![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 1JZKZ
Calculation Name: 2CX6-A-Xray307
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2CX6
Chain ID: A
UniProt ID: P64618
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 | 90 |
LigandCharge | |
Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
FMO2-HF: Electronic energy | -705866.175777 |
---|---|
FMO2-HF: Nuclear repulsion | 668302.463866 |
FMO2-HF: Total energy | -37563.711912 |
FMO2-MP2: Total energy | -37674.667874 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015097/ligand_interaction/ligand_F015097.png)
Ligand Interaction
![ligand interaction](./Kdata/F015097/ligand_interaction/ligand_interaction_F015097.png)
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:MET )
Summations of interaction energy for
fragment #1(A:1:MET )
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. |
-12.289 | -10.932 | 15.434 | -7.811 | -8.978 | -0.059 |
Interaction energy analysis for fragmet #1(A:1:MET )
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 | 0.012 | 0.016 | 3.883 | 1.192 | 2.854 | -0.004 | -0.687 | -0.972 | 0.002 |
4 | A | 4 | TYR | 0 | -0.009 | -0.007 | 6.236 | -0.591 | -0.591 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | THR | 0 | 0.011 | 0.006 | 9.563 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | PHE | 0 | -0.017 | -0.004 | 11.792 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ASP | -1 | -0.786 | -0.886 | 15.874 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PHE | 0 | -0.032 | -0.055 | 17.702 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASP | -1 | -0.935 | -0.948 | 21.548 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLU | -1 | -1.013 | -1.017 | 21.380 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | ILE | 0 | -0.065 | -0.010 | 19.017 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLU | -1 | -0.876 | -0.946 | 23.631 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.125 | -0.056 | 26.076 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLN | 0 | 0.053 | 0.002 | 23.518 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.891 | -0.964 | 23.161 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.867 | -0.942 | 23.892 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | PHE | 0 | 0.049 | 0.031 | 15.318 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | TYR | 0 | 0.024 | 0.014 | 19.370 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | ARG | 1 | 0.906 | 0.980 | 19.820 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASP | -1 | -0.845 | -0.932 | 18.324 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.010 | 0.007 | 12.583 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | SER | 0 | -0.029 | -0.043 | 15.528 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | -0.058 | -0.027 | 17.364 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | THR | 0 | -0.024 | 0.001 | 12.242 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | PHE | 0 | -0.063 | -0.025 | 8.591 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | -0.031 | 0.000 | 13.498 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | LEU | 0 | -0.036 | -0.015 | 14.771 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ALA | 0 | -0.050 | -0.043 | 18.049 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | LYS | 1 | 0.887 | 0.932 | 21.801 | 0.116 | 0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.859 | -0.929 | 23.931 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LYS | 1 | 0.882 | 0.951 | 18.302 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | 0.068 | 0.026 | 17.513 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ARG | 1 | 0.901 | 0.949 | 20.996 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | ASP | -1 | -0.871 | -0.930 | 23.402 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | 0.040 | -0.002 | 21.621 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ASP | -1 | -0.879 | -0.915 | 21.119 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | SER | 0 | -0.036 | -0.011 | 21.622 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LEU | 0 | -0.039 | -0.029 | 15.405 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | TRP | 0 | 0.041 | 0.006 | 16.657 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ASP | -1 | -0.904 | -0.943 | 17.368 | -0.182 | -0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | -0.102 | -0.052 | 13.947 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | -0.024 | -0.006 | 11.787 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | MET | 0 | 0.018 | 0.023 | 13.142 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASN | 0 | -0.114 | -0.079 | 15.394 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ASP | -1 | -0.933 | -0.971 | 11.508 | -0.883 | -0.883 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | -0.078 | -0.023 | 12.884 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | LEU | 0 | -0.020 | -0.003 | 9.069 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | PRO | 0 | 0.006 | 0.007 | 6.792 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | 0.011 | 0.030 | 4.850 | -0.799 | -0.799 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | -0.029 | -0.030 | 2.322 | -3.269 | -0.491 | 2.665 | -1.851 | -3.591 | -0.001 |
51 | A | 51 | LEU | 0 | -0.028 | -0.016 | 1.896 | -8.814 | -11.614 | 12.778 | -6.071 | -3.907 | -0.059 |
52 | A | 52 | GLU | -1 | -0.857 | -0.937 | 3.162 | 3.339 | 3.033 | -0.003 | 0.801 | -0.491 | -0.001 |
53 | A | 53 | ILE | 0 | -0.038 | -0.016 | 5.732 | -0.782 | -0.819 | -0.001 | -0.001 | 0.040 | 0.000 |
54 | A | 54 | GLU | -1 | -0.895 | -0.952 | 9.414 | 0.832 | 0.832 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | PHE | 0 | -0.022 | -0.017 | 11.754 | -0.150 | -0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | 0.032 | 0.009 | 15.192 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | HIS | 0 | -0.081 | -0.051 | 17.619 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | LEU | 0 | 0.043 | 0.042 | 19.776 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLY | 0 | 0.017 | 0.005 | 22.134 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.915 | -0.979 | 25.382 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | LYS | 1 | 0.914 | 0.961 | 27.313 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | 0.016 | 0.007 | 24.303 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 1.049 | 1.036 | 21.158 | -0.212 | -0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ARG | 1 | 0.896 | 0.949 | 23.964 | -0.107 | -0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ARG | 1 | 0.798 | 0.900 | 26.868 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | PHE | 0 | 0.024 | 0.014 | 21.873 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | GLY | 0 | 0.039 | 0.017 | 22.075 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | -0.002 | 0.008 | 22.610 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | LEU | 0 | 0.022 | 0.007 | 18.420 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ILE | 0 | -0.063 | -0.026 | 17.933 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | LEU | 0 | -0.015 | 0.009 | 18.138 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | LEU | 0 | 0.017 | 0.007 | 16.626 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | PHE | 0 | -0.019 | -0.036 | 12.439 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ASP | -1 | -0.875 | -0.920 | 13.778 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.910 | -0.961 | 15.395 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ALA | 0 | -0.009 | -0.005 | 12.927 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | GLU | -1 | -0.898 | -0.956 | 10.125 | 0.791 | 0.791 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLU | -1 | -1.051 | -1.034 | 12.019 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.955 | -0.983 | 14.889 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | LEU | 0 | -0.082 | -0.016 | 9.938 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | GLU | -1 | -0.876 | -0.940 | 9.882 | -0.298 | -0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLY | 0 | -0.042 | -0.018 | 8.499 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | HIS | 0 | -0.158 | -0.096 | 5.806 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | LEU | 0 | 0.001 | 0.009 | 5.062 | -0.352 | -0.292 | -0.001 | -0.002 | -0.057 | 0.000 |
85 | A | 85 | ARG | 1 | 0.893 | 0.959 | 4.897 | -1.906 | -1.906 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | PHE | 0 | 0.021 | 0.010 | 7.601 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | ASN | 0 | 0.002 | 0.013 | 9.714 | -0.198 | -0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | VAL | 0 | -0.031 | -0.014 | 12.678 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ARG | 1 | 0.875 | 0.916 | 16.077 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | HIS | -1 | -0.980 | -0.968 | 16.702 | 0.356 | 0.356 | 0.000 | 0.000 | 0.000 | 0.000 |