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: 1V23Z

Calculation Name: 1FNG-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: 1FNG

Chain ID: B

ChEMBL ID:

UniProt ID: P04224

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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2152750.36712
FMO2-HF: Nuclear repulsion 2067784.756355
FMO2-HF: Total energy -84965.610765
FMO2-MP2: Total energy -85214.171818


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:6:LYS)


Summations of interaction energy for fragment #1(B:6:LYS)
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.
-249.935-246.5550.317-1.729-1.967-0.014
Interaction energy analysis for fragmet #1(B:6:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.839 / q_NPA : 1.907
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].
3B8VAL00.0060.0062.816-14.452-11.1560.318-1.726-1.888-0.014
4B1ILE00.0450.0295.1814.7284.812-0.001-0.003-0.0790.000
5B2THR0-0.016-0.0138.026-0.179-0.1790.0000.0000.0000.000
6B3ALA00.0060.00011.4080.4990.4990.0000.0000.0000.000
7B4PHE00.017-0.00714.1480.1890.1890.0000.0000.0000.000
8B5ASN0-0.018-0.00217.9420.5520.5520.0000.0000.0000.000
9B6GLU-1-0.796-0.86620.305-25.068-25.0680.0000.0000.0000.000
10B7GLY00.0410.02522.5630.2470.2470.0000.0000.0000.000
11B8LEU0-0.031-0.01626.1540.2530.2530.0000.0000.0000.000
12B9LYS10.8840.95328.49720.15420.1540.0000.0000.0000.000
13B9GLY0-0.0150.00431.6190.0030.0030.0000.0000.0000.000
14B9GLY0-0.011-0.00335.1780.1890.1890.0000.0000.0000.000
15B9GLY00.006-0.01138.2030.0140.0140.0000.0000.0000.000
16B9GLY0-0.014-0.00441.5500.4370.4370.0000.0000.0000.000
17B9SER0-0.056-0.02241.895-0.250-0.2500.0000.0000.0000.000
18B9LEU00.0340.02241.5420.2050.2050.0000.0000.0000.000
19B9VAL00.003-0.00344.9910.0520.0520.0000.0000.0000.000
20B9GLY0-0.020-0.01345.629-0.205-0.2050.0000.0000.0000.000
21B9GLY00.0310.02843.2690.1620.1620.0000.0000.0000.000
22B10GLY00.0240.00043.6460.2220.2220.0000.0000.0000.000
23B11SER0-0.048-0.03042.475-0.215-0.2150.0000.0000.0000.000
24B12GLY00.0370.01742.004-0.295-0.2950.0000.0000.0000.000
25B13GLY00.0180.00644.0810.0250.0250.0000.0000.0000.000
26B14GLY00.0020.02143.7980.2900.2900.0000.0000.0000.000
27B15GLY0-0.0030.00445.2610.0110.0110.0000.0000.0000.000
28B16SER0-0.015-0.02040.866-0.074-0.0740.0000.0000.0000.000
29B16ARG10.9300.96833.48816.99916.9990.0000.0000.0000.000
30B16PRO00.0170.00038.951-0.314-0.3140.0000.0000.0000.000
31B16TRP0-0.049-0.02632.280-0.423-0.4230.0000.0000.0000.000
32B16PHE00.0060.00333.8390.4000.4000.0000.0000.0000.000
33B16LEU0-0.0260.00027.247-0.424-0.4240.0000.0000.0000.000
34B16GLU-1-0.801-0.88527.600-19.942-19.9420.0000.0000.0000.000
35B16TYR0-0.028-0.02523.372-0.525-0.5250.0000.0000.0000.000
36B16CYS00.0090.00323.2160.6540.6540.0000.0000.0000.000
37B16LYS10.8260.92522.13722.29022.2900.0000.0000.0000.000
38B16SER00.0430.01919.7361.0981.0980.0000.0000.0000.000
39B16GLU-1-0.818-0.89420.028-24.721-24.7210.0000.0000.0000.000
40B16CYS0-0.034-0.00814.503-1.387-1.3870.0000.0000.0000.000
41B16HIS0-0.033-0.01820.874-0.179-0.1790.0000.0000.0000.000
42B17PHE0-0.008-0.00916.9230.2240.2240.0000.0000.0000.000
43B18TYR00.002-0.01022.5180.3980.3980.0000.0000.0000.000
44B19ASN0-0.035-0.02123.9100.0930.0930.0000.0000.0000.000
45B20GLY00.0810.04919.583-0.167-0.1670.0000.0000.0000.000
46B21THR00.0510.01216.1450.8550.8550.0000.0000.0000.000
47B22GLN0-0.0070.02019.3691.3241.3240.0000.0000.0000.000
48B23ARG10.9210.95622.89821.89121.8910.0000.0000.0000.000
49B24VAL0-0.005-0.00220.259-0.441-0.4410.0000.0000.0000.000
50B25ARG10.8320.90723.47021.65921.6590.0000.0000.0000.000
51B26LEU00.0000.00721.101-0.942-0.9420.0000.0000.0000.000
52B27LEU0-0.040-0.01923.9121.1831.1830.0000.0000.0000.000
53B28VAL00.0050.00623.243-0.661-0.6610.0000.0000.0000.000
54B29ARG10.7400.83525.48922.21622.2160.0000.0000.0000.000
55B30TYR00.019-0.01824.615-0.484-0.4840.0000.0000.0000.000
56B31PHE0-0.029-0.03727.0060.7740.7740.0000.0000.0000.000
57B32TYR00.0260.01330.265-0.365-0.3650.0000.0000.0000.000
58B33ASN0-0.011-0.01832.7390.1830.1830.0000.0000.0000.000
59B34LEU0-0.006-0.00932.776-0.407-0.4070.0000.0000.0000.000
60B35GLU-1-0.852-0.89034.933-15.986-15.9860.0000.0000.0000.000
61B36GLU-1-0.763-0.84130.934-20.077-20.0770.0000.0000.0000.000
62B37ASN00.0040.00232.4970.3060.3060.0000.0000.0000.000
63B38LEU00.0120.01630.4400.4420.4420.0000.0000.0000.000
64B39ARG10.8530.92129.97918.30918.3090.0000.0000.0000.000
65B40PHE00.0200.01426.1590.4750.4750.0000.0000.0000.000
66B41ASP-1-0.773-0.86128.006-21.163-21.1630.0000.0000.0000.000
67B42SER00.0410.01625.7330.0990.0990.0000.0000.0000.000
68B43ASP-1-0.910-0.95527.851-20.786-20.7860.0000.0000.0000.000
69B44VAL0-0.094-0.04431.1010.7350.7350.0000.0000.0000.000
70B45GLY00.0130.02229.7500.3460.3460.0000.0000.0000.000
71B46GLU-1-0.839-0.90030.827-17.595-17.5950.0000.0000.0000.000
72B47PHE00.0020.00927.341-0.173-0.1730.0000.0000.0000.000
73B48ARG10.7890.86932.56218.04718.0470.0000.0000.0000.000
74B49ALA00.0350.02434.424-0.435-0.4350.0000.0000.0000.000
75B50VAL0-0.099-0.04233.8300.1500.1500.0000.0000.0000.000
76B51THR0-0.034-0.06036.9580.3290.3290.0000.0000.0000.000
77B52GLU-1-0.779-0.86538.599-14.900-14.9000.0000.0000.0000.000
78B53LEU0-0.017-0.00836.4290.0320.0320.0000.0000.0000.000
79B54GLY00.0470.03035.327-0.242-0.2420.0000.0000.0000.000
80B55ARG10.7700.85835.86014.61214.6120.0000.0000.0000.000
81B56PRO00.0240.00537.747-0.107-0.1070.0000.0000.0000.000
82B57ASP-1-0.824-0.92732.504-18.687-18.6870.0000.0000.0000.000
83B58ALA0-0.007-0.00933.770-0.390-0.3900.0000.0000.0000.000
84B59GLU-1-0.946-0.98135.024-15.310-15.3100.0000.0000.0000.000
85B60ASN0-0.0010.00833.420-0.014-0.0140.0000.0000.0000.000
86B61TRP0-0.039-0.02628.401-0.289-0.2890.0000.0000.0000.000
87B62ASN00.034-0.00532.427-0.886-0.8860.0000.0000.0000.000
88B63SER0-0.078-0.03934.5750.2280.2280.0000.0000.0000.000
89B64GLN0-0.028-0.01231.287-0.361-0.3610.0000.0000.0000.000
90B65PRO00.0240.01431.306-0.625-0.6250.0000.0000.0000.000
91B66GLU-1-0.895-0.95828.398-21.315-21.3150.0000.0000.0000.000
92B67PHE0-0.040-0.01124.811-0.990-0.9900.0000.0000.0000.000
93B68LEU0-0.0010.00226.717-0.804-0.8040.0000.0000.0000.000
94B69GLU-1-0.835-0.91927.096-21.729-21.7290.0000.0000.0000.000
95B70GLN0-0.048-0.01321.955-1.408-1.4080.0000.0000.0000.000
96B71LYS10.7980.87021.76125.86225.8620.0000.0000.0000.000
97B72ARG10.7840.86824.02619.82119.8210.0000.0000.0000.000
98B73ALA00.0350.02521.402-0.371-0.3710.0000.0000.0000.000
99B74GLU-1-0.772-0.86619.010-30.641-30.6410.0000.0000.0000.000
100B75VAL00.005-0.00318.777-1.476-1.4760.0000.0000.0000.000
101B76ASP-1-0.849-0.90918.680-29.672-29.6720.0000.0000.0000.000
102B77THR00.000-0.01715.716-2.308-2.3080.0000.0000.0000.000
103B78VAL0-0.0080.01414.367-2.929-2.9290.0000.0000.0000.000
104B80ARG10.8210.88715.76226.97326.9730.0000.0000.0000.000
105B81HIS0-0.012-0.0048.7190.1440.1440.0000.0000.0000.000
106B82ASN00.000-0.02610.650-7.866-7.8660.0000.0000.0000.000
107B83TYR0-0.028-0.00211.550-1.450-1.4500.0000.0000.0000.000
108B84GLU-1-0.929-0.97111.028-42.971-42.9710.0000.0000.0000.000
109B85ILE0-0.099-0.0366.446-5.542-5.5420.0000.0000.0000.000
110B86PHE00.022-0.0118.734-2.462-2.4620.0000.0000.0000.000
111B87ASP-1-0.851-0.93111.074-35.916-35.9160.0000.0000.0000.000
112B88ASN0-0.089-0.0458.2562.0602.0600.0000.0000.0000.000
113B89PHE0-0.051-0.0417.799-1.044-1.0440.0000.0000.0000.000
114B90LEU0-0.048-0.00911.1412.3292.3290.0000.0000.0000.000
115B91VAL00.0180.02613.6512.3142.3140.0000.0000.0000.000
116B92PRO0-0.0030.00914.0432.3272.3270.0000.0000.0000.000
117B93ARG10.8730.95215.19233.86233.8620.0000.0000.0000.000
118B94ARG10.8040.88416.83130.40330.4030.0000.0000.0000.000
119B95VAL0-0.037-0.01319.861-1.069-1.0690.0000.0000.0000.000
120B96GLU-1-0.873-0.93822.238-22.452-22.4520.0000.0000.0000.000
121B97PRO0-0.030-0.00425.9590.0350.0350.0000.0000.0000.000
122B98THR00.0190.01928.5190.6000.6000.0000.0000.0000.000
123B99VAL00.0070.00030.6290.1750.1750.0000.0000.0000.000
124B100THR0-0.058-0.03734.1100.2150.2150.0000.0000.0000.000
125B101VAL00.0250.01537.318-0.063-0.0630.0000.0000.0000.000
126B102TYR0-0.028-0.00738.424-0.065-0.0650.0000.0000.0000.000
127B103PRO00.0400.03743.515-0.065-0.0650.0000.0000.0000.000
128B104THR0-0.064-0.05144.281-0.303-0.3030.0000.0000.0000.000
129B105LYS00.0220.02646.6580.0480.0480.0000.0000.0000.000
130B106THR0-0.025-0.01050.098-0.156-0.1560.0000.0000.0000.000
131B107GLN0-0.030-0.02452.4700.3320.3320.0000.0000.0000.000
132B108PRO0-0.0090.00354.407-0.026-0.0260.0000.0000.0000.000
133B109LEU00.0050.00154.332-0.092-0.0920.0000.0000.0000.000
134B110GLU-1-0.938-0.96755.219-10.594-10.5940.0000.0000.0000.000
135B111HIS0-0.049-0.01151.6580.1760.1760.0000.0000.0000.000
136B112HIS0-0.038-0.02649.9260.2570.2570.0000.0000.0000.000
137B113ASN00.013-0.01350.215-0.303-0.3030.0000.0000.0000.000
138B114LEU00.0160.01044.619-0.064-0.0640.0000.0000.0000.000
139B115LEU0-0.0080.00944.851-0.084-0.0840.0000.0000.0000.000
140B116VAL00.004-0.00239.590-0.207-0.2070.0000.0000.0000.000
141B117CYS0-0.0320.00338.143-0.229-0.2290.0000.0000.0000.000
142B118SER0-0.035-0.01435.128-0.372-0.3720.0000.0000.0000.000
143B119VAL00.0460.01731.008-0.075-0.0750.0000.0000.0000.000
144B120SER0-0.030-0.03029.500-0.312-0.3120.0000.0000.0000.000
145B121ASP-1-0.877-0.94623.667-24.992-24.9920.0000.0000.0000.000
146B122PHE00.0400.02924.536-0.177-0.1770.0000.0000.0000.000
147B123TYR00.006-0.01718.325-0.892-0.8920.0000.0000.0000.000
148B124PRO00.019-0.00220.781-0.275-0.2750.0000.0000.0000.000
149B125GLY00.0240.01322.5540.7000.7000.0000.0000.0000.000
150B126ASN0-0.076-0.04325.2470.0680.0680.0000.0000.0000.000
151B127ILE00.0080.00327.695-0.330-0.3300.0000.0000.0000.000
152B128GLU-1-0.867-0.89730.484-17.123-17.1230.0000.0000.0000.000
153B129VAL00.007-0.01233.789-0.086-0.0860.0000.0000.0000.000
154B130ARG10.7600.87136.38016.71816.7180.0000.0000.0000.000
155B131TRP00.0540.00840.1550.0180.0180.0000.0000.0000.000
156B132PHE0-0.027-0.01441.5980.2010.2010.0000.0000.0000.000
157B133ARG10.7700.88546.12211.88111.8810.0000.0000.0000.000
158B134ASN00.015-0.00649.6760.0920.0920.0000.0000.0000.000
159B135GLY00.0220.01548.2020.1560.1560.0000.0000.0000.000
160B136LYS10.8630.94348.61812.02612.0260.0000.0000.0000.000
161B137GLU-1-0.835-0.89743.715-14.578-14.5780.0000.0000.0000.000
162B138GLU-1-0.816-0.92146.523-12.129-12.1290.0000.0000.0000.000
163B139LYS10.8510.90744.27413.89513.8950.0000.0000.0000.000
164B140THR0-0.059-0.05347.0100.1920.1920.0000.0000.0000.000
165B141GLY00.0570.04948.4310.0180.0180.0000.0000.0000.000
166B142ILE0-0.0160.00541.881-0.114-0.1140.0000.0000.0000.000
167B143VAL00.0180.01342.633-0.051-0.0510.0000.0000.0000.000
168B144SER0-0.006-0.02437.175-0.314-0.3140.0000.0000.0000.000
169B145THR0-0.031-0.01334.3740.2000.2000.0000.0000.0000.000
170B146GLY00.0080.01434.795-0.259-0.2590.0000.0000.0000.000
171B147LEU0-0.0360.00227.254-0.134-0.1340.0000.0000.0000.000
172B148VAL00.0020.00528.941-0.193-0.1930.0000.0000.0000.000
173B149ARG10.9480.96921.72424.84424.8440.0000.0000.0000.000
174B150ASN00.0330.01923.9121.0881.0880.0000.0000.0000.000
175B151GLY0-0.033-0.01021.5230.0140.0140.0000.0000.0000.000
176B152ASP-1-0.829-0.89718.552-28.117-28.1170.0000.0000.0000.000
177B153TRP0-0.067-0.04114.650-1.434-1.4340.0000.0000.0000.000
178B154THR00.0030.01018.8900.0480.0480.0000.0000.0000.000
179B155PHE0-0.064-0.03622.189-0.029-0.0290.0000.0000.0000.000
180B156GLN0-0.024-0.02625.6660.5170.5170.0000.0000.0000.000
181B157THR0-0.046-0.03829.3140.1490.1490.0000.0000.0000.000
182B158LEU00.0310.03332.8900.1180.1180.0000.0000.0000.000
183B159VAL00.0220.01236.2220.1150.1150.0000.0000.0000.000
184B160MET0-0.028-0.00238.8730.1510.1510.0000.0000.0000.000
185B161LEU00.0220.02142.4560.0550.0550.0000.0000.0000.000
186B162GLU-1-0.913-0.95845.808-12.659-12.6590.0000.0000.0000.000
187B163THR0-0.029-0.02449.1430.1480.1480.0000.0000.0000.000
188B164VAL0-0.004-0.01051.718-0.025-0.0250.0000.0000.0000.000
189B165PRO0-0.0160.00251.3430.1320.1320.0000.0000.0000.000
190B166GLN0-0.030-0.02154.0020.4360.4360.0000.0000.0000.000
191B167SER00.008-0.00255.281-0.134-0.1340.0000.0000.0000.000
192B168GLY0-0.023-0.00755.736-0.118-0.1180.0000.0000.0000.000
193B169GLU-1-0.865-0.90253.164-11.514-11.5140.0000.0000.0000.000
194B170VAL00.0520.05048.393-0.050-0.0500.0000.0000.0000.000
195B171TYR0-0.040-0.04847.061-0.028-0.0280.0000.0000.0000.000
196B172THR00.017-0.00542.670-0.053-0.0530.0000.0000.0000.000
197B174GLN00.022-0.00137.737-0.128-0.1280.0000.0000.0000.000
198B175VAL00.010-0.00732.274-0.092-0.0920.0000.0000.0000.000
199B176GLU-1-0.842-0.90633.100-17.314-17.3140.0000.0000.0000.000
200B177HIS00.0500.01924.318-0.058-0.0580.0000.0000.0000.000
201B178PRO0-0.019-0.00125.091-0.018-0.0180.0000.0000.0000.000
202B179SER0-0.048-0.05724.040-0.917-0.9170.0000.0000.0000.000
203B180LEU0-0.0260.00725.304-0.185-0.1850.0000.0000.0000.000
204B181THR0-0.069-0.05228.822-0.444-0.4440.0000.0000.0000.000
205B182ASP-1-0.884-0.92130.660-17.857-17.8570.0000.0000.0000.000
206B183PRO0-0.042-0.03033.428-0.300-0.3000.0000.0000.0000.000
207B184VAL00.0290.03032.5400.3360.3360.0000.0000.0000.000
208B185THR0-0.041-0.03535.5710.3470.3470.0000.0000.0000.000
209B186VAL0-0.024-0.01138.007-0.112-0.1120.0000.0000.0000.000
210B187GLU-1-0.966-0.97840.837-13.397-13.3970.0000.0000.0000.000
211B188TRP-1-0.862-0.94044.550-12.913-12.9130.0000.0000.0000.000