![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: Z6QVN
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 | 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 | 113 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -993147.74879 |
---|---|
FMO2-HF: Nuclear repulsion | 945540.40296 |
FMO2-HF: Total energy | -47607.34583 |
FMO2-MP2: Total energy | -47744.577143 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031071/ligand_interaction/ligand_F031071.png)
Ligand Interaction
![ligand interaction](./Kdata/F031071/ligand_interaction/ligand_interaction_F031071.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. |
-50.653 | -46.652 | 1.487 | -1.987 | -3.501 | -0.011 |
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 | -0.009 | -0.027 | 3.871 | 2.604 | 3.616 | -0.003 | -0.407 | -0.603 | 0.002 |
4 | A | 19 | PRO | 0 | 0.061 | 0.011 | 6.058 | 1.798 | 1.798 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 20 | ILE | 0 | -0.007 | 0.004 | 8.691 | 1.650 | 1.650 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 21 | ASP | -1 | -0.751 | -0.844 | 8.269 | -25.087 | -25.087 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 22 | LYS | 1 | 0.905 | 0.964 | 7.858 | 22.432 | 22.432 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 23 | ARG | 1 | 0.967 | 0.987 | 9.748 | 17.862 | 17.862 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 24 | LYS | 1 | 0.830 | 0.928 | 12.891 | 20.855 | 20.855 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 25 | CYS | 0 | 0.016 | 0.030 | 11.587 | 1.457 | 1.457 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 26 | GLU | -1 | -0.826 | -0.927 | 12.768 | -17.096 | -17.096 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 27 | ARG | 1 | 0.916 | 0.962 | 15.241 | 14.007 | 14.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 28 | LEU | 0 | -0.005 | 0.000 | 15.537 | 0.712 | 0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 29 | LEU | 0 | 0.036 | 0.021 | 15.886 | 0.724 | 0.724 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 30 | LEU | 0 | -0.025 | -0.003 | 18.702 | 0.647 | 0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 31 | PHE | 0 | -0.017 | -0.022 | 21.103 | 0.542 | 0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 32 | LEU | 0 | 0.008 | 0.008 | 20.221 | 0.448 | 0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 33 | TYR | 0 | -0.028 | -0.033 | 20.518 | 0.190 | 0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 34 | CYS | 0 | -0.096 | -0.046 | 24.509 | 0.441 | 0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 35 | HIS | 0 | 0.032 | 0.029 | 26.705 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 36 | GLU | -1 | -0.804 | -0.888 | 28.540 | -8.845 | -8.845 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 37 | MET | 0 | -0.034 | 0.013 | 30.051 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 38 | SER | 0 | 0.015 | -0.005 | 25.699 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 39 | LEU | 0 | 0.016 | 0.004 | 27.162 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 40 | ALA | 0 | -0.029 | -0.012 | 29.186 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 41 | PHE | 0 | -0.002 | 0.000 | 24.738 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 42 | GLN | 0 | -0.035 | -0.025 | 23.935 | -0.502 | -0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 43 | ASP | -1 | -0.890 | -0.946 | 23.460 | -11.564 | -11.564 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 44 | PRO | 0 | -0.061 | -0.025 | 22.833 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 45 | VAL | 0 | 0.051 | 0.041 | 25.093 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 46 | PRO | 0 | 0.041 | 0.024 | 28.182 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 47 | LEU | 0 | 0.000 | -0.014 | 27.738 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 48 | THR | 0 | -0.024 | -0.008 | 31.307 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 49 | VAL | 0 | -0.012 | 0.007 | 32.290 | 0.273 | 0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 50 | PRO | 0 | 0.018 | 0.001 | 34.452 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 51 | ASP | -1 | -0.783 | -0.900 | 34.990 | -8.345 | -8.345 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 52 | TYR | 0 | 0.082 | 0.051 | 26.420 | -0.338 | -0.338 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 53 | TYR | 0 | -0.037 | -0.039 | 25.759 | -0.406 | -0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 54 | LYS | 1 | 0.757 | 0.870 | 30.036 | 8.434 | 8.434 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 55 | ILE | 0 | -0.024 | -0.005 | 31.243 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 56 | ILE | 0 | 0.033 | 0.029 | 25.546 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 57 | LYS | 1 | 0.839 | 0.917 | 24.898 | 10.451 | 10.451 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 58 | ASN | 0 | -0.045 | -0.019 | 20.292 | -0.704 | -0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 59 | PRO | 0 | 0.068 | 0.053 | 21.630 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 60 | MET | 0 | -0.050 | -0.015 | 16.876 | -0.679 | -0.679 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 61 | ASP | -1 | -0.696 | -0.798 | 19.972 | -12.524 | -12.524 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 62 | LEU | 0 | 0.047 | 0.010 | 19.368 | -0.796 | -0.796 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 63 | SER | 0 | -0.009 | -0.012 | 18.810 | -0.624 | -0.624 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 64 | THR | 0 | -0.050 | -0.075 | 16.773 | -0.489 | -0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 65 | ILE | 0 | 0.013 | 0.023 | 14.139 | -0.900 | -0.900 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 66 | LYS | 1 | 0.879 | 0.944 | 13.834 | 11.950 | 11.950 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 67 | LYS | 1 | 0.825 | 0.914 | 14.066 | 12.913 | 12.913 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 68 | ARG | 1 | 0.917 | 0.943 | 11.170 | 17.672 | 17.672 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 69 | LEU | 0 | -0.012 | 0.005 | 9.198 | -2.029 | -2.029 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 70 | GLN | 0 | -0.133 | -0.089 | 9.562 | -0.485 | -0.485 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 71 | GLU | -1 | -0.886 | -0.941 | 11.616 | -16.688 | -16.688 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 72 | ASP | -1 | -0.941 | -0.972 | 8.005 | -24.676 | -24.676 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 73 | TYR | 0 | -0.062 | -0.029 | 8.116 | -1.396 | -1.396 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 74 | SER | 0 | -0.042 | -0.021 | 4.202 | -2.318 | -2.199 | -0.001 | -0.008 | -0.110 | 0.000 |
60 | A | 75 | MET | 0 | -0.016 | 0.000 | 5.547 | -2.888 | -2.888 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 76 | TYR | 0 | -0.063 | -0.052 | 6.468 | 0.274 | 0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 77 | SER | 0 | -0.091 | -0.065 | 2.416 | -5.817 | -4.574 | 0.718 | -0.593 | -1.367 | 0.000 |
63 | A | 78 | LYS | 1 | 0.796 | 0.871 | 2.632 | 29.785 | 31.353 | 0.774 | -0.978 | -1.365 | -0.013 |
64 | A | 79 | PRO | 0 | 0.024 | 0.009 | 5.376 | 2.002 | 2.061 | -0.001 | -0.001 | -0.056 | 0.000 |
65 | A | 80 | GLU | -1 | -0.738 | -0.876 | 8.666 | -26.529 | -26.529 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 81 | ASP | -1 | -0.757 | -0.835 | 6.677 | -35.179 | -35.179 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 82 | PHE | 0 | 0.074 | 0.029 | 9.324 | 1.317 | 1.317 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 83 | VAL | 0 | -0.040 | -0.014 | 11.941 | 1.541 | 1.541 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 84 | ALA | 0 | -0.016 | -0.001 | 13.545 | 1.226 | 1.226 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 85 | ASP | -1 | -0.706 | -0.819 | 13.899 | -17.923 | -17.923 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 86 | PHE | 0 | -0.008 | -0.029 | 14.853 | 0.846 | 0.846 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 87 | ARG | 1 | 0.766 | 0.840 | 17.965 | 16.107 | 16.107 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 88 | LEU | 0 | -0.012 | 0.009 | 18.087 | 0.693 | 0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 89 | ILE | 0 | -0.038 | -0.009 | 19.774 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 90 | PHE | 0 | 0.054 | 0.023 | 21.867 | 0.494 | 0.494 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 91 | GLN | 0 | -0.019 | -0.010 | 21.362 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 92 | ASN | 0 | -0.019 | -0.028 | 22.338 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 93 | CYS | 0 | -0.085 | -0.018 | 26.078 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 94 | ALA | 0 | 0.014 | -0.007 | 28.253 | 0.379 | 0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 95 | GLU | -1 | -0.984 | -0.981 | 27.725 | -10.730 | -10.730 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 96 | PHE | 0 | -0.040 | -0.022 | 30.431 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 97 | ASN | 0 | -0.060 | -0.029 | 31.583 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 98 | GLU | -1 | -0.833 | -0.920 | 34.069 | -7.991 | -7.991 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 99 | PRO | 0 | 0.020 | 0.015 | 36.149 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 100 | ASP | -1 | -0.898 | -0.945 | 37.201 | -7.496 | -7.496 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 101 | SER | 0 | -0.095 | -0.055 | 36.425 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 102 | GLU | -1 | -0.880 | -0.951 | 36.211 | -8.359 | -8.359 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 103 | VAL | 0 | -0.025 | -0.017 | 31.600 | -0.173 | -0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 104 | ALA | 0 | 0.073 | 0.036 | 32.017 | -0.344 | -0.344 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 105 | ASN | 0 | -0.044 | -0.028 | 32.307 | -0.261 | -0.261 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 106 | ALA | 0 | -0.022 | -0.017 | 31.750 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 107 | GLY | 0 | 0.053 | 0.015 | 28.414 | -0.278 | -0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 108 | ILE | 0 | 0.006 | 0.012 | 28.203 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 109 | LYS | 1 | 0.799 | 0.878 | 29.482 | 8.507 | 8.507 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 110 | LEU | 0 | -0.043 | -0.016 | 24.621 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 111 | GLU | -1 | -0.922 | -0.961 | 24.422 | -11.910 | -11.910 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 112 | ASN | 0 | -0.048 | -0.040 | 24.654 | -0.386 | -0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 113 | TYR | 0 | 0.029 | 0.022 | 25.460 | -0.235 | -0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 114 | PHE | 0 | 0.003 | -0.010 | 17.005 | -0.502 | -0.502 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 115 | GLU | -1 | -0.766 | -0.858 | 20.515 | -15.050 | -15.050 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 116 | GLU | -1 | -0.930 | -0.959 | 22.186 | -10.751 | -10.751 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 117 | LEU | 0 | -0.035 | -0.008 | 21.376 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 118 | LEU | 0 | -0.027 | -0.005 | 15.314 | -0.619 | -0.619 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 119 | LYS | 1 | 0.839 | 0.914 | 18.357 | 12.700 | 12.700 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 120 | ASN | 0 | -0.050 | -0.039 | 20.783 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 121 | LEU | 0 | -0.033 | -0.014 | 16.696 | -0.145 | -0.145 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 122 | TYR | 0 | -0.103 | -0.100 | 10.978 | -1.370 | -1.370 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 123 | PRO | 0 | -0.002 | 0.024 | 16.799 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 124 | GLU | -1 | -0.861 | -0.931 | 17.311 | -14.848 | -14.848 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 125 | LYS | 1 | 0.784 | 0.876 | 9.190 | 26.571 | 26.571 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 126 | ARG | 1 | 0.991 | 0.998 | 15.699 | 13.660 | 13.660 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 127 | PHE | 0 | 0.046 | 0.023 | 11.523 | -0.887 | -0.887 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 128 | PRO | 0 | 0.013 | 0.022 | 15.146 | 0.771 | 0.771 | 0.000 | 0.000 | 0.000 | 0.000 |