![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 5J69Z
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 | OptHSide |
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 | -989878.209901 |
---|---|
FMO2-HF: Nuclear repulsion | 942060.303571 |
FMO2-HF: Total energy | -47817.906331 |
FMO2-MP2: Total energy | -47958.572052 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037406/ligand_interaction/ligand_F037406.png)
Ligand Interaction
![ligand interaction](./Kdata/F037406/ligand_interaction/ligand_interaction_F037406.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. |
-4.616 | -0.9 | 2.47 | -1.877 | -4.307 | 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 | 0.974 | 0.971 | 2.167 | -4.616 | -1.045 | 2.471 | -1.868 | -4.173 | 0.009 |
4 | A | 5 | THR | 0 | -0.032 | -0.001 | 5.057 | 0.099 | 0.244 | -0.001 | -0.009 | -0.134 | 0.000 |
5 | A | 6 | VAL | 0 | 0.043 | 0.026 | 8.591 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 7 | HIS | 0 | -0.002 | -0.001 | 9.214 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 8 | HIS | 0 | 0.013 | 0.001 | 13.604 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 9 | GLN | 0 | -0.008 | -0.006 | 14.259 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 10 | GLN | 0 | 0.009 | -0.007 | 18.749 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 11 | THR | 0 | 0.074 | 0.035 | 22.176 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 12 | ALA | 0 | 0.036 | 0.032 | 20.270 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 13 | GLU | -1 | -0.829 | -0.909 | 20.054 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 14 | ILE | 0 | -0.050 | -0.033 | 22.688 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 15 | THR | 0 | -0.006 | -0.007 | 25.532 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 16 | GLN | 0 | 0.008 | 0.000 | 23.457 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 17 | GLN | 0 | -0.074 | -0.049 | 26.016 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 18 | ALA | 0 | 0.014 | 0.000 | 27.646 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 19 | ALA | 0 | 0.086 | 0.052 | 28.901 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 20 | ASP | -1 | -0.813 | -0.888 | 26.870 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 21 | PHE | 0 | -0.024 | -0.016 | 30.410 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 22 | ILE | 0 | 0.006 | 0.005 | 33.115 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 23 | ARG | 1 | 0.847 | 0.924 | 29.060 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 24 | TYR | 0 | -0.018 | -0.053 | 30.688 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 25 | MET | 0 | -0.022 | 0.003 | 35.813 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 26 | ASN | 0 | 0.026 | 0.006 | 38.398 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 27 | ALA | 0 | 0.036 | 0.031 | 38.202 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 28 | ILE | 0 | -0.027 | -0.030 | 37.925 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 29 | ASN | 0 | -0.058 | -0.033 | 41.549 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 30 | ASP | -1 | -0.850 | -0.926 | 43.420 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 31 | TYR | 0 | -0.002 | 0.001 | 43.781 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 32 | LEU | 0 | -0.043 | -0.056 | 45.119 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 33 | TYR | 0 | -0.044 | -0.009 | 47.655 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 34 | GLN | 0 | -0.012 | -0.006 | 46.316 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 35 | HIS | 1 | 0.801 | 0.914 | 48.833 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 36 | PRO | 0 | 0.061 | 0.035 | 50.707 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 37 | GLU | -1 | -0.801 | -0.902 | 52.431 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 38 | ARG | 1 | 0.797 | 0.889 | 44.647 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 39 | ARG | 1 | 0.852 | 0.907 | 48.200 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 40 | ALA | 0 | 0.009 | 0.002 | 50.172 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 41 | ALA | 0 | -0.013 | 0.002 | 49.454 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 42 | GLY | 0 | -0.008 | 0.018 | 47.354 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 43 | GLY | 0 | 0.028 | 0.026 | 43.520 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 44 | GLN | 0 | 0.007 | -0.025 | 38.459 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 45 | LEU | 0 | -0.025 | -0.004 | 40.872 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 46 | THR | 0 | -0.001 | -0.027 | 39.234 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 47 | SER | 0 | 0.022 | -0.012 | 34.522 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 48 | ALA | 0 | -0.015 | -0.007 | 37.054 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 49 | GLN | 0 | -0.016 | 0.004 | 39.764 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 50 | LEU | 0 | -0.008 | -0.005 | 37.070 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 51 | GLY | 0 | 0.029 | 0.033 | 37.787 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 52 | LEU | 0 | -0.034 | -0.002 | 32.948 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 53 | PRO | 0 | 0.016 | 0.021 | 29.607 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 54 | ALA | 0 | 0.040 | 0.022 | 29.699 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 55 | THR | 0 | 0.022 | 0.017 | 28.057 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 56 | LYS | 1 | 0.929 | 0.958 | 24.131 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 57 | ASN | 0 | -0.075 | -0.054 | 25.711 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 58 | VAL | 0 | 0.049 | 0.054 | 27.907 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 59 | SER | 0 | -0.042 | -0.005 | 31.675 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 60 | HIS | 0 | 0.054 | 0.021 | 34.479 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 61 | LEU | 0 | 0.003 | 0.015 | 38.179 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 62 | ILE | 0 | -0.015 | 0.014 | 41.417 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 63 | SER | 0 | -0.008 | -0.012 | 45.028 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 64 | GLN | 0 | 0.029 | 0.003 | 47.423 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 65 | GLN | 0 | -0.013 | -0.006 | 50.408 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 66 | ARG | 1 | 0.946 | 0.988 | 47.776 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 67 | VAL | 0 | 0.022 | 0.007 | 42.350 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 68 | PHE | 0 | -0.015 | -0.004 | 41.465 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 69 | VAL | 0 | 0.024 | 0.003 | 36.507 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 70 | TRP | 0 | 0.025 | 0.002 | 34.414 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 71 | ALA | 0 | 0.049 | 0.022 | 30.732 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 72 | LYS | 1 | 0.936 | 0.970 | 25.625 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 73 | GLU | -1 | -0.910 | -0.954 | 30.130 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 74 | LYS | 1 | 0.872 | 0.925 | 23.219 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 75 | PRO | 0 | 0.056 | 0.027 | 27.397 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 76 | GLY | 0 | 0.027 | 0.006 | 29.166 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 77 | LEU | 0 | -0.009 | 0.004 | 29.458 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 78 | MET | 0 | 0.016 | 0.009 | 31.492 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 79 | GLY | 0 | 0.037 | 0.016 | 34.647 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 80 | ALA | 0 | 0.051 | 0.034 | 30.962 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 81 | LEU | 0 | -0.026 | -0.011 | 32.955 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 82 | LEU | 0 | -0.018 | 0.004 | 35.123 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 83 | GLU | -1 | -0.892 | -0.936 | 32.686 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 84 | GLN | 0 | -0.069 | -0.041 | 29.956 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 85 | SER | 0 | -0.045 | -0.034 | 35.671 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 86 | GLY | 0 | -0.001 | 0.024 | 39.120 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 87 | ASP | -1 | -0.942 | -0.983 | 40.429 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 88 | SER | 0 | -0.081 | -0.055 | 42.166 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 89 | ALA | 0 | -0.030 | -0.008 | 40.077 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 90 | LEU | 0 | 0.005 | -0.003 | 42.089 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 91 | LEU | 0 | -0.047 | -0.026 | 37.841 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 92 | ALA | 0 | -0.002 | -0.004 | 40.976 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 93 | ARG | 1 | 0.916 | 0.945 | 38.032 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 94 | VAL | 0 | -0.021 | 0.002 | 38.881 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 95 | GLU | -1 | -0.847 | -0.908 | 38.533 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 96 | ASN | 0 | -0.010 | -0.005 | 39.630 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 97 | GLY | 0 | 0.018 | -0.002 | 41.286 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 98 | ARG | 1 | 0.793 | 0.890 | 43.147 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 99 | LEU | 0 | 0.050 | 0.036 | 43.409 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 100 | LEU | 0 | -0.022 | -0.009 | 42.216 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 101 | ASP | -1 | -0.742 | -0.883 | 43.876 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 102 | THR | 0 | 0.004 | -0.007 | 41.608 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 103 | HIS | 0 | -0.033 | -0.009 | 42.906 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 104 | GLY | 0 | -0.038 | -0.019 | 44.028 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 105 | ARG | 1 | 0.911 | 0.961 | 44.847 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 106 | ARG | 1 | 0.957 | 0.973 | 47.801 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 107 | ILE | 0 | 0.047 | 0.032 | 46.960 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 108 | SER | 0 | -0.065 | -0.040 | 49.563 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 109 | ILE | 0 | -0.005 | 0.000 | 48.474 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 110 | THR | 0 | -0.017 | -0.018 | 49.395 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 111 | LEU | 0 | 0.014 | 0.017 | 42.870 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 112 | PRO | 0 | -0.019 | -0.009 | 43.429 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 113 | ALA | 0 | 0.032 | 0.008 | 43.331 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 114 | VAL | 0 | -0.023 | -0.014 | 39.577 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | A | 115 | ILE | 0 | -0.045 | -0.007 | 38.486 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | A | 116 | PRO | 0 | -0.012 | 0.004 | 34.293 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
116 | A | 117 | ASP | -1 | -0.747 | -0.876 | 36.824 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
117 | A | 118 | GLN | 0 | -0.057 | -0.035 | 32.775 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
118 | A | 119 | VAL | 0 | -0.047 | -0.013 | 33.349 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
119 | A | 120 | ILE | 0 | 0.033 | 0.019 | 33.783 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
120 | A | 121 | ILE | 0 | -0.047 | -0.041 | 36.204 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
121 | A | 122 | TRP | 0 | 0.067 | 0.035 | 38.959 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
122 | A | 123 | MET | 0 | -0.004 | -0.015 | 41.225 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
123 | A | 124 | ASN | 0 | 0.017 | 0.046 | 44.399 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |