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: G8721

Calculation Name: 1FNG-A-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: 1FNG

Chain ID: A

ChEMBL ID:

UniProt ID: P04224

Base Structure: X-ray

Registration Date: 2025-09-02

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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1916119.819707
FMO2-HF: Nuclear repulsion 1842403.981574
FMO2-HF: Total energy -73715.838132
FMO2-MP2: Total energy -73933.143958


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:1:ILE)


Summations of interaction energy for fragment #1(A:1:ILE)
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.
-196.789-192.9830.145-1.59-2.36-0.009
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.913
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].
3A3GLU-1-0.842-0.9013.034-47.204-43.4710.146-1.579-2.299-0.009
4A4GLU-1-0.913-0.9474.589-28.848-28.775-0.001-0.011-0.0610.000
5A5HIS10.7970.8606.43428.96628.9660.0000.0000.0000.000
6A6THR0-0.0080.00410.6190.2580.2580.0000.0000.0000.000
7A7ILE0-0.019-0.00814.2040.0680.0680.0000.0000.0000.000
8A8ILE0-0.015-0.00616.8880.2110.2110.0000.0000.0000.000
9A9GLN0-0.0220.00120.623-0.057-0.0570.0000.0000.0000.000
10A10ALA00.003-0.00623.6420.1280.1280.0000.0000.0000.000
11A11GLU-1-0.776-0.84326.331-9.822-9.8220.0000.0000.0000.000
12A12PHE00.0030.00630.0130.0750.0750.0000.0000.0000.000
13A13TYR00.040-0.00433.5370.1600.1600.0000.0000.0000.000
14A14LEU00.0160.02937.249-0.017-0.0170.0000.0000.0000.000
15A15LEU0-0.090-0.04339.7130.2060.2060.0000.0000.0000.000
16A16PRO00.0520.01643.263-0.056-0.0560.0000.0000.0000.000
17A17ASP-1-0.827-0.93541.943-7.062-7.0620.0000.0000.0000.000
18A18LYS10.8720.93643.0086.4506.4500.0000.0000.0000.000
19A19ARG10.9520.98838.4757.2127.2120.0000.0000.0000.000
20A20GLY00.0310.01236.430-0.028-0.0280.0000.0000.0000.000
21A21GLU0-0.010-0.02129.5310.1250.1250.0000.0000.0000.000
22A22PHE00.0160.00326.858-0.053-0.0530.0000.0000.0000.000
23A23MET0-0.034-0.00323.5410.0450.0450.0000.0000.0000.000
24A24PHE00.0240.00820.222-0.164-0.1640.0000.0000.0000.000
25A25ASP-1-0.834-0.92119.145-14.256-14.2560.0000.0000.0000.000
26A26PHE0-0.010-0.02510.954-0.617-0.6170.0000.0000.0000.000
27A27ASP-1-0.801-0.88211.670-22.228-22.2280.0000.0000.0000.000
28A28GLY00.0390.03515.2160.0160.0160.0000.0000.0000.000
29A29ASP-1-0.920-0.94818.082-13.717-13.7170.0000.0000.0000.000
30A30GLU-1-0.870-0.93819.700-11.197-11.1970.0000.0000.0000.000
31A31ILE0-0.017-0.01817.989-0.123-0.1230.0000.0000.0000.000
32A32PHE0-0.019-0.02521.1530.2870.2870.0000.0000.0000.000
33A33HIS0-0.013-0.01124.8270.1490.1490.0000.0000.0000.000
34A34VAL0-0.042-0.02128.065-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.838-0.91631.189-8.016-8.0160.0000.0000.0000.000
36A36ILE0-0.034-0.04133.3540.0480.0480.0000.0000.0000.000
37A37GLU-1-0.955-0.97236.584-7.270-7.2700.0000.0000.0000.000
38A38LYS10.8450.93337.7088.0598.0590.0000.0000.0000.000
39A39SER0-0.052-0.01435.7400.0090.0090.0000.0000.0000.000
40A40GLU-1-0.884-0.94533.921-8.404-8.4040.0000.0000.0000.000
41A41THR0-0.027-0.03227.3500.0400.0400.0000.0000.0000.000
42A42ILE0-0.0090.01029.368-0.056-0.0560.0000.0000.0000.000
43A43TRP00.014-0.00521.777-0.401-0.4010.0000.0000.0000.000
44A44ARG10.8830.95523.08211.57811.5780.0000.0000.0000.000
45A45LEU00.0000.00120.4370.2410.2410.0000.0000.0000.000
46A46GLU-1-0.907-0.95724.149-10.214-10.2140.0000.0000.0000.000
47A47GLU-1-0.976-0.99119.847-13.628-13.6280.0000.0000.0000.000
48A48PHE00.0350.01218.463-0.400-0.4000.0000.0000.0000.000
49A49ALA00.0320.02321.779-0.182-0.1820.0000.0000.0000.000
50A50LYS10.8250.92221.34013.09113.0910.0000.0000.0000.000
51A51PHE0-0.058-0.03618.737-0.202-0.2020.0000.0000.0000.000
52A52ALA0-0.0090.00420.341-0.405-0.4050.0000.0000.0000.000
53A53SER0-0.025-0.01222.2800.5550.5550.0000.0000.0000.000
54A54PHE00.0460.01124.848-0.349-0.3490.0000.0000.0000.000
55A55GLU-1-0.952-0.96026.940-8.810-8.8100.0000.0000.0000.000
56A56ALA00.0400.02130.560-0.011-0.0110.0000.0000.0000.000
57A57GLN00.021-0.00932.3310.2270.2270.0000.0000.0000.000
58A58GLY00.0190.01431.3620.1360.1360.0000.0000.0000.000
59A59ALA00.0280.01830.445-0.001-0.0010.0000.0000.0000.000
60A60LEU0-0.0030.00332.0200.1440.1440.0000.0000.0000.000
61A61ALA0-0.024-0.00634.7950.2050.2050.0000.0000.0000.000
62A62ASN0-0.036-0.03030.1560.2740.2740.0000.0000.0000.000
63A63ILE00.0210.01233.0150.1500.1500.0000.0000.0000.000
64A64ALA0-0.033-0.01335.9420.2160.2160.0000.0000.0000.000
65A65VAL0-0.019-0.01035.8790.2060.2060.0000.0000.0000.000
66A66ASP0-0.054-0.07832.7240.1230.1230.0000.0000.0000.000
67A67LYS10.9040.96336.8257.0827.0820.0000.0000.0000.000
68A68ALA0-0.030-0.01140.3700.1540.1540.0000.0000.0000.000
69A69ASN00.008-0.00736.1550.2730.2730.0000.0000.0000.000
70A70LEU00.0030.01239.6820.0750.0750.0000.0000.0000.000
71A71ASP-1-0.907-0.95741.031-6.717-6.7170.0000.0000.0000.000
72A72VAL00.004-0.00242.5230.1120.1120.0000.0000.0000.000
73A73MET0-0.020-0.01938.6090.0670.0670.0000.0000.0000.000
74A74LYS10.9461.00042.4866.7026.7020.0000.0000.0000.000
75A75GLU-1-0.967-0.96945.359-6.305-6.3050.0000.0000.0000.000
76A76ARG10.9110.95239.8807.5997.5990.0000.0000.0000.000
77A77SER00.001-0.00844.0720.0330.0330.0000.0000.0000.000
78A78ASN0-0.054-0.02146.1470.1200.1200.0000.0000.0000.000
79A79ASN0-0.067-0.05247.4770.0410.0410.0000.0000.0000.000
80A80THR0-0.022-0.01446.6170.0960.0960.0000.0000.0000.000
81A81PRO0-0.048-0.01044.837-0.141-0.1410.0000.0000.0000.000
82A82ASP-1-0.896-0.94840.704-7.534-7.5340.0000.0000.0000.000
83A83ALA0-0.054-0.03142.7000.1190.1190.0000.0000.0000.000
84A84ASN0-0.031-0.01141.099-0.268-0.2680.0000.0000.0000.000
85A85VAL0-0.018-0.00535.9280.0860.0860.0000.0000.0000.000
86A86ALA00.0420.01537.954-0.119-0.1190.0000.0000.0000.000
87A87PRO0-0.0100.00535.622-0.172-0.1720.0000.0000.0000.000
88A88GLU-1-0.833-0.88932.437-9.242-9.2420.0000.0000.0000.000
89A89VAL00.0200.00034.216-0.177-0.1770.0000.0000.0000.000
90A90THR0-0.026-0.00831.0070.2010.2010.0000.0000.0000.000
91A91VAL00.004-0.00133.134-0.115-0.1150.0000.0000.0000.000
92A92LEU0-0.0010.01527.5210.0010.0010.0000.0000.0000.000
93A93SER00.0170.00631.0720.0740.0740.0000.0000.0000.000
94A94ARG10.9460.97424.59310.88710.8870.0000.0000.0000.000
95A95SER0-0.047-0.03526.483-0.492-0.4920.0000.0000.0000.000
96A96PRO00.0360.02427.2340.2870.2870.0000.0000.0000.000
97A97VAL00.0120.01230.4160.0370.0370.0000.0000.0000.000
98A98ASN0-0.010-0.00132.6220.1650.1650.0000.0000.0000.000
99A99LEU00.0140.00336.2370.0430.0430.0000.0000.0000.000
100A100GLY0-0.035-0.01239.8930.0260.0260.0000.0000.0000.000
101A101GLU-1-0.900-0.94333.987-8.738-8.7380.0000.0000.0000.000
102A102PRO0-0.080-0.04934.865-0.056-0.0560.0000.0000.0000.000
103A103ASN0-0.0010.00731.679-0.420-0.4200.0000.0000.0000.000
104A104ILE0-0.033-0.02929.8850.1270.1270.0000.0000.0000.000
105A105LEU00.0170.03031.781-0.258-0.2580.0000.0000.0000.000
106A106ILE0-0.026-0.02327.184-0.059-0.0590.0000.0000.0000.000
107A107CYS0-0.056-0.01931.4980.0880.0880.0000.0000.0000.000
108A108PHE0-0.018-0.00926.884-0.129-0.1290.0000.0000.0000.000
109A109ILE00.0140.01230.9850.2410.2410.0000.0000.0000.000
110A110ASP-1-0.752-0.88928.687-10.916-10.9160.0000.0000.0000.000
111A111LYS10.7770.87529.63610.19710.1970.0000.0000.0000.000
112A112PHE00.0270.03232.0300.2340.2340.0000.0000.0000.000
113A113SER00.0220.00033.744-0.203-0.2030.0000.0000.0000.000
114A114PRO00.0520.03136.2800.1590.1590.0000.0000.0000.000
115A115PRO0-0.033-0.00733.6620.0230.0230.0000.0000.0000.000
116A116VAL0-0.042-0.03335.5830.0330.0330.0000.0000.0000.000
117A117VAL0-0.005-0.00736.454-0.013-0.0130.0000.0000.0000.000
118A118ASN0-0.0480.00439.310-0.023-0.0230.0000.0000.0000.000
119A119VAL00.0270.00237.044-0.060-0.0600.0000.0000.0000.000
120A120THR0-0.055-0.03140.3720.1760.1760.0000.0000.0000.000
121A121TRP00.0220.02434.5250.0020.0020.0000.0000.0000.000
122A122LEU0-0.053-0.03041.2300.2030.2030.0000.0000.0000.000
123A123ARG10.9570.98041.1836.9856.9850.0000.0000.0000.000
124A124ASN0-0.031-0.02544.8540.1090.1090.0000.0000.0000.000
125A125GLY00.0210.00647.1640.1760.1760.0000.0000.0000.000
126A126ARG10.8370.92048.1506.1976.1970.0000.0000.0000.000
127A127PRO00.0420.01245.811-0.115-0.1150.0000.0000.0000.000
128A128VAL0-0.064-0.01841.8730.0970.0970.0000.0000.0000.000
129A129THR0-0.008-0.03342.396-0.095-0.0950.0000.0000.0000.000
130A130GLU-1-0.895-0.91541.771-7.063-7.0630.0000.0000.0000.000
131A131GLY00.0100.00037.961-0.037-0.0370.0000.0000.0000.000
132A132VAL0-0.0140.00736.452-0.210-0.2100.0000.0000.0000.000
133A133SER0-0.012-0.01032.102-0.038-0.0380.0000.0000.0000.000
134A134GLU-1-0.879-0.93632.160-8.376-8.3760.0000.0000.0000.000
135A135THR0-0.0100.00426.921-0.133-0.1330.0000.0000.0000.000
136A136VAL00.0060.01528.3270.3460.3460.0000.0000.0000.000
137A137PHE00.0100.00729.612-0.171-0.1710.0000.0000.0000.000
138A138LEU00.0040.01824.459-0.117-0.1170.0000.0000.0000.000
139A139PRO00.0380.01623.1670.3330.3330.0000.0000.0000.000
140A140ARG10.7550.83724.34110.51110.5110.0000.0000.0000.000
141A141ASP-1-0.889-0.94221.120-13.979-13.9790.0000.0000.0000.000
142A142ASP-1-0.852-0.89623.934-10.491-10.4910.0000.0000.0000.000
143A143HIS0-0.022-0.02227.762-0.280-0.2800.0000.0000.0000.000
144A144LEU0-0.081-0.02229.7820.3830.3830.0000.0000.0000.000
145A145PHE0-0.007-0.01829.128-0.334-0.3340.0000.0000.0000.000
146A146ARG10.8090.90821.99512.67112.6710.0000.0000.0000.000
147A147LYS10.7450.86129.3468.8508.8500.0000.0000.0000.000
148A148PHE00.0230.01124.7820.0280.0280.0000.0000.0000.000
149A149HIS00.0730.04230.2650.0550.0550.0000.0000.0000.000
150A150TYR00.002-0.00726.712-0.248-0.2480.0000.0000.0000.000
151A151LEU00.0270.02133.2230.2460.2460.0000.0000.0000.000
152A152THR0-0.034-0.02134.978-0.208-0.2080.0000.0000.0000.000
153A153PHE0-0.051-0.03634.3410.2630.2630.0000.0000.0000.000
154A154LEU00.0070.01037.204-0.173-0.1730.0000.0000.0000.000
155A155PRO0-0.025-0.00436.6870.1840.1840.0000.0000.0000.000
156A156SER00.0430.01939.7440.0660.0660.0000.0000.0000.000
157A157THR00.0360.00843.009-0.107-0.1070.0000.0000.0000.000
158A158ASP-1-0.991-0.98645.064-6.234-6.2340.0000.0000.0000.000
159A159ASP-1-0.930-0.94743.615-6.717-6.7170.0000.0000.0000.000
160A160PHE0-0.0130.00343.307-0.049-0.0490.0000.0000.0000.000
161A161TYR0-0.001-0.01840.1560.0530.0530.0000.0000.0000.000
162A162ASP-1-0.768-0.87741.359-6.896-6.8960.0000.0000.0000.000
163A164GLU-1-0.901-0.95839.685-6.653-6.6530.0000.0000.0000.000
164A165VAL00.004-0.01237.476-0.099-0.0990.0000.0000.0000.000
165A166ASP-1-0.851-0.93940.782-6.717-6.7170.0000.0000.0000.000
166A167HIS00.016-0.00538.371-0.031-0.0310.0000.0000.0000.000
167A168TRP0-0.017-0.00342.2170.1730.1730.0000.0000.0000.000
168A169GLY00.000-0.00942.2530.1110.1110.0000.0000.0000.000
169A170LEU0-0.081-0.02941.279-0.050-0.0500.0000.0000.0000.000
170A171GLU-1-0.983-0.98544.711-6.298-6.2980.0000.0000.0000.000
171A172GLU-1-0.977-0.98747.177-6.108-6.1080.0000.0000.0000.000
172A173PRO0-0.008-0.01044.996-0.155-0.1550.0000.0000.0000.000
173A174LEU00.0010.01739.2310.0400.0400.0000.0000.0000.000
174A175ARG10.8280.89741.7996.5046.5040.0000.0000.0000.000
175A176LYS10.8220.90036.9178.1608.1600.0000.0000.0000.000
176A177HIS00.009-0.02040.097-0.060-0.0600.0000.0000.0000.000
177A178TRP0-0.009-0.01235.208-0.141-0.1410.0000.0000.0000.000
178A179GLU-1-0.858-0.92439.640-6.792-6.7920.0000.0000.0000.000
179A180PHE0-0.014-0.01237.869-0.180-0.1800.0000.0000.0000.000
180A181GLU-1-0.985-0.99037.595-7.698-7.6980.0000.0000.0000.000
181A182GLU-2-1.950-1.96337.164-15.742-15.7420.0000.0000.0000.000