![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 5JV8Z
Calculation Name: 2J9W-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2J9W
Chain ID: A
UniProt ID: Q7T0W4
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 | 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 | 101 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -814934.344118 |
---|---|
FMO2-HF: Nuclear repulsion | 771509.433162 |
FMO2-HF: Total energy | -43424.910955 |
FMO2-MP2: Total energy | -43545.814844 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037206/ligand_interaction/ligand_F037206.png)
Ligand Interaction
![ligand interaction](./Kdata/F037206/ligand_interaction/ligand_interaction_F037206.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:120:HIS)
Summations of interaction energy for
fragment #1(A:120:HIS)
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. |
-3.112 | 0.28 | 0.858 | -1.369 | -2.881 | 0.011 |
Interaction energy analysis for fragmet #1(A:120:HIS)
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 | 122 | MET | 0 | -0.003 | 0.020 | 2.893 | -1.474 | 1.867 | 0.859 | -1.358 | -2.842 | 0.011 |
4 | A | 123 | GLY | 0 | 0.066 | 0.026 | 5.143 | -1.665 | -1.614 | -0.001 | -0.011 | -0.039 | 0.000 |
5 | A | 124 | ASN | 0 | 0.031 | 0.001 | 8.894 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 125 | LEU | 0 | 0.047 | 0.032 | 11.474 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 126 | ASN | 0 | 0.022 | -0.004 | 7.942 | -0.358 | -0.358 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 127 | ARG | 1 | 0.873 | 0.939 | 6.074 | 0.674 | 0.674 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 128 | CYS | 0 | 0.029 | 0.025 | 9.528 | -0.153 | -0.153 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 129 | ILE | 0 | 0.018 | 0.013 | 12.570 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 130 | ALA | 0 | -0.029 | -0.009 | 10.114 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 131 | ASP | -1 | -0.884 | -0.948 | 11.925 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 132 | ILE | 0 | -0.029 | -0.010 | 13.920 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 133 | VAL | 0 | -0.023 | -0.010 | 15.421 | -0.047 | -0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 134 | SER | 0 | -0.036 | -0.021 | 14.492 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 135 | LEU | 0 | 0.035 | -0.007 | 16.739 | -0.042 | -0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 136 | PHE | 0 | 0.029 | 0.000 | 19.258 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 137 | ILE | 0 | -0.044 | -0.020 | 18.924 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 138 | THR | 0 | 0.005 | 0.041 | 20.014 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 139 | VAL | 0 | 0.026 | 0.008 | 21.986 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 140 | MET | 0 | -0.045 | -0.026 | 24.207 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 141 | ASP | -1 | -0.870 | -0.945 | 23.561 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 142 | LYS | 1 | 0.845 | 0.908 | 23.924 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 143 | LEU | 0 | 0.006 | 0.000 | 27.826 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 144 | ARG | 1 | 0.846 | 0.919 | 26.048 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 145 | LEU | 0 | -0.084 | -0.032 | 27.414 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 146 | GLU | -1 | -0.975 | -0.983 | 31.440 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 147 | ILE | 0 | -0.003 | 0.022 | 28.569 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 148 | ARG | 1 | 0.824 | 0.879 | 32.463 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 149 | ALA | 0 | 0.070 | 0.059 | 34.068 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 150 | MET | 0 | -0.023 | -0.003 | 32.754 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 151 | ASP | -1 | -0.902 | -0.977 | 31.574 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 152 | GLU | -1 | -0.944 | -0.969 | 29.402 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 153 | ILE | 0 | -0.063 | -0.024 | 28.103 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 154 | GLN | 0 | -0.028 | -0.024 | 27.321 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 155 | PRO | 0 | 0.027 | 0.015 | 25.406 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 156 | ASP | -1 | -0.765 | -0.870 | 22.304 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 157 | LEU | 0 | -0.004 | 0.005 | 22.699 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 158 | ARG | 1 | 0.830 | 0.905 | 24.586 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 159 | GLU | -1 | -0.921 | -0.953 | 19.525 | -0.114 | -0.114 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 160 | LEU | 0 | -0.019 | -0.014 | 20.090 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 161 | MET | 0 | 0.002 | 0.005 | 21.113 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 162 | GLU | -1 | -0.838 | -0.928 | 21.254 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 163 | THR | 0 | -0.081 | -0.025 | 15.862 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 164 | MET | 0 | 0.020 | 0.005 | 18.314 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 165 | ASN | 0 | -0.051 | -0.030 | 20.609 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 166 | ARG | 1 | 0.922 | 0.974 | 15.274 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 167 | MET | 0 | -0.040 | -0.002 | 16.697 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 168 | SER | 0 | 0.012 | -0.006 | 18.365 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 169 | HIS | 0 | -0.040 | -0.026 | 16.506 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 170 | LEU | 0 | -0.027 | 0.006 | 20.573 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 171 | PRO | 0 | 0.037 | 0.021 | 22.797 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 172 | PRO | 0 | -0.001 | -0.018 | 26.527 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 173 | ASP | -1 | -0.935 | -0.963 | 28.514 | 0.174 | 0.174 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 174 | PHE | 0 | -0.044 | -0.018 | 23.761 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 175 | GLU | -1 | -0.827 | -0.932 | 27.943 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 176 | GLY | 0 | 0.025 | 0.000 | 25.904 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 177 | ARG | 1 | 0.910 | 0.950 | 23.800 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 178 | GLU | -1 | -0.959 | -0.957 | 26.717 | 0.098 | 0.098 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 179 | LYS | 1 | 1.002 | 0.999 | 29.400 | -0.156 | -0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 180 | VAL | 0 | 0.002 | 0.001 | 25.082 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 181 | SER | 0 | 0.018 | -0.008 | 28.291 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 182 | GLN | 0 | -0.037 | -0.009 | 30.132 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 183 | TRP | 0 | -0.008 | -0.026 | 30.695 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 184 | LEU | 0 | -0.029 | -0.019 | 26.922 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 185 | GLN | 0 | -0.019 | -0.009 | 31.324 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 186 | LYS | 1 | 0.954 | 1.006 | 34.703 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 187 | LEU | 0 | 0.034 | -0.008 | 31.028 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 188 | SER | 0 | -0.109 | -0.056 | 34.488 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 189 | SER | 0 | -0.105 | -0.055 | 35.733 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 190 | MET | 0 | -0.052 | -0.007 | 37.156 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 191 | SER | 0 | 0.015 | 0.001 | 38.053 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 192 | ALA | 0 | -0.031 | -0.029 | 35.489 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 193 | SER | 0 | 0.039 | 0.009 | 35.923 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 194 | ASP | -1 | -0.881 | -0.914 | 38.551 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 195 | GLU | -1 | -0.940 | -0.979 | 37.343 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 196 | LEU | 0 | -0.064 | -0.028 | 33.399 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 197 | ASP | -1 | -0.798 | -0.908 | 37.790 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 198 | ASP | -1 | -0.827 | -0.916 | 38.995 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 199 | SER | 0 | -0.098 | -0.042 | 39.303 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 200 | GLN | 0 | 0.006 | -0.003 | 37.512 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 201 | VAL | 0 | 0.065 | 0.035 | 33.841 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 202 | ARG | 1 | 0.952 | 0.984 | 34.459 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 203 | GLN | 0 | -0.058 | -0.024 | 35.473 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 204 | MET | 0 | 0.030 | 0.016 | 29.219 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 205 | LEU | 0 | -0.012 | -0.002 | 29.621 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 206 | PHE | 0 | -0.028 | 0.000 | 30.780 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 207 | ASP | -1 | -0.818 | -0.897 | 31.797 | 0.109 | 0.109 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 208 | LEU | 0 | -0.013 | -0.018 | 26.058 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 209 | GLU | -1 | -0.912 | -0.951 | 26.826 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 210 | SER | 0 | -0.063 | -0.018 | 27.754 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 211 | ALA | 0 | -0.002 | -0.008 | 26.302 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 212 | TYR | 0 | 0.030 | 0.013 | 19.787 | 0.029 | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 213 | ASN | 0 | -0.016 | -0.019 | 23.633 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 214 | ALA | 0 | -0.026 | -0.008 | 25.630 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 215 | PHE | 0 | 0.006 | -0.009 | 17.231 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 216 | ASN | 0 | 0.035 | -0.001 | 20.184 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 217 | ARG | 1 | 0.880 | 0.959 | 22.094 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 218 | PHE | 0 | -0.029 | -0.011 | 19.558 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 219 | LEU | 0 | -0.055 | -0.018 | 16.787 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 220 | HIS | 0 | -0.100 | -0.044 | 19.722 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |