![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 2J8KR
Calculation Name: 6EHR-E-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 6EHR
Chain ID: E
UniProt ID: Q6IAA8
Base Structure: X-ray
Registration Date: 2023-06-26
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 | 115 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -531743.438694 |
---|---|
FMO2-HF: Nuclear repulsion | 487602.870368 |
FMO2-HF: Total energy | -44140.568325 |
FMO2-MP2: Total energy | -44270.156392 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F028418/ligand_interaction/ligand_F028418.png)
Ligand Interaction
![ligand interaction](./Kdata/F028418/ligand_interaction/ligand_interaction_F028418.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(E:46:ALA)
Summations of interaction energy for
fragment #1(E:46:ALA)
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. |
-2.349 | 0.817 | 0 | -1.337 | -1.828 | 0.002 |
Interaction energy analysis for fragmet #1(E:46:ALA)
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 | E | 48 | THR | 0 | -0.007 | -0.015 | 3.170 | -1.422 | 1.406 | 0.001 | -1.311 | -1.518 | 0.002 |
4 | E | 49 | ASP | -1 | -0.845 | -0.922 | 4.030 | -1.991 | -1.653 | -0.001 | -0.026 | -0.310 | 0.000 |
5 | E | 50 | GLU | -1 | -0.926 | -0.960 | 6.057 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 51 | GLN | 0 | -0.013 | -0.006 | 7.760 | 0.315 | 0.315 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 52 | ALA | 0 | 0.012 | 0.017 | 8.536 | 0.146 | 0.146 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 53 | LEU | 0 | 0.007 | 0.008 | 9.758 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 54 | LEU | 0 | 0.016 | 0.003 | 11.907 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 55 | SER | 0 | -0.013 | -0.017 | 12.871 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 56 | SER | 0 | -0.057 | -0.027 | 14.478 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 57 | ILE | 0 | -0.009 | -0.002 | 15.745 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 58 | LEU | 0 | 0.011 | 0.016 | 17.383 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 59 | ALA | 0 | 0.004 | 0.007 | 18.976 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 60 | LYS | 1 | 0.944 | 0.965 | 19.723 | 0.229 | 0.229 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 61 | THR | 0 | -0.047 | -0.042 | 21.890 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 62 | ALA | 0 | -0.015 | -0.010 | 23.550 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 63 | SER | 0 | -0.013 | 0.004 | 25.069 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 64 | ASN | 0 | -0.063 | -0.035 | 25.897 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 65 | ILE | 0 | -0.024 | -0.003 | 27.495 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 66 | ILE | 0 | -0.005 | 0.002 | 30.055 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 67 | ASP | -1 | -0.845 | -0.915 | 33.530 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 68 | VAL | 0 | -0.048 | -0.028 | 34.999 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 69 | SER | 0 | -0.063 | -0.032 | 37.695 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 70 | ALA | 0 | -0.021 | -0.009 | 38.749 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 71 | ALA | 0 | -0.017 | -0.018 | 41.215 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 72 | ASP | -1 | -0.917 | -0.938 | 40.649 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 73 | SER | 0 | -0.016 | -0.023 | 43.376 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 74 | GLN | 0 | -0.005 | -0.010 | 42.059 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 75 | GLY | 0 | 0.000 | 0.010 | 43.871 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 76 | MET | 0 | -0.027 | -0.003 | 46.611 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 77 | GLU | -1 | -0.910 | -0.976 | 48.660 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 78 | GLN | 0 | -0.048 | -0.020 | 41.371 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 79 | HIS | 0 | 0.083 | 0.025 | 39.844 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | E | 80 | GLU | -1 | -0.806 | -0.885 | 38.859 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | E | 81 | TYR | 0 | -0.027 | -0.001 | 42.230 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | E | 82 | MET | 0 | 0.034 | 0.012 | 44.782 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 83 | ASP | -1 | -0.844 | -0.916 | 43.283 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | E | 84 | ARG | 1 | 0.812 | 0.898 | 36.461 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 85 | ALA | 0 | -0.006 | -0.011 | 43.036 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 86 | ARG | 1 | 0.913 | 0.939 | 46.346 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 87 | GLN | 0 | 0.076 | 0.063 | 39.979 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 88 | TYR | 0 | 0.003 | 0.006 | 39.334 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 89 | SER | 0 | 0.004 | 0.005 | 45.353 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 90 | THR | 0 | -0.051 | -0.037 | 47.167 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 91 | ARG | 1 | 0.883 | 0.911 | 38.355 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 92 | LEU | 0 | 0.026 | 0.036 | 46.091 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 93 | ALA | 0 | 0.046 | 0.027 | 48.245 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 94 | VAL | 0 | -0.018 | -0.018 | 46.636 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 95 | LEU | 0 | 0.041 | 0.016 | 44.650 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 96 | SER | 0 | -0.040 | 0.004 | 49.357 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 97 | SER | 0 | -0.045 | -0.038 | 52.247 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 98 | SER | 0 | -0.049 | -0.023 | 50.846 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 99 | LEU | 0 | 0.020 | 0.028 | 47.903 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 100 | THR | 0 | -0.002 | 0.001 | 50.056 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 101 | HIS | 0 | 0.012 | 0.001 | 52.509 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 102 | TRP | 0 | -0.004 | -0.007 | 48.328 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 103 | LYS | 1 | 0.898 | 0.942 | 54.820 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 104 | LYS | 1 | 0.934 | 0.970 | 57.394 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 105 | LEU | 0 | 0.022 | 0.021 | 59.592 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 106 | PRO | 0 | 0.011 | -0.001 | 58.790 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 107 | PRO | 0 | -0.018 | -0.002 | 61.638 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 108 | LEU | 0 | 0.040 | 0.018 | 64.287 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 109 | PRO | 0 | -0.022 | -0.018 | 63.155 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 110 | SER | 0 | 0.025 | 0.013 | 65.808 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 111 | LEU | 0 | 0.001 | 0.000 | 67.067 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 112 | THR | 0 | 0.022 | 0.011 | 69.471 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 113 | SER | 0 | 0.010 | 0.017 | 72.344 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 114 | GLN | 0 | -0.025 | -0.013 | 74.632 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 115 | PRO | 0 | 0.044 | 0.019 | 76.804 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | E | 116 | HIS | 0 | 0.044 | 0.007 | 77.973 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | E | 117 | GLN | 0 | -0.001 | -0.012 | 79.796 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | E | 118 | VAL | 0 | -0.001 | 0.002 | 74.849 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | E | 119 | LEU | 0 | -0.040 | -0.014 | 77.715 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | E | 120 | ALA | 0 | -0.030 | -0.005 | 79.976 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | E | 121 | SER | 0 | -0.088 | -0.037 | 78.597 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | E | 122 | GLU | -1 | -0.904 | -0.954 | 80.785 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 123 | PRO | 0 | -0.030 | -0.005 | 79.629 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 124 | ILE | 0 | -0.004 | -0.002 | 74.271 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 125 | PRO | 0 | 0.040 | 0.020 | 77.448 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 126 | PHE | 0 | 0.037 | 0.006 | 79.079 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 127 | SER | 0 | -0.014 | -0.015 | 79.123 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 128 | ASP | -1 | -0.828 | -0.920 | 75.023 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 129 | LEU | 0 | 0.017 | 0.010 | 75.121 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | E | 130 | GLN | 0 | -0.003 | 0.016 | 76.397 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | E | 131 | GLN | 0 | 0.003 | 0.004 | 71.841 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | E | 132 | VAL | 0 | 0.041 | 0.012 | 70.352 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | E | 133 | SER | 0 | -0.024 | -0.023 | 72.200 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | E | 134 | ARG | 1 | 0.884 | 0.935 | 74.463 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | E | 135 | ILE | 0 | 0.010 | 0.016 | 68.269 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | E | 136 | ALA | 0 | 0.016 | 0.013 | 69.062 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | E | 137 | ALA | 0 | 0.019 | 0.011 | 69.845 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | E | 138 | TYR | 0 | -0.041 | -0.019 | 67.838 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | E | 139 | ALA | 0 | 0.009 | 0.000 | 65.709 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | E | 140 | TYR | 0 | -0.002 | -0.007 | 66.634 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | E | 141 | SER | 0 | -0.023 | -0.023 | 68.496 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | E | 142 | ALA | 0 | -0.019 | -0.007 | 65.224 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | E | 143 | LEU | 0 | -0.012 | -0.011 | 62.994 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | E | 144 | SER | 0 | -0.022 | 0.003 | 64.875 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | E | 145 | GLN | 0 | 0.002 | 0.001 | 64.141 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | E | 146 | ILE | 0 | -0.040 | -0.001 | 59.483 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | E | 147 | ARG | 1 | 0.825 | 0.903 | 62.066 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | E | 148 | VAL | 0 | 0.008 | 0.001 | 59.156 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | E | 149 | ASP | -1 | -0.878 | -0.929 | 61.646 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | E | 150 | ALA | 0 | -0.010 | -0.010 | 62.577 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | E | 151 | LYS | 1 | 0.916 | 0.957 | 60.128 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | E | 152 | GLU | -1 | -0.911 | -0.957 | 61.892 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | E | 153 | GLU | -1 | -0.974 | -0.980 | 62.930 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | E | 154 | LEU | 0 | -0.019 | -0.009 | 58.802 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | E | 155 | VAL | 0 | -0.034 | -0.018 | 61.690 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | E | 156 | VAL | 0 | 0.055 | 0.021 | 63.772 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | E | 157 | GLN | 0 | -0.043 | -0.012 | 65.132 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | E | 158 | PHE | 0 | 0.005 | 0.003 | 62.056 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | E | 159 | GLY | 0 | 0.004 | -0.002 | 66.933 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | E | 160 | ILE | 0 | -0.010 | 0.003 | 70.011 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |