![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R9158
Calculation Name: 5I27-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5I27
Chain ID: A
UniProt ID: P10258
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 | 87 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -640643.282807 |
---|---|
FMO2-HF: Nuclear repulsion | 605766.151213 |
FMO2-HF: Total energy | -34877.131595 |
FMO2-MP2: Total energy | -34981.565573 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024435/ligand_interaction/ligand_F024435.png)
Ligand Interaction
![ligand interaction](./Kdata/F024435/ligand_interaction/ligand_interaction_F024435.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:7:SER)
Summations of interaction energy for
fragment #1(A:7:SER)
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. |
1.195 | 5.531 | 2.147 | -2.343 | -4.139 | -0.011 |
Interaction energy analysis for fragmet #1(A:7:SER)
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 | 9 | GLY | 0 | 0.079 | 0.046 | 3.815 | -0.328 | 1.116 | -0.023 | -0.650 | -0.771 | 0.002 |
4 | A | 10 | GLN | 0 | 0.058 | 0.022 | 2.726 | -3.097 | -0.601 | 2.167 | -1.575 | -3.088 | -0.013 |
5 | A | 11 | LYS | 1 | 0.981 | 0.988 | 4.594 | 2.243 | 2.363 | -0.001 | -0.012 | -0.106 | 0.000 |
6 | A | 12 | LEU | 0 | 0.042 | 0.031 | 6.392 | 0.460 | 0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | PHE | 0 | 0.089 | 0.053 | 8.151 | 0.260 | 0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | VAL | 0 | -0.001 | -0.017 | 7.048 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | SER | 0 | -0.071 | -0.037 | 9.516 | 0.236 | 0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | VAL | 0 | 0.015 | 0.001 | 11.970 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | LEU | 0 | 0.008 | 0.008 | 12.385 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | GLN | 0 | -0.018 | -0.014 | 12.714 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ARG | 1 | 0.967 | 0.998 | 15.372 | 0.415 | 0.415 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | LEU | 0 | 0.029 | 0.008 | 17.168 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LEU | 0 | 0.020 | -0.005 | 16.801 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | SER | 0 | 0.014 | 0.021 | 19.002 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | GLU | -1 | -0.981 | -0.992 | 21.114 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ARG | 1 | 0.857 | 0.946 | 22.816 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | GLY | 0 | -0.023 | -0.007 | 24.529 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | LEU | 0 | -0.055 | -0.018 | 21.637 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | HIS | 0 | 0.023 | 0.007 | 19.240 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | VAL | 0 | 0.006 | -0.004 | 14.327 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | LYS | 1 | 0.981 | 0.986 | 14.514 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | GLU | -1 | -0.848 | -0.929 | 9.046 | -0.986 | -0.986 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | SER | 0 | 0.018 | 0.003 | 9.591 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | SER | 0 | -0.005 | -0.005 | 10.542 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | ALA | 0 | 0.060 | 0.025 | 10.676 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ILE | 0 | -0.036 | -0.018 | 5.232 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | GLU | -1 | -0.795 | -0.901 | 7.234 | -0.463 | -0.463 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | PHE | 0 | -0.028 | -0.007 | 9.674 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | TYR | 0 | 0.040 | 0.017 | 3.976 | -0.191 | -0.108 | 0.000 | -0.023 | -0.060 | 0.000 |
32 | A | 38 | GLN | 0 | -0.022 | -0.025 | 3.423 | 0.462 | 0.655 | 0.004 | -0.083 | -0.114 | 0.000 |
33 | A | 39 | PHE | 0 | -0.005 | -0.004 | 6.755 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | LEU | 0 | -0.002 | 0.000 | 9.737 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ILE | 0 | 0.011 | -0.001 | 4.811 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | LYS | 1 | 0.873 | 0.966 | 9.033 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | VAL | 0 | -0.061 | -0.037 | 10.818 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | SER | 0 | -0.023 | -0.016 | 12.447 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | PRO | 0 | -0.014 | -0.005 | 10.770 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | TRP | 0 | 0.005 | -0.014 | 11.683 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | PHE | 0 | -0.034 | -0.017 | 11.271 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | PRO | 0 | -0.069 | -0.051 | 8.247 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | GLU | -1 | -0.972 | -0.964 | 10.582 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | GLU | -1 | -0.917 | -0.978 | 13.434 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | GLY | 0 | -0.038 | -0.019 | 14.765 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | GLY | 0 | -0.048 | -0.028 | 15.402 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | LEU | 0 | -0.047 | -0.031 | 15.236 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | ASN | 0 | 0.037 | 0.025 | 17.791 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | LEU | 0 | 0.067 | 0.022 | 20.795 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | GLN | 0 | 0.008 | -0.008 | 22.948 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | ASP | -1 | -0.754 | -0.858 | 18.016 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | TRP | 0 | -0.027 | -0.015 | 14.106 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | LYS | 1 | 0.932 | 0.947 | 19.304 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | ARG | 1 | 0.881 | 0.961 | 19.247 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | VAL | 0 | 0.072 | 0.037 | 14.979 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | GLY | 0 | 0.011 | 0.012 | 17.677 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | ARG | 1 | 0.888 | 0.936 | 20.018 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLU | -1 | -0.800 | -0.885 | 17.262 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | MET | 0 | -0.034 | 0.004 | 14.259 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | LYS | 1 | 0.931 | 0.961 | 18.371 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | ARG | 1 | 0.956 | 0.994 | 19.931 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | TYR | 0 | 0.082 | 0.033 | 15.811 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ALA | 0 | -0.019 | -0.027 | 19.703 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | ALA | 0 | -0.068 | -0.020 | 21.872 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | GLU | -1 | -0.962 | -0.979 | 20.735 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | HIS | 0 | -0.049 | -0.037 | 19.092 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | GLY | 0 | 0.046 | 0.046 | 22.034 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | THR | 0 | -0.040 | -0.040 | 22.012 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | ASP | -1 | -0.885 | -0.931 | 21.514 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | SER | 0 | -0.028 | -0.043 | 16.795 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | ILE | 0 | -0.025 | 0.028 | 16.628 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | PRO | 0 | -0.059 | -0.017 | 13.426 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | LYS | 1 | 0.918 | 0.952 | 15.401 | 0.284 | 0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | GLN | 0 | -0.033 | -0.033 | 13.277 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | ALA | 0 | -0.016 | -0.001 | 15.293 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | TYR | 0 | 0.056 | 0.022 | 16.471 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | PRO | 0 | 0.021 | -0.002 | 19.718 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | ILE | 0 | 0.027 | 0.015 | 14.470 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | TRP | 0 | -0.014 | -0.001 | 17.006 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | LEU | 0 | -0.012 | -0.001 | 18.317 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | GLN | 0 | 0.034 | 0.010 | 20.529 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | LEU | 0 | -0.010 | -0.004 | 15.661 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | ARG | 1 | 0.835 | 0.904 | 20.029 | 0.129 | 0.129 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | GLU | -1 | -0.865 | -0.920 | 22.381 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | ILE | 0 | -0.023 | -0.010 | 20.766 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | LEU | 0 | -0.104 | -0.035 | 19.323 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 93 | THR | 0 | -0.028 | -0.005 | 23.794 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |