![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 668MZ
Calculation Name: 2GMQ-A-Xray372
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: 2023-06-19
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 | 102 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -815842.263288 |
---|---|
FMO2-HF: Nuclear repulsion | 774750.688549 |
FMO2-HF: Total energy | -41091.57474 |
FMO2-MP2: Total energy | -41212.583055 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020717/ligand_interaction/ligand_F020717.png)
Ligand Interaction
![ligand interaction](./Kdata/F020717/ligand_interaction/ligand_interaction_F020717.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:12:GLY)
Summations of interaction energy for
fragment #1(A:12:GLY)
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. |
-0.636 | 0.72 | -0.011 | -0.783 | -0.563 | 0.004 |
Interaction energy analysis for fragmet #1(A:12:GLY)
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 | 14 | LYS | 1 | 0.898 | 0.940 | 3.830 | 1.436 | 2.792 | -0.011 | -0.783 | -0.563 | 0.004 |
4 | A | 15 | GLU | -1 | -0.877 | -0.918 | 6.772 | -0.648 | -0.648 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 16 | ILE | 0 | -0.006 | -0.005 | 10.169 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 17 | ALA | 0 | 0.010 | 0.019 | 13.549 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 18 | ILE | 0 | -0.039 | -0.022 | 16.884 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 19 | GLN | 0 | 0.014 | 0.011 | 19.735 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 20 | GLU | -1 | -0.730 | -0.884 | 23.266 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 21 | LYS | 1 | 0.911 | 0.948 | 24.528 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 22 | ASP | -1 | -0.819 | -0.892 | 23.889 | -0.316 | -0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 23 | LEU | 0 | -0.022 | -0.006 | 20.631 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 24 | THR | 0 | -0.069 | -0.032 | 24.606 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 25 | LEU | 0 | 0.036 | 0.020 | 23.529 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 26 | GLN | 0 | 0.036 | 0.030 | 24.789 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 27 | TRP | 0 | 0.044 | 0.030 | 24.697 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 28 | ARG | 1 | 0.953 | 0.960 | 24.939 | 0.197 | 0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 29 | GLY | 0 | 0.045 | 0.019 | 28.601 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 30 | ASN | 0 | -0.040 | -0.015 | 31.156 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 31 | THR | 0 | 0.057 | 0.011 | 31.533 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 32 | GLY | 0 | 0.013 | 0.023 | 29.069 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 33 | LYS | 1 | 0.938 | 0.957 | 19.270 | 0.302 | 0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 34 | LEU | 0 | 0.013 | 0.018 | 20.775 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 35 | VAL | 0 | -0.100 | -0.046 | 21.475 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 36 | LYS | 1 | 0.915 | 0.952 | 20.278 | 0.248 | 0.248 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 37 | VAL | 0 | 0.037 | 0.039 | 19.047 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 38 | ARG | 1 | 0.889 | 0.954 | 20.561 | 0.231 | 0.231 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 39 | LEU | 0 | 0.045 | 0.026 | 19.277 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 40 | LYS | 1 | 0.848 | 0.909 | 23.103 | 0.283 | 0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 41 | ASN | 0 | 0.003 | -0.022 | 26.066 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 42 | THR | 0 | 0.025 | 0.011 | 27.905 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 43 | ARG | 1 | 0.815 | 0.889 | 21.121 | 0.407 | 0.407 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 44 | ALA | 0 | 0.032 | 0.020 | 23.204 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 45 | MET | 0 | 0.009 | 0.000 | 24.043 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 46 | GLU | -1 | -0.842 | -0.894 | 23.622 | -0.353 | -0.353 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 47 | MET | 0 | -0.001 | -0.009 | 19.518 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 48 | TRP | 0 | 0.031 | 0.027 | 21.158 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 49 | TYR | 0 | -0.008 | -0.009 | 23.227 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 50 | ASN | 0 | -0.032 | -0.019 | 21.435 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 51 | LYS | 1 | 0.846 | 0.928 | 18.700 | 0.300 | 0.300 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 52 | GLN | 0 | 0.017 | 0.024 | 17.056 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 53 | ILE | 0 | -0.027 | -0.025 | 14.613 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 54 | THR | 0 | -0.038 | -0.030 | 15.445 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 55 | GLU | -1 | -0.888 | -0.970 | 15.503 | -0.453 | -0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 56 | GLU | -1 | -0.921 | -0.951 | 13.705 | -0.474 | -0.474 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 57 | ASN | 0 | 0.021 | 0.030 | 11.350 | -0.079 | -0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 58 | ILE | 0 | -0.054 | -0.019 | 10.721 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 59 | GLN | 0 | -0.050 | -0.054 | 10.043 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 60 | GLU | -1 | -0.791 | -0.872 | 6.359 | -1.952 | -1.952 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 61 | ILE | 0 | -0.100 | -0.034 | 6.282 | -0.939 | -0.939 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 62 | THR | 0 | 0.054 | 0.019 | 4.818 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 63 | THR | 0 | -0.038 | -0.027 | 8.166 | 0.359 | 0.359 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 64 | LEU | 0 | 0.011 | 0.014 | 10.859 | -0.039 | -0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 65 | ASN | 0 | -0.016 | -0.033 | 14.350 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 66 | ILE | 0 | -0.014 | -0.008 | 16.322 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 67 | ILE | 0 | 0.044 | 0.019 | 19.285 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 68 | LYS | 1 | 0.846 | 0.913 | 22.515 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 69 | ASN | 0 | -0.049 | -0.032 | 26.267 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 70 | GLY | 0 | 0.019 | 0.011 | 27.239 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 71 | LYS | 1 | 0.914 | 0.978 | 25.118 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 72 | SER | 0 | 0.021 | 0.004 | 19.705 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 73 | LEU | 0 | -0.020 | -0.010 | 19.570 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 74 | ALA | 0 | 0.038 | 0.030 | 13.943 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 75 | LEU | 0 | -0.053 | -0.035 | 15.069 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 76 | GLU | -1 | -0.763 | -0.872 | 9.447 | -0.840 | -0.840 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 77 | VAL | 0 | -0.019 | -0.012 | 11.010 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 78 | TYR | 0 | -0.010 | -0.026 | 11.138 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 79 | PRO | 0 | 0.068 | 0.036 | 7.352 | 0.189 | 0.189 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 80 | GLU | -1 | -0.872 | -0.936 | 8.834 | -0.782 | -0.782 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 81 | LYS | 1 | 0.814 | 0.915 | 12.132 | 0.479 | 0.479 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 82 | SER | 0 | -0.034 | -0.004 | 12.127 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 83 | ILE | 0 | 0.022 | 0.022 | 14.933 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 84 | TYR | 0 | 0.066 | 0.029 | 16.982 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 85 | VAL | 0 | -0.042 | -0.019 | 20.739 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 86 | LYS | 1 | 1.036 | 1.007 | 24.220 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 87 | PRO | 0 | -0.033 | -0.004 | 27.785 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 88 | ASN | 0 | -0.026 | -0.011 | 29.173 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 89 | LEU | 0 | 0.023 | -0.002 | 32.416 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 90 | GLY | 0 | 0.048 | 0.018 | 33.379 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 91 | ARG | 1 | 0.911 | 0.970 | 31.189 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 92 | ILE | 0 | 0.039 | 0.024 | 24.336 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 93 | ASN | 0 | 0.021 | 0.007 | 24.071 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 94 | VAL | 0 | -0.017 | -0.012 | 23.101 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 95 | PRO | 0 | 0.047 | 0.039 | 17.954 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 96 | VAL | 0 | -0.065 | -0.036 | 18.791 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 97 | PHE | 0 | 0.085 | 0.039 | 12.962 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 98 | PHE | 0 | -0.008 | -0.019 | 15.940 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 99 | ILE | 0 | 0.012 | -0.005 | 15.646 | -0.074 | -0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 100 | LYS | 1 | 0.801 | 0.889 | 9.682 | 0.773 | 0.773 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 101 | THR | 0 | 0.034 | 0.024 | 14.623 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 102 | PRO | 0 | -0.037 | -0.028 | 16.379 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 103 | ILE | 0 | 0.062 | 0.041 | 20.108 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 104 | ASN | 0 | 0.020 | -0.004 | 22.417 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 105 | ARG | 1 | 0.811 | 0.908 | 26.091 | 0.176 | 0.176 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 106 | GLY | 0 | 0.043 | 0.024 | 28.421 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 107 | VAL | 0 | 0.061 | 0.029 | 25.441 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 108 | PHE | 0 | -0.011 | -0.011 | 22.538 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 109 | GLU | -1 | -0.812 | -0.906 | 26.339 | -0.197 | -0.197 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 110 | GLU | -1 | -0.945 | -0.952 | 29.581 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 111 | ILE | 0 | -0.061 | -0.029 | 23.550 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 112 | PHE | 0 | -0.051 | -0.032 | 22.392 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 113 | GLY | 0 | -0.001 | 0.015 | 28.435 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |