![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: YVGM2
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 | 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 | 101 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -816152.402706 |
---|---|
FMO2-HF: Nuclear repulsion | 772726.975205 |
FMO2-HF: Total energy | -43425.4275 |
FMO2-MP2: Total energy | -43546.354335 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037205/ligand_interaction/ligand_F037205.png)
Ligand Interaction
![ligand interaction](./Kdata/F037205/ligand_interaction/ligand_interaction_F037205.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. |
-4.801 | -0.241 | 0.76 | -2.046 | -3.275 | 0.016 |
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 | 0.017 | 0.043 | 2.875 | -2.923 | 1.569 | 0.761 | -2.024 | -3.230 | 0.016 |
4 | A | 123 | GLY | 0 | 0.059 | 0.027 | 4.934 | -2.046 | -1.978 | -0.001 | -0.022 | -0.045 | 0.000 |
5 | A | 124 | ASN | 0 | 0.033 | -0.001 | 8.661 | 0.099 | 0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 125 | LEU | 0 | 0.053 | 0.038 | 11.427 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 126 | ASN | 0 | 0.026 | -0.011 | 7.282 | -0.481 | -0.481 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 127 | ARG | 1 | 0.863 | 0.932 | 6.669 | 0.827 | 0.827 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 128 | CYS | 0 | 0.027 | 0.022 | 9.454 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 129 | ILE | 0 | 0.019 | 0.008 | 12.499 | -0.065 | -0.065 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 130 | ALA | 0 | -0.023 | -0.005 | 9.970 | -0.070 | -0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 131 | ASP | -1 | -0.889 | -0.941 | 11.961 | -0.094 | -0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 132 | ILE | 0 | -0.017 | -0.011 | 13.860 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 133 | VAL | 0 | -0.021 | -0.010 | 15.277 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 134 | SER | 0 | -0.032 | -0.024 | 14.274 | -0.078 | -0.078 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 135 | LEU | 0 | 0.012 | 0.003 | 16.661 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 136 | PHE | 0 | 0.037 | 0.003 | 19.205 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 137 | ILE | 0 | -0.036 | -0.015 | 18.743 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 138 | THR | 0 | 0.017 | 0.021 | 19.960 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 139 | VAL | 0 | -0.006 | 0.003 | 21.938 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 140 | MET | 0 | -0.039 | -0.025 | 24.047 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 141 | ASP | -1 | -0.841 | -0.920 | 23.774 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 142 | LYS | 1 | 0.819 | 0.901 | 24.415 | 0.049 | 0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 143 | LEU | 0 | 0.003 | -0.005 | 27.795 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 144 | ARG | 1 | 0.819 | 0.893 | 25.803 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 145 | LEU | 0 | -0.084 | -0.032 | 27.360 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 146 | GLU | -1 | -0.909 | -0.943 | 31.405 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 147 | ILE | 0 | -0.001 | 0.022 | 28.684 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 148 | ARG | 1 | 0.764 | 0.846 | 32.453 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 149 | ALA | 0 | 0.049 | 0.050 | 34.078 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 150 | MET | 0 | -0.015 | -0.002 | 32.764 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 151 | ASP | -1 | -0.897 | -0.975 | 31.591 | -0.076 | -0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 152 | GLU | -1 | -0.913 | -0.956 | 29.457 | -0.068 | -0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 153 | ILE | 0 | -0.053 | -0.025 | 28.116 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 154 | GLN | 0 | -0.027 | -0.019 | 27.316 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 155 | PRO | 0 | 0.025 | 0.014 | 25.357 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 156 | ASP | -1 | -0.800 | -0.892 | 22.504 | -0.067 | -0.067 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 157 | LEU | 0 | 0.013 | 0.013 | 22.685 | 0.021 | 0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 158 | ARG | 1 | 0.820 | 0.889 | 24.627 | 0.092 | 0.092 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 159 | GLU | -1 | -0.914 | -0.957 | 19.276 | -0.160 | -0.160 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 160 | LEU | 0 | -0.027 | -0.012 | 20.078 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 161 | MET | 0 | -0.003 | 0.002 | 21.064 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 162 | GLU | -1 | -0.794 | -0.884 | 21.321 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 163 | THR | 0 | -0.078 | -0.029 | 15.552 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 164 | MET | 0 | 0.019 | 0.011 | 18.261 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 165 | ASN | 0 | -0.056 | -0.049 | 20.540 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 166 | ARG | 1 | 0.923 | 0.979 | 15.584 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 167 | MET | 0 | -0.057 | -0.010 | 16.868 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 168 | SER | 0 | 0.010 | -0.005 | 18.285 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 169 | HIS | 0 | -0.036 | -0.025 | 16.673 | -0.023 | -0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 170 | LEU | 0 | -0.031 | 0.009 | 20.393 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 171 | PRO | 0 | 0.036 | 0.019 | 22.590 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 172 | PRO | 0 | -0.001 | -0.015 | 26.268 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 173 | ASP | -1 | -0.928 | -0.961 | 28.414 | 0.137 | 0.137 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 174 | PHE | 0 | -0.042 | -0.016 | 23.525 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 175 | GLU | -1 | -0.769 | -0.903 | 27.820 | 0.168 | 0.168 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 176 | GLY | 0 | 0.039 | 0.010 | 25.784 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 177 | ARG | 1 | 0.895 | 0.944 | 23.254 | -0.148 | -0.148 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 178 | GLU | -1 | -0.895 | -0.931 | 26.627 | 0.084 | 0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 179 | LYS | 1 | 0.873 | 0.929 | 29.255 | -0.143 | -0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 180 | VAL | 0 | 0.011 | 0.003 | 24.944 | -0.014 | -0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 181 | SER | 0 | 0.006 | -0.015 | 28.222 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 182 | GLN | 0 | -0.030 | -0.008 | 30.079 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 183 | TRP | 0 | 0.005 | -0.014 | 30.706 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 184 | LEU | 0 | -0.029 | -0.017 | 26.842 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 185 | GLN | 0 | -0.014 | 0.001 | 31.298 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 186 | LYS | 1 | 0.939 | 1.005 | 34.677 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 187 | LEU | 0 | 0.038 | 0.003 | 30.959 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 188 | SER | 0 | -0.100 | -0.052 | 34.421 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 189 | SER | 0 | -0.104 | -0.060 | 35.737 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 190 | MET | 0 | -0.066 | -0.019 | 37.165 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 191 | SER | 0 | 0.000 | -0.015 | 38.074 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 192 | ALA | 0 | -0.053 | -0.034 | 35.589 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 193 | SER | 0 | 0.046 | 0.016 | 35.956 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 194 | ASP | -1 | -0.871 | -0.908 | 38.587 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 195 | GLU | -1 | -0.904 | -0.960 | 37.353 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 196 | LEU | 0 | -0.071 | -0.032 | 33.465 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 197 | ASP | -1 | -0.766 | -0.867 | 37.765 | 0.020 | 0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 198 | ASP | -1 | -0.806 | -0.906 | 38.946 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 199 | SER | 0 | -0.060 | -0.026 | 39.236 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 200 | GLN | 0 | -0.092 | -0.080 | 37.486 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 201 | VAL | 0 | 0.077 | 0.043 | 33.811 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 202 | ARG | 1 | 0.956 | 0.983 | 34.384 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 203 | GLN | 0 | -0.066 | -0.040 | 35.378 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 204 | MET | 0 | 0.036 | 0.023 | 29.141 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 205 | LEU | 0 | -0.010 | -0.002 | 29.590 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 206 | PHE | 0 | -0.029 | 0.002 | 30.674 | 0.017 | 0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 207 | ASP | -1 | -0.816 | -0.899 | 31.657 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 208 | LEU | 0 | -0.024 | -0.018 | 25.901 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 209 | GLU | -1 | -0.925 | -0.962 | 26.710 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 210 | SER | 0 | -0.025 | -0.005 | 27.614 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 211 | ALA | 0 | -0.046 | -0.022 | 26.250 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 212 | TYR | 0 | 0.032 | 0.015 | 19.443 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 213 | ASN | 0 | -0.013 | -0.015 | 23.480 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 214 | ALA | 0 | -0.028 | -0.010 | 25.428 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 215 | PHE | 0 | 0.010 | -0.008 | 16.980 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 216 | ASN | 0 | 0.024 | -0.005 | 20.226 | 0.093 | 0.093 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 217 | ARG | 1 | 0.892 | 0.963 | 21.887 | -0.202 | -0.202 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 218 | PHE | 0 | -0.004 | -0.002 | 19.007 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 219 | LEU | 0 | -0.041 | -0.012 | 16.413 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 220 | HIS | 0 | -0.148 | -0.062 | 19.458 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |