Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2J5GR

Calculation Name: 4YE4-H-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4YE4

Chain ID: H

ChEMBL ID:

UniProt ID: Q69994

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2326785.522083
FMO2-HF: Nuclear repulsion 2240366.568132
FMO2-HF: Total energy -86418.953951
FMO2-MP2: Total energy -86668.970937


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:2:MET)


Summations of interaction energy for fragment #1(H:2:MET)
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.
-15.053-5.62311.06-6.956-13.533-0.037
Interaction energy analysis for fragmet #1(H:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / 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].
3H4LEU00.0560.0273.805-1.2521.051-0.032-1.139-1.1330.004
4H5MET0-0.048-0.0206.9040.1250.1250.0000.0000.0000.000
5H6GLN00.039-0.0029.792-0.046-0.0460.0000.0000.0000.000
6H7SER00.0360.00313.1020.0520.0520.0000.0000.0000.000
7H8GLY0-0.0380.04116.3830.0260.0260.0000.0000.0000.000
8H9GLY00.015-0.00719.4560.0120.0120.0000.0000.0000.000
9H10VAL0-0.008-0.02821.6180.0180.0180.0000.0000.0000.000
10H11MET0-0.0180.00224.866-0.010-0.0100.0000.0000.0000.000
11H12VAL0-0.021-0.00628.5240.0060.0060.0000.0000.0000.000
12H13ARG10.9200.96130.8360.0640.0640.0000.0000.0000.000
13H14PRO0-0.024-0.03133.430-0.004-0.0040.0000.0000.0000.000
14H15GLY0-0.023-0.00833.5630.0070.0070.0000.0000.0000.000
15H16GLU-1-0.858-0.91832.215-0.076-0.0760.0000.0000.0000.000
16H17SER0-0.022-0.01428.731-0.009-0.0090.0000.0000.0000.000
17H18ALA00.0070.00525.1340.0070.0070.0000.0000.0000.000
18H19THR0-0.023-0.01421.000-0.010-0.0100.0000.0000.0000.000
19H20LEU0-0.0240.00317.9180.0070.0070.0000.0000.0000.000
20H21SER00.002-0.00915.8810.0100.0100.0000.0000.0000.000
21H22CYS0-0.059-0.02310.480-0.063-0.0630.0000.0000.0000.000
22H23VAL00.0350.0299.8230.0200.0200.0000.0000.0000.000
23H24ALA00.0190.0206.287-0.070-0.0700.0000.0000.0000.000
24H25SER0-0.042-0.0284.5320.4350.607-0.001-0.048-0.1220.000
25H26GLY00.0600.0162.403-2.280-0.3732.736-2.472-2.172-0.016
26H27PHE00.0160.0062.094-5.687-3.2294.935-1.783-5.610-0.018
27H28ASP-1-0.805-0.8903.954-0.0170.1520.004-0.059-0.1130.000
28H29PHE00.0110.0087.288-0.265-0.2650.0000.0000.0000.000
29H30SER0-0.033-0.0478.775-0.113-0.1130.0000.0000.0000.000
30H31ARG10.8640.9589.354-0.001-0.0010.0000.0000.0000.000
31H32ASN00.004-0.0055.778-0.470-0.4700.0000.0000.0000.000
32H33GLY00.0160.0418.5210.1890.1890.0000.0000.0000.000
33H34PHE0-0.024-0.0256.283-0.237-0.2370.0000.0000.0000.000
34H35GLU-1-0.759-0.86410.743-0.491-0.4910.0000.0000.0000.000
35H36TRP0-0.044-0.02612.996-0.071-0.0710.0000.0000.0000.000
36H37LEU00.002-0.00213.7300.0470.0470.0000.0000.0000.000
37H38ARG10.8240.91016.6680.2490.2490.0000.0000.0000.000
38H39GLN00.0210.00018.976-0.002-0.0020.0000.0000.0000.000
39H40GLY00.012-0.01421.1050.0190.0190.0000.0000.0000.000
40H41PRO00.0320.01224.623-0.010-0.0100.0000.0000.0000.000
41H42GLY00.000-0.00326.7150.0080.0080.0000.0000.0000.000
42H43LYS10.8781.00424.6700.2100.2100.0000.0000.0000.000
43H44GLY00.0340.00822.401-0.001-0.0010.0000.0000.0000.000
44H45LEU00.015-0.01815.944-0.002-0.0020.0000.0000.0000.000
45H46GLN00.0250.01220.0100.0210.0210.0000.0000.0000.000
46H47TRP00.0310.02416.2290.0280.0280.0000.0000.0000.000
47H48LEU0-0.033-0.01418.3050.0490.0490.0000.0000.0000.000
48H49ALA00.008-0.00518.1180.0470.0470.0000.0000.0000.000
49H50THR00.0200.00814.293-0.044-0.0440.0000.0000.0000.000
50H51VAL0-0.042-0.01213.8760.0740.0740.0000.0000.0000.000
51H52THR00.1050.04313.501-0.074-0.0740.0000.0000.0000.000
52H53PHE00.0410.00411.9380.0310.0310.0000.0000.0000.000
53H54GLU-1-0.852-0.90613.630-0.137-0.1370.0000.0000.0000.000
54H55SER0-0.050-0.04316.4080.0190.0190.0000.0000.0000.000
55H56LYS10.8500.93518.0710.1970.1970.0000.0000.0000.000
56H57THR0-0.005-0.00718.162-0.036-0.0360.0000.0000.0000.000
57H58HIS00.0030.01619.4080.0090.0090.0000.0000.0000.000
58H59VAL00.0240.00620.233-0.028-0.0280.0000.0000.0000.000
59H60THR00.0340.01422.6660.0250.0250.0000.0000.0000.000
60H61ALA00.020-0.01124.3760.0120.0120.0000.0000.0000.000
61H62SER0-0.0150.00127.2170.0080.0080.0000.0000.0000.000
62H63ALA00.0120.00325.3070.0080.0080.0000.0000.0000.000
63H64ARG10.8920.94625.5440.1940.1940.0000.0000.0000.000
64H65GLY00.0120.01227.8360.0100.0100.0000.0000.0000.000
65H66ARG10.8050.88127.9490.1680.1680.0000.0000.0000.000
66H67PHE0-0.016-0.00823.255-0.002-0.0020.0000.0000.0000.000
67H68THR00.000-0.00523.0260.0080.0080.0000.0000.0000.000
68H69ILE0-0.0220.01315.210-0.001-0.0010.0000.0000.0000.000
69H70SER0-0.007-0.00918.2760.0290.0290.0000.0000.0000.000
70H71ARG10.8290.89911.2410.3310.3310.0000.0000.0000.000
71H72ASP-1-0.777-0.87215.7680.0530.0530.0000.0000.0000.000
72H73ASN00.0540.00114.041-0.030-0.0300.0000.0000.0000.000
73H74SER0-0.064-0.02213.9270.0530.0530.0000.0000.0000.000
74H75ARG10.9340.96114.385-0.009-0.0090.0000.0000.0000.000
75H76ARG10.8840.9557.289-0.633-0.6330.0000.0000.0000.000
76H77THR0-0.031-0.01710.530-0.034-0.0340.0000.0000.0000.000
77H78VAL0-0.0150.00011.128-0.008-0.0080.0000.0000.0000.000
78H79TYR00.001-0.01914.2750.0230.0230.0000.0000.0000.000
79H80LEU00.0040.00517.623-0.021-0.0210.0000.0000.0000.000
80H81GLN00.0100.00619.7560.0160.0160.0000.0000.0000.000
81H82MET0-0.032-0.01122.065-0.012-0.0120.0000.0000.0000.000
82H83THR00.0550.01325.6860.0190.0190.0000.0000.0000.000
83H84ASN0-0.006-0.00929.450-0.005-0.0050.0000.0000.0000.000
84H85LEU00.0080.01026.365-0.006-0.0060.0000.0000.0000.000
85H86GLN00.0520.00930.5440.0150.0150.0000.0000.0000.000
86H87PRO00.0360.01230.815-0.011-0.0110.0000.0000.0000.000
87H88ASP-1-0.907-0.93829.477-0.182-0.1820.0000.0000.0000.000
88H89ASP-1-0.763-0.83926.949-0.184-0.1840.0000.0000.0000.000
89H90THR0-0.0150.01726.115-0.015-0.0150.0000.0000.0000.000
90H91ALA0-0.012-0.00923.028-0.004-0.0040.0000.0000.0000.000
91H92MET0-0.038-0.00118.2070.0100.0100.0000.0000.0000.000
92H93TYR0-0.011-0.02318.297-0.031-0.0310.0000.0000.0000.000
93H94PHE00.0080.01113.2490.0120.0120.0000.0000.0000.000
94H96VAL00.011-0.0038.783-0.126-0.1260.0000.0000.0000.000
95H97LYS10.8270.9182.3953.4283.8750.764-0.187-1.0250.001
96H98ASP-1-0.893-0.9327.223-1.053-1.0530.0000.0000.0000.000
97H99GLN0-0.061-0.0535.943-0.467-0.4670.0000.0000.0000.000
98H100THR0-0.002-0.0058.5820.2150.2150.0000.0000.0000.000
99H101ILE0-0.008-0.0019.9260.0100.0100.0000.0000.0000.000
100H102PHE00.0310.00711.0500.0560.0560.0000.0000.0000.000
101H103HIS0-0.009-0.01114.7460.0560.0560.0000.0000.0000.000
102H104LYS10.9500.96217.9640.0280.0280.0000.0000.0000.000
103H105ASN0-0.044-0.03420.5440.0050.0050.0000.0000.0000.000
104H106GLY00.0430.02620.4760.0050.0050.0000.0000.0000.000
105H107ALA0-0.0300.00620.179-0.012-0.0120.0000.0000.0000.000
106H108VAL0-0.014-0.02314.7670.0050.0050.0000.0000.0000.000
107H109ASP-1-0.858-0.88915.091-0.241-0.2410.0000.0000.0000.000
108H110PHE0-0.016-0.02613.529-0.039-0.0390.0000.0000.0000.000
109H111PHE00.007-0.00612.0100.0430.0430.0000.0000.0000.000
110H112SER0-0.006-0.02011.488-0.114-0.1140.0000.0000.0000.000
111H113TYR0-0.011-0.0029.2190.0860.0860.0000.0000.0000.000
112H114PHE00.0230.0038.187-0.131-0.1310.0000.0000.0000.000
113H115ASP-1-0.814-0.8782.892-6.799-5.6740.342-0.610-0.857-0.007
114H116LEU0-0.038-0.0172.235-1.176-0.4022.313-0.656-2.430-0.001
115H117TRP00.014-0.0075.1060.4860.561-0.001-0.002-0.0710.000
116H118GLY00.0020.0067.971-0.107-0.1070.0000.0000.0000.000
117H119ARG10.8510.9169.8990.2570.2570.0000.0000.0000.000
118H120GLY00.0040.02012.6970.0470.0470.0000.0000.0000.000
119H121ALA0-0.058-0.04615.3590.0580.0580.0000.0000.0000.000
120H122PRO00.0140.00618.208-0.009-0.0090.0000.0000.0000.000
121H123VAL00.0110.01321.7240.0200.0200.0000.0000.0000.000
122H124ILE0-0.004-0.00824.147-0.004-0.0040.0000.0000.0000.000
123H125VAL00.0020.01027.7250.0100.0100.0000.0000.0000.000
124H126SER0-0.001-0.01030.6180.0020.0020.0000.0000.0000.000
125H127ALA00.0490.02534.1470.0040.0040.0000.0000.0000.000
126H128ALA0-0.0050.00836.3320.0070.0070.0000.0000.0000.000
127H129SER00.0160.01436.470-0.001-0.0010.0000.0000.0000.000
128H130THR0-0.032-0.03534.301-0.004-0.0040.0000.0000.0000.000
129H131LYS10.8110.90836.4870.0580.0580.0000.0000.0000.000
130H132GLY00.0910.05137.468-0.004-0.0040.0000.0000.0000.000
131H133PRO0-0.056-0.02137.2520.0000.0000.0000.0000.0000.000
132H134SER0-0.012-0.00139.9470.0040.0040.0000.0000.0000.000
133H135VAL00.007-0.00641.190-0.003-0.0030.0000.0000.0000.000
134H136PHE0-0.012-0.01043.8460.0040.0040.0000.0000.0000.000
135H137PRO0-0.0030.00345.604-0.002-0.0020.0000.0000.0000.000
136H138LEU0-0.0200.00543.623-0.001-0.0010.0000.0000.0000.000
137H139ALA00.0220.00647.5850.0000.0000.0000.0000.0000.000
138H140PRO00.0330.02849.632-0.001-0.0010.0000.0000.0000.000
139H141SER00.020-0.02451.2960.0020.0020.0000.0000.0000.000
140H142SER00.0600.02354.119-0.001-0.0010.0000.0000.0000.000
141H143LYS10.9430.97254.5310.0370.0370.0000.0000.0000.000
142H144SER0-0.0110.00949.793-0.002-0.0020.0000.0000.0000.000
143H145THR0-0.038-0.02250.110-0.001-0.0010.0000.0000.0000.000
144H146SER0-0.0020.01650.4690.0010.0010.0000.0000.0000.000
145H147GLY00.0330.00651.6900.0000.0000.0000.0000.0000.000
146H148GLY00.0270.01152.2750.0010.0010.0000.0000.0000.000
147H149THR0-0.0130.00046.1890.0010.0010.0000.0000.0000.000
148H150ALA00.0040.00748.6730.0000.0000.0000.0000.0000.000
149H151ALA00.0050.00945.684-0.002-0.0020.0000.0000.0000.000
150H152LEU0-0.022-0.00244.5120.0020.0020.0000.0000.0000.000
151H153GLY00.0530.00043.065-0.003-0.0030.0000.0000.0000.000
152H154CYS0-0.088-0.00640.4100.0040.0040.0000.0000.0000.000
153H155LEU00.0240.03041.315-0.005-0.0050.0000.0000.0000.000
154H156VAL0-0.005-0.01037.3900.0040.0040.0000.0000.0000.000
155H157LYS10.9180.94539.1070.0530.0530.0000.0000.0000.000
156H158ASP-1-0.813-0.89540.128-0.058-0.0580.0000.0000.0000.000
157H159TYR0-0.020-0.02332.5600.0070.0070.0000.0000.0000.000
158H160PHE00.0650.03532.296-0.009-0.0090.0000.0000.0000.000
159H161PRO00.0220.02229.9720.0080.0080.0000.0000.0000.000
160H162GLU-1-0.776-0.87628.480-0.113-0.1130.0000.0000.0000.000
161H163PRO0-0.058-0.02726.6870.0000.0000.0000.0000.0000.000
162H164VAL00.0390.00829.4930.0100.0100.0000.0000.0000.000
163H165THR0-0.048-0.01929.262-0.005-0.0050.0000.0000.0000.000
164H166VAL00.029-0.00131.9720.0050.0050.0000.0000.0000.000
165H167SER0-0.039-0.01634.011-0.002-0.0020.0000.0000.0000.000
166H168TRP00.0360.00935.8980.0030.0030.0000.0000.0000.000
167H169ASN00.005-0.00639.0060.0020.0020.0000.0000.0000.000
168H170SER0-0.023-0.02538.4090.0020.0020.0000.0000.0000.000
169H171GLY0-0.002-0.00135.6070.0020.0020.0000.0000.0000.000
170H172ALA0-0.0320.00136.047-0.001-0.0010.0000.0000.0000.000
171H173LEU0-0.037-0.01038.7280.0000.0000.0000.0000.0000.000
172H174THR00.015-0.00433.547-0.003-0.0030.0000.0000.0000.000
173H175SER00.0230.00036.130-0.006-0.0060.0000.0000.0000.000
174H176GLY00.0340.01737.4960.0030.0030.0000.0000.0000.000
175H177VAL0-0.032-0.00835.0320.0000.0000.0000.0000.0000.000
176H178HIS00.0000.00735.058-0.009-0.0090.0000.0000.0000.000
177H179THR00.0120.00333.2960.0070.0070.0000.0000.0000.000
178H180PHE0-0.033-0.00733.082-0.007-0.0070.0000.0000.0000.000
179H181PRO00.027-0.00430.3770.0020.0020.0000.0000.0000.000
180H182ALA0-0.0040.01831.5710.0070.0070.0000.0000.0000.000
181H183VAL0-0.017-0.00132.646-0.009-0.0090.0000.0000.0000.000
182H184LEU0-0.038-0.01932.7750.0060.0060.0000.0000.0000.000
183H185GLN0-0.041-0.04735.2360.0030.0030.0000.0000.0000.000
184H186SER00.0300.01038.656-0.002-0.0020.0000.0000.0000.000
185H187SER00.0100.00441.144-0.001-0.0010.0000.0000.0000.000
186H188GLY00.0120.01837.0430.0020.0020.0000.0000.0000.000
187H189LEU0-0.070-0.03136.294-0.002-0.0020.0000.0000.0000.000
188H190TYR00.0330.00630.092-0.002-0.0020.0000.0000.0000.000
189H191SER0-0.042-0.02036.0410.0080.0080.0000.0000.0000.000
190H192LEU00.0390.02933.639-0.006-0.0060.0000.0000.0000.000
191H193SER00.0290.00737.3270.0080.0080.0000.0000.0000.000
192H194SER0-0.025-0.01436.763-0.004-0.0040.0000.0000.0000.000
193H195VAL00.021-0.00138.6040.0050.0050.0000.0000.0000.000
194H196VAL00.0210.00839.472-0.002-0.0020.0000.0000.0000.000
195H197THR0-0.031-0.00841.5970.0010.0010.0000.0000.0000.000
196H198VAL0-0.0100.00043.3890.0000.0000.0000.0000.0000.000
197H199PRO00.0720.03445.997-0.001-0.0010.0000.0000.0000.000
198H200SER00.0050.01249.0650.0020.0020.0000.0000.0000.000
199H201SER00.0160.00651.9810.0000.0000.0000.0000.0000.000
200H202SER0-0.036-0.03049.4720.0010.0010.0000.0000.0000.000
201H203LEU0-0.009-0.01150.2130.0000.0000.0000.0000.0000.000
202H204GLY0-0.0040.00152.5560.0000.0000.0000.0000.0000.000
203H205THR0-0.013-0.01552.8580.0010.0010.0000.0000.0000.000
204H206GLN0-0.0220.01546.8830.0020.0020.0000.0000.0000.000
205H207THR0-0.0220.00247.371-0.001-0.0010.0000.0000.0000.000
206H208TYR00.0500.00344.470-0.001-0.0010.0000.0000.0000.000
207H209ILE00.002-0.00743.3680.0000.0000.0000.0000.0000.000
208H211ASN00.026-0.00337.4790.0010.0010.0000.0000.0000.000
209H212VAL00.0020.00636.713-0.004-0.0040.0000.0000.0000.000
210H213ASN0-0.025-0.02333.1420.0100.0100.0000.0000.0000.000
211H214HIS00.0400.04933.1860.0000.0000.0000.0000.0000.000
212H215LYS10.9980.97426.8300.0420.0420.0000.0000.0000.000
213H216PRO00.0080.01729.7860.0070.0070.0000.0000.0000.000
214H217SER0-0.014-0.02132.1180.0030.0030.0000.0000.0000.000
215H218ASN0-0.061-0.02934.5050.0040.0040.0000.0000.0000.000
216H219THR00.015-0.00435.8130.0030.0030.0000.0000.0000.000
217H220LYS10.8850.94636.8610.0200.0200.0000.0000.0000.000
218H221VAL0-0.010-0.00838.8900.0020.0020.0000.0000.0000.000
219H222ASP-1-0.809-0.89340.817-0.026-0.0260.0000.0000.0000.000
220H223LYS10.9090.95043.2250.0320.0320.0000.0000.0000.000
221H224ARG10.8350.89145.1450.0190.0190.0000.0000.0000.000
222H225VAL0-0.042-0.02645.7630.0000.0000.0000.0000.0000.000
223H226GLU-1-0.810-0.87548.633-0.022-0.0220.0000.0000.0000.000
224H227PRO00.0220.00652.161-0.002-0.0020.0000.0000.0000.000
225H228LYS10.9580.98954.1990.0280.0280.0000.0000.0000.000