![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 6N83Z
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 | 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 | 115 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -532196.731003 |
---|---|
FMO2-HF: Nuclear repulsion | 488055.819299 |
FMO2-HF: Total energy | -44140.911704 |
FMO2-MP2: Total energy | -44270.427616 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F028417/ligand_interaction/ligand_F028417.png)
Ligand Interaction
![ligand interaction](./Kdata/F028417/ligand_interaction/ligand_interaction_F028417.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. |
-2.337 | 0.472 | 0.016 | -1.196 | -1.629 | 0.001 |
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 | -0.024 | -0.011 | 3.129 | -1.192 | 1.164 | 0.016 | -1.110 | -1.262 | 0.001 |
4 | E | 49 | ASP | -1 | -0.852 | -0.920 | 4.089 | -2.488 | -2.035 | 0.000 | -0.086 | -0.367 | 0.000 |
5 | E | 50 | GLU | -1 | -0.904 | -0.956 | 5.914 | 0.065 | 0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 51 | GLN | 0 | -0.007 | -0.004 | 7.534 | 0.416 | 0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 52 | ALA | 0 | 0.019 | 0.021 | 8.898 | 0.151 | 0.151 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 53 | LEU | 0 | 0.007 | 0.005 | 9.368 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 54 | LEU | 0 | 0.026 | 0.019 | 11.562 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 55 | SER | 0 | -0.021 | -0.023 | 13.013 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 56 | SER | 0 | -0.079 | -0.048 | 14.529 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 57 | ILE | 0 | -0.018 | -0.012 | 15.548 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 58 | LEU | 0 | 0.013 | 0.017 | 17.081 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 59 | ALA | 0 | 0.007 | 0.003 | 19.130 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 60 | LYS | 1 | 0.947 | 0.972 | 19.140 | 0.239 | 0.239 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 61 | THR | 0 | -0.034 | -0.024 | 21.969 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 62 | ALA | 0 | -0.015 | -0.016 | 23.706 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 63 | SER | 0 | -0.036 | -0.024 | 25.042 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 64 | ASN | 0 | -0.047 | -0.014 | 26.361 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 65 | ILE | 0 | -0.026 | -0.009 | 27.449 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 66 | ILE | 0 | -0.010 | 0.000 | 30.291 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 67 | ASP | -1 | -0.825 | -0.892 | 33.763 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 68 | VAL | 0 | -0.009 | -0.012 | 35.049 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 69 | SER | 0 | -0.074 | -0.046 | 37.231 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 70 | ALA | 0 | -0.051 | -0.023 | 39.520 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 71 | ALA | 0 | -0.025 | -0.019 | 41.341 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 72 | ASP | -1 | -0.910 | -0.939 | 41.048 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 73 | SER | 0 | -0.024 | -0.025 | 43.443 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | E | 74 | GLN | 0 | -0.022 | -0.007 | 42.823 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | E | 75 | GLY | 0 | 0.030 | 0.019 | 44.095 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | E | 76 | MET | 0 | -0.033 | -0.012 | 46.884 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | E | 77 | GLU | -1 | -0.923 | -0.982 | 48.884 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | E | 78 | GLN | 0 | -0.039 | -0.015 | 41.665 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | E | 79 | HIS | 0 | 0.077 | 0.025 | 40.153 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | E | 80 | GLU | -1 | -0.800 | -0.874 | 39.356 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | E | 81 | TYR | 0 | -0.007 | 0.006 | 42.552 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | E | 82 | MET | 0 | 0.027 | 0.012 | 45.073 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | E | 83 | ASP | -1 | -0.848 | -0.928 | 43.778 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | E | 84 | ARG | 1 | 0.804 | 0.888 | 36.898 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | E | 85 | ALA | 0 | 0.035 | 0.020 | 43.525 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | E | 86 | ARG | 1 | 0.860 | 0.925 | 46.871 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | E | 87 | GLN | 0 | 0.062 | 0.043 | 40.225 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | E | 88 | TYR | 0 | -0.006 | -0.010 | 39.958 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | E | 89 | SER | 0 | 0.022 | 0.014 | 45.793 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | E | 90 | THR | 0 | -0.026 | -0.021 | 47.705 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | E | 91 | ARG | 1 | 0.892 | 0.927 | 38.893 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | E | 92 | LEU | 0 | 0.020 | 0.021 | 46.539 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | E | 93 | ALA | 0 | 0.013 | 0.012 | 48.671 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | E | 94 | VAL | 0 | 0.001 | 0.001 | 47.545 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | E | 95 | LEU | 0 | 0.023 | 0.020 | 44.725 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | E | 96 | SER | 0 | -0.008 | 0.000 | 49.444 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | E | 97 | SER | 0 | -0.008 | -0.024 | 52.452 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | E | 98 | SER | 0 | -0.083 | -0.041 | 51.328 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | E | 99 | LEU | 0 | -0.010 | 0.016 | 48.651 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | E | 100 | THR | 0 | 0.005 | 0.002 | 50.287 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | E | 101 | HIS | 0 | 0.043 | 0.008 | 52.742 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | E | 102 | TRP | 0 | -0.025 | -0.009 | 48.203 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | E | 103 | LYS | 1 | 0.893 | 0.944 | 54.929 | 0.022 | 0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | E | 104 | LYS | 1 | 0.932 | 0.967 | 57.459 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | E | 105 | LEU | 0 | 0.030 | 0.023 | 59.566 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | E | 106 | PRO | 0 | 0.004 | -0.007 | 59.090 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | E | 107 | PRO | 0 | -0.010 | 0.007 | 61.895 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | E | 108 | LEU | 0 | 0.033 | 0.013 | 64.387 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | E | 109 | PRO | 0 | -0.017 | -0.017 | 63.330 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | E | 110 | SER | 0 | 0.002 | 0.002 | 66.071 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | E | 111 | LEU | 0 | -0.012 | -0.010 | 66.770 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | E | 112 | THR | 0 | 0.025 | 0.021 | 69.355 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | E | 113 | SER | 0 | 0.029 | 0.021 | 72.208 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | E | 114 | GLN | 0 | -0.013 | -0.004 | 74.378 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | E | 115 | PRO | 0 | 0.041 | 0.015 | 76.621 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | E | 116 | HIS | 0 | 0.039 | 0.004 | 77.836 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | E | 117 | GLN | 0 | -0.010 | -0.009 | 79.542 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | E | 118 | VAL | 0 | 0.003 | 0.003 | 74.782 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | E | 119 | LEU | 0 | -0.041 | -0.020 | 77.974 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | E | 120 | ALA | 0 | -0.025 | 0.003 | 80.150 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | E | 121 | SER | 0 | -0.073 | -0.035 | 78.523 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | E | 122 | GLU | -1 | -0.903 | -0.959 | 80.612 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | E | 123 | PRO | 0 | -0.034 | -0.004 | 79.388 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | E | 124 | ILE | 0 | -0.008 | -0.010 | 73.928 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | E | 125 | PRO | 0 | 0.046 | 0.026 | 77.499 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | E | 126 | PHE | 0 | 0.023 | -0.006 | 78.850 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | E | 127 | SER | 0 | -0.009 | -0.022 | 78.820 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | E | 128 | ASP | -1 | -0.820 | -0.891 | 74.754 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | E | 129 | LEU | 0 | 0.030 | 0.014 | 74.827 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | E | 130 | GLN | 0 | 0.024 | 0.037 | 75.988 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | E | 131 | GLN | 0 | -0.006 | -0.004 | 71.511 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | E | 132 | VAL | 0 | 0.024 | 0.005 | 70.353 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | E | 133 | SER | 0 | -0.021 | -0.023 | 71.857 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | E | 134 | ARG | 1 | 0.856 | 0.918 | 73.877 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | E | 135 | ILE | 0 | 0.006 | 0.007 | 68.151 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | E | 136 | ALA | 0 | 0.012 | 0.011 | 69.007 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | E | 137 | ALA | 0 | 0.016 | 0.009 | 69.810 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | E | 138 | TYR | 0 | -0.027 | -0.002 | 67.412 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | E | 139 | ALA | 0 | 0.013 | -0.004 | 65.596 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | E | 140 | TYR | 0 | -0.006 | -0.010 | 66.419 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | E | 141 | SER | 0 | -0.011 | -0.021 | 68.246 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | E | 142 | ALA | 0 | -0.012 | 0.004 | 65.165 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | E | 143 | LEU | 0 | -0.005 | -0.003 | 62.949 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | E | 144 | SER | 0 | -0.032 | -0.010 | 64.784 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | E | 145 | GLN | 0 | 0.012 | 0.005 | 63.704 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | E | 146 | ILE | 0 | -0.049 | -0.010 | 59.424 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | E | 147 | ARG | 1 | 0.808 | 0.889 | 61.732 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | E | 148 | VAL | 0 | 0.007 | -0.002 | 58.750 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | E | 149 | ASP | -1 | -0.881 | -0.920 | 61.361 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | E | 150 | ALA | 0 | -0.009 | -0.012 | 62.555 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | E | 151 | LYS | 1 | 0.905 | 0.948 | 60.448 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | E | 152 | GLU | -1 | -0.907 | -0.946 | 61.327 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | E | 153 | GLU | -1 | -0.957 | -0.977 | 63.064 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | E | 154 | LEU | 0 | -0.026 | -0.020 | 58.253 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | E | 155 | VAL | 0 | -0.038 | -0.019 | 60.757 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | E | 156 | VAL | 0 | 0.044 | 0.028 | 63.398 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | E | 157 | GLN | 0 | -0.020 | -0.007 | 64.803 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | E | 158 | PHE | 0 | 0.008 | 0.000 | 62.151 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
114 | E | 159 | GLY | 0 | 0.003 | -0.009 | 66.403 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
115 | E | 160 | ILE | 0 | -0.030 | 0.007 | 69.882 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |