![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2J1NR
Calculation Name: 2YYN-A-Xray372
Preferred Name: Transcription intermediary factor 1-alpha
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2YYN
Chain ID: A
ChEMBL ID: CHEMBL3108638
UniProt ID: O15164
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 | 113 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -989211.415097 |
---|---|
FMO2-HF: Nuclear repulsion | 941605.197783 |
FMO2-HF: Total energy | -47606.217315 |
FMO2-MP2: Total energy | -47743.479748 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031073/ligand_interaction/ligand_F031073.png)
Ligand Interaction
![ligand interaction](./Kdata/F031073/ligand_interaction/ligand_interaction_F031073.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:16:LYS)
Summations of interaction energy for
fragment #1(A:16:LYS)
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. |
-48.618 | -45.249 | 1.531 | -1.832 | -3.068 | -0.012 |
Interaction energy analysis for fragmet #1(A:16:LYS)
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 | 18 | THR | 0 | -0.037 | -0.034 | 3.821 | 4.924 | 5.872 | -0.008 | -0.272 | -0.668 | 0.002 |
4 | A | 19 | PRO | 0 | 0.070 | 0.016 | 5.651 | 1.720 | 1.720 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 20 | ILE | 0 | -0.010 | 0.001 | 8.461 | 1.476 | 1.476 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 21 | ASP | -1 | -0.759 | -0.867 | 7.942 | -25.044 | -25.044 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 22 | LYS | 1 | 0.947 | 0.989 | 8.514 | 20.568 | 20.568 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 23 | ARG | 1 | 0.999 | 0.995 | 10.186 | 16.888 | 16.888 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 24 | LYS | 1 | 0.834 | 0.911 | 13.045 | 19.096 | 19.096 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 25 | CYS | 0 | 0.019 | 0.026 | 11.974 | 1.289 | 1.289 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 26 | GLU | -1 | -0.891 | -0.962 | 13.641 | -15.864 | -15.864 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 27 | ARG | 1 | 0.877 | 0.956 | 16.002 | 13.676 | 13.676 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 28 | LEU | 0 | 0.001 | 0.008 | 15.842 | 0.659 | 0.659 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 29 | LEU | 0 | 0.049 | 0.020 | 15.673 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 30 | LEU | 0 | -0.029 | -0.003 | 19.167 | 0.603 | 0.603 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 31 | PHE | 0 | -0.021 | -0.038 | 21.806 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 32 | LEU | 0 | 0.016 | 0.014 | 20.864 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 33 | TYR | 0 | -0.023 | -0.003 | 20.843 | 0.407 | 0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 34 | CYS | 0 | -0.087 | -0.053 | 25.270 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 35 | HIS | 0 | 0.008 | 0.030 | 27.309 | 0.338 | 0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 36 | GLU | -1 | -0.904 | -0.971 | 29.134 | -8.394 | -8.394 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 37 | MET | 0 | -0.062 | -0.014 | 30.735 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 38 | SER | 0 | 0.041 | 0.014 | 26.281 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 39 | LEU | 0 | 0.019 | 0.007 | 27.791 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 40 | ALA | 0 | -0.020 | -0.006 | 29.468 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 41 | PHE | 0 | -0.020 | -0.013 | 25.286 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 42 | GLN | 0 | -0.038 | -0.018 | 24.333 | -0.564 | -0.564 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 43 | ASP | -1 | -0.901 | -0.946 | 23.783 | -10.941 | -10.941 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 44 | PRO | 0 | -0.048 | -0.015 | 23.288 | 0.112 | 0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 45 | VAL | 0 | 0.037 | 0.031 | 25.581 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 46 | PRO | 0 | 0.030 | 0.008 | 28.697 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 47 | LEU | 0 | 0.011 | -0.011 | 28.591 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 48 | THR | 0 | -0.036 | -0.021 | 31.781 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 49 | VAL | 0 | -0.003 | 0.026 | 32.523 | 0.254 | 0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 50 | PRO | 0 | 0.018 | -0.008 | 34.828 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 51 | ASP | -1 | -0.877 | -0.954 | 35.745 | -8.128 | -8.128 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 52 | TYR | 0 | 0.157 | 0.083 | 27.446 | -0.347 | -0.347 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 53 | TYR | 0 | -0.015 | -0.002 | 26.168 | -0.401 | -0.401 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 54 | LYS | 1 | 0.696 | 0.850 | 30.391 | 8.486 | 8.486 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 55 | ILE | 0 | 0.001 | -0.007 | 31.233 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 56 | ILE | 0 | 0.031 | 0.036 | 25.672 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 57 | LYS | 1 | 0.893 | 0.937 | 24.804 | 10.543 | 10.543 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 58 | ASN | 0 | -0.032 | -0.017 | 20.474 | -0.521 | -0.521 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 59 | PRO | 0 | 0.043 | 0.041 | 22.266 | -0.163 | -0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 60 | MET | 0 | -0.038 | -0.011 | 17.170 | -0.697 | -0.697 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 61 | ASP | -1 | -0.709 | -0.833 | 20.392 | -12.152 | -12.152 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 62 | LEU | 0 | 0.053 | 0.006 | 19.796 | -0.735 | -0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 63 | SER | 0 | -0.090 | -0.043 | 19.042 | -0.668 | -0.668 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 64 | THR | 0 | -0.050 | -0.057 | 17.152 | -0.550 | -0.550 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 65 | ILE | 0 | -0.003 | 0.002 | 14.409 | -0.864 | -0.864 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 66 | LYS | 1 | 0.896 | 0.951 | 14.273 | 11.839 | 11.839 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 67 | LYS | 1 | 0.944 | 0.970 | 14.594 | 12.623 | 12.623 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 68 | ARG | 1 | 0.936 | 0.977 | 11.605 | 17.408 | 17.408 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 69 | LEU | 0 | -0.060 | -0.012 | 9.586 | -1.611 | -1.611 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 70 | GLN | 0 | -0.095 | -0.065 | 9.958 | -0.585 | -0.585 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 71 | GLU | -1 | -0.943 | -0.955 | 12.027 | -16.544 | -16.544 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 72 | ASP | -1 | -0.972 | -0.982 | 8.494 | -24.555 | -24.555 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 73 | TYR | 0 | 0.012 | 0.000 | 9.569 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 74 | SER | 0 | -0.063 | -0.036 | 4.421 | -2.838 | -2.742 | -0.001 | -0.002 | -0.093 | 0.000 |
60 | A | 75 | MET | 0 | -0.002 | 0.003 | 6.115 | -2.706 | -2.706 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 76 | TYR | 0 | -0.073 | -0.060 | 6.955 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 77 | SER | 0 | -0.073 | -0.048 | 2.280 | -4.578 | -4.089 | 1.301 | -0.442 | -1.348 | -0.001 |
63 | A | 78 | LYS | 1 | 0.863 | 0.924 | 2.891 | 28.023 | 29.795 | 0.240 | -1.115 | -0.898 | -0.013 |
64 | A | 79 | PRO | 0 | -0.002 | -0.004 | 5.355 | 2.000 | 2.064 | -0.001 | -0.001 | -0.061 | 0.000 |
65 | A | 80 | GLU | -1 | -0.837 | -0.947 | 8.641 | -25.609 | -25.609 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 81 | ASP | -1 | -0.815 | -0.880 | 6.787 | -32.692 | -32.692 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 82 | PHE | 0 | 0.086 | 0.023 | 9.782 | 1.320 | 1.320 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 83 | VAL | 0 | -0.046 | -0.010 | 12.098 | 1.494 | 1.494 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 84 | ALA | 0 | -0.024 | -0.013 | 13.372 | 1.220 | 1.220 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 85 | ASP | -1 | -0.727 | -0.842 | 14.417 | -17.665 | -17.665 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 86 | PHE | 0 | -0.010 | -0.025 | 15.230 | 0.843 | 0.843 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 87 | ARG | 1 | 0.791 | 0.842 | 17.851 | 15.454 | 15.454 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 88 | LEU | 0 | -0.022 | 0.017 | 18.288 | 0.600 | 0.600 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 89 | ILE | 0 | -0.040 | -0.013 | 20.447 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 90 | PHE | 0 | 0.055 | 0.011 | 21.463 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 91 | GLN | 0 | -0.023 | -0.001 | 21.142 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 92 | ASN | 0 | 0.010 | -0.011 | 23.126 | 0.488 | 0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 93 | CYS | 0 | -0.103 | -0.013 | 26.461 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 94 | ALA | 0 | 0.016 | -0.006 | 28.316 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 95 | GLU | -1 | -1.011 | -0.992 | 28.039 | -10.372 | -10.372 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 96 | PHE | 0 | -0.038 | -0.029 | 30.411 | 0.303 | 0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 97 | ASN | 0 | -0.067 | -0.029 | 31.946 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 98 | GLU | -1 | -0.866 | -0.930 | 34.338 | -7.872 | -7.872 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 99 | PRO | 0 | 0.003 | -0.015 | 35.824 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 100 | ASP | -1 | -0.896 | -0.930 | 36.863 | -7.325 | -7.325 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 101 | SER | 0 | -0.085 | -0.054 | 36.515 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 102 | GLU | -1 | -0.859 | -0.933 | 36.578 | -8.099 | -8.099 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 103 | VAL | 0 | 0.001 | -0.007 | 31.809 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 104 | ALA | 0 | 0.072 | 0.039 | 32.530 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 105 | ASN | 0 | 0.005 | 0.006 | 32.786 | -0.265 | -0.265 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 106 | ALA | 0 | -0.055 | -0.053 | 32.203 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 107 | GLY | 0 | 0.026 | -0.004 | 28.915 | -0.262 | -0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 108 | ILE | 0 | 0.003 | 0.012 | 28.320 | -0.321 | -0.321 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 109 | LYS | 1 | 0.893 | 0.950 | 29.450 | 8.380 | 8.380 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 110 | LEU | 0 | 0.014 | -0.002 | 24.998 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 111 | GLU | -1 | -0.920 | -0.933 | 24.240 | -11.827 | -11.827 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 112 | ASN | 0 | 0.003 | 0.007 | 24.967 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 113 | TYR | 0 | -0.031 | -0.005 | 25.856 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 114 | PHE | 0 | 0.010 | -0.023 | 17.251 | -0.471 | -0.471 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 115 | GLU | -1 | -0.784 | -0.886 | 21.498 | -14.175 | -14.175 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 116 | GLU | -1 | -0.967 | -0.971 | 22.618 | -10.403 | -10.403 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 117 | LEU | 0 | -0.072 | -0.037 | 21.682 | -0.286 | -0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 118 | LEU | 0 | -0.020 | -0.007 | 15.673 | -0.562 | -0.562 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 119 | LYS | 1 | 0.905 | 0.972 | 18.898 | 12.037 | 12.037 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 120 | ASN | 0 | -0.008 | -0.020 | 21.171 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 121 | LEU | 0 | -0.037 | -0.015 | 17.149 | -0.128 | -0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 122 | TYR | 0 | -0.118 | -0.080 | 11.474 | -1.116 | -1.116 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 123 | PRO | 0 | -0.025 | 0.016 | 17.487 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 124 | GLU | -1 | -0.839 | -0.942 | 18.155 | -13.876 | -13.876 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 125 | LYS | 1 | 0.880 | 0.960 | 10.174 | 23.900 | 23.900 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 126 | ARG | 1 | 1.008 | 0.995 | 16.461 | 13.973 | 13.973 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 127 | PHE | 0 | 0.017 | 0.007 | 11.653 | -0.702 | -0.702 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 128 | PRO | 0 | 0.034 | 0.038 | 15.511 | 0.570 | 0.570 | 0.000 | 0.000 | 0.000 | 0.000 |