FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 4QKMN

Calculation Name: 1JAK-A-Xray547

Preferred Name: B-N-acetylhexosaminidase

Target Type: SINGLE PROTEIN

Ligand Name: (2r,3r,4s,5r)-2-acetamido-3,4-dihydroxy-5-hydroxymethyl-piperidine | sulfate ion | glycerol | chloride ion

Ligand 3-letter code: IFG | SO4 | GOL | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JAK

Chain ID: A

ChEMBL ID: CHEMBL1075027

UniProt ID: O85361

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 498
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -9914296.398049
FMO2-HF: Nuclear repulsion 9725332.886469
FMO2-HF: Total energy -188963.51158
FMO2-MP2: Total energy -189525.754345


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:8:ASP)


Summations of interaction energy for fragment #1(A:8:ASP)
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.
-39.72-36.93714.145-6.906-10.0230.05
Interaction energy analysis for fragmet #1(A:8:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.026
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
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].
3A10LYS00.0870.0593.9221.9773.881-0.009-0.811-1.084-0.001
4A11ALA00.0010.0013.8432.6453.0940.000-0.087-0.3620.000
5A12PRO0-0.0130.0052.225-5.563-2.3545.481-4.612-4.0780.003
6A13VAL00.005-0.0031.891-14.759-17.9738.663-1.181-4.2680.047
7A14ARG10.8550.9233.978-16.016-15.5810.010-0.215-0.2310.001
8A15PRO00.0120.0115.9871.0781.0780.0000.0000.0000.000
9A16THR00.0260.0188.5721.1031.1030.0000.0000.0000.000
10A17PRO0-0.013-0.0229.768-0.386-0.3860.0000.0000.0000.000
11A18LEU0-0.0080.00612.681-0.246-0.2460.0000.0000.0000.000
12A19ASP-1-0.849-0.92916.0391.9281.9280.0000.0000.0000.000
13A20ARG10.8780.94910.589-3.328-3.3280.0000.0000.0000.000
14A21VAL0-0.022-0.01114.8100.0120.0120.0000.0000.0000.000
15A22ILE0-0.0080.00917.595-0.048-0.0480.0000.0000.0000.000
16A23PRO0-0.016-0.01820.753-0.045-0.0450.0000.0000.0000.000
17A24ALA00.0090.01421.7430.0830.0830.0000.0000.0000.000
18A25PRO0-0.0060.01121.024-0.085-0.0850.0000.0000.0000.000
19A26ALA0-0.029-0.02024.0130.0260.0260.0000.0000.0000.000
20A27SER0-0.0220.00026.1260.0110.0110.0000.0000.0000.000
21A28VAL0-0.005-0.02119.4780.0310.0310.0000.0000.0000.000
22A29ASP-1-0.897-0.93322.5211.2341.2340.0000.0000.0000.000
23A30PRO0-0.022-0.00917.5490.0670.0670.0000.0000.0000.000
24A31GLY00.0340.00019.109-0.043-0.0430.0000.0000.0000.000
25A32GLY0-0.013-0.00119.515-0.035-0.0350.0000.0000.0000.000
26A33ALA0-0.028-0.01616.2300.2560.2560.0000.0000.0000.000
27A34PRO00.008-0.00812.281-0.136-0.1360.0000.0000.0000.000
28A35TYR00.0080.03515.240-0.187-0.1870.0000.0000.0000.000
29A36ARG10.9520.95311.142-1.951-1.9510.0000.0000.0000.000
30A37ILE00.0290.03315.315-0.224-0.2240.0000.0000.0000.000
31A38THR00.008-0.00215.704-0.021-0.0210.0000.0000.0000.000
32A39ARG11.0271.00418.188-0.237-0.2370.0000.0000.0000.000
33A40GLY0-0.0240.00120.502-0.075-0.0750.0000.0000.0000.000
34A41THR0-0.042-0.02220.2850.0430.0430.0000.0000.0000.000
35A42HIS0-0.044-0.03622.820-0.104-0.1040.0000.0000.0000.000
36A43ILE00.0320.02423.1200.0630.0630.0000.0000.0000.000
37A44ARG10.8040.90526.505-0.425-0.4250.0000.0000.0000.000
38A45VAL00.0610.03229.5600.0320.0320.0000.0000.0000.000
39A46ASP-1-0.743-0.86431.7770.3790.3790.0000.0000.0000.000
40A47ASP-1-0.820-0.89835.3810.1880.1880.0000.0000.0000.000
41A48SER00.0110.00837.202-0.018-0.0180.0000.0000.0000.000
42A49ARG10.9630.96237.081-0.104-0.1040.0000.0000.0000.000
43A50GLU-1-0.934-0.97935.8850.2160.2160.0000.0000.0000.000
44A51ALA00.0490.02632.9610.0060.0060.0000.0000.0000.000
45A52ARG10.8090.89531.629-0.178-0.1780.0000.0000.0000.000
46A53ARG11.0051.01231.260-0.119-0.1190.0000.0000.0000.000
47A54VAL00.0110.01427.773-0.020-0.0200.0000.0000.0000.000
48A55GLY00.0160.00027.3260.0210.0210.0000.0000.0000.000
49A56ASP-1-0.919-0.97326.6860.1500.1500.0000.0000.0000.000
50A57TYR00.0170.02424.738-0.008-0.0080.0000.0000.0000.000
51A58LEU00.0160.00421.000-0.011-0.0110.0000.0000.0000.000
52A59ALA0-0.018-0.01922.2090.0090.0090.0000.0000.0000.000
53A60ASP-1-0.885-0.94222.760-0.040-0.0400.0000.0000.0000.000
54A61LEU0-0.039-0.01720.288-0.067-0.0670.0000.0000.0000.000
55A62LEU0-0.0010.00516.856-0.005-0.0050.0000.0000.0000.000
56A63ARG10.8030.90718.435-0.112-0.1120.0000.0000.0000.000
57A64PRO0-0.0090.00819.377-0.022-0.0220.0000.0000.0000.000
58A65ALA00.0690.06014.339-0.056-0.0560.0000.0000.0000.000
59A66THR0-0.041-0.05914.682-0.040-0.0400.0000.0000.0000.000
60A67GLY00.0270.02216.278-0.006-0.0060.0000.0000.0000.000
61A68TYR0-0.074-0.03615.6620.1140.1140.0000.0000.0000.000
62A69ARG10.9860.98420.824-0.161-0.1610.0000.0000.0000.000
63A70LEU00.0300.02619.893-0.009-0.0090.0000.0000.0000.000
64A71PRO0-0.045-0.00224.229-0.036-0.0360.0000.0000.0000.000
65A72VAL00.0580.03327.8480.0530.0530.0000.0000.0000.000
66A73THR0-0.034-0.02829.659-0.040-0.0400.0000.0000.0000.000
67A74ALA00.0050.01032.2900.0290.0290.0000.0000.0000.000
68A75HIS0-0.013-0.00834.3430.0190.0190.0000.0000.0000.000
69A76GLY00.0380.02233.0370.0080.0080.0000.0000.0000.000
70A77HIS00.010-0.00130.253-0.011-0.0110.0000.0000.0000.000
71A78GLY0-0.007-0.00227.3620.0270.0270.0000.0000.0000.000
72A79GLY00.0310.01723.4350.0150.0150.0000.0000.0000.000
73A80ILE00.0250.01819.7680.0950.0950.0000.0000.0000.000
74A81ARG10.7990.89323.979-0.556-0.5560.0000.0000.0000.000
75A82LEU00.0190.01925.3660.0400.0400.0000.0000.0000.000
76A83ARG10.8780.92528.741-0.558-0.5580.0000.0000.0000.000
77A84LEU00.0290.01731.9420.0180.0180.0000.0000.0000.000
78A85ALA0-0.040-0.03034.777-0.001-0.0010.0000.0000.0000.000
79A86GLY0-0.0090.00036.475-0.009-0.0090.0000.0000.0000.000
80A87GLY00.0340.00435.0350.0260.0260.0000.0000.0000.000
81A88PRO0-0.0030.01233.938-0.038-0.0380.0000.0000.0000.000
82A89TYR0-0.005-0.03131.060-0.002-0.0020.0000.0000.0000.000
83A90GLY00.0570.03133.988-0.008-0.0080.0000.0000.0000.000
84A91ASP-1-0.869-0.93635.9010.2640.2640.0000.0000.0000.000
85A92GLU-1-0.762-0.84932.4090.2560.2560.0000.0000.0000.000
86A93GLY00.0820.05230.2850.0180.0180.0000.0000.0000.000
87A94TYR0-0.171-0.10523.7360.0030.0030.0000.0000.0000.000
88A95ARG10.8500.91326.691-0.717-0.7170.0000.0000.0000.000
89A96LEU0-0.036-0.02319.944-0.058-0.0580.0000.0000.0000.000
90A97ASP-1-0.764-0.83823.0610.9540.9540.0000.0000.0000.000
91A98SER0-0.034-0.04117.459-0.080-0.0800.0000.0000.0000.000
92A99GLY00.0800.04419.0020.0800.0800.0000.0000.0000.000
93A100PRO0-0.048-0.03718.600-0.088-0.0880.0000.0000.0000.000
94A101ALA0-0.025-0.00620.213-0.085-0.0850.0000.0000.0000.000
95A102GLY0-0.005-0.00721.786-0.119-0.1190.0000.0000.0000.000
96A103VAL00.0100.00918.9840.0940.0940.0000.0000.0000.000
97A104THR0-0.065-0.04022.054-0.150-0.1500.0000.0000.0000.000
98A105ILE00.0160.02922.7860.0310.0310.0000.0000.0000.000
99A106THR0-0.023-0.01626.354-0.075-0.0750.0000.0000.0000.000
100A107ALA00.0370.03129.8610.0200.0200.0000.0000.0000.000
101A108ARG10.9030.95932.079-0.354-0.3540.0000.0000.0000.000
102A109LYS10.8700.91734.481-0.260-0.2600.0000.0000.0000.000
103A110ALA00.0290.00932.9190.0280.0280.0000.0000.0000.000
104A111ALA00.0600.03631.4260.0140.0140.0000.0000.0000.000
105A112GLY00.0650.04830.1900.0150.0150.0000.0000.0000.000
106A113LEU0-0.074-0.04928.3590.0470.0470.0000.0000.0000.000
107A114PHE00.0100.01226.7980.0510.0510.0000.0000.0000.000
108A115HIS0-0.025-0.03325.823-0.014-0.0140.0000.0000.0000.000
109A116GLY00.0540.03024.0730.0490.0490.0000.0000.0000.000
110A117VAL0-0.053-0.03122.1530.0990.0990.0000.0000.0000.000
111A118GLN00.005-0.00820.9870.0280.0280.0000.0000.0000.000
112A119THR00.0160.01219.421-0.009-0.0090.0000.0000.0000.000
113A120LEU00.000-0.00717.4230.1510.1510.0000.0000.0000.000
114A121ARG10.8430.91616.4900.0610.0610.0000.0000.0000.000
115A122GLN00.0450.02314.736-0.019-0.0190.0000.0000.0000.000
116A123LEU0-0.0160.00513.3180.3380.3380.0000.0000.0000.000
117A124LEU0-0.035-0.00212.1300.5160.5160.0000.0000.0000.000
118A125PRO0-0.0280.0077.5870.0600.0600.0000.0000.0000.000
119A126PRO00.0530.0137.279-0.491-0.4910.0000.0000.0000.000
120A127ALA0-0.014-0.0098.361-0.222-0.2220.0000.0000.0000.000
121A128VAL0-0.047-0.03410.1620.0100.0100.0000.0000.0000.000
122A129GLU-1-0.777-0.85913.306-0.169-0.1690.0000.0000.0000.000
123A130LYS10.9020.97012.0301.9131.9130.0000.0000.0000.000
124A131ASP-1-0.846-0.92415.209-1.021-1.0210.0000.0000.0000.000
125A132SER0-0.030-0.02216.3330.0480.0480.0000.0000.0000.000
126A133ALA0-0.015-0.00115.365-0.083-0.0830.0000.0000.0000.000
127A134GLN0-0.043-0.02410.407-0.703-0.7030.0000.0000.0000.000
128A135PRO0-0.037-0.0358.9420.3530.3530.0000.0000.0000.000
129A136GLY0-0.0120.0289.5150.5160.5160.0000.0000.0000.000
130A137PRO0-0.013-0.0396.143-0.819-0.8190.0000.0000.0000.000
131A138TRP00.0050.0219.0340.6740.6740.0000.0000.0000.000
132A139LEU0-0.082-0.0478.219-0.270-0.2700.0000.0000.0000.000
133A140VAL00.0430.02111.7680.0010.0010.0000.0000.0000.000
134A141ALA00.0140.00613.0830.0130.0130.0000.0000.0000.000
135A142GLY00.0240.02614.239-0.330-0.3300.0000.0000.0000.000
136A143GLY00.0260.02617.3650.1070.1070.0000.0000.0000.000
137A144THR0-0.017-0.04020.578-0.048-0.0480.0000.0000.0000.000
138A145ILE0-0.0230.00719.0180.0350.0350.0000.0000.0000.000
139A146GLU-1-0.851-0.91823.3890.6320.6320.0000.0000.0000.000
140A147ASP-1-0.738-0.84125.3650.6860.6860.0000.0000.0000.000
141A148THR0-0.033-0.03627.588-0.049-0.0490.0000.0000.0000.000
142A149PRO0-0.0370.01130.3370.0190.0190.0000.0000.0000.000
143A150ARG10.7880.88431.899-0.326-0.3260.0000.0000.0000.000
144A151TYR00.0240.02033.839-0.024-0.0240.0000.0000.0000.000
145A152ALA00.0310.01534.8320.0060.0060.0000.0000.0000.000
146A153TRP0-0.045-0.02737.297-0.007-0.0070.0000.0000.0000.000
147A154ARG10.7650.85330.755-0.260-0.2600.0000.0000.0000.000
148A155SER0-0.004-0.03933.7360.0080.0080.0000.0000.0000.000
149A156ALA00.0230.02530.8820.0020.0020.0000.0000.0000.000
150A157MET0-0.058-0.01833.0290.0120.0120.0000.0000.0000.000
151A158LEU00.0240.01833.038-0.017-0.0170.0000.0000.0000.000
152A159ASP-1-0.744-0.86835.621-0.140-0.1400.0000.0000.0000.000
153A160VAL0-0.0100.01937.314-0.021-0.0210.0000.0000.0000.000
154A161SER00.012-0.00639.363-0.002-0.0020.0000.0000.0000.000
155A162ARG10.7380.85940.0400.1370.1370.0000.0000.0000.000
156A163HIS10.8370.91637.2440.2550.2550.0000.0000.0000.000
157A164PHE0-0.0030.01138.8140.0130.0130.0000.0000.0000.000
158A165PHE00.0470.02833.399-0.019-0.0190.0000.0000.0000.000
159A166GLY00.0600.03936.1730.0280.0280.0000.0000.0000.000
160A167VAL00.002-0.01835.539-0.001-0.0010.0000.0000.0000.000
161A168ASP-1-0.871-0.95332.109-0.219-0.2190.0000.0000.0000.000
162A169GLU-1-0.842-0.91931.010-0.350-0.3500.0000.0000.0000.000
163A170VAL00.0100.00731.1060.0010.0010.0000.0000.0000.000
164A171LYS10.7990.91530.9500.1760.1760.0000.0000.0000.000
165A172ARG10.8300.89124.9500.5780.5780.0000.0000.0000.000
166A173TYR00.0420.01426.9890.0190.0190.0000.0000.0000.000
167A174ILE0-0.014-0.00928.4050.0350.0350.0000.0000.0000.000
168A175ASP-1-0.789-0.86925.078-0.070-0.0700.0000.0000.0000.000
169A176ARG10.7320.86121.6940.5710.5710.0000.0000.0000.000
170A177VAL00.0280.00924.3460.0390.0390.0000.0000.0000.000
171A178ALA00.000-0.00226.4300.0590.0590.0000.0000.0000.000
172A179ARG10.7550.85318.0950.2810.2810.0000.0000.0000.000
173A180TYR00.0130.00418.9370.0260.0260.0000.0000.0000.000
174A181LYS10.8540.94022.664-0.621-0.6210.0000.0000.0000.000
175A182TYR00.001-0.01227.3320.0120.0120.0000.0000.0000.000
176A183ASN0-0.033-0.03930.426-0.018-0.0180.0000.0000.0000.000
177A184LYS10.8320.94533.566-0.142-0.1420.0000.0000.0000.000
178A185LEU00.0090.00033.200-0.006-0.0060.0000.0000.0000.000
179A186HIS10.8060.87535.8570.0200.0200.0000.0000.0000.000
180A187LEU0-0.021-0.01236.709-0.017-0.0170.0000.0000.0000.000
181A188HIS10.8590.89939.7340.0920.0920.0000.0000.0000.000
182A189LEU0-0.038-0.00842.000-0.017-0.0170.0000.0000.0000.000
183A190SER00.0190.01044.229-0.002-0.0020.0000.0000.0000.000
184A191ASP-1-0.754-0.84644.859-0.106-0.1060.0000.0000.0000.000
185A192ASP-1-0.798-0.88346.978-0.102-0.1020.0000.0000.0000.000
186A193GLN0-0.025-0.04245.1390.0070.0070.0000.0000.0000.000
187A194GLY00.0170.01445.957-0.010-0.0100.0000.0000.0000.000
188A195TRP00.000-0.00346.7040.0080.0080.0000.0000.0000.000
189A196ARG10.7320.84942.8540.1610.1610.0000.0000.0000.000
190A197ILE0-0.023-0.00244.715-0.002-0.0020.0000.0000.0000.000
191A198ALA00.0130.00147.1660.0010.0010.0000.0000.0000.000
192A199ILE0-0.045-0.01150.0240.0080.0080.0000.0000.0000.000
193A200ASP-1-0.911-0.97353.348-0.061-0.0610.0000.0000.0000.000
194A201SER0-0.017-0.03556.211-0.003-0.0030.0000.0000.0000.000
195A202TRP0-0.041-0.03856.681-0.004-0.0040.0000.0000.0000.000
196A203PRO00.0620.01855.473-0.006-0.0060.0000.0000.0000.000
197A204ARG10.8400.92954.8380.0880.0880.0000.0000.0000.000
198A205LEU00.0250.03152.697-0.008-0.0080.0000.0000.0000.000
199A206ALA00.0040.00650.145-0.006-0.0060.0000.0000.0000.000
200A207THR0-0.063-0.05350.568-0.009-0.0090.0000.0000.0000.000
201A208TYR0-0.011-0.00352.790-0.008-0.0080.0000.0000.0000.000
202A209GLY00.0710.04251.915-0.008-0.0080.0000.0000.0000.000
203A210GLY00.0330.02747.872-0.004-0.0040.0000.0000.0000.000
204A211SER0-0.100-0.06647.092-0.014-0.0140.0000.0000.0000.000
205A212THR0-0.010-0.02046.659-0.011-0.0110.0000.0000.0000.000
206A213GLU-1-0.762-0.88440.743-0.245-0.2450.0000.0000.0000.000
207A214VAL0-0.054-0.02041.2980.0030.0030.0000.0000.0000.000
208A215GLY0-0.038-0.01341.929-0.018-0.0180.0000.0000.0000.000
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