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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V56Y1

Calculation Name: 4XHJ-H-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4XHJ

Chain ID: H

ChEMBL ID:

UniProt ID: Q775J3

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2117391.044846
FMO2-HF: Nuclear repulsion 2036345.003117
FMO2-HF: Total energy -81046.04173
FMO2-MP2: Total energy -81275.424822


3D Structure
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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
-8.017-3.7291.35-2.26-3.3780.018
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.017
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].
3H3GLN0-0.019-0.0032.410-7.672-3.7731.340-2.132-3.1070.018
4H4LEU0-0.007-0.0085.609-0.524-0.5240.0000.0000.0000.000
5H5VAL0-0.0040.0109.2850.2090.2090.0000.0000.0000.000
6H6GLN00.024-0.02511.531-0.160-0.1600.0000.0000.0000.000
7H7SER0-0.0410.00215.1690.0650.0650.0000.0000.0000.000
8H8GLY00.0290.00818.121-0.043-0.0430.0000.0000.0000.000
9H9ALA00.020-0.02619.2160.0380.0380.0000.0000.0000.000
10H10GLU-1-0.930-0.96822.1120.2710.2710.0000.0000.0000.000
11H11MET00.0060.02025.724-0.002-0.0020.0000.0000.0000.000
12H12LYS10.9110.95728.159-0.187-0.1870.0000.0000.0000.000
13H13LYS10.9490.98331.637-0.121-0.1210.0000.0000.0000.000
14H14PRO00.0530.00634.6680.0020.0020.0000.0000.0000.000
15H15GLY0-0.0150.01236.289-0.003-0.0030.0000.0000.0000.000
16H16ALA0-0.042-0.00333.435-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.011-0.04231.322-0.003-0.0030.0000.0000.0000.000
18H18VAL0-0.060-0.01725.7380.0050.0050.0000.0000.0000.000
19H19LYS10.8990.92824.227-0.109-0.1090.0000.0000.0000.000
20H20VAL00.0050.02418.9120.0210.0210.0000.0000.0000.000
21H21SER0-0.001-0.00618.076-0.034-0.0340.0000.0000.0000.000
22H22CYS0-0.081-0.00613.9030.0320.0320.0000.0000.0000.000
23H23LYS10.8590.92611.029-0.145-0.1450.0000.0000.0000.000
24H24ALA00.0480.03410.0090.1210.1210.0000.0000.0000.000
25H25SER00.023-0.0105.6730.3660.3660.0000.0000.0000.000
26H26GLY00.0100.0113.562-0.655-0.4460.011-0.099-0.1210.000
27H27TYR00.0180.0024.2010.0530.233-0.001-0.029-0.1500.000
28H28THR00.0020.0026.9550.1820.1820.0000.0000.0000.000
29H29PHE00.0260.01510.6270.0530.0530.0000.0000.0000.000
30H30ILE00.036-0.00312.6550.0450.0450.0000.0000.0000.000
31H31GLY0-0.010-0.00213.7220.0430.0430.0000.0000.0000.000
32H32TYR0-0.038-0.01310.640-0.037-0.0370.0000.0000.0000.000
33H33HIS0-0.046-0.02214.4440.0060.0060.0000.0000.0000.000
34H34LEU00.0000.00013.628-0.028-0.0280.0000.0000.0000.000
35H35HIS00.0180.00716.7590.0290.0290.0000.0000.0000.000
36H36TRP00.0290.00817.9430.0440.0440.0000.0000.0000.000
37H37VAL0-0.013-0.00319.735-0.022-0.0220.0000.0000.0000.000
38H38ARG10.8080.89420.768-0.093-0.0930.0000.0000.0000.000
39H39GLN0-0.007-0.01221.7870.0120.0120.0000.0000.0000.000
40H40ALA00.0470.03424.3820.0160.0160.0000.0000.0000.000
41H41PRO00.022-0.00826.8600.0080.0080.0000.0000.0000.000
42H42GLY0-0.0040.00627.185-0.015-0.0150.0000.0000.0000.000
43H43GLN0-0.019-0.00127.894-0.019-0.0190.0000.0000.0000.000
44H44GLY00.0370.01726.0590.0160.0160.0000.0000.0000.000
45H45LEU0-0.015-0.01020.5400.0080.0080.0000.0000.0000.000
46H46GLU-1-0.743-0.86224.4130.0820.0820.0000.0000.0000.000
47H47TRP0-0.029-0.00821.5560.0130.0130.0000.0000.0000.000
48H48MET0-0.044-0.02523.817-0.001-0.0010.0000.0000.0000.000
49H49GLY00.0830.02023.733-0.010-0.0100.0000.0000.0000.000
50H50TRP0-0.042-0.00820.6510.0050.0050.0000.0000.0000.000
51H51ILE00.0240.00719.7120.0020.0020.0000.0000.0000.000
52H52ASN0-0.019-0.00419.723-0.035-0.0350.0000.0000.0000.000
53H53PRO00.0410.02915.9770.0250.0250.0000.0000.0000.000
54H54ASN00.0330.02418.762-0.001-0.0010.0000.0000.0000.000
55H55SER0-0.046-0.02120.3310.0180.0180.0000.0000.0000.000
56H56GLY0-0.020-0.01622.7870.0080.0080.0000.0000.0000.000
57H57GLU-1-0.847-0.90524.266-0.013-0.0130.0000.0000.0000.000
58H58THR0-0.103-0.05724.406-0.003-0.0030.0000.0000.0000.000
59H59ASN0-0.004-0.00525.5920.0030.0030.0000.0000.0000.000
60H60TYR00.0760.02626.2340.0110.0110.0000.0000.0000.000
61H61ALA00.0210.01828.464-0.005-0.0050.0000.0000.0000.000
62H62GLN00.0560.00330.1130.0050.0050.0000.0000.0000.000
63H63LYS10.8490.92031.349-0.087-0.0870.0000.0000.0000.000
64H64PHE0-0.016-0.03328.3150.0050.0050.0000.0000.0000.000
65H65GLN0-0.0410.00431.323-0.002-0.0020.0000.0000.0000.000
66H66ASP-1-0.831-0.91033.1000.0340.0340.0000.0000.0000.000
67H67TRP0-0.043-0.03332.8940.0030.0030.0000.0000.0000.000
68H68VAL0-0.026-0.01826.7770.0120.0120.0000.0000.0000.000
69H69THR0-0.0020.00428.168-0.009-0.0090.0000.0000.0000.000
70H70MET0-0.0310.00323.2010.0100.0100.0000.0000.0000.000
71H71THR00.0230.00623.481-0.011-0.0110.0000.0000.0000.000
72H72ARG10.8420.91119.0050.0790.0790.0000.0000.0000.000
73H73ASP-1-0.810-0.88419.143-0.004-0.0040.0000.0000.0000.000
74H74THR0-0.024-0.03417.901-0.007-0.0070.0000.0000.0000.000
75H75SER0-0.014-0.00917.192-0.039-0.0390.0000.0000.0000.000
76H76ILE0-0.030-0.01015.941-0.024-0.0240.0000.0000.0000.000
77H77ASN0-0.030-0.01412.4480.0130.0130.0000.0000.0000.000
78H78THR00.0380.01513.6980.0010.0010.0000.0000.0000.000
79H79ALA0-0.001-0.00916.311-0.036-0.0360.0000.0000.0000.000
80H80TYR00.011-0.00418.4910.0600.0600.0000.0000.0000.000
81H81MET0-0.0240.01321.445-0.027-0.0270.0000.0000.0000.000
82H82GLU-1-0.783-0.88223.4180.1070.1070.0000.0000.0000.000
83H83LEU00.0180.00926.988-0.011-0.0110.0000.0000.0000.000
84H84ARG10.9000.95429.161-0.071-0.0710.0000.0000.0000.000
85H85LEU0-0.064-0.02629.2910.0000.0000.0000.0000.0000.000
86H86ARG10.9440.97033.092-0.083-0.0830.0000.0000.0000.000
87H87SER0-0.090-0.05034.502-0.004-0.0040.0000.0000.0000.000
88H88ASP-1-0.841-0.90134.5150.0970.0970.0000.0000.0000.000
89H89ASP-1-0.871-0.92430.0720.1110.1110.0000.0000.0000.000
90H90THR00.0070.02328.9440.0150.0150.0000.0000.0000.000
91H91ALA00.004-0.00125.687-0.007-0.0070.0000.0000.0000.000
92H92VAL00.0050.00820.0090.0110.0110.0000.0000.0000.000
93H93TYR0-0.018-0.04221.105-0.027-0.0270.0000.0000.0000.000
94H94TYR00.0170.02115.8390.0590.0590.0000.0000.0000.000
95H96ALA00.0470.00513.2470.0710.0710.0000.0000.0000.000
96H97ARG10.8150.9168.2970.5790.5790.0000.0000.0000.000
97H98GLY0-0.011-0.01112.9000.0250.0250.0000.0000.0000.000
98H99GLY0-0.022-0.02012.612-0.069-0.0690.0000.0000.0000.000
99H100MET00.004-0.00113.466-0.039-0.0390.0000.0000.0000.000
100H101THR00.0230.00915.8050.0230.0230.0000.0000.0000.000
101H102MET00.0200.00518.2180.0150.0150.0000.0000.0000.000
102H103VAL00.0010.01020.3140.0160.0160.0000.0000.0000.000
103H104ARG10.8750.93819.8630.0940.0940.0000.0000.0000.000
104H105GLY00.0530.01320.0190.0070.0070.0000.0000.0000.000
105H106VAL00.0070.01815.2050.0200.0200.0000.0000.0000.000
106H107MET0-0.0120.00414.837-0.037-0.0370.0000.0000.0000.000
107H108MET0-0.035-0.0089.7220.0510.0510.0000.0000.0000.000
108H109ASP-1-0.767-0.8736.976-0.399-0.3990.0000.0000.0000.000
109H110TRP00.016-0.0129.887-0.087-0.0870.0000.0000.0000.000
110H111GLY00.0290.02410.0390.1630.1630.0000.0000.0000.000
111H112GLN00.0010.01011.8940.0630.0630.0000.0000.0000.000
112H113GLY0-0.0080.00413.295-0.065-0.0650.0000.0000.0000.000
113H114THR0-0.029-0.01916.7520.0400.0400.0000.0000.0000.000
114H115LEU0-0.028-0.00519.617-0.038-0.0380.0000.0000.0000.000
115H116VAL00.0040.00123.0290.0000.0000.0000.0000.0000.000
116H117THR00.005-0.00125.980-0.015-0.0150.0000.0000.0000.000
117H118VAL0-0.005-0.00229.455-0.004-0.0040.0000.0000.0000.000
118H119SER00.0360.00732.618-0.008-0.0080.0000.0000.0000.000
119H120SER00.0570.00835.7850.0030.0030.0000.0000.0000.000
120H121ALA0-0.0130.01537.212-0.003-0.0030.0000.0000.0000.000
121H122SER00.004-0.00836.9070.0050.0050.0000.0000.0000.000
122H123THR00.006-0.00331.4850.0000.0000.0000.0000.0000.000
123H124LYS10.9190.95533.798-0.138-0.1380.0000.0000.0000.000
124H125GLY00.0520.02832.4280.0120.0120.0000.0000.0000.000
125H126PRO0-0.009-0.00629.709-0.009-0.0090.0000.0000.0000.000
126H127SER0-0.026-0.00432.927-0.006-0.0060.0000.0000.0000.000
127H128VAL0-0.010-0.02030.8950.0000.0000.0000.0000.0000.000
128H129PHE0-0.016-0.02234.113-0.008-0.0080.0000.0000.0000.000
129H130PRO0-0.039-0.02533.965-0.001-0.0010.0000.0000.0000.000
130H131LEU00.0230.00934.987-0.008-0.0080.0000.0000.0000.000
131H132ALA00.0060.00536.5800.0030.0030.0000.0000.0000.000
132H133PRO00.0300.02635.7250.0010.0010.0000.0000.0000.000
133H145LEU00.0490.01829.867-0.005-0.0050.0000.0000.0000.000
134H146GLY0-0.072-0.01032.8750.0030.0030.0000.0000.0000.000
135H147CYS0-0.070-0.02625.2220.0230.0230.0000.0000.0000.000
136H148LEU00.0670.02231.9270.0040.0040.0000.0000.0000.000
137H149VAL0-0.0110.01329.214-0.005-0.0050.0000.0000.0000.000
138H150LYS10.8510.91132.675-0.133-0.1330.0000.0000.0000.000
139H151ASP-1-0.843-0.91435.3700.1320.1320.0000.0000.0000.000
140H152TYR0-0.014-0.01129.276-0.004-0.0040.0000.0000.0000.000
141H153PHE0-0.005-0.00132.538-0.005-0.0050.0000.0000.0000.000
142H154PRO0-0.027-0.00929.3470.0000.0000.0000.0000.0000.000
143H155GLU-1-0.744-0.85226.6380.2750.2750.0000.0000.0000.000
144H156PRO0-0.036-0.03122.493-0.006-0.0060.0000.0000.0000.000
145H157VAL00.002-0.02124.838-0.008-0.0080.0000.0000.0000.000
146H158THR00.0010.01219.3030.0140.0140.0000.0000.0000.000
147H159VAL00.002-0.01522.024-0.020-0.0200.0000.0000.0000.000
148H160SER0-0.0090.00518.8040.0390.0390.0000.0000.0000.000
149H161TRP00.0470.01820.748-0.032-0.0320.0000.0000.0000.000
150H162ASN00.0360.00620.5490.0100.0100.0000.0000.0000.000
151H163SER0-0.009-0.01517.7720.0110.0110.0000.0000.0000.000
152H164GLY0-0.012-0.00216.4180.0830.0830.0000.0000.0000.000
153H165ALA0-0.0170.00816.1470.0190.0190.0000.0000.0000.000
154H166LEU0-0.063-0.02517.966-0.037-0.0370.0000.0000.0000.000
155H167THR00.0180.01615.8950.0430.0430.0000.0000.0000.000
156H168SER00.0210.00318.3480.0060.0060.0000.0000.0000.000
157H169GLY00.008-0.00921.299-0.004-0.0040.0000.0000.0000.000
158H170VAL0-0.033-0.01220.969-0.014-0.0140.0000.0000.0000.000
159H171HIS0-0.0090.00423.8780.0160.0160.0000.0000.0000.000
160H172THR0-0.018-0.01222.921-0.001-0.0010.0000.0000.0000.000
161H173PHE0-0.017-0.01025.7310.0040.0040.0000.0000.0000.000
162H174PRO00.0320.00327.8520.0120.0120.0000.0000.0000.000
163H175ALA0-0.0090.01128.839-0.011-0.0110.0000.0000.0000.000
164H176VAL0-0.0010.00130.628-0.009-0.0090.0000.0000.0000.000
165H177LEU0-0.020-0.02033.7820.0010.0010.0000.0000.0000.000
166H178GLN0-0.0120.00236.444-0.014-0.0140.0000.0000.0000.000
167H179SER00.0360.00639.573-0.002-0.0020.0000.0000.0000.000
168H180SER0-0.014-0.01140.817-0.002-0.0020.0000.0000.0000.000
169H181GLY00.0200.01539.701-0.002-0.0020.0000.0000.0000.000
170H182LEU0-0.090-0.03436.4820.0070.0070.0000.0000.0000.000
171H183TYR00.0140.00330.953-0.001-0.0010.0000.0000.0000.000
172H184SER0-0.039-0.01333.563-0.004-0.0040.0000.0000.0000.000
173H185LEU00.0470.03027.625-0.003-0.0030.0000.0000.0000.000
174H186SER00.0540.01631.4550.0010.0010.0000.0000.0000.000
175H187SER0-0.020-0.02025.9190.0140.0140.0000.0000.0000.000
176H188VAL00.0410.03028.266-0.011-0.0110.0000.0000.0000.000
177H189VAL00.0190.01124.7290.0180.0180.0000.0000.0000.000
178H190THR00.004-0.00426.050-0.017-0.0170.0000.0000.0000.000
179H191VAL0-0.011-0.00428.6200.0000.0000.0000.0000.0000.000
180H192PRO00.0010.01930.070-0.003-0.0030.0000.0000.0000.000
181H200THR0-0.010-0.00629.9620.0010.0010.0000.0000.0000.000
182H201TYR00.004-0.00425.2830.0080.0080.0000.0000.0000.000
183H202ILE00.005-0.00724.778-0.012-0.0120.0000.0000.0000.000
184H204ASN0-0.003-0.02422.1080.0040.0040.0000.0000.0000.000
185H205VAL00.0280.01823.3670.0280.0280.0000.0000.0000.000
186H206ASN0-0.011-0.01420.846-0.023-0.0230.0000.0000.0000.000
187H207HIS00.0180.02324.0790.0040.0040.0000.0000.0000.000
188H208LYS10.9310.95221.365-0.341-0.3410.0000.0000.0000.000
189H209PRO0-0.0150.00324.599-0.010-0.0100.0000.0000.0000.000
190H210SER0-0.030-0.02527.786-0.008-0.0080.0000.0000.0000.000
191H211ASN0-0.063-0.01825.9740.0140.0140.0000.0000.0000.000
192H212THR00.0280.02027.138-0.019-0.0190.0000.0000.0000.000
193H213LYS10.9330.95421.724-0.366-0.3660.0000.0000.0000.000
194H214VAL0-0.021-0.00726.784-0.020-0.0200.0000.0000.0000.000
195H215ASP-1-0.791-0.87725.8490.2920.2920.0000.0000.0000.000
196H216LYS10.8830.93728.449-0.182-0.1820.0000.0000.0000.000
197H217ARG10.8710.92229.773-0.119-0.1190.0000.0000.0000.000
198H218VAL0-0.047-0.01830.953-0.006-0.0060.0000.0000.0000.000
199H219GLU-1-0.803-0.88633.3220.1060.1060.0000.0000.0000.000
200H220PRO0-0.0050.00236.6890.0010.0010.0000.0000.0000.000
201H221LYS10.9200.95338.935-0.114-0.1140.0000.0000.0000.000
202H222SER00.0060.00942.630-0.001-0.0010.0000.0000.0000.000
203H223CYS0-0.063-0.02944.7650.0040.0040.0000.0000.0000.000
204H224ASP-1-0.912-0.94847.5400.0620.0620.0000.0000.0000.000