![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 493GN
Calculation Name: 3FBN-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FBN
Chain ID: B
UniProt ID: P38633
Base Structure: X-ray
Registration Date: 2023-06-21
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 | 94 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -685714.914582 |
---|---|
FMO2-HF: Nuclear repulsion | 646821.771795 |
FMO2-HF: Total energy | -38893.142787 |
FMO2-MP2: Total energy | -39006.010729 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F024972/ligand_interaction/ligand_F024972.png)
Ligand Interaction
![ligand interaction](./Kdata/F024972/ligand_interaction/ligand_interaction_F024972.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(B:17:SER)
Summations of interaction energy for
fragment #1(B:17:SER)
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. |
-0.979 | 2.541 | 0.228 | -1.557 | -2.19 | 0.002 |
Interaction energy analysis for fragmet #1(B:17:SER)
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 | B | 19 | GLN | 0 | -0.047 | -0.002 | 2.731 | -0.460 | 2.990 | 0.229 | -1.548 | -2.131 | 0.002 |
4 | B | 20 | ASN | 0 | -0.029 | -0.028 | 4.844 | 0.120 | 0.190 | -0.001 | -0.009 | -0.059 | 0.000 |
5 | B | 21 | PRO | 0 | -0.025 | -0.015 | 8.302 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | B | 22 | LEU | 0 | 0.018 | 0.018 | 11.652 | -0.098 | -0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 23 | PRO | 0 | 0.030 | 0.032 | 13.781 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 24 | THR | 0 | -0.029 | -0.034 | 16.400 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 25 | ARG | 1 | 0.865 | 0.903 | 19.931 | 0.050 | 0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 26 | PHE | 0 | 0.003 | -0.003 | 22.632 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 27 | GLU | -1 | -0.796 | -0.883 | 17.385 | -0.175 | -0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 28 | VAL | 0 | 0.072 | 0.036 | 19.084 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 29 | GLU | -1 | -0.765 | -0.817 | 21.083 | -0.100 | -0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 30 | LEU | 0 | 0.002 | 0.012 | 22.083 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 31 | GLU | -1 | -0.939 | -0.968 | 17.156 | -0.356 | -0.356 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 32 | PHE | 0 | -0.031 | -0.011 | 21.802 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 33 | ILE | 0 | 0.016 | 0.017 | 24.368 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 34 | GLN | 0 | 0.049 | -0.009 | 23.557 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 35 | SER | 0 | -0.050 | -0.029 | 23.508 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 36 | LEU | 0 | -0.009 | -0.011 | 25.327 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 37 | ALA | 0 | -0.029 | -0.016 | 27.783 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 38 | ASN | 0 | -0.042 | -0.015 | 26.051 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 39 | ILE | 0 | 0.086 | 0.023 | 29.178 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 40 | GLN | 0 | 0.020 | 0.028 | 29.558 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 41 | TYR | 0 | -0.017 | 0.002 | 25.994 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 42 | VAL | 0 | 0.022 | 0.005 | 29.196 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 43 | THR | 0 | 0.004 | -0.009 | 32.130 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 44 | TYR | 0 | 0.006 | 0.000 | 28.139 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 45 | LEU | 0 | -0.018 | -0.011 | 28.835 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 46 | LEU | 0 | -0.003 | -0.009 | 32.460 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 47 | THR | 0 | -0.021 | 0.000 | 34.467 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 48 | GLN | 0 | -0.070 | -0.026 | 30.715 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 49 | GLN | 0 | 0.074 | 0.041 | 34.285 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 50 | GLN | 0 | 0.027 | -0.005 | 34.221 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | B | 51 | ILE | 0 | -0.058 | -0.033 | 31.695 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | B | 52 | TRP | 0 | 0.014 | 0.003 | 35.061 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 53 | LYS | 1 | 0.898 | 0.964 | 38.609 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 54 | SER | 0 | -0.039 | -0.023 | 37.747 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 55 | PRO | 0 | 0.034 | 0.013 | 38.819 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 56 | ASN | 0 | -0.020 | 0.003 | 34.805 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 57 | PHE | 0 | 0.090 | 0.047 | 29.806 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 58 | LYS | 1 | 0.962 | 0.977 | 34.631 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 59 | ASN | 0 | -0.016 | -0.021 | 37.593 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 60 | TYR | 0 | -0.046 | -0.029 | 27.874 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 61 | LEU | 0 | 0.022 | 0.011 | 32.172 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 62 | LYS | 1 | 0.862 | 0.910 | 34.322 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 63 | TYR | 0 | -0.087 | -0.061 | 29.587 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 64 | LEU | 0 | -0.001 | -0.006 | 28.748 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 65 | GLU | -1 | -0.815 | -0.897 | 32.618 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 66 | TYR | 0 | -0.075 | -0.054 | 28.390 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | B | 67 | TRP | 0 | 0.048 | 0.006 | 25.846 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | B | 68 | CYS | 0 | -0.080 | -0.030 | 32.029 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | B | 69 | ASN | 0 | -0.054 | -0.014 | 34.748 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | B | 70 | PRO | 0 | 0.014 | 0.035 | 33.982 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | B | 71 | PRO | 0 | 0.031 | -0.016 | 31.102 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | B | 72 | TYR | 0 | -0.012 | 0.003 | 29.343 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | B | 73 | SER | 0 | 0.052 | 0.020 | 29.464 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | B | 74 | GLN | 0 | -0.050 | -0.036 | 30.262 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | B | 75 | CYS | 0 | -0.044 | -0.009 | 25.274 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | B | 76 | ILE | 0 | -0.046 | -0.012 | 25.453 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | B | 77 | VAL | 0 | 0.015 | 0.015 | 22.918 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | B | 78 | TYR | 0 | -0.004 | -0.002 | 21.415 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | B | 79 | PRO | 0 | 0.044 | 0.008 | 27.951 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | B | 80 | ASN | 0 | 0.004 | -0.001 | 31.503 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | B | 81 | CYS | 0 | -0.032 | 0.004 | 29.209 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | B | 82 | LEU | 0 | 0.043 | 0.021 | 31.357 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | B | 83 | PHE | 0 | -0.029 | -0.011 | 33.904 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | B | 84 | ILE | 0 | 0.030 | 0.011 | 32.791 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | B | 85 | LEU | 0 | 0.005 | 0.013 | 32.509 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | B | 86 | LYS | 1 | 0.859 | 0.920 | 35.223 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | B | 87 | LEU | 0 | -0.039 | -0.012 | 38.751 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | B | 88 | LEU | 0 | 0.005 | 0.014 | 34.502 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | B | 89 | ASN | 0 | -0.010 | -0.035 | 36.521 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | B | 90 | GLY | 0 | 0.007 | 0.004 | 39.778 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | B | 91 | PHE | 0 | 0.014 | 0.008 | 40.726 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | B | 92 | MET | 0 | 0.033 | 0.014 | 37.679 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | B | 93 | GLU | -1 | -0.935 | -0.946 | 42.090 | -0.056 | -0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | B | 94 | SER | 0 | -0.073 | -0.034 | 44.983 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | B | 95 | ALA | 0 | -0.021 | 0.003 | 43.613 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | B | 96 | ILE | 0 | 0.013 | 0.022 | 45.611 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | B | 97 | VAL | 0 | -0.073 | -0.038 | 42.600 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | B | 98 | ASN | 0 | 0.003 | -0.001 | 45.218 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | B | 99 | GLU | -1 | -0.946 | -0.978 | 45.302 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | B | 100 | ASP | -1 | -0.898 | -0.940 | 43.043 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | B | 101 | GLY | 0 | -0.061 | -0.039 | 40.614 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | B | 102 | LEU | 0 | -0.006 | -0.004 | 40.655 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | B | 103 | LEU | 0 | -0.022 | -0.019 | 38.557 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | B | 104 | GLU | -1 | -0.884 | -0.949 | 42.724 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | B | 105 | GLY | 0 | 0.024 | 0.021 | 46.379 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | B | 106 | LEU | 0 | -0.079 | -0.067 | 40.223 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | B | 107 | ASP | -1 | -0.904 | -0.949 | 43.238 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | B | 108 | GLU | -1 | -0.984 | -0.979 | 45.085 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | B | 109 | LEU | 0 | -0.064 | -0.019 | 41.708 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | B | 110 | PRO | 0 | -0.057 | -0.026 | 38.700 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |