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: Q585Y

Calculation Name: 5THF-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | beta-d-mannopyranose

Ligand 3-letter code: NAG | BMA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5THF

Chain ID: B

ChEMBL ID:

UniProt ID: Q91MA7

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1502518.015339
FMO2-HF: Nuclear repulsion 1432132.227551
FMO2-HF: Total energy -70385.787789
FMO2-MP2: Total energy -70589.546078


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:1:GLY)


Summations of interaction energy for fragment #1(B:1:GLY)
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.
-290.564-285.30511.501-8.883-7.872-0.105
Interaction energy analysis for fragmet #1(B:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.895
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].
3B3PHE0-0.045-0.0203.52012.42413.728-0.005-0.579-0.720-0.002
4B4GLY00.0100.0202.83410.18210.7110.016-0.214-0.330-0.001
5B5ALA00.0230.0254.1279.6559.802-0.001-0.013-0.1320.000
6B6ILE0-0.017-0.0284.1625.3205.444-0.001-0.019-0.1040.000
7B7ALA0-0.048-0.0253.243-19.938-18.9130.071-0.553-0.542-0.005
8B8GLY0-0.007-0.0034.987-4.750-4.734-0.001-0.003-0.0110.000
108B108ILE00.0170.0232.876-1.664-1.2990.122-0.198-0.289-0.001
109B109ASP-1-0.792-0.9012.389-78.839-77.2082.914-2.438-2.106-0.026
110B110LEU0-0.058-0.0254.0711.0460.998-0.001-0.0140.0620.000
112B112ASP-1-0.720-0.8611.899-111.417-111.2448.388-4.850-3.710-0.070
113B113SER0-0.0250.0035.1415.7495.742-0.001-0.0020.0100.000
9B9PHE0-0.030-0.0056.0954.9174.9170.0000.0000.0000.000
10B10ILE0-0.047-0.0217.8243.9463.9460.0000.0000.0000.000
11B11GLU-1-0.917-0.9598.484-24.457-24.4570.0000.0000.0000.000
12B12ASN0-0.060-0.04410.444-0.493-0.4930.0000.0000.0000.000
13B13GLY00.0250.02111.4930.2570.2570.0000.0000.0000.000
14B14TRP0-0.006-0.02612.4941.5881.5880.0000.0000.0000.000
15B15GLU-1-0.869-0.94016.260-16.517-16.5170.0000.0000.0000.000
16B16GLY0-0.030-0.01018.3240.6980.6980.0000.0000.0000.000
17B17MET0-0.084-0.01817.5770.3750.3750.0000.0000.0000.000
18B18ILE00.002-0.00118.800-0.526-0.5260.0000.0000.0000.000
19B19ASP-1-0.915-0.96021.301-13.963-13.9630.0000.0000.0000.000
20B20GLY0-0.029-0.02519.0550.3290.3290.0000.0000.0000.000
21B21TRP0-0.016-0.01612.871-0.564-0.5640.0000.0000.0000.000
22B22TYR00.001-0.0069.525-0.683-0.6830.0000.0000.0000.000
23B23GLY00.011-0.00514.6101.5021.5020.0000.0000.0000.000
24B24PHE00.0070.00816.329-0.877-0.8770.0000.0000.0000.000
25B25ARG10.8720.93018.85816.41816.4180.0000.0000.0000.000
26B26HIS00.0010.00720.769-0.751-0.7510.0000.0000.0000.000
27B27GLN00.024-0.00223.661-0.089-0.0890.0000.0000.0000.000
28B28ASN0-0.016-0.00426.3840.0030.0030.0000.0000.0000.000
29B29SER0-0.010-0.01329.6410.0650.0650.0000.0000.0000.000
30B30GLU-1-0.911-0.95132.461-9.081-9.0810.0000.0000.0000.000
31B31GLY0-0.0050.01631.2490.1150.1150.0000.0000.0000.000
32B32THR0-0.006-0.01726.190-0.234-0.2340.0000.0000.0000.000
33B33GLY0-0.010-0.00225.7580.3980.3980.0000.0000.0000.000
34B34GLN00.000-0.00620.815-0.933-0.9330.0000.0000.0000.000
35B35ALA00.0110.00921.6920.6400.6400.0000.0000.0000.000
36B36ALA00.0620.04619.300-0.765-0.7650.0000.0000.0000.000
37B37ASP-1-0.806-0.88417.345-16.128-16.1280.0000.0000.0000.000
38B38LEU00.0350.01018.305-0.784-0.7840.0000.0000.0000.000
39B39LYS10.9420.97319.88314.63714.6370.0000.0000.0000.000
40B40SER00.021-0.01914.266-0.329-0.3290.0000.0000.0000.000
41B41THR0-0.0060.00215.094-1.236-1.2360.0000.0000.0000.000
42B42GLN0-0.035-0.02316.497-0.268-0.2680.0000.0000.0000.000
43B43ALA0-0.0010.00715.5050.0470.0470.0000.0000.0000.000
44B44ALA00.0220.02512.353-0.476-0.4760.0000.0000.0000.000
45B45ILE00.0090.01013.7180.0580.0580.0000.0000.0000.000
46B46ASP-1-0.856-0.93216.675-14.576-14.5760.0000.0000.0000.000
47B47GLN0-0.117-0.06712.621-0.282-0.2820.0000.0000.0000.000
48B48ILE0-0.012-0.00611.286-0.060-0.0600.0000.0000.0000.000
49B49ASN00.0190.00515.2190.5420.5420.0000.0000.0000.000
50B50GLY0-0.025-0.01118.6380.7010.7010.0000.0000.0000.000
51B51LYS10.7450.86611.68823.77123.7710.0000.0000.0000.000
52B52LEU00.0290.01317.4320.5300.5300.0000.0000.0000.000
53B53ASN0-0.007-0.02119.3420.6410.6410.0000.0000.0000.000
54B54ARG10.8200.90116.95316.68216.6820.0000.0000.0000.000
55B55VAL0-0.0080.00318.6770.3240.3240.0000.0000.0000.000
56B56ILE0-0.029-0.00821.9630.4920.4920.0000.0000.0000.000
57B57GLU-1-0.806-0.86724.966-10.287-10.2870.0000.0000.0000.000
58B58LYS10.7400.83827.06010.68610.6860.0000.0000.0000.000
59B59THR00.0160.00329.150-0.132-0.1320.0000.0000.0000.000
60B60ASN0-0.023-0.01831.432-0.058-0.0580.0000.0000.0000.000
61B61GLU-1-0.825-0.88733.516-7.727-7.7270.0000.0000.0000.000
62B62LYS10.8130.87937.1478.0338.0330.0000.0000.0000.000
63B63PHE00.0120.00839.6330.0020.0020.0000.0000.0000.000
64B64HIS00.0170.01942.814-0.120-0.1200.0000.0000.0000.000
65B65GLN0-0.054-0.03739.512-0.303-0.3030.0000.0000.0000.000
66B66ILE0-0.0010.01041.3170.1560.1560.0000.0000.0000.000
67B67GLU-1-0.890-0.94043.974-6.807-6.8070.0000.0000.0000.000
68B68LYS10.7900.87138.3297.9397.9390.0000.0000.0000.000
69B69GLU-1-0.963-0.97042.712-7.427-7.4270.0000.0000.0000.000
70B70PHE00.006-0.01244.7370.0820.0820.0000.0000.0000.000
71B71SER0-0.042-0.03848.707-0.076-0.0760.0000.0000.0000.000
72B72GLU-1-0.889-0.91251.812-5.764-5.7640.0000.0000.0000.000
73B73VAL0-0.029-0.01551.474-0.129-0.1290.0000.0000.0000.000
74B74GLU-1-0.864-0.92151.481-6.024-6.0240.0000.0000.0000.000
75B75GLY0-0.022-0.00150.4580.0810.0810.0000.0000.0000.000
76B76ARG10.9580.95949.4916.0806.0800.0000.0000.0000.000
77B77ILE0-0.022-0.00148.576-0.086-0.0860.0000.0000.0000.000
78B78GLN00.0570.01246.983-0.240-0.2400.0000.0000.0000.000
79B79ASP-1-0.930-0.97145.373-6.796-6.7960.0000.0000.0000.000
80B80LEU0-0.047-0.02042.921-0.195-0.1950.0000.0000.0000.000
81B81GLU-1-0.898-0.96142.631-6.872-6.8720.0000.0000.0000.000
82B82LYS10.8980.95241.5116.7716.7710.0000.0000.0000.000
83B83TYR00.0090.01237.334-0.188-0.1880.0000.0000.0000.000
84B84VAL0-0.026-0.00837.988-0.252-0.2520.0000.0000.0000.000
85B85GLU-1-0.750-0.85536.953-8.718-8.7180.0000.0000.0000.000
86B86ASP-1-0.931-0.96135.402-9.027-9.0270.0000.0000.0000.000
87B87THR00.012-0.00833.588-0.339-0.3390.0000.0000.0000.000
88B88LYS10.8070.88732.2188.3728.3720.0000.0000.0000.000
89B89ILE00.0030.00031.187-0.363-0.3630.0000.0000.0000.000
90B90ASP-1-0.855-0.90529.061-10.516-10.5160.0000.0000.0000.000
91B91LEU0-0.060-0.03427.446-0.524-0.5240.0000.0000.0000.000
92B92TRP0-0.037-0.02526.106-0.607-0.6070.0000.0000.0000.000
93B93SER0-0.012-0.00925.477-0.476-0.4760.0000.0000.0000.000
94B94TYR0-0.021-0.00821.448-0.798-0.7980.0000.0000.0000.000
95B95ASN0-0.039-0.03121.655-0.872-0.8720.0000.0000.0000.000
96B96ALA0-0.013-0.00221.164-0.648-0.6480.0000.0000.0000.000
97B97GLU-1-0.913-0.95418.650-16.332-16.3320.0000.0000.0000.000
98B98LEU0-0.011-0.01216.399-1.167-1.1670.0000.0000.0000.000
99B99LEU0-0.025-0.00516.168-1.170-1.1700.0000.0000.0000.000
100B100VAL00.010-0.00415.600-1.241-1.2410.0000.0000.0000.000
101B101ALA00.0020.01212.935-1.630-1.6300.0000.0000.0000.000
102B102LEU0-0.010-0.01011.366-2.388-2.3880.0000.0000.0000.000
103B103GLU-1-0.766-0.86211.142-21.047-21.0470.0000.0000.0000.000
104B104ASN00.0060.00210.596-1.300-1.3000.0000.0000.0000.000
105B105GLN0-0.0210.0014.807-0.132-0.1320.0000.0000.0000.000
106B106HIS00.0490.0266.166-4.024-4.0240.0000.0000.0000.000
107B107THR00.0140.0027.739-0.860-0.8600.0000.0000.0000.000
111B111THR0-0.010-0.0306.8200.4670.4670.0000.0000.0000.000
114B114GLU-1-0.836-0.9207.748-20.087-20.0870.0000.0000.0000.000
115B115MET0-0.0120.0227.4023.0153.0150.0000.0000.0000.000
116B116ASN00.0260.0077.6211.9391.9390.0000.0000.0000.000
117B117LYS10.8170.8979.50327.06727.0670.0000.0000.0000.000
118B118LEU0-0.029-0.00612.5652.1102.1100.0000.0000.0000.000
119B119PHE00.0140.03412.0161.5611.5610.0000.0000.0000.000
120B120GLU-1-0.773-0.89612.950-20.880-20.8800.0000.0000.0000.000
121B121LYS10.8030.90015.40517.87017.8700.0000.0000.0000.000
122B122THR0-0.039-0.02517.1211.3491.3490.0000.0000.0000.000
123B123GLY00.0640.02817.7870.8610.8610.0000.0000.0000.000
124B124ARG10.7960.87816.20318.98218.9820.0000.0000.0000.000
125B125GLN0-0.049-0.02721.4111.1941.1940.0000.0000.0000.000
126B126LEU00.0240.01321.0370.6100.6100.0000.0000.0000.000
127B127ARG10.8790.95123.72811.99811.9980.0000.0000.0000.000
128B128GLU-1-0.877-0.92324.705-12.079-12.0790.0000.0000.0000.000
129B129ASN0-0.007-0.03026.7630.3060.3060.0000.0000.0000.000
130B130ALA0-0.007-0.01623.0510.1680.1680.0000.0000.0000.000
131B131GLU-1-0.812-0.86422.085-12.508-12.5080.0000.0000.0000.000
132B132ASP-1-0.865-0.94115.280-20.501-20.5010.0000.0000.0000.000
133B133MET0-0.061-0.02918.0630.6890.6890.0000.0000.0000.000
134B134GLY0-0.021-0.00314.9540.2200.2200.0000.0000.0000.000
135B135ASN0-0.004-0.01312.780-1.188-1.1880.0000.0000.0000.000
136B136GLY00.0240.01212.797-0.500-0.5000.0000.0000.0000.000
137B137CYS0-0.058-0.01013.4991.1231.1230.0000.0000.0000.000
138B138PHE00.009-0.00316.7190.1520.1520.0000.0000.0000.000
139B139LYS10.9500.97519.90312.39012.3900.0000.0000.0000.000
140B140ILE00.005-0.00423.2870.1090.1090.0000.0000.0000.000
141B141TYR0-0.071-0.05225.3540.3660.3660.0000.0000.0000.000
142B142HIS00.0300.03329.1700.0630.0630.0000.0000.0000.000
143B143LYS10.9240.94530.7388.2488.2480.0000.0000.0000.000
144B144CYS0-0.0380.01528.654-0.300-0.3000.0000.0000.0000.000
145B145ASP-1-0.823-0.90930.260-9.694-9.6940.0000.0000.0000.000
146B146ASN00.020-0.00630.139-0.725-0.7250.0000.0000.0000.000
147B147ALA00.0480.03630.135-0.301-0.3010.0000.0000.0000.000
148B149ILE00.0170.00624.996-0.471-0.4710.0000.0000.0000.000
149B150GLU-1-0.965-0.99226.000-10.996-10.9960.0000.0000.0000.000
150B151SER0-0.062-0.03527.278-0.235-0.2350.0000.0000.0000.000
151B152ILE00.0180.01122.424-0.302-0.3020.0000.0000.0000.000
152B153ARG10.8740.95522.42012.00112.0010.0000.0000.0000.000
153B154ASN0-0.0250.00323.274-0.376-0.3760.0000.0000.0000.000
154B155GLY0-0.028-0.00224.8520.0980.0980.0000.0000.0000.000
155B156THR0-0.084-0.06325.6230.3540.3540.0000.0000.0000.000
156B157TYR0-0.027-0.01926.5660.3380.3380.0000.0000.0000.000
157B158ASP-1-0.873-0.94028.553-9.792-9.7920.0000.0000.0000.000
158B159HIS0-0.046-0.04628.308-0.187-0.1870.0000.0000.0000.000
159B160ASP-1-0.841-0.91930.183-9.504-9.5040.0000.0000.0000.000
160B161VAL0-0.059-0.02033.8040.2420.2420.0000.0000.0000.000
161B162TYR00.011-0.00731.2180.2450.2450.0000.0000.0000.000
162B163ARG10.9290.98930.00710.01810.0180.0000.0000.0000.000
163B164ASP-1-0.909-0.95633.167-8.605-8.6050.0000.0000.0000.000
164B165GLU-1-0.904-0.95134.563-9.172-9.1720.0000.0000.0000.000
165B166ALA0-0.0050.00129.792-0.052-0.0520.0000.0000.0000.000
166B167LEU00.001-0.00630.910-0.162-0.1620.0000.0000.0000.000
167B168ASN0-0.045-0.01232.8100.1500.1500.0000.0000.0000.000
168B169ASN0-0.056-0.04032.6090.2660.2660.0000.0000.0000.000
169B170ARG10.7400.85826.36111.66411.6640.0000.0000.0000.000
170B171PHE0-0.093-0.05129.600-0.083-0.0830.0000.0000.0000.000
171B172GLN0-0.0130.00333.6850.3970.3970.0000.0000.0000.000
172B173ILE-1-0.967-0.97135.364-8.406-8.4060.0000.0000.0000.000