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: 3GQNL

Calculation Name: 7DDP-C-Other547

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: 7DDP

Chain ID: C

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2065487.928004
FMO2-HF: Nuclear repulsion 1989019.601027
FMO2-HF: Total energy -76468.326978
FMO2-MP2: Total energy -76689.575637


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(C:333:THR)


Summations of interaction energy for fragment #1(C:333:THR)
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.
-21.215-19.5731.916-1.19-2.368-0.008
Interaction energy analysis for fragmet #1(C:333:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.921
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].
3C335LEU00.0720.0483.8420.3031.553-0.020-0.479-0.752-0.001
4C336CYS0-0.126-0.0364.165-5.240-5.167-0.002-0.022-0.0490.000
29C362VAL00.0670.0392.240-0.3020.0171.938-0.689-1.567-0.007
5C337PRO00.0070.0198.7732.0512.0510.0000.0000.0000.000
6C338PHE00.053-0.00611.9771.7991.7990.0000.0000.0000.000
7C339GLY00.0430.02514.3581.4101.4100.0000.0000.0000.000
8C340GLU-1-0.827-0.92814.837-18.965-18.9650.0000.0000.0000.000
9C341VAL0-0.043-0.01216.4770.5010.5010.0000.0000.0000.000
10C342PHE00.010-0.00916.8810.8850.8850.0000.0000.0000.000
11C343ASN0-0.065-0.03619.5640.6600.6600.0000.0000.0000.000
12C344ALA00.0390.04221.2380.3860.3860.0000.0000.0000.000
13C345SER00.0370.00922.7330.4940.4940.0000.0000.0000.000
14C346LYS10.9130.94826.28810.67810.6780.0000.0000.0000.000
15C347PHE00.0420.03223.024-0.434-0.4340.0000.0000.0000.000
16C348ALA00.0080.01726.8760.3720.3720.0000.0000.0000.000
17C349SER00.0250.00028.6650.2490.2490.0000.0000.0000.000
18C350VAL00.0100.01130.898-0.235-0.2350.0000.0000.0000.000
19C351TYR0-0.0030.00132.089-0.134-0.1340.0000.0000.0000.000
20C352ALA0-0.052-0.02431.1570.0030.0030.0000.0000.0000.000
21C353TRP0-0.0240.01224.944-0.548-0.5480.0000.0000.0000.000
22C354ASN00.0540.02423.1300.0970.0970.0000.0000.0000.000
23C355ARG10.7780.89820.73513.88713.8870.0000.0000.0000.000
24C356LYS10.8280.93214.31020.22320.2230.0000.0000.0000.000
25C357ARG10.9060.94714.66918.56018.5600.0000.0000.0000.000
26C358ILE0-0.014-0.01110.711-0.786-0.7860.0000.0000.0000.000
27C359SER00.012-0.0149.9811.7781.7780.0000.0000.0000.000
28C360ASN00.0150.0155.7390.9690.9690.0000.0000.0000.000
30C363ALA0-0.008-0.0265.4511.9341.9340.0000.0000.0000.000
31C364ASP-1-0.715-0.8209.028-20.164-20.1640.0000.0000.0000.000
32C365TYR0-0.004-0.02210.6420.6830.6830.0000.0000.0000.000
33C366SER0-0.017-0.02213.9121.7871.7870.0000.0000.0000.000
34C367VAL0-0.023-0.01112.7701.2221.2220.0000.0000.0000.000
35C368LEU0-0.038-0.01414.2030.7760.7760.0000.0000.0000.000
36C369TYR0-0.029-0.01217.3000.9350.9350.0000.0000.0000.000
37C370ASN00.025-0.01119.0180.8530.8530.0000.0000.0000.000
38C371SER0-0.0020.03219.5760.5960.5960.0000.0000.0000.000
39C372THR0-0.051-0.03221.0790.5310.5310.0000.0000.0000.000
40C373SER0-0.036-0.01123.9710.6090.6090.0000.0000.0000.000
41C374PHE0-0.053-0.03220.3400.1120.1120.0000.0000.0000.000
42C375SER0-0.018-0.00826.2180.3230.3230.0000.0000.0000.000
43C376THR0-0.070-0.04427.6910.3950.3950.0000.0000.0000.000
44C377PHE00.0430.02319.543-0.333-0.3330.0000.0000.0000.000
45C378LYS10.9390.97425.54010.20510.2050.0000.0000.0000.000
46C379CYS0-0.049-0.02821.5590.1580.1580.0000.0000.0000.000
47C380TYR00.0020.00225.5340.1790.1790.0000.0000.0000.000
48C381GLY00.0360.02925.141-0.323-0.3230.0000.0000.0000.000
49C382VAL00.000-0.00619.401-0.039-0.0390.0000.0000.0000.000
50C383SER0-0.027-0.00822.2200.0370.0370.0000.0000.0000.000
51C384PRO00.0660.01119.088-0.521-0.5210.0000.0000.0000.000
52C385THR0-0.010-0.01117.495-0.791-0.7910.0000.0000.0000.000
53C386LYS10.9360.95917.12312.00912.0090.0000.0000.0000.000
54C387LEU00.0170.01715.6300.0940.0940.0000.0000.0000.000
55C388ASN0-0.081-0.04511.445-2.022-2.0220.0000.0000.0000.000
56C389ASP-1-0.881-0.93211.382-19.349-19.3490.0000.0000.0000.000
57C390LEU0-0.050-0.01913.0330.8360.8360.0000.0000.0000.000
58C391CYS0-0.033-0.0197.2532.7372.7370.0000.0000.0000.000
59C392PHE00.0300.00213.3231.0991.0990.0000.0000.0000.000
60C393THR0-0.0350.00713.075-1.207-1.2070.0000.0000.0000.000
61C394ASN0-0.029-0.02413.375-2.346-2.3460.0000.0000.0000.000
62C395VAL00.0270.02612.5940.8390.8390.0000.0000.0000.000
63C396TYR0-0.059-0.04715.311-0.525-0.5250.0000.0000.0000.000
64C397ALA00.0190.01517.2860.1320.1320.0000.0000.0000.000
65C398ASP-1-0.752-0.85618.974-13.133-13.1330.0000.0000.0000.000
66C399SER0-0.028-0.01922.419-0.155-0.1550.0000.0000.0000.000
67C400PHE0-0.022-0.01624.2860.2450.2450.0000.0000.0000.000
68C401VAL00.0110.01727.929-0.160-0.1600.0000.0000.0000.000
69C402VAL0-0.005-0.00130.8570.1830.1830.0000.0000.0000.000
70C403LYS10.8400.91833.8317.7657.7650.0000.0000.0000.000
71C404GLY00.0480.02135.261-0.181-0.1810.0000.0000.0000.000
72C405ASP-1-0.914-0.96536.340-7.914-7.9140.0000.0000.0000.000
73C406GLU-1-0.784-0.87636.114-8.180-8.1800.0000.0000.0000.000
74C407VAL00.0010.00231.601-0.172-0.1720.0000.0000.0000.000
75C408ARG10.8600.93232.4197.8267.8260.0000.0000.0000.000
76C409GLN00.000-0.00534.873-0.065-0.0650.0000.0000.0000.000
77C410ILE0-0.045-0.00228.289-0.078-0.0780.0000.0000.0000.000
78C411ALA00.011-0.01530.182-0.262-0.2620.0000.0000.0000.000
79C412PRO00.0370.03629.7260.2050.2050.0000.0000.0000.000
80C413GLY00.007-0.00232.3780.1760.1760.0000.0000.0000.000
81C414GLN0-0.097-0.01934.7200.4480.4480.0000.0000.0000.000
82C415THR0-0.020-0.01936.8060.0210.0210.0000.0000.0000.000
83C416GLY00.011-0.00439.5100.0210.0210.0000.0000.0000.000
84C417VAL00.0400.01138.888-0.190-0.1900.0000.0000.0000.000
85C418ILE00.0070.02033.683-0.115-0.1150.0000.0000.0000.000
86C419ALA00.0510.02534.428-0.195-0.1950.0000.0000.0000.000
87C420ASP-1-0.792-0.88135.441-8.096-8.0960.0000.0000.0000.000
88C421TYR0-0.021-0.02737.9220.0350.0350.0000.0000.0000.000
89C422ASN0-0.059-0.03434.055-0.058-0.0580.0000.0000.0000.000
90C423TYR00.003-0.04325.019-0.120-0.1200.0000.0000.0000.000
91C424LYS10.9200.99531.7789.0829.0820.0000.0000.0000.000
92C425LEU00.0060.00926.907-0.303-0.3030.0000.0000.0000.000
93C426PRO0-0.007-0.00527.9700.4200.4200.0000.0000.0000.000
94C427ASP-1-0.843-0.95430.609-9.159-9.1590.0000.0000.0000.000
95C428ASP-1-0.958-0.96928.632-10.632-10.6320.0000.0000.0000.000
96C429PHE0-0.046-0.02424.085-0.474-0.4740.0000.0000.0000.000
97C430THR00.024-0.01121.5110.0850.0850.0000.0000.0000.000
98C431GLY0-0.0010.01021.351-0.710-0.7100.0000.0000.0000.000
99C433VAL00.0100.01122.964-0.301-0.3010.0000.0000.0000.000
100C434ILE0-0.005-0.00320.3190.0670.0670.0000.0000.0000.000
101C435ALA00.0140.01024.2560.0370.0370.0000.0000.0000.000
102C436TRP00.0190.00522.879-0.028-0.0280.0000.0000.0000.000
103C437ASN0-0.030-0.00728.4470.0610.0610.0000.0000.0000.000
104C438SER00.012-0.02529.618-0.141-0.1410.0000.0000.0000.000
105C439VAL00.0380.02431.3890.0630.0630.0000.0000.0000.000
106C440LYS10.9310.95332.1039.2089.2080.0000.0000.0000.000
107C441GLN0-0.016-0.00526.477-0.006-0.0060.0000.0000.0000.000
108C442ASP-1-0.745-0.79431.006-10.424-10.4240.0000.0000.0000.000
109C443ALA00.0040.01434.0480.2080.2080.0000.0000.0000.000
110C444LEU00.0090.01037.094-0.048-0.0480.0000.0000.0000.000
111C445THR00.004-0.01840.1540.0830.0830.0000.0000.0000.000
112C446GLY00.0050.01143.757-0.002-0.0020.0000.0000.0000.000
113C447GLY00.0050.00842.7800.0920.0920.0000.0000.0000.000
114C448ASN0-0.093-0.06535.5530.0890.0890.0000.0000.0000.000
115C449TYR0-0.006-0.00539.739-0.040-0.0400.0000.0000.0000.000
116C450GLY00.0170.00537.3460.0770.0770.0000.0000.0000.000
117C451TYR0-0.077-0.05630.855-0.240-0.2400.0000.0000.0000.000
118C452LEU00.019-0.00535.4810.2530.2530.0000.0000.0000.000
119C453TYR0-0.049-0.05535.555-0.377-0.3770.0000.0000.0000.000
120C454ARG10.8040.90036.3008.6308.6300.0000.0000.0000.000
121C455LEU0-0.0110.01739.546-0.078-0.0780.0000.0000.0000.000
122C456PHE00.0170.00042.7630.0930.0930.0000.0000.0000.000
123C457ARG10.8720.90738.0658.1178.1170.0000.0000.0000.000
124C458LYS10.9620.98843.1166.7666.7660.0000.0000.0000.000
125C459SER00.0130.00842.4370.1100.1100.0000.0000.0000.000
126C460LYS10.8780.93639.6087.6687.6680.0000.0000.0000.000
127C461LEU0-0.042-0.01033.8960.0580.0580.0000.0000.0000.000
128C462LYS10.9220.97433.9908.7838.7830.0000.0000.0000.000
129C463PRO00.032-0.00530.497-0.075-0.0750.0000.0000.0000.000
130C464PHE00.0080.01223.922-0.291-0.2910.0000.0000.0000.000
131C465GLU-1-0.882-0.93828.446-10.069-10.0690.0000.0000.0000.000
132C466ARG10.8180.91125.18711.71111.7110.0000.0000.0000.000
133C467ASP-1-0.786-0.86331.268-8.328-8.3280.0000.0000.0000.000
134C468ILE00.013-0.00131.5200.0310.0310.0000.0000.0000.000
135C469SER0-0.046-0.03235.1620.1600.1600.0000.0000.0000.000
136C470THR00.005-0.01138.778-0.018-0.0180.0000.0000.0000.000
137C471GLU-1-0.932-0.95541.405-6.840-6.8400.0000.0000.0000.000
138C472ILE0-0.027-0.01844.576-0.060-0.0600.0000.0000.0000.000
139C473TYR0-0.004-0.00645.914-0.016-0.0160.0000.0000.0000.000
140C474GLN00.016-0.01047.9730.1900.1900.0000.0000.0000.000
141C475ALA0-0.016-0.01351.170-0.053-0.0530.0000.0000.0000.000
142C476GLY0-0.0180.00252.5950.0830.0830.0000.0000.0000.000
143C477SER0-0.018-0.01655.064-0.043-0.0430.0000.0000.0000.000
144C478THR0-0.0040.00857.2500.0850.0850.0000.0000.0000.000
145C479PRO00.006-0.00154.807-0.104-0.1040.0000.0000.0000.000
146C480CYS00.0130.01352.201-0.012-0.0120.0000.0000.0000.000
147C481ASN0-0.029-0.02153.703-0.070-0.0700.0000.0000.0000.000
148C482GLY00.0350.02749.934-0.017-0.0170.0000.0000.0000.000
149C483GLN00.0030.01250.253-0.190-0.1900.0000.0000.0000.000
150C484VAL0-0.025-0.01550.179-0.006-0.0060.0000.0000.0000.000
151C485GLY00.011-0.01452.9650.1170.1170.0000.0000.0000.000
152C486LEU0-0.0050.00355.638-0.068-0.0680.0000.0000.0000.000
153C487ASN0-0.017-0.00755.009-0.031-0.0310.0000.0000.0000.000
154C489TYR00.0810.03649.1690.0810.0810.0000.0000.0000.000
155C490TYR00.0400.01741.084-0.082-0.0820.0000.0000.0000.000
156C491PRO0-0.033-0.00142.7310.0110.0110.0000.0000.0000.000
157C492LEU0-0.037-0.01938.184-0.191-0.1910.0000.0000.0000.000
158C493GLU-1-0.827-0.88841.483-6.963-6.9630.0000.0000.0000.000
159C494ARG10.9040.95440.0266.9756.9750.0000.0000.0000.000
160C495TYR0-0.012-0.02935.1980.0820.0820.0000.0000.0000.000
161C496GLY00.0420.01540.133-0.002-0.0020.0000.0000.0000.000
162C497PHE0-0.0120.00335.4000.0970.0970.0000.0000.0000.000
163C498HIS00.0490.01839.9320.0600.0600.0000.0000.0000.000
164C499PRO0-0.020-0.01039.540-0.042-0.0420.0000.0000.0000.000
165C500THR00.002-0.00140.703-0.084-0.0840.0000.0000.0000.000
166C501THR0-0.021-0.00241.1180.0780.0780.0000.0000.0000.000
167C502GLY00.0730.04041.884-0.095-0.0950.0000.0000.0000.000
168C503VAL00.0370.00636.995-0.082-0.0820.0000.0000.0000.000
169C504ASN00.000-0.00938.363-0.238-0.2380.0000.0000.0000.000
170C505TYR00.013-0.01140.291-0.024-0.0240.0000.0000.0000.000
171C506GLN0-0.0090.01736.783-0.259-0.2590.0000.0000.0000.000
172C507PRO00.0010.00833.602-0.036-0.0360.0000.0000.0000.000
173C508PHE00.012-0.00131.168-0.052-0.0520.0000.0000.0000.000
174C509ARG10.7580.87026.22711.46811.4680.0000.0000.0000.000
175C510VAL0-0.007-0.01126.400-0.042-0.0420.0000.0000.0000.000
176C511VAL0-0.012-0.01019.816-0.168-0.1680.0000.0000.0000.000
177C512VAL0-0.013-0.00522.8320.2100.2100.0000.0000.0000.000
178C513LEU0-0.0020.00516.179-0.463-0.4630.0000.0000.0000.000
179C514SER0-0.017-0.00819.1060.6250.6250.0000.0000.0000.000
180C515PHE00.0590.01914.907-1.154-1.1540.0000.0000.0000.000
181C516GLU-1-0.779-0.85517.827-14.876-14.8760.0000.0000.0000.000
182C517LEU00.009-0.00717.703-1.070-1.0700.0000.0000.0000.000
183C518LEU00.0430.02218.9140.8220.8220.0000.0000.0000.000
184C519ASN0-0.027-0.02819.607-0.453-0.4530.0000.0000.0000.000
185C520GLY0-0.0010.01217.0360.1370.1370.0000.0000.0000.000
186C521PRO0-0.005-0.00812.3420.3410.3410.0000.0000.0000.000
187C522ALA00.0240.00912.176-0.125-0.1250.0000.0000.0000.000
188C523THR0-0.038-0.0348.104-3.176-3.1760.0000.0000.0000.000
189C524VAL0-0.071-0.0406.823-4.608-4.6080.0000.0000.0000.000
190C526GLY-1-0.884-0.9236.222-39.063-39.0630.0000.0000.0000.000