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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: G64V1

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 OptH
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 -2123339.900255
FMO2-HF: Nuclear repulsion 2042048.724011
FMO2-HF: Total energy -81291.176244
FMO2-MP2: Total energy -81521.287314


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.
-5.129-1.7550.304-1.341-2.3370.007
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 : -0.001 / q_NPA : -0.021
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].
3D3GLN0-0.0100.0012.777-4.555-1.6100.297-1.193-2.0490.007
4D4LEU00.003-0.0075.656-0.162-0.1620.0000.0000.0000.000
5D5VAL00.0090.0199.4150.0560.0560.0000.0000.0000.000
6D6GLN0-0.034-0.04711.573-0.100-0.1000.0000.0000.0000.000
7D7SER0-0.078-0.01615.2190.0320.0320.0000.0000.0000.000
8D8GLY00.0510.02618.224-0.026-0.0260.0000.0000.0000.000
9D9ALA0-0.002-0.04819.4180.0210.0210.0000.0000.0000.000
10D10GLU-1-0.924-0.94922.3220.2840.2840.0000.0000.0000.000
11D11MET00.0130.02625.974-0.006-0.0060.0000.0000.0000.000
12D12LYS10.8990.94828.773-0.197-0.1970.0000.0000.0000.000
13D13LYS10.9520.98531.872-0.127-0.1270.0000.0000.0000.000
14D14PRO00.0520.00534.8520.0050.0050.0000.0000.0000.000
15D15GLY0-0.0110.01336.452-0.003-0.0030.0000.0000.0000.000
16D16ALA0-0.038-0.00133.4720.0000.0000.0000.0000.0000.000
17D17SER0-0.015-0.02431.182-0.002-0.0020.0000.0000.0000.000
18D18VAL0-0.055-0.01425.8610.0020.0020.0000.0000.0000.000
19D19LYS10.9590.97524.432-0.213-0.2130.0000.0000.0000.000
20D20VAL00.0260.03819.0750.0130.0130.0000.0000.0000.000
21D21SER0-0.003-0.00618.233-0.011-0.0110.0000.0000.0000.000
22D22CYS0-0.047-0.00913.7500.0350.0350.0000.0000.0000.000
23D23LYS10.8590.92910.914-0.670-0.6700.0000.0000.0000.000
24D24ALA00.0540.03110.1710.1050.1050.0000.0000.0000.000
25D25SER0-0.018-0.0295.9770.2360.2360.0000.0000.0000.000
26D26GLY00.0520.0243.494-0.696-0.4410.008-0.133-0.1310.000
27D27TYR0-0.006-0.0044.1191.2971.471-0.001-0.015-0.1570.000
28D28THR00.0010.0017.459-0.126-0.1260.0000.0000.0000.000
29D29PHE00.0350.01011.003-0.025-0.0250.0000.0000.0000.000
30D30ILE00.0380.00212.954-0.012-0.0120.0000.0000.0000.000
31D31GLY0-0.0050.00214.431-0.028-0.0280.0000.0000.0000.000
32D32TYR0-0.043-0.01511.7540.0280.0280.0000.0000.0000.000
33D33HIS0-0.042-0.02115.128-0.001-0.0010.0000.0000.0000.000
34D34LEU00.0150.01013.9740.0230.0230.0000.0000.0000.000
35D35HIS00.0280.00316.810-0.037-0.0370.0000.0000.0000.000
36D36TRP00.0380.01718.0570.0330.0330.0000.0000.0000.000
37D37VAL0-0.011-0.00419.905-0.026-0.0260.0000.0000.0000.000
38D38ARG10.8750.96220.865-0.123-0.1230.0000.0000.0000.000
39D39GLN0-0.022-0.01322.1440.0070.0070.0000.0000.0000.000
40D40ALA00.0510.03224.5930.0100.0100.0000.0000.0000.000
41D41PRO00.017-0.01127.228-0.001-0.0010.0000.0000.0000.000
42D42GLY00.0040.01027.751-0.009-0.0090.0000.0000.0000.000
43D43GLN0-0.0220.00028.249-0.010-0.0100.0000.0000.0000.000
44D44GLY00.0250.00926.3950.0040.0040.0000.0000.0000.000
45D45LEU0-0.022-0.01820.8360.0110.0110.0000.0000.0000.000
46D46GLU-1-0.825-0.92124.6520.1100.1100.0000.0000.0000.000
47D47TRP0-0.039-0.01321.8530.0110.0110.0000.0000.0000.000
48D48MET0-0.043-0.02223.991-0.004-0.0040.0000.0000.0000.000
49D49GLY00.0720.01723.847-0.012-0.0120.0000.0000.0000.000
50D50TRP0-0.053-0.01220.6780.0160.0160.0000.0000.0000.000
51D51ILE00.0310.00819.875-0.011-0.0110.0000.0000.0000.000
52D52ASN0-0.015-0.01319.9450.0340.0340.0000.0000.0000.000
53D53PRO00.0340.03216.496-0.016-0.0160.0000.0000.0000.000
54D54ASN00.0410.01519.1520.0030.0030.0000.0000.0000.000
55D55SER0-0.067-0.02620.676-0.009-0.0090.0000.0000.0000.000
56D56GLY0-0.009-0.00323.120-0.007-0.0070.0000.0000.0000.000
57D57GLU-1-0.917-0.95224.4560.1340.1340.0000.0000.0000.000
58D58THR0-0.034-0.02224.6130.0150.0150.0000.0000.0000.000
59D59ASN0-0.025-0.01925.558-0.015-0.0150.0000.0000.0000.000
60D60TYR00.0720.03226.2100.0160.0160.0000.0000.0000.000
61D61ALA00.0310.02528.422-0.009-0.0090.0000.0000.0000.000
62D62GLN00.046-0.00230.0650.0000.0000.0000.0000.0000.000
63D63LYS10.9150.97731.706-0.104-0.1040.0000.0000.0000.000
64D64PHE00.015-0.02028.4100.0010.0010.0000.0000.0000.000
65D65GLN0-0.0060.01931.5110.0050.0050.0000.0000.0000.000
66D66ASP-1-0.851-0.92133.2380.1030.1030.0000.0000.0000.000
67D67TRP0-0.064-0.04533.0360.0000.0000.0000.0000.0000.000
68D68VAL0-0.040-0.01127.0410.0090.0090.0000.0000.0000.000
69D69THR0-0.018-0.00628.353-0.009-0.0090.0000.0000.0000.000
70D70MET0-0.042-0.00423.2700.0150.0150.0000.0000.0000.000
71D71THR00.0330.01423.644-0.006-0.0060.0000.0000.0000.000
72D72ARG10.8400.92019.085-0.201-0.2010.0000.0000.0000.000
73D73ASP-1-0.838-0.92319.2700.2410.2410.0000.0000.0000.000
74D74THR0-0.042-0.04117.8790.0250.0250.0000.0000.0000.000
75D75SER00.0040.02716.9920.0050.0050.0000.0000.0000.000
76D76ILE0-0.0060.00815.8020.0190.0190.0000.0000.0000.000
77D77ASN0-0.019-0.00411.0390.0390.0390.0000.0000.0000.000
78D78THR00.0130.00013.6890.0440.0440.0000.0000.0000.000
79D79ALA00.006-0.00416.316-0.039-0.0390.0000.0000.0000.000
80D80TYR00.006-0.01018.5010.0270.0270.0000.0000.0000.000
81D81MET0-0.0430.00221.476-0.024-0.0240.0000.0000.0000.000
82D82GLU-1-0.844-0.94323.4200.1870.1870.0000.0000.0000.000
83D83LEU00.002-0.00627.018-0.009-0.0090.0000.0000.0000.000
84D84ARG10.9320.96329.182-0.141-0.1410.0000.0000.0000.000
85D85LEU0-0.050-0.01629.540-0.003-0.0030.0000.0000.0000.000
86D86ARG10.9840.98333.296-0.114-0.1140.0000.0000.0000.000
87D87SER0-0.104-0.05834.745-0.008-0.0080.0000.0000.0000.000
88D88ASP-1-0.828-0.89934.7120.0970.0970.0000.0000.0000.000
89D89ASP-1-0.921-0.97430.2170.1360.1360.0000.0000.0000.000
90D90THR0-0.0120.02629.1250.0160.0160.0000.0000.0000.000
91D91ALA00.0050.00025.776-0.010-0.0100.0000.0000.0000.000
92D92VAL00.0020.01120.1730.0130.0130.0000.0000.0000.000
93D93TYR0-0.010-0.05321.234-0.015-0.0150.0000.0000.0000.000
94D94TYR00.0500.03015.6930.0490.0490.0000.0000.0000.000
95D96ALA00.0460.00913.4200.0420.0420.0000.0000.0000.000
96D97ARG10.8700.9598.382-0.555-0.5550.0000.0000.0000.000
97D98GLY0-0.018-0.00913.039-0.023-0.0230.0000.0000.0000.000
98D99GLY0-0.026-0.03212.6070.0380.0380.0000.0000.0000.000
99D100MET0-0.007-0.00713.4230.0100.0100.0000.0000.0000.000
100D101THR0-0.001-0.00316.490-0.012-0.0120.0000.0000.0000.000
101D102MET00.0520.01018.614-0.005-0.0050.0000.0000.0000.000
102D103VAL0-0.0050.01220.368-0.016-0.0160.0000.0000.0000.000
103D104ARG10.8940.94919.923-0.145-0.1450.0000.0000.0000.000
104D105GLY00.0510.01420.043-0.012-0.0120.0000.0000.0000.000
105D106VAL00.0090.02015.288-0.004-0.0040.0000.0000.0000.000
106D107MET0-0.018-0.00214.8230.0230.0230.0000.0000.0000.000
107D108MET0-0.044-0.0079.665-0.039-0.0390.0000.0000.0000.000
108D109ASP-1-0.818-0.9027.1040.3940.3940.0000.0000.0000.000
109D110TRP00.008-0.0169.866-0.005-0.0050.0000.0000.0000.000
110D111GLY00.0310.02810.0640.1000.1000.0000.0000.0000.000
111D112GLN0-0.0160.00912.0140.0460.0460.0000.0000.0000.000
112D113GLY0-0.004-0.00413.448-0.063-0.0630.0000.0000.0000.000
113D114THR0-0.024-0.01816.9140.0400.0400.0000.0000.0000.000
114D115LEU0-0.028-0.00719.795-0.025-0.0250.0000.0000.0000.000
115D116VAL00.0070.01023.1910.0050.0050.0000.0000.0000.000
116D117THR00.012-0.00626.192-0.016-0.0160.0000.0000.0000.000
117D118VAL00.0110.00729.6020.0010.0010.0000.0000.0000.000
118D119SER00.0280.00432.816-0.010-0.0100.0000.0000.0000.000
119D120SER00.041-0.00135.9340.0060.0060.0000.0000.0000.000
120D121ALA0-0.0130.01437.252-0.002-0.0020.0000.0000.0000.000
121D122SER0-0.016-0.01836.9990.0070.0070.0000.0000.0000.000
122D123THR0-0.039-0.00732.340-0.001-0.0010.0000.0000.0000.000
123D124LYS11.0030.98734.034-0.108-0.1080.0000.0000.0000.000
124D125GLY00.0040.01432.5530.0090.0090.0000.0000.0000.000
125D126PRO0-0.0060.00429.666-0.008-0.0080.0000.0000.0000.000
126D127SER0-0.027-0.00932.742-0.003-0.0030.0000.0000.0000.000
127D128VAL0-0.006-0.00930.204-0.003-0.0030.0000.0000.0000.000
128D129PHE0-0.004-0.02033.370-0.004-0.0040.0000.0000.0000.000
129D130PRO0-0.018-0.01833.299-0.002-0.0020.0000.0000.0000.000
130D131LEU00.0150.02333.765-0.004-0.0040.0000.0000.0000.000
131D132ALA0-0.008-0.00435.475-0.001-0.0010.0000.0000.0000.000
132D133PRO00.0420.02434.9930.0010.0010.0000.0000.0000.000
133D144ALA00.002-0.03032.090-0.002-0.0020.0000.0000.0000.000
134D145LEU0-0.037-0.01630.1030.0020.0020.0000.0000.0000.000
135D146GLY0-0.0030.01129.4620.0070.0070.0000.0000.0000.000
136D147CYS0-0.038-0.00425.4790.0000.0000.0000.0000.0000.000
137D148LEU00.0690.06831.542-0.001-0.0010.0000.0000.0000.000
138D149VAL0-0.0180.00328.6530.0020.0020.0000.0000.0000.000
139D150LYS10.9110.95232.061-0.084-0.0840.0000.0000.0000.000
140D151ASP-1-0.848-0.94134.8970.0910.0910.0000.0000.0000.000
141D152TYR0-0.053-0.06529.3920.0020.0020.0000.0000.0000.000
142D153PHE00.0250.00932.538-0.004-0.0040.0000.0000.0000.000
143D154PRO0-0.040-0.02729.0460.0010.0010.0000.0000.0000.000
144D155GLU-1-0.773-0.85126.8750.1730.1730.0000.0000.0000.000
145D156PRO0-0.009-0.01922.4620.0060.0060.0000.0000.0000.000
146D157VAL0-0.007-0.01024.7310.0030.0030.0000.0000.0000.000
147D158THR0-0.041-0.00719.3940.0110.0110.0000.0000.0000.000
148D159VAL00.012-0.00422.160-0.001-0.0010.0000.0000.0000.000
149D160SER0-0.0130.00519.0420.0040.0040.0000.0000.0000.000
150D161TRP00.0450.02520.830-0.012-0.0120.0000.0000.0000.000
151D162ASN00.0500.02520.7860.0020.0020.0000.0000.0000.000
152D163SER00.0060.00117.9310.0210.0210.0000.0000.0000.000
153D164GLY00.0270.01916.2620.0430.0430.0000.0000.0000.000
154D165ALA0-0.035-0.01616.553-0.033-0.0330.0000.0000.0000.000
155D166LEU0-0.033-0.01018.828-0.035-0.0350.0000.0000.0000.000
156D167THR00.0230.01815.9090.0300.0300.0000.0000.0000.000
157D168SER00.0150.00218.5260.0230.0230.0000.0000.0000.000
158D169GLY00.0370.01121.4110.0080.0080.0000.0000.0000.000
159D170VAL0-0.037-0.01920.6900.0080.0080.0000.0000.0000.000
160D171HIS00.0200.01223.3970.0080.0080.0000.0000.0000.000
161D172THR0-0.031-0.03022.9740.0060.0060.0000.0000.0000.000
162D173PHE0-0.017-0.00625.6130.0010.0010.0000.0000.0000.000
163D174PRO00.0330.00327.9770.0120.0120.0000.0000.0000.000
164D175ALA00.0120.01128.946-0.007-0.0070.0000.0000.0000.000
165D176VAL0-0.014-0.01130.801-0.006-0.0060.0000.0000.0000.000
166D177LEU0-0.035-0.02034.5920.0040.0040.0000.0000.0000.000
167D178GLN0-0.0190.00936.531-0.009-0.0090.0000.0000.0000.000
168D179SER00.034-0.00439.7450.0010.0010.0000.0000.0000.000
169D180SER0-0.013-0.00740.7080.0000.0000.0000.0000.0000.000
170D181GLY00.0100.01339.7730.0010.0010.0000.0000.0000.000
171D182LEU0-0.090-0.03336.3610.0080.0080.0000.0000.0000.000
172D183TYR00.0180.01232.338-0.006-0.0060.0000.0000.0000.000
173D184SER0-0.072-0.03833.2630.0000.0000.0000.0000.0000.000
174D185LEU00.0610.06227.408-0.004-0.0040.0000.0000.0000.000
175D186SER0-0.013-0.05430.9910.0000.0000.0000.0000.0000.000
176D187SER0-0.035-0.03326.1250.0150.0150.0000.0000.0000.000
177D188VAL00.0330.01827.922-0.002-0.0020.0000.0000.0000.000
178D189VAL00.0530.04225.1890.0010.0010.0000.0000.0000.000
179D190THR0-0.011-0.02927.6770.0020.0020.0000.0000.0000.000
180D191VAL00.0000.01529.304-0.006-0.0060.0000.0000.0000.000
181D192PRO00.0210.02431.028-0.008-0.0080.0000.0000.0000.000
182D200THR00.0190.00830.214-0.003-0.0030.0000.0000.0000.000
183D201TYR0-0.057-0.02926.1070.0010.0010.0000.0000.0000.000
184D202ILE0-0.0030.00124.475-0.004-0.0040.0000.0000.0000.000
185D204ASN0-0.007-0.01821.075-0.021-0.0210.0000.0000.0000.000
186D205VAL00.0310.01823.4990.0170.0170.0000.0000.0000.000
187D206ASN0-0.002-0.01721.8750.0090.0090.0000.0000.0000.000
188D207HIS00.0360.06423.8940.0130.0130.0000.0000.0000.000
189D208LYS10.9710.97718.095-0.471-0.4710.0000.0000.0000.000
190D209PRO00.0100.00424.489-0.002-0.0020.0000.0000.0000.000
191D210SER00.006-0.04327.723-0.008-0.0080.0000.0000.0000.000
192D211ASN0-0.061-0.01626.3690.0080.0080.0000.0000.0000.000
193D212THR00.0150.01727.285-0.017-0.0170.0000.0000.0000.000
194D213LYS10.9290.96721.882-0.261-0.2610.0000.0000.0000.000
195D214VAL0-0.027-0.01226.772-0.013-0.0130.0000.0000.0000.000
196D215ASP-1-0.855-0.91825.6830.1940.1940.0000.0000.0000.000
197D216LYS10.8480.93228.393-0.110-0.1100.0000.0000.0000.000
198D217ARG10.8660.89429.823-0.054-0.0540.0000.0000.0000.000
199D218VAL0-0.0090.00130.623-0.002-0.0020.0000.0000.0000.000
200D219GLU-1-0.829-0.90332.9170.0370.0370.0000.0000.0000.000
201D220PRO0-0.016-0.00535.6160.0020.0020.0000.0000.0000.000
202D221LYS10.9430.96538.456-0.039-0.0390.0000.0000.0000.000
203D222SER0-0.0070.00042.086-0.001-0.0010.0000.0000.0000.000
204D223CYS0-0.036-0.00743.9240.0030.0030.0000.0000.0000.000
205D224ASP-1-0.917-0.95146.7800.0210.0210.0000.0000.0000.000