![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZY1JN
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 | 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 | 102 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -817187.844887 |
---|---|
FMO2-HF: Nuclear repulsion | 776095.868414 |
FMO2-HF: Total energy | -41091.976473 |
FMO2-MP2: Total energy | -41212.858922 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020716/ligand_interaction/ligand_F020716.png)
Ligand Interaction
![ligand interaction](./Kdata/F020716/ligand_interaction/ligand_interaction_F020716.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. |
-0.223 | 1.119 | -0.007 | -0.757 | -0.579 | 0.003 |
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 | 0.853 | 0.920 | 3.851 | 1.531 | 2.873 | -0.007 | -0.757 | -0.579 | 0.003 |
4 | A | 15 | GLU | -1 | -0.872 | -0.930 | 6.728 | -0.693 | -0.693 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 16 | ILE | 0 | -0.006 | -0.003 | 10.323 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 17 | ALA | 0 | 0.011 | 0.012 | 13.766 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 18 | ILE | 0 | -0.025 | -0.015 | 17.092 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 19 | GLN | 0 | 0.022 | 0.020 | 20.041 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 20 | GLU | -1 | -0.771 | -0.899 | 23.621 | -0.257 | -0.257 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 21 | LYS | 1 | 0.914 | 0.956 | 25.053 | 0.228 | 0.228 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 22 | ASP | -1 | -0.759 | -0.861 | 23.871 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 23 | LEU | 0 | -0.039 | -0.009 | 20.746 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 24 | THR | 0 | -0.025 | -0.007 | 24.833 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 25 | LEU | 0 | 0.030 | 0.014 | 23.890 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 26 | GLN | 0 | 0.020 | 0.020 | 24.940 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 27 | TRP | 0 | 0.069 | 0.036 | 24.852 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 28 | ARG | 1 | 0.955 | 0.971 | 25.022 | 0.252 | 0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 29 | GLY | 0 | 0.038 | 0.016 | 28.821 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 30 | ASN | 0 | -0.034 | -0.020 | 31.341 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 31 | THR | 0 | 0.026 | 0.004 | 31.892 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 32 | GLY | 0 | 0.054 | 0.034 | 29.509 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 33 | LYS | 1 | 0.865 | 0.917 | 19.544 | 0.396 | 0.396 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 34 | LEU | 0 | 0.006 | 0.016 | 21.257 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 35 | VAL | 0 | -0.074 | -0.031 | 21.852 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 36 | LYS | 1 | 0.898 | 0.944 | 20.329 | 0.297 | 0.297 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 37 | VAL | 0 | 0.024 | 0.023 | 19.362 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 38 | ARG | 1 | 0.861 | 0.926 | 21.134 | 0.244 | 0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 39 | LEU | 0 | 0.031 | 0.017 | 19.818 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 40 | LYS | 1 | 0.845 | 0.913 | 23.665 | 0.281 | 0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 41 | ASN | 0 | 0.022 | -0.009 | 26.601 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 42 | THR | 0 | 0.031 | 0.015 | 28.003 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 43 | ARG | 1 | 0.785 | 0.865 | 21.504 | 0.361 | 0.361 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 44 | ALA | 0 | 0.020 | 0.012 | 23.209 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 45 | MET | 0 | 0.015 | 0.011 | 24.000 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 46 | GLU | -1 | -0.814 | -0.863 | 23.851 | -0.306 | -0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 47 | MET | 0 | 0.004 | -0.006 | 19.808 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 48 | TRP | 0 | 0.028 | 0.028 | 21.159 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 49 | TYR | 0 | -0.014 | -0.018 | 23.007 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 50 | ASN | 0 | -0.032 | -0.033 | 21.784 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 51 | LYS | 1 | 0.834 | 0.920 | 18.792 | 0.258 | 0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 52 | GLN | 0 | 0.022 | 0.022 | 17.250 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 53 | ILE | 0 | -0.026 | -0.022 | 15.075 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 54 | THR | 0 | -0.026 | -0.024 | 15.740 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 55 | GLU | -1 | -0.896 | -0.969 | 15.537 | -0.467 | -0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 56 | GLU | -1 | -0.916 | -0.946 | 13.739 | -0.458 | -0.458 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 57 | ASN | 0 | -0.001 | 0.013 | 11.307 | -0.096 | -0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 58 | ILE | 0 | -0.064 | -0.029 | 10.857 | -0.236 | -0.236 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 59 | GLN | 0 | -0.045 | -0.042 | 10.572 | -0.110 | -0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 60 | GLU | -1 | -0.776 | -0.875 | 6.542 | -1.786 | -1.786 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 61 | ILE | 0 | -0.090 | -0.028 | 6.396 | -0.921 | -0.921 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 62 | THR | 0 | 0.057 | 0.029 | 5.184 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 63 | THR | 0 | -0.047 | -0.028 | 8.336 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 64 | LEU | 0 | -0.004 | 0.007 | 11.022 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 65 | ASN | 0 | -0.008 | -0.031 | 14.465 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 66 | ILE | 0 | 0.005 | 0.006 | 16.689 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 67 | ILE | 0 | 0.005 | 0.001 | 19.306 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 68 | LYS | 1 | 0.830 | 0.896 | 22.801 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 69 | ASN | 0 | -0.040 | -0.035 | 26.543 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 70 | GLY | 0 | 0.024 | 0.021 | 28.033 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 71 | LYS | 1 | 0.888 | 0.959 | 25.251 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 72 | SER | 0 | 0.013 | -0.006 | 19.866 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 73 | LEU | 0 | -0.009 | -0.002 | 19.772 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 74 | ALA | 0 | 0.038 | 0.033 | 14.116 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 75 | LEU | 0 | -0.037 | -0.029 | 15.257 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 76 | GLU | -1 | -0.757 | -0.861 | 10.618 | -1.024 | -1.024 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 77 | VAL | 0 | -0.032 | -0.015 | 11.405 | 0.226 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 78 | TYR | 0 | -0.012 | -0.029 | 11.532 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 79 | PRO | 0 | 0.095 | 0.057 | 7.553 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 80 | GLU | -1 | -0.849 | -0.926 | 9.167 | -1.071 | -1.071 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 81 | LYS | 1 | 0.808 | 0.917 | 12.376 | 0.661 | 0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 82 | SER | 0 | -0.038 | -0.010 | 12.467 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 83 | ILE | 0 | 0.012 | 0.019 | 15.155 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 84 | TYR | 0 | 0.074 | 0.026 | 17.223 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 85 | VAL | 0 | -0.040 | -0.018 | 20.886 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 86 | LYS | 1 | 1.035 | 1.018 | 24.518 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 87 | PRO | 0 | -0.006 | 0.012 | 28.075 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 88 | ASN | 0 | -0.001 | 0.001 | 29.349 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 89 | LEU | 0 | 0.025 | 0.000 | 32.555 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 90 | GLY | 0 | 0.022 | 0.009 | 33.176 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 91 | ARG | 1 | 0.931 | 0.971 | 31.443 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 92 | ILE | 0 | 0.023 | 0.012 | 24.399 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 93 | ASN | 0 | 0.013 | 0.009 | 24.026 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 94 | VAL | 0 | -0.008 | -0.010 | 23.572 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 95 | PRO | 0 | 0.040 | 0.036 | 18.408 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 96 | VAL | 0 | -0.068 | -0.046 | 19.108 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 97 | PHE | 0 | 0.101 | 0.048 | 13.378 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 98 | PHE | 0 | -0.003 | -0.015 | 16.614 | 0.095 | 0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 99 | ILE | 0 | 0.024 | 0.014 | 15.804 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 100 | LYS | 1 | 0.804 | 0.888 | 10.658 | 1.015 | 1.015 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 101 | THR | 0 | 0.049 | 0.026 | 15.150 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 102 | PRO | 0 | -0.030 | -0.029 | 17.117 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 103 | ILE | 0 | 0.065 | 0.044 | 20.834 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 104 | ASN | 0 | 0.008 | -0.007 | 23.026 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 105 | ARG | 1 | 0.805 | 0.900 | 26.681 | 0.196 | 0.196 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 106 | GLY | 0 | 0.028 | 0.014 | 28.749 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 107 | VAL | 0 | 0.054 | 0.026 | 25.706 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 108 | PHE | 0 | 0.009 | -0.001 | 23.122 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 109 | GLU | -1 | -0.828 | -0.914 | 26.740 | -0.201 | -0.201 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 110 | GLU | -1 | -0.928 | -0.946 | 30.074 | -0.132 | -0.132 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 111 | ILE | 0 | -0.047 | -0.009 | 23.747 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 112 | PHE | 0 | -0.053 | -0.033 | 22.759 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 113 | GLY | 0 | 0.002 | 0.016 | 28.788 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |