![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZY8MN
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 | OptHSide |
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 | -919787.088145 |
---|---|
FMO2-HF: Nuclear repulsion | 873735.423093 |
FMO2-HF: Total energy | -46051.665052 |
FMO2-MP2: Total energy | -46184.583973 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021976/ligand_interaction/ligand_F021976.png)
Ligand Interaction
![ligand interaction](./Kdata/F021976/ligand_interaction/ligand_interaction_F021976.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. |
-16.51 | -6.964 | 2.771 | -5.172 | -7.147 | -0.032 |
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 | 0.799 | 0.892 | 3.048 | -2.113 | 2.276 | 0.120 | -2.278 | -2.231 | -0.002 |
4 | A | 36 | ASP | -1 | -0.848 | -0.903 | 5.307 | -0.987 | -0.941 | -0.001 | -0.002 | -0.043 | 0.000 |
5 | A | 37 | MET | 0 | -0.082 | -0.029 | 8.267 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 38 | LYS | 1 | 0.869 | 0.922 | 11.237 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 39 | ASN | 0 | 0.016 | -0.010 | 13.679 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 40 | ILE | 0 | 0.096 | 0.054 | 15.981 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 41 | ASN | 0 | -0.008 | -0.007 | 18.147 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 42 | GLU | -1 | -0.845 | -0.905 | 12.142 | -0.284 | -0.284 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 43 | SER | 0 | 0.023 | 0.008 | 13.559 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 44 | VAL | 0 | 0.042 | 0.022 | 14.603 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 45 | GLY | 0 | -0.032 | -0.012 | 15.986 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 46 | ALA | 0 | 0.010 | -0.001 | 10.660 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 47 | LEU | 0 | 0.038 | 0.019 | 12.618 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 48 | GLN | 0 | 0.006 | 0.009 | 14.515 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 49 | VAL | 0 | -0.019 | -0.011 | 13.510 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 50 | LEU | 0 | 0.048 | 0.023 | 10.310 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 51 | GLN | 0 | 0.033 | 0.019 | 13.626 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 52 | ILE | 0 | -0.057 | -0.036 | 17.104 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 53 | ALA | 0 | 0.008 | 0.007 | 14.593 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 54 | CYS | 0 | 0.021 | 0.008 | 14.552 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 55 | LYS | 1 | 0.943 | 0.972 | 16.970 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 56 | LYS | 1 | 0.887 | 0.955 | 19.467 | 0.238 | 0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 57 | LEU | 0 | 0.003 | 0.007 | 14.992 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 58 | PHE | 0 | 0.028 | 0.026 | 19.558 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 59 | ASN | 0 | 0.008 | -0.010 | 21.648 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 60 | LYS | 1 | 0.770 | 0.873 | 22.330 | 0.153 | 0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 61 | SER | 0 | -0.035 | -0.016 | 22.230 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 62 | MET | 0 | 0.005 | 0.012 | 24.360 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 63 | GLY | 0 | 0.057 | 0.020 | 27.526 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 64 | LEU | 0 | -0.082 | -0.038 | 24.150 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 65 | GLU | -1 | -0.863 | -0.944 | 28.112 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 66 | ASP | -1 | -0.923 | -0.949 | 29.666 | -0.103 | -0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 67 | LYS | 1 | 0.750 | 0.895 | 28.484 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 68 | ASP | -1 | -0.806 | -0.901 | 32.154 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 69 | ALA | 0 | 0.034 | -0.009 | 31.453 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 70 | LEU | 0 | -0.022 | 0.007 | 30.680 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 71 | GLN | 0 | 0.019 | 0.000 | 30.361 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 72 | ALA | 0 | 0.026 | 0.018 | 27.812 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 73 | SER | 0 | -0.085 | -0.051 | 26.134 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 74 | ILE | 0 | 0.009 | -0.003 | 25.475 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 75 | ILE | 0 | 0.036 | 0.015 | 24.091 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 76 | LYS | 1 | 0.946 | 0.970 | 21.929 | 0.119 | 0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 77 | GLN | 0 | -0.025 | -0.025 | 20.200 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 78 | GLU | -1 | -0.808 | -0.886 | 20.367 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 79 | LEU | 0 | -0.046 | -0.024 | 18.672 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 80 | ARG | 1 | 0.808 | 0.876 | 16.000 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 81 | GLU | -1 | -0.840 | -0.894 | 15.297 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 82 | ILE | 0 | -0.069 | -0.031 | 15.957 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 83 | VAL | 0 | -0.010 | -0.006 | 10.982 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 84 | GLU | -1 | -0.828 | -0.893 | 11.351 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 85 | ASN | 0 | -0.091 | -0.051 | 12.098 | 0.139 | 0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 86 | CYS | 0 | -0.087 | -0.010 | 11.131 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 87 | GLN | 0 | -0.006 | -0.007 | 9.868 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 88 | PHE | 0 | 0.014 | 0.001 | 9.824 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 89 | LEU | 0 | -0.018 | -0.015 | 9.662 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 90 | ALA | 0 | 0.002 | 0.012 | 9.778 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 91 | SER | 0 | 0.005 | 0.010 | 4.787 | -0.171 | -0.056 | -0.001 | -0.007 | -0.107 | 0.000 |
60 | A | 92 | PRO | 0 | 0.071 | 0.029 | 3.839 | -0.783 | -0.345 | 0.003 | -0.044 | -0.398 | 0.000 |
61 | A | 93 | LEU | 0 | -0.021 | -0.015 | 5.521 | -0.418 | -0.418 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 94 | PHE | 0 | 0.065 | 0.024 | 7.129 | -0.360 | -0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 95 | ASP | -1 | -0.845 | -0.913 | 4.122 | -2.073 | -1.816 | -0.001 | -0.041 | -0.215 | 0.000 |
64 | A | 96 | THR | 0 | -0.076 | -0.043 | 2.297 | -10.918 | -7.181 | 2.648 | -2.647 | -3.738 | -0.030 |
65 | A | 97 | GLN | 0 | -0.054 | -0.033 | 3.755 | 1.870 | 2.434 | 0.003 | -0.153 | -0.415 | 0.000 |
66 | A | 98 | LEU | 0 | -0.024 | -0.021 | 5.792 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 99 | ASN | 0 | 0.007 | 0.010 | 7.949 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 100 | ILE | 0 | 0.030 | -0.005 | 10.500 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 101 | ALA | 0 | -0.004 | 0.016 | 13.681 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 102 | ILE | 0 | -0.014 | -0.023 | 16.994 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 103 | ASN | 0 | -0.016 | -0.020 | 20.121 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 104 | ASP | -1 | -0.936 | -0.955 | 21.846 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 105 | GLU | -1 | -0.940 | -0.948 | 20.379 | -0.371 | -0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 106 | ILE | 0 | -0.055 | -0.043 | 13.792 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 107 | PHE | 0 | 0.017 | 0.015 | 15.551 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 108 | SER | 0 | -0.011 | -0.032 | 10.646 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 109 | MET | 0 | -0.037 | 0.008 | 10.763 | 0.170 | 0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 110 | ILE | 0 | -0.007 | -0.005 | 5.063 | -0.391 | -0.391 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 111 | VAL | 0 | 0.001 | 0.007 | 8.380 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 112 | VAL | 0 | 0.019 | 0.005 | 7.576 | -0.351 | -0.351 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 113 | ASN | 0 | 0.051 | -0.009 | 8.208 | 0.293 | 0.293 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 114 | PRO | 0 | -0.010 | 0.002 | 10.116 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 115 | LEU | 0 | -0.048 | -0.032 | 13.569 | 0.090 | 0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 116 | ASP | -1 | -0.898 | -0.947 | 13.067 | -0.273 | -0.273 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 117 | LEU | 0 | 0.010 | 0.004 | 15.518 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 118 | LEU | 0 | -0.069 | -0.032 | 18.116 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 119 | GLU | -1 | -1.032 | -1.007 | 20.323 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 120 | ASN | 0 | -0.005 | -0.004 | 22.009 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 121 | VAL | 0 | 0.027 | 0.001 | 22.427 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 122 | GLY | 0 | 0.054 | 0.026 | 23.278 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 123 | GLU | -1 | -0.875 | -0.926 | 20.421 | -0.303 | -0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 124 | PHE | 0 | -0.035 | -0.019 | 17.089 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 125 | GLN | 0 | -0.033 | -0.026 | 18.967 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 126 | ALA | 0 | 0.037 | 0.020 | 21.190 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 127 | TYR | 0 | 0.042 | 0.032 | 11.644 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 128 | LEU | 0 | -0.022 | -0.021 | 15.560 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 129 | GLU | -1 | -0.957 | -0.973 | 17.733 | -0.345 | -0.345 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 130 | GLU | -1 | -0.913 | -0.953 | 18.141 | -0.542 | -0.542 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 131 | LYS | 1 | 0.803 | 0.880 | 12.434 | 1.030 | 1.030 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 132 | LEU | 0 | -0.050 | -0.036 | 16.292 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 133 | ASN | 0 | -0.061 | -0.036 | 18.721 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 134 | GLU | -1 | -0.788 | -0.869 | 14.792 | -0.933 | -0.933 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 135 | ILE | 0 | 0.010 | -0.007 | 14.155 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 136 | LYS | 1 | 0.855 | 0.927 | 17.362 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 137 | GLU | -1 | -0.852 | -0.914 | 20.629 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 138 | LEU | 0 | 0.019 | 0.014 | 14.936 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 139 | LEU | 0 | -0.040 | -0.028 | 18.186 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 140 | GLY | 0 | -0.009 | 0.017 | 20.267 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 141 | TYR | 0 | 0.026 | -0.004 | 20.690 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 142 | LEU | 0 | -0.004 | -0.004 | 16.895 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 143 | SER | 0 | -0.041 | -0.047 | 21.603 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 144 | GLU | -1 | -0.934 | -0.955 | 24.625 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 145 | SER | 0 | -0.043 | -0.021 | 23.336 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 146 | LEU | 0 | -0.103 | -0.044 | 22.691 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 147 | SER | 0 | -0.119 | -0.041 | 26.029 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |