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: 3GN5L

Calculation Name: 1F3J-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: 1F3J

Chain ID: B

ChEMBL ID:

UniProt ID: P04228

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1838785.743238
FMO2-HF: Nuclear repulsion 1760963.623092
FMO2-HF: Total energy -77822.120146
FMO2-MP2: Total energy -78049.261846


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:4:GLU)


Summations of interaction energy for fragment #1(B:4:GLU)
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.
-13.639-14.01411.766-5.667-5.7230.054
Interaction energy analysis for fragmet #1(B:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.004
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].
3B6HIS00.0100.0071.799-12.077-12.44411.767-5.665-5.7340.054
4B7PHE0-0.018-0.0105.740-3.259-3.267-0.001-0.0020.0110.000
5B8VAL00.0260.0159.4370.7690.7690.0000.0000.0000.000
6B9HIS00.0520.04012.285-0.501-0.5010.0000.0000.0000.000
7B10GLN0-0.045-0.03015.9590.1190.1190.0000.0000.0000.000
8B11PHE00.0310.01918.874-0.070-0.0700.0000.0000.0000.000
9B12LYS10.9070.96320.387-0.082-0.0820.0000.0000.0000.000
10B13GLY00.0580.03325.073-0.024-0.0240.0000.0000.0000.000
11B14GLU-1-0.821-0.86027.0520.0420.0420.0000.0000.0000.000
12B15CYS0-0.045-0.01530.780-0.014-0.0140.0000.0000.0000.000
13B16TYR0-0.060-0.04530.234-0.029-0.0290.0000.0000.0000.000
14B17PHE00.0550.02436.3390.0080.0080.0000.0000.0000.000
15B18THR0-0.074-0.05139.851-0.028-0.0280.0000.0000.0000.000
16B19ASN0-0.0080.00342.8840.0080.0080.0000.0000.0000.000
17B20GLY00.0510.03544.6250.0070.0070.0000.0000.0000.000
18B21THR0-0.031-0.05342.941-0.008-0.0080.0000.0000.0000.000
19B22GLN0-0.041-0.01544.810-0.004-0.0040.0000.0000.0000.000
20B23ARG10.9320.95240.7950.0130.0130.0000.0000.0000.000
21B24ILE00.0050.01739.245-0.003-0.0030.0000.0000.0000.000
22B25ARG10.7370.84335.7350.0200.0200.0000.0000.0000.000
23B26LEU00.0350.02332.697-0.003-0.0030.0000.0000.0000.000
24B27VAL0-0.028-0.01029.975-0.021-0.0210.0000.0000.0000.000
25B28THR00.0000.00028.7720.0310.0310.0000.0000.0000.000
26B29ARG10.7630.83624.768-0.025-0.0250.0000.0000.0000.000
27B30TYR00.0370.01322.9840.1210.1210.0000.0000.0000.000
28B31ILE00.0090.00118.011-0.122-0.1220.0000.0000.0000.000
29B32TYR00.0390.02612.7700.0170.0170.0000.0000.0000.000
30B33ASN00.010-0.01211.907-0.029-0.0290.0000.0000.0000.000
31B34ARG10.9170.94514.1761.4491.4490.0000.0000.0000.000
32B35GLU-1-0.828-0.86716.763-0.538-0.5380.0000.0000.0000.000
33B36GLU-1-0.754-0.86219.4660.0850.0850.0000.0000.0000.000
34B37TYR00.014-0.01320.332-0.080-0.0800.0000.0000.0000.000
35B38LEU0-0.021-0.00623.995-0.011-0.0110.0000.0000.0000.000
36B39ARG10.8510.91526.4440.1180.1180.0000.0000.0000.000
37B40PHE00.0200.02429.217-0.001-0.0010.0000.0000.0000.000
38B41ASP-1-0.772-0.87632.236-0.010-0.0100.0000.0000.0000.000
39B42SER00.0190.01134.8240.0110.0110.0000.0000.0000.000
40B43ASP-1-0.858-0.92238.136-0.003-0.0030.0000.0000.0000.000
41B44VAL0-0.097-0.03536.063-0.014-0.0140.0000.0000.0000.000
42B45GLY00.0600.03338.4410.0010.0010.0000.0000.0000.000
43B46GLU-1-0.857-0.92436.9490.1000.1000.0000.0000.0000.000
44B47TYR0-0.029-0.03029.963-0.006-0.0060.0000.0000.0000.000
45B48ARG10.7980.87432.009-0.034-0.0340.0000.0000.0000.000
46B49ALA00.0080.01228.8990.0210.0210.0000.0000.0000.000
47B50VAL0-0.083-0.03226.299-0.028-0.0280.0000.0000.0000.000
48B51THR0-0.030-0.05722.724-0.042-0.0420.0000.0000.0000.000
49B52GLU-1-0.800-0.89424.003-0.158-0.1580.0000.0000.0000.000
50B53LEU0-0.0110.00319.0290.0910.0910.0000.0000.0000.000
51B54GLY00.0180.01523.7400.1170.1170.0000.0000.0000.000
52B55ARG10.8100.89426.6970.1710.1710.0000.0000.0000.000
53B56HIS00.0230.00029.059-0.023-0.0230.0000.0000.0000.000
54B57SER0-0.023-0.00725.4970.0530.0530.0000.0000.0000.000
55B58ALA00.0230.00828.4040.0340.0340.0000.0000.0000.000
56B59GLU-1-0.913-0.94931.3310.2230.2230.0000.0000.0000.000
57B60TYR00.005-0.00329.4330.0070.0070.0000.0000.0000.000
58B61TYR00.017-0.01225.5860.0340.0340.0000.0000.0000.000
59B62ASN00.0350.01331.8710.0140.0140.0000.0000.0000.000
60B63LYS10.9260.97035.419-0.354-0.3540.0000.0000.0000.000
61B64GLN0-0.020-0.00132.916-0.019-0.0190.0000.0000.0000.000
62B67TYR0-0.004-0.00528.7750.0330.0330.0000.0000.0000.000
63B68LEU0-0.0210.03434.707-0.006-0.0060.0000.0000.0000.000
64B69GLU-1-0.930-0.96037.0520.2300.2300.0000.0000.0000.000
65B70ARG10.9250.93934.556-0.472-0.4720.0000.0000.0000.000
66B71THR00.0130.00833.3150.0110.0110.0000.0000.0000.000
67B72ARG10.8540.91335.750-0.178-0.1780.0000.0000.0000.000
68B73ALA00.0380.03339.126-0.016-0.0160.0000.0000.0000.000
69B74GLU-1-0.904-0.94732.9200.4170.4170.0000.0000.0000.000
70B75LEU0-0.025-0.01137.147-0.004-0.0040.0000.0000.0000.000
71B76ASP-1-0.814-0.90938.9000.1660.1660.0000.0000.0000.000
72B77THR00.003-0.02037.609-0.001-0.0010.0000.0000.0000.000
73B78ALA0-0.0060.01034.6830.0240.0240.0000.0000.0000.000
74B80ARG10.8380.91137.816-0.158-0.1580.0000.0000.0000.000
75B81HIS00.0210.02339.026-0.018-0.0180.0000.0000.0000.000
76B82ASN00.0450.02234.646-0.001-0.0010.0000.0000.0000.000
77B83TYR00.0240.02838.870-0.014-0.0140.0000.0000.0000.000
78B84GLU-1-0.831-0.91440.7530.1410.1410.0000.0000.0000.000
79B84GLU-1-0.915-0.95442.2960.2140.2140.0000.0000.0000.000
80B85THR0-0.094-0.07138.6640.0190.0190.0000.0000.0000.000
81B86GLU-1-0.851-0.89636.0540.2240.2240.0000.0000.0000.000
82B87VAL0-0.0100.00140.350-0.018-0.0180.0000.0000.0000.000
83B88PRO0-0.032-0.00342.869-0.014-0.0140.0000.0000.0000.000
84B89THR00.007-0.01439.4000.0000.0000.0000.0000.0000.000
85B90SER00.006-0.01937.048-0.019-0.0190.0000.0000.0000.000
86B91LEU0-0.075-0.04639.089-0.025-0.0250.0000.0000.0000.000
87B92ARG10.8240.92242.145-0.152-0.1520.0000.0000.0000.000
88B93ARG10.8050.90637.246-0.135-0.1350.0000.0000.0000.000
89B94LEU0-0.030-0.03342.240-0.019-0.0190.0000.0000.0000.000
90B95GLU-1-0.865-0.91039.7260.1220.1220.0000.0000.0000.000
91B96GLN00.000-0.01843.024-0.008-0.0080.0000.0000.0000.000
92B97PRO0-0.044-0.01443.5190.0010.0010.0000.0000.0000.000
93B98ASN0-0.021-0.00242.2260.0060.0060.0000.0000.0000.000
94B99VAL0-0.011-0.02544.405-0.016-0.0160.0000.0000.0000.000
95B100ALA00.0240.01945.5890.0080.0080.0000.0000.0000.000
96B101ILE0-0.018-0.00646.785-0.012-0.0120.0000.0000.0000.000
97B102SER0-0.0140.00245.3410.0070.0070.0000.0000.0000.000
98B103LEU0-0.0070.00247.389-0.003-0.0030.0000.0000.0000.000
99B104SER0-0.021-0.03145.077-0.003-0.0030.0000.0000.0000.000
100B105ARG10.9010.94244.0780.2610.2610.0000.0000.0000.000
101B106THR00.000-0.00547.6760.0060.0060.0000.0000.0000.000
102B107GLU-1-0.854-0.91050.186-0.134-0.1340.0000.0000.0000.000
103B108ALA0-0.009-0.01952.770-0.013-0.0130.0000.0000.0000.000
104B109LEU0-0.034-0.00954.0180.0080.0080.0000.0000.0000.000
105B110ASN00.0210.02057.7000.0080.0080.0000.0000.0000.000
106B111HIS0-0.040-0.02254.502-0.011-0.0110.0000.0000.0000.000
107B112HIS10.8920.94151.1690.2470.2470.0000.0000.0000.000
108B113ASN00.0250.01050.090-0.018-0.0180.0000.0000.0000.000
109B114THR00.0270.03046.441-0.004-0.0040.0000.0000.0000.000
110B115LEU00.0290.04248.1710.0030.0030.0000.0000.0000.000
111B116VAL0-0.013-0.02042.596-0.011-0.0110.0000.0000.0000.000
112B117CYS0-0.0470.00845.9000.0100.0100.0000.0000.0000.000
113B118SER0-0.021-0.01141.990-0.019-0.0190.0000.0000.0000.000
114B119VAL00.0090.00442.4470.0180.0180.0000.0000.0000.000
115B120THR0-0.007-0.02538.792-0.011-0.0110.0000.0000.0000.000
116B121ASP-1-0.802-0.89938.3930.0020.0020.0000.0000.0000.000
117B122PHE0-0.0060.01939.4550.0160.0160.0000.0000.0000.000
118B123TYR00.001-0.01336.099-0.005-0.0050.0000.0000.0000.000
119B124PRO00.0150.01439.6900.0070.0070.0000.0000.0000.000
120B125ALA00.0320.00337.630-0.008-0.0080.0000.0000.0000.000
121B126LYS10.9150.96639.7480.0250.0250.0000.0000.0000.000
122B127ILE00.0150.01042.5630.0140.0140.0000.0000.0000.000
123B128LYS10.8190.91344.9620.0690.0690.0000.0000.0000.000
124B129VAL00.0220.01045.1340.0110.0110.0000.0000.0000.000
125B130ARG10.7820.87948.1130.0800.0800.0000.0000.0000.000
126B131TRP00.0530.00947.9820.0130.0130.0000.0000.0000.000
127B132PHE0-0.025-0.01752.7280.0000.0000.0000.0000.0000.000
128B133ARG10.8830.93656.3930.1290.1290.0000.0000.0000.000
129B134ASN0-0.016-0.01458.8060.0040.0040.0000.0000.0000.000
130B135GLY00.0080.01160.7380.0030.0030.0000.0000.0000.000
131B136GLN0-0.027-0.01360.9630.0000.0000.0000.0000.0000.000
132B137GLU-1-0.874-0.92654.816-0.117-0.1170.0000.0000.0000.000
133B138GLU-1-0.872-0.93154.333-0.151-0.1510.0000.0000.0000.000
134B139THR0-0.015-0.01653.623-0.007-0.0070.0000.0000.0000.000
135B140VAL0-0.009-0.00952.348-0.010-0.0100.0000.0000.0000.000
136B141GLY00.0370.02850.4670.0060.0060.0000.0000.0000.000
137B142VAL0-0.0070.00348.694-0.006-0.0060.0000.0000.0000.000
138B143SER0-0.042-0.01143.680-0.017-0.0170.0000.0000.0000.000
139B144SER00.001-0.01142.1250.0140.0140.0000.0000.0000.000
140B145THR0-0.0020.00736.626-0.017-0.0170.0000.0000.0000.000
141B146GLN0-0.015-0.01134.7040.0190.0190.0000.0000.0000.000
142B147LEU0-0.031-0.00735.604-0.002-0.0020.0000.0000.0000.000
143B148ILE00.0180.01431.774-0.016-0.0160.0000.0000.0000.000
144B149ARG10.9450.96329.5520.0680.0680.0000.0000.0000.000
145B150ASN00.0320.02230.403-0.053-0.0530.0000.0000.0000.000
146B151GLY0-0.031-0.00828.6430.0100.0100.0000.0000.0000.000
147B152ASP-1-0.825-0.89629.5810.1140.1140.0000.0000.0000.000
148B153TRP0-0.047-0.02431.068-0.006-0.0060.0000.0000.0000.000
149B154THR0-0.0050.00034.104-0.013-0.0130.0000.0000.0000.000
150B155PHE0-0.068-0.04734.077-0.012-0.0120.0000.0000.0000.000
151B156GLN0-0.027-0.02034.466-0.002-0.0020.0000.0000.0000.000
152B157VAL0-0.050-0.02837.375-0.019-0.0190.0000.0000.0000.000
153B158LEU00.0260.03137.9160.0130.0130.0000.0000.0000.000
154B159VAL00.025-0.01441.152-0.016-0.0160.0000.0000.0000.000
155B160MET0-0.0230.00341.1380.0150.0150.0000.0000.0000.000
156B161LEU00.0210.01045.8630.0000.0000.0000.0000.0000.000
157B162GLU-1-0.945-0.98749.061-0.233-0.2330.0000.0000.0000.000
158B163MET0-0.0090.00350.4160.0070.0070.0000.0000.0000.000
159B164THR0-0.005-0.00853.799-0.009-0.0090.0000.0000.0000.000
160B165PRO0-0.061-0.00955.2560.0060.0060.0000.0000.0000.000
161B166HIS0-0.007-0.01258.188-0.005-0.0050.0000.0000.0000.000
162B167GLN00.0370.00361.1910.0000.0000.0000.0000.0000.000
163B168GLY0-0.059-0.02963.7660.0020.0020.0000.0000.0000.000
164B169GLU-1-0.819-0.88960.514-0.126-0.1260.0000.0000.0000.000
165B170VAL0-0.025-0.01359.3020.0010.0010.0000.0000.0000.000
166B171TYR0-0.003-0.01754.822-0.006-0.0060.0000.0000.0000.000
167B172THR0-0.015-0.02055.0010.0060.0060.0000.0000.0000.000
168B174HIS00.003-0.00151.8640.0060.0060.0000.0000.0000.000
169B175VAL00.0370.00747.147-0.010-0.0100.0000.0000.0000.000
170B176GLU-1-0.797-0.88949.600-0.056-0.0560.0000.0000.0000.000
171B177HIS00.0530.02642.929-0.004-0.0040.0000.0000.0000.000
172B178PRO0-0.027-0.02045.9250.0050.0050.0000.0000.0000.000
173B179SER00.006-0.00646.0950.0080.0080.0000.0000.0000.000
174B180LEU0-0.039-0.01248.2040.0070.0070.0000.0000.0000.000
175B181LYS10.9420.98051.134-0.033-0.0330.0000.0000.0000.000
176B182SER00.006-0.01554.791-0.003-0.0030.0000.0000.0000.000
177B183PRO0-0.013-0.00852.8160.0020.0020.0000.0000.0000.000
178B184ILE00.0240.02749.1990.0030.0030.0000.0000.0000.000
179B185THR0-0.007-0.00552.675-0.009-0.0090.0000.0000.0000.000
180B186VAL0-0.016-0.00350.3670.0070.0070.0000.0000.0000.000
181B187GLU-1-0.829-0.91253.448-0.072-0.0720.0000.0000.0000.000
182B188TRP00.0330.00552.7310.0000.0000.0000.0000.0000.000
183B189ARG10.8620.90555.4730.0700.0700.0000.0000.0000.000
184B190ALA0-0.0080.00857.606-0.001-0.0010.0000.0000.0000.000
185B191GLN-1-0.918-0.93858.627-0.092-0.0920.0000.0000.0000.000