![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 3JRYL
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 | 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 | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -648217.1246 |
---|---|
FMO2-HF: Nuclear repulsion | 612341.04613 |
FMO2-HF: Total energy | -35876.07847 |
FMO2-MP2: Total energy | -35983.049107 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037738/ligand_interaction/ligand_F037738.png)
Ligand Interaction
![ligand interaction](./Kdata/F037738/ligand_interaction/ligand_interaction_F037738.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. |
-128.273 | -131.227 | 37.44 | -16.487 | -17.997 | 0.158 |
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 | -0.030 | -0.014 | 2.100 | -24.549 | -19.783 | 4.594 | -4.015 | -5.345 | 0.039 |
4 | A | 10 | THR | 0 | -0.030 | -0.042 | 2.642 | 12.232 | 13.391 | 3.774 | -1.248 | -3.685 | -0.009 |
5 | A | 11 | VAL | 0 | 0.018 | 0.015 | 3.754 | -5.205 | -5.038 | 0.018 | -0.030 | -0.154 | 0.000 |
6 | A | 12 | THR | 0 | -0.019 | -0.003 | 7.562 | -0.529 | -0.529 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 13 | LEU | 0 | -0.025 | -0.009 | 9.813 | -1.085 | -1.085 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 14 | VAL | 0 | -0.001 | -0.018 | 13.327 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 15 | GLY | 0 | 0.020 | 0.012 | 16.720 | -0.323 | -0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 16 | LYS | 1 | 0.802 | 0.885 | 19.457 | -11.570 | -11.570 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 17 | VAL | 0 | -0.001 | 0.016 | 20.526 | 0.301 | 0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 18 | PHE | 0 | 0.013 | -0.004 | 22.235 | -0.623 | -0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 19 | THR | 0 | -0.035 | -0.011 | 23.523 | -0.308 | -0.308 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 20 | PRO | 0 | 0.035 | 0.002 | 23.769 | 0.360 | 0.360 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 21 | LEU | 0 | 0.000 | 0.003 | 19.934 | 0.385 | 0.385 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 22 | GLU | -1 | -0.895 | -0.936 | 22.963 | 12.079 | 12.079 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 23 | PHE | 0 | -0.020 | -0.011 | 22.366 | 0.703 | 0.703 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 24 | SER | 0 | -0.042 | -0.022 | 19.496 | -0.311 | -0.311 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 25 | HIS | 0 | -0.067 | -0.044 | 17.749 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 26 | GLU | -1 | -0.808 | -0.893 | 21.037 | 12.871 | 12.871 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 27 | LEU | 0 | -0.021 | -0.002 | 15.794 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 28 | TYR | 0 | -0.035 | -0.034 | 19.509 | 0.205 | 0.205 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 29 | GLY | 0 | 0.066 | 0.048 | 22.503 | -0.301 | -0.301 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 30 | GLU | -1 | -0.808 | -0.829 | 16.376 | 18.456 | 18.456 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 31 | LYS | 1 | 0.811 | 0.888 | 20.374 | -12.465 | -12.465 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 32 | PHE | 0 | -0.006 | -0.009 | 13.747 | 0.856 | 0.856 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 33 | PHE | 0 | 0.016 | 0.004 | 18.227 | -1.031 | -1.031 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 34 | ASN | 0 | -0.012 | -0.009 | 17.750 | 1.153 | 1.153 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 35 | PHE | 0 | 0.057 | 0.029 | 16.649 | -0.645 | -0.645 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 36 | ILE | 0 | -0.004 | 0.007 | 18.860 | 0.979 | 0.979 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 37 | LEU | 0 | 0.001 | 0.008 | 15.774 | -0.399 | -0.399 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 38 | GLU | -1 | -0.852 | -0.915 | 19.431 | 11.949 | 11.949 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 39 | VAL | 0 | -0.002 | -0.010 | 16.789 | 0.269 | 0.269 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 40 | PRO | 0 | 0.001 | 0.009 | 20.203 | -0.219 | -0.219 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 41 | ARG | 1 | 0.824 | 0.865 | 21.173 | -12.935 | -12.935 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 42 | LEU | 0 | 0.014 | -0.004 | 22.638 | -0.365 | -0.365 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 43 | SER | 0 | -0.021 | -0.022 | 24.792 | -0.238 | -0.238 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 44 | GLU | -1 | -0.842 | -0.913 | 26.521 | 10.750 | 10.750 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 45 | THR | 0 | -0.057 | -0.018 | 25.578 | -0.091 | -0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 46 | LYS | 1 | 0.819 | 0.924 | 23.686 | -10.933 | -10.933 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 47 | ASP | -1 | -0.817 | -0.855 | 19.211 | 14.448 | 14.448 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 48 | TYR | 0 | -0.033 | -0.049 | 21.037 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 49 | LEU | 0 | 0.003 | 0.004 | 14.755 | 0.215 | 0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 50 | PRO | 0 | 0.016 | 0.016 | 16.028 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 51 | ILE | 0 | 0.010 | 0.024 | 13.465 | 2.004 | 2.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 52 | THR | 0 | -0.024 | -0.034 | 13.480 | -1.675 | -1.675 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 53 | ILE | 0 | -0.018 | -0.005 | 13.117 | 2.138 | 2.138 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 54 | SER | 0 | 0.017 | -0.024 | 14.826 | -1.439 | -1.439 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 55 | ASN | 0 | 0.026 | -0.020 | 16.597 | 0.348 | 0.348 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 56 | ARG | 1 | 0.843 | 0.897 | 15.190 | -17.912 | -17.912 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 57 | LEU | 0 | -0.063 | -0.030 | 11.981 | 0.340 | 0.340 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 58 | PHE | 0 | 0.005 | -0.003 | 16.096 | 0.158 | 0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 59 | GLU | -1 | -0.879 | -0.929 | 19.099 | 12.772 | 12.772 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 60 | GLY | 0 | 0.004 | 0.010 | 21.833 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 61 | MET | 0 | -0.097 | -0.030 | 18.370 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 62 | ASN | 0 | -0.048 | -0.044 | 23.358 | 0.349 | 0.349 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 63 | LEU | 0 | 0.025 | -0.002 | 19.021 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 64 | GLU | -1 | -0.842 | -0.894 | 23.229 | 10.495 | 10.495 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 65 | VAL | 0 | -0.022 | -0.009 | 25.427 | 0.295 | 0.295 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 66 | GLY | 0 | 0.002 | 0.008 | 25.682 | -0.448 | -0.448 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 67 | THR | 0 | -0.060 | -0.041 | 22.312 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 68 | ARG | 1 | 0.866 | 0.931 | 21.465 | -11.882 | -11.882 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 69 | VAL | 0 | 0.017 | -0.002 | 17.166 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 70 | LYS | 1 | 0.897 | 0.955 | 10.813 | -22.057 | -22.057 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 71 | ILE | 0 | 0.008 | -0.005 | 10.871 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 72 | GLU | -1 | -0.741 | -0.832 | 4.790 | 45.642 | 45.715 | -0.001 | -0.004 | -0.068 | 0.000 |
67 | A | 73 | GLY | 0 | 0.067 | 0.026 | 6.976 | -1.513 | -1.513 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 74 | GLN | 0 | -0.022 | 0.012 | 1.776 | -31.261 | -34.538 | 11.739 | -4.734 | -3.728 | 0.062 |
69 | A | 75 | LEU | 0 | 0.015 | 0.012 | 5.487 | -6.891 | -6.885 | -0.001 | -0.001 | -0.003 | 0.000 |
70 | A | 76 | ARG | 1 | 0.834 | 0.918 | 6.017 | -38.083 | -38.083 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 77 | SER | 0 | 0.020 | 0.002 | 9.836 | -2.245 | -2.245 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 78 | TYR | 0 | 0.011 | -0.003 | 13.282 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 79 | ASN | 0 | 0.009 | -0.002 | 15.590 | -1.112 | -1.112 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 80 | ARG | 1 | 0.995 | 1.010 | 19.327 | -14.816 | -14.816 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 89 | LYS | 1 | 1.000 | 1.002 | 22.691 | -12.680 | -12.680 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 90 | LEU | 0 | 0.000 | -0.006 | 16.610 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 91 | ILE | 0 | -0.082 | -0.030 | 17.221 | -0.875 | -0.875 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 92 | LEU | 0 | 0.025 | 0.006 | 14.071 | 1.110 | 1.110 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 93 | THR | 0 | -0.073 | -0.036 | 12.136 | -1.375 | -1.375 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 94 | VAL | 0 | 0.039 | 0.028 | 9.185 | 2.542 | 2.542 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 95 | PHE | 0 | 0.011 | -0.003 | 8.358 | -2.444 | -2.444 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 96 | ALA | 0 | 0.014 | 0.001 | 8.321 | 4.512 | 4.512 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 97 | ARG | 1 | 0.663 | 0.771 | 1.706 | -87.750 | -93.598 | 17.317 | -6.455 | -5.014 | 0.066 |
84 | A | 98 | ASP | -1 | -0.855 | -0.925 | 8.949 | 20.538 | 20.538 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 99 | ILE | 0 | 0.009 | 0.006 | 11.029 | 0.452 | 0.452 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 100 | SER | 0 | 0.001 | 0.003 | 14.308 | -0.941 | -0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 101 | VAL | 0 | 0.014 | 0.011 | 16.853 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 102 | VAL | 0 | -0.040 | -0.013 | 19.374 | -0.125 | -0.125 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 103 | PRO | 0 | 0.027 | 0.020 | 22.063 | -0.233 | -0.233 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 104 | GLU | -1 | -0.804 | -0.878 | 24.853 | 11.497 | 11.497 | 0.000 | 0.000 | 0.000 | 0.000 |