FMODB ID: 8JZ3Y
Calculation Name: 2OYZ-A-Xray311
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OYZ
Chain ID: A
UniProt ID: Q87K41
Base Structure: X-ray
Registration Date: 2021-09-06
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. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -625685.074012 |
---|---|
FMO2-HF: Nuclear repulsion | 589824.796368 |
FMO2-HF: Total energy | -35860.277644 |
FMO2-MP2: Total energy | -35964.279306 |
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:1:ALA )
Summations of interaction energy for
fragment #1(A:1: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. |
0.257 | 1.966 | -0.014 | -0.837 | -0.86 | 0.002 |
Interaction energy analysis for fragmet #1(A:1: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 | 3 | ILE | 0 | 0.028 | 0.009 | 3.855 | -0.607 | 0.866 | -0.016 | -0.788 | -0.670 | 0.002 |
4 | A | 4 | LYS | 1 | 0.929 | 0.980 | 7.030 | -0.860 | -0.860 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | GLU | -1 | -0.897 | -0.941 | 9.466 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | ASN | 0 | -0.063 | -0.028 | 13.063 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | SER | 0 | 0.014 | -0.004 | 16.015 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | TYR | 0 | 0.001 | -0.006 | 16.957 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | PHE | 0 | 0.037 | 0.012 | 22.408 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | ALA | 0 | -0.012 | -0.001 | 26.011 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | GLY | 0 | -0.029 | -0.010 | 23.480 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLY | 0 | -0.009 | 0.005 | 24.515 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | VAL | 0 | 0.042 | 0.023 | 20.232 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | LYS | 1 | 0.890 | 0.949 | 18.283 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | SER | 0 | 0.025 | 0.010 | 14.945 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | LEU | 0 | 0.006 | 0.000 | 11.076 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | GLY | 0 | 0.007 | 0.002 | 9.559 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | PHE | 0 | -0.047 | -0.030 | 5.553 | 0.169 | 0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | ASN | 0 | -0.013 | -0.007 | 3.741 | 0.404 | 0.640 | 0.002 | -0.049 | -0.190 | 0.000 |
20 | A | 20 | GLN | 0 | -0.006 | -0.019 | 5.303 | -0.428 | -0.428 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | HIS | 0 | -0.015 | -0.019 | 7.764 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | GLY | 0 | -0.030 | -0.015 | 7.723 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | 0.030 | 0.024 | 8.732 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | ASP | -1 | -0.902 | -0.933 | 8.090 | 0.913 | 0.913 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | VAL | 0 | 0.028 | 0.026 | 9.225 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | SER | 0 | -0.032 | -0.022 | 10.108 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | VAL | 0 | 0.026 | 0.025 | 12.457 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | GLY | 0 | 0.041 | 0.004 | 14.735 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | VAL | 0 | -0.064 | -0.022 | 17.429 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | MET | 0 | 0.004 | 0.012 | 21.007 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LEU | 0 | 0.022 | 0.003 | 24.088 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | PRO | 0 | -0.024 | -0.013 | 27.301 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLY | 0 | 0.008 | 0.014 | 30.702 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | GLU | -1 | -0.909 | -0.954 | 31.252 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | TYR | 0 | -0.092 | -0.055 | 26.780 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | THR | 0 | 0.041 | 0.019 | 28.486 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | PHE | 0 | -0.025 | -0.023 | 22.663 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | GLY | 0 | 0.008 | -0.002 | 24.331 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | THR | 0 | -0.018 | -0.034 | 22.475 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLN | 0 | -0.006 | -0.007 | 19.165 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ALA | 0 | -0.020 | -0.010 | 18.685 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | PRO | 0 | 0.009 | -0.010 | 20.776 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | GLU | -1 | -0.872 | -0.936 | 18.689 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ARG | 1 | 0.894 | 0.950 | 19.274 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | MET | 0 | -0.018 | -0.007 | 19.184 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | THR | 0 | 0.000 | -0.029 | 19.872 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | VAL | 0 | -0.011 | -0.004 | 21.108 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | VAL | 0 | -0.023 | -0.008 | 18.696 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LYS | 1 | 0.928 | 0.940 | 22.101 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | GLY | 0 | 0.006 | 0.010 | 25.007 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ALA | 0 | -0.008 | -0.025 | 27.761 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | LEU | 0 | -0.034 | 0.001 | 23.716 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.033 | -0.010 | 28.425 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | VAL | 0 | 0.018 | 0.006 | 27.805 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | LYS | 1 | 0.961 | 0.997 | 30.759 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.820 | 0.891 | 28.341 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | VAL | 0 | 0.004 | 0.003 | 31.123 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLY | 0 | -0.032 | -0.013 | 33.548 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLU | -1 | -0.850 | -0.897 | 33.290 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | ALA | 0 | -0.025 | -0.012 | 36.948 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | ASP | -1 | -0.954 | -0.976 | 38.498 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | TRP | 0 | -0.010 | -0.013 | 32.348 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | THR | 0 | -0.005 | -0.004 | 32.823 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | THR | 0 | -0.070 | -0.031 | 32.220 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | TYR | 0 | 0.051 | 0.039 | 28.061 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | SER | 0 | 0.012 | -0.012 | 29.074 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | SER | 0 | -0.025 | -0.030 | 26.176 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | GLY | 0 | -0.026 | -0.005 | 24.623 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | GLU | -1 | -0.901 | -0.934 | 25.564 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | SER | 0 | 0.012 | 0.006 | 23.268 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | PHE | 0 | -0.063 | -0.026 | 24.420 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | ASP | -1 | -0.772 | -0.865 | 23.976 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | VAL | 0 | -0.046 | -0.028 | 23.162 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | GLU | -1 | -0.918 | -0.954 | 24.475 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLY | 0 | 0.071 | 0.043 | 24.300 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ASN | 0 | -0.106 | -0.063 | 24.794 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | SER | 0 | 0.047 | 0.035 | 26.344 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | SER | 0 | -0.037 | -0.005 | 26.949 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | PHE | 0 | 0.028 | 0.000 | 22.993 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.925 | -0.950 | 28.156 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | LEU | 0 | -0.021 | -0.022 | 24.666 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLN | 0 | -0.046 | -0.015 | 29.284 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | VAL | 0 | -0.033 | -0.015 | 26.973 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | LYS | 1 | 0.963 | 0.971 | 30.172 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | ASP | -1 | -0.881 | -0.939 | 31.020 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | ALA | 0 | -0.039 | -0.017 | 26.399 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | THR | 0 | -0.012 | -0.006 | 24.312 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | ALA | 0 | -0.035 | -0.011 | 20.153 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | TYR | 0 | -0.007 | -0.001 | 17.659 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | LEU | 0 | 0.013 | -0.007 | 14.147 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | CYS | 0 | -0.019 | -0.002 | 15.627 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | GLU | -1 | -0.942 | -0.969 | 14.578 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | TYR | 0 | -0.017 | -0.019 | 13.502 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | LEU | -1 | -0.953 | -0.959 | 15.468 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |