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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: JLRR9

Calculation Name: 4ZXB-D-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4ZXB

Chain ID: D

ChEMBL ID:

UniProt ID: P01865

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1655499.634616
FMO2-HF: Nuclear repulsion 1585900.593698
FMO2-HF: Total energy -69599.040918
FMO2-MP2: Total energy -69801.481792


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:ASP)


Summations of interaction energy for fragment #1(D:1:ASP)
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.
-21.959-16.0683.321-3.804-5.4090.026
Interaction energy analysis for fragmet #1(D:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.913 / q_NPA : -0.972
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].
3D3GLN00.0450.0393.353-5.264-3.1700.018-0.870-1.2420.004
4D4MET00.0070.0165.603-2.638-2.6380.0000.0000.0000.000
5D5THR00.010-0.0058.946-0.658-0.6580.0000.0000.0000.000
6D6GLN00.004-0.02511.5330.1340.1340.0000.0000.0000.000
7D7SER0-0.063-0.00214.206-0.224-0.2240.0000.0000.0000.000
8D8PRO00.0370.01117.815-0.077-0.0770.0000.0000.0000.000
9D9SER00.0700.02317.3910.1020.1020.0000.0000.0000.000
10D10SER0-0.016-0.00819.375-0.030-0.0300.0000.0000.0000.000
11D11LEU0-0.034-0.01623.033-0.080-0.0800.0000.0000.0000.000
12D12SER0-0.013-0.01625.6210.0080.0080.0000.0000.0000.000
13D13ALA0-0.034-0.02329.340-0.169-0.1690.0000.0000.0000.000
14D14SER00.0260.00931.321-0.097-0.0970.0000.0000.0000.000
15D15LEU00.010-0.00434.2100.1260.1260.0000.0000.0000.000
16D16GLY0-0.0040.00735.631-0.215-0.2150.0000.0000.0000.000
17D17GLU-1-0.844-0.88932.2479.2979.2970.0000.0000.0000.000
18D18ARG10.9510.98529.324-9.874-9.8740.0000.0000.0000.000
19D19VAL0-0.018-0.01026.8450.0050.0050.0000.0000.0000.000
20D20SER0-0.010-0.03124.032-0.104-0.1040.0000.0000.0000.000
21D21LEU00.0110.01719.715-0.026-0.0260.0000.0000.0000.000
22D22THR0-0.011-0.00317.443-0.175-0.1750.0000.0000.0000.000
23D23CYS0-0.0430.00312.7420.3150.3150.0000.0000.0000.000
24D24ARG10.8810.94413.261-17.714-17.7140.0000.0000.0000.000
25D25ALA00.001-0.0069.8181.3371.3370.0000.0000.0000.000
26D26SER0-0.069-0.0356.351-2.228-2.2280.0000.0000.0000.000
27D27GLN00.0290.0145.9141.7041.7040.0000.0000.0000.000
28D28ASP-1-0.804-0.9008.87519.70619.7060.0000.0000.0000.000
29D29ILE00.0350.0048.4131.6201.6200.0000.0000.0000.000
30D30GLY0-0.018-0.00610.991-0.725-0.7250.0000.0000.0000.000
31D31GLY00.0150.01014.600-1.111-1.1110.0000.0000.0000.000
32D32ASN0-0.063-0.01712.161-1.659-1.6590.0000.0000.0000.000
33D33LEU00.011-0.00412.0412.0922.0920.0000.0000.0000.000
34D34TYR0-0.009-0.01113.784-2.240-2.2400.0000.0000.0000.000
35D35TRP0-0.006-0.00715.3530.9640.9640.0000.0000.0000.000
36D36LEU0-0.005-0.01115.570-0.650-0.6500.0000.0000.0000.000
37D37GLN00.0150.00619.0500.0320.0320.0000.0000.0000.000
38D38GLN0-0.024-0.01819.8470.6590.6590.0000.0000.0000.000
39D39GLY00.0480.03022.497-0.290-0.2900.0000.0000.0000.000
40D40PRO00.016-0.00825.3300.3370.3370.0000.0000.0000.000
41D41ASP-1-0.856-0.90227.59911.20911.2090.0000.0000.0000.000
42D42GLY00.0220.02523.8300.0460.0460.0000.0000.0000.000
43D43THR0-0.072-0.06122.6350.8270.8270.0000.0000.0000.000
44D44ILE0-0.011-0.01217.9280.1140.1140.0000.0000.0000.000
45D45LYS10.9040.96421.942-11.687-11.6870.0000.0000.0000.000
46D46ARG10.7850.86518.518-14.822-14.8220.0000.0000.0000.000
47D47LEU0-0.014-0.01121.187-0.741-0.7410.0000.0000.0000.000
48D48ILE0-0.0110.00020.010-0.607-0.6070.0000.0000.0000.000
49D49TYR0-0.004-0.00518.2671.0531.0530.0000.0000.0000.000
50D50ALA00.0400.01817.640-0.669-0.6690.0000.0000.0000.000
51D51THR0-0.007-0.00617.079-0.530-0.5300.0000.0000.0000.000
52D52SER0-0.040-0.03818.641-0.064-0.0640.0000.0000.0000.000
53D53SER0-0.0470.00021.861-0.835-0.8350.0000.0000.0000.000
54D54LEU00.0000.00022.9450.4340.4340.0000.0000.0000.000
55D55ASP-1-0.762-0.85122.43113.68113.6810.0000.0000.0000.000
56D56SER0-0.006-0.01125.632-0.548-0.5480.0000.0000.0000.000
57D57GLY00.0250.00528.7980.1580.1580.0000.0000.0000.000
58D58VAL0-0.058-0.01025.9300.0380.0380.0000.0000.0000.000
59D59PRO00.0390.02129.272-0.194-0.1940.0000.0000.0000.000
60D60LYS10.9460.95730.274-9.301-9.3010.0000.0000.0000.000
61D61ARG10.7060.82530.276-9.874-9.8740.0000.0000.0000.000
62D62PHE00.0100.01625.4580.1910.1910.0000.0000.0000.000
63D63SER0-0.055-0.02926.118-0.232-0.2320.0000.0000.0000.000
64D64GLY00.0570.01522.2230.3800.3800.0000.0000.0000.000
65D65SER0-0.054-0.02421.274-0.554-0.5540.0000.0000.0000.000
66D66ARG10.8350.89515.873-16.614-16.6140.0000.0000.0000.000
67D67SER0-0.0100.00419.794-0.841-0.8410.0000.0000.0000.000
68D68GLY00.0490.02819.0790.2920.2920.0000.0000.0000.000
69D69SER00.0170.00813.818-0.045-0.0450.0000.0000.0000.000
70D70ASP-1-0.845-0.89814.42017.58217.5820.0000.0000.0000.000
71D71TYR00.010-0.00513.774-0.941-0.9410.0000.0000.0000.000
72D72SER00.005-0.03117.3690.3370.3370.0000.0000.0000.000
73D73LEU00.0080.04020.108-0.459-0.4590.0000.0000.0000.000
74D74THR0-0.045-0.02721.687-0.311-0.3110.0000.0000.0000.000
75D75ILE00.0260.03025.362-0.045-0.0450.0000.0000.0000.000
76D76SER0-0.043-0.04428.297-0.164-0.1640.0000.0000.0000.000
77D77SER00.0380.00031.665-0.322-0.3220.0000.0000.0000.000
78D78LEU0-0.0500.00028.6280.0730.0730.0000.0000.0000.000
79D79GLU-1-0.817-0.90232.3278.5188.5180.0000.0000.0000.000
80D80SER00.008-0.02332.5510.2450.2450.0000.0000.0000.000
81D81GLU-1-0.837-0.89831.4809.7709.7700.0000.0000.0000.000
82D82ASP-1-0.746-0.84728.41610.76210.7620.0000.0000.0000.000
83D83PHE0-0.0270.00427.3320.4530.4530.0000.0000.0000.000
84D84VAL0-0.038-0.01924.901-0.066-0.0660.0000.0000.0000.000
85D85ASP-1-0.854-0.92620.70913.42313.4230.0000.0000.0000.000
86D86TYR0-0.020-0.03119.676-0.047-0.0470.0000.0000.0000.000
87D87TYR0-0.0040.00114.2780.6800.6800.0000.0000.0000.000
88D89LEU00.000-0.0069.9351.0211.0210.0000.0000.0000.000
89D90GLN00.0000.0015.366-6.109-6.1090.0000.0000.0000.000
90D91TYR0-0.006-0.0289.1921.5691.5690.0000.0000.0000.000
91D92SER00.0120.0238.850-2.260-2.2600.0000.0000.0000.000
92D93SER0-0.066-0.0465.602-0.408-0.4080.0000.0000.0000.000
93D94SER00.0030.0046.6200.8190.8190.0000.0000.0000.000
94D95PRO00.0140.0362.400-12.131-8.9903.282-2.766-3.6570.022
95D96TRP00.001-0.0014.642-0.622-0.542-0.001-0.023-0.0570.000
96D97THR0-0.023-0.0183.308-0.1170.4590.022-0.145-0.4530.000
97D98PHE00.024-0.0056.751-3.890-3.8900.0000.0000.0000.000
98D99GLY00.0110.0058.5151.9621.9620.0000.0000.0000.000
99D100GLY0-0.045-0.04011.122-0.143-0.1430.0000.0000.0000.000
100D101GLY00.0160.02212.658-0.703-0.7030.0000.0000.0000.000
101D102THR0-0.073-0.05315.9990.0150.0150.0000.0000.0000.000
102D103LYS10.8640.95519.511-12.050-12.0500.0000.0000.0000.000
103D104LEU0-0.023-0.00822.851-0.168-0.1680.0000.0000.0000.000
104D105GLU-1-0.785-0.82325.96010.04310.0430.0000.0000.0000.000
105D106ILE00.004-0.00429.178-0.081-0.0810.0000.0000.0000.000
106D107LYS10.8000.88532.154-9.409-9.4090.0000.0000.0000.000
107D108ARG10.7980.88434.046-7.894-7.8940.0000.0000.0000.000
108D109ALA00.0170.00537.5760.0450.0450.0000.0000.0000.000
109D110ASP-1-0.817-0.88038.2068.1138.1130.0000.0000.0000.000
110D111ALA0-0.022-0.01539.932-0.200-0.2000.0000.0000.0000.000
111D112ALA00.0230.01740.3970.1830.1830.0000.0000.0000.000
112D113PRO0-0.0060.01540.346-0.060-0.0600.0000.0000.0000.000
113D114THR00.0240.00642.256-0.221-0.2210.0000.0000.0000.000
114D115VAL0-0.053-0.02742.9830.0090.0090.0000.0000.0000.000
115D116SER0-0.027-0.00645.065-0.281-0.2810.0000.0000.0000.000
116D117ILE0-0.011-0.00645.7560.1460.1460.0000.0000.0000.000
117D118PHE0-0.002-0.00346.322-0.181-0.1810.0000.0000.0000.000
118D119PRO00.014-0.00548.2300.1280.1280.0000.0000.0000.000
119D120PRO0-0.0010.00948.7700.0380.0380.0000.0000.0000.000
120D121SER00.0210.02149.851-0.182-0.1820.0000.0000.0000.000
121D122SER00.0440.01051.8320.0530.0530.0000.0000.0000.000
122D123GLU-1-0.823-0.90352.9425.7725.7720.0000.0000.0000.000
123D124GLN0-0.025-0.01345.6750.0100.0100.0000.0000.0000.000
124D125LEU0-0.001-0.00250.6960.0170.0170.0000.0000.0000.000
125D126THR0-0.052-0.03753.395-0.003-0.0030.0000.0000.0000.000
126D127SER0-0.046-0.02550.290-0.029-0.0290.0000.0000.0000.000
127D128GLY0-0.0200.00250.8340.0950.0950.0000.0000.0000.000
128D129GLY0-0.033-0.01748.1770.0930.0930.0000.0000.0000.000
129D130ALA0-0.036-0.03647.596-0.116-0.1160.0000.0000.0000.000
130D131SER0-0.035-0.01043.6780.1250.1250.0000.0000.0000.000
131D132VAL0-0.0170.01044.780-0.064-0.0640.0000.0000.0000.000
132D133VAL00.0250.01141.8740.2070.2070.0000.0000.0000.000
133D134CYS0-0.052-0.02342.259-0.248-0.2480.0000.0000.0000.000
134D135PHE00.0080.01441.3060.2170.2170.0000.0000.0000.000
135D136LEU00.004-0.02238.476-0.198-0.1980.0000.0000.0000.000
136D137ASN00.0410.00439.4110.3580.3580.0000.0000.0000.000
137D138ASN00.008-0.01139.933-0.281-0.2810.0000.0000.0000.000
138D139PHE0-0.0210.00234.651-0.164-0.1640.0000.0000.0000.000
139D140TYR00.031-0.01732.1410.1120.1120.0000.0000.0000.000
140D141PRO00.006-0.00532.585-0.253-0.2530.0000.0000.0000.000
141D142LYS10.9210.94026.704-11.069-11.0690.0000.0000.0000.000
142D143ASP-1-0.876-0.90428.93010.52510.5250.0000.0000.0000.000
143D144ILE0-0.019-0.01131.880-0.344-0.3440.0000.0000.0000.000
144D145ASN0-0.0080.00133.4070.3840.3840.0000.0000.0000.000
145D146VAL00.0440.01735.659-0.247-0.2470.0000.0000.0000.000
146D147LYS10.9150.96436.298-8.335-8.3350.0000.0000.0000.000
147D159VAL0-0.0020.00236.107-0.108-0.1080.0000.0000.0000.000
148D160LEU0-0.038-0.02133.5910.3020.3020.0000.0000.0000.000
149D161ASN0-0.005-0.01732.804-0.500-0.5000.0000.0000.0000.000
150D162SER0-0.0060.00332.5100.3360.3360.0000.0000.0000.000
151D163TRP00.026-0.01629.670-0.214-0.2140.0000.0000.0000.000
152D164THR00.0060.00932.2600.0870.0870.0000.0000.0000.000
153D165ASP-1-0.892-0.94430.0149.9969.9960.0000.0000.0000.000
154D166GLN0-0.040-0.02131.380-0.078-0.0780.0000.0000.0000.000
155D167ASP-1-0.829-0.92633.1858.1588.1580.0000.0000.0000.000
156D168SER00.002-0.00136.076-0.180-0.1800.0000.0000.0000.000
157D169LYS10.9170.96337.152-7.317-7.3170.0000.0000.0000.000
158D170ASP-1-0.837-0.90539.6367.4827.4820.0000.0000.0000.000
159D171SER00.0080.02235.827-0.109-0.1090.0000.0000.0000.000
160D172THR0-0.106-0.04935.9440.1810.1810.0000.0000.0000.000
161D173TYR0-0.014-0.03030.0030.2780.2780.0000.0000.0000.000
162D174SER00.0400.02835.736-0.366-0.3660.0000.0000.0000.000
163D175MET0-0.048-0.00234.3740.2770.2770.0000.0000.0000.000
164D176SER0-0.0060.00236.489-0.343-0.3430.0000.0000.0000.000
165D177SER00.0150.00836.7100.2550.2550.0000.0000.0000.000
166D178THR0-0.008-0.00938.507-0.313-0.3130.0000.0000.0000.000
167D179LEU00.0240.02039.3480.1470.1470.0000.0000.0000.000
168D196ALA00.0190.00940.1540.0410.0410.0000.0000.0000.000
169D197THR0-0.052-0.03838.410-0.151-0.1510.0000.0000.0000.000
170D198HIS00.0640.03836.3540.0190.0190.0000.0000.0000.000
171D199LYS10.8880.92336.036-8.406-8.4060.0000.0000.0000.000
172D200THR0-0.022-0.02538.357-0.169-0.1690.0000.0000.0000.000
173D201SER0-0.042-0.00941.652-0.254-0.2540.0000.0000.0000.000
174D202THR00.0150.00842.5510.0920.0920.0000.0000.0000.000
175D203SER0-0.043-0.02844.467-0.066-0.0660.0000.0000.0000.000
176D204PRO0-0.020-0.01642.4730.0110.0110.0000.0000.0000.000
177D205ILE00.0340.03243.601-0.188-0.1880.0000.0000.0000.000
178D206VAL0-0.009-0.00645.2620.1010.1010.0000.0000.0000.000
179D207LYS10.8850.93247.122-6.553-6.5530.0000.0000.0000.000
180D208SER0-0.015-0.01747.8910.1220.1220.0000.0000.0000.000
181D209PHE00.0280.03149.318-0.070-0.0700.0000.0000.0000.000