![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: R1318
Calculation Name: 3FB9-A-Xray312
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: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 90 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -628770.999273 |
---|---|
FMO2-HF: Nuclear repulsion | 592586.411144 |
FMO2-HF: Total energy | -36184.588129 |
FMO2-MP2: Total energy | -36289.994661 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015624/ligand_interaction/ligand_F015624.png)
Ligand Interaction
![ligand interaction](./Kdata/F015624/ligand_interaction/ligand_interaction_F015624.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:-1:ACE )
Summations of interaction energy for
fragment #1(A:-1:ACE )
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. |
0.446 | 1.403 | -0.004 | -0.48 | -0.473 | -0.001 |
Interaction energy analysis for fragmet #1(A:-1:ACE )
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 | 1 | MET | 0 | -0.033 | 0.008 | 3.876 | 0.882 | 1.839 | -0.004 | -0.480 | -0.473 | -0.001 |
4 | A | 2 | SER | 0 | 0.046 | 0.013 | 7.089 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 3 | ASP | -1 | -0.880 | -0.964 | 9.261 | -0.294 | -0.294 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 4 | ALA | 0 | 0.004 | 0.010 | 12.485 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 5 | PHE | 0 | -0.037 | -0.031 | 10.888 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 6 | THR | 0 | -0.031 | -0.001 | 12.666 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 7 | ASP | -1 | -0.832 | -0.923 | 14.353 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 8 | VAL | 0 | -0.047 | -0.026 | 17.625 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 9 | ALA | 0 | 0.000 | 0.014 | 16.575 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 10 | LYS | 1 | 0.972 | 0.988 | 15.514 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 11 | MET | 0 | 0.000 | 0.008 | 19.101 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 12 | LYS | 1 | 0.874 | 0.950 | 22.122 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 13 | LYS | 1 | 0.911 | 0.966 | 21.078 | 0.110 | 0.110 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 14 | ILE | 0 | 0.050 | 0.037 | 21.567 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 15 | LYS | 1 | 0.845 | 0.920 | 24.603 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 16 | GLU | -1 | -0.945 | -0.978 | 25.604 | -0.088 | -0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 17 | GLU | -1 | -0.900 | -0.961 | 23.472 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 18 | ILE | 0 | 0.019 | 0.007 | 27.804 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 19 | LYS | 1 | 0.930 | 0.968 | 30.327 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 20 | ALA | 0 | -0.075 | -0.043 | 30.673 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 21 | HIS | 0 | 0.036 | 0.027 | 31.301 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 22 | GLU | -1 | -0.927 | -0.959 | 33.380 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 23 | GLY | 0 | -0.056 | -0.034 | 36.353 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 24 | GLN | 0 | -0.023 | -0.012 | 35.117 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 25 | VAL | 0 | 0.023 | 0.007 | 34.848 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 26 | VAL | 0 | -0.005 | 0.009 | 31.088 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 27 | GLU | -1 | -0.833 | -0.901 | 29.875 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 28 | MET | 0 | -0.046 | -0.029 | 28.979 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 29 | THR | 0 | -0.029 | -0.018 | 26.749 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 30 | LEU | 0 | -0.042 | -0.023 | 27.379 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 31 | GLU | -1 | -0.927 | -0.933 | 20.202 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 32 | ASN | 0 | 0.023 | -0.011 | 24.402 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 33 | GLY | 0 | -0.006 | 0.013 | 23.383 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 34 | ARG | 1 | 0.940 | 0.954 | 20.790 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 35 | LYS | 1 | 0.852 | 0.938 | 23.270 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 36 | ARG | 1 | 1.015 | 1.015 | 20.514 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 37 | GLN | 0 | 0.025 | -0.007 | 27.557 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 38 | LYS | 1 | 0.919 | 0.952 | 31.015 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 39 | ASN | 0 | -0.001 | -0.010 | 28.763 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 40 | ARG | 1 | 0.810 | 0.925 | 32.237 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 41 | LEU | 0 | 0.024 | 0.008 | 33.441 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 42 | GLY | 0 | 0.013 | -0.005 | 35.351 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 43 | LYS | 1 | 0.936 | 0.986 | 36.242 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 44 | LEU | 0 | -0.012 | -0.002 | 32.624 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 45 | ILE | 0 | -0.067 | -0.040 | 36.455 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 46 | GLU | -1 | -0.874 | -0.929 | 38.217 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 47 | VAL | 0 | 0.013 | 0.007 | 33.617 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 48 | TYR | 0 | 0.013 | 0.011 | 35.471 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 49 | PRO | 0 | -0.020 | -0.014 | 34.074 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 50 | SER | 0 | -0.066 | -0.039 | 32.435 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 51 | LEU | 0 | -0.020 | -0.012 | 32.304 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 52 | PHE | 0 | 0.020 | 0.023 | 29.241 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 53 | ILE | 0 | 0.022 | 0.006 | 34.502 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 54 | VAL | 0 | 0.010 | 0.010 | 33.590 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 55 | GLU | -1 | -0.964 | -0.976 | 36.999 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 56 | PHE | 0 | 0.021 | -0.013 | 33.995 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 57 | GLY | 0 | 0.052 | 0.015 | 39.702 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 58 | ASP | -1 | -0.820 | -0.919 | 42.196 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 59 | VAL | 0 | -0.004 | 0.024 | 38.090 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 60 | GLU | -1 | -0.944 | -0.981 | 41.378 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 61 | GLY | 0 | -0.017 | -0.012 | 40.469 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 62 | ASP | -1 | -0.866 | -0.943 | 37.843 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 63 | LYS | 1 | 0.816 | 0.931 | 40.362 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 64 | GLN | 0 | -0.082 | -0.047 | 40.536 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 65 | VAL | 0 | -0.041 | -0.019 | 44.523 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 66 | ASN | 0 | -0.047 | -0.021 | 44.201 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 67 | VAL | 0 | 0.060 | 0.039 | 44.050 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 68 | TYR | 0 | -0.075 | -0.021 | 38.348 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 69 | VAL | 0 | 0.047 | 0.024 | 40.425 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 70 | GLU | -1 | -0.883 | -0.944 | 34.761 | -0.062 | -0.062 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 71 | SER | 0 | -0.055 | -0.023 | 36.010 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 72 | PHE | 0 | 0.058 | 0.031 | 30.476 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 73 | THR | 0 | -0.004 | -0.003 | 29.406 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 74 | TYR | 0 | 0.052 | -0.016 | 26.763 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 75 | SER | 0 | 0.000 | -0.004 | 24.987 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 76 | ASP | -1 | -0.843 | -0.905 | 24.567 | -0.118 | -0.118 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 77 | ILE | 0 | 0.002 | 0.006 | 23.349 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 78 | LEU | 0 | -0.018 | -0.025 | 19.261 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 79 | THR | 0 | -0.115 | -0.076 | 19.863 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 80 | GLU | -1 | -0.953 | -0.973 | 17.479 | -0.249 | -0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 81 | LYS | 1 | 1.001 | 1.025 | 21.765 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 82 | ASN | 0 | -0.053 | -0.049 | 25.089 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 83 | LEU | 0 | -0.015 | -0.006 | 21.772 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 84 | ILE | 0 | -0.004 | -0.014 | 24.708 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 85 | HIS | 0 | -0.008 | 0.002 | 25.075 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 86 | TYR | 0 | 0.018 | -0.004 | 25.426 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 87 | LEU | 0 | -0.084 | -0.029 | 29.468 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 88 | ASP | -2 | -1.855 | -1.926 | 31.546 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |