![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6NQYZ
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 | 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 | 113 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -990497.431113 |
---|---|
FMO2-HF: Nuclear repulsion | 942890.40322 |
FMO2-HF: Total energy | -47607.027893 |
FMO2-MP2: Total energy | -47744.271247 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F031072/ligand_interaction/ligand_F031072.png)
Ligand Interaction
![ligand interaction](./Kdata/F031072/ligand_interaction/ligand_interaction_F031072.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. |
-47.903 | -44.042 | 1.022 | -1.82 | -3.063 | -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 | -0.043 | -0.052 | 3.821 | 4.053 | 5.146 | -0.007 | -0.378 | -0.709 | 0.002 |
4 | A | 19 | PRO | 0 | 0.084 | 0.022 | 5.658 | 1.632 | 1.632 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 20 | ILE | 0 | -0.009 | 0.002 | 8.450 | 1.631 | 1.631 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 21 | ASP | -1 | -0.765 | -0.838 | 7.959 | -25.772 | -25.772 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 22 | LYS | 1 | 0.920 | 0.968 | 7.840 | 23.387 | 23.387 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 23 | ARG | 1 | 0.993 | 0.993 | 9.742 | 17.644 | 17.644 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 24 | LYS | 1 | 0.830 | 0.911 | 13.033 | 20.022 | 20.022 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 25 | CYS | 0 | 0.005 | 0.021 | 11.940 | 1.445 | 1.445 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 26 | GLU | -1 | -0.860 | -0.943 | 13.265 | -16.622 | -16.622 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 27 | ARG | 1 | 0.897 | 0.958 | 15.603 | 14.030 | 14.030 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 28 | LEU | 0 | 0.003 | 0.009 | 15.766 | 0.708 | 0.708 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 29 | LEU | 0 | 0.038 | 0.022 | 15.944 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 30 | LEU | 0 | -0.016 | -0.001 | 19.048 | 0.635 | 0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 31 | PHE | 0 | -0.025 | -0.032 | 21.520 | 0.537 | 0.537 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 32 | LEU | 0 | 0.011 | 0.012 | 20.656 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 33 | TYR | 0 | -0.006 | -0.003 | 21.003 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 34 | CYS | 0 | -0.095 | -0.056 | 25.153 | 0.423 | 0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 35 | HIS | 0 | 0.016 | 0.029 | 27.192 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 36 | GLU | -1 | -0.835 | -0.936 | 29.017 | -8.693 | -8.693 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 37 | MET | 0 | -0.052 | 0.000 | 30.650 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 38 | SER | 0 | 0.055 | 0.024 | 26.211 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 39 | LEU | 0 | 0.008 | 0.011 | 27.690 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 40 | ALA | 0 | -0.018 | -0.008 | 29.369 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 41 | PHE | 0 | -0.018 | -0.013 | 25.234 | -0.146 | -0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 42 | GLN | 0 | -0.033 | -0.026 | 24.241 | -0.535 | -0.535 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 43 | ASP | -1 | -0.902 | -0.949 | 23.688 | -11.358 | -11.358 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 44 | PRO | 0 | -0.045 | -0.018 | 23.192 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 45 | VAL | 0 | 0.041 | 0.037 | 25.510 | 0.421 | 0.421 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 46 | PRO | 0 | 0.039 | 0.024 | 28.629 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 47 | LEU | 0 | 0.004 | -0.012 | 28.358 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 48 | THR | 0 | -0.028 | -0.017 | 31.732 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 49 | VAL | 0 | -0.013 | 0.018 | 32.772 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 50 | PRO | 0 | 0.035 | 0.000 | 34.779 | -0.183 | -0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 51 | ASP | -1 | -0.831 | -0.911 | 35.632 | -8.238 | -8.238 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 52 | TYR | 0 | 0.157 | 0.077 | 27.378 | -0.352 | -0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 53 | TYR | 0 | 0.003 | 0.001 | 26.071 | -0.405 | -0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 54 | LYS | 1 | 0.657 | 0.812 | 30.357 | 8.525 | 8.525 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 55 | ILE | 0 | 0.009 | 0.000 | 31.615 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 56 | ILE | 0 | 0.027 | 0.035 | 25.924 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 57 | LYS | 1 | 0.839 | 0.906 | 24.801 | 10.465 | 10.465 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 58 | ASN | 0 | -0.038 | -0.017 | 20.626 | -0.638 | -0.638 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 59 | PRO | 0 | 0.058 | 0.050 | 22.449 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 60 | MET | 0 | -0.044 | -0.015 | 17.390 | -0.723 | -0.723 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 61 | ASP | -1 | -0.697 | -0.810 | 20.296 | -12.464 | -12.464 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 62 | LEU | 0 | 0.048 | 0.006 | 19.705 | -0.765 | -0.765 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 63 | SER | 0 | -0.024 | -0.016 | 18.942 | -0.701 | -0.701 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 64 | THR | 0 | -0.102 | -0.105 | 17.249 | -0.560 | -0.560 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 65 | ILE | 0 | -0.005 | 0.008 | 14.467 | -0.882 | -0.882 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 66 | LYS | 1 | 0.882 | 0.946 | 14.175 | 12.052 | 12.052 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 67 | LYS | 1 | 0.893 | 0.951 | 14.454 | 12.744 | 12.744 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 68 | ARG | 1 | 0.921 | 0.950 | 11.553 | 17.799 | 17.799 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 69 | LEU | 0 | -0.044 | -0.006 | 9.351 | -1.887 | -1.887 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 70 | GLN | 0 | -0.123 | -0.083 | 9.577 | -0.879 | -0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 71 | GLU | -1 | -0.903 | -0.935 | 11.760 | -17.073 | -17.073 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 72 | ASP | -1 | -0.972 | -0.987 | 7.787 | -25.598 | -25.598 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 73 | TYR | 0 | -0.005 | -0.003 | 9.540 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 74 | SER | 0 | -0.056 | -0.032 | 4.382 | -2.626 | -2.527 | -0.001 | -0.003 | -0.095 | 0.000 |
60 | A | 75 | MET | 0 | 0.003 | 0.012 | 6.088 | -2.527 | -2.527 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 76 | TYR | 0 | -0.075 | -0.063 | 6.890 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 77 | SER | 0 | -0.068 | -0.047 | 2.595 | -5.513 | -4.616 | 0.691 | -0.385 | -1.203 | -0.001 |
63 | A | 78 | LYS | 1 | 0.800 | 0.867 | 2.818 | 30.770 | 32.482 | 0.340 | -1.052 | -1.000 | -0.013 |
64 | A | 79 | PRO | 0 | 0.033 | 0.006 | 5.254 | 1.924 | 1.984 | -0.001 | -0.002 | -0.056 | 0.000 |
65 | A | 80 | GLU | -1 | -0.771 | -0.893 | 8.646 | -25.723 | -25.723 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 81 | ASP | -1 | -0.768 | -0.834 | 6.611 | -34.699 | -34.699 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 82 | PHE | 0 | 0.098 | 0.035 | 9.591 | 1.315 | 1.315 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 83 | VAL | 0 | -0.039 | -0.010 | 12.168 | 1.554 | 1.554 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 84 | ALA | 0 | -0.019 | -0.009 | 13.409 | 1.271 | 1.271 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 85 | ASP | -1 | -0.709 | -0.820 | 14.419 | -18.078 | -18.078 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 86 | PHE | 0 | -0.016 | -0.027 | 15.218 | 0.844 | 0.844 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 87 | ARG | 1 | 0.786 | 0.834 | 18.038 | 15.795 | 15.795 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 88 | LEU | 0 | -0.023 | 0.013 | 18.790 | 0.621 | 0.621 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 89 | ILE | 0 | -0.043 | -0.018 | 20.236 | 0.635 | 0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 90 | PHE | 0 | 0.052 | 0.012 | 21.780 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 91 | GLN | 0 | -0.022 | 0.001 | 21.334 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 92 | ASN | 0 | 0.013 | -0.007 | 23.130 | 0.537 | 0.537 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 93 | CYS | 0 | -0.108 | -0.023 | 26.615 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 94 | ALA | 0 | 0.025 | -0.003 | 28.416 | 0.381 | 0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 95 | GLU | -1 | -1.009 | -0.987 | 28.062 | -10.611 | -10.611 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 96 | PHE | 0 | -0.041 | -0.032 | 30.563 | 0.311 | 0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 97 | ASN | 0 | -0.059 | -0.027 | 32.151 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 98 | GLU | -1 | -0.854 | -0.922 | 34.476 | -7.999 | -7.999 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 99 | PRO | 0 | 0.013 | -0.009 | 35.877 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 100 | ASP | -1 | -0.913 | -0.944 | 36.931 | -7.440 | -7.440 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 101 | SER | 0 | -0.068 | -0.048 | 36.696 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 102 | GLU | -1 | -0.849 | -0.930 | 36.643 | -8.288 | -8.288 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 103 | VAL | 0 | 0.002 | -0.004 | 31.947 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 104 | ALA | 0 | 0.076 | 0.043 | 32.608 | -0.319 | -0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 105 | ASN | 0 | -0.042 | -0.023 | 32.833 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 106 | ALA | 0 | -0.049 | -0.033 | 32.257 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 107 | GLY | 0 | 0.022 | -0.008 | 28.968 | -0.282 | -0.282 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 108 | ILE | 0 | 0.015 | 0.017 | 28.339 | -0.342 | -0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 109 | LYS | 1 | 0.839 | 0.931 | 29.420 | 8.484 | 8.484 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 110 | LEU | 0 | 0.007 | -0.007 | 24.937 | -0.250 | -0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 111 | GLU | -1 | -0.915 | -0.935 | 24.293 | -12.051 | -12.051 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 112 | ASN | 0 | -0.039 | -0.028 | 24.900 | -0.340 | -0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 113 | TYR | 0 | -0.005 | 0.005 | 26.048 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 114 | PHE | 0 | -0.005 | -0.026 | 17.184 | -0.510 | -0.510 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 115 | GLU | -1 | -0.775 | -0.874 | 20.955 | -14.687 | -14.687 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 116 | GLU | -1 | -0.944 | -0.958 | 22.453 | -10.649 | -10.649 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 117 | LEU | 0 | -0.054 | -0.025 | 21.630 | -0.305 | -0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 118 | LEU | 0 | -0.027 | -0.012 | 15.542 | -0.610 | -0.610 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 119 | LYS | 1 | 0.878 | 0.939 | 18.674 | 12.451 | 12.451 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 120 | ASN | 0 | -0.050 | -0.043 | 20.899 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 121 | LEU | 0 | -0.041 | -0.009 | 17.017 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 122 | TYR | 0 | -0.101 | -0.091 | 11.142 | -1.057 | -1.057 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 123 | PRO | 0 | 0.003 | 0.028 | 17.194 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 124 | GLU | -1 | -0.859 | -0.932 | 17.959 | -14.290 | -14.290 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 125 | LYS | 1 | 0.800 | 0.900 | 9.389 | 25.792 | 25.792 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 126 | ARG | 1 | 0.990 | 0.987 | 16.148 | 14.143 | 14.143 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 127 | PHE | 0 | 0.035 | 0.013 | 11.515 | -0.827 | -0.827 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 128 | PRO | 0 | 0.028 | 0.037 | 15.374 | 0.569 | 0.569 | 0.000 | 0.000 | 0.000 | 0.000 |