![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R5MK8
Calculation Name: 2CX6-A-Xray372
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: 2023-03-13
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 | OptH |
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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -706076.615884 |
---|---|
FMO2-HF: Nuclear repulsion | 668512.06641 |
FMO2-HF: Total energy | -37564.549474 |
FMO2-MP2: Total energy | -37675.492899 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F019005/ligand_interaction/ligand_F019005.png)
Ligand Interaction
![ligand interaction](./Kdata/F019005/ligand_interaction/ligand_interaction_F019005.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. |
-12.329 | -10.89 | 15.278 | -7.731 | -8.985 | -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 | 0.009 | 0.015 | 3.881 | 1.316 | 2.980 | -0.002 | -0.683 | -0.979 | 0.002 |
4 | A | 4 | TYR | 0 | -0.003 | -0.003 | 6.211 | -0.608 | -0.608 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | THR | 0 | 0.007 | 0.004 | 9.546 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | PHE | 0 | -0.010 | -0.001 | 11.777 | -0.082 | -0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ASP | -1 | -0.789 | -0.888 | 15.845 | 0.206 | 0.206 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | PHE | 0 | -0.032 | -0.055 | 17.672 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | ASP | -1 | -0.935 | -0.948 | 21.517 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | GLU | -1 | -1.008 | -1.014 | 21.358 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | ILE | 0 | -0.064 | -0.010 | 19.002 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLU | -1 | -0.876 | -0.946 | 23.615 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.123 | -0.055 | 26.062 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLN | 0 | 0.051 | 0.001 | 23.507 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | GLU | -1 | -0.887 | -0.962 | 23.150 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.865 | -0.942 | 23.878 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | PHE | 0 | 0.045 | 0.029 | 15.307 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | TYR | 0 | 0.025 | 0.014 | 19.358 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | ARG | 1 | 0.909 | 0.982 | 19.810 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | ASP | -1 | -0.845 | -0.932 | 18.309 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | PHE | 0 | 0.007 | 0.005 | 12.574 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | SER | 0 | -0.026 | -0.042 | 15.517 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | -0.056 | -0.026 | 17.355 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | THR | 0 | -0.026 | -0.001 | 12.230 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | PHE | 0 | -0.064 | -0.026 | 8.582 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | GLY | 0 | -0.029 | 0.001 | 13.489 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | LEU | 0 | -0.036 | -0.015 | 14.768 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ALA | 0 | -0.048 | -0.042 | 18.043 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | LYS | 1 | 0.889 | 0.933 | 21.796 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | ASP | -1 | -0.859 | -0.929 | 23.923 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | LYS | 1 | 0.883 | 0.952 | 18.302 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | VAL | 0 | 0.066 | 0.025 | 17.508 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | ARG | 1 | 0.903 | 0.950 | 20.991 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | ASP | -1 | -0.871 | -0.930 | 23.396 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | LEU | 0 | 0.037 | -0.004 | 21.615 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ASP | -1 | -0.878 | -0.914 | 21.116 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | SER | 0 | -0.034 | -0.010 | 21.622 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LEU | 0 | -0.041 | -0.030 | 15.399 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | TRP | 0 | 0.040 | 0.005 | 16.658 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | ASP | -1 | -0.902 | -0.942 | 17.370 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | VAL | 0 | -0.101 | -0.051 | 13.945 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | -0.027 | -0.007 | 11.785 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | MET | 0 | 0.017 | 0.023 | 13.147 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | ASN | 0 | -0.111 | -0.078 | 15.407 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | ASP | -1 | -0.932 | -0.971 | 11.519 | -0.881 | -0.881 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | VAL | 0 | -0.076 | -0.022 | 12.892 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | LEU | 0 | -0.022 | -0.004 | 9.067 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | PRO | 0 | 0.008 | 0.008 | 6.788 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | LEU | 0 | 0.011 | 0.029 | 4.857 | -0.779 | -0.779 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | PRO | 0 | -0.025 | -0.028 | 2.313 | -3.337 | -0.521 | 2.606 | -1.839 | -3.582 | -0.001 |
51 | A | 51 | LEU | 0 | -0.026 | -0.014 | 1.900 | -8.799 | -11.499 | 12.680 | -6.073 | -3.907 | -0.059 |
52 | A | 52 | GLU | -1 | -0.859 | -0.938 | 3.154 | 3.454 | 3.090 | -0.004 | 0.867 | -0.499 | -0.001 |
53 | A | 53 | ILE | 0 | -0.033 | -0.013 | 5.701 | -0.810 | -0.848 | -0.001 | -0.001 | 0.040 | 0.000 |
54 | A | 54 | GLU | -1 | -0.899 | -0.955 | 9.383 | 0.871 | 0.871 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | PHE | 0 | -0.016 | -0.012 | 11.723 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | 0.021 | 0.002 | 15.140 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | HIS | 0 | -0.077 | -0.050 | 17.588 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | LEU | 0 | 0.046 | 0.045 | 19.745 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | GLY | 0 | 0.008 | -0.001 | 22.103 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.919 | -0.980 | 25.351 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | LYS | 1 | 0.923 | 0.965 | 27.282 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | 0.019 | 0.009 | 24.272 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | ARG | 1 | 1.037 | 1.029 | 21.127 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | ARG | 1 | 0.898 | 0.950 | 23.933 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | ARG | 1 | 0.804 | 0.904 | 26.838 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | PHE | 0 | 0.026 | 0.014 | 21.862 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | GLY | 0 | 0.035 | 0.014 | 22.065 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ALA | 0 | 0.003 | 0.011 | 22.602 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | LEU | 0 | 0.025 | 0.009 | 18.411 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | ILE | 0 | -0.071 | -0.031 | 17.913 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | LEU | 0 | -0.014 | 0.010 | 18.121 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | LEU | 0 | 0.021 | 0.010 | 16.623 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | PHE | 0 | -0.018 | -0.036 | 12.432 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | ASP | -1 | -0.881 | -0.924 | 13.775 | 0.392 | 0.392 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.907 | -0.959 | 15.367 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ALA | 0 | -0.006 | -0.003 | 12.927 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | GLU | -1 | -0.900 | -0.958 | 10.097 | 0.849 | 0.849 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | GLU | -1 | -1.051 | -1.034 | 11.994 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.952 | -0.982 | 14.868 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | LEU | 0 | -0.080 | -0.015 | 9.946 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | GLU | -1 | -0.874 | -0.938 | 9.872 | -0.288 | -0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLY | 0 | -0.044 | -0.020 | 8.445 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | HIS | 0 | -0.155 | -0.094 | 5.802 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | LEU | 0 | 0.003 | 0.010 | 5.069 | -0.314 | -0.253 | -0.001 | -0.002 | -0.058 | 0.000 |
85 | A | 85 | ARG | 1 | 0.894 | 0.960 | 4.870 | -2.006 | -2.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | PHE | 0 | 0.026 | 0.014 | 7.568 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | ASN | 0 | 0.001 | 0.013 | 9.686 | -0.222 | -0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | VAL | 0 | -0.020 | -0.003 | 12.648 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | ARG | 1 | 0.894 | 0.924 | 16.046 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | HIS | 0 | -0.050 | -0.006 | 16.645 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |