![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: M3K8Z
Calculation Name: 1T4A-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1T4A
Chain ID: A
UniProt ID: P12049
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 80 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -491882.345612 |
---|---|
FMO2-HF: Nuclear repulsion | 458311.483056 |
FMO2-HF: Total energy | -33570.862556 |
FMO2-MP2: Total energy | -33665.961383 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F023740/ligand_interaction/ligand_F023740.png)
Ligand Interaction
![ligand interaction](./Kdata/F023740/ligand_interaction/ligand_interaction_F023740.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. |
-19.244 | -11.119 | 5.939 | -5.498 | -8.567 | -0.027 |
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 | LYS | 1 | 0.951 | 0.996 | 3.552 | 0.403 | 2.548 | 0.007 | -1.019 | -1.133 | -0.001 |
4 | A | 4 | VAL | 0 | -0.009 | -0.024 | 5.603 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 5 | LYS | 1 | 0.914 | 0.982 | 8.857 | 0.833 | 0.833 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 6 | VAL | 0 | 0.007 | -0.009 | 12.032 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | TYR | 0 | -0.046 | -0.033 | 14.993 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | VAL | 0 | 0.010 | 0.006 | 18.582 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 9 | SER | 0 | 0.021 | 0.010 | 21.226 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | LEU | 0 | 0.011 | 0.013 | 24.839 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | LYS | 1 | 0.932 | 0.978 | 27.627 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | GLU | -1 | -0.922 | -0.956 | 29.748 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | SER | 0 | -0.057 | -0.027 | 32.330 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | VAL | 0 | -0.039 | -0.007 | 31.604 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | LEU | 0 | 0.012 | -0.003 | 33.775 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | ASP | -1 | -0.749 | -0.880 | 31.037 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | PRO | 0 | -0.012 | -0.012 | 33.821 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | GLN | 0 | 0.003 | 0.007 | 28.718 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | GLY | 0 | 0.064 | 0.024 | 32.951 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | SER | 0 | -0.005 | -0.001 | 33.477 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ALA | 0 | -0.012 | -0.003 | 36.521 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | VAL | 0 | 0.000 | -0.005 | 32.513 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | GLN | 0 | 0.011 | 0.010 | 35.841 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | HIS | 0 | 0.011 | 0.016 | 37.565 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | ALA | 0 | -0.005 | -0.005 | 38.247 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | 0.003 | -0.007 | 34.424 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | HIS | 0 | -0.024 | -0.018 | 39.042 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | SER | 0 | -0.045 | -0.015 | 42.247 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | MET | 0 | -0.115 | -0.045 | 38.439 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | THR | 0 | -0.078 | -0.049 | 42.203 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | TYR | 0 | 0.023 | 0.024 | 38.716 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | ASN | 0 | 0.000 | -0.018 | 40.120 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | GLU | -1 | -0.912 | -0.952 | 38.989 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | VAL | 0 | -0.044 | -0.019 | 35.472 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLN | 0 | -0.046 | -0.016 | 37.457 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ASP | -1 | -0.888 | -0.959 | 34.064 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | VAL | 0 | -0.043 | -0.006 | 31.601 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | ARG | 1 | 0.840 | 0.931 | 29.222 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | ILE | 0 | -0.040 | -0.032 | 26.963 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | GLY | 0 | 0.012 | 0.003 | 24.427 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | LYS | 1 | 0.886 | 0.939 | 20.243 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | TYR | 0 | -0.035 | -0.042 | 13.453 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | MET | 0 | -0.040 | -0.021 | 14.209 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | GLU | -1 | -0.842 | -0.884 | 9.838 | -0.431 | -0.431 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | LEU | 0 | -0.010 | -0.006 | 8.604 | 0.135 | 0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | THR | 0 | -0.009 | 0.002 | 3.033 | -0.781 | -0.423 | 1.259 | -0.324 | -1.294 | 0.001 |
47 | A | 47 | ILE | 0 | -0.030 | -0.019 | 3.575 | -0.336 | 0.354 | 0.007 | -0.160 | -0.537 | 0.000 |
48 | A | 48 | GLU | -1 | -0.914 | -0.950 | 2.374 | -6.985 | -4.536 | 4.448 | -3.208 | -3.689 | -0.035 |
49 | A | 49 | LYS | 1 | 0.929 | 0.955 | 3.256 | -7.108 | -5.273 | 0.218 | -0.696 | -1.356 | 0.008 |
50 | A | 50 | SER | 0 | -0.021 | -0.020 | 4.946 | -0.567 | -0.508 | -0.001 | -0.004 | -0.054 | 0.000 |
51 | A | 51 | ASP | -1 | -0.941 | -0.976 | 8.633 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ARG | 1 | 0.949 | 0.991 | 10.927 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | ASP | -1 | -0.850 | -0.904 | 10.563 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | -0.042 | -0.039 | 7.370 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | ASP | -1 | -0.868 | -0.944 | 10.230 | -0.192 | -0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | VAL | 0 | -0.001 | -0.006 | 13.685 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | LEU | 0 | -0.004 | -0.003 | 8.531 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | VAL | 0 | -0.005 | -0.010 | 10.527 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LYS | 1 | 1.000 | 1.000 | 12.884 | 0.167 | 0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | GLU | -1 | -0.897 | -0.937 | 15.766 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | MET | 0 | -0.030 | -0.010 | 9.922 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | CYS | 0 | -0.042 | -0.025 | 15.292 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | GLU | -1 | -0.979 | -0.987 | 17.560 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LYS | 1 | 0.849 | 0.928 | 18.878 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | LEU | 0 | -0.068 | -0.028 | 16.114 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | LEU | 0 | -0.042 | -0.028 | 13.798 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | 0.022 | 0.015 | 18.357 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ASN | 0 | 0.027 | 0.037 | 21.600 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | THR | 0 | 0.042 | 0.002 | 23.118 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | VAL | 0 | -0.052 | -0.019 | 25.654 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ILE | 0 | -0.043 | -0.032 | 28.099 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | GLU | -1 | -0.915 | -0.954 | 24.053 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | ASP | -1 | -0.848 | -0.934 | 24.573 | -0.133 | -0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | TYR | 0 | -0.008 | -0.029 | 17.856 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | ARG | 1 | 0.889 | 0.957 | 18.218 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | TYR | 0 | 0.008 | -0.012 | 12.618 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | GLU | -1 | -0.887 | -0.933 | 13.381 | -0.439 | -0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | VAL | 0 | -0.037 | -0.024 | 7.613 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | GLU | -1 | -0.858 | -0.929 | 8.040 | -0.747 | -0.747 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLU | -1 | -0.966 | -0.982 | 3.609 | -3.945 | -3.356 | 0.001 | -0.087 | -0.504 | 0.000 |