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: 8GQYY

Calculation Name: 1CFB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | sulfate ion

Ligand 3-letter code: NAG | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CFB

Chain ID: A

ChEMBL ID:

UniProt ID: P20241

Base Structure: X-ray

Registration Date: 2025-09-02

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2096197.859482
FMO2-HF: Nuclear repulsion 2015855.499018
FMO2-HF: Total energy -80342.360463
FMO2-MP2: Total energy -80579.249888


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(A:610:ILE)


Summations of interaction energy for fragment #1(A:610:ILE)
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.
-54.302-48.0022.954-3.219-6.035-0.028
Interaction energy analysis for fragmet #1(A:610:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.911
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].
3A612GLN0-0.052-0.0342.4080.6423.8951.185-1.504-2.934-0.011
4A613ASP-1-0.824-0.8945.016-23.760-23.653-0.001-0.010-0.0960.000
32A641ARG10.8960.9292.27536.24737.5271.151-0.640-1.791-0.004
33A642SER0-0.013-0.0032.753-8.527-6.8670.619-1.065-1.214-0.013
5A614VAL00.0070.0168.571-0.934-0.9340.0000.0000.0000.000
6A615PRO0-0.051-0.01410.922-0.751-0.7510.0000.0000.0000.000
7A616ASN0-0.012-0.01811.8540.6650.6650.0000.0000.0000.000
8A617ALA0-0.0060.00214.2790.2030.2030.0000.0000.0000.000
9A618PRO0-0.044-0.02217.725-0.050-0.0500.0000.0000.0000.000
10A619LYS10.8630.92619.12912.80612.8060.0000.0000.0000.000
11A620LEU0-0.015-0.00521.934-0.029-0.0290.0000.0000.0000.000
12A621THR0-0.045-0.03723.9840.1700.1700.0000.0000.0000.000
13A622GLY00.0300.01726.6740.3140.3140.0000.0000.0000.000
14A623ILE0-0.038-0.02229.381-0.262-0.2620.0000.0000.0000.000
15A624THR0-0.0120.01832.0950.2760.2760.0000.0000.0000.000
16A625CYS0-0.027-0.00634.996-0.046-0.0460.0000.0000.0000.000
17A626GLN0-0.006-0.01236.6780.0710.0710.0000.0000.0000.000
18A627ALA0-0.018-0.01940.164-0.021-0.0210.0000.0000.0000.000
19A628ASP-1-0.795-0.88041.178-7.276-7.2760.0000.0000.0000.000
20A629LYS10.8270.91436.3307.4847.4840.0000.0000.0000.000
21A630ALA00.0490.02134.0630.1370.1370.0000.0000.0000.000
22A631GLU-1-0.856-0.89930.020-9.558-9.5580.0000.0000.0000.000
23A632ILE0-0.010-0.00426.4560.0680.0680.0000.0000.0000.000
24A633HIS00.001-0.01126.361-0.423-0.4230.0000.0000.0000.000
25A634TRP0-0.051-0.02619.4830.2210.2210.0000.0000.0000.000
26A635GLU-1-0.814-0.88719.831-12.607-12.6070.0000.0000.0000.000
27A636GLN00.0320.01613.556-0.723-0.7230.0000.0000.0000.000
28A637GLN0-0.018-0.01915.5340.5890.5890.0000.0000.0000.000
29A638GLY00.0210.02211.315-0.458-0.4580.0000.0000.0000.000
30A639ASP-1-0.823-0.9227.165-29.177-29.1770.0000.0000.0000.000
31A640ASN0-0.047-0.0337.448-2.060-2.0600.0000.0000.0000.000
34A643PRO00.0080.0175.3952.3662.3660.0000.0000.0000.000
35A644ILE00.027-0.0028.1170.4670.4670.0000.0000.0000.000
36A645LEU0-0.061-0.02410.6770.2490.2490.0000.0000.0000.000
37A646HIS0-0.028-0.00313.6620.5360.5360.0000.0000.0000.000
38A647TYR00.0130.00416.676-1.088-1.0880.0000.0000.0000.000
39A648THR0-0.040-0.01819.3310.2040.2040.0000.0000.0000.000
40A649ILE0-0.0010.01622.497-0.204-0.2040.0000.0000.0000.000
41A650GLN00.0730.03325.3820.0840.0840.0000.0000.0000.000
42A651PHE0-0.020-0.01927.7150.0330.0330.0000.0000.0000.000
43A652ASN00.0550.05631.265-0.063-0.0630.0000.0000.0000.000
44A653THR00.0350.00134.0560.1780.1780.0000.0000.0000.000
45A654SER00.001-0.01437.822-0.004-0.0040.0000.0000.0000.000
46A655PHE0-0.0130.01440.9450.1000.1000.0000.0000.0000.000
47A656THR0-0.0010.00337.3550.1000.1000.0000.0000.0000.000
48A657PRO00.0200.02236.786-0.252-0.2520.0000.0000.0000.000
49A658ALA0-0.009-0.01134.771-0.227-0.2270.0000.0000.0000.000
50A659SER0-0.027-0.00633.448-0.230-0.2300.0000.0000.0000.000
51A660TRP0-0.040-0.03228.861-0.120-0.1200.0000.0000.0000.000
52A661ASP-1-0.879-0.92529.715-9.255-9.2550.0000.0000.0000.000
53A662ALA0-0.012-0.02127.943-0.204-0.2040.0000.0000.0000.000
54A663ALA0-0.030-0.01328.7810.2970.2970.0000.0000.0000.000
55A664TYR00.022-0.00625.5330.3550.3550.0000.0000.0000.000
56A665GLU-1-0.933-0.96323.996-11.919-11.9190.0000.0000.0000.000
57A666LYS10.8760.93419.95613.40513.4050.0000.0000.0000.000
58A667VAL00.0250.03421.6760.1380.1380.0000.0000.0000.000
59A668PRO00.0500.01719.597-0.803-0.8030.0000.0000.0000.000
60A669ASN0-0.033-0.03313.4920.9180.9180.0000.0000.0000.000
61A670THR0-0.042-0.02316.969-0.398-0.3980.0000.0000.0000.000
62A671ASP-1-0.892-0.93818.985-11.689-11.6890.0000.0000.0000.000
63A672SER0-0.024-0.02820.382-0.392-0.3920.0000.0000.0000.000
64A673SER0-0.045-0.02922.5590.1170.1170.0000.0000.0000.000
65A674PHE00.017-0.00325.672-0.169-0.1690.0000.0000.0000.000
66A675VAL0-0.0120.00327.7550.1760.1760.0000.0000.0000.000
67A676VAL0-0.016-0.00230.065-0.122-0.1220.0000.0000.0000.000
68A677GLN00.007-0.00932.7910.1390.1390.0000.0000.0000.000
69A678MET0-0.067-0.03035.924-0.203-0.2030.0000.0000.0000.000
70A679SER00.012-0.00138.4010.1710.1710.0000.0000.0000.000
71A680PRO00.0110.01741.536-0.045-0.0450.0000.0000.0000.000
72A681TRP0-0.038-0.02344.8360.0170.0170.0000.0000.0000.000
73A682ALA00.0380.02640.852-0.018-0.0180.0000.0000.0000.000
74A683ASN0-0.024-0.00340.0700.0730.0730.0000.0000.0000.000
75A684TYR00.0390.02634.7610.0310.0310.0000.0000.0000.000
76A685THR0-0.047-0.02332.6870.1180.1180.0000.0000.0000.000
77A686PHE00.0410.00529.231-0.087-0.0870.0000.0000.0000.000
78A687ARG10.8640.93625.45410.94610.9460.0000.0000.0000.000
79A688VAL00.0210.01420.7070.0360.0360.0000.0000.0000.000
80A689ILE0-0.0120.00318.662-0.216-0.2160.0000.0000.0000.000
81A690ALA00.0440.01814.8710.2040.2040.0000.0000.0000.000
82A691PHE00.015-0.00414.677-0.272-0.2720.0000.0000.0000.000
83A692ASN00.020-0.0038.5870.8610.8610.0000.0000.0000.000
84A693LYS10.9190.9528.35926.20026.2000.0000.0000.0000.000
85A694ILE0-0.049-0.0086.8190.0330.0330.0000.0000.0000.000
86A695GLY00.0290.00910.6821.3771.3770.0000.0000.0000.000
87A696ALA00.0010.00513.724-0.405-0.4050.0000.0000.0000.000
88A697SER00.0050.00215.275-0.349-0.3490.0000.0000.0000.000
89A698PRO00.005-0.00516.1600.8200.8200.0000.0000.0000.000
90A699PRO0-0.010-0.00819.168-0.249-0.2490.0000.0000.0000.000
91A700SER0-0.0180.00421.827-0.023-0.0230.0000.0000.0000.000
92A701ALA00.002-0.00222.9180.3190.3190.0000.0000.0000.000
93A702HIS0-0.059-0.02726.245-0.173-0.1730.0000.0000.0000.000
94A703SER0-0.015-0.01928.891-0.006-0.0060.0000.0000.0000.000
95A704ASP-1-0.865-0.91930.879-8.572-8.5720.0000.0000.0000.000
96A705SER0-0.022-0.01634.372-0.099-0.0990.0000.0000.0000.000
97A707THR0-0.006-0.01738.152-0.034-0.0340.0000.0000.0000.000
98A708THR0-0.033-0.03340.6360.0610.0610.0000.0000.0000.000
99A709GLN0-0.021-0.02143.2440.2100.2100.0000.0000.0000.000
100A710PRO00.006-0.00946.682-0.065-0.0650.0000.0000.0000.000
101A711ASP-1-0.890-0.94048.655-6.034-6.0340.0000.0000.0000.000
102A712VAL00.0300.02450.350-0.003-0.0030.0000.0000.0000.000
103A713PRO0-0.024-0.00849.129-0.156-0.1560.0000.0000.0000.000
104A714PHE0-0.009-0.01944.4210.0380.0380.0000.0000.0000.000
105A715LYS10.8150.90543.9276.8016.8010.0000.0000.0000.000
106A716ASN00.0550.04748.6260.1130.1130.0000.0000.0000.000
107A717PRO00.019-0.00449.203-0.119-0.1190.0000.0000.0000.000
108A718ASP-1-0.806-0.87345.192-6.682-6.6820.0000.0000.0000.000
109A719ASN0-0.072-0.04545.9830.0530.0530.0000.0000.0000.000
110A720VAL00.0290.02550.1970.0480.0480.0000.0000.0000.000
111A721VAL0-0.0020.00153.4550.0300.0300.0000.0000.0000.000
112A722GLY00.0120.00456.1350.0290.0290.0000.0000.0000.000
113A723GLN0-0.021-0.03559.560-0.051-0.0510.0000.0000.0000.000
114A724GLY00.0530.04061.311-0.018-0.0180.0000.0000.0000.000
115A725THR0-0.053-0.03560.435-0.065-0.0650.0000.0000.0000.000
116A726GLU-1-0.926-0.95663.136-4.666-4.6660.0000.0000.0000.000
117A727PRO0-0.010-0.00366.8710.0090.0090.0000.0000.0000.000
118A728ASN0-0.019-0.01769.7610.0310.0310.0000.0000.0000.000
119A729ASN00.0300.03264.630-0.003-0.0030.0000.0000.0000.000
120A730LEU00.0190.00762.957-0.014-0.0140.0000.0000.0000.000
121A731VAL0-0.030-0.01059.2630.0120.0120.0000.0000.0000.000
122A732ILE00.0130.00958.471-0.036-0.0360.0000.0000.0000.000
123A733SER0-0.028-0.02154.686-0.040-0.0400.0000.0000.0000.000
124A734TRP00.0040.00251.6600.0660.0660.0000.0000.0000.000
125A735THR00.014-0.00845.688-0.056-0.0560.0000.0000.0000.000
126A736PRO0-0.061-0.03347.7050.0130.0130.0000.0000.0000.000
127A737MET00.0260.04446.229-0.088-0.0880.0000.0000.0000.000
128A738PRO00.0220.00641.8880.0730.0730.0000.0000.0000.000
129A739GLU-1-0.881-0.97343.999-6.694-6.6940.0000.0000.0000.000
130A740ILE0-0.0030.00739.1030.0820.0820.0000.0000.0000.000
131A741GLU-1-0.826-0.91642.499-7.007-7.0070.0000.0000.0000.000
132A742HIS10.8290.92344.9226.6116.6110.0000.0000.0000.000
133A743ASN00.0150.01545.9340.0750.0750.0000.0000.0000.000
134A744ALA00.005-0.00447.7840.0240.0240.0000.0000.0000.000
135A745PRO00.0020.00550.629-0.031-0.0310.0000.0000.0000.000
136A746ASN0-0.042-0.04452.7190.0360.0360.0000.0000.0000.000
137A747PHE0-0.0040.01050.3330.0750.0750.0000.0000.0000.000
138A748HIS10.8130.91853.4535.3835.3830.0000.0000.0000.000
139A749TYR00.0500.00650.458-0.056-0.0560.0000.0000.0000.000
140A750TYR0-0.039-0.02056.0990.1200.1200.0000.0000.0000.000
141A751VAL00.0170.02058.317-0.053-0.0530.0000.0000.0000.000
142A752SER00.004-0.01360.5050.0650.0650.0000.0000.0000.000
143A753TRP0-0.020-0.01562.751-0.113-0.1130.0000.0000.0000.000
144A754LYS10.9420.98565.3174.6914.6910.0000.0000.0000.000
145A755ARG10.9680.99567.7074.3054.3050.0000.0000.0000.000
146A756ASP-1-0.849-0.91468.112-4.580-4.5800.0000.0000.0000.000
147A757ILE0-0.014-0.00970.0150.0530.0530.0000.0000.0000.000
148A758PRO00.001-0.01473.320-0.024-0.0240.0000.0000.0000.000
149A759ALA0-0.019-0.01874.9230.0370.0370.0000.0000.0000.000
150A760ALA0-0.0110.02472.0170.0190.0190.0000.0000.0000.000
151A761ALA0-0.009-0.01271.792-0.051-0.0510.0000.0000.0000.000
152A762TRP0-0.050-0.02863.847-0.014-0.0140.0000.0000.0000.000
153A763GLU-1-0.876-0.92968.658-4.468-4.4680.0000.0000.0000.000
154A764ASN0-0.003-0.00864.938-0.131-0.1310.0000.0000.0000.000
155A765ASN0-0.016-0.00462.707-0.007-0.0070.0000.0000.0000.000
156A766ASN00.000-0.00160.913-0.120-0.1200.0000.0000.0000.000
157A767ILE00.0010.01456.5370.0380.0380.0000.0000.0000.000
158A768PHE00.021-0.01856.830-0.080-0.0800.0000.0000.0000.000
159A769ASP-1-0.876-0.91353.295-5.951-5.9510.0000.0000.0000.000
160A770TRP0-0.016-0.01445.243-0.006-0.0060.0000.0000.0000.000
161A771ARG10.9470.97846.4786.3666.3660.0000.0000.0000.000
162A772GLN0-0.025-0.00650.941-0.029-0.0290.0000.0000.0000.000
163A773ASN00.0140.00251.4260.0800.0800.0000.0000.0000.000
164A774ASN0-0.016-0.02053.5530.0880.0880.0000.0000.0000.000
165A775ILE0-0.0030.01157.1610.0190.0190.0000.0000.0000.000
166A776VAL00.0200.01460.934-0.013-0.0130.0000.0000.0000.000
167A777ILE0-0.0140.00363.7040.0500.0500.0000.0000.0000.000
168A778ALA00.0420.01266.921-0.008-0.0080.0000.0000.0000.000
169A779ASP-1-0.897-0.94569.826-4.293-4.2930.0000.0000.0000.000
170A780GLN0-0.0110.02469.0950.0480.0480.0000.0000.0000.000
171A781PRO0-0.029-0.02072.3380.0290.0290.0000.0000.0000.000
172A782THR00.0120.00970.786-0.068-0.0680.0000.0000.0000.000
173A783PHE0-0.0120.00566.3140.0760.0760.0000.0000.0000.000
174A784VAL0-0.046-0.01669.8360.0550.0550.0000.0000.0000.000
175A785LYS10.8820.92265.1104.6674.6670.0000.0000.0000.000
176A786TYR0-0.056-0.06865.1110.0820.0820.0000.0000.0000.000
177A787LEU0-0.044-0.00763.643-0.059-0.0590.0000.0000.0000.000
178A788ILE00.0270.00459.4410.0610.0610.0000.0000.0000.000
179A789LYS10.8590.94058.8544.9884.9880.0000.0000.0000.000
180A790VAL00.008-0.00154.9810.0450.0450.0000.0000.0000.000
181A791VAL0-0.012-0.00255.352-0.088-0.0880.0000.0000.0000.000
182A792ALA00.0200.01151.9260.0080.0080.0000.0000.0000.000
183A793ILE0-0.015-0.01853.8950.0350.0350.0000.0000.0000.000
184A794ASN0-0.037-0.03650.9730.0650.0650.0000.0000.0000.000
185A795ASP-1-0.821-0.90554.866-5.411-5.4110.0000.0000.0000.000
186A796ARG10.8100.91351.7495.8975.8970.0000.0000.0000.000
187A797GLY00.0080.01155.8030.0590.0590.0000.0000.0000.000
188A798GLU-1-0.940-0.97655.813-5.297-5.2970.0000.0000.0000.000
189A799SER0-0.017-0.02651.615-0.024-0.0240.0000.0000.0000.000
190A800ASN0-0.023-0.00848.8780.0580.0580.0000.0000.0000.000
191A801VAL0-0.013-0.00449.408-0.016-0.0160.0000.0000.0000.000
192A802ALA00.0040.00552.7600.0440.0440.0000.0000.0000.000
193A803ALA0-0.018-0.00554.652-0.072-0.0720.0000.0000.0000.000
194A804GLU-1-0.920-0.96353.747-5.607-5.6070.0000.0000.0000.000
195A805GLU-1-0.895-0.95956.562-4.869-4.8690.0000.0000.0000.000
196A806VAL00.0070.01355.9280.0320.0320.0000.0000.0000.000
197A807VAL0-0.016-0.01558.9920.0960.0960.0000.0000.0000.000
198A808GLY0-0.0050.00760.512-0.092-0.0920.0000.0000.0000.000
199A809TYR0-0.015-0.01562.5550.1120.1120.0000.0000.0000.000
200A810SER0-0.002-0.01564.423-0.070-0.0700.0000.0000.0000.000
201A811GLY00.0160.00667.0370.0380.0380.0000.0000.0000.000
202A812GLU-1-0.928-0.96163.336-4.932-4.9320.0000.0000.0000.000
203A813ASP-1-0.947-0.95762.599-4.891-4.8910.0000.0000.0000.000
204A814ARG0-0.139-0.07859.4290.3110.3110.0000.0000.0000.000