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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: 72Z4K

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2325507.130992
FMO2-HF: Nuclear repulsion 2239089.181259
FMO2-HF: Total energy -86417.949733
FMO2-MP2: Total energy -86667.983345


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.
-11.773-5.2514.354-7.055-13.823-0.039
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 : -0.034 / q_NPA : -0.012
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].
3H4LEU00.0510.0243.805-1.3550.907-0.032-1.123-1.1060.004
4H5MET0-0.045-0.0186.8100.1230.1230.0000.0000.0000.000
5H6GLN00.008-0.0129.775-0.049-0.0490.0000.0000.0000.000
6H7SER00.0320.00813.0580.0420.0420.0000.0000.0000.000
7H8GLY0-0.0510.03116.3640.0190.0190.0000.0000.0000.000
8H9GLY00.002-0.01719.3620.0130.0130.0000.0000.0000.000
9H10VAL0-0.002-0.02321.5170.0140.0140.0000.0000.0000.000
10H11MET0-0.0190.00124.770-0.007-0.0070.0000.0000.0000.000
11H12VAL0-0.011-0.00128.4270.0050.0050.0000.0000.0000.000
12H13ARG10.9350.97230.7450.0430.0430.0000.0000.0000.000
13H14PRO0-0.021-0.03333.348-0.003-0.0030.0000.0000.0000.000
14H15GLY0-0.023-0.00733.4690.0050.0050.0000.0000.0000.000
15H16GLU-1-0.862-0.91732.087-0.053-0.0530.0000.0000.0000.000
16H17SER0-0.012-0.01028.639-0.007-0.0070.0000.0000.0000.000
17H18ALA00.0030.00224.9900.0070.0070.0000.0000.0000.000
18H19THR0-0.020-0.01121.019-0.012-0.0120.0000.0000.0000.000
19H20LEU0-0.040-0.00517.8610.0100.0100.0000.0000.0000.000
20H21SER00.009-0.00415.9010.0010.0010.0000.0000.0000.000
21H22CYS0-0.052-0.02510.379-0.051-0.0510.0000.0000.0000.000
22H23VAL00.0460.0389.5030.0000.0000.0000.0000.0000.000
23H24ALA00.0150.0156.156-0.026-0.0260.0000.0000.0000.000
24H25SER0-0.045-0.0334.5190.4860.659-0.001-0.048-0.1240.000
25H26GLY00.0570.0142.419-2.320-0.4462.751-2.458-2.167-0.016
26H27PHE00.001-0.0042.074-5.843-3.1964.614-1.581-5.681-0.016
27H28ASP-1-0.832-0.9033.978-0.0750.1320.004-0.066-0.1460.000
28H29PHE00.0110.0016.731-0.252-0.2520.0000.0000.0000.000
29H30SER0-0.026-0.0378.386-0.048-0.0480.0000.0000.0000.000
30H31ARG10.9100.9728.3590.2840.2840.0000.0000.0000.000
31H32ASN00.0110.0025.094-0.483-0.4830.0000.0000.0000.000
32H33GLY00.0260.0348.2000.2090.2090.0000.0000.0000.000
33H34PHE0-0.022-0.0226.236-0.216-0.2160.0000.0000.0000.000
34H35GLU-1-0.763-0.89010.519-0.450-0.4500.0000.0000.0000.000
35H36TRP0-0.038-0.01712.667-0.046-0.0460.0000.0000.0000.000
36H37LEU00.0030.00113.5120.0370.0370.0000.0000.0000.000
37H38ARG10.8660.93316.6860.1920.1920.0000.0000.0000.000
38H39GLN00.0370.00919.2800.0000.0000.0000.0000.0000.000
39H40GLY00.011-0.02521.4270.0140.0140.0000.0000.0000.000
40H41PRO00.0390.01924.852-0.006-0.0060.0000.0000.0000.000
41H42GLY00.004-0.00626.7990.0050.0050.0000.0000.0000.000
42H43LYS10.8661.01724.7930.1560.1560.0000.0000.0000.000
43H44GLY00.0460.00822.9540.0020.0020.0000.0000.0000.000
44H45LEU00.024-0.01817.496-0.002-0.0020.0000.0000.0000.000
45H46GLN00.0220.01120.2640.0140.0140.0000.0000.0000.000
46H47TRP00.0190.01015.9420.0310.0310.0000.0000.0000.000
47H48LEU0-0.047-0.01818.1180.0380.0380.0000.0000.0000.000
48H49ALA00.022-0.00117.7820.0360.0360.0000.0000.0000.000
49H50THR00.0390.04214.047-0.029-0.0290.0000.0000.0000.000
50H51VAL0-0.046-0.00513.6940.0650.0650.0000.0000.0000.000
51H52THR00.0940.03213.424-0.072-0.0720.0000.0000.0000.000
52H53PHE00.0370.00111.5900.0190.0190.0000.0000.0000.000
53H54GLU-1-0.963-0.97513.322-0.179-0.1790.0000.0000.0000.000
54H55SER0-0.057-0.04316.2190.0320.0320.0000.0000.0000.000
55H56LYS10.9651.00117.9480.2200.2200.0000.0000.0000.000
56H57THR0-0.005-0.01118.113-0.032-0.0320.0000.0000.0000.000
57H58HIS0-0.0070.01419.2350.0110.0110.0000.0000.0000.000
58H59VAL00.0200.00719.976-0.022-0.0220.0000.0000.0000.000
59H60THR00.016-0.00122.3710.0220.0220.0000.0000.0000.000
60H61ALA00.021-0.01424.0200.0090.0090.0000.0000.0000.000
61H62SER0-0.041-0.00726.5830.0100.0100.0000.0000.0000.000
62H63ALA00.0300.01324.9690.0070.0070.0000.0000.0000.000
63H64ARG10.9290.96825.6030.1660.1660.0000.0000.0000.000
64H65GLY00.0020.00727.5200.0090.0090.0000.0000.0000.000
65H66ARG10.8280.89827.6350.1340.1340.0000.0000.0000.000
66H67PHE0-0.014-0.00922.5350.0000.0000.0000.0000.0000.000
67H68THR00.009-0.00122.6040.0030.0030.0000.0000.0000.000
68H69ILE0-0.0290.00714.9510.0030.0030.0000.0000.0000.000
69H70SER0-0.013-0.01518.0720.0230.0230.0000.0000.0000.000
70H71ARG10.8230.91110.7050.4150.4150.0000.0000.0000.000
71H72ASP-1-0.809-0.88115.7650.0010.0010.0000.0000.0000.000
72H73ASN00.071-0.00513.863-0.027-0.0270.0000.0000.0000.000
73H74SER0-0.063-0.01813.9190.0400.0400.0000.0000.0000.000
74H75ARG10.9720.98714.432-0.025-0.0250.0000.0000.0000.000
75H76ARG10.9260.9817.511-0.491-0.4910.0000.0000.0000.000
76H77THR0-0.039-0.02410.516-0.011-0.0110.0000.0000.0000.000
77H78VAL0-0.0150.00011.121-0.020-0.0200.0000.0000.0000.000
78H79TYR00.016-0.01314.1200.0310.0310.0000.0000.0000.000
79H80LEU0-0.0020.00117.451-0.023-0.0230.0000.0000.0000.000
80H81GLN00.0130.00519.4940.0200.0200.0000.0000.0000.000
81H82MET0-0.031-0.01022.563-0.011-0.0110.0000.0000.0000.000
82H83THR00.0550.01325.4850.0170.0170.0000.0000.0000.000
83H84ASN00.001-0.00529.195-0.003-0.0030.0000.0000.0000.000
84H85LEU00.0090.01126.339-0.005-0.0050.0000.0000.0000.000
85H86GLN00.0430.01030.4720.0120.0120.0000.0000.0000.000
86H87PRO00.0280.00530.738-0.007-0.0070.0000.0000.0000.000
87H88ASP-1-0.941-0.95029.628-0.132-0.1320.0000.0000.0000.000
88H89ASP-1-0.799-0.87126.933-0.142-0.1420.0000.0000.0000.000
89H90THR0-0.0240.00426.038-0.010-0.0100.0000.0000.0000.000
90H91ALA0-0.001-0.01022.968-0.002-0.0020.0000.0000.0000.000
91H92MET0-0.050-0.00618.1420.0090.0090.0000.0000.0000.000
92H93TYR0-0.001-0.01018.161-0.026-0.0260.0000.0000.0000.000
93H94PHE00.0030.00413.0650.0140.0140.0000.0000.0000.000
94H96VAL00.0190.0048.771-0.072-0.0720.0000.0000.0000.000
95H97LYS10.8540.9302.2733.1713.1531.525-0.250-1.2570.000
96H98ASP-1-0.908-0.9296.839-0.935-0.9350.0000.0000.0000.000
97H99GLN0-0.070-0.0455.509-0.416-0.4160.0000.0000.0000.000
98H100THR0-0.008-0.0108.2360.2070.2070.0000.0000.0000.000
99H101ILE0-0.0060.0049.563-0.053-0.0530.0000.0000.0000.000
100H102PHE0-0.001-0.00610.6120.0690.0690.0000.0000.0000.000
101H103HIS0-0.0020.00414.3030.0420.0420.0000.0000.0000.000
102H104LYS10.9550.96717.5510.0940.0940.0000.0000.0000.000
103H105ASN0-0.053-0.04120.1130.0010.0010.0000.0000.0000.000
104H106GLY00.0430.02619.8080.0100.0100.0000.0000.0000.000
105H107ALA0-0.0260.01019.615-0.012-0.0120.0000.0000.0000.000
106H108VAL0-0.009-0.01814.335-0.009-0.0090.0000.0000.0000.000
107H109ASP-1-0.873-0.90814.911-0.267-0.2670.0000.0000.0000.000
108H110PHE0-0.012-0.02913.235-0.057-0.0570.0000.0000.0000.000
109H111PHE0-0.003-0.00811.8150.0530.0530.0000.0000.0000.000
110H112SER0-0.004-0.02511.369-0.096-0.0960.0000.0000.0000.000
111H113TYR0-0.028-0.0099.5110.0480.0480.0000.0000.0000.000
112H114PHE00.011-0.0158.322-0.117-0.1170.0000.0000.0000.000
113H115ASP-1-0.827-0.8873.283-4.275-3.4580.044-0.359-0.503-0.003
114H116LEU0-0.032-0.0172.107-0.066-1.5055.449-1.170-2.839-0.008
115H117TRP00.004-0.0105.7030.1870.1870.0000.0000.0000.000
116H118GLY00.0020.0047.874-0.084-0.0840.0000.0000.0000.000
117H119ARG10.8910.9359.8020.1750.1750.0000.0000.0000.000
118H120GLY00.0000.02312.5900.0370.0370.0000.0000.0000.000
119H121ALA0-0.055-0.04915.2600.0440.0440.0000.0000.0000.000
120H122PRO00.0240.01518.109-0.010-0.0100.0000.0000.0000.000
121H123VAL00.0140.01621.7510.0140.0140.0000.0000.0000.000
122H124ILE00.004-0.00324.056-0.003-0.0030.0000.0000.0000.000
123H125VAL00.0030.01127.6320.0080.0080.0000.0000.0000.000
124H126SER00.003-0.00930.5290.0010.0010.0000.0000.0000.000
125H127ALA00.0420.02134.0560.0030.0030.0000.0000.0000.000
126H128ALA0-0.029-0.00836.3040.0050.0050.0000.0000.0000.000
127H129SER00.0070.00536.371-0.002-0.0020.0000.0000.0000.000
128H130THR0-0.030-0.03234.139-0.003-0.0030.0000.0000.0000.000
129H131LYS10.9100.96536.3820.0340.0340.0000.0000.0000.000
130H132GLY00.0790.04037.359-0.003-0.0030.0000.0000.0000.000
131H133PRO0-0.065-0.02037.191-0.001-0.0010.0000.0000.0000.000
132H134SER0-0.0040.00139.8370.0040.0040.0000.0000.0000.000
133H135VAL00.003-0.00641.200-0.002-0.0020.0000.0000.0000.000
134H136PHE0-0.015-0.02043.7600.0020.0020.0000.0000.0000.000
135H137PRO00.0050.00645.496-0.001-0.0010.0000.0000.0000.000
136H138LEU0-0.0250.00643.545-0.001-0.0010.0000.0000.0000.000
137H139ALA00.0290.00847.5590.0000.0000.0000.0000.0000.000
138H140PRO00.0310.02349.653-0.001-0.0010.0000.0000.0000.000
139H141SER00.038-0.01851.2690.0010.0010.0000.0000.0000.000
140H142SER00.0730.01954.1720.0000.0000.0000.0000.0000.000
141H143LYS10.9060.94954.4180.0200.0200.0000.0000.0000.000
142H144SER0-0.0290.01349.883-0.001-0.0010.0000.0000.0000.000
143H145THR0-0.0030.00250.1640.0000.0000.0000.0000.0000.000
144H146SER0-0.0110.01250.5490.0000.0000.0000.0000.0000.000
145H147GLY00.0320.00551.7440.0000.0000.0000.0000.0000.000
146H148GLY00.0250.00852.2580.0010.0010.0000.0000.0000.000
147H149THR0-0.0170.00346.2180.0010.0010.0000.0000.0000.000
148H150ALA0-0.0030.00348.636-0.001-0.0010.0000.0000.0000.000
149H151ALA00.0100.00845.705-0.001-0.0010.0000.0000.0000.000
150H152LEU0-0.0110.00644.3610.0010.0010.0000.0000.0000.000
151H153GLY00.040-0.00743.038-0.002-0.0020.0000.0000.0000.000
152H154CYS0-0.084-0.00740.3830.0030.0030.0000.0000.0000.000
153H155LEU00.0100.02441.222-0.003-0.0030.0000.0000.0000.000
154H156VAL0-0.008-0.01237.2400.0030.0030.0000.0000.0000.000
155H157LYS10.9630.97639.0010.0290.0290.0000.0000.0000.000
156H158ASP-1-0.877-0.95040.086-0.034-0.0340.0000.0000.0000.000
157H159TYR0-0.024-0.00432.5530.0040.0040.0000.0000.0000.000
158H160PHE00.0650.02932.360-0.007-0.0070.0000.0000.0000.000
159H161PRO00.0120.01829.8620.0060.0060.0000.0000.0000.000
160H162GLU-1-0.809-0.91628.402-0.069-0.0690.0000.0000.0000.000
161H163PRO0-0.047-0.02226.6610.0010.0010.0000.0000.0000.000
162H164VAL00.0350.00829.3830.0070.0070.0000.0000.0000.000
163H165THR0-0.057-0.02529.401-0.003-0.0030.0000.0000.0000.000
164H166VAL00.0380.00131.9370.0030.0030.0000.0000.0000.000
165H167SER0-0.032-0.01133.9780.0000.0000.0000.0000.0000.000
166H168TRP00.0330.01135.8640.0010.0010.0000.0000.0000.000
167H169ASN00.0160.00338.9720.0010.0010.0000.0000.0000.000
168H170SER0-0.025-0.02438.4010.0020.0020.0000.0000.0000.000
169H171GLY0-0.012-0.00735.5720.0030.0030.0000.0000.0000.000
170H172ALA0-0.0310.00036.0140.0000.0000.0000.0000.0000.000
171H173LEU0-0.035-0.01038.6940.0000.0000.0000.0000.0000.000
172H174THR00.013-0.00733.522-0.002-0.0020.0000.0000.0000.000
173H175SER00.024-0.00536.104-0.004-0.0040.0000.0000.0000.000
174H176GLY00.0370.02137.4680.0010.0010.0000.0000.0000.000
175H177VAL0-0.033-0.00235.107-0.001-0.0010.0000.0000.0000.000
176H178HIS00.0060.00835.103-0.005-0.0050.0000.0000.0000.000
177H179THR00.0150.00933.2960.0040.0040.0000.0000.0000.000
178H180PHE0-0.040-0.01033.135-0.004-0.0040.0000.0000.0000.000
179H181PRO00.022-0.00730.3480.0020.0020.0000.0000.0000.000
180H182ALA00.0060.02231.4630.0040.0040.0000.0000.0000.000
181H183VAL0-0.0160.00432.550-0.007-0.0070.0000.0000.0000.000
182H184LEU0-0.029-0.01632.5360.0040.0040.0000.0000.0000.000
183H185GLN0-0.039-0.03335.1410.0010.0010.0000.0000.0000.000
184H186SER00.0330.01438.563-0.002-0.0020.0000.0000.0000.000
185H187SER00.003-0.00140.846-0.001-0.0010.0000.0000.0000.000
186H188GLY00.0160.02036.9500.0010.0010.0000.0000.0000.000
187H189LEU0-0.079-0.03536.1960.0000.0000.0000.0000.0000.000
188H190TYR00.012-0.00530.715-0.005-0.0050.0000.0000.0000.000
189H191SER0-0.031-0.01735.9390.0060.0060.0000.0000.0000.000
190H192LEU00.0320.03033.447-0.004-0.0040.0000.0000.0000.000
191H193SER00.0350.00737.2240.0050.0050.0000.0000.0000.000
192H194SER0-0.026-0.02236.680-0.002-0.0020.0000.0000.0000.000
193H195VAL00.0220.00138.6230.0030.0030.0000.0000.0000.000
194H196VAL00.0180.00939.446-0.001-0.0010.0000.0000.0000.000
195H197THR0-0.033-0.01241.5710.0000.0000.0000.0000.0000.000
196H198VAL00.0010.00543.3650.0010.0010.0000.0000.0000.000
197H199PRO00.0710.03245.972-0.001-0.0010.0000.0000.0000.000
198H200SER00.0110.02149.0410.0010.0010.0000.0000.0000.000
199H201SER00.0130.00551.9560.0000.0000.0000.0000.0000.000
200H202SER0-0.030-0.03349.4720.0010.0010.0000.0000.0000.000
201H203LEU0-0.013-0.01250.3120.0010.0010.0000.0000.0000.000
202H204GLY0-0.0040.00052.5270.0000.0000.0000.0000.0000.000
203H205THR0-0.009-0.01852.5420.0010.0010.0000.0000.0000.000
204H206GLN0-0.0190.02846.8330.0020.0020.0000.0000.0000.000
205H207THR0-0.038-0.01147.479-0.001-0.0010.0000.0000.0000.000
206H208TYR00.031-0.01344.4950.0000.0000.0000.0000.0000.000
207H209ILE00.008-0.00643.204-0.001-0.0010.0000.0000.0000.000
208H211ASN00.016-0.02037.4460.0010.0010.0000.0000.0000.000
209H212VAL0-0.0010.00436.675-0.002-0.0020.0000.0000.0000.000
210H213ASN0-0.018-0.01533.1620.0060.0060.0000.0000.0000.000
211H214HIS00.0610.07333.0370.0000.0000.0000.0000.0000.000
212H215LYS10.9920.97126.8800.0030.0030.0000.0000.0000.000
213H216PRO00.0010.01229.8550.0050.0050.0000.0000.0000.000
214H217SER0-0.009-0.01632.1180.0020.0020.0000.0000.0000.000
215H218ASN0-0.059-0.02534.5060.0030.0030.0000.0000.0000.000
216H219THR0-0.002-0.02535.8130.0010.0010.0000.0000.0000.000
217H220LYS10.9030.95736.861-0.002-0.0020.0000.0000.0000.000
218H221VAL0-0.007-0.00838.8720.0000.0000.0000.0000.0000.000
219H222ASP-1-0.810-0.88540.779-0.003-0.0030.0000.0000.0000.000
220H223LYS10.9060.95143.1880.0120.0120.0000.0000.0000.000
221H224ARG10.8450.91245.1100.0040.0040.0000.0000.0000.000
222H225VAL0-0.046-0.02545.769-0.001-0.0010.0000.0000.0000.000
223H226GLU-1-0.822-0.89648.601-0.006-0.0060.0000.0000.0000.000
224H227PRO00.0150.00152.129-0.001-0.0010.0000.0000.0000.000
225H228LYS10.9570.99154.1690.0140.0140.0000.0000.0000.000