![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2K1VR
Calculation Name: 2GMQ-A-Xray311
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2GMQ
Chain ID: A
UniProt ID: Q8KUD5
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 104 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -823405.09315 |
---|---|
FMO2-HF: Nuclear repulsion | 782143.487254 |
FMO2-HF: Total energy | -41261.605896 |
FMO2-MP2: Total energy | -41383.274044 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015507/ligand_interaction/ligand_F015507.png)
Ligand Interaction
![ligand interaction](./Kdata/F015507/ligand_interaction/ligand_interaction_F015507.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:11:ACE )
Summations of interaction energy for
fragment #1(A:11:ACE )
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. |
2.195 | 2.979 | -0.005 | -0.378 | -0.401 | 0 |
Interaction energy analysis for fragmet #1(A:11:ACE )
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 | 13 | MET | 0 | -0.034 | -0.016 | 3.840 | 1.070 | 1.854 | -0.005 | -0.378 | -0.401 | 0.000 |
4 | A | 14 | LYS | 1 | 0.996 | 1.008 | 7.136 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 15 | GLU | -1 | -0.902 | -0.943 | 8.807 | -0.228 | -0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 16 | ILE | 0 | -0.025 | -0.019 | 12.615 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 17 | ALA | 0 | 0.015 | 0.023 | 15.448 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 18 | ILE | 0 | -0.055 | -0.030 | 18.764 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 19 | GLN | 0 | -0.019 | -0.019 | 21.732 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 20 | GLU | -1 | -0.797 | -0.921 | 25.438 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 21 | LYS | 1 | 0.966 | 0.990 | 26.899 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 22 | ASP | -1 | -0.851 | -0.914 | 25.789 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 23 | LEU | 0 | -0.038 | -0.010 | 22.409 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 24 | THR | 0 | -0.084 | -0.037 | 26.322 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 25 | LEU | 0 | 0.044 | 0.020 | 25.733 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 26 | GLN | 0 | 0.017 | 0.014 | 26.461 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 27 | TRP | 0 | 0.051 | 0.034 | 27.103 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 28 | ARG | 1 | 0.951 | 0.955 | 25.724 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 29 | GLY | 0 | 0.050 | 0.023 | 30.468 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 30 | ASN | 0 | -0.014 | 0.006 | 33.032 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 31 | THR | 0 | 0.038 | 0.019 | 33.877 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 32 | GLY | 0 | 0.012 | 0.017 | 31.545 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 33 | LYS | 1 | 0.981 | 0.987 | 21.905 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 34 | LEU | 0 | 0.013 | 0.006 | 23.327 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 35 | VAL | 0 | -0.105 | -0.039 | 23.646 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 36 | LYS | 1 | 0.934 | 0.967 | 21.851 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 37 | VAL | 0 | 0.050 | 0.044 | 20.743 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 38 | ARG | 1 | 0.879 | 0.944 | 22.013 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 39 | LEU | 0 | 0.061 | 0.031 | 20.933 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 40 | LYS | 1 | 0.900 | 0.936 | 24.494 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 41 | ASN | 0 | 0.030 | -0.013 | 27.316 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 42 | THR | 0 | 0.015 | 0.007 | 28.919 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 43 | ARG | 1 | 0.911 | 0.961 | 22.361 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 44 | ALA | 0 | 0.024 | 0.009 | 24.179 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 45 | MET | 0 | -0.006 | -0.005 | 24.757 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 46 | GLU | -1 | -0.912 | -0.952 | 25.176 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 47 | MET | 0 | -0.013 | -0.017 | 20.630 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 48 | TRP | 0 | 0.027 | 0.026 | 21.691 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 49 | TYR | 0 | -0.008 | -0.019 | 23.526 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 50 | ASN | 0 | -0.019 | -0.013 | 22.141 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 51 | LYS | 1 | 0.867 | 0.944 | 18.828 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 52 | GLN | 0 | 0.027 | 0.031 | 17.622 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 53 | ILE | 0 | -0.043 | -0.032 | 15.566 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 54 | THR | 0 | -0.049 | -0.026 | 15.328 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 55 | GLU | -1 | -0.903 | -0.980 | 15.849 | 0.114 | 0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 56 | GLU | -1 | -0.943 | -0.967 | 12.749 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 57 | ASN | 0 | 0.084 | 0.061 | 11.297 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 58 | ILE | 0 | -0.054 | -0.025 | 11.270 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 59 | GLN | 0 | -0.048 | -0.062 | 10.210 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 60 | GLU | -1 | -0.890 | -0.934 | 7.074 | 0.498 | 0.498 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 61 | ILE | 0 | -0.118 | -0.042 | 7.777 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 62 | THR | 0 | 0.043 | 0.010 | 7.244 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 63 | THR | 0 | -0.017 | -0.010 | 10.248 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 64 | LEU | 0 | -0.004 | 0.000 | 13.615 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 65 | ASN | 0 | 0.030 | 0.005 | 16.900 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 66 | ILE | 0 | -0.016 | -0.007 | 19.245 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 67 | ILE | 0 | 0.040 | 0.024 | 22.255 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 68 | LYS | 1 | 0.919 | 0.938 | 25.244 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 69 | ASN | 0 | -0.068 | -0.043 | 29.048 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 70 | GLY | 0 | 0.017 | 0.011 | 30.144 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 71 | LYS | 1 | 0.903 | 0.969 | 28.467 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 72 | SER | 0 | -0.025 | -0.020 | 22.923 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 73 | LEU | 0 | 0.024 | 0.016 | 22.700 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 74 | ALA | 0 | 0.036 | 0.031 | 17.413 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 75 | LEU | 0 | -0.058 | -0.040 | 18.140 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 76 | GLU | -1 | -0.845 | -0.933 | 13.276 | -0.381 | -0.381 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 77 | VAL | 0 | -0.004 | -0.003 | 12.660 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 78 | TYR | 0 | -0.045 | -0.042 | 13.068 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 79 | PRO | 0 | 0.073 | 0.030 | 8.836 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 80 | GLU | -1 | -0.873 | -0.930 | 8.774 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 81 | LYS | 1 | 0.843 | 0.929 | 12.543 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 82 | SER | 0 | -0.039 | -0.005 | 13.396 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 83 | ILE | 0 | 0.030 | 0.033 | 15.785 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 84 | TYR | 0 | 0.066 | 0.028 | 17.482 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 85 | VAL | 0 | -0.047 | -0.018 | 21.273 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 86 | LYS | 1 | 1.046 | 1.012 | 24.824 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 87 | PRO | 0 | -0.044 | -0.013 | 28.344 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 88 | ASN | 0 | -0.017 | 0.005 | 29.977 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 89 | LEU | 0 | 0.012 | 0.005 | 33.213 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 90 | GLY | 0 | -0.012 | -0.007 | 34.001 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 91 | ARG | 1 | 0.926 | 0.958 | 32.478 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 92 | ILE | 0 | 0.055 | 0.040 | 25.172 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 93 | ASN | 0 | 0.008 | -0.005 | 24.403 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 94 | VAL | 0 | -0.029 | -0.018 | 23.981 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 95 | PRO | 0 | 0.060 | 0.042 | 18.882 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 96 | VAL | 0 | -0.080 | -0.034 | 19.771 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 97 | PHE | 0 | 0.081 | 0.037 | 14.300 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 98 | PHE | 0 | -0.015 | -0.025 | 17.280 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 99 | ILE | 0 | -0.012 | -0.012 | 17.205 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 100 | LYS | 1 | 0.873 | 0.946 | 11.930 | 0.336 | 0.336 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 101 | THR | 0 | 0.031 | 0.018 | 17.840 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 102 | PRO | 0 | -0.056 | -0.025 | 19.456 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 103 | ILE | 0 | 0.085 | 0.045 | 23.116 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 104 | ASN | 0 | 0.024 | -0.003 | 25.498 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 105 | ARG | 1 | 0.838 | 0.911 | 29.028 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 106 | GLY | 0 | 0.046 | 0.024 | 31.216 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 107 | VAL | 0 | 0.067 | 0.032 | 28.757 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 108 | PHE | 0 | -0.021 | -0.018 | 25.238 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 109 | GLU | -1 | -0.823 | -0.920 | 29.472 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 110 | GLU | -1 | -0.959 | -0.966 | 33.012 | -0.055 | -0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 111 | ILE | 0 | -0.067 | -0.025 | 26.999 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 112 | PHE | 0 | -0.042 | -0.030 | 25.551 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 113 | GLY | 0 | 0.048 | 0.051 | 31.625 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 114 | NME | 0 | -0.041 | -0.022 | 34.894 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |