![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: JQGJ9
Calculation Name: 4GS3-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4GS3
Chain ID: A
UniProt ID: Q8RBI8
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -648578.96567 |
---|---|
FMO2-HF: Nuclear repulsion | 612703.161328 |
FMO2-HF: Total energy | -35875.804342 |
FMO2-MP2: Total energy | -35982.757994 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037739/ligand_interaction/ligand_F037739.png)
Ligand Interaction
![ligand interaction](./Kdata/F037739/ligand_interaction/ligand_interaction_F037739.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:7:GLU)
Summations of interaction energy for
fragment #1(A:7:GLU)
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. |
-106.965 | -105.645 | 26.48 | -13.047 | -14.755 | 0.107 |
Interaction energy analysis for fragmet #1(A:7:GLU)
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 | 9 | ASN | 0 | -0.004 | -0.014 | 1.638 | -15.181 | -13.852 | 5.964 | -3.361 | -3.932 | 0.010 |
4 | A | 10 | THR | 0 | -0.053 | -0.045 | 2.496 | 9.248 | 9.959 | 2.786 | -0.936 | -2.562 | -0.013 |
5 | A | 11 | VAL | 0 | 0.010 | 0.018 | 4.198 | -4.782 | -4.599 | 0.003 | -0.055 | -0.132 | 0.000 |
6 | A | 12 | THR | 0 | -0.009 | -0.009 | 7.913 | 0.192 | 0.192 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | LEU | 0 | -0.018 | 0.002 | 10.396 | -1.188 | -1.188 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | VAL | 0 | 0.000 | -0.011 | 13.843 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | GLY | 0 | 0.011 | 0.003 | 17.095 | -0.411 | -0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | LYS | 1 | 0.844 | 0.915 | 19.870 | -11.104 | -11.104 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | VAL | 0 | -0.014 | 0.012 | 20.704 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | PHE | 0 | 0.012 | -0.003 | 22.428 | -0.607 | -0.607 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | THR | 0 | 0.018 | 0.007 | 23.676 | -0.342 | -0.342 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | PRO | 0 | 0.019 | -0.001 | 23.834 | 0.417 | 0.417 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LEU | 0 | -0.024 | 0.001 | 20.178 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | GLU | -1 | -0.949 | -0.958 | 22.938 | 11.507 | 11.507 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | PHE | 0 | -0.020 | -0.018 | 22.613 | 0.752 | 0.752 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | SER | 0 | -0.037 | -0.026 | 19.116 | -0.227 | -0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | HIS | 0 | -0.042 | -0.034 | 18.043 | -0.349 | -0.349 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | GLU | -1 | -0.844 | -0.921 | 20.932 | 12.993 | 12.993 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | LEU | 0 | -0.010 | 0.005 | 15.822 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | TYR | 0 | -0.006 | -0.016 | 19.405 | 0.263 | 0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | GLY | 0 | 0.038 | 0.033 | 22.287 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | GLU | -1 | -0.802 | -0.833 | 16.141 | 18.507 | 18.507 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | LYS | 1 | 0.849 | 0.908 | 20.343 | -12.577 | -12.577 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | PHE | 0 | -0.007 | -0.005 | 13.694 | 0.939 | 0.939 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | PHE | 0 | 0.027 | 0.019 | 18.347 | -1.004 | -1.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ASN | 0 | -0.007 | 0.002 | 18.006 | 2.043 | 2.043 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PHE | 0 | 0.049 | 0.022 | 16.985 | -0.711 | -0.711 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | 0.004 | 0.008 | 18.937 | 0.898 | 0.898 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | 0.002 | 0.007 | 16.023 | -0.475 | -0.475 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | GLU | -1 | -0.852 | -0.910 | 19.614 | 11.693 | 11.693 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | VAL | 0 | -0.009 | -0.023 | 17.034 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | PRO | 0 | -0.001 | 0.006 | 20.449 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ARG | 1 | 0.828 | 0.869 | 21.398 | -12.872 | -12.872 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | LEU | 0 | 0.020 | 0.002 | 23.049 | -0.389 | -0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | SER | 0 | -0.029 | -0.023 | 25.079 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.820 | -0.897 | 26.581 | 10.533 | 10.533 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | THR | 0 | -0.082 | -0.037 | 25.556 | -0.105 | -0.105 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | LYS | 1 | 0.833 | 0.925 | 23.899 | -10.723 | -10.723 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | ASP | -1 | -0.813 | -0.850 | 19.388 | 14.200 | 14.200 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | TYR | 0 | -0.039 | -0.050 | 21.242 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | LEU | 0 | -0.023 | -0.016 | 15.266 | 0.306 | 0.306 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | PRO | 0 | 0.000 | 0.014 | 15.809 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | ILE | 0 | 0.012 | 0.016 | 13.586 | 1.729 | 1.729 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | THR | 0 | -0.028 | -0.020 | 13.579 | -1.040 | -1.040 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | ILE | 0 | -0.010 | 0.001 | 13.463 | 1.928 | 1.928 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | SER | 0 | 0.018 | -0.019 | 14.677 | -1.525 | -1.525 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.035 | -0.002 | 16.365 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | ARG | 1 | 0.833 | 0.886 | 15.198 | -17.883 | -17.883 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | -0.038 | -0.027 | 12.055 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | PHE | 0 | 0.027 | 0.019 | 16.366 | 0.115 | 0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.920 | -0.948 | 19.119 | 12.532 | 12.532 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | GLY | 0 | -0.028 | -0.009 | 21.457 | 0.250 | 0.250 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | MET | 0 | -0.091 | -0.025 | 18.475 | -0.272 | -0.272 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | ASN | 0 | -0.049 | -0.034 | 23.300 | 0.213 | 0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | 0.012 | -0.011 | 18.916 | 0.319 | 0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLU | -1 | -0.838 | -0.899 | 23.246 | 10.314 | 10.314 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | VAL | 0 | -0.002 | -0.009 | 25.444 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | GLY | 0 | -0.028 | -0.008 | 25.791 | -0.389 | -0.389 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | THR | 0 | -0.040 | -0.020 | 22.456 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ARG | 1 | 0.850 | 0.924 | 21.469 | -12.041 | -12.041 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | VAL | 0 | 0.031 | 0.007 | 17.237 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | LYS | 1 | 0.965 | 0.987 | 11.434 | -20.876 | -20.876 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ILE | 0 | 0.005 | -0.004 | 10.984 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | GLU | -1 | -0.731 | -0.823 | 4.851 | 44.196 | 44.267 | -0.001 | -0.003 | -0.066 | 0.000 |
67 | A | 73 | GLY | 0 | 0.046 | 0.014 | 6.636 | -0.979 | -0.979 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | GLN | 0 | 0.003 | 0.036 | 2.027 | -25.079 | -23.972 | 4.572 | -2.900 | -2.780 | 0.046 |
69 | A | 75 | LEU | 0 | 0.007 | 0.001 | 6.016 | -5.631 | -5.631 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | ARG | 1 | 0.855 | 0.930 | 6.215 | -36.681 | -36.681 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | SER | 0 | 0.014 | 0.005 | 10.100 | -2.052 | -2.052 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | TYR | 0 | 0.017 | 0.001 | 12.866 | 0.449 | 0.449 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | ASN | 0 | 0.002 | 0.003 | 15.350 | -1.275 | -1.275 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | ARG | 1 | 0.993 | 1.007 | 19.017 | -14.384 | -14.384 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | LYS | 1 | 1.005 | 1.000 | 22.655 | -12.568 | -12.568 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | LEU | 0 | -0.012 | -0.011 | 16.638 | 0.456 | 0.456 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | ILE | 0 | -0.082 | -0.036 | 17.235 | -0.822 | -0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | LEU | 0 | 0.037 | 0.013 | 13.982 | 1.058 | 1.058 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | THR | 0 | -0.026 | -0.042 | 12.363 | -1.339 | -1.339 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | VAL | 0 | 0.023 | 0.023 | 9.510 | 2.616 | 2.616 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | PHE | 0 | -0.010 | -0.016 | 8.372 | -2.227 | -2.227 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | 0.000 | -0.008 | 8.551 | 3.898 | 3.898 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ARG | 1 | 0.692 | 0.795 | 1.853 | -83.072 | -85.153 | 13.156 | -5.792 | -5.283 | 0.064 |
84 | A | 98 | ASP | -1 | -0.930 | -0.968 | 8.815 | 20.750 | 20.750 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | 0.001 | -0.005 | 11.131 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | SER | 0 | 0.010 | 0.015 | 14.327 | -0.813 | -0.813 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | VAL | 0 | 0.019 | 0.010 | 17.200 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | VAL | 0 | -0.045 | -0.020 | 19.471 | -0.154 | -0.154 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | PRO | 0 | 0.026 | 0.019 | 22.220 | -0.252 | -0.252 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.803 | -0.891 | 24.832 | 11.332 | 11.332 | 0.000 | 0.000 | 0.000 | 0.000 |