![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 94792
Calculation Name: 3K1I-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3K1I
Chain ID: A
UniProt ID: O25709
Base Structure: X-ray
Registration Date: 2023-06-22
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 | 106 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -838716.034463 |
---|---|
FMO2-HF: Nuclear repulsion | 796353.696559 |
FMO2-HF: Total energy | -42362.337904 |
FMO2-MP2: Total energy | -42487.594785 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F027081/ligand_interaction/ligand_F027081.png)
Ligand Interaction
![ligand interaction](./Kdata/F027081/ligand_interaction/ligand_interaction_F027081.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:19:SER)
Summations of interaction energy for
fragment #1(A:19: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. |
-8.23 | -3.881 | 3.501 | -3.269 | -4.58 | 0.006 |
Interaction energy analysis for fragmet #1(A:19: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 | 21 | ALA | 0 | 0.028 | 0.024 | 3.238 | -0.777 | 0.919 | 0.023 | -0.686 | -1.031 | 0.000 |
4 | A | 22 | LYS | 1 | 1.072 | 1.039 | 2.030 | -3.904 | -2.124 | 3.474 | -2.246 | -3.008 | 0.008 |
5 | A | 23 | LEU | 0 | -0.019 | -0.020 | 3.992 | 1.514 | 1.777 | -0.001 | -0.046 | -0.216 | 0.000 |
6 | A | 24 | ILE | 0 | 0.030 | 0.040 | 5.583 | 0.867 | 0.867 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 25 | GLU | -1 | -0.822 | -0.890 | 7.862 | -1.026 | -1.026 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 26 | MET | 0 | 0.011 | -0.001 | 7.515 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 27 | LEU | 0 | -0.052 | -0.025 | 9.074 | 0.298 | 0.298 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 28 | TYR | 0 | 0.052 | 0.011 | 11.519 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 29 | GLU | -1 | -0.902 | -0.974 | 11.974 | -0.635 | -0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 30 | GLY | 0 | -0.076 | -0.046 | 13.730 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 31 | ILE | 0 | 0.015 | 0.010 | 15.462 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 32 | LEU | 0 | 0.000 | -0.007 | 17.136 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 33 | ARG | 1 | 0.902 | 0.957 | 13.887 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 34 | PHE | 0 | 0.003 | -0.004 | 17.124 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 35 | SER | 0 | 0.048 | 0.035 | 21.110 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 36 | SER | 0 | -0.003 | 0.007 | 22.989 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 37 | GLN | 0 | -0.044 | -0.012 | 23.575 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 38 | ALA | 0 | 0.025 | -0.015 | 25.257 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 39 | LYS | 1 | 0.878 | 0.946 | 27.046 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 40 | ARG | 1 | 0.952 | 0.980 | 28.697 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 41 | CYS | 0 | -0.095 | -0.027 | 29.184 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 42 | ILE | 0 | -0.007 | 0.012 | 30.699 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 43 | GLU | -1 | -0.937 | -0.973 | 33.231 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 44 | ASN | 0 | -0.070 | -0.045 | 34.067 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 45 | GLU | -1 | -0.948 | -0.957 | 35.860 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 46 | ASP | -1 | -0.917 | -0.945 | 33.484 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 47 | ILE | 0 | 0.036 | -0.014 | 33.244 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 48 | GLU | -1 | -0.871 | -0.939 | 32.525 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 49 | LYS | 1 | 0.927 | 0.973 | 29.107 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 50 | LYS | 1 | 0.903 | 0.961 | 28.331 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 51 | ILE | 0 | -0.015 | -0.005 | 28.300 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 52 | TYR | 0 | -0.024 | -0.006 | 22.360 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 53 | TYR | 0 | -0.002 | -0.030 | 23.355 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 54 | ILE | 0 | 0.017 | 0.009 | 23.323 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 55 | ASN | 0 | 0.045 | -0.011 | 23.586 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 56 | ARG | 1 | 0.928 | 0.992 | 16.803 | 0.127 | 0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 57 | VAL | 0 | -0.033 | -0.021 | 19.223 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 58 | THR | 0 | -0.024 | -0.011 | 19.383 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 59 | ASP | -1 | -0.888 | -0.922 | 17.773 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 60 | ILE | 0 | -0.032 | 0.001 | 13.632 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 61 | PHE | 0 | -0.008 | -0.017 | 15.011 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 62 | THR | 0 | -0.023 | -0.010 | 17.554 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 63 | GLU | -1 | -0.978 | -0.995 | 11.243 | -0.275 | -0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 64 | LEU | 0 | -0.030 | -0.029 | 11.579 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 65 | LEU | 0 | -0.046 | -0.020 | 13.705 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 66 | ASN | 0 | -0.019 | -0.008 | 15.015 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 67 | ILE | 0 | -0.065 | -0.010 | 8.869 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 68 | LEU | 0 | -0.076 | -0.029 | 12.528 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 69 | ASP | -1 | -0.834 | -0.913 | 13.973 | 0.286 | 0.286 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 70 | TYR | 0 | -0.083 | -0.042 | 16.056 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 71 | GLU | -1 | -0.968 | -1.000 | 17.804 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 72 | LYS | 1 | 0.926 | 0.968 | 12.743 | -0.381 | -0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 73 | GLY | 0 | 0.008 | 0.016 | 17.078 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 74 | GLY | 0 | 0.030 | 0.002 | 17.873 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 75 | GLU | -1 | -0.906 | -0.932 | 21.291 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 76 | VAL | 0 | 0.033 | 0.008 | 16.611 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 77 | ALA | 0 | 0.007 | 0.021 | 18.226 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 78 | VAL | 0 | 0.035 | 0.024 | 19.124 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 79 | TYR | 0 | -0.008 | 0.004 | 20.794 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 80 | LEU | 0 | 0.019 | -0.007 | 15.841 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 81 | THR | 0 | 0.019 | -0.020 | 19.931 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 82 | GLY | 0 | -0.009 | 0.008 | 21.298 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 83 | LEU | 0 | 0.008 | 0.005 | 20.433 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 84 | TYR | 0 | 0.053 | 0.017 | 14.595 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 85 | THR | 0 | -0.030 | -0.021 | 20.870 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 86 | HIS | 0 | -0.029 | -0.007 | 23.848 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 87 | GLN | 0 | 0.038 | 0.002 | 21.743 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 88 | ILE | 0 | 0.035 | 0.021 | 21.133 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 89 | LYS | 1 | 0.937 | 0.965 | 24.678 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 90 | VAL | 0 | -0.018 | -0.004 | 27.088 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 91 | LEU | 0 | 0.027 | 0.009 | 22.802 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 92 | THR | 0 | -0.038 | -0.010 | 27.396 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 93 | GLN | 0 | -0.014 | -0.017 | 30.053 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 94 | ALA | 0 | 0.037 | 0.025 | 29.929 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 95 | ASN | 0 | -0.020 | 0.003 | 30.477 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 96 | VAL | 0 | -0.055 | -0.035 | 32.434 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 97 | GLU | -1 | -0.944 | -0.973 | 35.507 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 98 | ASN | 0 | -0.016 | -0.016 | 34.744 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 99 | ASP | -1 | -0.795 | -0.889 | 33.979 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 100 | ALA | 0 | 0.028 | -0.007 | 31.988 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 101 | SER | 0 | -0.043 | -0.022 | 31.125 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 102 | LYS | 1 | 0.930 | 0.959 | 30.959 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 103 | ILE | 0 | 0.054 | 0.023 | 26.383 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 104 | ASP | -1 | -0.876 | -0.942 | 26.420 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 105 | LEU | 0 | -0.061 | -0.026 | 26.860 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 106 | VAL | 0 | 0.010 | 0.016 | 22.556 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 107 | LEU | 0 | -0.054 | -0.041 | 22.446 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 108 | ASN | 0 | -0.008 | -0.002 | 22.400 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 109 | VAL | 0 | 0.020 | 0.026 | 21.193 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 110 | ALA | 0 | -0.021 | -0.008 | 18.938 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 111 | ARG | 1 | 0.933 | 0.943 | 18.283 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 112 | GLY | 0 | 0.014 | 0.015 | 19.135 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 113 | LEU | 0 | -0.038 | -0.022 | 16.301 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 114 | LEU | 0 | -0.023 | -0.007 | 13.076 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 115 | GLU | -1 | -0.974 | -0.997 | 14.475 | -0.456 | -0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 116 | ALA | 0 | 0.049 | 0.052 | 16.451 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 117 | TRP | 0 | -0.041 | -0.043 | 7.193 | 0.224 | 0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 118 | ARG | 1 | 0.849 | 0.904 | 11.163 | 0.636 | 0.636 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 119 | GLU | -1 | -0.922 | -0.950 | 12.795 | -0.422 | -0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 120 | ILE | 0 | -0.098 | -0.046 | 11.566 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 121 | HIS | 1 | 0.825 | 0.915 | 7.465 | 1.194 | 1.194 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 122 | SER | 0 | 0.030 | 0.029 | 9.162 | -0.176 | -0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 123 | ASP | -1 | -0.954 | -0.954 | 8.598 | -0.940 | -0.940 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 124 | GLU | -1 | -0.975 | -0.994 | 3.701 | -5.670 | -5.060 | 0.005 | -0.291 | -0.325 | -0.002 |