![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 4JRNN
Calculation Name: 1TBX-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1TBX
Chain ID: A
UniProt ID: P20222
Base Structure: X-ray
Registration Date: 2023-09-20
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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -723091.919307 |
---|---|
FMO2-HF: Nuclear repulsion | 685000.131731 |
FMO2-HF: Total energy | -38091.787576 |
FMO2-MP2: Total energy | -38206.053495 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031807/ligand_interaction/ligand_F031807.png)
Ligand Interaction
![ligand interaction](./Kdata/F031807/ligand_interaction/ligand_interaction_F031807.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:3:SER)
Summations of interaction energy for
fragment #1(A:3:SER)
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. |
-1.712 | -0.198 | -0.009 | -0.876 | -0.629 | 0.004 |
Interaction energy analysis for fragmet #1(A:3:SER)
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 | 5 | PRO | 0 | 0.013 | 0.016 | 3.868 | -2.145 | -0.687 | -0.008 | -0.853 | -0.596 | 0.004 |
4 | A | 6 | PHE | 0 | 0.003 | -0.001 | 6.200 | 0.232 | 0.232 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | PHE | 0 | -0.055 | -0.025 | 8.388 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | TYR | 0 | 0.086 | 0.051 | 6.832 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | PRO | 0 | 0.028 | -0.007 | 6.441 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | GLU | -1 | -0.852 | -0.938 | 8.975 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | ALA | 0 | -0.010 | 0.001 | 11.258 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | ILE | 0 | 0.020 | 0.013 | 7.747 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | VAL | 0 | -0.005 | -0.009 | 11.305 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | LEU | 0 | 0.003 | 0.000 | 13.665 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | ALA | 0 | -0.006 | -0.006 | 15.002 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | TYR | 0 | -0.053 | -0.048 | 13.066 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | -0.014 | 0.012 | 16.777 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | TYR | 0 | 0.029 | 0.015 | 19.479 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | ASP | -1 | -0.869 | -0.930 | 21.615 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | ASN | 0 | -0.183 | -0.097 | 20.568 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | GLU | -1 | -0.809 | -0.928 | 23.115 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | GLY | 0 | 0.013 | 0.015 | 25.035 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | ILE | 0 | -0.052 | -0.017 | 20.059 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | ALA | 0 | 0.046 | 0.010 | 22.990 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | THR | 0 | -0.007 | -0.045 | 18.396 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | TYR | 0 | 0.012 | 0.009 | 15.799 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | ASP | -1 | -0.861 | -0.937 | 17.237 | -0.178 | -0.178 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | LEU | 0 | -0.055 | -0.023 | 15.748 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | TYR | 0 | -0.053 | -0.036 | 9.691 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | LYS | 1 | 0.938 | 0.960 | 12.914 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | LYS | 1 | 0.934 | 0.978 | 14.001 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | VAL | 0 | 0.034 | 0.019 | 9.850 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ASN | 0 | 0.013 | 0.000 | 8.766 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ALA | 0 | -0.051 | -0.016 | 9.685 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.946 | -0.972 | 11.184 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | PHE | 0 | -0.047 | -0.032 | 7.274 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | PRO | 0 | -0.007 | 0.008 | 5.001 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | MET | 0 | -0.016 | 0.030 | 4.228 | -0.441 | -0.385 | -0.001 | -0.023 | -0.033 | 0.000 |
37 | A | 39 | SER | 0 | 0.061 | 0.041 | 5.899 | 0.134 | 0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | THR | 0 | 0.062 | 0.020 | 8.277 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | ALA | 0 | 0.062 | 0.035 | 10.820 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | THR | 0 | 0.031 | 0.009 | 6.058 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | PHE | 0 | 0.048 | 0.006 | 9.454 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | TYR | 0 | -0.062 | -0.064 | 11.243 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | ASP | -1 | -0.905 | -0.936 | 11.562 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | ALA | 0 | 0.001 | 0.004 | 11.280 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | LYS | 1 | 0.887 | 0.951 | 13.229 | 0.126 | 0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | LYS | 1 | 0.912 | 0.945 | 16.496 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | PHE | 0 | 0.045 | 0.026 | 15.015 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | LEU | 0 | 0.031 | 0.014 | 15.386 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | ILE | 0 | -0.053 | -0.016 | 18.516 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | GLN | 0 | -0.018 | -0.017 | 19.338 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | GLU | -1 | -0.932 | -0.950 | 19.089 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | GLY | 0 | -0.038 | -0.020 | 21.769 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | PHE | 0 | -0.010 | -0.038 | 19.418 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | VAL | 0 | 0.013 | 0.000 | 19.417 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | LYS | 1 | 0.935 | 0.968 | 22.684 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.791 | -0.896 | 22.136 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | ARG | 1 | 0.855 | 0.937 | 25.056 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | GLN | 0 | 0.023 | 0.019 | 27.454 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLU | -1 | -0.783 | -0.842 | 29.245 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | ARG | 1 | 0.915 | 0.942 | 30.032 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | GLY | 0 | 0.026 | 0.007 | 31.059 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | GLU | -1 | -0.850 | -0.913 | 25.353 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LYS | 1 | 0.901 | 0.965 | 24.067 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | ARG | 1 | 0.834 | 0.929 | 23.780 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | LEU | 0 | 0.015 | 0.018 | 19.138 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | TYR | 0 | -0.048 | -0.089 | 23.313 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | 0.022 | 0.028 | 21.130 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.097 | -0.011 | 24.629 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.880 | -0.950 | 26.491 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.989 | 0.984 | 23.279 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | -0.008 | -0.005 | 22.301 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | LYS | 1 | 0.886 | 0.943 | 22.694 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LEU | 0 | 0.002 | 0.009 | 24.691 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | PHE | 0 | 0.011 | 0.007 | 17.181 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | ALA | 0 | 0.050 | 0.013 | 19.472 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | ILE | 0 | 0.023 | 0.030 | 20.022 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | SER | 0 | -0.038 | -0.035 | 21.158 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | LEU | 0 | 0.003 | -0.002 | 14.940 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | LYS | 1 | 0.943 | 0.986 | 16.596 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | THR | 0 | -0.024 | 0.014 | 18.192 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | ALA | 0 | 0.061 | 0.052 | 16.145 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | ILE | 0 | -0.001 | -0.004 | 12.375 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | GLU | -1 | -0.864 | -0.931 | 14.778 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | THR | 0 | -0.015 | -0.023 | 17.451 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | TYR | 0 | 0.005 | -0.010 | 8.263 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LYS | 1 | 0.866 | 0.932 | 13.653 | 0.257 | 0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLN | 0 | -0.031 | -0.014 | 14.868 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ILE | 0 | -0.025 | -0.004 | 14.977 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | LYS | 1 | 0.937 | 0.963 | 10.085 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | LYS | 1 | 0.970 | 0.984 | 14.614 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ARG | 1 | 0.895 | 0.938 | 17.339 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | HIS | 0 | 0.005 | 0.008 | 16.967 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | HIS | 0 | -0.005 | 0.029 | 12.941 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | HIS | 0 | -0.061 | -0.030 | 17.214 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |