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: N6V5Q

Calculation Name: 4JUL-D-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JUL

Chain ID: D

ChEMBL ID:

UniProt ID: Q00G25

Base Structure: X-ray

Registration Date: 2025-10-06

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 171
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1511905.376124
FMO2-HF: Nuclear repulsion 1440937.83518
FMO2-HF: Total energy -70967.540944
FMO2-MP2: Total energy -71170.935991


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(D:1:GLY)


Summations of interaction energy for fragment #1(D:1: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.
-287.1-283.97519.637-12.568-10.198-0.145
Interaction energy analysis for fragmet #1(D:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / q_NPA : 0.877
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].
3D3PHE0-0.027-0.0193.84810.10411.309-0.011-0.543-0.652-0.001
4D4GLY0-0.001-0.0013.0447.8638.5200.073-0.286-0.444-0.002
5D5ALA00.0010.0112.8926.6107.4830.060-0.346-0.588-0.005
6D6ILE00.0050.0002.9277.3598.3280.050-0.463-0.556-0.003
7D7ALA0-0.016-0.0051.827-39.456-40.7779.074-4.597-3.156-0.057
8D8GLY0-0.054-0.0193.610-8.137-7.8490.005-0.119-0.174-0.001
9D9PHE0-0.039-0.0094.2188.0568.132-0.001-0.018-0.0580.000
109D109ASP-1-0.854-0.9324.435-51.761-51.637-0.001-0.019-0.1040.000
112D112ASP-1-0.773-0.8941.899-121.302-121.04010.389-6.173-4.479-0.076
113D113SER0-0.020-0.0015.0502.9142.906-0.001-0.0040.0130.000
10D10ILE0-0.0100.0006.5635.6665.6660.0000.0000.0000.000
11D11GLU-1-0.934-0.9716.551-29.829-29.8290.0000.0000.0000.000
12D12GLY00.001-0.0107.871-1.762-1.7620.0000.0000.0000.000
13D13GLY0-0.0110.0059.0820.4410.4410.0000.0000.0000.000
14D14TRP00.010-0.01110.7311.6781.6780.0000.0000.0000.000
15D15GLN00.0370.01314.472-0.400-0.4000.0000.0000.0000.000
16D16GLY0-0.010-0.00417.1190.7620.7620.0000.0000.0000.000
17D17MET0-0.071-0.01715.1601.0511.0510.0000.0000.0000.000
18D18VAL0-0.010-0.01717.355-0.435-0.4350.0000.0000.0000.000
19D19ASP-1-0.937-0.95920.067-13.072-13.0720.0000.0000.0000.000
20D20GLY0-0.013-0.01518.3230.3180.3180.0000.0000.0000.000
21D21TRP0-0.027-0.01112.986-0.585-0.5850.0000.0000.0000.000
22D22TYR00.009-0.01910.337-1.669-1.6690.0000.0000.0000.000
23D23GLY00.006-0.00713.5901.8161.8160.0000.0000.0000.000
24D24TYR0-0.043-0.03714.767-1.158-1.1580.0000.0000.0000.000
25D25HIS00.000-0.00117.3590.7370.7370.0000.0000.0000.000
26D26HIS00.0220.01218.793-0.217-0.2170.0000.0000.0000.000
27D27SER00.018-0.01221.8760.0840.0840.0000.0000.0000.000
28D28ASN0-0.048-0.02124.6810.1520.1520.0000.0000.0000.000
29D29GLU-1-0.856-0.93228.142-9.378-9.3780.0000.0000.0000.000
30D30GLN0-0.060-0.01931.1020.1340.1340.0000.0000.0000.000
31D31GLY00.0340.01929.2810.2100.2100.0000.0000.0000.000
32D32SER0-0.022-0.01424.002-0.310-0.3100.0000.0000.0000.000
33D33GLY0-0.0080.00523.4100.4120.4120.0000.0000.0000.000
34D34TYR0-0.013-0.00417.186-0.255-0.2550.0000.0000.0000.000
35D35ALA00.0160.00420.0660.7620.7620.0000.0000.0000.000
36D36ALA00.0670.04118.192-0.821-0.8210.0000.0000.0000.000
37D37ASP-1-0.856-0.88916.468-16.369-16.3690.0000.0000.0000.000
38D38LYS10.9270.94918.38113.50613.5060.0000.0000.0000.000
39D39GLU-1-0.877-0.93920.306-14.841-14.8410.0000.0000.0000.000
40D40SER0-0.034-0.04714.768-0.585-0.5850.0000.0000.0000.000
41D41THR00.0200.00315.884-1.277-1.2770.0000.0000.0000.000
42D42GLN0-0.025-0.02016.988-0.204-0.2040.0000.0000.0000.000
43D43LYS10.8910.94216.72715.75115.7510.0000.0000.0000.000
44D44ALA00.0270.01713.717-0.057-0.0570.0000.0000.0000.000
45D45ILE00.0160.00515.505-0.013-0.0130.0000.0000.0000.000
46D46ASP-1-0.864-0.90918.287-13.178-13.1780.0000.0000.0000.000
47D47GLY0-0.038-0.02016.8220.3390.3390.0000.0000.0000.000
48D48VAL0-0.026-0.02113.858-0.168-0.1680.0000.0000.0000.000
49D49THR0-0.013-0.01316.6410.5030.5030.0000.0000.0000.000
50D50ASN0-0.003-0.00920.3230.8230.8230.0000.0000.0000.000
51D51LYS10.8340.92612.86521.63021.6300.0000.0000.0000.000
52D52VAL00.012-0.00518.0640.3820.3820.0000.0000.0000.000
53D53ASN00.0140.00420.2940.4530.4530.0000.0000.0000.000
54D54SER00.0060.00121.3380.5270.5270.0000.0000.0000.000
55D55ILE0-0.043-0.02117.9370.3000.3000.0000.0000.0000.000
56D56ILE0-0.017-0.00422.5950.3850.3850.0000.0000.0000.000
57D57ASP-1-0.912-0.96425.995-10.725-10.7250.0000.0000.0000.000
58D58LYS10.8130.90124.95811.53911.5390.0000.0000.0000.000
59D59MET00.0150.01524.1830.1410.1410.0000.0000.0000.000
60D60ASN0-0.044-0.00628.2580.4920.4920.0000.0000.0000.000
61D61THR0-0.033-0.00731.6010.3010.3010.0000.0000.0000.000
62D62GLN00.007-0.01029.430-0.279-0.2790.0000.0000.0000.000
63D63PHE0-0.017-0.00633.7170.2250.2250.0000.0000.0000.000
64D64GLU-1-0.906-0.95436.529-8.158-8.1580.0000.0000.0000.000
65D65ALA0-0.0290.00138.7530.1740.1740.0000.0000.0000.000
66D66VAL0-0.066-0.04640.5640.1030.1030.0000.0000.0000.000
67D67GLY0-0.0080.00444.3360.0350.0350.0000.0000.0000.000
68D68ARG10.8010.87744.1137.0817.0810.0000.0000.0000.000
69D69GLU-1-0.938-0.96049.522-6.050-6.0500.0000.0000.0000.000
70D70PHE00.012-0.00549.0500.0550.0550.0000.0000.0000.000
71D71ASN00.0200.00054.3070.0700.0700.0000.0000.0000.000
72D72ASN00.017-0.00656.583-0.150-0.1500.0000.0000.0000.000
73D73LEU0-0.026-0.01058.062-0.019-0.0190.0000.0000.0000.000
74D74GLU-1-0.870-0.92754.962-5.616-5.6160.0000.0000.0000.000
75D75ARG10.9040.95052.7085.6955.6950.0000.0000.0000.000
76D76ARG10.9290.96551.2055.5775.5770.0000.0000.0000.000
77D77ILE00.0230.00950.087-0.128-0.1280.0000.0000.0000.000
78D78GLU-1-0.847-0.90849.212-6.338-6.3380.0000.0000.0000.000
79D79ASN0-0.031-0.02346.011-0.255-0.2550.0000.0000.0000.000
80D80LEU0-0.024-0.00444.998-0.160-0.1600.0000.0000.0000.000
81D81ASN00.0650.03844.509-0.145-0.1450.0000.0000.0000.000
82D82LYS10.9290.96441.7217.3177.3170.0000.0000.0000.000
83D83LYS10.9450.96539.7557.5747.5740.0000.0000.0000.000
84D84MET0-0.0320.00239.770-0.161-0.1610.0000.0000.0000.000
85D85GLU-1-0.802-0.89138.957-7.622-7.6220.0000.0000.0000.000
86D86ASP-1-0.881-0.94637.290-8.224-8.2240.0000.0000.0000.000
87D87GLY00.0090.00835.454-0.262-0.2620.0000.0000.0000.000
88D88PHE0-0.015-0.02034.181-0.255-0.2550.0000.0000.0000.000
89D89LEU0-0.0010.00733.222-0.277-0.2770.0000.0000.0000.000
90D90ASP-1-0.895-0.92831.079-9.823-9.8230.0000.0000.0000.000
91D91VAL0-0.054-0.03029.485-0.437-0.4370.0000.0000.0000.000
92D92TRP00.009-0.00928.558-0.489-0.4890.0000.0000.0000.000
93D93THR0-0.0040.00026.736-0.364-0.3640.0000.0000.0000.000
94D94TYR0-0.011-0.00623.981-0.671-0.6710.0000.0000.0000.000
95D95ASN0-0.041-0.03023.709-0.783-0.7830.0000.0000.0000.000
96D96ALA0-0.008-0.00323.282-0.504-0.5040.0000.0000.0000.000
97D97GLU-1-0.933-0.97021.317-13.380-13.3800.0000.0000.0000.000
98D98LEU0-0.001-0.00318.199-0.976-0.9760.0000.0000.0000.000
99D99LEU0-0.0040.00517.959-1.022-1.0220.0000.0000.0000.000
100D100VAL00.0250.00317.317-0.980-0.9800.0000.0000.0000.000
101D101LEU0-0.035-0.01214.802-1.284-1.2840.0000.0000.0000.000
102D102MET00.0150.00013.364-1.278-1.2780.0000.0000.0000.000
103D103GLU-1-0.818-0.89212.603-21.118-21.1180.0000.0000.0000.000
104D104ASN00.0040.01111.932-0.993-0.9930.0000.0000.0000.000
105D105GLU-1-0.942-0.9548.012-29.784-29.7840.0000.0000.0000.000
106D106ARG10.9230.9367.65617.73817.7380.0000.0000.0000.000
107D107THR0-0.066-0.0429.280-0.175-0.1750.0000.0000.0000.000
108D108LEU0-0.021-0.0115.151-0.415-0.4150.0000.0000.0000.000
110D110PHE0-0.044-0.0115.473-0.384-0.3840.0000.0000.0000.000
111D111HIS00.0360.0457.0230.7390.7390.0000.0000.0000.000
114D114ASN0-0.012-0.0187.8173.1143.1140.0000.0000.0000.000
115D115VAL0-0.0050.0046.8602.5462.5460.0000.0000.0000.000
116D116LYS10.8930.9406.65732.93332.9330.0000.0000.0000.000
117D117ASN0-0.013-0.0148.4342.4792.4790.0000.0000.0000.000
118D118LEU0-0.040-0.00811.6052.1012.1010.0000.0000.0000.000
119D119TYR0-0.043-0.04810.6951.2891.2890.0000.0000.0000.000
120D120ASP-1-0.789-0.88512.023-23.268-23.2680.0000.0000.0000.000
121D121LYS10.9120.96614.11917.57617.5760.0000.0000.0000.000
122D122VAL0-0.032-0.01416.0891.2861.2860.0000.0000.0000.000
123D123ARG10.9120.94714.74320.38020.3800.0000.0000.0000.000
124D124LEU0-0.074-0.03917.5880.9580.9580.0000.0000.0000.000
125D125GLN0-0.048-0.01920.0211.3551.3550.0000.0000.0000.000
126D126LEU00.0090.00619.9760.6760.6760.0000.0000.0000.000
127D127ARG10.8860.95221.81512.43312.4330.0000.0000.0000.000
128D128ASP-1-0.790-0.86622.601-11.981-11.9810.0000.0000.0000.000
129D129ASN00.008-0.00325.1660.5310.5310.0000.0000.0000.000
130D130ALA0-0.050-0.02421.9140.1880.1880.0000.0000.0000.000
131D131LYS10.8640.94021.33612.87212.8720.0000.0000.0000.000
132D132GLU-1-0.832-0.90515.173-20.488-20.4880.0000.0000.0000.000
133D133LEU0-0.007-0.01816.8960.3130.3130.0000.0000.0000.000
134D134GLY0-0.0110.00713.4630.0190.0190.0000.0000.0000.000
135D135ASN00.006-0.00711.668-2.833-2.8330.0000.0000.0000.000
136D136GLY00.0290.00711.198-0.924-0.9240.0000.0000.0000.000
137D137CYS0-0.092-0.03511.9210.9030.9030.0000.0000.0000.000
138D138PHE00.0350.00715.517-0.016-0.0160.0000.0000.0000.000
139D139GLU-1-0.861-0.90918.939-12.715-12.7150.0000.0000.0000.000
140D140PHE00.007-0.01122.495-0.051-0.0510.0000.0000.0000.000
141D141TYR00.0140.00624.9540.1930.1930.0000.0000.0000.000
142D142HIS0-0.0180.00727.7400.0550.0550.0000.0000.0000.000
143D143LYS10.8540.90529.1789.6709.6700.0000.0000.0000.000
144D144CYS0-0.0010.02726.766-0.402-0.4020.0000.0000.0000.000
145D145ASP-1-0.830-0.91928.894-10.198-10.1980.0000.0000.0000.000
146D146ASN00.027-0.01128.801-0.594-0.5940.0000.0000.0000.000
147D147GLU-1-0.925-0.95028.949-9.694-9.6940.0000.0000.0000.000
148D149MET00.010-0.00424.147-0.698-0.6980.0000.0000.0000.000
149D150GLU-1-0.964-0.94724.467-11.637-11.6370.0000.0000.0000.000
150D151SER00.0560.04425.680-0.464-0.4640.0000.0000.0000.000
151D152VAL00.0170.00020.902-0.344-0.3440.0000.0000.0000.000
152D153ARG10.8400.90620.74212.59012.5900.0000.0000.0000.000
153D154ASN0-0.071-0.02822.111-0.717-0.7170.0000.0000.0000.000
154D155GLY0-0.082-0.02922.987-0.243-0.2430.0000.0000.0000.000
155D156THR0-0.022-0.01423.7260.1960.1960.0000.0000.0000.000
156D157TYR0-0.002-0.01424.9890.3700.3700.0000.0000.0000.000
157D158ASP-1-0.855-0.92026.871-9.833-9.8330.0000.0000.0000.000
158D159TYR0-0.026-0.05326.6600.2740.2740.0000.0000.0000.000
159D160PRO0-0.028-0.03629.2020.0950.0950.0000.0000.0000.000
160D161GLN0-0.0190.00832.5350.2280.2280.0000.0000.0000.000
161D162TYR0-0.001-0.00730.1920.1470.1470.0000.0000.0000.000
162D163SER0-0.0250.01031.520-0.198-0.1980.0000.0000.0000.000
163D164GLU-1-0.955-0.99832.533-8.901-8.9010.0000.0000.0000.000
164D165GLU-1-0.890-0.94433.358-9.584-9.5840.0000.0000.0000.000
165D166ALA0-0.014-0.00629.174-0.035-0.0350.0000.0000.0000.000
166D167ARG10.9530.97030.7508.5918.5910.0000.0000.0000.000
167D168LEU0-0.016-0.00132.7350.1070.1070.0000.0000.0000.000
168D169LYS10.9690.97431.05410.09110.0910.0000.0000.0000.000
169D170ARG10.7830.90928.46610.76910.7690.0000.0000.0000.000
170D171GLU-1-0.963-0.99530.758-9.776-9.7760.0000.0000.0000.000
171D172GLU-2-1.965-1.95633.473-18.495-18.4950.0000.0000.0000.000