FMODB ID: XYQM2
Calculation Name: 2DLB-A-Xray13
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: 2018-03-01
Reference:
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE. |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20181228 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 72 |
LigandCharge | |
Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
FMO2-HF: Electronic energy | -353010.101678 |
---|---|
FMO2-HF: Nuclear repulsion | 325344.948406 |
FMO2-HF: Total energy | -27665.153272 |
FMO2-MP2: Total energy | -27745.338762 |
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:2001:ACE)
Summations of interaction energy for
fragment #1(A:2001: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. |
1.188 | 1.763 | -0.01 | -0.229 | -0.336 | 0 |
Interaction energy analysis for fragmet #1(A:2001: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 | 2003 | GLY | 0 | 0.008 | 0.017 | 3.818 | 1.236 | 1.811 | -0.010 | -0.229 | -0.336 | 0.000 |
4 | A | 2004 | TYR | 0 | -0.008 | -0.008 | 4.820 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 2005 | LEU | 0 | -0.003 | 0.013 | 9.452 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 2006 | ASN | 0 | -0.013 | -0.021 | 12.455 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 2007 | ASN | 0 | -0.010 | -0.006 | 15.164 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 2008 | ILE | 0 | -0.005 | -0.012 | 17.211 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 2009 | ALA | 0 | 0.025 | 0.025 | 20.842 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 2010 | LEU | 0 | -0.021 | -0.017 | 23.132 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 2011 | ASN | 0 | 0.005 | 0.010 | 26.535 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 2012 | LEU | 0 | -0.022 | -0.018 | 28.723 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 2013 | GLU | -1 | -0.807 | -0.875 | 32.163 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 2014 | ILE | 0 | -0.048 | -0.025 | 35.330 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 2015 | VAL | 0 | 0.009 | 0.001 | 37.724 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 2016 | LEU | 0 | 0.032 | 0.008 | 41.369 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 2017 | LYS | 1 | 0.932 | 0.976 | 43.612 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 2018 | ASN | 0 | -0.040 | 0.003 | 47.326 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 2019 | LYS | 1 | 0.949 | 0.961 | 49.978 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 2020 | ALA | 0 | 0.010 | 0.003 | 53.495 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 2021 | ASP | -1 | -0.907 | -0.957 | 55.441 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 2022 | SER | 0 | 0.023 | 0.024 | 56.483 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 2023 | PRO | 0 | 0.053 | 0.023 | 52.655 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 2024 | GLU | -1 | -0.794 | -0.903 | 51.790 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 2025 | VAL | 0 | -0.030 | -0.008 | 52.013 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 2026 | SER | 0 | -0.058 | -0.053 | 50.079 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 2027 | GLU | -1 | -0.768 | -0.867 | 47.715 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 2028 | THR | 0 | -0.040 | -0.007 | 47.222 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 2029 | LEU | 0 | -0.097 | -0.059 | 47.901 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 2030 | VAL | 0 | 0.027 | 0.017 | 42.870 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 2031 | THR | 0 | 0.040 | 0.009 | 43.256 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 2032 | ARG | 1 | 0.914 | 0.968 | 43.102 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 2033 | ILE | 0 | -0.055 | -0.030 | 40.522 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 2034 | CYS | 0 | -0.010 | -0.008 | 38.952 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 2035 | GLU | -1 | -0.843 | -0.918 | 38.346 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 2036 | ASN | 0 | -0.084 | -0.042 | 39.138 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 2037 | LEU | 0 | -0.055 | -0.032 | 34.963 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 2038 | LEU | 0 | 0.014 | 0.024 | 34.088 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 2039 | LEU | 0 | -0.045 | -0.021 | 32.661 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 2040 | SER | 0 | -0.026 | -0.009 | 31.268 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 2041 | LYS | 1 | 0.956 | 0.967 | 27.362 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 2042 | GLU | -1 | -0.968 | -0.981 | 25.237 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 2043 | VAL | 0 | -0.006 | 0.012 | 25.916 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 2044 | SER | 0 | 0.005 | 0.002 | 26.197 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 2045 | PHE | 0 | 0.019 | 0.009 | 25.968 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 2046 | LEU | 0 | 0.000 | 0.001 | 28.067 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 2047 | LYS | 1 | 0.846 | 0.922 | 22.835 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 2048 | ALA | 0 | 0.039 | 0.017 | 29.016 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 2049 | ASP | -1 | -0.895 | -0.936 | 26.972 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 2050 | GLY | 0 | -0.021 | -0.009 | 30.490 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 2051 | SER | 0 | -0.102 | -0.052 | 26.446 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 2052 | VAL | 0 | 0.030 | -0.002 | 27.720 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 2053 | GLU | -1 | -0.919 | -0.955 | 20.018 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 2054 | ASN | 0 | 0.014 | 0.005 | 23.563 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 2055 | PHE | 0 | 0.007 | 0.005 | 19.696 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 2056 | LYS | 1 | 0.954 | 0.972 | 20.535 | 0.130 | 0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 2057 | LEU | 0 | -0.014 | 0.004 | 22.773 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 2058 | SER | 0 | -0.084 | -0.052 | 23.308 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 2059 | ASH | 0 | -0.099 | -0.122 | 25.456 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 2060 | MET | 0 | -0.014 | 0.000 | 28.493 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 2061 | GLU | -1 | -0.839 | -0.848 | 31.321 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 2062 | TYR | 0 | -0.068 | -0.055 | 34.059 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 2063 | GLU | -1 | -0.918 | -0.959 | 36.754 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 2064 | ILE | 0 | -0.045 | -0.016 | 39.765 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 2065 | THR | 0 | -0.013 | -0.006 | 39.729 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 2066 | ASN | 0 | -0.021 | -0.022 | 42.624 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 2067 | THR | 0 | -0.063 | -0.059 | 45.728 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 2068 | GLU | -1 | -0.998 | -1.000 | 47.856 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 2069 | GLU | -1 | -0.965 | -0.971 | 50.965 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 2070 | LEU | 0 | -0.052 | -0.036 | 50.190 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 2071 | PRO | 0 | 0.009 | 0.005 | 54.094 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 2072 | NME | 0 | -0.007 | 0.000 | 56.867 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |