FMODB ID: R5Z68
Calculation Name: 1VIT-L-Xray372
Preferred Name:
Target Type:
Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose
ligand 3-letter code: NAG
PDB ID: 1VIT
Chain ID: L
UniProt ID: P28507
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 36 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -130104.983854 |
---|---|
FMO2-HF: Nuclear repulsion | 115586.476228 |
FMO2-HF: Total energy | -14518.507626 |
FMO2-MP2: Total energy | -14560.697323 |
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(L:1:THR)
Summations of interaction energy for
fragment #1(L:1:THR)
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. |
-4.92 | -0.643 | 0.881 | -2.311 | -2.845 | 0.002 |
Interaction energy analysis for fragmet #1(L:1:THR)
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 | L | 1 | GLY | 0 | 0.126 | 0.061 | 2.384 | -3.166 | 0.278 | 0.847 | -2.028 | -2.263 | 0.004 |
4 | L | 1 | ALA | 0 | -0.060 | -0.025 | 3.464 | -0.620 | 0.172 | 0.035 | -0.282 | -0.544 | -0.002 |
5 | L | 1 | GLY | 0 | -0.005 | -0.008 | 5.691 | -0.775 | -0.734 | -0.001 | -0.001 | -0.038 | 0.000 |
6 | L | 1 | GLU | -1 | -1.005 | -1.007 | 6.659 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | L | 1 | ALA | 0 | 0.061 | 0.031 | 9.271 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | L | 1 | ASP | -1 | -0.893 | -0.952 | 7.844 | -0.495 | -0.495 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | L | 1 | CYS | 0 | -0.029 | -0.009 | 9.836 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | L | 2 | GLY | 0 | -0.007 | -0.006 | 12.162 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | L | 3 | LEU | 0 | 0.022 | 0.008 | 11.992 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | L | 4 | ARG | 1 | 0.840 | 0.909 | 12.567 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | L | 5 | PRO | 0 | 0.003 | -0.009 | 11.311 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | L | 6 | LEU | 0 | -0.039 | -0.027 | 13.505 | -0.036 | -0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | L | 7 | PHE | 0 | -0.014 | -0.018 | 16.613 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | L | 8 | GLU | -1 | -0.736 | -0.840 | 16.014 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | L | 9 | LYS | 1 | 0.833 | 0.939 | 8.182 | 0.193 | 0.193 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | L | 10 | LYS | 1 | 0.888 | 0.945 | 14.550 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | L | 11 | GLN | 0 | -0.028 | -0.018 | 17.240 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | L | 12 | VAL | 0 | -0.045 | 0.004 | 20.015 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | L | 13 | GLN | 0 | 0.038 | 0.019 | 21.357 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | L | 14 | ASP | -1 | -0.842 | -0.935 | 23.593 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | L | 14 | GLN | 0 | -0.061 | -0.053 | 25.325 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | L | 14 | THR | 0 | 0.027 | 0.012 | 28.109 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | L | 14 | GLU | -1 | -0.851 | -0.920 | 22.984 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | L | 14 | LYS | 1 | 0.870 | 0.922 | 27.212 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | L | 14 | GLU | -1 | -0.879 | -0.927 | 30.068 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | L | 14 | LEU | 0 | 0.007 | 0.009 | 26.099 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | L | 14 | PHE | 0 | -0.025 | 0.014 | 23.894 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | L | 14 | GLU | -1 | -0.952 | -0.956 | 29.988 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | L | 14 | SER | 0 | -0.063 | -0.076 | 32.092 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | L | 14 | TYR | 0 | -0.058 | -0.038 | 26.909 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | L | 14 | ILE | 0 | 0.005 | 0.022 | 32.801 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | L | 14 | GLU | -1 | -0.953 | -0.975 | 32.638 | -0.045 | -0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | L | 14 | GLY | 0 | 0.043 | 0.039 | 32.003 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | L | 15 | ARG | 1 | 0.843 | 0.906 | 28.098 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |