![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: G6LQ1
Calculation Name: 3H9W-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3H9W
Chain ID: A
UniProt ID: A1U4R9
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 | 109 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -927907.568728 |
---|---|
FMO2-HF: Nuclear repulsion | 882580.360238 |
FMO2-HF: Total energy | -45327.208489 |
FMO2-MP2: Total energy | -45458.747097 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024027/ligand_interaction/ligand_F024027.png)
Ligand Interaction
![ligand interaction](./Kdata/F024027/ligand_interaction/ligand_interaction_F024027.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:23:LYS)
Summations of interaction energy for
fragment #1(A:23:LYS)
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. |
-149.456 | -148.357 | 6.884 | -2.837 | -5.144 | -0.027 |
Interaction energy analysis for fragmet #1(A:23:LYS)
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 | 25 | ILE | 0 | 0.008 | 0.005 | 3.459 | 6.424 | 8.204 | 0.047 | -0.627 | -1.199 | 0.000 |
4 | A | 26 | PRO | 0 | -0.018 | 0.009 | 6.078 | 0.978 | 0.978 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 27 | TRP | 0 | 0.033 | 0.010 | 8.925 | 2.597 | 2.597 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 28 | LYS | 1 | 0.948 | 0.982 | 12.472 | 15.501 | 15.501 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 29 | ILE | 0 | -0.002 | 0.005 | 15.739 | 0.372 | 0.372 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 30 | ASN | 0 | 0.006 | 0.015 | 18.730 | 0.446 | 0.446 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 31 | TRP | 0 | 0.066 | 0.015 | 22.185 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 32 | GLN | 0 | 0.017 | 0.019 | 23.726 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 33 | THR | 0 | -0.052 | -0.043 | 25.423 | 0.154 | 0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 34 | MET | 0 | 0.016 | 0.017 | 22.308 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 35 | ALA | 0 | 0.012 | 0.005 | 22.362 | -0.377 | -0.377 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 36 | PHE | 0 | -0.027 | -0.023 | 14.658 | -0.380 | -0.380 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 37 | GLU | -1 | -0.946 | -0.971 | 17.877 | -13.742 | -13.742 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 38 | TYR | 0 | -0.061 | -0.047 | 12.049 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 39 | ILE | 0 | 0.045 | 0.022 | 10.899 | -0.744 | -0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 40 | GLY | 0 | -0.012 | 0.009 | 7.920 | 1.101 | 1.101 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 41 | PRO | 0 | 0.040 | 0.006 | 7.815 | -0.092 | -0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 42 | GLN | 0 | 0.012 | -0.003 | 2.959 | 4.440 | 4.937 | 0.019 | -0.126 | -0.390 | 0.000 |
21 | A | 43 | ILE | 0 | 0.041 | 0.025 | 6.093 | -1.186 | -1.186 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 44 | GLU | -1 | -0.886 | -0.919 | 8.515 | -16.789 | -16.789 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 45 | ALA | 0 | -0.063 | -0.027 | 6.698 | 0.879 | 0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 46 | LEU | 0 | -0.022 | 0.000 | 5.887 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 47 | LEU | 0 | 0.015 | -0.013 | 8.075 | 1.383 | 1.383 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 48 | GLY | 0 | -0.002 | -0.005 | 11.394 | 1.754 | 1.754 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 49 | TRP | 0 | -0.053 | -0.048 | 13.463 | 1.625 | 1.625 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 50 | PRO | 0 | 0.028 | 0.019 | 13.926 | -0.782 | -0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 51 | GLN | 0 | 0.041 | 0.022 | 11.921 | 0.692 | 0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 52 | GLY | 0 | -0.042 | -0.027 | 14.049 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 53 | SER | 0 | -0.109 | -0.081 | 16.587 | 0.637 | 0.637 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 54 | TRP | 0 | 0.028 | 0.013 | 13.451 | 0.262 | 0.262 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 55 | LYS | 1 | 0.931 | 0.974 | 17.226 | 13.108 | 13.108 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 56 | SER | 0 | 0.006 | 0.004 | 20.519 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 57 | VAL | 0 | 0.074 | 0.029 | 19.515 | -0.568 | -0.568 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 58 | GLU | -1 | -0.920 | -0.949 | 20.499 | -12.152 | -12.152 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 59 | ASP | -1 | -0.847 | -0.925 | 19.065 | -14.252 | -14.252 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 60 | TRP | 0 | -0.051 | -0.044 | 14.000 | 0.434 | 0.434 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 61 | ALA | 0 | 0.004 | 0.006 | 17.612 | -0.379 | -0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 62 | THR | 0 | -0.011 | -0.004 | 20.185 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 63 | ARG | 1 | 0.826 | 0.924 | 16.354 | 16.514 | 16.514 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 64 | MET | 0 | -0.012 | -0.002 | 16.087 | -1.173 | -1.173 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 65 | HIS | 0 | 0.019 | 0.012 | 17.805 | 0.812 | 0.812 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 66 | PRO | 0 | 0.025 | 0.008 | 19.745 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 67 | GLU | -1 | -0.910 | -0.962 | 22.469 | -12.574 | -12.574 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 68 | ASP | -1 | -0.788 | -0.892 | 17.717 | -17.409 | -17.409 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 69 | GLN | 0 | -0.046 | -0.033 | 20.405 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 70 | GLU | -1 | -0.981 | -0.986 | 21.941 | -11.497 | -11.497 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 71 | TRP | 0 | -0.095 | -0.042 | 16.997 | 0.410 | 0.410 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 72 | VAL | 0 | 0.000 | 0.009 | 16.825 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 73 | VAL | 0 | 0.055 | 0.024 | 19.836 | -0.205 | -0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 74 | ASN | 0 | 0.010 | -0.004 | 21.653 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 75 | PHE | 0 | -0.033 | -0.006 | 17.294 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 76 | CYS | 0 | 0.035 | 0.007 | 17.322 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 77 | VAL | 0 | 0.012 | 0.031 | 19.778 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 78 | LYS | 1 | 0.940 | 0.962 | 23.038 | 11.862 | 11.862 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 79 | GLN | 0 | -0.048 | -0.033 | 20.121 | 0.329 | 0.329 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 80 | SER | 0 | 0.032 | 0.010 | 20.009 | -0.166 | -0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 81 | GLU | -1 | -0.933 | -0.961 | 21.733 | -11.169 | -11.169 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 82 | CYS | 0 | -0.131 | -0.048 | 24.755 | 0.656 | 0.656 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 83 | GLY | 0 | -0.028 | -0.018 | 22.854 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 84 | VAL | 0 | -0.068 | -0.021 | 20.464 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 85 | ASP | -1 | -0.770 | -0.869 | 15.902 | -18.431 | -18.431 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 86 | HIS | 0 | -0.104 | -0.066 | 15.747 | 0.365 | 0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 87 | GLU | -1 | -0.924 | -0.970 | 11.599 | -27.569 | -27.569 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 88 | ALA | 0 | -0.017 | -0.005 | 12.641 | 1.786 | 1.786 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 89 | ASP | -1 | -0.803 | -0.865 | 11.427 | -28.578 | -28.578 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 90 | TYR | 0 | 0.020 | -0.004 | 12.410 | 1.645 | 1.645 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 91 | ARG | 1 | 0.804 | 0.900 | 12.823 | 14.397 | 14.397 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 92 | ALA | 0 | 0.045 | 0.023 | 12.147 | 1.188 | 1.188 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 93 | LEU | 0 | -0.010 | 0.000 | 14.115 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 94 | HIS | 0 | 0.048 | 0.051 | 12.375 | 0.364 | 0.364 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 95 | ARG | 1 | 0.949 | 0.989 | 15.334 | 15.653 | 15.653 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 96 | ASP | -1 | -0.966 | -0.974 | 16.920 | -15.658 | -15.658 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 97 | GLY | 0 | 0.021 | 0.010 | 18.820 | 0.642 | 0.642 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 98 | HIS | 1 | 0.790 | 0.881 | 12.975 | 18.765 | 18.765 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 99 | TYR | 0 | 0.045 | 0.005 | 15.837 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 100 | VAL | 0 | -0.031 | -0.020 | 9.142 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 101 | TRP | 0 | -0.002 | 0.008 | 10.858 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 102 | ILE | 0 | 0.012 | -0.005 | 7.793 | -3.372 | -3.372 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 103 | ARG | 1 | 0.771 | 0.865 | 7.134 | 34.390 | 34.390 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 104 | ASP | -1 | -0.873 | -0.956 | 7.809 | -30.301 | -30.301 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 105 | VAL | 0 | 0.002 | -0.011 | 8.000 | 1.235 | 1.235 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 106 | VAL | 0 | -0.003 | -0.011 | 10.319 | -0.744 | -0.744 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 107 | HIS | 0 | -0.047 | -0.024 | 13.378 | 0.991 | 0.991 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 108 | VAL | 0 | -0.022 | -0.023 | 15.404 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 109 | VAL | 0 | -0.016 | -0.004 | 18.451 | 0.173 | 0.173 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 110 | ARG | 1 | 0.905 | 0.946 | 20.954 | 12.482 | 12.482 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 111 | ASP | -1 | -0.712 | -0.817 | 24.758 | -10.924 | -10.924 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 112 | ASP | -1 | -0.927 | -0.980 | 27.381 | -10.474 | -10.474 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 113 | SER | 0 | -0.190 | -0.111 | 30.382 | 0.386 | 0.386 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 114 | GLY | 0 | -0.062 | -0.036 | 29.036 | 0.217 | 0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 115 | GLU | -1 | -0.967 | -0.978 | 28.897 | -10.052 | -10.052 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 116 | VAL | 0 | -0.055 | -0.021 | 22.994 | -0.379 | -0.379 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 117 | GLU | -1 | -0.907 | -0.955 | 24.018 | -12.084 | -12.084 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 118 | ALA | 0 | -0.067 | -0.062 | 19.932 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 119 | LEU | 0 | -0.002 | 0.028 | 16.842 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 120 | ILE | 0 | -0.020 | -0.009 | 14.236 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 121 | GLY | 0 | 0.062 | 0.030 | 10.842 | 0.243 | 0.243 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 122 | PHE | 0 | -0.052 | -0.028 | 5.486 | -1.874 | -1.874 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 123 | MET | 0 | -0.016 | 0.020 | 7.221 | 1.397 | 1.397 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 124 | PHE | 0 | -0.043 | -0.040 | 1.681 | -21.864 | -23.804 | 6.811 | -1.982 | -2.890 | -0.027 |
103 | A | 125 | ASP | -1 | -0.808 | -0.873 | 3.350 | -30.208 | -29.689 | 0.008 | -0.079 | -0.447 | 0.000 |
104 | A | 126 | ILE | 0 | -0.007 | -0.015 | 4.504 | -6.493 | -6.250 | -0.001 | -0.023 | -0.218 | 0.000 |
105 | A | 127 | SER | 0 | -0.008 | -0.048 | 6.767 | 5.531 | 5.531 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 128 | LEU | 0 | -0.049 | -0.030 | 6.115 | 2.584 | 2.584 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 129 | GLU | -1 | -0.870 | -0.914 | 7.598 | -31.129 | -31.129 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 130 | HIS | 1 | 0.830 | 0.925 | 10.481 | 24.638 | 24.638 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 131 | HIS | 0 | 0.012 | 0.027 | 10.818 | 1.974 | 1.974 | 0.000 | 0.000 | 0.000 | 0.000 |