![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YV862
Calculation Name: 3EOI-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3EOI
Chain ID: A
UniProt ID: Q68JC9
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 | 123 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -990641.06126 |
---|---|
FMO2-HF: Nuclear repulsion | 942822.837191 |
FMO2-HF: Total energy | -47818.22407 |
FMO2-MP2: Total energy | -47958.806195 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037405/ligand_interaction/ligand_F037405.png)
Ligand Interaction
![ligand interaction](./Kdata/F037405/ligand_interaction/ligand_interaction_F037405.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:2:LEU)
Summations of interaction energy for
fragment #1(A:2:LEU)
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. |
-3.491 | 0.185 | 1.228 | -1.507 | -3.397 | 0.009 |
Interaction energy analysis for fragmet #1(A:2:LEU)
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 | 4 | ARG | 1 | 0.953 | 0.974 | 2.153 | -3.427 | 0.101 | 1.229 | -1.498 | -3.259 | 0.009 |
4 | A | 5 | THR | 0 | -0.015 | -0.013 | 5.330 | 0.091 | 0.239 | -0.001 | -0.009 | -0.138 | 0.000 |
5 | A | 6 | VAL | 0 | 0.024 | 0.021 | 8.837 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | HIS | 0 | 0.015 | 0.005 | 9.172 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | HIS | 0 | 0.028 | 0.000 | 13.672 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | GLN | 0 | -0.006 | 0.004 | 14.629 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | GLN | 0 | -0.016 | -0.023 | 18.584 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | THR | 0 | 0.044 | 0.020 | 22.127 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | ALA | 0 | 0.040 | 0.034 | 20.819 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.850 | -0.915 | 20.730 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | ILE | 0 | -0.033 | -0.022 | 23.302 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | THR | 0 | 0.012 | 0.005 | 25.860 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | GLN | 0 | -0.028 | -0.024 | 23.673 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | GLN | 0 | -0.085 | -0.061 | 26.237 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ALA | 0 | 0.027 | 0.014 | 28.065 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | ALA | 0 | 0.076 | 0.041 | 28.973 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ASP | -1 | -0.822 | -0.877 | 27.242 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | PHE | 0 | -0.055 | -0.024 | 30.727 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | ILE | 0 | 0.050 | 0.019 | 33.404 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | ARG | 1 | 0.842 | 0.933 | 29.573 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | -0.033 | -0.055 | 30.777 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | MET | 0 | -0.030 | -0.001 | 35.982 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | ASN | 0 | 0.036 | 0.011 | 38.663 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | ALA | 0 | 0.024 | 0.024 | 38.348 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | ILE | 0 | -0.022 | -0.031 | 38.050 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | ASN | 0 | -0.053 | -0.041 | 41.733 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | ASP | -1 | -0.814 | -0.906 | 43.732 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | TYR | 0 | -0.014 | 0.003 | 44.031 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | LEU | 0 | -0.024 | -0.038 | 45.083 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | TYR | 0 | -0.037 | 0.002 | 47.893 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | GLN | 0 | -0.036 | -0.027 | 46.434 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | HIS | 1 | 0.800 | 0.895 | 48.924 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | PRO | 0 | 0.054 | 0.027 | 50.688 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | GLU | -1 | -0.776 | -0.880 | 52.753 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | ARG | 1 | 0.787 | 0.876 | 44.848 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | ARG | 1 | 0.850 | 0.913 | 48.879 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | ALA | 0 | -0.012 | -0.008 | 50.581 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | ALA | 0 | -0.013 | 0.002 | 50.052 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.009 | 0.017 | 47.876 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | GLY | 0 | 0.052 | 0.035 | 43.799 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | GLN | 0 | -0.008 | -0.031 | 38.776 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | -0.011 | 0.010 | 40.917 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | THR | 0 | 0.005 | -0.022 | 39.440 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | SER | 0 | 0.023 | -0.016 | 34.856 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | ALA | 0 | -0.021 | -0.004 | 37.331 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | GLN | 0 | -0.014 | 0.003 | 40.212 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | LEU | 0 | -0.020 | -0.005 | 37.257 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | GLY | 0 | 0.036 | 0.032 | 38.270 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LEU | 0 | -0.010 | 0.001 | 33.103 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | PRO | 0 | 0.028 | 0.024 | 29.933 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ALA | 0 | 0.026 | 0.020 | 30.188 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | THR | 0 | 0.028 | 0.019 | 28.065 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | LYS | 1 | 0.922 | 0.951 | 24.672 | -0.057 | -0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | ASN | 0 | -0.052 | -0.044 | 26.063 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | VAL | 0 | 0.048 | 0.055 | 28.207 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | SER | 0 | -0.063 | -0.025 | 32.032 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | HIS | 0 | 0.062 | 0.034 | 34.853 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | -0.009 | 0.008 | 38.634 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | ILE | 0 | 0.003 | 0.026 | 41.968 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | SER | 0 | -0.016 | -0.021 | 45.531 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLN | 0 | 0.031 | 0.002 | 47.959 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | GLN | 0 | 0.024 | 0.010 | 51.292 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | ARG | 1 | 0.897 | 0.972 | 48.002 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | VAL | 0 | 0.011 | 0.006 | 42.770 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | PHE | 0 | -0.012 | -0.003 | 42.055 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | VAL | 0 | 0.031 | -0.004 | 37.052 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | TRP | 0 | 0.031 | 0.010 | 34.910 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ALA | 0 | 0.054 | 0.022 | 31.072 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | LYS | 1 | 0.934 | 0.973 | 26.053 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | GLU | -1 | -0.814 | -0.884 | 30.669 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | LYS | 1 | 0.879 | 0.928 | 23.065 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | PRO | 0 | 0.026 | 0.016 | 27.574 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | GLY | 0 | 0.047 | 0.015 | 29.176 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | LEU | 0 | -0.025 | -0.002 | 29.738 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | MET | 0 | 0.034 | 0.009 | 31.674 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | GLY | 0 | 0.012 | 0.015 | 34.496 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ALA | 0 | 0.034 | 0.016 | 31.212 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | LEU | 0 | -0.016 | -0.010 | 33.217 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | LEU | 0 | -0.021 | 0.017 | 35.462 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | GLU | -1 | -0.829 | -0.912 | 32.896 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | GLN | 0 | -0.092 | -0.056 | 30.518 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | SER | 0 | -0.046 | -0.039 | 35.939 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | GLY | 0 | -0.001 | 0.023 | 39.461 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | ASP | -1 | -0.942 | -0.985 | 40.803 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | SER | 0 | -0.073 | -0.042 | 42.446 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ALA | 0 | -0.014 | -0.010 | 40.186 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | LEU | 0 | -0.010 | -0.005 | 42.115 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | LEU | 0 | -0.027 | -0.017 | 38.311 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ALA | 0 | -0.023 | -0.011 | 41.333 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | ARG | 1 | 0.753 | 0.823 | 37.103 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | VAL | 0 | -0.027 | -0.004 | 38.745 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | GLU | -1 | -0.809 | -0.886 | 38.545 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | -0.023 | -0.026 | 39.274 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | GLY | 0 | 0.003 | 0.004 | 41.226 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | ARG | 1 | 0.789 | 0.894 | 42.966 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | LEU | 0 | 0.064 | 0.040 | 43.352 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | LEU | 0 | -0.042 | -0.016 | 42.415 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ASP | -1 | -0.739 | -0.874 | 43.771 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | THR | 0 | -0.006 | -0.019 | 41.310 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | HIS | 0 | -0.036 | -0.003 | 43.099 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | GLY | 0 | 0.009 | 0.013 | 44.155 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | ARG | 1 | 0.866 | 0.925 | 45.002 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | ARG | 1 | 0.971 | 0.975 | 47.715 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | ILE | 0 | 0.047 | 0.033 | 46.849 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | SER | 0 | -0.040 | -0.021 | 49.391 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | ILE | 0 | -0.030 | -0.022 | 48.741 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | THR | 0 | -0.018 | -0.015 | 49.131 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | LEU | 0 | 0.031 | 0.023 | 42.783 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | PRO | 0 | -0.003 | -0.005 | 43.904 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | ALA | 0 | 0.014 | 0.002 | 43.393 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | VAL | 0 | -0.018 | -0.005 | 40.141 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | ILE | 0 | -0.038 | -0.005 | 38.789 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | PRO | 0 | -0.023 | -0.004 | 34.514 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | ASP | -1 | -0.743 | -0.884 | 36.505 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 118 | GLN | 0 | -0.026 | -0.005 | 32.915 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 119 | VAL | 0 | -0.050 | -0.015 | 33.477 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 120 | ILE | 0 | 0.043 | 0.027 | 33.763 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 121 | ILE | 0 | -0.045 | -0.036 | 36.496 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 122 | TRP | 0 | 0.073 | 0.036 | 39.263 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 123 | MET | 0 | -0.009 | -0.012 | 41.639 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
123 | A | 124 | ASN | 0 | 0.016 | 0.045 | 44.934 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |