FMODB ID: 7GYRK
Calculation Name: 1LTT-C-Xray372
Preferred Name:
Target Type:
Ligand Name: beta-d-glucopyranose
ligand 3-letter code: BGC
PDB ID: 1LTT
Chain ID: C
UniProt ID: P06717
Base Structure: X-ray
Registration Date: 2023-03-13
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 | 41 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -157305.762243 |
---|---|
FMO2-HF: Nuclear repulsion | 139858.726025 |
FMO2-HF: Total energy | -17447.036218 |
FMO2-MP2: Total energy | -17497.736777 |
3D Structure
Ligand structure
Ligand Interaction
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(C:196:GLY)
Summations of interaction energy for
fragment #1(C:196:GLY)
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. |
2.248 | 4.607 | -0.02 | -1.164 | -1.176 | 0.001 |
Interaction energy analysis for fragmet #1(C:196:GLY)
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 | C | 198 | THR | 0 | 0.002 | -0.001 | 3.794 | -0.916 | 1.156 | -0.018 | -1.111 | -0.944 | 0.001 |
4 | C | 199 | CYS | 0 | -0.008 | -0.003 | 4.510 | 1.103 | 1.243 | -0.001 | -0.016 | -0.123 | 0.000 |
5 | C | 200 | ASN | 0 | -0.010 | -0.005 | 3.862 | 1.090 | 1.237 | -0.001 | -0.037 | -0.109 | 0.000 |
6 | C | 201 | GLU | -1 | -0.886 | -0.939 | 7.074 | -0.849 | -0.849 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | C | 202 | GLU | -1 | -0.829 | -0.920 | 8.838 | -0.422 | -0.422 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | C | 203 | THR | 0 | -0.042 | -0.011 | 9.722 | 0.371 | 0.371 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | C | 204 | GLN | 0 | -0.002 | 0.024 | 11.411 | 0.235 | 0.235 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | C | 205 | ASN | 0 | -0.035 | -0.020 | 13.044 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | C | 206 | LEU | 0 | 0.014 | -0.001 | 13.868 | 0.156 | 0.156 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | C | 207 | SER | 0 | -0.037 | -0.032 | 15.219 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | C | 208 | THR | 0 | -0.098 | -0.068 | 16.892 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | C | 209 | ILE | 0 | 0.017 | 0.013 | 18.306 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | C | 210 | TYR | 0 | 0.039 | 0.028 | 20.558 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | C | 211 | LEU | 0 | -0.023 | 0.002 | 21.863 | 0.047 | 0.047 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | C | 212 | ARG | 1 | 0.912 | 0.937 | 21.921 | 0.435 | 0.435 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | C | 213 | GLU | -1 | -0.836 | -0.907 | 24.999 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | C | 214 | TYR | 0 | 0.008 | 0.003 | 26.437 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | C | 215 | GLN | 0 | 0.002 | -0.019 | 26.216 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | C | 216 | SER | 0 | 0.000 | 0.012 | 29.465 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | C | 217 | LYS | 1 | 0.823 | 0.899 | 29.730 | 0.249 | 0.249 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | C | 218 | VAL | 0 | 0.055 | 0.027 | 32.060 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | C | 219 | LYS | 1 | 0.934 | 0.975 | 30.760 | 0.227 | 0.227 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | C | 220 | ARG | 1 | 0.949 | 0.978 | 34.757 | 0.172 | 0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | C | 221 | GLN | 0 | -0.038 | 0.016 | 37.274 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | C | 222 | ILE | 0 | 0.062 | 0.022 | 36.272 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | C | 223 | PHE | 0 | -0.036 | -0.041 | 35.448 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | C | 224 | SER | 0 | -0.031 | -0.041 | 40.299 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | C | 225 | ASP | -1 | -0.910 | -0.943 | 42.751 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | C | 226 | TYR | 0 | -0.087 | -0.038 | 42.061 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | C | 227 | GLN | 0 | -0.100 | -0.038 | 44.695 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | C | 228 | SER | 0 | 0.013 | 0.005 | 46.366 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | C | 229 | GLU | -1 | -0.921 | -0.949 | 48.908 | -0.090 | -0.090 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | C | 230 | VAL | 0 | -0.033 | -0.025 | 51.307 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | C | 231 | ASP | -1 | -0.847 | -0.917 | 53.839 | -0.058 | -0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | C | 232 | ILE | 0 | -0.014 | -0.033 | 52.417 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | C | 233 | TYR | 0 | 0.031 | 0.015 | 56.625 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | C | 234 | ASN | 0 | -0.029 | -0.021 | 60.166 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | C | 235 | ARG | 1 | 0.909 | 0.977 | 51.570 | 0.072 | 0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | C | 236 | ILE | 0 | -0.069 | -0.020 | 55.183 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |