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

tag_button

FMODB ID: 74JNK

Calculation Name: 1MUJ-B-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: 1MUJ

Chain ID: B

ChEMBL ID:

UniProt ID: P14434

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1906716.008621
FMO2-HF: Nuclear repulsion 1827213.595283
FMO2-HF: Total energy -79502.413338
FMO2-MP2: Total energy -79733.325418


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(B:3:SER)


Summations of interaction energy for fragment #1(B:3: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.
-16.985-12.9063.161-3.372-3.868-0.03
Interaction energy analysis for fragmet #1(B:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.816 / q_NPA : 0.892
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].
3B5ARG10.9860.9973.82046.76149.290-0.004-1.180-1.345-0.004
4B6HIS00.0430.0232.064-22.033-21.2363.113-1.921-1.989-0.028
5B7PHE0-0.004-0.0112.9871.4432.1960.052-0.271-0.5340.002
6B8VAL0-0.0040.0065.8530.0460.0460.0000.0000.0000.000
7B9TYR00.010-0.0199.2710.0830.0830.0000.0000.0000.000
8B10GLN0-0.053-0.03410.895-0.154-0.1540.0000.0000.0000.000
9B11PHE00.0110.00914.6640.0260.0260.0000.0000.0000.000
10B12MET0-0.0130.01017.726-0.028-0.0280.0000.0000.0000.000
11B13GLY00.0660.04721.3590.0720.0720.0000.0000.0000.000
12B14GLU-1-0.815-0.86624.689-11.440-11.4400.0000.0000.0000.000
13B15CYS0-0.069-0.03327.4790.2050.2050.0000.0000.0000.000
14B16TYR0-0.069-0.05727.6400.2920.2920.0000.0000.0000.000
15B17PHE00.0450.02733.5020.1720.1720.0000.0000.0000.000
16B18THR0-0.082-0.05636.9440.0330.0330.0000.0000.0000.000
17B19ASN0-0.013-0.00640.1600.0960.0960.0000.0000.0000.000
18B20GLY00.0460.02941.2200.0960.0960.0000.0000.0000.000
19B21THR0-0.021-0.05838.877-0.117-0.1170.0000.0000.0000.000
20B22GLN0-0.063-0.01840.9890.0720.0720.0000.0000.0000.000
21B23ARG10.9500.97738.6247.8777.8770.0000.0000.0000.000
22B24ILE00.004-0.00234.704-0.058-0.0580.0000.0000.0000.000
23B25ARG10.7470.86031.2199.3889.3880.0000.0000.0000.000
24B26TYR0-0.045-0.04826.402-0.152-0.1520.0000.0000.0000.000
25B27VAL0-0.014-0.00725.6740.0140.0140.0000.0000.0000.000
26B28THR0-0.0120.01022.217-0.326-0.3260.0000.0000.0000.000
27B29ARG10.8230.86920.71512.08012.0800.0000.0000.0000.000
28B30TYR00.0270.01116.192-0.173-0.1730.0000.0000.0000.000
29B31ILE0-0.013-0.01014.4510.2480.2480.0000.0000.0000.000
30B32TYR00.004-0.0066.263-0.926-0.9260.0000.0000.0000.000
31B33ASN0-0.011-0.0129.565-0.625-0.6250.0000.0000.0000.000
32B34ARG10.9050.94710.86216.97316.9730.0000.0000.0000.000
33B35GLU-1-0.853-0.90614.121-15.889-15.8890.0000.0000.0000.000
34B36GLU-1-0.776-0.85215.618-13.527-13.5270.0000.0000.0000.000
35B37TYR00.0130.01014.2000.1370.1370.0000.0000.0000.000
36B38VAL00.0030.00217.5690.6050.6050.0000.0000.0000.000
37B39ARG10.8110.88120.05011.64711.6470.0000.0000.0000.000
38B40TYR00.0200.02522.9530.2620.2620.0000.0000.0000.000
39B41ASP-1-0.780-0.87525.912-9.987-9.9870.0000.0000.0000.000
40B42SER00.0680.03729.2330.1200.1200.0000.0000.0000.000
41B43ASP-1-0.920-0.95332.483-8.466-8.4660.0000.0000.0000.000
42B44VAL0-0.070-0.03430.4310.1750.1750.0000.0000.0000.000
43B45GLY00.0250.02232.4480.1040.1040.0000.0000.0000.000
44B46GLU-1-0.879-0.92129.444-9.897-9.8970.0000.0000.0000.000
45B47HIS00.002-0.00423.356-0.311-0.3110.0000.0000.0000.000
46B48ARG10.7890.86124.94410.61210.6120.0000.0000.0000.000
47B49ALA00.0120.01821.816-0.407-0.4070.0000.0000.0000.000
48B50VAL0-0.096-0.03721.0990.5780.5780.0000.0000.0000.000
49B51THR0-0.010-0.00117.2160.3520.3520.0000.0000.0000.000
50B52GLU-1-0.869-0.94517.761-15.516-15.5160.0000.0000.0000.000
51B53LEU0-0.022-0.02612.3890.0200.0200.0000.0000.0000.000
52B54GLY00.0200.02316.835-0.502-0.5020.0000.0000.0000.000
53B55ARG10.9220.95718.61713.06213.0620.0000.0000.0000.000
54B56PRO00.0270.01317.7170.5220.5220.0000.0000.0000.000
55B57ASP-1-0.849-0.93116.407-17.433-17.4330.0000.0000.0000.000
56B58ALA0-0.016-0.00519.4330.5290.5290.0000.0000.0000.000
57B59GLU-1-0.925-0.96422.851-11.247-11.2470.0000.0000.0000.000
58B60TYR0-0.0040.01118.9630.2350.2350.0000.0000.0000.000
59B61TRP0-0.006-0.00817.0330.2600.2600.0000.0000.0000.000
60B62ASN00.0530.02023.6150.3950.3950.0000.0000.0000.000
61B63SER0-0.050-0.02825.9560.5540.5540.0000.0000.0000.000
62B64GLN0-0.067-0.04221.9110.0500.0500.0000.0000.0000.000
63B65PRO00.0150.01027.349-0.053-0.0530.0000.0000.0000.000
64B66GLU-1-0.880-0.93830.069-9.719-9.7190.0000.0000.0000.000
65B67ILE0-0.018-0.00123.078-0.056-0.0560.0000.0000.0000.000
66B68LEU0-0.0180.01326.836-0.031-0.0310.0000.0000.0000.000
67B69GLU-1-0.905-0.97228.244-8.783-8.7830.0000.0000.0000.000
68B70ARG10.9510.97723.66312.16712.1670.0000.0000.0000.000
69B71THR0-0.039-0.03925.948-0.113-0.1130.0000.0000.0000.000
70B72ARG10.8470.92628.1669.4869.4860.0000.0000.0000.000
71B73ALA00.0340.02331.7580.1980.1980.0000.0000.0000.000
72B74GLU-1-0.851-0.89426.467-11.488-11.4880.0000.0000.0000.000
73B75LEU0-0.004-0.00130.7100.0190.0190.0000.0000.0000.000
74B76ASP-1-0.862-0.92533.041-7.917-7.9170.0000.0000.0000.000
75B77THR0-0.024-0.03831.9200.1190.1190.0000.0000.0000.000
76B78VAL0-0.0110.00228.459-0.066-0.0660.0000.0000.0000.000
77B80ARG10.8780.92633.3787.9737.9730.0000.0000.0000.000
78B81HIS00.0140.01833.9680.3290.3290.0000.0000.0000.000
79B82ASN00.019-0.00230.7280.2440.2440.0000.0000.0000.000
80B83TYR00.0050.00535.1710.1640.1640.0000.0000.0000.000
81B84GLU-1-0.809-0.90337.571-7.337-7.3370.0000.0000.0000.000
82B84GLY00.0310.03639.2120.2130.2130.0000.0000.0000.000
83B85PRO00.015-0.00135.3190.1290.1290.0000.0000.0000.000
84B86GLU-1-0.866-0.89233.893-8.882-8.8820.0000.0000.0000.000
85B87THR0-0.051-0.02838.0360.1570.1570.0000.0000.0000.000
86B88HIS0-0.063-0.03040.7860.2880.2880.0000.0000.0000.000
87B89THR0-0.042-0.04537.5410.0070.0070.0000.0000.0000.000
88B90SER0-0.003-0.02335.5450.1580.1580.0000.0000.0000.000
89B91LEU0-0.060-0.03338.2420.1270.1270.0000.0000.0000.000
90B92ARG10.8770.95241.1397.2407.2400.0000.0000.0000.000
91B93ARG10.7810.89338.4297.9267.9260.0000.0000.0000.000
92B94LEU0-0.041-0.03942.2260.0040.0040.0000.0000.0000.000
93B95GLU-1-0.851-0.90141.810-7.081-7.0810.0000.0000.0000.000
94B96GLN0-0.013-0.03244.7350.0390.0390.0000.0000.0000.000
95B97PRO0-0.053-0.01346.036-0.059-0.0590.0000.0000.0000.000
96B98ASN00.0260.02445.9220.2870.2870.0000.0000.0000.000
97B99VAL0-0.020-0.01847.564-0.107-0.1070.0000.0000.0000.000
98B100VAL00.0010.00149.0270.1090.1090.0000.0000.0000.000
99B101ILE00.023-0.00450.862-0.104-0.1040.0000.0000.0000.000
100B102SER0-0.001-0.02550.6680.0800.0800.0000.0000.0000.000
101B103LEU0-0.083-0.01050.0350.0440.0440.0000.0000.0000.000
102B104SER00.0480.00752.6400.0970.0970.0000.0000.0000.000
103B105ARG10.9030.94152.5465.7265.7260.0000.0000.0000.000
104B106THR00.0400.01946.4650.0400.0400.0000.0000.0000.000
105B107GLU-1-0.835-0.92247.710-6.477-6.4770.0000.0000.0000.000
106B108ALA0-0.016-0.00449.5180.0410.0410.0000.0000.0000.000
107B109LEU0-0.036-0.01151.6010.1210.1210.0000.0000.0000.000
108B110ASN00.0010.01154.477-0.044-0.0440.0000.0000.0000.000
109B111HIS00.001-0.00857.7080.0900.0900.0000.0000.0000.000
110B112HIS10.8570.93656.7245.2895.2890.0000.0000.0000.000
111B113ASN00.0150.01255.275-0.012-0.0120.0000.0000.0000.000
112B114THR00.004-0.02554.4020.0650.0650.0000.0000.0000.000
113B115LEU00.0230.04053.9480.0240.0240.0000.0000.0000.000
114B116VAL00.0060.01747.408-0.040-0.0400.0000.0000.0000.000
115B117CYS0-0.0230.02249.8090.0020.0020.0000.0000.0000.000
116B118SER00.005-0.00346.212-0.126-0.1260.0000.0000.0000.000
117B119VAL00.0000.00845.7960.1020.1020.0000.0000.0000.000
118B120THR0-0.008-0.03742.857-0.177-0.1770.0000.0000.0000.000
119B121ASP-1-0.816-0.91541.247-7.120-7.1200.0000.0000.0000.000
120B122PHE00.0130.01941.778-0.012-0.0120.0000.0000.0000.000
121B123TYR00.0230.00235.703-0.222-0.2220.0000.0000.0000.000
122B124PRO00.0190.01239.8910.1420.1420.0000.0000.0000.000
123B125ALA00.021-0.00137.7100.1190.1190.0000.0000.0000.000
124B126LYS10.9190.97139.8376.6706.6700.0000.0000.0000.000
125B127ILE00.0160.00643.0970.1080.1080.0000.0000.0000.000
126B128LYS10.8140.90545.6035.7685.7680.0000.0000.0000.000
127B129VAL00.0150.01347.1110.0920.0920.0000.0000.0000.000
128B130ARG10.8320.90149.6765.5465.5460.0000.0000.0000.000
129B131TRP00.0460.01451.5650.0630.0630.0000.0000.0000.000
130B132PHE00.0020.01055.3150.0230.0230.0000.0000.0000.000
131B133ARG10.9190.97459.0894.8304.8300.0000.0000.0000.000
132B134ASN0-0.013-0.01462.057-0.001-0.0010.0000.0000.0000.000
133B135GLY00.0310.01663.7800.0650.0650.0000.0000.0000.000
134B136GLN0-0.059-0.02263.283-0.009-0.0090.0000.0000.0000.000
135B137GLU-1-0.862-0.91856.443-5.533-5.5330.0000.0000.0000.000
136B138GLU-1-0.903-0.96257.286-5.181-5.1810.0000.0000.0000.000
137B139THR0-0.033-0.02554.025-0.127-0.1270.0000.0000.0000.000
138B140VAL0-0.015-0.00854.392-0.101-0.1010.0000.0000.0000.000
139B141GLY0-0.010-0.00853.9320.0260.0260.0000.0000.0000.000
140B142VAL0-0.027-0.00750.370-0.056-0.0560.0000.0000.0000.000
141B143SER0-0.045-0.02046.985-0.087-0.0870.0000.0000.0000.000
142B144SER00.009-0.02243.5590.0770.0770.0000.0000.0000.000
143B145THR0-0.0070.01640.091-0.044-0.0440.0000.0000.0000.000
144B146GLN00.0100.00435.0100.0800.0800.0000.0000.0000.000
145B147LEU0-0.0170.00137.5470.0530.0530.0000.0000.0000.000
146B148ILE00.0010.01135.378-0.269-0.2690.0000.0000.0000.000
147B149ARG10.9480.96630.6559.4599.4590.0000.0000.0000.000
148B150ASN00.0400.02633.092-0.257-0.2570.0000.0000.0000.000
149B151GLY0-0.035-0.01130.950-0.157-0.1570.0000.0000.0000.000
150B152ASP-1-0.821-0.89431.300-8.685-8.6850.0000.0000.0000.000
151B153TRP0-0.049-0.02131.5510.2800.2800.0000.0000.0000.000
152B154THR0-0.0070.00335.4210.3140.3140.0000.0000.0000.000
153B155PHE0-0.046-0.03935.014-0.353-0.3530.0000.0000.0000.000
154B156GLN0-0.031-0.02538.2940.3380.3380.0000.0000.0000.000
155B157VAL0-0.045-0.02140.028-0.158-0.1580.0000.0000.0000.000
156B158LEU00.0090.01542.2460.1480.1480.0000.0000.0000.000
157B159VAL00.010-0.00744.808-0.048-0.0480.0000.0000.0000.000
158B160MET0-0.0120.01347.4120.1120.1120.0000.0000.0000.000
159B161LEU00.0360.03649.8990.0100.0100.0000.0000.0000.000
160B162GLU00.041-0.01652.842-0.001-0.0010.0000.0000.0000.000
161B163MET0-0.076-0.00555.1640.0530.0530.0000.0000.0000.000
162B164THR0-0.052-0.04258.9810.0080.0080.0000.0000.0000.000
163B165PRO00.0570.02661.2790.0570.0570.0000.0000.0000.000
164B166ARG10.8860.96363.8084.7264.7260.0000.0000.0000.000
165B167ARG11.0200.98567.2754.4304.4300.0000.0000.0000.000
166B168GLY0-0.0030.02369.0250.0680.0680.0000.0000.0000.000
167B169GLU-1-0.932-0.99164.080-4.716-4.7160.0000.0000.0000.000
168B170VAL00.0620.04563.428-0.009-0.0090.0000.0000.0000.000
169B171TYR0-0.004-0.01558.5940.0240.0240.0000.0000.0000.000
170B172THR00.0600.02858.068-0.018-0.0180.0000.0000.0000.000
171B174HIS0-0.026-0.03254.1380.0870.0870.0000.0000.0000.000
172B175VAL00.007-0.01249.042-0.104-0.1040.0000.0000.0000.000
173B176GLU-1-0.786-0.86350.909-5.668-5.6680.0000.0000.0000.000
174B177HIS00.0450.01843.4900.0200.0200.0000.0000.0000.000
175B178PRO0-0.020-0.01145.4390.1060.1060.0000.0000.0000.000
176B179SER00.0140.00146.7820.0970.0970.0000.0000.0000.000
177B180LEU0-0.054-0.01548.7310.0900.0900.0000.0000.0000.000
178B181LYS10.9510.97252.0465.4445.4440.0000.0000.0000.000
179B182SER0-0.032-0.03155.0300.1270.1270.0000.0000.0000.000
180B183PRO00.0000.00154.284-0.064-0.0640.0000.0000.0000.000
181B184ILE00.0340.03451.3900.0900.0900.0000.0000.0000.000
182B185THR00.0020.00154.718-0.043-0.0430.0000.0000.0000.000
183B186VAL0-0.030-0.01254.0590.0400.0400.0000.0000.0000.000
184B187GLU-1-0.941-0.98256.890-5.028-5.0280.0000.0000.0000.000
185B188TRP0-0.020-0.01558.142-0.038-0.0380.0000.0000.0000.000
186B189SER00.003-0.01160.1910.0480.0480.0000.0000.0000.000
187B190SER0-0.079-0.04662.830-0.036-0.0360.0000.0000.0000.000
188B191ALA0-0.095-0.04764.2020.0250.0250.0000.0000.0000.000
189B192GLU-2-1.742-1.83961.163-10.117-10.1170.0000.0000.0000.000