
FMODB ID: JLQ99
Calculation Name: 1ZBA-4-Xray372
Preferred Name:
Target Type:
Ligand Name: 2-deoxy-6-o-sulfo-2-(sulfoamino)-alpha-d-glucopyranose
ligand 3-letter code: SGN
PDB ID: 1ZBA
Chain ID: 4
UniProt ID: P03306
Base Structure: X-ray
Registration Date: 2023-06-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
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 | 49 |
LigandResidueName | |
LigandFragmentNumber | 0 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -157247.199089 |
---|---|
FMO2-HF: Nuclear repulsion | 138131.083332 |
FMO2-HF: Total energy | -19116.115758 |
FMO2-MP2: Total energy | -19170.63392 |
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(4:15:SER)
Summations of interaction energy for
fragment #1(4:15:SER)
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. |
-2.902 | 1.3 | 0.22 | -2.184 | -2.236 | 0.006 |
Interaction energy analysis for fragmet #1(4:15:SER)
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 | 4 | 17 | ASN | 0 | -0.052 | -0.014 | 3.804 | -0.593 | 2.134 | -0.025 | -1.494 | -1.208 | 0.004 |
4 | 4 | 18 | THR | 0 | 0.011 | 0.009 | 2.669 | -1.612 | -0.190 | 0.246 | -0.677 | -0.990 | 0.002 |
5 | 4 | 19 | GLY | 0 | 0.024 | 0.003 | 4.526 | -0.627 | -0.574 | -0.001 | -0.013 | -0.038 | 0.000 |
6 | 4 | 20 | SER | 0 | -0.036 | 0.003 | 6.990 | 0.111 | 0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | 4 | 21 | ILE | 0 | 0.020 | 0.000 | 7.997 | -0.121 | -0.121 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | 4 | 22 | ILE | 0 | -0.030 | -0.015 | 10.548 | 0.036 | 0.036 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | 4 | 23 | ASN | 0 | 0.036 | 0.019 | 10.207 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | 4 | 24 | ASN | 0 | 0.015 | 0.002 | 8.216 | 0.094 | 0.094 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | 4 | 25 | TYR | 0 | 0.015 | 0.017 | 10.857 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | 4 | 26 | TYR | 0 | -0.012 | 0.002 | 12.867 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | 4 | 27 | MET | 0 | 0.030 | 0.010 | 12.440 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | 4 | 28 | GLN | 0 | 0.076 | 0.015 | 9.438 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | 4 | 29 | GLN | 0 | -0.009 | -0.008 | 11.773 | 0.054 | 0.054 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | 4 | 30 | TYR | 0 | -0.053 | -0.023 | 13.885 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | 4 | 31 | GLN | 0 | -0.065 | -0.024 | 8.639 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | 4 | 32 | ASN | 0 | -0.029 | -0.011 | 7.192 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | 4 | 33 | SER | 0 | 0.041 | 0.033 | 10.914 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | 4 | 34 | MET | 0 | -0.011 | -0.012 | 12.244 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | 4 | 35 | SER | 0 | -0.005 | 0.000 | 11.253 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | 4 | 36 | THR | 0 | -0.007 | 0.001 | 14.065 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | 4 | 37 | GLN | 0 | -0.018 | -0.020 | 14.755 | 0.057 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | 4 | 38 | LEU | 0 | 0.028 | 0.010 | 18.683 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | 4 | 39 | GLY | 0 | -0.005 | 0.015 | 21.797 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | 4 | 62 | THR | 0 | 0.015 | -0.001 | 7.418 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | 4 | 63 | GLN | 0 | 0.020 | 0.008 | 10.674 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | 4 | 64 | ASN | 0 | 0.061 | 0.028 | 12.225 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | 4 | 65 | ASN | 0 | -0.013 | -0.003 | 13.601 | -0.033 | -0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | 4 | 66 | ASP | -1 | -0.829 | -0.919 | 12.462 | -0.217 | -0.217 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | 4 | 67 | TRP | 0 | -0.007 | -0.011 | 14.624 | -0.019 | -0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | 4 | 68 | PHE | 0 | 0.081 | 0.017 | 16.490 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | 4 | 69 | SER | 0 | 0.001 | 0.035 | 14.104 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | 4 | 70 | LYS | 1 | 0.846 | 0.912 | 16.255 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | 4 | 71 | LEU | 0 | -0.010 | -0.001 | 19.188 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | 4 | 72 | ALA | 0 | 0.014 | 0.017 | 18.788 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | 4 | 73 | SER | 0 | -0.040 | -0.032 | 18.466 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | 4 | 74 | SER | 0 | -0.109 | -0.053 | 21.080 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | 4 | 75 | ALA | 0 | 0.001 | 0.012 | 24.017 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | 4 | 76 | PHE | 0 | -0.002 | -0.005 | 26.004 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | 4 | 77 | THR | 0 | -0.007 | -0.020 | 27.296 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | 4 | 78 | GLY | 0 | -0.046 | -0.006 | 29.745 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | 4 | 79 | LEU | 0 | 0.037 | 0.013 | 33.202 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | 4 | 80 | PHE | 0 | -0.011 | -0.003 | 36.586 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | 4 | 81 | GLY | 0 | 0.005 | 0.005 | 38.800 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | 4 | 82 | ALA | 0 | -0.020 | -0.007 | 41.601 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | 4 | 83 | LEU | 0 | 0.007 | 0.001 | 40.421 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | 4 | 84 | LEU | 0 | 0.005 | 0.000 | 43.539 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | 4 | 85 | ALA | 0 | -0.001 | 0.011 | 42.459 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |