![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 725JK
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 | OptH |
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 | -531875.885009 |
---|---|
FMO2-HF: Nuclear repulsion | 487735.844481 |
FMO2-HF: Total energy | -44140.040528 |
FMO2-MP2: Total energy | -44269.650448 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F028419/ligand_interaction/ligand_F028419.png)
Ligand Interaction
![ligand interaction](./Kdata/F028419/ligand_interaction/ligand_interaction_F028419.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. |
-2.844 | 0.302 | 0.005 | -1.343 | -1.808 | 0.003 |
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 | -0.004 | -0.017 | 3.084 | -1.407 | 1.419 | 0.006 | -1.321 | -1.511 | 0.003 |
4 | E | 49 | ASP | -1 | -0.839 | -0.916 | 3.941 | -2.075 | -1.755 | -0.001 | -0.022 | -0.297 | 0.000 |
5 | E | 50 | GLU | -1 | -0.934 | -0.965 | 5.957 | -0.513 | -0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 51 | GLN | 0 | 0.006 | 0.002 | 7.761 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 52 | ALA | 0 | 0.010 | 0.046 | 8.436 | 0.159 | 0.159 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 53 | LEU | 0 | 0.019 | 0.013 | 9.869 | 0.120 | 0.120 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 54 | LEU | 0 | 0.016 | 0.011 | 11.804 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 55 | SER | 0 | -0.027 | -0.052 | 12.575 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 56 | SER | 0 | -0.052 | -0.033 | 14.371 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 57 | ILE | 0 | -0.013 | -0.003 | 15.682 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 58 | LEU | 0 | 0.010 | 0.023 | 17.430 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 59 | ALA | 0 | 0.015 | 0.017 | 18.876 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 60 | LYS | 1 | 0.945 | 0.957 | 19.987 | 0.241 | 0.241 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 61 | THR | 0 | -0.053 | -0.057 | 21.709 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 62 | ALA | 0 | -0.006 | -0.004 | 23.449 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 63 | SER | 0 | -0.061 | -0.014 | 24.661 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 64 | ASN | 0 | -0.030 | -0.018 | 25.321 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 65 | ILE | 0 | -0.033 | -0.009 | 27.688 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 66 | ILE | 0 | -0.006 | 0.002 | 29.953 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 67 | ASP | -1 | -0.877 | -0.940 | 33.429 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 68 | VAL | 0 | -0.048 | -0.027 | 34.898 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 69 | SER | 0 | -0.044 | -0.015 | 37.717 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 70 | ALA | 0 | -0.003 | 0.001 | 38.652 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 71 | ALA | 0 | -0.018 | -0.015 | 41.119 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 72 | ASP | -1 | -0.916 | -0.940 | 40.377 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 73 | SER | 0 | -0.033 | -0.037 | 43.282 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 74 | GLN | 0 | -0.024 | -0.010 | 41.785 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 75 | GLY | 0 | -0.016 | -0.005 | 43.790 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 76 | MET | 0 | -0.041 | -0.009 | 46.532 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 77 | GLU | -1 | -0.913 | -0.986 | 48.560 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 78 | GLN | 0 | -0.020 | 0.005 | 41.486 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 79 | HIS | 0 | 0.072 | 0.015 | 39.889 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | E | 80 | GLU | -1 | -0.872 | -0.931 | 38.707 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | E | 81 | TYR | 0 | -0.033 | -0.003 | 42.166 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | E | 82 | MET | 0 | 0.022 | 0.002 | 44.714 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 83 | ASP | -1 | -0.817 | -0.899 | 43.131 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | E | 84 | ARG | 1 | 0.954 | 0.982 | 36.280 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 85 | ALA | 0 | -0.039 | -0.030 | 42.975 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 86 | ARG | 1 | 0.916 | 0.942 | 46.283 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 87 | GLN | 0 | 0.037 | 0.035 | 40.132 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 88 | TYR | 0 | -0.010 | 0.001 | 39.218 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 89 | SER | 0 | 0.005 | 0.005 | 45.297 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 90 | THR | 0 | -0.046 | -0.029 | 47.166 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 91 | ARG | 1 | 0.923 | 0.938 | 38.186 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 92 | LEU | 0 | 0.030 | 0.037 | 46.045 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 93 | ALA | 0 | 0.048 | 0.027 | 48.195 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 94 | VAL | 0 | -0.028 | -0.022 | 46.457 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 95 | LEU | 0 | 0.026 | 0.007 | 44.696 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 96 | SER | 0 | -0.052 | -0.007 | 49.315 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 97 | SER | 0 | -0.068 | -0.053 | 52.200 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 98 | SER | 0 | -0.064 | -0.031 | 50.780 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 99 | LEU | 0 | 0.028 | 0.027 | 47.748 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 100 | THR | 0 | -0.008 | 0.000 | 50.014 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 101 | HIS | 0 | 0.006 | 0.000 | 52.802 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 102 | TRP | 0 | 0.003 | 0.000 | 48.450 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 103 | LYS | 1 | 0.966 | 0.984 | 54.769 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 104 | LYS | 1 | 0.932 | 0.967 | 57.344 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 105 | LEU | 0 | 0.017 | 0.018 | 59.540 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 106 | PRO | 0 | 0.008 | -0.001 | 58.757 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 107 | PRO | 0 | -0.010 | 0.001 | 61.586 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 108 | LEU | 0 | 0.043 | 0.016 | 64.232 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 109 | PRO | 0 | -0.026 | -0.016 | 63.165 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 110 | SER | 0 | 0.007 | 0.003 | 65.756 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 111 | LEU | 0 | 0.021 | 0.005 | 67.310 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 112 | THR | 0 | 0.029 | 0.016 | 69.419 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 113 | SER | 0 | 0.010 | 0.018 | 72.296 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 114 | GLN | 0 | -0.026 | -0.015 | 74.587 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 115 | PRO | 0 | 0.044 | 0.023 | 76.805 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | E | 116 | HIS | 0 | 0.041 | 0.002 | 77.922 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | E | 117 | GLN | 0 | -0.005 | -0.014 | 79.730 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | E | 118 | VAL | 0 | -0.009 | 0.002 | 74.847 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | E | 119 | LEU | 0 | -0.037 | -0.010 | 77.572 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | E | 120 | ALA | 0 | -0.028 | -0.001 | 79.920 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | E | 121 | SER | 0 | -0.087 | -0.041 | 78.634 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | E | 122 | GLU | -1 | -0.909 | -0.958 | 80.767 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 123 | PRO | 0 | -0.034 | -0.004 | 79.571 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 124 | ILE | 0 | 0.003 | 0.001 | 74.289 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 125 | PRO | 0 | 0.055 | 0.023 | 77.363 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 126 | PHE | 0 | 0.051 | 0.012 | 79.013 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 127 | SER | 0 | -0.022 | -0.024 | 79.009 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 128 | ASP | -1 | -0.839 | -0.914 | 74.977 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 129 | LEU | 0 | 0.005 | 0.001 | 75.052 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | E | 130 | GLN | 0 | -0.040 | -0.010 | 76.325 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | E | 131 | GLN | 0 | 0.009 | 0.008 | 72.282 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | E | 132 | VAL | 0 | 0.043 | 0.012 | 70.426 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | E | 133 | SER | 0 | -0.026 | -0.026 | 72.126 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | E | 134 | ARG | 1 | 0.924 | 0.962 | 74.386 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | E | 135 | ILE | 0 | 0.004 | 0.016 | 68.188 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | E | 136 | ALA | 0 | 0.016 | 0.013 | 68.984 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | E | 137 | ALA | 0 | 0.019 | 0.011 | 69.765 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | E | 138 | TYR | 0 | -0.042 | -0.017 | 68.018 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | E | 139 | ALA | 0 | 0.011 | 0.002 | 65.591 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | E | 140 | TYR | 0 | -0.004 | -0.007 | 66.552 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | E | 141 | SER | 0 | -0.029 | -0.032 | 68.411 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | E | 142 | ALA | 0 | -0.013 | -0.003 | 65.133 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | E | 143 | LEU | 0 | -0.008 | -0.009 | 62.862 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | E | 144 | SER | 0 | -0.017 | 0.007 | 64.786 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | E | 145 | GLN | 0 | -0.013 | -0.015 | 64.097 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | E | 146 | ILE | 0 | -0.027 | 0.005 | 59.409 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | E | 147 | ARG | 1 | 0.909 | 0.953 | 61.976 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | E | 148 | VAL | 0 | 0.001 | 0.001 | 59.162 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | E | 149 | ASP | -1 | -0.950 | -0.965 | 61.573 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | E | 150 | ALA | 0 | -0.026 | -0.020 | 62.503 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | E | 151 | LYS | 1 | 0.921 | 0.962 | 60.208 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | E | 152 | GLU | -1 | -0.914 | -0.963 | 61.690 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | E | 153 | GLU | -1 | -0.976 | -0.981 | 62.854 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | E | 154 | LEU | 0 | -0.020 | -0.010 | 58.816 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | E | 155 | VAL | 0 | -0.035 | -0.019 | 61.612 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | E | 156 | VAL | 0 | 0.066 | 0.029 | 63.694 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | E | 157 | GLN | 0 | -0.047 | -0.015 | 65.055 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | E | 158 | PHE | 0 | 0.005 | 0.003 | 61.729 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | E | 159 | GLY | 0 | 0.004 | -0.002 | 66.896 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | E | 160 | ILE | 0 | -0.013 | 0.001 | 69.972 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |