![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: K9R33
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 | 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 | 87 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -643095.157909 |
---|---|
FMO2-HF: Nuclear repulsion | 608217.249811 |
FMO2-HF: Total energy | -34877.908098 |
FMO2-MP2: Total energy | -34982.326493 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024433/ligand_interaction/ligand_F024433.png)
Ligand Interaction
![ligand interaction](./Kdata/F024433/ligand_interaction/ligand_interaction_F024433.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. |
-1.569 | 3.051 | 2.217 | -2.495 | -4.342 | -0.013 |
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 | 0.070 | 0.044 | 3.866 | -1.153 | -0.074 | -0.007 | -0.468 | -0.605 | 0.003 |
4 | A | 10 | GLN | 0 | 0.036 | 0.028 | 2.646 | -3.934 | -1.081 | 2.195 | -1.801 | -3.248 | -0.016 |
5 | A | 11 | LYS | 1 | 0.908 | 0.927 | 4.863 | 1.695 | 1.789 | -0.001 | -0.009 | -0.084 | 0.000 |
6 | A | 12 | LEU | 0 | 0.036 | 0.036 | 6.810 | 0.198 | 0.198 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | PHE | 0 | 0.068 | 0.039 | 8.252 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | VAL | 0 | -0.004 | -0.006 | 7.480 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | SER | 0 | -0.045 | -0.025 | 10.120 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | VAL | 0 | 0.019 | 0.011 | 12.536 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | LEU | 0 | 0.010 | 0.007 | 11.704 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | GLN | 0 | -0.023 | -0.030 | 12.592 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | ARG | 1 | 0.879 | 0.947 | 15.733 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | LEU | 0 | -0.005 | -0.004 | 17.598 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LEU | 0 | 0.026 | 0.016 | 17.269 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | SER | 0 | 0.011 | -0.003 | 19.222 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | GLU | -1 | -0.852 | -0.918 | 21.689 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | ARG | 1 | 0.793 | 0.894 | 22.626 | 0.162 | 0.162 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | GLY | 0 | 0.011 | 0.016 | 25.077 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | LEU | 0 | -0.047 | -0.009 | 22.163 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | HIS | 0 | 0.030 | 0.007 | 19.609 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | VAL | 0 | 0.000 | -0.005 | 14.454 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | LYS | 1 | 0.991 | 0.998 | 15.013 | 0.450 | 0.450 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | GLU | -1 | -0.778 | -0.883 | 8.795 | -1.477 | -1.477 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | SER | 0 | 0.021 | 0.006 | 9.706 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | SER | 0 | 0.002 | 0.002 | 10.346 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | ALA | 0 | 0.052 | 0.032 | 10.869 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ILE | 0 | -0.023 | -0.013 | 5.292 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | GLU | -1 | -0.767 | -0.855 | 7.171 | -0.595 | -0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | PHE | 0 | -0.001 | -0.001 | 9.677 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | TYR | 0 | 0.023 | 0.000 | 3.401 | -0.440 | -0.252 | 0.010 | -0.058 | -0.140 | 0.000 |
32 | A | 38 | GLN | 0 | -0.024 | -0.035 | 3.168 | 0.541 | 0.885 | 0.021 | -0.154 | -0.210 | 0.000 |
33 | A | 39 | PHE | 0 | 0.008 | -0.001 | 6.587 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | LEU | 0 | -0.003 | 0.003 | 9.646 | 0.123 | 0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ILE | 0 | 0.007 | -0.009 | 4.580 | 0.101 | 0.163 | -0.001 | -0.005 | -0.055 | 0.000 |
36 | A | 42 | LYS | 1 | 0.872 | 0.957 | 8.864 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | VAL | 0 | -0.068 | -0.031 | 10.801 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | SER | 0 | -0.026 | -0.040 | 12.552 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | PRO | 0 | -0.020 | -0.011 | 10.657 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | TRP | 0 | 0.029 | -0.002 | 11.255 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | PHE | 0 | -0.033 | -0.018 | 10.766 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | PRO | 0 | -0.077 | -0.057 | 8.053 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | GLU | -1 | -0.984 | -0.973 | 10.555 | 0.926 | 0.926 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | GLU | -1 | -0.835 | -0.917 | 13.751 | 0.364 | 0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | GLY | 0 | -0.031 | 0.005 | 15.097 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | GLY | 0 | 0.001 | 0.004 | 15.614 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | LEU | 0 | -0.049 | -0.029 | 15.256 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | ASN | 0 | 0.009 | -0.007 | 17.497 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | LEU | 0 | 0.063 | 0.024 | 20.623 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | GLN | 0 | 0.033 | 0.023 | 23.048 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | ASP | -1 | -0.736 | -0.874 | 17.887 | 0.234 | 0.234 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | TRP | 0 | -0.028 | -0.015 | 14.015 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | LYS | 1 | 0.889 | 0.933 | 19.334 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | ARG | 1 | 0.749 | 0.880 | 18.732 | -0.352 | -0.352 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | VAL | 0 | 0.072 | 0.028 | 14.936 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | GLY | 0 | -0.005 | 0.002 | 17.495 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | ARG | 1 | 0.901 | 0.948 | 20.223 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLU | -1 | -0.776 | -0.846 | 17.196 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | MET | 0 | -0.026 | -0.003 | 14.067 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | LYS | 1 | 0.928 | 0.960 | 18.133 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | ARG | 1 | 0.829 | 0.895 | 18.137 | -0.220 | -0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | TYR | 0 | 0.072 | 0.037 | 15.667 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | ALA | 0 | 0.005 | -0.013 | 19.520 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | ALA | 0 | -0.050 | -0.018 | 21.639 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | GLU | -1 | -0.857 | -0.896 | 19.989 | 0.177 | 0.177 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | HIS | 0 | -0.060 | -0.031 | 18.382 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | GLY | 0 | 0.051 | 0.050 | 21.797 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | THR | 0 | -0.045 | -0.043 | 21.902 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 75 | ASP | -1 | -0.904 | -0.947 | 21.406 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | SER | 0 | -0.019 | -0.026 | 16.193 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | ILE | 0 | -0.024 | 0.010 | 16.220 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | PRO | 0 | -0.039 | -0.016 | 12.899 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | LYS | 1 | 0.855 | 0.913 | 15.349 | 0.536 | 0.536 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | GLN | 0 | -0.031 | -0.036 | 13.536 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 81 | ALA | 0 | -0.017 | -0.010 | 15.100 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 82 | TYR | 0 | 0.058 | 0.024 | 16.413 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 83 | PRO | 0 | 0.015 | -0.003 | 19.802 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 84 | ILE | 0 | 0.017 | 0.010 | 14.864 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 85 | TRP | 0 | -0.021 | -0.008 | 17.298 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 86 | LEU | 0 | 0.017 | 0.013 | 18.462 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 87 | GLN | 0 | 0.019 | 0.001 | 20.664 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 88 | LEU | 0 | 0.005 | -0.005 | 15.463 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 89 | ARG | 1 | 0.767 | 0.861 | 19.965 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 90 | GLU | -1 | -0.784 | -0.852 | 22.536 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 91 | ILE | 0 | -0.045 | -0.021 | 21.048 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 92 | LEU | 0 | -0.080 | -0.019 | 19.187 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 93 | THR | 0 | -0.041 | -0.027 | 23.713 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |