![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YV662
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 | OptAll |
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 | -723165.765479 |
---|---|
FMO2-HF: Nuclear repulsion | 685072.025946 |
FMO2-HF: Total energy | -38093.739532 |
FMO2-MP2: Total energy | -38207.815773 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031805/ligand_interaction/ligand_F031805.png)
Ligand Interaction
![ligand interaction](./Kdata/F031805/ligand_interaction/ligand_interaction_F031805.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. |
0.049000000000001 | 1.657 | -0.007 | -0.83 | -0.77 | 0.003 |
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 | 0.020 | 0.014 | 3.835 | -1.063 | 0.452 | -0.006 | -0.823 | -0.686 | 0.003 |
4 | A | 6 | PHE | 0 | -0.027 | -0.016 | 6.208 | 0.476 | 0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | PHE | 0 | -0.005 | 0.002 | 8.125 | 0.354 | 0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | TYR | 0 | 0.074 | 0.049 | 6.839 | -0.485 | -0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | PRO | 0 | 0.033 | -0.008 | 6.279 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | GLU | -1 | -0.837 | -0.920 | 8.789 | -0.519 | -0.519 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | ALA | 0 | 0.001 | -0.003 | 11.615 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | ILE | 0 | -0.011 | -0.006 | 7.517 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | VAL | 0 | -0.001 | -0.007 | 11.606 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | LEU | 0 | -0.021 | -0.005 | 13.903 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | ALA | 0 | -0.015 | -0.003 | 14.807 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | TYR | 0 | -0.082 | -0.091 | 13.234 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | -0.044 | -0.009 | 16.891 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | TYR | 0 | 0.026 | 0.007 | 19.826 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | ASP | -1 | -0.899 | -0.939 | 21.703 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | ASN | 0 | -0.041 | -0.028 | 21.300 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | GLU | -1 | -0.772 | -0.867 | 23.405 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | GLY | 0 | 0.018 | 0.016 | 25.277 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | ILE | 0 | -0.059 | -0.018 | 20.034 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | ALA | 0 | 0.033 | 0.013 | 23.100 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | THR | 0 | -0.003 | -0.046 | 18.457 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | TYR | 0 | 0.029 | 0.009 | 16.325 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | ASP | -1 | -0.820 | -0.895 | 17.750 | 0.223 | 0.223 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | LEU | 0 | -0.010 | 0.003 | 16.112 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | TYR | 0 | -0.060 | -0.039 | 10.313 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | LYS | 1 | 0.854 | 0.898 | 13.430 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | LYS | 1 | 0.883 | 0.941 | 14.614 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | VAL | 0 | 0.017 | 0.011 | 9.974 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ASN | 0 | 0.013 | 0.001 | 9.574 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ALA | 0 | -0.014 | -0.002 | 10.277 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.816 | -0.866 | 10.941 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | PHE | 0 | -0.042 | -0.028 | 6.705 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | PRO | 0 | -0.009 | 0.007 | 5.905 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | MET | 0 | -0.009 | 0.013 | 4.858 | 1.002 | 1.095 | -0.001 | -0.007 | -0.084 | 0.000 |
37 | A | 39 | SER | 0 | 0.035 | 0.021 | 6.396 | -0.892 | -0.892 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | THR | 0 | 0.064 | 0.014 | 8.501 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | ALA | 0 | 0.035 | 0.026 | 10.604 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | THR | 0 | 0.038 | 0.015 | 5.885 | 0.117 | 0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | PHE | 0 | -0.003 | -0.003 | 9.159 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | TYR | 0 | 0.010 | -0.008 | 11.502 | -0.144 | -0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | ASP | -1 | -0.815 | -0.898 | 12.022 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | ALA | 0 | -0.003 | 0.013 | 11.004 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | LYS | 1 | 0.815 | 0.890 | 13.080 | -0.195 | -0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | LYS | 1 | 0.862 | 0.928 | 16.273 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | PHE | 0 | 0.038 | 0.018 | 15.298 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | LEU | 0 | 0.008 | 0.000 | 15.407 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | ILE | 0 | -0.057 | -0.019 | 18.618 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | GLN | 0 | -0.034 | -0.022 | 20.447 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | GLU | -1 | -0.899 | -0.936 | 19.309 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | GLY | 0 | -0.009 | 0.005 | 22.067 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | PHE | 0 | 0.003 | -0.015 | 19.983 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | VAL | 0 | -0.008 | -0.006 | 19.161 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | LYS | 1 | 0.929 | 0.968 | 22.387 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.742 | -0.848 | 21.872 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | ARG | 1 | 0.807 | 0.908 | 24.902 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | GLN | 0 | 0.044 | 0.051 | 27.773 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLU | -1 | -0.764 | -0.862 | 29.421 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | ARG | 1 | 0.938 | 0.961 | 30.371 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | GLY | 0 | 0.054 | 0.028 | 31.497 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | GLU | -1 | -0.878 | -0.916 | 25.184 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LYS | 1 | 0.855 | 0.911 | 23.896 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | ARG | 1 | 0.823 | 0.906 | 23.997 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | LEU | 0 | 0.021 | 0.012 | 19.101 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | TYR | 0 | 0.005 | -0.031 | 23.355 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | -0.013 | -0.004 | 21.097 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.038 | -0.030 | 24.769 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.856 | -0.923 | 26.333 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.882 | 0.932 | 22.952 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | 0.000 | 0.005 | 22.428 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | LYS | 1 | 0.849 | 0.897 | 22.707 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LEU | 0 | 0.028 | 0.016 | 24.451 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | PHE | 0 | 0.006 | 0.008 | 17.204 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | ALA | 0 | 0.054 | 0.028 | 19.540 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | ILE | 0 | 0.025 | 0.025 | 20.018 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | SER | 0 | -0.063 | -0.040 | 21.087 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | LEU | 0 | -0.002 | 0.000 | 15.272 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | LYS | 1 | 0.874 | 0.944 | 15.674 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | THR | 0 | 0.028 | 0.011 | 17.870 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | ALA | 0 | -0.025 | 0.010 | 16.532 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | ILE | 0 | 0.019 | 0.007 | 12.102 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | GLU | -1 | -0.785 | -0.882 | 14.343 | -0.164 | -0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | THR | 0 | -0.023 | -0.027 | 16.841 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | TYR | 0 | 0.019 | 0.008 | 8.333 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LYS | 1 | 0.782 | 0.876 | 12.970 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLN | 0 | 0.029 | 0.019 | 14.479 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ILE | 0 | -0.035 | -0.016 | 15.189 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | LYS | 1 | 0.883 | 0.940 | 10.253 | 0.768 | 0.768 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | LYS | 1 | 0.937 | 0.956 | 14.528 | 0.164 | 0.164 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ARG | 1 | 0.911 | 0.961 | 17.349 | 0.221 | 0.221 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | HIS | 0 | 0.027 | 0.014 | 16.501 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | HIS | 0 | -0.018 | 0.019 | 13.131 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | HIS | 0 | -0.059 | -0.028 | 17.067 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |