![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: ZY5MN
Calculation Name: 1UB9-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1UB9
Chain ID: A
UniProt ID: O58788
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 100 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -727798.532866 |
---|---|
FMO2-HF: Nuclear repulsion | 688012.754252 |
FMO2-HF: Total energy | -39785.778614 |
FMO2-MP2: Total energy | -39901.694421 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F021576/ligand_interaction/ligand_F021576.png)
Ligand Interaction
![ligand interaction](./Kdata/F021576/ligand_interaction/ligand_interaction_F021576.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:MET)
Summations of interaction energy for
fragment #1(A:1:MET)
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. |
-12.815 | -10.978 | 11.087 | -5.428 | -7.496 | -0.056 |
Interaction energy analysis for fragmet #1(A:1:MET)
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 | 3 | GLU | -1 | -0.762 | -0.895 | 1.878 | -15.225 | -15.386 | 8.855 | -4.461 | -4.233 | -0.057 |
4 | A | 4 | LEU | 0 | 0.013 | 0.009 | 2.500 | -0.189 | 0.867 | 2.193 | -0.762 | -2.486 | 0.000 |
5 | A | 5 | LYS | 1 | 0.815 | 0.890 | 3.086 | 1.111 | 1.973 | 0.040 | -0.201 | -0.702 | 0.001 |
6 | A | 6 | GLU | -1 | -0.886 | -0.908 | 5.970 | -0.285 | -0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 7 | ILE | 0 | 0.002 | 0.005 | 7.090 | 0.305 | 0.305 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 8 | MET | 0 | -0.037 | -0.026 | 5.791 | 0.074 | 0.154 | -0.001 | -0.004 | -0.075 | 0.000 |
9 | A | 9 | LYS | 1 | 0.921 | 0.967 | 9.219 | 0.589 | 0.589 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 10 | SER | 0 | -0.003 | 0.014 | 11.484 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 11 | HIS | 0 | 0.003 | -0.007 | 13.980 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 12 | ILE | 0 | -0.075 | -0.039 | 16.180 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 13 | LEU | 0 | 0.012 | -0.007 | 17.056 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 14 | GLY | 0 | 0.069 | 0.031 | 15.202 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 15 | ASN | 0 | -0.041 | -0.015 | 16.089 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 16 | PRO | 0 | 0.078 | 0.035 | 18.369 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 17 | VAL | 0 | 0.019 | 0.015 | 20.538 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 18 | ARG | 1 | 0.889 | 0.934 | 21.354 | 0.128 | 0.128 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 19 | LEU | 0 | 0.054 | 0.039 | 17.215 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 20 | GLY | 0 | 0.035 | 0.021 | 21.102 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 21 | ILE | 0 | -0.021 | -0.020 | 24.201 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 22 | MET | 0 | -0.043 | -0.010 | 22.468 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 23 | ILE | 0 | 0.030 | 0.015 | 20.318 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 24 | PHE | 0 | -0.021 | -0.011 | 24.525 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 25 | LEU | 0 | -0.004 | -0.010 | 27.781 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 26 | LEU | 0 | 0.005 | 0.013 | 22.773 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 27 | PRO | 0 | -0.024 | -0.012 | 26.939 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 28 | ARG | 1 | 0.899 | 0.944 | 29.365 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 29 | ARG | 1 | 0.785 | 0.893 | 30.973 | 0.091 | 0.091 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 30 | LYS | 1 | 0.876 | 0.904 | 32.093 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 31 | ALA | 0 | 0.033 | 0.026 | 34.225 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 32 | PRO | 0 | -0.014 | -0.010 | 36.024 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 33 | PHE | 0 | 0.048 | 0.020 | 34.355 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 34 | SER | 0 | 0.000 | -0.014 | 36.243 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 35 | GLN | 0 | -0.002 | -0.001 | 37.078 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 36 | ILE | 0 | 0.036 | 0.017 | 31.099 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 37 | GLN | 0 | -0.042 | -0.038 | 33.070 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 38 | LYS | 1 | 0.921 | 0.971 | 34.973 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 39 | VAL | 0 | -0.015 | -0.005 | 32.399 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 40 | LEU | 0 | -0.035 | -0.019 | 28.088 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 41 | ASP | -1 | -0.931 | -0.943 | 30.562 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 42 | LEU | 0 | 0.019 | 0.018 | 28.524 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 43 | THR | 0 | 0.058 | 0.024 | 32.462 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 44 | PRO | 0 | 0.032 | -0.007 | 33.684 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 45 | GLY | 0 | 0.059 | 0.032 | 34.648 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 46 | ASN | 0 | -0.008 | 0.002 | 29.303 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 47 | LEU | 0 | 0.005 | 0.020 | 29.950 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 48 | ASP | -1 | -0.806 | -0.889 | 30.923 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 49 | SER | 0 | -0.014 | -0.010 | 29.562 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 50 | HIS | 0 | 0.014 | 0.015 | 24.859 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 51 | ILE | 0 | 0.009 | 0.006 | 27.108 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 52 | ARG | 1 | 0.888 | 0.909 | 29.306 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 53 | VAL | 0 | -0.075 | -0.025 | 23.648 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 54 | LEU | 0 | 0.036 | 0.016 | 23.013 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 55 | GLU | -1 | -0.816 | -0.879 | 26.051 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 56 | ARG | 1 | 0.897 | 0.945 | 27.176 | 0.096 | 0.096 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 57 | ASN | 0 | -0.043 | -0.024 | 23.176 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 58 | GLY | 0 | 0.054 | 0.037 | 25.268 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 59 | LEU | 0 | 0.005 | 0.028 | 21.688 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 60 | VAL | 0 | -0.028 | -0.032 | 25.762 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 61 | LYS | 1 | 0.887 | 0.943 | 29.011 | 0.077 | 0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 62 | THR | 0 | -0.071 | -0.068 | 32.686 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 63 | TYR | 0 | 0.000 | -0.021 | 35.578 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 64 | LYS | 1 | 0.867 | 0.916 | 39.331 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 65 | VAL | 0 | 0.029 | 0.018 | 42.029 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 66 | ILE | 0 | 0.028 | -0.008 | 44.579 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 67 | ALA | 0 | 0.030 | 0.040 | 48.010 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 68 | ASP | -1 | -0.863 | -0.938 | 50.089 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 69 | ARG | 1 | 0.874 | 0.926 | 48.498 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 70 | PRO | 0 | 0.023 | 0.021 | 47.292 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 71 | ARG | 1 | 0.921 | 0.965 | 42.471 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 72 | THR | 0 | 0.008 | 0.011 | 37.691 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 73 | VAL | 0 | -0.051 | -0.004 | 37.098 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 74 | VAL | 0 | 0.045 | 0.019 | 31.548 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 75 | GLU | -1 | -0.786 | -0.867 | 32.771 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 76 | ILE | 0 | 0.017 | 0.022 | 24.836 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 77 | THR | 0 | -0.029 | -0.042 | 27.665 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 78 | ASP | -1 | -0.767 | -0.871 | 27.336 | -0.097 | -0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 79 | PHE | 0 | 0.065 | 0.041 | 21.846 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 80 | GLY | 0 | 0.062 | 0.024 | 23.259 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 81 | MET | 0 | -0.081 | -0.046 | 22.954 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 82 | GLU | -1 | -0.877 | -0.899 | 21.245 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 83 | GLU | -1 | -0.822 | -0.914 | 18.463 | -0.274 | -0.274 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 84 | ALA | 0 | -0.031 | -0.013 | 17.850 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 85 | LYS | 1 | 0.884 | 0.930 | 18.157 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 86 | ARG | 1 | 0.820 | 0.904 | 15.273 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 87 | PHE | 0 | 0.058 | 0.032 | 12.139 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 88 | LEU | 0 | -0.022 | -0.021 | 13.274 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 89 | SER | 0 | -0.040 | -0.023 | 13.846 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 90 | SER | 0 | -0.015 | -0.034 | 9.110 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 91 | LEU | 0 | -0.027 | -0.019 | 9.147 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 92 | LYS | 1 | 0.815 | 0.888 | 10.992 | 0.225 | 0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 93 | ALA | 0 | 0.017 | 0.012 | 8.628 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 94 | VAL | 0 | 0.002 | -0.003 | 5.380 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 95 | ILE | 0 | -0.052 | -0.029 | 7.886 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 96 | ASP | -1 | -0.829 | -0.895 | 11.526 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 97 | GLY | 0 | -0.025 | -0.007 | 8.368 | 0.056 | 0.056 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 98 | LEU | 0 | -0.074 | -0.045 | 7.923 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 99 | ASP | -1 | -0.939 | -0.951 | 10.872 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 100 | LEU | 0 | -0.085 | -0.030 | 13.545 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |