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: G7Q81

Calculation Name: 1IEB-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: 1IEB

Chain ID: B

ChEMBL ID:

UniProt ID: P01904

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2247516.898348
FMO2-HF: Nuclear repulsion 2160192.253239
FMO2-HF: Total energy -87324.645109
FMO2-MP2: Total energy -87579.465506


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:ARG)


Summations of interaction energy for fragment #1(B:4:ARG)
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.
-76.775-74.5130.058-0.91-1.409-0.006
Interaction energy analysis for fragmet #1(B:4:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.759 / q_NPA : 1.871
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].
3B6ARG10.9390.9703.16150.57052.7800.059-0.886-1.382-0.006
113B88ASN0-0.034-0.0143.779-1.972-1.920-0.001-0.024-0.0270.000
4B7MET00.0090.0085.212-5.356-5.3560.0000.0000.0000.000
5B1VAL00.0190.0116.4883.5963.5960.0000.0000.0000.000
6B2ASN0-0.0110.00410.071-0.264-0.2640.0000.0000.0000.000
7B3HIS00.0050.00413.069-1.163-1.1630.0000.0000.0000.000
8B4PHE00.021-0.00816.2070.3790.3790.0000.0000.0000.000
9B5ILE0-0.0080.00119.1820.0010.0010.0000.0000.0000.000
10B6ALA0-0.032-0.01621.5080.7740.7740.0000.0000.0000.000
11B7GLU-1-0.859-0.92824.682-21.379-21.3790.0000.0000.0000.000
12B8PHE0-0.047-0.03427.7440.3010.3010.0000.0000.0000.000
13B9LYS10.8780.95530.77118.58218.5820.0000.0000.0000.000
14B9ARG10.8990.94933.79216.94216.9420.0000.0000.0000.000
15B9LYS10.9130.95636.87814.67514.6750.0000.0000.0000.000
16B9GLY00.0830.05739.2360.1030.1030.0000.0000.0000.000
17B9GLY0-0.010-0.00442.1230.1730.1730.0000.0000.0000.000
18B9SER0-0.053-0.05444.687-0.169-0.1690.0000.0000.0000.000
19B9LEU00.0160.02344.0080.2300.2300.0000.0000.0000.000
20B9VAL00.0240.01247.332-0.036-0.0360.0000.0000.0000.000
21B9PRO0-0.0150.00046.993-0.158-0.1580.0000.0000.0000.000
22B9ARG10.8270.87242.85714.66914.6690.0000.0000.0000.000
23B10GLY00.0360.02148.1250.2910.2910.0000.0000.0000.000
24B11SER0-0.058-0.03046.208-0.329-0.3290.0000.0000.0000.000
25B12GLY00.0360.03045.9840.2770.2770.0000.0000.0000.000
26B13GLY00.0630.02047.156-0.115-0.1150.0000.0000.0000.000
27B14GLY0-0.025-0.01248.778-0.163-0.1630.0000.0000.0000.000
28B15GLY00.0440.02348.6600.0260.0260.0000.0000.0000.000
29B16SER0-0.059-0.02144.922-0.398-0.3980.0000.0000.0000.000
30B16ARG10.9230.95937.88016.18316.1830.0000.0000.0000.000
31B16PRO00.025-0.00242.825-0.314-0.3140.0000.0000.0000.000
32B16TRP0-0.017-0.01135.557-0.385-0.3850.0000.0000.0000.000
33B16PHE00.0110.01637.6230.3350.3350.0000.0000.0000.000
34B16LEU0-0.0050.01030.886-0.306-0.3060.0000.0000.0000.000
35B16GLU-1-0.812-0.89130.421-18.783-18.7830.0000.0000.0000.000
36B16TYR0-0.010-0.01326.414-0.447-0.4470.0000.0000.0000.000
37B16CYS0-0.006-0.00126.5630.2600.2600.0000.0000.0000.000
38B16LYS10.8570.93924.46621.77221.7720.0000.0000.0000.000
39B16SER00.0310.01221.7870.9770.9770.0000.0000.0000.000
40B16GLU-1-0.809-0.88221.443-24.046-24.0460.0000.0000.0000.000
41B16CYS0-0.031-0.00615.609-1.268-1.2680.0000.0000.0000.000
42B16HIS0-0.027-0.01820.352-0.845-0.8450.0000.0000.0000.000
43B17PHE00.0150.00416.5630.4760.4760.0000.0000.0000.000
44B18TYR0-0.032-0.02320.5280.4060.4060.0000.0000.0000.000
45B19ASN0-0.038-0.02520.8470.1680.1680.0000.0000.0000.000
46B20GLY00.0750.05316.822-0.280-0.2800.0000.0000.0000.000
47B21THR0-0.015-0.02815.0422.1512.1510.0000.0000.0000.000
48B22GLN0-0.0470.00517.6761.9921.9920.0000.0000.0000.000
49B23ARG10.9570.96920.98523.17223.1720.0000.0000.0000.000
50B24VAL00.004-0.00819.313-0.447-0.4470.0000.0000.0000.000
51B25ARG10.8250.91422.56421.23921.2390.0000.0000.0000.000
52B26LEU00.0160.01022.336-0.773-0.7730.0000.0000.0000.000
53B27LEU0-0.034-0.01824.6031.1871.1870.0000.0000.0000.000
54B28VAL0-0.022-0.00124.997-0.594-0.5940.0000.0000.0000.000
55B29ARG10.8030.87927.17221.52221.5220.0000.0000.0000.000
56B30TYR00.0480.00528.071-0.722-0.7220.0000.0000.0000.000
57B31PHE0-0.004-0.02029.3330.6020.6020.0000.0000.0000.000
58B32TYR00.014-0.00133.591-0.146-0.1460.0000.0000.0000.000
59B33ASN0-0.041-0.03436.1300.1510.1510.0000.0000.0000.000
60B34LEU0-0.005-0.00235.863-0.390-0.3900.0000.0000.0000.000
61B35GLU-1-0.755-0.81237.551-15.146-15.1460.0000.0000.0000.000
62B36GLU-1-0.759-0.84732.872-19.479-19.4790.0000.0000.0000.000
63B37ASN0-0.007-0.01235.4100.3230.3230.0000.0000.0000.000
64B38LEU00.0190.02533.1220.3950.3950.0000.0000.0000.000
65B39ARG10.8430.90731.56618.30618.3060.0000.0000.0000.000
66B40PHE00.0410.02728.2190.4730.4730.0000.0000.0000.000
67B41ASP-1-0.797-0.87429.329-20.781-20.7810.0000.0000.0000.000
68B42SER00.0200.01126.8760.1090.1090.0000.0000.0000.000
69B43ASP-1-0.913-0.96228.984-20.449-20.4490.0000.0000.0000.000
70B44VAL0-0.091-0.04331.8020.6460.6460.0000.0000.0000.000
71B45GLY00.0140.02131.8260.4190.4190.0000.0000.0000.000
72B46GLU-1-0.852-0.90532.884-16.569-16.5690.0000.0000.0000.000
73B47PHE00.005-0.00729.596-0.317-0.3170.0000.0000.0000.000
74B48ARG10.7890.87634.76317.22517.2250.0000.0000.0000.000
75B49ALA00.0360.02136.423-0.407-0.4070.0000.0000.0000.000
76B50VAL0-0.083-0.03235.3770.1340.1340.0000.0000.0000.000
77B51THR0-0.035-0.06138.6880.3710.3710.0000.0000.0000.000
78B52GLU-1-0.774-0.86841.059-14.332-14.3320.0000.0000.0000.000
79B53LEU0-0.048-0.02239.3650.0460.0460.0000.0000.0000.000
80B54GLY00.0660.04237.952-0.146-0.1460.0000.0000.0000.000
81B55ARG10.7710.86138.22114.03814.0380.0000.0000.0000.000
82B56PRO0-0.011-0.01339.983-0.046-0.0460.0000.0000.0000.000
83B57ASP-1-0.828-0.92334.845-17.351-17.3510.0000.0000.0000.000
84B58ALA00.000-0.00735.994-0.314-0.3140.0000.0000.0000.000
85B59GLU-1-0.894-0.95637.188-14.634-14.6340.0000.0000.0000.000
86B60ASN0-0.012-0.00135.1040.3780.3780.0000.0000.0000.000
87B61TRP0-0.018-0.00930.770-0.142-0.1420.0000.0000.0000.000
88B62ASN00.0630.02134.200-0.795-0.7950.0000.0000.0000.000
89B63SER0-0.092-0.05336.4520.1290.1290.0000.0000.0000.000
90B64GLN0-0.023-0.00831.6480.5490.5490.0000.0000.0000.000
91B65PRO00.0400.02632.861-0.567-0.5670.0000.0000.0000.000
92B66GLU-1-0.859-0.94629.689-19.479-19.4790.0000.0000.0000.000
93B67PHE0-0.0130.00226.407-0.798-0.7980.0000.0000.0000.000
94B68LEU0-0.021-0.01528.480-0.726-0.7260.0000.0000.0000.000
95B69GLU-1-0.840-0.90628.721-20.577-20.5770.0000.0000.0000.000
96B70GLN0-0.060-0.03023.506-0.579-0.5790.0000.0000.0000.000
97B71LYS10.7930.88124.41223.45223.4520.0000.0000.0000.000
98B72ARG10.8330.90325.90619.38719.3870.0000.0000.0000.000
99B73ALA00.0530.02623.084-0.666-0.6660.0000.0000.0000.000
100B74GLU-1-0.801-0.87320.918-27.558-27.5580.0000.0000.0000.000
101B75VAL00.0110.01320.310-1.605-1.6050.0000.0000.0000.000
102B76ASP-1-0.796-0.88219.312-29.764-29.7640.0000.0000.0000.000
103B77THR0-0.043-0.05117.421-2.267-2.2670.0000.0000.0000.000
104B78VAL0-0.0090.01016.145-2.198-2.1980.0000.0000.0000.000
105B80ARG10.8120.87115.58827.16427.1640.0000.0000.0000.000
106B81HIS0-0.037-0.01310.339-1.191-1.1910.0000.0000.0000.000
107B82ASN0-0.004-0.02511.237-6.576-6.5760.0000.0000.0000.000
108B83TYR0-0.052-0.02710.882-1.758-1.7580.0000.0000.0000.000
109B84GLU-1-0.829-0.9289.998-42.987-42.9870.0000.0000.0000.000
110B85ILE0-0.078-0.0155.633-5.565-5.5650.0000.0000.0000.000
111B86PHE00.002-0.0146.490-4.897-4.8970.0000.0000.0000.000
112B87ASP-1-0.828-0.9139.034-42.268-42.2680.0000.0000.0000.000
114B89PHE0-0.055-0.0405.001-1.697-1.6970.0000.0000.0000.000
115B90LEU0-0.056-0.0157.1584.9774.9770.0000.0000.0000.000
116B91VAL00.0020.01810.6273.3123.3120.0000.0000.0000.000
117B92PRO00.0050.0118.8583.5023.5020.0000.0000.0000.000
118B93ARG10.8810.95911.90038.13438.1340.0000.0000.0000.000
119B94ARG10.8040.88212.81636.22436.2240.0000.0000.0000.000
120B95VAL0-0.022-0.01115.714-1.387-1.3870.0000.0000.0000.000
121B96GLU-1-0.877-0.93918.506-25.899-25.8990.0000.0000.0000.000
122B97PRO0-0.045-0.01021.8200.2640.2640.0000.0000.0000.000
123B98THR00.0490.02625.0770.6280.6280.0000.0000.0000.000
124B99VAL0-0.034-0.01827.3200.4560.4560.0000.0000.0000.000
125B100THR0-0.0120.00330.5360.3090.3090.0000.0000.0000.000
126B101VAL00.007-0.00333.6100.1300.1300.0000.0000.0000.000
127B102TYR0-0.003-0.00335.6830.2560.2560.0000.0000.0000.000
128B103PRO0-0.0170.01340.3170.0360.0360.0000.0000.0000.000
129B104THR00.0420.01042.296-0.023-0.0230.0000.0000.0000.000
130B105LYS10.8410.91044.62312.33812.3380.0000.0000.0000.000
131B106THR00.0880.04247.9860.0710.0710.0000.0000.0000.000
132B107GLN0-0.029-0.02350.565-0.063-0.0630.0000.0000.0000.000
133B108PRO00.0370.02654.1900.0750.0750.0000.0000.0000.000
134B109LEU0-0.015-0.01149.976-0.112-0.1120.0000.0000.0000.000
135B110GLU-1-0.911-0.94054.487-10.548-10.5480.0000.0000.0000.000
136B111HIS10.8490.91849.21212.37912.3790.0000.0000.0000.000
137B112HIS10.8670.94149.19912.20412.2040.0000.0000.0000.000
138B113ASN0-0.0190.00446.516-0.328-0.3280.0000.0000.0000.000
139B114LEU00.0340.02742.8900.1640.1640.0000.0000.0000.000
140B115LEU00.002-0.00241.423-0.123-0.1230.0000.0000.0000.000
141B116VAL0-0.0070.00336.941-0.191-0.1910.0000.0000.0000.000
142B117CYS0-0.0290.00334.638-0.228-0.2280.0000.0000.0000.000
143B118SER0-0.033-0.01832.851-0.312-0.3120.0000.0000.0000.000
144B119VAL00.0430.02428.089-0.178-0.1780.0000.0000.0000.000
145B120SER0-0.017-0.02727.680-0.288-0.2880.0000.0000.0000.000
146B121ASP-1-0.869-0.94521.988-26.245-26.2450.0000.0000.0000.000
147B122PHE00.0160.02221.597-0.324-0.3240.0000.0000.0000.000
148B123TYR00.001-0.01515.508-0.624-0.6240.0000.0000.0000.000
149B124PRO00.0340.01817.668-0.759-0.7590.0000.0000.0000.000
150B125GLY00.0270.00419.5260.8710.8710.0000.0000.0000.000
151B126ASN0-0.047-0.02822.0800.2330.2330.0000.0000.0000.000
152B127ILE00.0240.00924.310-0.524-0.5240.0000.0000.0000.000
153B128GLU-1-0.885-0.90627.045-18.373-18.3730.0000.0000.0000.000
154B129VAL00.0220.00630.550-0.146-0.1460.0000.0000.0000.000
155B130ARG10.7410.85832.93717.83917.8390.0000.0000.0000.000
156B131TRP00.0340.00336.4880.0480.0480.0000.0000.0000.000
157B132PHE0-0.003-0.00537.3170.3110.3110.0000.0000.0000.000
158B133ARG10.9050.95141.97912.54512.5450.0000.0000.0000.000
159B134ASN0-0.008-0.01545.6020.1590.1590.0000.0000.0000.000
160B135GLY00.0510.02844.2480.0610.0610.0000.0000.0000.000
161B136LYS10.9250.97543.76412.55712.5570.0000.0000.0000.000
162B137GLU-1-0.771-0.88239.023-15.413-15.4130.0000.0000.0000.000
163B138GLU0-0.029-0.01942.5540.4400.4400.0000.0000.0000.000
164B139LYS10.8090.89539.97314.82214.8220.0000.0000.0000.000
165B140THR0-0.021-0.02243.5360.0930.0930.0000.0000.0000.000
166B141GLY00.0670.03845.141-0.062-0.0620.0000.0000.0000.000
167B142ILE0-0.036-0.00639.040-0.102-0.1020.0000.0000.0000.000
168B143VAL00.0420.03140.970-0.173-0.1730.0000.0000.0000.000
169B144SER00.018-0.00235.511-0.380-0.3800.0000.0000.0000.000
170B145THR0-0.0110.00033.0830.2360.2360.0000.0000.0000.000
171B146GLY00.0050.01633.454-0.201-0.2010.0000.0000.0000.000
172B147LEU0-0.0430.00025.355-0.149-0.1490.0000.0000.0000.000
173B148VAL00.0090.00828.672-0.031-0.0310.0000.0000.0000.000
174B149ARG10.9440.96421.32125.15525.1550.0000.0000.0000.000
175B150ASN00.0420.02523.8911.3341.3340.0000.0000.0000.000
176B151GLY0-0.024-0.00222.1730.2030.2030.0000.0000.0000.000
177B152ASP-1-0.827-0.89719.587-28.230-28.2300.0000.0000.0000.000
178B153TRP0-0.075-0.04813.903-1.793-1.7930.0000.0000.0000.000
179B154THR00.0080.01818.501-0.498-0.4980.0000.0000.0000.000
180B155PHE0-0.063-0.03820.3710.5060.5060.0000.0000.0000.000
181B156GLN0-0.028-0.02524.2380.4220.4220.0000.0000.0000.000
182B157THR0-0.060-0.04027.6800.2680.2680.0000.0000.0000.000
183B158LEU00.0090.01931.1000.0760.0760.0000.0000.0000.000
184B159VAL00.0250.01233.8300.3330.3330.0000.0000.0000.000
185B160MET0-0.022-0.01336.5690.2230.2230.0000.0000.0000.000
186B161LEU00.0170.02340.1170.2430.2430.0000.0000.0000.000
187B162GLU-1-0.907-0.96943.113-12.909-12.9090.0000.0000.0000.000
188B163THR0-0.014-0.01246.2810.1710.1710.0000.0000.0000.000
189B164VAL00.038-0.00348.762-0.006-0.0060.0000.0000.0000.000
190B165PRO0-0.036-0.01047.4640.1410.1410.0000.0000.0000.000
191B166GLN0-0.020-0.00450.1590.3700.3700.0000.0000.0000.000
192B167SER00.0470.00851.793-0.250-0.2500.0000.0000.0000.000
193B168GLY00.0110.00952.8520.0860.0860.0000.0000.0000.000
194B169GLU0-0.104-0.04649.4300.0580.0580.0000.0000.0000.000
195B170VAL00.0580.05944.3890.0540.0540.0000.0000.0000.000
196B171TYR0-0.054-0.05242.8610.1300.1300.0000.0000.0000.000
197B172THR00.0330.00837.920-0.041-0.0410.0000.0000.0000.000
198B174GLN0-0.052-0.04033.6450.2200.2200.0000.0000.0000.000
199B175VAL00.0280.00628.1670.0160.0160.0000.0000.0000.000
200B176GLU-1-0.770-0.86828.456-18.408-18.4080.0000.0000.0000.000
201B177HIS00.0410.01420.8750.0570.0570.0000.0000.0000.000
202B178PRO0-0.021-0.01020.179-0.206-0.2060.0000.0000.0000.000
203B179SER0-0.036-0.04519.659-1.287-1.2870.0000.0000.0000.000
204B180LEU0-0.0230.00320.605-0.148-0.1480.0000.0000.0000.000
205B181THR0-0.058-0.05323.311-0.248-0.2480.0000.0000.0000.000
206B182ASP-1-0.881-0.91125.344-19.520-19.5200.0000.0000.0000.000
207B183PRO0-0.030-0.01728.334-0.405-0.4050.0000.0000.0000.000
208B184VAL00.0280.01927.5710.4020.4020.0000.0000.0000.000
209B185THR0-0.022-0.02330.5930.3750.3750.0000.0000.0000.000
210B186VAL0-0.025-0.00833.435-0.004-0.0040.0000.0000.0000.000
211B187GLU-1-0.940-0.97636.192-14.324-14.3240.0000.0000.0000.000
212B188TRP-1-0.852-0.93340.024-13.676-13.6760.0000.0000.0000.000