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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: N97LQ

Calculation Name: 4XHJ-D-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4XHJ

Chain ID: D

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 OptAll
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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2130202.010117
FMO2-HF: Nuclear repulsion 2048909.152173
FMO2-HF: Total energy -81292.857944
FMO2-MP2: Total energy -81523.101707


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(D:1:GLN)


Summations of interaction energy for fragment #1(D: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.
-10.404-8.0534.596-2.93-4.0160.024
Interaction energy analysis for fragmet #1(D:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.019
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].
3D3GLN0-0.023-0.0162.058-9.464-7.4214.598-2.814-3.8270.024
4D4LEU0-0.010-0.0065.345-0.745-0.729-0.001-0.001-0.0140.000
5D5VAL00.0070.0128.7840.3280.3280.0000.0000.0000.000
6D6GLN0-0.007-0.02611.194-0.203-0.2030.0000.0000.0000.000
7D7SER0-0.0350.00214.8540.0600.0600.0000.0000.0000.000
8D8GLY00.0510.01918.043-0.052-0.0520.0000.0000.0000.000
9D9ALA0-0.013-0.02419.5850.0630.0630.0000.0000.0000.000
10D10GLU-1-0.873-0.92622.1340.2670.2670.0000.0000.0000.000
11D11MET0-0.0020.00925.8710.0000.0000.0000.0000.0000.000
12D12LYS10.8290.90627.975-0.221-0.2210.0000.0000.0000.000
13D13LYS10.9030.96032.039-0.138-0.1380.0000.0000.0000.000
14D14PRO00.0570.00335.0400.0020.0020.0000.0000.0000.000
15D15GLY0-0.0140.01136.473-0.004-0.0040.0000.0000.0000.000
16D16ALA0-0.031-0.00133.841-0.005-0.0050.0000.0000.0000.000
17D17SER0-0.025-0.03731.0650.0030.0030.0000.0000.0000.000
18D18VAL0-0.042-0.01625.7870.0060.0060.0000.0000.0000.000
19D19LYS10.8870.92724.646-0.137-0.1370.0000.0000.0000.000
20D20VAL00.0180.02319.2120.0230.0230.0000.0000.0000.000
21D21SER0-0.006-0.00318.367-0.034-0.0340.0000.0000.0000.000
22D22CYS0-0.047-0.01513.8830.0420.0420.0000.0000.0000.000
23D23LYS10.8390.93511.067-0.165-0.1650.0000.0000.0000.000
24D24ALA00.0590.03610.2960.1750.1750.0000.0000.0000.000
25D25SER0-0.008-0.0175.7850.2750.2750.0000.0000.0000.000
26D26GLY00.0570.0284.066-0.473-0.2920.000-0.101-0.0800.000
27D27TYR0-0.008-0.0044.672-0.161-0.050-0.001-0.014-0.0950.000
28D28THR00.0300.0067.4910.1960.1960.0000.0000.0000.000
29D29PHE0-0.0060.00611.1460.0920.0920.0000.0000.0000.000
30D30ILE00.028-0.00113.0250.0540.0540.0000.0000.0000.000
31D31GLY0-0.0010.00614.2510.0500.0500.0000.0000.0000.000
32D32TYR0-0.028-0.02111.159-0.052-0.0520.0000.0000.0000.000
33D33HIS00.0190.01515.2690.0060.0060.0000.0000.0000.000
34D34LEU0-0.016-0.00613.644-0.017-0.0170.0000.0000.0000.000
35D35HIS00.0320.01216.9600.0260.0260.0000.0000.0000.000
36D36TRP00.0150.00017.6630.0580.0580.0000.0000.0000.000
37D37VAL0-0.011-0.00719.338-0.031-0.0310.0000.0000.0000.000
38D38ARG10.7910.87420.627-0.138-0.1380.0000.0000.0000.000
39D39GLN00.0030.00221.8430.0220.0220.0000.0000.0000.000
40D40ALA00.0540.04524.3810.0160.0160.0000.0000.0000.000
41D41PRO00.004-0.02127.2820.0100.0100.0000.0000.0000.000
42D42GLY00.0110.01227.879-0.018-0.0180.0000.0000.0000.000
43D43GLN0-0.028-0.00327.867-0.024-0.0240.0000.0000.0000.000
44D44GLY00.0370.01725.7960.0220.0220.0000.0000.0000.000
45D45LEU0-0.017-0.01220.0370.0060.0060.0000.0000.0000.000
46D46GLU-1-0.747-0.85624.0540.1220.1220.0000.0000.0000.000
47D47TRP0-0.020-0.00721.6290.0170.0170.0000.0000.0000.000
48D48MET0-0.031-0.01223.658-0.001-0.0010.0000.0000.0000.000
49D49GLY00.0660.01123.774-0.014-0.0140.0000.0000.0000.000
50D50TRP0-0.045-0.01120.9100.0120.0120.0000.0000.0000.000
51D51ILE00.0000.00619.701-0.001-0.0010.0000.0000.0000.000
52D52ASN0-0.015-0.00320.140-0.038-0.0380.0000.0000.0000.000
53D53PRO00.0060.00316.5310.0190.0190.0000.0000.0000.000
54D54ASN00.0390.02519.442-0.003-0.0030.0000.0000.0000.000
55D55SER0-0.023-0.00320.7340.0150.0150.0000.0000.0000.000
56D56GLY0-0.029-0.01523.3330.0090.0090.0000.0000.0000.000
57D57GLU-1-0.870-0.93324.757-0.043-0.0430.0000.0000.0000.000
58D58THR0-0.032-0.01224.692-0.003-0.0030.0000.0000.0000.000
59D59ASN0-0.007-0.00325.7350.0010.0010.0000.0000.0000.000
60D60TYR00.0720.01226.2440.0150.0150.0000.0000.0000.000
61D61ALA00.0240.02128.246-0.007-0.0070.0000.0000.0000.000
62D62GLN00.0530.00629.9630.0070.0070.0000.0000.0000.000
63D63LYS10.8540.92330.966-0.129-0.1290.0000.0000.0000.000
64D64PHE0-0.007-0.02328.2430.0080.0080.0000.0000.0000.000
65D65GLN0-0.0370.00031.503-0.002-0.0020.0000.0000.0000.000
66D66ASP-1-0.854-0.91333.1890.0520.0520.0000.0000.0000.000
67D67TRP00.005-0.00632.6790.0030.0030.0000.0000.0000.000
68D68VAL0-0.040-0.01826.5990.0110.0110.0000.0000.0000.000
69D69THR0-0.0060.00227.913-0.013-0.0130.0000.0000.0000.000
70D70MET0-0.0360.01023.0390.0150.0150.0000.0000.0000.000
71D71THR00.0260.00523.137-0.015-0.0150.0000.0000.0000.000
72D72ARG10.8400.90619.1760.0870.0870.0000.0000.0000.000
73D73ASP-1-0.762-0.85719.685-0.037-0.0370.0000.0000.0000.000
74D74THR00.002-0.01417.9130.0000.0000.0000.0000.0000.000
75D75SER0-0.032-0.02317.304-0.050-0.0500.0000.0000.0000.000
76D76ILE0-0.022-0.01416.409-0.031-0.0310.0000.0000.0000.000
77D77ASN0-0.066-0.02913.054-0.043-0.0430.0000.0000.0000.000
78D78THR00.0320.01113.7970.0260.0260.0000.0000.0000.000
79D79ALA00.0170.00616.263-0.048-0.0480.0000.0000.0000.000
80D80TYR00.006-0.01018.1410.0740.0740.0000.0000.0000.000
81D81MET0-0.0180.01520.938-0.036-0.0360.0000.0000.0000.000
82D82GLU-1-0.773-0.85623.1590.1330.1330.0000.0000.0000.000
83D83LEU00.011-0.00526.662-0.012-0.0120.0000.0000.0000.000
84D84ARG10.8410.90629.004-0.092-0.0920.0000.0000.0000.000
85D85LEU0-0.020-0.00729.1030.0000.0000.0000.0000.0000.000
86D86ARG10.8570.90632.194-0.117-0.1170.0000.0000.0000.000
87D87SER0-0.050-0.02534.331-0.004-0.0040.0000.0000.0000.000
88D88ASP-1-0.842-0.92233.8640.1300.1300.0000.0000.0000.000
89D89ASP-1-0.829-0.87929.9940.1450.1450.0000.0000.0000.000
90D90THR0-0.0110.00928.9590.0190.0190.0000.0000.0000.000
91D91ALA00.000-0.00325.577-0.005-0.0050.0000.0000.0000.000
92D92VAL0-0.0040.00519.9740.0120.0120.0000.0000.0000.000
93D93TYR00.007-0.02121.011-0.034-0.0340.0000.0000.0000.000
94D94TYR00.005-0.00415.9320.0770.0770.0000.0000.0000.000
95D96ALA00.0540.00913.0990.1020.1020.0000.0000.0000.000
96D97ARG10.7940.9038.8640.5380.5380.0000.0000.0000.000
97D98GLY00.024-0.00312.9970.0240.0240.0000.0000.0000.000
98D99GLY0-0.048-0.02512.607-0.055-0.0550.0000.0000.0000.000
99D100MET00.0150.00413.286-0.060-0.0600.0000.0000.0000.000
100D101THR00.0350.01416.0400.0370.0370.0000.0000.0000.000
101D102MET00.0230.02218.4200.0180.0180.0000.0000.0000.000
102D103VAL00.0010.00420.0990.0190.0190.0000.0000.0000.000
103D104ARG10.8100.89819.8330.1030.1030.0000.0000.0000.000
104D105GLY00.0740.02920.0650.0090.0090.0000.0000.0000.000
105D106VAL0-0.0080.00015.2740.0300.0300.0000.0000.0000.000
106D107MET0-0.022-0.01015.014-0.062-0.0620.0000.0000.0000.000
107D108MET0-0.0440.0039.9070.0640.0640.0000.0000.0000.000
108D109ASP-1-0.762-0.8657.059-0.326-0.3260.0000.0000.0000.000
109D110TRP00.009-0.0209.639-0.127-0.1270.0000.0000.0000.000
110D111GLY00.0270.0229.7410.2570.2570.0000.0000.0000.000
111D112GLN0-0.018-0.01211.7420.0390.0390.0000.0000.0000.000
112D113GLY00.0350.02613.086-0.093-0.0930.0000.0000.0000.000
113D114THR0-0.087-0.06116.6030.0360.0360.0000.0000.0000.000
114D115LEU0-0.0150.00919.542-0.042-0.0420.0000.0000.0000.000
115D116VAL00.0140.00523.0260.0030.0030.0000.0000.0000.000
116D117THR00.0110.00826.005-0.017-0.0170.0000.0000.0000.000
117D118VAL0-0.002-0.00229.432-0.005-0.0050.0000.0000.0000.000
118D119SER00.0230.00432.584-0.010-0.0100.0000.0000.0000.000
119D120SER00.0530.00535.7590.0030.0030.0000.0000.0000.000
120D121ALA00.0150.03136.781-0.005-0.0050.0000.0000.0000.000
121D122SER0-0.008-0.02436.2260.0020.0020.0000.0000.0000.000
122D123THR0-0.034-0.02031.3900.0030.0030.0000.0000.0000.000
123D124LYS10.8590.91933.118-0.180-0.1800.0000.0000.0000.000
124D125GLY00.0690.03831.7560.0130.0130.0000.0000.0000.000
125D126PRO0-0.048-0.02628.923-0.013-0.0130.0000.0000.0000.000
126D127SER0-0.0300.00132.209-0.012-0.0120.0000.0000.0000.000
127D128VAL0-0.003-0.01529.7340.0070.0070.0000.0000.0000.000
128D129PHE00.002-0.00432.879-0.010-0.0100.0000.0000.0000.000
129D130PRO00.012-0.00932.2800.0060.0060.0000.0000.0000.000
130D131LEU0-0.0170.00933.588-0.009-0.0090.0000.0000.0000.000
131D132ALA0-0.004-0.00835.1130.0010.0010.0000.0000.0000.000
132D133PRO00.0100.00034.9090.0000.0000.0000.0000.0000.000
133D144ALA00.014-0.00531.8810.0010.0010.0000.0000.0000.000
134D145LEU0-0.051-0.00529.526-0.008-0.0080.0000.0000.0000.000
135D146GLY00.0480.01929.5010.0130.0130.0000.0000.0000.000
136D147CYS0-0.048-0.00624.8360.0020.0020.0000.0000.0000.000
137D148LEU00.0260.03330.7300.0110.0110.0000.0000.0000.000
138D149VAL00.001-0.00128.042-0.002-0.0020.0000.0000.0000.000
139D150LYS10.8750.90731.430-0.151-0.1510.0000.0000.0000.000
140D151ASP-1-0.758-0.85034.0800.1570.1570.0000.0000.0000.000
141D152TYR00.002-0.01428.844-0.007-0.0070.0000.0000.0000.000
142D153PHE00.0560.02932.127-0.003-0.0030.0000.0000.0000.000
143D154PRO0-0.0010.01528.839-0.004-0.0040.0000.0000.0000.000
144D155GLU-1-0.713-0.85026.3020.3230.3230.0000.0000.0000.000
145D156PRO0-0.044-0.02422.049-0.007-0.0070.0000.0000.0000.000
146D157VAL0-0.020-0.01724.548-0.002-0.0020.0000.0000.0000.000
147D158THR0-0.065-0.03319.0770.0440.0440.0000.0000.0000.000
148D159VAL00.024-0.00221.464-0.033-0.0330.0000.0000.0000.000
149D160SER0-0.0160.01318.7850.0390.0390.0000.0000.0000.000
150D161TRP00.0560.01619.987-0.050-0.0500.0000.0000.0000.000
151D162ASN00.0310.01320.2270.0030.0030.0000.0000.0000.000
152D163SER00.0070.00317.3270.0290.0290.0000.0000.0000.000
153D164GLY00.0270.01615.8010.0560.0560.0000.0000.0000.000
154D165ALA0-0.050-0.02516.5570.0010.0010.0000.0000.0000.000
155D166LEU0-0.030-0.00718.389-0.037-0.0370.0000.0000.0000.000
156D167THR00.0300.01315.0930.0140.0140.0000.0000.0000.000
157D168SER00.0120.01518.0230.0160.0160.0000.0000.0000.000
158D169GLY00.0210.00121.070-0.017-0.0170.0000.0000.0000.000
159D170VAL0-0.032-0.01220.274-0.016-0.0160.0000.0000.0000.000
160D171HIS00.0120.00523.2200.0250.0250.0000.0000.0000.000
161D172THR0-0.026-0.01421.883-0.006-0.0060.0000.0000.0000.000
162D173PHE0-0.007-0.00624.8340.0050.0050.0000.0000.0000.000
163D174PRO00.024-0.00427.1500.0160.0160.0000.0000.0000.000
164D175ALA0-0.0150.00828.139-0.014-0.0140.0000.0000.0000.000
165D176VAL0-0.002-0.00229.805-0.010-0.0100.0000.0000.0000.000
166D177LEU0-0.048-0.01833.6560.0010.0010.0000.0000.0000.000
167D178GLN00.001-0.00335.527-0.016-0.0160.0000.0000.0000.000
168D179SER00.021-0.00738.7790.0000.0000.0000.0000.0000.000
169D180SER0-0.016-0.01439.709-0.003-0.0030.0000.0000.0000.000
170D181GLY00.0100.01339.080-0.002-0.0020.0000.0000.0000.000
171D182LEU0-0.070-0.02435.8280.0100.0100.0000.0000.0000.000
172D183TYR00.0250.00831.366-0.004-0.0040.0000.0000.0000.000
173D184SER0-0.078-0.03732.384-0.009-0.0090.0000.0000.0000.000
174D185LEU00.0290.03226.4950.0000.0000.0000.0000.0000.000
175D186SER00.008-0.00530.077-0.010-0.0100.0000.0000.0000.000
176D187SER0-0.011-0.01425.5720.0340.0340.0000.0000.0000.000
177D188VAL00.0180.00927.286-0.017-0.0170.0000.0000.0000.000
178D189VAL00.0600.03424.8000.0190.0190.0000.0000.0000.000
179D190THR0-0.009-0.01327.309-0.011-0.0110.0000.0000.0000.000
180D191VAL00.0420.03828.903-0.002-0.0020.0000.0000.0000.000
181D192PRO0-0.028-0.00930.466-0.009-0.0090.0000.0000.0000.000
182D200THR0-0.018-0.00430.423-0.002-0.0020.0000.0000.0000.000
183D201TYR00.0470.01625.8500.0060.0060.0000.0000.0000.000
184D202ILE00.0030.01023.534-0.014-0.0140.0000.0000.0000.000
185D204ASN0-0.016-0.04120.701-0.056-0.0560.0000.0000.0000.000
186D205VAL00.0060.01223.0970.0400.0400.0000.0000.0000.000
187D206ASN00.010-0.01121.644-0.003-0.0030.0000.0000.0000.000
188D207HIS00.0130.03023.3690.0270.0270.0000.0000.0000.000
189D208LYS10.9680.99317.695-0.653-0.6530.0000.0000.0000.000
190D209PRO00.0210.00924.067-0.018-0.0180.0000.0000.0000.000
191D210SER0-0.010-0.02827.275-0.021-0.0210.0000.0000.0000.000
192D211ASN0-0.048-0.02025.7080.0040.0040.0000.0000.0000.000
193D212THR00.0110.01726.981-0.020-0.0200.0000.0000.0000.000
194D213LYS10.8250.89722.303-0.338-0.3380.0000.0000.0000.000
195D214VAL0-0.037-0.01826.457-0.026-0.0260.0000.0000.0000.000
196D215ASP-1-0.749-0.84724.9430.3330.3330.0000.0000.0000.000
197D216LYS10.8580.91627.769-0.217-0.2170.0000.0000.0000.000
198D217ARG10.8500.90829.056-0.127-0.1270.0000.0000.0000.000
199D218VAL00.0060.00629.937-0.007-0.0070.0000.0000.0000.000
200D219GLU-1-0.813-0.90532.2970.1120.1120.0000.0000.0000.000
201D220PRO00.0160.00835.165-0.002-0.0020.0000.0000.0000.000
202D221LYS10.8410.92238.197-0.112-0.1120.0000.0000.0000.000
203D222SER00.0300.01141.7310.0020.0020.0000.0000.0000.000
204D223CYS0-0.047-0.02243.7890.0060.0060.0000.0000.0000.000
205D224ASP-1-0.926-0.94346.3740.0740.0740.0000.0000.0000.000