![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 7G81K
Calculation Name: 2V1Y-A-Xray372
Preferred Name: PI3-kinase p85-alpha subunit
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 2V1Y
Chain ID: A
ChEMBL ID: CHEMBL2506
UniProt ID: P27986
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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -690535.737452 |
---|---|
FMO2-HF: Nuclear repulsion | 652799.456254 |
FMO2-HF: Total energy | -37736.281198 |
FMO2-MP2: Total energy | -37844.73224 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F023899/ligand_interaction/ligand_F023899.png)
Ligand Interaction
![ligand interaction](./Kdata/F023899/ligand_interaction/ligand_interaction_F023899.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:MET)
Summations of interaction energy for
fragment #1(A:16: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. |
-13.267 | -6.477 | 9.47 | -3.566 | -12.697 | -0.014 |
Interaction energy analysis for fragmet #1(A:16: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 | 18 | PRO | 0 | -0.019 | -0.014 | 3.333 | -1.843 | -0.156 | 0.038 | -0.862 | -0.863 | 0.000 |
4 | A | 19 | ARG | 1 | 0.842 | 0.891 | 5.585 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 20 | ILE | 0 | -0.042 | -0.023 | 2.830 | -2.039 | -0.489 | 1.167 | -0.533 | -2.184 | -0.003 |
6 | A | 21 | LEU | 0 | 0.031 | 0.011 | 5.558 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 22 | VAL | 0 | 0.005 | -0.006 | 5.432 | -0.218 | -0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 23 | GLU | -1 | -0.950 | -0.972 | 7.888 | -0.271 | -0.271 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 24 | CYS | 0 | -0.016 | 0.003 | 10.384 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 25 | LEU | 0 | -0.001 | -0.009 | 12.568 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 26 | LEU | 0 | 0.044 | 0.018 | 15.485 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 27 | PRO | 0 | 0.010 | 0.007 | 18.142 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 28 | ASN | 0 | -0.018 | -0.019 | 20.935 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 29 | GLY | 0 | -0.024 | -0.018 | 21.765 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 30 | MET | 0 | -0.054 | -0.012 | 20.683 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 31 | ILE | 0 | 0.005 | 0.007 | 14.594 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 32 | VAL | 0 | 0.017 | 0.003 | 14.961 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 33 | THR | 0 | -0.022 | -0.005 | 11.965 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 34 | LEU | 0 | 0.047 | 0.021 | 11.261 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 35 | GLU | -1 | -0.824 | -0.869 | 8.942 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 36 | CYS | 0 | -0.018 | 0.003 | 6.740 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 37 | LEU | 0 | 0.039 | 0.018 | 6.285 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 38 | ARG | 1 | 0.933 | 0.963 | 2.348 | -1.633 | -0.055 | 2.606 | -1.219 | -2.965 | 0.001 |
24 | A | 39 | GLU | -1 | -0.937 | -0.983 | 4.235 | 0.805 | 1.118 | 0.002 | 0.024 | -0.339 | 0.000 |
25 | A | 40 | ALA | 0 | -0.020 | 0.004 | 7.297 | -0.382 | -0.382 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 41 | THR | 0 | 0.014 | 0.004 | 7.902 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 42 | LEU | 0 | 0.048 | 0.027 | 7.456 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 43 | ILE | 0 | 0.036 | 0.020 | 10.187 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 44 | THR | 0 | -0.044 | -0.021 | 12.614 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 45 | ILE | 0 | 0.046 | 0.020 | 7.263 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 46 | LYS | 1 | 0.881 | 0.952 | 11.578 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 47 | HIS | 0 | 0.020 | 0.009 | 14.068 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 48 | GLU | -1 | -0.942 | -0.983 | 13.158 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 49 | LEU | 0 | -0.028 | -0.011 | 13.478 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 50 | PHE | 0 | 0.027 | 0.007 | 15.418 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 51 | LYS | 1 | 0.820 | 0.926 | 18.625 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 52 | GLU | -1 | -0.894 | -0.953 | 16.824 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 53 | ALA | 0 | 0.027 | 0.004 | 19.231 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 54 | ARG | 1 | 0.931 | 0.960 | 20.602 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 55 | LYS | 1 | 0.866 | 0.954 | 21.151 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 56 | TYR | 0 | -0.028 | -0.001 | 18.733 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 57 | PRO | 0 | -0.004 | -0.015 | 23.733 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 58 | LEU | 0 | 0.034 | 0.006 | 24.943 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 59 | HIS | 0 | 0.037 | 0.039 | 24.720 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 60 | GLN | 0 | -0.015 | -0.017 | 25.688 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 61 | LEU | 0 | -0.049 | -0.026 | 26.590 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 62 | LEU | 0 | -0.061 | -0.010 | 21.441 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 63 | GLN | 0 | 0.034 | 0.019 | 24.448 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 64 | ASP | -1 | -0.810 | -0.896 | 23.682 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 65 | GLU | -1 | -0.880 | -0.952 | 18.595 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 66 | SER | 0 | -0.121 | -0.095 | 19.137 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 67 | SER | 0 | -0.037 | -0.011 | 20.995 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 68 | TYR | 0 | -0.036 | -0.017 | 17.956 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 69 | ILE | 0 | 0.028 | 0.027 | 15.168 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 70 | PHE | 0 | -0.010 | -0.008 | 10.714 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 71 | VAL | 0 | -0.005 | -0.005 | 12.550 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 72 | SER | 0 | -0.038 | -0.025 | 8.065 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 73 | VAL | 0 | -0.002 | 0.006 | 9.579 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 74 | THR | 0 | 0.061 | 0.040 | 8.403 | -0.320 | -0.320 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 75 | GLN | 0 | -0.049 | -0.046 | 6.232 | -0.298 | -0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 76 | GLU | -1 | -0.937 | -0.976 | 9.630 | -0.729 | -0.729 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 77 | ALA | 0 | -0.035 | -0.013 | 12.323 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 78 | GLU | -1 | -0.901 | -0.929 | 13.385 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 79 | ARG | 1 | 0.896 | 0.947 | 12.867 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 80 | GLU | -1 | -0.858 | -0.945 | 11.059 | -0.759 | -0.759 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 81 | GLU | -1 | -0.918 | -0.970 | 12.488 | -0.406 | -0.406 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 82 | PHE | 0 | -0.035 | -0.027 | 8.307 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 83 | PHE | 0 | 0.063 | 0.013 | 12.813 | 0.041 | 0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 84 | ASP | -1 | -0.881 | -0.911 | 13.853 | -0.169 | -0.169 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 85 | GLU | -1 | -0.896 | -0.970 | 12.338 | -0.300 | -0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 86 | THR | 0 | -0.067 | -0.053 | 12.647 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 87 | ARG | 1 | 0.905 | 0.967 | 9.248 | 0.767 | 0.767 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 88 | ARG | 1 | 0.884 | 0.939 | 7.606 | -0.458 | -0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 89 | LEU | 0 | 0.034 | 0.020 | 2.396 | -1.448 | -0.521 | 1.370 | -0.414 | -1.883 | -0.001 |
75 | A | 90 | CYS | 0 | -0.042 | -0.049 | 2.668 | -5.852 | -3.928 | 4.218 | -2.986 | -3.157 | -0.010 |
76 | A | 91 | ASP | -1 | -0.869 | -0.919 | 3.778 | 0.402 | -1.879 | 0.000 | 2.564 | -0.284 | -0.001 |
77 | A | 92 | LEU | 0 | -0.052 | -0.028 | 4.165 | -0.073 | 0.041 | -0.001 | -0.007 | -0.106 | 0.000 |
78 | A | 93 | ARG | 1 | 0.883 | 0.961 | 4.613 | 1.173 | 1.243 | -0.001 | -0.002 | -0.067 | 0.000 |
79 | A | 94 | LEU | 0 | 0.014 | 0.014 | 3.147 | -0.037 | 0.540 | 0.072 | -0.103 | -0.547 | 0.000 |
80 | A | 95 | PHE | 0 | -0.015 | -0.002 | 4.962 | -0.346 | -0.279 | -0.001 | 0.000 | -0.067 | 0.000 |
81 | A | 96 | GLN | 0 | -0.046 | -0.034 | 6.370 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 97 | PRO | 0 | 0.011 | 0.013 | 3.729 | -0.708 | -0.481 | 0.001 | -0.026 | -0.202 | 0.000 |
83 | A | 98 | PHE | 0 | 0.022 | 0.009 | 4.976 | 0.591 | 0.628 | -0.001 | -0.002 | -0.033 | 0.000 |
84 | A | 99 | LEU | 0 | 0.000 | 0.004 | 6.864 | -0.279 | -0.279 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 100 | LYS | 1 | 0.940 | 0.973 | 9.933 | 0.505 | 0.505 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 101 | VAL | 0 | -0.007 | 0.004 | 13.591 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 102 | ILE | 0 | -0.063 | -0.035 | 15.721 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 103 | GLU | -1 | -0.899 | -0.949 | 18.638 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 104 | PRO | 0 | -0.009 | -0.007 | 19.277 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 105 | VAL | 0 | -0.040 | -0.002 | 21.579 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |