![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 66KZZ
Calculation Name: 3FB9-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FB9
Chain ID: A
UniProt ID: A0A0H2
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 | 89 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -626723.405406 |
---|---|
FMO2-HF: Nuclear repulsion | 590688.766546 |
FMO2-HF: Total energy | -36034.638861 |
FMO2-MP2: Total energy | -36139.598104 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F020917/ligand_interaction/ligand_F020917.png)
Ligand Interaction
![ligand interaction](./Kdata/F020917/ligand_interaction/ligand_interaction_F020917.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:0:GLY)
Summations of interaction energy for
fragment #1(A:0: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. |
-0.375 | 0.504 | -0.002 | -0.395 | -0.482 | 0.001 |
Interaction energy analysis for fragmet #1(A:0: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 | 2 | SER | 0 | 0.002 | -0.015 | 3.849 | -0.825 | 0.054 | -0.002 | -0.395 | -0.482 | 0.001 |
4 | A | 3 | ASP | -1 | -0.794 | -0.903 | 6.260 | -0.409 | -0.409 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 4 | ALA | 0 | -0.030 | 0.003 | 9.294 | 0.184 | 0.184 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 5 | PHE | 0 | -0.012 | -0.012 | 7.489 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 6 | THR | 0 | -0.028 | -0.021 | 8.322 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 7 | ASP | -1 | -0.812 | -0.923 | 10.054 | 0.148 | 0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 8 | VAL | 0 | -0.025 | -0.013 | 13.376 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 9 | ALA | 0 | -0.003 | 0.010 | 12.629 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 10 | LYS | 1 | 0.855 | 0.932 | 12.027 | -0.137 | -0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 11 | MET | 0 | 0.002 | 0.010 | 15.385 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 12 | LYS | 1 | 0.783 | 0.871 | 18.052 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 13 | LYS | 1 | 0.881 | 0.925 | 17.540 | 0.118 | 0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 14 | ILE | 0 | 0.056 | 0.028 | 17.873 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 15 | LYS | 1 | 0.823 | 0.917 | 21.068 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 16 | GLU | -1 | -0.867 | -0.916 | 21.562 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 17 | GLU | -1 | -0.824 | -0.876 | 20.631 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 18 | ILE | 0 | 0.011 | 0.003 | 24.680 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 19 | LYS | 1 | 0.933 | 0.964 | 26.935 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 20 | ALA | 0 | -0.069 | -0.032 | 27.518 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 21 | HIS | 0 | 0.003 | 0.003 | 28.570 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 22 | GLU | -1 | -0.860 | -0.936 | 30.580 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 23 | GLY | 0 | -0.044 | -0.015 | 33.264 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 24 | GLN | 0 | -0.049 | -0.019 | 32.350 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 25 | VAL | 0 | 0.002 | -0.004 | 33.043 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 26 | VAL | 0 | 0.006 | 0.009 | 28.514 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 27 | GLU | -1 | -0.855 | -0.911 | 28.075 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 28 | MET | 0 | -0.043 | -0.020 | 26.236 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 29 | THR | 0 | -0.021 | -0.023 | 24.954 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 30 | LEU | 0 | -0.015 | -0.003 | 25.174 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 31 | GLU | -1 | -0.736 | -0.833 | 19.124 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 32 | ASN | 0 | -0.100 | -0.061 | 22.473 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 33 | GLY | 0 | 0.037 | 0.020 | 22.220 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 34 | ARG | 1 | 0.960 | 0.977 | 19.743 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 35 | LYS | 1 | 0.870 | 0.944 | 22.240 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 36 | ARG | 1 | 0.871 | 0.915 | 19.359 | -0.179 | -0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 37 | GLN | 0 | 0.029 | -0.003 | 26.312 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 38 | LYS | 1 | 0.921 | 0.951 | 29.649 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 39 | ASN | 0 | -0.006 | 0.000 | 26.904 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 40 | ARG | 1 | 0.771 | 0.870 | 30.168 | -0.054 | -0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 41 | LEU | 0 | 0.006 | -0.005 | 31.527 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 42 | GLY | 0 | 0.033 | -0.007 | 33.109 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 43 | LYS | 1 | 0.845 | 0.933 | 33.598 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 44 | LEU | 0 | 0.000 | -0.001 | 29.245 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 45 | ILE | 0 | -0.047 | -0.017 | 33.235 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 46 | GLU | -1 | -0.833 | -0.885 | 34.609 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 47 | VAL | 0 | -0.020 | -0.005 | 29.668 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 48 | TYR | 0 | -0.042 | -0.038 | 31.326 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 49 | PRO | 0 | -0.028 | -0.021 | 29.747 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 50 | SER | 0 | -0.036 | -0.025 | 28.038 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 51 | LEU | 0 | -0.015 | -0.008 | 27.755 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 52 | PHE | 0 | 0.042 | 0.027 | 25.366 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 53 | ILE | 0 | 0.003 | -0.006 | 30.646 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 54 | VAL | 0 | -0.009 | -0.005 | 30.502 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 55 | GLU | -1 | -0.844 | -0.912 | 33.855 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 56 | PHE | 0 | 0.019 | -0.006 | 31.005 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 57 | GLY | 0 | 0.048 | 0.012 | 37.081 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 58 | ASP | -1 | -0.824 | -0.919 | 39.852 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 59 | VAL | 0 | 0.009 | 0.032 | 35.926 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 60 | GLU | -1 | -0.895 | -0.963 | 39.230 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 61 | GLY | 0 | -0.011 | -0.005 | 38.655 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 62 | ASP | -1 | -0.872 | -0.933 | 36.052 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 63 | LYS | 1 | 0.777 | 0.910 | 38.879 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 64 | GLN | 0 | -0.074 | -0.053 | 39.028 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 65 | VAL | 0 | -0.034 | -0.020 | 42.897 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 66 | ASN | 0 | -0.048 | -0.019 | 41.744 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 67 | VAL | 0 | 0.024 | 0.023 | 41.656 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 68 | TYR | 0 | -0.066 | -0.019 | 35.705 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 69 | VAL | 0 | 0.027 | 0.010 | 37.416 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 70 | GLU | -1 | -0.798 | -0.865 | 31.810 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 71 | SER | 0 | -0.013 | -0.005 | 32.233 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 72 | PHE | 0 | -0.006 | 0.001 | 26.858 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 73 | THR | 0 | -0.002 | -0.031 | 25.488 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 74 | TYR | 0 | 0.046 | -0.016 | 22.519 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 75 | SER | 0 | 0.025 | 0.007 | 20.925 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 76 | ASP | -1 | -0.811 | -0.840 | 20.925 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 77 | ILE | 0 | 0.029 | 0.024 | 19.914 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 78 | LEU | 0 | -0.025 | -0.006 | 15.724 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 79 | THR | 0 | -0.068 | -0.052 | 16.225 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 80 | GLU | -1 | -0.915 | -0.961 | 14.266 | 0.290 | 0.290 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 81 | LYS | 1 | 0.861 | 0.937 | 18.716 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 82 | ASN | 0 | -0.047 | -0.043 | 21.986 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 83 | LEU | 0 | -0.024 | -0.003 | 19.438 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 84 | ILE | 0 | 0.009 | -0.012 | 22.325 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 85 | HIS | 0 | 0.012 | 0.017 | 22.761 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 86 | TYR | 0 | -0.016 | -0.039 | 22.052 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 87 | LEU | 0 | -0.043 | -0.012 | 27.227 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 88 | ASP | -1 | -0.941 | -0.972 | 29.928 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |