FMODB ID: YYQY2
Calculation Name: 4EVX-A-Xray321
Preferred Name:
Target Type:
Ligand Name: n-dimethyl-lysine
ligand 3-letter code: MLY
PDB ID: 4EVX
Chain ID: A
UniProt ID: Q8ZLC6
Base Structure: X-ray
Registration Date: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200129 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 99 |
LigandCharge | MLY=1 |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -721188.7667 |
---|---|
FMO2-HF: Nuclear repulsion | 680916.865247 |
FMO2-HF: Total energy | -40271.901452 |
FMO2-MP2: Total energy | -40387.741194 |
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:6:ACE )
Summations of interaction energy for
fragment #1(A:6: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. |
0.974 | 2.151 | 0.001 | -0.487 | -0.691 | -0.001 |
Interaction energy analysis for fragmet #1(A:6: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 | 8 | PHE | 0 | 0.029 | 0.023 | 3.829 | 0.586 | 1.586 | -0.005 | -0.424 | -0.571 | -0.001 |
4 | A | 9 | SER | 0 | -0.082 | -0.063 | 4.905 | 0.192 | 0.259 | 0.000 | -0.005 | -0.062 | 0.000 |
5 | A | 10 | SER | 0 | 0.038 | 0.003 | 7.503 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 11 | ALA | 0 | 0.014 | 0.007 | 8.073 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 12 | CSO | 0 | -0.001 | 0.016 | 9.558 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 13 | ILE | 0 | 0.024 | 0.005 | 5.219 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 14 | ALA | 0 | -0.015 | -0.015 | 9.816 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 15 | PHE | 0 | -0.017 | 0.001 | 12.870 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 16 | ILE | 0 | 0.023 | 0.010 | 11.542 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 17 | MLY | 1 | 0.814 | 0.879 | 10.058 | -0.450 | -0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 18 | GLN | 0 | -0.034 | 0.015 | 15.092 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 19 | TRP | 0 | -0.043 | -0.024 | 17.849 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 20 | GLN | 0 | -0.046 | -0.016 | 16.445 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 21 | GLY | 0 | 0.006 | 0.009 | 17.835 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 22 | LEU | 0 | -0.007 | -0.003 | 16.191 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 23 | SER | 0 | -0.024 | -0.012 | 18.979 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 24 | LEU | 0 | 0.001 | -0.010 | 18.743 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 25 | GLU | -1 | -0.910 | -0.952 | 21.277 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 26 | MLY | 1 | 0.848 | 0.942 | 23.331 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 27 | TYR | 0 | 0.005 | -0.008 | 22.319 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 28 | ARG | 1 | 0.888 | 0.948 | 25.755 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 29 | ASP | -1 | -0.826 | -0.915 | 25.359 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 30 | ARG | 1 | 0.958 | 0.966 | 27.559 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 31 | GLN | 0 | -0.073 | -0.040 | 28.523 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 32 | GLY | 0 | 0.009 | 0.020 | 30.106 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 33 | ASN | 0 | 0.010 | 0.007 | 25.229 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 34 | TRP | 0 | 0.010 | -0.004 | 24.750 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 35 | VAL | 0 | -0.013 | 0.001 | 20.272 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 36 | ILE | 0 | 0.025 | 0.014 | 18.115 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 37 | GLY | 0 | 0.041 | 0.019 | 16.474 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 38 | TYR | 0 | 0.014 | 0.000 | 13.031 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 39 | GLY | 0 | -0.020 | -0.015 | 15.743 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 40 | HIS | 1 | 0.902 | 0.940 | 14.611 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 41 | MET | 0 | -0.019 | -0.014 | 16.973 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 42 | LEU | 0 | -0.033 | -0.012 | 18.892 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 43 | THR | 0 | -0.036 | -0.033 | 19.622 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 44 | PRO | 0 | -0.012 | -0.026 | 22.230 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 45 | ASP | -1 | -0.892 | -0.941 | 25.500 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 46 | GLU | -1 | -0.915 | -0.936 | 19.397 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 47 | THR | 0 | -0.013 | -0.018 | 24.102 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 48 | LEU | 0 | -0.038 | 0.008 | 19.678 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 49 | THR | 0 | 0.026 | -0.012 | 24.047 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 50 | PHE | 0 | 0.029 | 0.010 | 23.196 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 51 | ILE | 0 | -0.019 | -0.002 | 16.382 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 52 | THR | 0 | 0.017 | 0.001 | 16.757 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 53 | PRO | 0 | 0.045 | 0.001 | 15.968 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 54 | ASP | -1 | -0.875 | -0.928 | 12.359 | 0.551 | 0.551 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 55 | GLN | 0 | 0.003 | 0.003 | 11.809 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 56 | ALA | 0 | 0.000 | -0.002 | 13.005 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 57 | GLU | -1 | -0.822 | -0.898 | 8.045 | 0.649 | 0.649 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 58 | ALA | 0 | -0.009 | -0.008 | 8.216 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 59 | PHE | 0 | 0.028 | 0.006 | 9.160 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 60 | LEU | 0 | 0.000 | 0.022 | 9.390 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 61 | LEU | 0 | -0.025 | -0.022 | 3.530 | -0.157 | 0.000 | 0.006 | -0.054 | -0.109 | 0.000 |
57 | A | 62 | ASP | -1 | -0.894 | -0.937 | 6.901 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 63 | ASP | -1 | -0.810 | -0.890 | 9.298 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 64 | LEU | 0 | -0.048 | -0.031 | 7.790 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 65 | ASN | 0 | -0.036 | -0.047 | 4.596 | -0.421 | -0.468 | 0.000 | -0.004 | 0.051 | 0.000 |
61 | A | 66 | SER | 0 | 0.003 | 0.020 | 8.605 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 67 | CYS | 0 | -0.054 | -0.035 | 12.198 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 68 | ASP | -1 | -0.865 | -0.946 | 10.153 | -0.599 | -0.599 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 69 | ILE | 0 | 0.000 | 0.002 | 10.688 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 70 | LEU | 0 | -0.027 | -0.020 | 13.523 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 71 | LEU | 0 | -0.032 | -0.001 | 14.982 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 72 | GLN | 0 | -0.029 | -0.019 | 14.408 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 73 | ASN | 0 | -0.001 | -0.017 | 16.966 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 74 | CYS | 0 | -0.025 | 0.014 | 19.805 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 75 | LEU | 0 | -0.048 | -0.031 | 19.327 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 76 | PRO | 0 | 0.007 | 0.011 | 19.998 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 77 | GLU | -1 | -0.940 | -0.970 | 20.837 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 78 | LEU | 0 | -0.058 | -0.008 | 18.081 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 79 | ASN | 0 | 0.035 | -0.005 | 17.059 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 80 | ASP | -1 | -0.887 | -0.934 | 16.270 | -0.255 | -0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 81 | ARG | 1 | 0.993 | 0.968 | 7.355 | 0.967 | 0.967 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 82 | PHE | 0 | -0.001 | 0.021 | 13.569 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 83 | GLN | 0 | 0.042 | 0.008 | 15.545 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 84 | ARG | 1 | 0.865 | 0.946 | 12.672 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 85 | GLU | -1 | -0.769 | -0.864 | 9.227 | -0.451 | -0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 86 | THR | 0 | -0.060 | -0.031 | 13.154 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 87 | LEU | 0 | 0.023 | 0.020 | 16.639 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 88 | ILE | 0 | 0.023 | 0.012 | 11.550 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 89 | ALA | 0 | 0.008 | 0.002 | 14.683 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 90 | LEU | 0 | -0.016 | 0.000 | 15.658 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 91 | MET | 0 | 0.008 | 0.001 | 16.340 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 92 | PHE | 0 | -0.031 | -0.005 | 13.810 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 93 | SER | 0 | -0.067 | -0.052 | 17.244 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 94 | ILE | 0 | 0.002 | -0.001 | 20.186 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 95 | GLY | 0 | -0.008 | 0.002 | 20.763 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 96 | HIS | 1 | 0.850 | 0.957 | 16.775 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 97 | GLN | 0 | 0.041 | 0.026 | 21.365 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 98 | ARG | 1 | 0.849 | 0.918 | 20.661 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 99 | PHE | 0 | 0.001 | -0.008 | 24.309 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 100 | LEU | 0 | 0.006 | 0.010 | 26.920 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 101 | SER | 0 | 0.035 | 0.006 | 27.698 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 102 | LEU | 0 | -0.016 | -0.009 | 29.684 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 103 | ILE | 0 | -0.015 | 0.002 | 30.529 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 104 | NME | 0 | 0.003 | 0.009 | 30.709 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |