![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 766JK
Calculation Name: 3QMQ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3QMQ
Chain ID: A
UniProt ID: P64461
Base Structure: X-ray
Registration Date: 2023-09-21
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 | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -752817.134957 |
---|---|
FMO2-HF: Nuclear repulsion | 712808.061793 |
FMO2-HF: Total energy | -40009.073164 |
FMO2-MP2: Total energy | -40125.102826 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F033414/ligand_interaction/ligand_F033414.png)
Ligand Interaction
![ligand interaction](./Kdata/F033414/ligand_interaction/ligand_interaction_F033414.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:0:SER)
Summations of interaction energy for
fragment #1(A:0: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. |
-23.316 | -26.389 | 23.232 | -10.339 | -9.821 | -0.024 |
Interaction energy analysis for fragmet #1(A:0: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 | 2 | HIS | 0 | -0.012 | 0.000 | 3.877 | 2.390 | 3.867 | -0.016 | -0.734 | -0.728 | 0.001 |
4 | A | 3 | VAL | 0 | 0.017 | 0.002 | 6.033 | -0.161 | -0.161 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | THR | 0 | -0.051 | -0.036 | 8.768 | 0.326 | 0.326 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | LEU | 0 | 0.028 | 0.030 | 12.328 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | VAL | 0 | -0.061 | -0.047 | 15.062 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | GLU | -1 | -0.768 | -0.845 | 18.548 | -0.196 | -0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | ILE | 0 | -0.017 | -0.025 | 21.737 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | ASN | 0 | -0.017 | -0.007 | 24.736 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | VAL | 0 | 0.001 | -0.001 | 28.374 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | HIS | 0 | 0.063 | 0.035 | 31.283 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | GLU | -1 | -0.847 | -0.916 | 34.706 | -0.117 | -0.117 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | ASP | -1 | -0.937 | -0.968 | 36.397 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | LYS | 1 | 0.811 | 0.888 | 34.097 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | VAL | 0 | 0.008 | 0.012 | 31.449 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | ASP | -1 | -0.862 | -0.937 | 31.334 | -0.136 | -0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | GLU | -1 | -0.853 | -0.911 | 32.296 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | PHE | 0 | 0.003 | -0.006 | 24.477 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | ILE | 0 | 0.006 | 0.008 | 27.734 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | GLU | -1 | -0.837 | -0.884 | 27.953 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | VAL | 0 | -0.033 | -0.020 | 27.791 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | PHE | 0 | 0.026 | -0.019 | 20.681 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | ARG | 1 | 0.844 | 0.907 | 23.764 | 0.138 | 0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLN | 0 | -0.002 | -0.005 | 24.471 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | ASN | 0 | -0.014 | -0.018 | 21.714 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | HIS | 0 | -0.046 | -0.021 | 18.660 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | LEU | 0 | -0.010 | -0.011 | 19.975 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | GLY | 0 | 0.011 | 0.017 | 21.710 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | SER | 0 | -0.017 | -0.037 | 17.031 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | VAL | 0 | -0.056 | -0.025 | 15.720 | -0.066 | -0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLN | 0 | -0.035 | -0.008 | 16.393 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | GLU | -1 | -0.787 | -0.862 | 15.362 | -0.440 | -0.440 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLU | -1 | -0.885 | -0.938 | 14.172 | -0.350 | -0.350 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | GLY | 0 | 0.010 | 0.004 | 10.957 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | ASN | 0 | -0.058 | -0.050 | 9.922 | -0.324 | -0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | LEU | 0 | -0.039 | -0.017 | 5.203 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | ARG | 1 | 0.875 | 0.940 | 9.103 | 1.033 | 1.033 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | PHE | 0 | 0.034 | 0.025 | 12.127 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASP | -1 | -0.814 | -0.899 | 14.095 | -0.583 | -0.583 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | VAL | 0 | -0.011 | -0.010 | 16.858 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | LEU | 0 | -0.009 | 0.002 | 17.185 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLN | 0 | -0.014 | -0.028 | 21.368 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | ASP | -1 | -0.799 | -0.880 | 24.667 | -0.190 | -0.190 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | PRO | 0 | -0.043 | -0.028 | 25.088 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | GLU | -1 | -0.950 | -0.961 | 28.176 | -0.116 | -0.116 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | VAL | 0 | -0.056 | -0.022 | 29.716 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | ASN | 0 | 0.048 | 0.024 | 29.775 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | SER | 0 | 0.020 | 0.006 | 30.541 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | ARG | 1 | 0.799 | 0.890 | 25.411 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | PHE | 0 | 0.017 | -0.001 | 23.891 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | TYR | 0 | -0.047 | -0.056 | 19.342 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | ILE | 0 | -0.013 | 0.005 | 17.351 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | TYR | 0 | -0.017 | -0.012 | 9.579 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | GLU | -1 | -0.774 | -0.872 | 13.548 | -0.528 | -0.528 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | ALA | 0 | -0.013 | -0.010 | 8.028 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | TYR | 0 | 0.005 | -0.016 | 8.839 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | LYS | 1 | 0.912 | 0.952 | 5.550 | 0.150 | 0.150 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.838 | -0.915 | 5.813 | -1.141 | -1.141 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | GLU | -1 | -0.891 | -0.966 | 8.431 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | ASP | -1 | -0.895 | -0.934 | 11.514 | -0.149 | -0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | ALA | 0 | -0.013 | 0.000 | 11.193 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | VAL | 0 | -0.034 | -0.017 | 11.103 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | ALA | 0 | -0.029 | -0.021 | 13.811 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | PHE | 0 | 0.034 | 0.012 | 16.362 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | HIS | 1 | 0.859 | 0.934 | 15.873 | 0.503 | 0.503 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | LYS | 1 | 0.904 | 0.971 | 16.145 | 0.334 | 0.334 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | THR | 0 | -0.108 | -0.072 | 20.516 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | THR | 0 | 0.020 | 0.014 | 19.981 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | PRO | 0 | 0.050 | 0.007 | 22.961 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | HIS | 0 | 0.007 | 0.015 | 19.700 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | TYR | 0 | 0.030 | 0.027 | 20.255 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | LYS | 1 | 0.828 | 0.906 | 23.514 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | THR | 0 | -0.026 | -0.029 | 26.925 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | CYS | 0 | -0.075 | -0.007 | 25.039 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | VAL | 0 | -0.001 | -0.014 | 24.641 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ALA | 0 | 0.025 | 0.010 | 27.263 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | LYS | 1 | 0.949 | 0.985 | 30.377 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | LEU | 0 | 0.006 | 0.006 | 25.570 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | GLU | -1 | -0.930 | -0.965 | 29.727 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | SER | 0 | -0.080 | -0.038 | 31.793 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | LEU | 0 | -0.031 | -0.016 | 30.612 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | MET | 0 | -0.057 | -0.021 | 26.172 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | THR | 0 | 0.028 | 0.016 | 31.225 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | GLY | 0 | -0.015 | -0.007 | 30.612 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | PRO | 0 | -0.024 | -0.020 | 27.226 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | ARG | 1 | 0.956 | 1.001 | 22.412 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | LYS | 1 | 0.863 | 0.920 | 21.893 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | LYS | 1 | 0.819 | 0.917 | 15.662 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 89 | ARG | 1 | 0.949 | 0.971 | 15.060 | 0.362 | 0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 90 | LEU | 0 | 0.047 | 0.018 | 10.868 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 91 | PHE | 0 | -0.044 | -0.024 | 8.516 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 92 | ASN | 0 | 0.047 | 0.027 | 5.191 | -0.134 | -0.134 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 93 | GLY | 0 | 0.038 | 0.017 | 3.860 | -0.214 | 0.255 | 0.000 | -0.219 | -0.250 | 0.000 |
95 | A | 94 | LEU | 0 | -0.009 | -0.014 | 1.936 | -8.885 | -11.814 | 10.955 | -4.200 | -3.826 | -0.047 |
96 | A | 95 | MET | 0 | -0.012 | -0.010 | 2.762 | -0.711 | 0.484 | 0.818 | -0.459 | -1.554 | -0.009 |
97 | A | 96 | PRO | 0 | -0.007 | -0.004 | 1.784 | -15.079 | -18.364 | 11.475 | -4.727 | -3.463 | 0.031 |