FMODB ID: R8GQ8
Calculation Name: 2DLB-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2DLB
Chain ID: A
UniProt ID: O34498
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 70 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -350247.065926 |
---|---|
FMO2-HF: Nuclear repulsion | 322752.525761 |
FMO2-HF: Total energy | -27494.540165 |
FMO2-MP2: Total energy | -27574.191779 |
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:2002:ALA)
Summations of interaction energy for
fragment #1(A:2002:ALA)
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. |
-3.877 | 0.786 | 1.042 | -2.499 | -3.207 | -0.001 |
Interaction energy analysis for fragmet #1(A:2002:ALA)
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 | 2004 | TYR | 0 | -0.010 | -0.017 | 2.718 | -3.257 | 1.406 | 1.042 | -2.499 | -3.207 | -0.001 |
4 | A | 2005 | LEU | 0 | 0.003 | 0.019 | 6.063 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 2006 | ASN | 0 | -0.022 | -0.025 | 9.617 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 2007 | ASN | 0 | -0.003 | -0.001 | 12.173 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 2008 | ILE | 0 | -0.001 | -0.010 | 14.860 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 2009 | ALA | 0 | 0.023 | 0.023 | 18.251 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 2010 | LEU | 0 | -0.023 | -0.015 | 21.411 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 2011 | ASN | 0 | 0.005 | 0.007 | 24.319 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 2012 | LEU | 0 | -0.023 | -0.019 | 26.934 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 2013 | GLU | -1 | -0.810 | -0.867 | 30.207 | -0.120 | -0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 2014 | ILE | 0 | -0.041 | -0.023 | 33.380 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 2015 | VAL | 0 | 0.016 | 0.004 | 35.930 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 2016 | LEU | 0 | 0.012 | 0.004 | 38.843 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 2017 | LYS | 1 | 0.947 | 0.977 | 41.760 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 2018 | ASN | 0 | -0.035 | 0.007 | 45.543 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 2019 | LYS | 1 | 0.947 | 0.962 | 48.093 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 2020 | ALA | 0 | 0.019 | 0.005 | 51.167 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 2021 | ASP | -1 | -0.893 | -0.941 | 53.207 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 2022 | SER | 0 | 0.003 | 0.007 | 54.091 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 2023 | PRO | 0 | 0.042 | 0.017 | 50.175 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 2024 | GLU | -1 | -0.785 | -0.901 | 49.263 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 2025 | VAL | 0 | -0.019 | 0.002 | 49.308 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 2026 | SER | 0 | -0.048 | -0.049 | 47.958 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 2027 | GLU | -1 | -0.773 | -0.863 | 45.093 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 2028 | THR | 0 | -0.053 | -0.009 | 44.533 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 2029 | LEU | 0 | -0.087 | -0.048 | 45.045 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 2030 | VAL | 0 | 0.028 | 0.009 | 40.565 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 2031 | THR | 0 | 0.044 | 0.009 | 40.573 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 2032 | ARG | 1 | 0.926 | 0.976 | 40.113 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 2033 | ILE | 0 | -0.030 | -0.008 | 38.290 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 2034 | CYS | 0 | -0.029 | -0.015 | 36.239 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 2035 | GLU | -1 | -0.812 | -0.884 | 35.396 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 2036 | ASN | 0 | -0.154 | -0.091 | 35.875 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 2037 | LEU | 0 | -0.032 | -0.022 | 32.487 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 2038 | LEU | 0 | 0.020 | 0.035 | 31.208 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 2039 | LEU | 0 | -0.030 | -0.011 | 29.210 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 2040 | SER | 0 | 0.006 | 0.005 | 28.763 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 2041 | LYS | 1 | 0.888 | 0.927 | 24.639 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 2042 | GLU | -1 | -0.906 | -0.941 | 23.600 | -0.315 | -0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 2043 | VAL | 0 | -0.006 | 0.011 | 24.017 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 2044 | SER | 0 | 0.007 | 0.000 | 24.643 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 2045 | PHE | 0 | 0.009 | 0.007 | 24.167 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 2046 | LEU | 0 | 0.001 | 0.004 | 26.984 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 2047 | LYS | 1 | 0.843 | 0.911 | 22.179 | 0.331 | 0.331 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 2048 | ALA | 0 | 0.030 | 0.012 | 28.099 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 2049 | ASP | -1 | -0.877 | -0.915 | 26.427 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 2050 | GLY | 0 | -0.016 | -0.007 | 30.045 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 2051 | SER | 0 | -0.120 | -0.076 | 25.965 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 2052 | VAL | 0 | 0.017 | -0.006 | 26.884 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 2053 | GLU | -1 | -0.902 | -0.930 | 19.185 | -0.445 | -0.445 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 2054 | ASN | 0 | -0.025 | -0.027 | 22.562 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 2055 | PHE | 0 | -0.007 | -0.004 | 18.327 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 2056 | LYS | 1 | 0.949 | 0.970 | 17.079 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 2057 | LEU | 0 | -0.006 | 0.007 | 20.330 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 2058 | SER | 0 | -0.086 | -0.053 | 19.782 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 2059 | ASH | 0 | -0.096 | -0.104 | 21.922 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 2060 | MET | 0 | -0.007 | 0.005 | 24.973 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 2061 | GLU | -1 | -0.838 | -0.859 | 27.911 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 2062 | TYR | 0 | -0.086 | -0.095 | 30.954 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 2063 | GLU | -1 | -0.916 | -0.954 | 33.908 | -0.106 | -0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 2064 | ILE | 0 | -0.045 | -0.019 | 37.001 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 2065 | THR | 0 | -0.021 | -0.018 | 37.612 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 2066 | ASN | 0 | -0.078 | -0.055 | 40.227 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 2067 | THR | 0 | -0.048 | -0.056 | 43.519 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 2068 | GLU | -1 | -0.954 | -0.973 | 45.842 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 2069 | GLU | -1 | -0.974 | -0.976 | 48.961 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 2070 | LEU | 0 | -0.048 | -0.030 | 48.474 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 2071 | PRO | 0 | 0.003 | 0.003 | 52.525 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |