![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: NNQ5Q
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 | OptH |
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 | -648030.638249 |
---|---|
FMO2-HF: Nuclear repulsion | 612155.434998 |
FMO2-HF: Total energy | -35875.203251 |
FMO2-MP2: Total energy | -35982.173668 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037740/ligand_interaction/ligand_F037740.png)
Ligand Interaction
![ligand interaction](./Kdata/F037740/ligand_interaction/ligand_interaction_F037740.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. |
-44.921 | -38.697 | 0.636 | -2.731 | -4.128 | 0.005 |
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 | -0.024 | -0.027 | 2.519 | -12.296 | -8.440 | 0.303 | -1.873 | -2.286 | 0.006 |
4 | A | 10 | THR | 0 | -0.065 | -0.045 | 3.027 | 3.306 | 4.523 | 0.114 | -0.489 | -0.842 | -0.002 |
5 | A | 11 | VAL | 0 | 0.019 | 0.025 | 4.622 | -3.357 | -3.275 | -0.001 | -0.016 | -0.065 | 0.000 |
6 | A | 12 | THR | 0 | -0.018 | -0.020 | 8.314 | 0.681 | 0.681 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | LEU | 0 | -0.012 | 0.005 | 10.710 | -1.101 | -1.101 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | VAL | 0 | -0.007 | -0.016 | 14.305 | 0.216 | 0.216 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | GLY | 0 | 0.013 | 0.005 | 17.591 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | LYS | 1 | 0.855 | 0.918 | 20.502 | -10.550 | -10.550 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | VAL | 0 | -0.009 | 0.013 | 21.707 | 0.207 | 0.207 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | PHE | 0 | 0.012 | -0.005 | 23.459 | -0.530 | -0.530 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | THR | 0 | 0.023 | 0.008 | 24.634 | -0.302 | -0.302 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | PRO | 0 | 0.029 | 0.004 | 24.724 | 0.409 | 0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LEU | 0 | -0.026 | 0.002 | 20.935 | 0.222 | 0.222 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | GLU | -1 | -0.961 | -0.964 | 23.533 | 10.592 | 10.592 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | PHE | 0 | -0.021 | -0.006 | 23.296 | 0.647 | 0.647 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | SER | 0 | -0.048 | -0.029 | 20.774 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | HIS | 0 | -0.057 | -0.065 | 19.369 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | GLU | -1 | -0.921 | -0.970 | 21.805 | 12.548 | 12.548 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | LEU | 0 | -0.006 | 0.009 | 16.881 | -0.081 | -0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | TYR | 0 | -0.025 | -0.026 | 20.253 | 0.308 | 0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | GLY | 0 | 0.036 | 0.024 | 23.013 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | GLU | -1 | -0.866 | -0.895 | 16.488 | 18.820 | 18.820 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | LYS | 1 | 0.972 | 0.991 | 21.181 | -11.977 | -11.977 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | PHE | 0 | 0.025 | 0.017 | 14.591 | 0.741 | 0.741 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | PHE | 0 | -0.002 | 0.004 | 19.016 | -0.979 | -0.979 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ASN | 0 | 0.004 | 0.012 | 18.638 | 1.728 | 1.728 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PHE | 0 | 0.031 | 0.009 | 18.085 | -0.598 | -0.598 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | 0.005 | 0.014 | 19.716 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | 0.001 | 0.006 | 16.872 | -0.366 | -0.366 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | GLU | -1 | -0.876 | -0.941 | 20.496 | 10.996 | 10.996 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | VAL | 0 | -0.016 | -0.024 | 17.555 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | PRO | 0 | -0.019 | 0.001 | 20.887 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ARG | 1 | 0.844 | 0.885 | 21.788 | -11.871 | -11.871 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | LEU | 0 | 0.037 | 0.013 | 23.343 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | SER | 0 | -0.030 | -0.017 | 25.243 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.871 | -0.930 | 26.870 | 10.037 | 10.037 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | THR | 0 | -0.100 | -0.055 | 25.372 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | LYS | 1 | 0.900 | 0.963 | 24.353 | -10.099 | -10.099 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | ASP | -1 | -0.817 | -0.864 | 20.087 | 12.980 | 12.980 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | TYR | 0 | -0.018 | -0.017 | 21.801 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | LEU | 0 | -0.028 | -0.021 | 15.943 | 0.220 | 0.220 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | PRO | 0 | -0.005 | 0.016 | 16.271 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | ILE | 0 | 0.020 | 0.018 | 14.468 | 1.328 | 1.328 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | THR | 0 | -0.015 | -0.014 | 14.285 | -0.879 | -0.879 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | ILE | 0 | -0.012 | 0.002 | 14.017 | 1.564 | 1.564 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | SER | 0 | 0.004 | -0.024 | 15.235 | -1.406 | -1.406 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.028 | -0.007 | 16.963 | 0.501 | 0.501 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | ARG | 1 | 0.928 | 0.956 | 16.457 | -17.153 | -17.153 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | -0.027 | -0.017 | 12.448 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | PHE | 0 | 0.007 | 0.005 | 16.913 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.931 | -0.951 | 19.866 | 12.371 | 12.371 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | GLY | 0 | -0.034 | -0.012 | 22.019 | 0.288 | 0.288 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | MET | 0 | -0.072 | -0.018 | 19.753 | -0.244 | -0.244 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | ASN | 0 | 0.010 | 0.002 | 24.236 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | 0.011 | -0.008 | 19.877 | 0.292 | 0.292 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLU | -1 | -0.912 | -0.951 | 24.235 | 9.783 | 9.783 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | VAL | 0 | 0.002 | 0.001 | 26.533 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | GLY | 0 | -0.029 | -0.007 | 26.820 | -0.333 | -0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | THR | 0 | -0.035 | -0.019 | 23.350 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ARG | 1 | 0.876 | 0.939 | 22.073 | -11.909 | -11.909 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | VAL | 0 | 0.026 | 0.005 | 18.103 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | LYS | 1 | 0.958 | 0.984 | 13.062 | -19.178 | -19.178 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ILE | 0 | 0.019 | 0.005 | 11.949 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | GLU | -1 | -0.734 | -0.832 | 5.465 | 39.657 | 39.657 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 73 | GLY | 0 | 0.049 | 0.016 | 7.615 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | GLN | 0 | 0.027 | 0.051 | 4.150 | -2.662 | -2.570 | -0.001 | -0.015 | -0.075 | 0.000 |
69 | A | 75 | LEU | 0 | -0.004 | -0.007 | 6.554 | -3.189 | -3.189 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 76 | ARG | 1 | 0.892 | 0.942 | 7.853 | -28.795 | -28.795 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | SER | 0 | 0.007 | 0.005 | 10.933 | -1.417 | -1.417 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | TYR | 0 | 0.015 | 0.000 | 13.862 | 0.520 | 0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | ASN | 0 | 0.000 | 0.000 | 16.360 | -1.194 | -1.194 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | ARG | 1 | 1.014 | 1.017 | 20.051 | -12.975 | -12.975 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | LYS | 1 | 1.002 | 0.987 | 23.356 | -11.623 | -11.623 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | LEU | 0 | -0.025 | -0.004 | 17.631 | 0.390 | 0.390 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | ILE | 0 | -0.077 | -0.034 | 18.065 | -0.684 | -0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | LEU | 0 | 0.039 | 0.011 | 14.576 | 0.831 | 0.831 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | THR | 0 | -0.024 | -0.042 | 13.137 | -1.020 | -1.020 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | VAL | 0 | 0.019 | 0.017 | 10.421 | 1.801 | 1.801 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | PHE | 0 | -0.018 | -0.015 | 9.121 | -1.423 | -1.423 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | -0.005 | -0.009 | 9.139 | 2.816 | 2.816 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ARG | 1 | 0.761 | 0.852 | 2.542 | -51.216 | -50.239 | 0.221 | -0.338 | -0.860 | 0.001 |
84 | A | 98 | ASP | -1 | -0.901 | -0.957 | 9.533 | 21.108 | 21.108 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | -0.012 | -0.012 | 12.158 | -0.341 | -0.341 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | SER | 0 | 0.003 | 0.015 | 15.465 | -0.559 | -0.559 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | VAL | 0 | 0.023 | 0.008 | 18.154 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | VAL | 0 | -0.055 | -0.023 | 20.212 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | PRO | 0 | 0.032 | 0.019 | 22.997 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.840 | -0.908 | 25.444 | 10.579 | 10.579 | 0.000 | 0.000 | 0.000 | 0.000 |