![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 5JZ9Z
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 | OptHSide |
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 | -723747.961599 |
---|---|
FMO2-HF: Nuclear repulsion | 685654.826465 |
FMO2-HF: Total energy | -38093.135134 |
FMO2-MP2: Total energy | -38207.330439 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031806/ligand_interaction/ligand_F031806.png)
Ligand Interaction
![ligand interaction](./Kdata/F031806/ligand_interaction/ligand_interaction_F031806.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. |
-0.331 | 1.141 | -0.009 | -0.861 | -0.602 | 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 | 0.005 | 0.009 | 3.868 | -2.231 | -0.773 | -0.008 | -0.854 | -0.596 | 0.004 |
4 | A | 6 | PHE | 0 | 0.007 | 0.000 | 6.201 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 7 | PHE | 0 | -0.062 | -0.020 | 8.577 | 0.202 | 0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 8 | TYR | 0 | 0.082 | 0.050 | 6.854 | -0.762 | -0.762 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 9 | PRO | 0 | 0.037 | -0.007 | 6.056 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 10 | GLU | -1 | -0.839 | -0.933 | 8.749 | -0.818 | -0.818 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 11 | ALA | 0 | 0.009 | 0.011 | 11.285 | 0.144 | 0.144 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 12 | ILE | 0 | -0.001 | 0.000 | 7.988 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 13 | VAL | 0 | -0.005 | -0.004 | 11.658 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 14 | LEU | 0 | -0.004 | -0.005 | 13.983 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 15 | ALA | 0 | -0.018 | -0.011 | 15.461 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 16 | TYR | 0 | -0.102 | -0.101 | 13.934 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 17 | LEU | 0 | -0.016 | 0.005 | 17.207 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 18 | TYR | 0 | 0.014 | 0.014 | 19.846 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 19 | ASP | -1 | -0.873 | -0.931 | 22.059 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 20 | ASN | 0 | -0.106 | -0.058 | 21.390 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 21 | GLU | -1 | -0.734 | -0.862 | 23.544 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 22 | GLY | 0 | 0.013 | 0.014 | 25.378 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 23 | ILE | 0 | -0.070 | -0.021 | 20.211 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 24 | ALA | 0 | 0.041 | 0.011 | 23.418 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 25 | THR | 0 | 0.014 | -0.037 | 18.650 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 26 | TYR | 0 | 0.014 | 0.007 | 16.436 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 27 | ASP | -1 | -0.815 | -0.904 | 17.865 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 28 | LEU | 0 | -0.043 | -0.011 | 16.271 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 29 | TYR | 0 | -0.059 | -0.048 | 10.309 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 30 | LYS | 1 | 0.862 | 0.910 | 13.586 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 31 | LYS | 1 | 0.882 | 0.939 | 14.804 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 32 | VAL | 0 | 0.036 | 0.016 | 10.345 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 33 | ASN | 0 | 0.013 | 0.009 | 9.545 | 0.251 | 0.251 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 34 | ALA | 0 | -0.038 | -0.014 | 10.574 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 35 | GLU | -1 | -0.819 | -0.875 | 11.686 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 36 | PHE | 0 | -0.036 | -0.022 | 7.462 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 37 | PRO | 0 | -0.015 | 0.006 | 6.167 | 0.067 | 0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 38 | MET | 0 | -0.019 | 0.008 | 5.017 | 1.276 | 1.290 | -0.001 | -0.007 | -0.006 | 0.000 |
37 | A | 39 | SER | 0 | 0.069 | 0.049 | 6.506 | -0.373 | -0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 40 | THR | 0 | 0.058 | 0.022 | 8.628 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 41 | ALA | 0 | 0.038 | 0.027 | 10.366 | -0.093 | -0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 42 | THR | 0 | 0.045 | 0.008 | 5.715 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 43 | PHE | 0 | -0.022 | -0.011 | 8.944 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 44 | TYR | 0 | 0.012 | -0.022 | 11.224 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 45 | ASP | -1 | -0.895 | -0.930 | 11.537 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 46 | ALA | 0 | 0.003 | 0.002 | 11.112 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 47 | LYS | 1 | 0.816 | 0.894 | 13.085 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 48 | LYS | 1 | 0.921 | 0.958 | 16.389 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 49 | PHE | 0 | 0.052 | 0.028 | 14.881 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 50 | LEU | 0 | 0.026 | 0.011 | 15.362 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 51 | ILE | 0 | -0.061 | -0.024 | 18.299 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 52 | GLN | 0 | -0.028 | -0.021 | 19.929 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 53 | GLU | -1 | -0.906 | -0.936 | 18.836 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 54 | GLY | 0 | -0.024 | -0.009 | 21.524 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 55 | PHE | 0 | -0.018 | -0.035 | 19.497 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 56 | VAL | 0 | 0.012 | -0.003 | 19.338 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 57 | LYS | 1 | 0.937 | 0.974 | 22.479 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 58 | GLU | -1 | -0.756 | -0.855 | 22.015 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 59 | ARG | 1 | 0.815 | 0.916 | 25.036 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 60 | GLN | 0 | 0.034 | 0.038 | 27.666 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 61 | GLU | -1 | -0.792 | -0.865 | 29.569 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 62 | ARG | 1 | 0.941 | 0.957 | 30.466 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 63 | GLY | 0 | 0.030 | 0.011 | 31.579 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 64 | GLU | -1 | -0.854 | -0.911 | 25.528 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 65 | LYS | 1 | 0.861 | 0.924 | 24.221 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 66 | ARG | 1 | 0.840 | 0.917 | 24.178 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 67 | LEU | 0 | 0.020 | 0.017 | 19.201 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 68 | TYR | 0 | -0.006 | -0.037 | 23.574 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 69 | LEU | 0 | 0.001 | 0.012 | 21.170 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 70 | THR | 0 | -0.056 | -0.020 | 24.437 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 71 | GLU | -1 | -0.871 | -0.940 | 26.254 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 72 | LYS | 1 | 0.912 | 0.945 | 23.002 | 0.233 | 0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 73 | GLY | 0 | -0.005 | 0.002 | 22.081 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 74 | LYS | 1 | 0.845 | 0.912 | 22.489 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 75 | LEU | 0 | 0.012 | 0.011 | 24.632 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 76 | PHE | 0 | 0.011 | 0.006 | 17.105 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 77 | ALA | 0 | 0.056 | 0.019 | 19.411 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 78 | ILE | 0 | 0.029 | 0.033 | 20.161 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 79 | SER | 0 | -0.052 | -0.033 | 21.185 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 80 | LEU | 0 | 0.004 | -0.002 | 15.114 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 81 | LYS | 1 | 0.881 | 0.943 | 16.732 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 82 | THR | 0 | 0.031 | 0.021 | 18.400 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 83 | ALA | 0 | -0.002 | 0.023 | 16.267 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 84 | ILE | 0 | 0.015 | 0.004 | 12.458 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 85 | GLU | -1 | -0.780 | -0.879 | 14.778 | -0.130 | -0.130 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 86 | THR | 0 | -0.028 | -0.024 | 17.385 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 87 | TYR | 0 | 0.013 | -0.006 | 8.203 | 0.125 | 0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 88 | LYS | 1 | 0.789 | 0.889 | 13.267 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 89 | GLN | 0 | 0.016 | 0.006 | 14.599 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 90 | ILE | 0 | -0.028 | -0.003 | 15.484 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 91 | LYS | 1 | 0.916 | 0.953 | 10.192 | 0.532 | 0.532 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 92 | LYS | 1 | 0.923 | 0.954 | 14.461 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 93 | ARG | 1 | 0.903 | 0.949 | 17.166 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 94 | HIS | 0 | 0.001 | -0.001 | 16.987 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 95 | HIS | 0 | -0.028 | 0.020 | 12.595 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 96 | HIS | 0 | -0.030 | -0.014 | 17.168 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |