![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R5238
Calculation Name: 3K1H-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3K1H
Chain ID: A
UniProt ID: O25709
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 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 | 115 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -924231.453749 |
---|---|
FMO2-HF: Nuclear repulsion | 878179.659311 |
FMO2-HF: Total energy | -46051.794438 |
FMO2-MP2: Total energy | -46184.678823 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021975/ligand_interaction/ligand_F021975.png)
Ligand Interaction
![ligand interaction](./Kdata/F021975/ligand_interaction/ligand_interaction_F021975.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:33:PHE)
Summations of interaction energy for
fragment #1(A:33:PHE)
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. |
-19.022 | -11.788 | 9.11 | -7.558 | -8.785 | -0.055 |
Interaction energy analysis for fragmet #1(A:33:PHE)
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 | 35 | ARG | 1 | 0.788 | 0.885 | 2.694 | -2.263 | 2.486 | 0.745 | -2.686 | -2.808 | -0.007 |
4 | A | 36 | ASP | -1 | -0.844 | -0.902 | 5.062 | -1.043 | -1.012 | -0.001 | -0.005 | -0.025 | 0.000 |
5 | A | 37 | MET | 0 | -0.068 | -0.023 | 7.841 | 0.219 | 0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 38 | LYS | 1 | 0.842 | 0.913 | 11.258 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 39 | ASN | 0 | -0.031 | -0.024 | 13.887 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 40 | ILE | 0 | 0.120 | 0.070 | 15.788 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 41 | ASN | 0 | 0.000 | 0.002 | 17.848 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 42 | GLU | -1 | -0.822 | -0.911 | 12.418 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 43 | SER | 0 | 0.016 | 0.000 | 13.301 | -0.109 | -0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 44 | VAL | 0 | 0.039 | 0.019 | 14.497 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 45 | GLY | 0 | -0.019 | -0.011 | 15.597 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 46 | ALA | 0 | 0.018 | -0.001 | 10.565 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 47 | LEU | 0 | 0.031 | 0.019 | 12.480 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 48 | GLN | 0 | 0.022 | 0.022 | 14.296 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 49 | VAL | 0 | -0.028 | -0.016 | 13.477 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 50 | LEU | 0 | 0.054 | 0.032 | 9.900 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 51 | GLN | 0 | 0.035 | 0.019 | 13.365 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 52 | ILE | 0 | -0.061 | -0.040 | 16.945 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 53 | ALA | 0 | -0.002 | -0.003 | 14.193 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 54 | CYS | 0 | 0.030 | 0.009 | 14.213 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 55 | LYS | 1 | 0.931 | 0.966 | 16.846 | 0.427 | 0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 56 | LYS | 1 | 0.886 | 0.952 | 19.273 | 0.289 | 0.289 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 57 | LEU | 0 | 0.003 | 0.008 | 14.749 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 58 | PHE | 0 | 0.029 | 0.026 | 19.394 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 59 | ASN | 0 | 0.000 | -0.011 | 21.450 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 60 | LYS | 1 | 0.766 | 0.875 | 22.454 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 61 | SER | 0 | -0.035 | -0.029 | 21.735 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 62 | MET | 0 | 0.024 | 0.025 | 23.852 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 63 | GLY | 0 | 0.065 | 0.035 | 27.064 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 64 | LEU | 0 | -0.122 | -0.055 | 23.629 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 65 | GLU | -1 | -0.824 | -0.928 | 27.670 | -0.159 | -0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 66 | ASP | -1 | -0.925 | -0.952 | 29.209 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 67 | LYS | 1 | 0.771 | 0.900 | 28.088 | 0.147 | 0.147 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 68 | ASP | -1 | -0.814 | -0.909 | 31.652 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 69 | ALA | 0 | 0.034 | -0.002 | 30.893 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 70 | LEU | 0 | -0.031 | 0.009 | 30.132 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 71 | GLN | 0 | 0.023 | 0.000 | 29.844 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 72 | ALA | 0 | 0.036 | 0.018 | 27.515 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 73 | SER | 0 | -0.084 | -0.049 | 25.831 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 74 | ILE | 0 | 0.007 | -0.005 | 25.004 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 75 | ILE | 0 | 0.036 | 0.021 | 23.969 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 76 | LYS | 1 | 0.930 | 0.966 | 21.686 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 77 | GLN | 0 | -0.009 | -0.003 | 19.972 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 78 | GLU | -1 | -0.809 | -0.894 | 20.004 | -0.122 | -0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 79 | LEU | 0 | -0.039 | -0.018 | 18.548 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 80 | ARG | 1 | 0.784 | 0.858 | 15.959 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 81 | GLU | -1 | -0.848 | -0.901 | 15.222 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 82 | ILE | 0 | -0.067 | -0.035 | 16.074 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 83 | VAL | 0 | 0.008 | 0.002 | 10.821 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 84 | GLU | -1 | -0.827 | -0.893 | 11.396 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 85 | ASN | 0 | -0.095 | -0.051 | 12.187 | 0.121 | 0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 86 | CYS | 0 | -0.075 | -0.012 | 10.698 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 87 | GLN | 0 | -0.018 | -0.008 | 9.595 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 88 | PHE | 0 | 0.030 | 0.007 | 9.739 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 89 | LEU | 0 | -0.029 | -0.017 | 9.570 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 90 | ALA | 0 | 0.006 | 0.008 | 9.237 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 91 | SER | 0 | 0.015 | 0.019 | 4.379 | -0.192 | -0.072 | -0.001 | -0.010 | -0.109 | 0.000 |
60 | A | 92 | PRO | 0 | 0.048 | 0.018 | 3.838 | -0.649 | -0.245 | 0.002 | -0.039 | -0.366 | 0.000 |
61 | A | 93 | LEU | 0 | -0.026 | -0.014 | 6.017 | -0.414 | -0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 94 | PHE | 0 | 0.082 | 0.036 | 7.073 | -0.248 | -0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 95 | ASP | -1 | -0.838 | -0.906 | 3.816 | -2.323 | -1.874 | 0.000 | -0.157 | -0.293 | 0.000 |
64 | A | 96 | THR | 0 | -0.065 | -0.040 | 1.900 | -12.971 | -12.130 | 8.354 | -4.495 | -4.700 | -0.048 |
65 | A | 97 | GLN | 0 | -0.038 | -0.029 | 3.584 | 1.793 | 2.433 | 0.011 | -0.166 | -0.484 | 0.000 |
66 | A | 98 | LEU | 0 | -0.021 | -0.020 | 5.944 | 0.086 | 0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 99 | ASN | 0 | 0.016 | 0.020 | 8.115 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 100 | ILE | 0 | 0.004 | -0.017 | 10.535 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 101 | ALA | 0 | 0.012 | 0.020 | 13.607 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 102 | ILE | 0 | -0.028 | -0.025 | 16.763 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 103 | ASN | 0 | 0.004 | 0.002 | 20.050 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 104 | ASP | -1 | -0.926 | -0.956 | 21.846 | -0.241 | -0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 105 | GLU | -1 | -0.952 | -0.950 | 20.722 | -0.373 | -0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 106 | ILE | 0 | -0.062 | -0.049 | 14.141 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 107 | PHE | 0 | 0.020 | 0.019 | 15.744 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 108 | SER | 0 | -0.007 | -0.034 | 10.349 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 109 | MET | 0 | -0.035 | 0.015 | 10.934 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 110 | ILE | 0 | -0.003 | -0.012 | 4.944 | -0.449 | -0.449 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 111 | VAL | 0 | -0.016 | -0.002 | 7.863 | 0.467 | 0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 112 | VAL | 0 | 0.025 | 0.008 | 7.106 | -0.422 | -0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 113 | ASN | 0 | 0.026 | -0.028 | 7.893 | 0.218 | 0.218 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 114 | PRO | 0 | -0.001 | 0.009 | 9.809 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 115 | LEU | 0 | -0.064 | -0.033 | 13.228 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 116 | ASP | -1 | -0.875 | -0.924 | 12.309 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 117 | LEU | 0 | -0.001 | 0.000 | 15.021 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 118 | LEU | 0 | -0.100 | -0.035 | 17.481 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 119 | GLU | -1 | -0.998 | -0.998 | 19.677 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 120 | ASN | 0 | 0.025 | -0.004 | 21.867 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 121 | VAL | 0 | 0.007 | -0.012 | 22.047 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 122 | GLY | 0 | 0.061 | 0.037 | 22.953 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 123 | GLU | -1 | -0.890 | -0.936 | 19.758 | -0.278 | -0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 124 | PHE | 0 | -0.036 | -0.023 | 16.729 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 125 | GLN | 0 | -0.054 | -0.034 | 18.788 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 126 | ALA | 0 | 0.047 | 0.020 | 20.762 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 127 | TYR | 0 | 0.044 | 0.029 | 11.219 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 128 | LEU | 0 | -0.026 | -0.020 | 15.267 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 129 | GLU | -1 | -0.952 | -0.971 | 17.521 | -0.350 | -0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 130 | GLU | -1 | -0.913 | -0.959 | 17.603 | -0.542 | -0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 131 | LYS | 1 | 0.806 | 0.885 | 11.977 | 1.075 | 1.075 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 132 | LEU | 0 | -0.032 | -0.022 | 15.856 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 133 | ASN | 0 | -0.035 | -0.019 | 18.403 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 134 | GLU | -1 | -0.794 | -0.876 | 14.238 | -0.981 | -0.981 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 135 | ILE | 0 | 0.005 | -0.013 | 13.723 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 136 | LYS | 1 | 0.804 | 0.896 | 16.907 | 0.426 | 0.426 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 137 | GLU | -1 | -0.829 | -0.882 | 20.357 | -0.361 | -0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 138 | LEU | 0 | 0.015 | 0.011 | 14.844 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 139 | LEU | 0 | -0.030 | -0.023 | 18.001 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 140 | GLY | 0 | -0.003 | 0.022 | 20.176 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 141 | TYR | 0 | 0.005 | -0.025 | 21.017 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 142 | LEU | 0 | -0.008 | -0.005 | 16.983 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 143 | SER | 0 | -0.031 | -0.035 | 21.639 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 144 | GLU | -1 | -0.935 | -0.953 | 24.774 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 145 | SER | 0 | -0.048 | -0.028 | 22.966 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 146 | LEU | 0 | -0.091 | -0.041 | 22.525 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 147 | SER | 0 | -0.136 | -0.065 | 25.612 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |