Manual

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: 72Z8K

Calculation Name: 5UG0-D-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 5UG0

Chain ID: D

ChEMBL ID:

UniProt ID: A7UPX0

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2218393.338751
FMO2-HF: Nuclear repulsion 2133954.828267
FMO2-HF: Total energy -84438.510484
FMO2-MP2: Total energy -84683.802094


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:GLU)


Summations of interaction energy for fragment #1(D:1:GLU)
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.
-28.037-25.8280.019-1.006-1.2220.005
Interaction energy analysis for fragmet #1(D:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.894 / q_NPA : -0.951
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].
3D3GLN0-0.0020.0043.899-2.604-0.984-0.008-0.798-0.8140.004
4D4LEU00.000-0.0226.415-1.588-1.5880.0000.0000.0000.000
5D5VAL00.0410.0248.509-0.630-0.6300.0000.0000.0000.000
6D6GLU-1-0.802-0.90311.07915.86015.8600.0000.0000.0000.000
7D7SER00.014-0.00214.856-0.235-0.2350.0000.0000.0000.000
8D8GLY00.0480.02117.772-0.174-0.1740.0000.0000.0000.000
9D9GLY0-0.0100.00421.589-0.182-0.1820.0000.0000.0000.000
10D10GLY00.0510.01824.7140.1650.1650.0000.0000.0000.000
11D11LEU0-0.065-0.02826.624-0.188-0.1880.0000.0000.0000.000
12D12VAL00.0150.01930.086-0.038-0.0380.0000.0000.0000.000
13D13GLN00.0360.00232.759-0.007-0.0070.0000.0000.0000.000
14D14PRO00.0050.01835.5580.1820.1820.0000.0000.0000.000
15D15GLY00.0160.00236.965-0.212-0.2120.0000.0000.0000.000
16D16GLY0-0.0030.00235.155-0.071-0.0710.0000.0000.0000.000
17D17SER0-0.050-0.03731.9470.0520.0520.0000.0000.0000.000
18D18LEU0-0.0130.00725.885-0.100-0.1000.0000.0000.0000.000
19D19ARG10.8450.92023.272-11.300-11.3000.0000.0000.0000.000
20D20LEU00.0060.01620.5660.0290.0290.0000.0000.0000.000
21D21SER0-0.045-0.04018.141-0.172-0.1720.0000.0000.0000.000
22D22CYS0-0.0170.01013.9250.0280.0280.0000.0000.0000.000
23D23ALA00.0230.03411.904-0.304-0.3040.0000.0000.0000.000
24D24ALA00.0060.0019.5231.0321.0320.0000.0000.0000.000
25D25SER0-0.009-0.0134.430-1.423-1.284-0.001-0.010-0.1270.000
26D26GLY00.0270.0063.4381.1661.4150.029-0.193-0.0850.001
27D27PHE0-0.006-0.0014.1782.3662.567-0.001-0.005-0.1960.000
28D28THR00.0580.0327.380-1.347-1.3470.0000.0000.0000.000
29D29PHE00.0120.00011.107-1.104-1.1040.0000.0000.0000.000
30D30ASN0-0.027-0.03112.6230.0540.0540.0000.0000.0000.000
31D31ILE0-0.0010.01813.505-0.966-0.9660.0000.0000.0000.000
32D32TYR0-0.071-0.08110.9530.3670.3670.0000.0000.0000.000
33D33ASP-1-0.819-0.90315.43613.54313.5430.0000.0000.0000.000
34D34MET0-0.058-0.02213.0391.3151.3150.0000.0000.0000.000
35D35HIS0-0.035-0.03816.749-0.445-0.4450.0000.0000.0000.000
36D36TRP0-0.0070.00918.1700.6850.6850.0000.0000.0000.000
37D37VAL0-0.004-0.00819.539-0.684-0.6840.0000.0000.0000.000
38D38ARG10.7830.86220.921-10.182-10.1820.0000.0000.0000.000
39D39GLN00.0380.02022.278-0.323-0.3230.0000.0000.0000.000
40D40ALA00.0240.02224.441-0.062-0.0620.0000.0000.0000.000
41D41PRO0-0.009-0.02427.2180.2340.2340.0000.0000.0000.000
42D42GLY0-0.0170.02528.847-0.053-0.0530.0000.0000.0000.000
43D43LYS10.9430.95325.849-11.440-11.4400.0000.0000.0000.000
44D44GLY0-0.0120.00126.082-0.390-0.3900.0000.0000.0000.000
45D45LEU0-0.012-0.00720.6910.0210.0210.0000.0000.0000.000
46D46GLU-1-0.776-0.85024.5259.9409.9400.0000.0000.0000.000
47D47TRP00.0060.00122.8600.0410.0410.0000.0000.0000.000
48D48VAL0-0.023-0.02624.052-0.526-0.5260.0000.0000.0000.000
49D49SER0-0.008-0.02923.851-0.289-0.2890.0000.0000.0000.000
50D50SER0-0.017-0.00521.9920.7090.7090.0000.0000.0000.000
51D51ILE0-0.048-0.01520.624-0.666-0.6660.0000.0000.0000.000
52D52THR00.0270.00220.7980.6710.6710.0000.0000.0000.000
53D53THR0-0.066-0.06118.3660.0170.0170.0000.0000.0000.000
54D54ALA0-0.0300.00020.884-0.130-0.1300.0000.0000.0000.000
55D55GLY00.0100.00124.400-0.325-0.3250.0000.0000.0000.000
56D56ASP-1-0.873-0.90325.45810.56010.5600.0000.0000.0000.000
57D57THR0-0.052-0.03625.4600.3610.3610.0000.0000.0000.000
58D58TYR0-0.0050.00725.762-0.535-0.5350.0000.0000.0000.000
59D59TYR00.0260.00526.8050.4580.4580.0000.0000.0000.000
60D60PRO00.0290.04428.031-0.339-0.3390.0000.0000.0000.000
61D61GLY00.002-0.01730.978-0.152-0.1520.0000.0000.0000.000
62D62SER0-0.023-0.02430.897-0.224-0.2240.0000.0000.0000.000
63D63VAL00.0150.00128.730-0.155-0.1550.0000.0000.0000.000
64D64LYS10.9480.96832.049-8.661-8.6610.0000.0000.0000.000
65D65GLY00.0050.01433.140-0.062-0.0620.0000.0000.0000.000
66D66ARG10.8390.91933.267-8.366-8.3660.0000.0000.0000.000
67D67PHE00.0300.01327.5160.0500.0500.0000.0000.0000.000
68D68THR00.0090.00428.329-0.083-0.0830.0000.0000.0000.000
69D69THR00.0320.02922.2330.2390.2390.0000.0000.0000.000
70D70SER0-0.016-0.00723.004-0.378-0.3780.0000.0000.0000.000
71D71ARG10.8110.89116.330-15.009-15.0090.0000.0000.0000.000
72D72GLU-1-0.868-0.95219.04311.79511.7950.0000.0000.0000.000
73D73ASN00.0510.02517.3091.0481.0480.0000.0000.0000.000
74D74ALA00.0160.02117.0010.5990.5990.0000.0000.0000.000
75D75LYS10.8920.94616.474-12.832-12.8320.0000.0000.0000.000
76D76ASN0-0.0050.01311.9790.7780.7780.0000.0000.0000.000
77D77SER00.0180.00713.1380.8040.8040.0000.0000.0000.000
78D78LEU0-0.009-0.00115.718-0.646-0.6460.0000.0000.0000.000
79D79TYR0-0.009-0.03017.7990.1010.1010.0000.0000.0000.000
80D80LEU00.0080.01320.765-0.146-0.1460.0000.0000.0000.000
81D81GLN00.0200.03023.5680.1460.1460.0000.0000.0000.000
82D82MET0-0.005-0.00125.8580.0320.0320.0000.0000.0000.000
83D83ASN00.022-0.01229.026-0.016-0.0160.0000.0000.0000.000
84D84SER0-0.006-0.00332.758-0.028-0.0280.0000.0000.0000.000
85D85LEU00.0280.02929.652-0.094-0.0940.0000.0000.0000.000
86D86ARG10.7760.83732.855-9.117-9.1170.0000.0000.0000.000
87D87ALA00.0290.00034.3880.2000.2000.0000.0000.0000.000
88D88GLY00.0100.00434.1140.1110.1110.0000.0000.0000.000
89D89ASP-1-0.781-0.83230.6099.4909.4900.0000.0000.0000.000
90D90THR0-0.0030.02129.2790.3390.3390.0000.0000.0000.000
91D91GLY00.0360.01126.640-0.032-0.0320.0000.0000.0000.000
92D92VAL0-0.045-0.01120.225-0.055-0.0550.0000.0000.0000.000
93D93TYR0-0.010-0.03621.537-0.079-0.0790.0000.0000.0000.000
94D94TYR00.0350.01516.300-0.030-0.0300.0000.0000.0000.000
95D96THR00.012-0.01613.7960.6930.6930.0000.0000.0000.000
96D97ARG10.8990.9579.967-26.049-26.0490.0000.0000.0000.000
97D98GLY0-0.016-0.01013.0401.5901.5900.0000.0000.0000.000
98D99VAL00.0020.01415.455-0.847-0.8470.0000.0000.0000.000
99D100ARG10.8280.91314.602-16.581-16.5810.0000.0000.0000.000
100D101GLU-1-0.802-0.87916.96813.79213.7920.0000.0000.0000.000
101D102VAL00.002-0.00120.280-0.297-0.2970.0000.0000.0000.000
102D103GLY0-0.003-0.00921.6450.3530.3530.0000.0000.0000.000
103D104ALA00.0080.02517.234-0.134-0.1340.0000.0000.0000.000
104D105THR0-0.001-0.00817.6130.4650.4650.0000.0000.0000.000
105D106GLY0-0.070-0.04717.519-0.649-0.6490.0000.0000.0000.000
106D107ASP-1-0.835-0.90214.04119.17519.1750.0000.0000.0000.000
107D108ASP-1-0.790-0.86810.68527.15427.1540.0000.0000.0000.000
108D109PRO0-0.015-0.01011.464-1.891-1.8910.0000.0000.0000.000
109D110PHE0-0.0200.00414.3340.1870.1870.0000.0000.0000.000
110D111TYR00.0160.00410.804-0.293-0.2930.0000.0000.0000.000
111D112TYR00.0150.00117.4190.2110.2110.0000.0000.0000.000
112D113GLY00.005-0.00217.171-0.398-0.3980.0000.0000.0000.000
113D114MET0-0.051-0.01514.9580.6190.6190.0000.0000.0000.000
114D115TYR00.0100.0186.197-2.183-2.1830.0000.0000.0000.000
115D116VAL00.0040.0077.3991.3281.3280.0000.0000.0000.000
116D117TRP0-0.005-0.0289.862-3.240-3.2400.0000.0000.0000.000
117D118GLY00.0510.04110.0891.8311.8310.0000.0000.0000.000
118D119GLN0-0.058-0.03612.1070.6280.6280.0000.0000.0000.000
119D120GLY00.0190.01513.650-0.903-0.9030.0000.0000.0000.000
120D121THR0-0.085-0.05517.031-0.104-0.1040.0000.0000.0000.000
121D122THR0-0.036-0.00419.950-0.202-0.2020.0000.0000.0000.000
122D123VAL0-0.012-0.00623.437-0.169-0.1690.0000.0000.0000.000
123D124THR00.005-0.00326.471-0.025-0.0250.0000.0000.0000.000
124D125VAL00.0030.00530.169-0.038-0.0380.0000.0000.0000.000
125D126SER0-0.048-0.05233.574-0.151-0.1510.0000.0000.0000.000
126D127GLY00.0320.00336.517-0.034-0.0340.0000.0000.0000.000
127D128ALA0-0.016-0.01739.774-0.196-0.1960.0000.0000.0000.000
128D129SER00.0250.01836.2900.0390.0390.0000.0000.0000.000
129D130THR0-0.0220.00135.568-0.130-0.1300.0000.0000.0000.000
130D131LYS10.9520.99237.774-7.217-7.2170.0000.0000.0000.000
131D132GLY00.0670.03838.6400.1990.1990.0000.0000.0000.000
132D133PRO0-0.048-0.02038.091-0.118-0.1180.0000.0000.0000.000
133D134SER00.0200.02640.724-0.113-0.1130.0000.0000.0000.000
134D135VAL00.008-0.01741.6720.1350.1350.0000.0000.0000.000
135D136PHE0-0.021-0.01244.503-0.139-0.1390.0000.0000.0000.000
136D137PRO0-0.021-0.00946.1200.0550.0550.0000.0000.0000.000
137D138LEU0-0.0040.01347.846-0.128-0.1280.0000.0000.0000.000
138D139ALA0-0.005-0.01350.9250.0360.0360.0000.0000.0000.000
139D140PRO0-0.016-0.02754.0720.0010.0010.0000.0000.0000.000
140D141SER0-0.0220.01356.783-0.113-0.1130.0000.0000.0000.000
141D142SER00.0150.01153.263-0.054-0.0540.0000.0000.0000.000
142D143LYS10.9240.97055.575-5.764-5.7640.0000.0000.0000.000
143D144SER0-0.002-0.02456.136-0.133-0.1330.0000.0000.0000.000
144D145THR0-0.0120.00454.4210.1440.1440.0000.0000.0000.000
145D146SER0-0.028-0.03253.862-0.138-0.1380.0000.0000.0000.000
146D147GLY00.0440.02351.8690.0940.0940.0000.0000.0000.000
147D148GLY00.0170.01750.6630.1130.1130.0000.0000.0000.000
148D149THR0-0.065-0.04250.6760.0280.0280.0000.0000.0000.000
149D150ALA00.0360.03549.001-0.082-0.0820.0000.0000.0000.000
150D151ALA00.0250.00646.1600.1790.1790.0000.0000.0000.000
151D152LEU0-0.0110.00946.552-0.145-0.1450.0000.0000.0000.000
152D153GLY00.0230.00144.4420.1880.1880.0000.0000.0000.000
153D154CYS0-0.060-0.03441.7660.0110.0110.0000.0000.0000.000
154D155LEU00.0160.02242.7420.1780.1780.0000.0000.0000.000
155D156VAL0-0.0050.00438.213-0.105-0.1050.0000.0000.0000.000
156D157LYS10.8530.88540.778-6.736-6.7360.0000.0000.0000.000
157D158ASP-1-0.815-0.88741.8326.8416.8410.0000.0000.0000.000
158D159TYR00.0540.03433.753-0.059-0.0590.0000.0000.0000.000
159D160PHE00.0170.00834.8250.1130.1130.0000.0000.0000.000
160D161PRO0-0.0010.00631.455-0.150-0.1500.0000.0000.0000.000
161D162GLU-1-0.805-0.88429.8139.6499.6490.0000.0000.0000.000
162D163PRO0-0.033-0.03127.5640.1330.1330.0000.0000.0000.000
163D164VAL00.010-0.00930.531-0.147-0.1470.0000.0000.0000.000
164D165THR0-0.042-0.01330.3590.1700.1700.0000.0000.0000.000
165D166VAL00.0290.01032.547-0.305-0.3050.0000.0000.0000.000
166D167SER0-0.039-0.03034.0090.3050.3050.0000.0000.0000.000
167D168TRP00.0620.02436.345-0.316-0.3160.0000.0000.0000.000
168D169ASN00.014-0.00238.7720.1180.1180.0000.0000.0000.000
169D170SER0-0.010-0.01037.1830.0060.0060.0000.0000.0000.000
170D171GLY00.0180.01834.8300.2210.2210.0000.0000.0000.000
171D172ALA0-0.0110.01035.5550.1280.1280.0000.0000.0000.000
172D173LEU0-0.019-0.00238.309-0.001-0.0010.0000.0000.0000.000
173D174THR00.0190.00534.0900.1890.1890.0000.0000.0000.000
174D175SER0-0.032-0.03435.5770.1400.1400.0000.0000.0000.000
175D176GLY00.0330.02337.915-0.151-0.1510.0000.0000.0000.000
176D177VAL0-0.029-0.01436.588-0.153-0.1530.0000.0000.0000.000
177D178HIS0-0.0090.00536.6250.2860.2860.0000.0000.0000.000
178D179THR00.005-0.00533.026-0.288-0.2880.0000.0000.0000.000
179D180PHE0-0.019-0.01434.2710.2410.2410.0000.0000.0000.000
180D181PRO00.012-0.00632.2000.0540.0540.0000.0000.0000.000
181D182ALA0-0.0170.00932.505-0.301-0.3010.0000.0000.0000.000
182D183VAL00.002-0.00634.1610.1500.1500.0000.0000.0000.000
183D184LEU0-0.039-0.00935.847-0.184-0.1840.0000.0000.0000.000
184D185GLN00.0010.01037.719-0.132-0.1320.0000.0000.0000.000
185D186SER00.019-0.00741.3500.0820.0820.0000.0000.0000.000
186D187SER0-0.007-0.01343.874-0.121-0.1210.0000.0000.0000.000
187D188GLY0-0.0160.01039.9730.0030.0030.0000.0000.0000.000
188D189LEU0-0.046-0.02438.780-0.133-0.1330.0000.0000.0000.000
189D190TYR0-0.033-0.04231.608-0.114-0.1140.0000.0000.0000.000
190D191SER0-0.074-0.03137.914-0.252-0.2520.0000.0000.0000.000
191D192LEU00.0240.02134.7840.1570.1570.0000.0000.0000.000
192D193SER00.0390.01938.536-0.232-0.2320.0000.0000.0000.000
193D194SER0-0.021-0.00538.3330.2470.2470.0000.0000.0000.000
194D195VAL00.0110.00139.786-0.244-0.2440.0000.0000.0000.000
195D196VAL00.0200.01140.5590.2340.2340.0000.0000.0000.000
196D197THR00.0060.00242.625-0.134-0.1340.0000.0000.0000.000
197D198VAL0-0.035-0.01244.8610.0670.0670.0000.0000.0000.000
198D199PRO00.0430.00947.190-0.074-0.0740.0000.0000.0000.000
199D200SER00.026-0.00849.858-0.036-0.0360.0000.0000.0000.000
200D201SER00.0090.01753.496-0.123-0.1230.0000.0000.0000.000
201D202SER0-0.036-0.01150.558-0.052-0.0520.0000.0000.0000.000
202D203LEU00.0080.01151.7270.0850.0850.0000.0000.0000.000
203D204GLY00.0390.01653.0160.0320.0320.0000.0000.0000.000
204D205THR0-0.040-0.01151.836-0.010-0.0100.0000.0000.0000.000
205D206GLN00.024-0.00347.2780.0280.0280.0000.0000.0000.000
206D207THR0-0.042-0.00148.7550.0590.0590.0000.0000.0000.000
207D208TYR00.0600.03544.4090.0960.0960.0000.0000.0000.000
208D209ILE0-0.041-0.04242.489-0.111-0.1110.0000.0000.0000.000
209D211ASN00.0070.00338.2130.0210.0210.0000.0000.0000.000
210D212VAL00.0080.00337.3900.1990.1990.0000.0000.0000.000
211D213ASN00.015-0.00332.051-0.305-0.3050.0000.0000.0000.000
212D214HIS00.003-0.00633.8610.0970.0970.0000.0000.0000.000
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