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About

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: 856QY

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2125277.317566
FMO2-HF: Nuclear repulsion 2043985.119546
FMO2-HF: Total energy -81292.19802
FMO2-MP2: Total energy -81522.323158


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.
-9.038-4.9851.967-2.435-3.5840.02
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 : 0.051 / q_NPA : 0.018
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].
3D3GLN0-0.024-0.0062.297-8.157-4.5881.960-2.247-3.2820.020
4D4LEU00.005-0.0055.556-0.564-0.5640.0000.0000.0000.000
5D5VAL0-0.0020.0099.1960.2070.2070.0000.0000.0000.000
6D6GLN00.013-0.03611.476-0.167-0.1670.0000.0000.0000.000
7D7SER0-0.0500.00115.1250.0540.0540.0000.0000.0000.000
8D8GLY00.0400.01418.129-0.044-0.0440.0000.0000.0000.000
9D9ALA00.007-0.04019.3390.0410.0410.0000.0000.0000.000
10D10GLU-1-0.885-0.92022.2430.2310.2310.0000.0000.0000.000
11D11MET0-0.0020.01625.8910.0000.0000.0000.0000.0000.000
12D12LYS10.8500.91727.921-0.204-0.2040.0000.0000.0000.000
13D13LYS10.9080.96831.785-0.129-0.1290.0000.0000.0000.000
14D14PRO00.0530.00334.7640.0020.0020.0000.0000.0000.000
15D15GLY0-0.0190.00936.359-0.003-0.0030.0000.0000.0000.000
16D16ALA0-0.0350.00133.458-0.004-0.0040.0000.0000.0000.000
17D17SER0-0.016-0.04831.299-0.003-0.0030.0000.0000.0000.000
18D18VAL0-0.064-0.01525.8120.0050.0050.0000.0000.0000.000
19D19LYS10.9080.93324.387-0.127-0.1270.0000.0000.0000.000
20D20VAL00.0070.02318.9860.0250.0250.0000.0000.0000.000
21D21SER00.003-0.00318.214-0.032-0.0320.0000.0000.0000.000
22D22CYS0-0.084-0.01413.9710.0430.0430.0000.0000.0000.000
23D23LYS10.8650.92811.049-0.211-0.2110.0000.0000.0000.000
24D24ALA00.0440.03210.1670.1410.1410.0000.0000.0000.000
25D25SER00.026-0.0085.6330.3590.3590.0000.0000.0000.000
26D26GLY00.0190.0123.642-0.601-0.3060.008-0.155-0.1480.000
27D27TYR00.0070.0004.252-0.0990.090-0.001-0.033-0.1540.000
28D28THR00.0020.0016.9800.1860.1860.0000.0000.0000.000
29D29PHE00.0230.01210.5990.0660.0660.0000.0000.0000.000
30D30ILE00.0330.00012.7720.0480.0480.0000.0000.0000.000
31D31GLY0-0.0040.00213.9200.0430.0430.0000.0000.0000.000
32D32TYR0-0.035-0.01510.743-0.042-0.0420.0000.0000.0000.000
33D33HIS0-0.041-0.02014.5720.0080.0080.0000.0000.0000.000
34D34LEU00.0020.00113.840-0.023-0.0230.0000.0000.0000.000
35D35HIS00.0220.00616.8250.0260.0260.0000.0000.0000.000
36D36TRP00.0360.01417.9770.0500.0500.0000.0000.0000.000
37D37VAL0-0.015-0.00419.813-0.024-0.0240.0000.0000.0000.000
38D38ARG10.8200.90420.800-0.102-0.1020.0000.0000.0000.000
39D39GLN0-0.025-0.02122.0710.0120.0120.0000.0000.0000.000
40D40ALA00.0480.03424.5420.0160.0160.0000.0000.0000.000
41D41PRO00.022-0.00927.1870.0080.0080.0000.0000.0000.000
42D42GLY00.0000.00727.723-0.015-0.0150.0000.0000.0000.000
43D43GLN0-0.022-0.00128.218-0.019-0.0190.0000.0000.0000.000
44D44GLY00.0360.01926.3670.0160.0160.0000.0000.0000.000
45D45LEU0-0.015-0.01220.7410.0090.0090.0000.0000.0000.000
46D46GLU-1-0.743-0.86524.6130.0910.0910.0000.0000.0000.000
47D47TRP0-0.028-0.00821.7430.0150.0150.0000.0000.0000.000
48D48MET0-0.043-0.02023.923-0.001-0.0010.0000.0000.0000.000
49D49GLY00.0710.01523.862-0.011-0.0110.0000.0000.0000.000
50D50TRP0-0.040-0.00820.7530.0070.0070.0000.0000.0000.000
51D51ILE00.0080.00019.8310.0010.0010.0000.0000.0000.000
52D52ASN00.0000.00519.830-0.035-0.0350.0000.0000.0000.000
53D53PRO00.0410.02516.0320.0250.0250.0000.0000.0000.000
54D54ASN00.0380.02818.900-0.004-0.0040.0000.0000.0000.000
55D55SER0-0.056-0.02220.3480.0160.0160.0000.0000.0000.000
56D56GLY0-0.026-0.01522.7970.0090.0090.0000.0000.0000.000
57D57GLU-1-0.910-0.95024.240-0.033-0.0330.0000.0000.0000.000
58D58THR0-0.033-0.01924.401-0.004-0.0040.0000.0000.0000.000
59D59ASN0-0.021-0.01525.5640.0020.0020.0000.0000.0000.000
60D60TYR00.0770.02826.2240.0120.0120.0000.0000.0000.000
61D61ALA00.0260.02328.434-0.006-0.0060.0000.0000.0000.000
62D62GLN00.048-0.00130.0800.0050.0050.0000.0000.0000.000
63D63LYS10.8490.92431.386-0.097-0.0970.0000.0000.0000.000
64D64PHE0-0.002-0.02628.4340.0050.0050.0000.0000.0000.000
65D65GLN0-0.0380.00131.430-0.002-0.0020.0000.0000.0000.000
66D66ASP-1-0.842-0.91233.1860.0410.0410.0000.0000.0000.000
67D67TRP0-0.025-0.02633.0490.0030.0030.0000.0000.0000.000
68D68VAL0-0.047-0.02126.9770.0120.0120.0000.0000.0000.000
69D69THR00.0080.00828.389-0.010-0.0100.0000.0000.0000.000
70D70MET0-0.0320.00023.3180.0110.0110.0000.0000.0000.000
71D71THR00.0280.00923.615-0.013-0.0130.0000.0000.0000.000
72D72ARG10.8430.91819.1850.0760.0760.0000.0000.0000.000
73D73ASP-1-0.803-0.89219.390-0.002-0.0020.0000.0000.0000.000
74D74THR0-0.030-0.03618.018-0.002-0.0020.0000.0000.0000.000
75D75SER0-0.0080.00317.122-0.044-0.0440.0000.0000.0000.000
76D76ILE0-0.028-0.00615.876-0.025-0.0250.0000.0000.0000.000
77D77ASN0-0.025-0.01112.4230.0160.0160.0000.0000.0000.000
78D78THR00.0330.01313.8030.0140.0140.0000.0000.0000.000
79D79ALA0-0.005-0.01116.388-0.041-0.0410.0000.0000.0000.000
80D80TYR00.016-0.00318.4750.0650.0650.0000.0000.0000.000
81D81MET0-0.0390.00321.368-0.030-0.0300.0000.0000.0000.000
82D82GLU-1-0.767-0.86623.3190.1200.1200.0000.0000.0000.000
83D83LEU00.006-0.00126.917-0.012-0.0120.0000.0000.0000.000
84D84ARG10.8980.94729.087-0.079-0.0790.0000.0000.0000.000
85D85LEU0-0.057-0.02029.3530.0000.0000.0000.0000.0000.000
86D86ARG10.9390.96833.209-0.091-0.0910.0000.0000.0000.000
87D87SER0-0.090-0.04834.682-0.004-0.0040.0000.0000.0000.000
88D88ASP-1-0.842-0.90334.6430.1040.1040.0000.0000.0000.000
89D89ASP-1-0.868-0.92330.1840.1210.1210.0000.0000.0000.000
90D90THR00.0060.02229.0510.0160.0160.0000.0000.0000.000
91D91ALA00.0050.00025.760-0.007-0.0070.0000.0000.0000.000
92D92VAL0-0.0020.00620.0840.0120.0120.0000.0000.0000.000
93D93TYR0-0.001-0.03721.161-0.026-0.0260.0000.0000.0000.000
94D94TYR00.0090.01815.9310.0640.0640.0000.0000.0000.000
95D96ALA00.0420.00113.3480.0750.0750.0000.0000.0000.000
96D97ARG10.8190.9258.4790.5570.5570.0000.0000.0000.000
97D98GLY0-0.005-0.00613.0520.0220.0220.0000.0000.0000.000
98D99GLY0-0.018-0.01712.607-0.070-0.0700.0000.0000.0000.000
99D100MET0-0.004-0.00213.429-0.045-0.0450.0000.0000.0000.000
100D101THR00.0220.00815.7490.0260.0260.0000.0000.0000.000
101D102MET00.0260.01118.1830.0170.0170.0000.0000.0000.000
102D103VAL00.0060.01520.2880.0160.0160.0000.0000.0000.000
103D104ARG10.8660.92919.9290.0950.0950.0000.0000.0000.000
104D105GLY00.0540.01320.0350.0070.0070.0000.0000.0000.000
105D106VAL00.0050.01815.2950.0230.0230.0000.0000.0000.000
106D107MET0-0.013-0.00114.820-0.048-0.0480.0000.0000.0000.000
107D108MET0-0.035-0.0069.6900.0490.0490.0000.0000.0000.000
108D109ASP-1-0.768-0.8757.000-0.358-0.3580.0000.0000.0000.000
109D110TRP00.006-0.0179.883-0.091-0.0910.0000.0000.0000.000
110D111GLY00.0310.02810.0060.1860.1860.0000.0000.0000.000
111D112GLN0-0.0020.00711.9420.0710.0710.0000.0000.0000.000
112D113GLY0-0.0010.00813.390-0.069-0.0690.0000.0000.0000.000
113D114THR0-0.061-0.03816.8480.0360.0360.0000.0000.0000.000
114D115LEU0-0.0160.00219.721-0.038-0.0380.0000.0000.0000.000
115D116VAL00.0070.00523.1240.0010.0010.0000.0000.0000.000
116D117THR00.007-0.00126.117-0.014-0.0140.0000.0000.0000.000
117D118VAL00.0020.00229.531-0.004-0.0040.0000.0000.0000.000
118D119SER00.0240.00332.740-0.009-0.0090.0000.0000.0000.000
119D120SER00.0580.00835.8600.0030.0030.0000.0000.0000.000
120D121ALA00.0010.01937.143-0.004-0.0040.0000.0000.0000.000
121D122SER0-0.012-0.02536.9230.0040.0040.0000.0000.0000.000
122D123THR0-0.032-0.00431.9630.0030.0030.0000.0000.0000.000
123D124LYS10.9070.95633.736-0.161-0.1610.0000.0000.0000.000
124D125GLY00.0440.02932.2960.0130.0130.0000.0000.0000.000
125D126PRO0-0.028-0.01629.275-0.010-0.0100.0000.0000.0000.000
126D127SER0-0.027-0.00832.478-0.008-0.0080.0000.0000.0000.000
127D128VAL0-0.013-0.01629.8680.0000.0000.0000.0000.0000.000
128D129PHE00.001-0.00933.125-0.009-0.0090.0000.0000.0000.000
129D130PRO0-0.017-0.01732.9030.0010.0010.0000.0000.0000.000
130D131LEU00.0050.01934.054-0.009-0.0090.0000.0000.0000.000
131D132ALA0-0.012-0.00635.3880.0020.0020.0000.0000.0000.000
132D133PRO00.0380.02134.8440.0010.0010.0000.0000.0000.000
133D144ALA0-0.008-0.03232.1140.0010.0010.0000.0000.0000.000
134D145LEU0-0.035-0.01029.880-0.004-0.0040.0000.0000.0000.000
135D146GLY00.0140.01429.4210.0080.0080.0000.0000.0000.000
136D147CYS0-0.067-0.01525.3310.0020.0020.0000.0000.0000.000
137D148LEU00.0470.02931.3550.0040.0040.0000.0000.0000.000
138D149VAL0-0.0110.00428.297-0.004-0.0040.0000.0000.0000.000
139D150LYS10.8850.92631.748-0.140-0.1400.0000.0000.0000.000
140D151ASP-1-0.803-0.89234.5710.1410.1410.0000.0000.0000.000
141D152TYR0-0.007-0.02329.155-0.002-0.0020.0000.0000.0000.000
142D153PHE00.0560.02932.227-0.005-0.0050.0000.0000.0000.000
143D154PRO0-0.019-0.01528.984-0.003-0.0030.0000.0000.0000.000
144D155GLU-1-0.753-0.86526.7590.2820.2820.0000.0000.0000.000
145D156PRO0-0.028-0.01922.278-0.002-0.0020.0000.0000.0000.000
146D157VAL0-0.002-0.02024.415-0.007-0.0070.0000.0000.0000.000
147D158THR0-0.0290.00518.8860.0180.0180.0000.0000.0000.000
148D159VAL00.008-0.01321.827-0.016-0.0160.0000.0000.0000.000
149D160SER00.0030.01418.7370.0230.0230.0000.0000.0000.000
150D161TRP00.0440.02320.682-0.039-0.0390.0000.0000.0000.000
151D162ASN00.0380.01620.6590.0020.0020.0000.0000.0000.000
152D163SER00.0160.01317.6810.0230.0230.0000.0000.0000.000
153D164GLY00.0240.01716.1300.0640.0640.0000.0000.0000.000
154D165ALA0-0.035-0.01516.470-0.005-0.0050.0000.0000.0000.000
155D166LEU0-0.039-0.01318.730-0.033-0.0330.0000.0000.0000.000
156D167THR00.0280.01815.7920.0290.0290.0000.0000.0000.000
157D168SER00.0350.01918.5680.0110.0110.0000.0000.0000.000
158D169GLY00.006-0.01121.509-0.006-0.0060.0000.0000.0000.000
159D170VAL0-0.040-0.01920.725-0.012-0.0120.0000.0000.0000.000
160D171HIS00.0210.01323.4690.0230.0230.0000.0000.0000.000
161D172THR0-0.033-0.02622.464-0.003-0.0030.0000.0000.0000.000
162D173PHE0-0.0040.00125.3040.0070.0070.0000.0000.0000.000
163D174PRO00.0370.00227.5140.0120.0120.0000.0000.0000.000
164D175ALA0-0.0100.00428.485-0.013-0.0130.0000.0000.0000.000
165D176VAL0-0.003-0.01130.366-0.008-0.0080.0000.0000.0000.000
166D177LEU0-0.049-0.02234.1540.0020.0020.0000.0000.0000.000
167D178GLN0-0.013-0.00436.175-0.014-0.0140.0000.0000.0000.000
168D179SER00.036-0.00139.3360.0000.0000.0000.0000.0000.000
169D180SER0-0.024-0.01840.187-0.002-0.0020.0000.0000.0000.000
170D181GLY00.0210.01739.556-0.002-0.0020.0000.0000.0000.000
171D182LEU0-0.080-0.02936.0560.0090.0090.0000.0000.0000.000
172D183TYR00.0300.01431.894-0.004-0.0040.0000.0000.0000.000
173D184SER0-0.078-0.03632.881-0.004-0.0040.0000.0000.0000.000
174D185LEU00.0420.06126.767-0.004-0.0040.0000.0000.0000.000
175D186SER00.019-0.00930.626-0.002-0.0020.0000.0000.0000.000
176D187SER0-0.023-0.02825.9520.0290.0290.0000.0000.0000.000
177D188VAL00.0310.01227.877-0.011-0.0110.0000.0000.0000.000
178D189VAL00.0460.04225.1790.0150.0150.0000.0000.0000.000
179D190THR00.010-0.01427.691-0.010-0.0100.0000.0000.0000.000
180D191VAL00.0160.02429.3490.0000.0000.0000.0000.0000.000
181D192PRO0-0.0140.00431.045-0.009-0.0090.0000.0000.0000.000
182D200THR0-0.026-0.01130.473-0.001-0.0010.0000.0000.0000.000
183D201TYR00.0220.01226.1500.0070.0070.0000.0000.0000.000
184D202ILE00.011-0.00624.296-0.015-0.0150.0000.0000.0000.000
185D204ASN0-0.014-0.02220.730-0.049-0.0490.0000.0000.0000.000
186D205VAL00.0200.01123.2650.0300.0300.0000.0000.0000.000
187D206ASN0-0.001-0.01721.5460.0140.0140.0000.0000.0000.000
188D207HIS00.0100.02623.6670.0130.0130.0000.0000.0000.000
189D208LYS10.9710.97317.894-0.608-0.6080.0000.0000.0000.000
190D209PRO00.0150.01124.254-0.012-0.0120.0000.0000.0000.000
191D210SER0-0.002-0.02627.476-0.015-0.0150.0000.0000.0000.000
192D211ASN0-0.058-0.01926.0570.0060.0060.0000.0000.0000.000
193D212THR00.0150.01727.100-0.021-0.0210.0000.0000.0000.000
194D213LYS10.8520.90922.638-0.328-0.3280.0000.0000.0000.000
195D214VAL0-0.034-0.01226.625-0.021-0.0210.0000.0000.0000.000
196D215ASP-1-0.764-0.85325.4910.3130.3130.0000.0000.0000.000
197D216LYS10.8530.92428.265-0.203-0.2030.0000.0000.0000.000
198D217ARG10.8610.89729.646-0.128-0.1280.0000.0000.0000.000
199D218VAL00.0020.00830.476-0.006-0.0060.0000.0000.0000.000
200D219GLU-1-0.810-0.89632.7760.1100.1100.0000.0000.0000.000
201D220PRO00.0050.01535.478-0.002-0.0020.0000.0000.0000.000
202D221LYS10.8680.92138.345-0.104-0.1040.0000.0000.0000.000
203D222SER00.0140.00641.9680.0010.0010.0000.0000.0000.000
204D223CYS0-0.036-0.00643.9100.0030.0030.0000.0000.0000.000
205D224ASP-1-0.923-0.95346.7020.0660.0660.0000.0000.0000.000