![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: GQMY1
Calculation Name: 3OFE-A-Xray313
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3OFE
Chain ID: A
UniProt ID: Q8T9B6
Base Structure: X-ray
Registration Date: 2021-09-06
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 1.20200116 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 82 |
LigandCharge | |
Software | ABINIT-MP - Open Ver.1 Rev. 15 / 20190524 |
Total energy (hartree)
FMO2-HF: Electronic energy | -587797.554067 |
---|---|
FMO2-HF: Nuclear repulsion | 554104.14166 |
FMO2-HF: Total energy | -33693.412407 |
FMO2-MP2: Total energy | -33791.250517 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F015716/ligand_interaction/ligand_F015716.png)
Ligand Interaction
![ligand interaction](./Kdata/F015716/ligand_interaction/ligand_interaction_F015716.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:91:ACE )
Summations of interaction energy for
fragment #1(A:91:ACE )
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. |
-1.188 | 0.43 | 0 | -0.782 | -0.836 | -0.002 |
Interaction energy analysis for fragmet #1(A:91:ACE )
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 | 93 | THR | 0 | -0.011 | 0.028 | 3.639 | -0.090 | 1.528 | 0.000 | -0.782 | -0.836 | -0.002 |
4 | A | 94 | LEU | 0 | 0.030 | 0.025 | 5.736 | -0.040 | -0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 95 | MET | 0 | -0.042 | -0.011 | 8.515 | 0.078 | 0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 96 | THR | 0 | -0.019 | -0.005 | 11.190 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 97 | PHE | 0 | 0.013 | -0.011 | 14.738 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 98 | VAL | 0 | 0.050 | 0.027 | 18.240 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 99 | SER | 0 | 0.011 | 0.001 | 20.941 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 100 | VAL | 0 | -0.011 | 0.004 | 24.509 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 101 | THR | 0 | -0.020 | -0.004 | 27.765 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 102 | GLY | 0 | 0.009 | 0.001 | 31.125 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 103 | ASN | 0 | -0.043 | -0.033 | 33.375 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 104 | PRO | 0 | -0.002 | 0.015 | 30.190 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 105 | THR | 0 | 0.046 | 0.024 | 32.437 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 106 | ARG | 1 | 0.924 | 0.949 | 25.481 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 107 | GLU | -1 | -0.900 | -0.947 | 28.449 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 108 | GLU | -1 | -0.897 | -0.950 | 30.118 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 109 | SER | 0 | 0.027 | -0.020 | 26.634 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 110 | ASP | -1 | -0.846 | -0.886 | 24.674 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 111 | THR | 0 | -0.018 | -0.009 | 25.580 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 112 | ILE | 0 | -0.017 | -0.012 | 27.243 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 113 | THR | 0 | -0.007 | -0.011 | 22.382 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 114 | LYS | 1 | 0.980 | 0.989 | 22.495 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 115 | LEU | 0 | 0.010 | 0.025 | 23.478 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 116 | TRP | 0 | 0.028 | 0.006 | 22.879 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 117 | GLN | 0 | 0.014 | 0.006 | 17.071 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 118 | THR | 0 | -0.057 | -0.034 | 19.863 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 119 | SER | 0 | -0.039 | -0.011 | 22.352 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 120 | LEU | 0 | 0.022 | 0.021 | 17.934 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 121 | TRP | 0 | 0.004 | 0.009 | 14.800 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 122 | ASN | 0 | -0.067 | -0.042 | 19.061 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 123 | ASN | 0 | -0.073 | -0.034 | 20.887 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 124 | HIS | 0 | -0.036 | -0.018 | 17.582 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 125 | ILE | 0 | 0.010 | 0.017 | 14.812 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 126 | GLN | 0 | -0.022 | -0.009 | 12.761 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 127 | ALA | 0 | 0.011 | -0.003 | 12.345 | -0.051 | -0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 128 | GLU | -1 | -0.895 | -0.932 | 10.931 | 0.211 | 0.211 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 129 | ARG | 1 | 0.805 | 0.886 | 14.144 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 130 | TYR | 0 | -0.040 | -0.037 | 13.041 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 131 | MET | 0 | -0.004 | 0.020 | 18.670 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 132 | VAL | 0 | -0.055 | -0.030 | 18.887 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 133 | ASP | -1 | -0.813 | -0.894 | 22.116 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 134 | ASP | -1 | -0.844 | -0.925 | 25.569 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 135 | ASN | 0 | -0.026 | 0.005 | 27.534 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 136 | ARG | 1 | 0.859 | 0.930 | 21.499 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 137 | ALA | 0 | 0.028 | 0.001 | 20.250 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 138 | ILE | 0 | -0.024 | -0.011 | 14.097 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 139 | PHE | 0 | 0.003 | 0.003 | 15.475 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 140 | LEU | 0 | -0.014 | -0.004 | 8.551 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 141 | PHE | 0 | 0.038 | 0.012 | 10.828 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 142 | LYS | 1 | 0.912 | 0.948 | 7.633 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 143 | ASP | -1 | -0.781 | -0.877 | 6.641 | -1.319 | -1.319 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 144 | GLY | 0 | 0.030 | -0.005 | 7.673 | 0.194 | 0.194 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 145 | THR | 0 | -0.103 | -0.061 | 9.315 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 146 | GLN | 0 | 0.053 | 0.014 | 11.742 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 147 | ALA | 0 | -0.029 | 0.003 | 12.408 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 148 | TRP | 0 | -0.013 | -0.027 | 12.553 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 149 | ASP | -1 | -0.829 | -0.899 | 17.373 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 150 | ALA | 0 | -0.037 | -0.025 | 16.899 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 151 | LYS | 1 | 0.811 | 0.896 | 18.434 | 0.181 | 0.181 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 152 | ASP | -1 | -0.830 | -0.902 | 20.143 | -0.140 | -0.140 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 153 | PHE | 0 | 0.006 | 0.009 | 22.321 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 154 | LEU | 0 | -0.040 | -0.039 | 19.255 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 155 | ILE | 0 | -0.020 | -0.030 | 23.383 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 156 | GLU | -1 | -0.906 | -0.930 | 25.781 | -0.071 | -0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 157 | GLN | 0 | -0.134 | -0.048 | 26.257 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 158 | GLU | -1 | -0.882 | -0.945 | 28.845 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 159 | ARG | 1 | 0.845 | 0.896 | 30.300 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 160 | CYS | 0 | 0.002 | 0.026 | 24.506 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 161 | LYS | 1 | 0.937 | 0.955 | 27.021 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 162 | GLY | 0 | 0.078 | 0.044 | 24.988 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 163 | VAL | 0 | -0.042 | -0.020 | 18.697 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 164 | THR | 0 | -0.023 | -0.005 | 18.039 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 165 | ILE | 0 | 0.018 | -0.007 | 14.040 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 166 | GLU | -1 | -0.924 | -0.957 | 12.192 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 167 | ASN | 0 | -0.043 | -0.042 | 15.203 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 168 | LYS | 1 | 0.896 | 0.973 | 16.780 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 169 | GLU | -1 | -0.934 | -0.975 | 20.027 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 170 | TYR | 0 | -0.049 | -0.035 | 18.991 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 171 | PRO | 0 | -0.033 | -0.028 | 23.966 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 172 | GLY | -1 | -0.885 | -0.925 | 27.171 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |