.026 | 0.018 | 45.177 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 59 | SER | 0 | -0.026 | -0.009 | 47.593 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 60 | ILE | 0 | -0.033 | -0.027 | 46.943 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 61 | GLU | -1 | -0.938 | -0.959 | 49.238 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 62 | ASP | -1 | -0.797 | -0.893 | 51.363 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 63 | LYS | 1 | 0.839 | 0.919 | 52.485 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 64 | ALA | 0 | -0.015 | -0.004 | 53.495 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 65 | ASP | -1 | -0.901 | -0.941 | 55.411 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 66 | ASN | 0 | -0.033 | -0.037 | 57.418 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 67 | LEU | 0 | -0.022 | 0.004 | 57.409 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 68 | ALA | 0 | 0.030 | 0.017 | 59.278 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 69 | VAL | 0 | 0.011 | 0.009 | 61.051 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 70 | SER | 0 | -0.025 | -0.025 | 62.934 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 71 | ALA | 0 | -0.006 | 0.005 | 63.223 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 72 | GLN | 0 | -0.012 | -0.006 | 65.144 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 73 | GLY | 0 | 0.000 | -0.012 | 67.160 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 74 | PHE | 0 | 0.032 | 0.022 | 68.123 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 75 | LYS | 1 | 0.979 | 0.993 | 67.789 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 76 | ARG | 1 | 0.877 | 0.923 | 69.762 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 77 | GLY | 0 | 0.016 | 0.012 | 72.958 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 78 | ALA | 0 | 0.063 | 0.031 | 73.550 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 79 | ASN | 0 | 0.001 | 0.003 | 75.103 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 80 | ARG | 1 | 0.940 | 0.965 | 76.099 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 81 | VAL | 0 | 0.061 | 0.039 | 78.539 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 82 | ARG | 1 | 0.894 | 0.948 | 78.071 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 83 | LYS | 1 | 0.917 | 0.944 | 80.729 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 84 | ALA | 0 | 0.001 | 0.006 | 82.898 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 85 | MET | 0 | -0.024 | -0.018 | 83.010 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 86 | TRP | 0 | -0.063 | -0.003 | 84.984 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |