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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: 1739Z

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2122030.415797
FMO2-HF: Nuclear repulsion 2040983.624749
FMO2-HF: Total energy -81046.791049
FMO2-MP2: Total energy -81276.285088


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.
-9.956-7.1764.072-2.876-3.9730.023
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 : 0.051 / 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].
3H3GLN0-0.019-0.0132.094-9.424-6.9664.074-2.755-3.7770.023
4H4LEU0-0.011-0.0085.360-0.729-0.711-0.001-0.001-0.0140.000
5H5VAL00.0090.0138.8170.3270.3270.0000.0000.0000.000
6H6GLN0-0.011-0.02711.246-0.197-0.1970.0000.0000.0000.000
7H7SER0-0.038-0.02014.9470.0680.0680.0000.0000.0000.000
8H8GLY00.0620.00318.110-0.056-0.0560.0000.0000.0000.000
9H9ALA0-0.074-0.01419.5100.0440.0440.0000.0000.0000.000
10H10GLU-1-0.840-0.93822.2560.3490.3490.0000.0000.0000.000
11H11MET00.0030.02625.908-0.004-0.0040.0000.0000.0000.000
12H12LYS10.8760.93228.124-0.220-0.2200.0000.0000.0000.000
13H13LYS10.9180.97331.699-0.139-0.1390.0000.0000.0000.000
14H14PRO00.0650.01334.7480.0020.0020.0000.0000.0000.000
15H15GLY0-0.0160.00836.507-0.004-0.0040.0000.0000.0000.000
16H16ALA0-0.038-0.00533.722-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.018-0.03731.0500.0030.0030.0000.0000.0000.000
18H18VAL0-0.046-0.01925.7010.0070.0070.0000.0000.0000.000
19H19LYS10.8880.93024.483-0.131-0.1310.0000.0000.0000.000
20H20VAL00.0100.01919.1780.0200.0200.0000.0000.0000.000
21H21SER00.003-0.00318.236-0.035-0.0350.0000.0000.0000.000
22H22CYS0-0.037-0.00813.8280.0360.0360.0000.0000.0000.000
23H23LYS10.8430.93411.088-0.172-0.1720.0000.0000.0000.000
24H24ALA00.0580.03510.2870.1660.1660.0000.0000.0000.000
25H25SER0-0.009-0.0175.8720.2680.2680.0000.0000.0000.000
26H26GLY00.0590.0304.024-0.484-0.2960.000-0.104-0.0830.000
27H27TYR0-0.011-0.0044.619-0.171-0.055-0.001-0.016-0.0990.000
28H28THR00.0300.0067.4180.2050.2050.0000.0000.0000.000
29H29PHE0-0.0010.00711.1140.0890.0890.0000.0000.0000.000
30H30ILE00.032-0.00212.9190.0500.0500.0000.0000.0000.000
31H31GLY0-0.0070.00414.1850.0490.0490.0000.0000.0000.000
32H32TYR0-0.033-0.02211.145-0.047-0.0470.0000.0000.0000.000
33H33HIS00.0050.01315.2730.0060.0060.0000.0000.0000.000
34H34LEU0-0.008-0.00113.607-0.020-0.0200.0000.0000.0000.000
35H35HIS00.0180.00616.9130.0250.0250.0000.0000.0000.000
36H36TRP00.0130.00017.6330.0550.0550.0000.0000.0000.000
37H37VAL0-0.013-0.00819.295-0.032-0.0320.0000.0000.0000.000
38H38ARG10.7920.87520.618-0.136-0.1360.0000.0000.0000.000
39H39GLN00.0060.00621.6910.0210.0210.0000.0000.0000.000
40H40ALA00.0510.04424.3080.0150.0150.0000.0000.0000.000
41H41PRO00.009-0.01927.0920.0100.0100.0000.0000.0000.000
42H42GLY00.0110.01227.427-0.018-0.0180.0000.0000.0000.000
43H43GLN0-0.030-0.00427.601-0.024-0.0240.0000.0000.0000.000
44H44GLY00.0370.01825.7440.0220.0220.0000.0000.0000.000
45H45LEU0-0.015-0.01120.0140.0060.0060.0000.0000.0000.000
46H46GLU-1-0.747-0.85624.0570.1190.1190.0000.0000.0000.000
47H47TRP0-0.022-0.00521.6170.0170.0170.0000.0000.0000.000
48H48MET0-0.031-0.01323.596-0.002-0.0020.0000.0000.0000.000
49H49GLY00.0770.01323.680-0.014-0.0140.0000.0000.0000.000
50H50TRP0-0.050-0.01820.9240.0090.0090.0000.0000.0000.000
51H51ILE00.0170.01619.748-0.001-0.0010.0000.0000.0000.000
52H52ASN0-0.013-0.00420.071-0.027-0.0270.0000.0000.0000.000
53H53PRO00.0200.01316.3650.0200.0200.0000.0000.0000.000
54H54ASN00.0180.01919.282-0.008-0.0080.0000.0000.0000.000
55H55SER0-0.016-0.00420.7170.0180.0180.0000.0000.0000.000
56H56GLY0-0.038-0.03223.2910.0080.0080.0000.0000.0000.000
57H57GLU-1-0.815-0.88524.6650.0010.0010.0000.0000.0000.000
58H58THR0-0.109-0.06824.667-0.001-0.0010.0000.0000.0000.000
59H59ASN00.0130.00125.771-0.001-0.0010.0000.0000.0000.000
60H60TYR00.0670.01626.2550.0160.0160.0000.0000.0000.000
61H61ALA00.0230.02128.237-0.007-0.0070.0000.0000.0000.000
62H62GLN00.0600.01229.9910.0070.0070.0000.0000.0000.000
63H63LYS10.8450.91630.926-0.126-0.1260.0000.0000.0000.000
64H64PHE0-0.021-0.03328.1700.0090.0090.0000.0000.0000.000
65H65GLN0-0.046-0.00631.494-0.001-0.0010.0000.0000.0000.000
66H66ASP-1-0.825-0.90133.0950.0490.0490.0000.0000.0000.000
67H67TRP0-0.012-0.01032.6450.0030.0030.0000.0000.0000.000
68H68VAL0-0.031-0.01426.5420.0120.0120.0000.0000.0000.000
69H69THR0-0.0050.00227.833-0.013-0.0130.0000.0000.0000.000
70H70MET0-0.0330.01023.0550.0160.0160.0000.0000.0000.000
71H71THR00.0170.00323.134-0.014-0.0140.0000.0000.0000.000
72H72ARG10.8450.90519.4270.0820.0820.0000.0000.0000.000
73H73ASP-1-0.793-0.85819.498-0.014-0.0140.0000.0000.0000.000
74H74THR00.004-0.02018.082-0.003-0.0030.0000.0000.0000.000
75H75SER0-0.009-0.01117.467-0.049-0.0490.0000.0000.0000.000
76H76ILE0-0.022-0.01416.467-0.029-0.0290.0000.0000.0000.000
77H77ASN0-0.068-0.03513.015-0.035-0.0350.0000.0000.0000.000
78H78THR00.0310.01113.7900.0230.0230.0000.0000.0000.000
79H79ALA00.0190.01016.238-0.051-0.0510.0000.0000.0000.000
80H80TYR00.000-0.01118.1540.0740.0740.0000.0000.0000.000
81H81MET0-0.0080.02120.924-0.035-0.0350.0000.0000.0000.000
82H82GLU-1-0.778-0.86223.1480.1310.1310.0000.0000.0000.000
83H83LEU00.014-0.00126.626-0.012-0.0120.0000.0000.0000.000
84H84ARG10.8450.91628.966-0.090-0.0900.0000.0000.0000.000
85H85LEU0-0.040-0.01729.1730.0010.0010.0000.0000.0000.000
86H86ARG10.8550.90532.135-0.116-0.1160.0000.0000.0000.000
87H87SER0-0.031-0.01634.261-0.004-0.0040.0000.0000.0000.000
88H88ASP-1-0.842-0.92733.6910.1310.1310.0000.0000.0000.000
89H89ASP-1-0.825-0.87629.9730.1440.1440.0000.0000.0000.000
90H90THR0-0.0030.01928.8200.0190.0190.0000.0000.0000.000
91H91ALA00.0060.00025.510-0.005-0.0050.0000.0000.0000.000
92H92VAL00.0030.00819.8610.0120.0120.0000.0000.0000.000
93H93TYR0-0.003-0.02620.932-0.036-0.0360.0000.0000.0000.000
94H94TYR00.008-0.00515.8500.0750.0750.0000.0000.0000.000
95H96ALA00.0570.01113.1180.0970.0970.0000.0000.0000.000
96H97ARG10.7940.9028.7490.5410.5410.0000.0000.0000.000
97H98GLY00.015-0.00712.9890.0240.0240.0000.0000.0000.000
98H99GLY0-0.046-0.02512.724-0.053-0.0530.0000.0000.0000.000
99H100MET00.0220.00613.334-0.056-0.0560.0000.0000.0000.000
100H101THR00.0360.01716.1500.0350.0350.0000.0000.0000.000
101H102MET00.0310.02118.5280.0170.0170.0000.0000.0000.000
102H103VAL0-0.0070.00320.0630.0180.0180.0000.0000.0000.000
103H104ARG10.8120.89919.8580.0980.0980.0000.0000.0000.000
104H105GLY00.0750.02920.0750.0080.0080.0000.0000.0000.000
105H106VAL0-0.0040.00215.1250.0280.0280.0000.0000.0000.000
106H107MET0-0.024-0.00815.084-0.046-0.0460.0000.0000.0000.000
107H108MET0-0.0390.00110.0000.0620.0620.0000.0000.0000.000
108H109ASP-1-0.760-0.8627.010-0.345-0.3450.0000.0000.0000.000
109H110TRP00.011-0.0219.598-0.122-0.1220.0000.0000.0000.000
110H111GLY00.0260.0219.6950.2480.2480.0000.0000.0000.000
111H112GLN0-0.008-0.00511.7020.0380.0380.0000.0000.0000.000
112H113GLY00.0310.02612.978-0.093-0.0930.0000.0000.0000.000
113H114THR0-0.074-0.05116.5060.0360.0360.0000.0000.0000.000
114H115LEU0-0.0210.00719.470-0.043-0.0430.0000.0000.0000.000
115H116VAL00.0010.00422.934-0.001-0.0010.0000.0000.0000.000
116H117THR00.0100.00625.820-0.017-0.0170.0000.0000.0000.000
117H118VAL0-0.013-0.00229.353-0.005-0.0050.0000.0000.0000.000
118H119SER00.0380.00632.457-0.011-0.0110.0000.0000.0000.000
119H120SER00.0480.00335.6830.0040.0040.0000.0000.0000.000
120H121ALA00.0110.02636.844-0.004-0.0040.0000.0000.0000.000
121H122SER0-0.005-0.01836.6040.0040.0040.0000.0000.0000.000
122H123THR00.005-0.01330.8320.0000.0000.0000.0000.0000.000
123H124LYS10.8780.93133.053-0.163-0.1630.0000.0000.0000.000
124H125GLY00.0550.03331.5380.0130.0130.0000.0000.0000.000
125H126PRO0-0.029-0.01629.243-0.010-0.0100.0000.0000.0000.000
126H127SER0-0.0250.00832.546-0.008-0.0080.0000.0000.0000.000
127H128VAL00.007-0.02030.6170.0080.0080.0000.0000.0000.000
128H129PHE00.001-0.00233.799-0.009-0.0090.0000.0000.0000.000
129H130PRO0-0.021-0.01733.2180.0010.0010.0000.0000.0000.000
130H131LEU00.0210.01534.530-0.011-0.0110.0000.0000.0000.000
131H132ALA0-0.002-0.00235.9390.0030.0030.0000.0000.0000.000
132H133PRO00.0340.02835.5040.0020.0020.0000.0000.0000.000
133H145LEU00.0620.03129.693-0.005-0.0050.0000.0000.0000.000
134H146GLY0-0.069-0.03732.2000.0030.0030.0000.0000.0000.000
135H147CYS0-0.036-0.02324.7670.0270.0270.0000.0000.0000.000
136H148LEU00.0220.03130.9270.0110.0110.0000.0000.0000.000
137H149VAL0-0.009-0.01028.864-0.004-0.0040.0000.0000.0000.000
138H150LYS10.8190.88232.288-0.147-0.1470.0000.0000.0000.000
139H151ASP-1-0.790-0.88534.9160.1520.1520.0000.0000.0000.000
140H152TYR0-0.010-0.00429.071-0.007-0.0070.0000.0000.0000.000
141H153PHE0-0.002-0.00532.371-0.005-0.0050.0000.0000.0000.000
142H154PRO0-0.0170.00229.201-0.003-0.0030.0000.0000.0000.000
143H155GLU-1-0.700-0.83826.2090.3190.3190.0000.0000.0000.000
144H156PRO0-0.041-0.02822.127-0.010-0.0100.0000.0000.0000.000
145H157VAL0-0.035-0.02524.616-0.003-0.0030.0000.0000.0000.000
146H158THR0-0.042-0.01519.3860.0370.0370.0000.0000.0000.000
147H159VAL00.0330.00021.709-0.032-0.0320.0000.0000.0000.000
148H160SER0-0.024-0.00418.6610.0740.0740.0000.0000.0000.000
149H161TRP00.0420.01820.198-0.045-0.0450.0000.0000.0000.000
150H162ASN00.0450.01020.0930.0120.0120.0000.0000.0000.000
151H163SER0-0.018-0.02517.5630.0050.0050.0000.0000.0000.000
152H164GLY0-0.008-0.00115.7770.0900.0900.0000.0000.0000.000
153H165ALA0-0.0260.00016.2670.0080.0080.0000.0000.0000.000
154H166LEU0-0.050-0.01517.560-0.036-0.0360.0000.0000.0000.000
155H167THR00.0220.00814.9930.0020.0020.0000.0000.0000.000
156H168SER00.0040.00617.7950.0130.0130.0000.0000.0000.000
157H169GLY00.010-0.00520.925-0.010-0.0100.0000.0000.0000.000
158H170VAL0-0.030-0.01120.404-0.017-0.0170.0000.0000.0000.000
159H171HIS0-0.0010.00023.8220.0150.0150.0000.0000.0000.000
160H172THR0-0.021-0.00622.711-0.006-0.0060.0000.0000.0000.000
161H173PHE0-0.007-0.00925.4870.0050.0050.0000.0000.0000.000
162H174PRO00.022-0.00427.4800.0150.0150.0000.0000.0000.000
163H175ALA0-0.0110.00928.379-0.014-0.0140.0000.0000.0000.000
164H176VAL0-0.0060.00030.089-0.009-0.0090.0000.0000.0000.000
165H177LEU0-0.020-0.01333.1840.0000.0000.0000.0000.0000.000
166H178GLN00.0060.00635.937-0.017-0.0170.0000.0000.0000.000
167H179SER00.0250.00039.112-0.001-0.0010.0000.0000.0000.000
168H180SER0-0.005-0.00140.500-0.003-0.0030.0000.0000.0000.000
169H181GLY0-0.0050.00239.031-0.001-0.0010.0000.0000.0000.000
170H182LEU0-0.072-0.02236.1720.0090.0090.0000.0000.0000.000
171H183TYR00.005-0.00930.5740.0010.0010.0000.0000.0000.000
172H184SER0-0.044-0.02033.083-0.008-0.0080.0000.0000.0000.000
173H185LEU00.0310.02627.0380.0020.0020.0000.0000.0000.000
174H186SER00.0460.01330.559-0.006-0.0060.0000.0000.0000.000
175H187SER00.0190.01025.9530.0260.0260.0000.0000.0000.000
176H188VAL00.0160.03027.893-0.013-0.0130.0000.0000.0000.000
177H189VAL00.0210.00024.4070.0230.0230.0000.0000.0000.000
178H190THR0-0.001-0.00825.743-0.017-0.0170.0000.0000.0000.000
179H191VAL00.0030.01028.362-0.002-0.0020.0000.0000.0000.000
180H192PRO0-0.0050.01329.354-0.007-0.0070.0000.0000.0000.000
181H200THR00.004-0.00829.4810.0010.0010.0000.0000.0000.000
182H201TYR00.0030.00825.0720.0050.0050.0000.0000.0000.000
183H202ILE0-0.004-0.01023.910-0.011-0.0110.0000.0000.0000.000
184H204ASN00.013-0.01422.080-0.005-0.0050.0000.0000.0000.000
185H205VAL00.0240.01023.1740.0360.0360.0000.0000.0000.000
186H206ASN00.008-0.00420.659-0.039-0.0390.0000.0000.0000.000
187H207HIS00.0410.03823.6520.0200.0200.0000.0000.0000.000
188H208LYS10.9210.96320.893-0.401-0.4010.0000.0000.0000.000
189H209PRO0-0.0100.00824.205-0.017-0.0170.0000.0000.0000.000
190H210SER0-0.010-0.00227.474-0.023-0.0230.0000.0000.0000.000
191H211ASN0-0.043-0.02125.3500.0140.0140.0000.0000.0000.000
192H212THR00.0250.01026.3760.0030.0030.0000.0000.0000.000
193H213LYS10.9010.94221.713-0.372-0.3720.0000.0000.0000.000
194H214VAL0-0.030-0.01826.655-0.026-0.0260.0000.0000.0000.000
195H215ASP-1-0.785-0.86625.3250.3120.3120.0000.0000.0000.000
196H216LYS10.8640.92027.938-0.200-0.2000.0000.0000.0000.000
197H217ARG10.8440.91729.242-0.119-0.1190.0000.0000.0000.000
198H218VAL0-0.030-0.00730.362-0.004-0.0040.0000.0000.0000.000
199H219GLU-1-0.814-0.89332.7440.1110.1110.0000.0000.0000.000
200H220PRO00.0070.00536.0350.0030.0030.0000.0000.0000.000
201H221LYS10.8940.93838.242-0.126-0.1260.0000.0000.0000.000
202H222SER00.0320.02642.301-0.001-0.0010.0000.0000.0000.000
203H223CYS0-0.078-0.05444.4680.0060.0060.0000.0000.0000.000
204H224ASP-1-0.912-0.93447.1360.0700.0700.0000.0000.0000.000