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

tag_button

FMODB ID: 94252

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 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 -2209928.48085
FMO2-HF: Nuclear repulsion 2125492.060052
FMO2-HF: Total energy -84436.420798
FMO2-MP2: Total energy -84681.800676


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.
-27.321-25.9390.029-0.497-0.9130.002
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 : -0.938 / q_NPA : -0.981
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].
3D3GLN00.0140.0033.750-0.7390.275-0.006-0.366-0.6420.002
4D4LEU00.001-0.0076.359-2.352-2.3520.0000.0000.0000.000
5D5VAL0-0.019-0.0068.862-0.324-0.3240.0000.0000.0000.000
6D6GLU-1-0.794-0.91311.39216.39116.3910.0000.0000.0000.000
7D7SER0-0.010-0.00815.156-0.273-0.2730.0000.0000.0000.000
8D8GLY00.0490.01217.917-0.212-0.2120.0000.0000.0000.000
9D9GLY0-0.0140.00121.697-0.147-0.1470.0000.0000.0000.000
10D10GLY00.0260.01324.4200.3130.3130.0000.0000.0000.000
11D11LEU0-0.059-0.01527.038-0.203-0.2030.0000.0000.0000.000
12D12VAL00.0340.01630.165-0.009-0.0090.0000.0000.0000.000
13D13GLN00.0220.00332.8390.0230.0230.0000.0000.0000.000
14D14PRO00.0070.00335.7200.1850.1850.0000.0000.0000.000
15D15GLY00.0360.03436.636-0.235-0.2350.0000.0000.0000.000
16D16GLY0-0.030-0.01234.900-0.098-0.0980.0000.0000.0000.000
17D17SER0-0.038-0.04531.8580.0890.0890.0000.0000.0000.000
18D18LEU0-0.0150.00225.983-0.061-0.0610.0000.0000.0000.000
19D19ARG10.9260.97422.848-11.406-11.4060.0000.0000.0000.000
20D20LEU0-0.0120.00420.6720.0660.0660.0000.0000.0000.000
21D21SER0-0.021-0.02117.948-0.313-0.3130.0000.0000.0000.000
22D22CYS0-0.056-0.01214.364-0.099-0.0990.0000.0000.0000.000
23D23ALA00.0400.03611.308-0.098-0.0980.0000.0000.0000.000
24D24ALA00.0270.0139.3440.9700.9700.0000.0000.0000.000
25D25SER0-0.049-0.0285.201-0.402-0.4020.0000.0000.0000.000
26D26GLY00.0810.0253.4031.5181.6600.036-0.128-0.0500.000
27D27PHE0-0.017-0.0054.1212.4582.684-0.001-0.003-0.2210.000
28D28THR00.0380.0267.199-1.400-1.4000.0000.0000.0000.000
29D29PHE00.0670.02610.935-0.543-0.5430.0000.0000.0000.000
30D30ASN0-0.017-0.03612.7630.4150.4150.0000.0000.0000.000
31D31ILE00.0190.02413.270-0.834-0.8340.0000.0000.0000.000
32D32TYR0-0.053-0.05310.9900.1590.1590.0000.0000.0000.000
33D33ASP-1-0.864-0.91615.45313.98913.9890.0000.0000.0000.000
34D34MET0-0.064-0.02713.1041.3071.3070.0000.0000.0000.000
35D35HIS0-0.023-0.03916.962-0.441-0.4410.0000.0000.0000.000
36D36TRP00.0060.01618.2010.6440.6440.0000.0000.0000.000
37D37VAL0-0.013-0.01219.434-0.718-0.7180.0000.0000.0000.000
38D38ARG10.8460.92521.028-10.205-10.2050.0000.0000.0000.000
39D39GLN00.0150.00621.734-0.626-0.6260.0000.0000.0000.000
40D40ALA00.0190.01624.440-0.004-0.0040.0000.0000.0000.000
41D41PRO0-0.008-0.01527.0680.2440.2440.0000.0000.0000.000
42D42GLY0-0.0260.00828.6330.0650.0650.0000.0000.0000.000
43D43LYS10.9700.97526.651-11.287-11.2870.0000.0000.0000.000
44D44GLY0-0.008-0.00426.595-0.337-0.3370.0000.0000.0000.000
45D45LEU0-0.008-0.00320.517-0.062-0.0620.0000.0000.0000.000
46D46GLU-1-0.835-0.91524.60110.19110.1910.0000.0000.0000.000
47D47TRP00.0030.00223.0080.1340.1340.0000.0000.0000.000
48D48VAL0-0.017-0.01824.137-0.525-0.5250.0000.0000.0000.000
49D49SER00.008-0.00723.647-0.292-0.2920.0000.0000.0000.000
50D50SER0-0.046-0.02421.9560.6890.6890.0000.0000.0000.000
51D51ILE0-0.0170.01120.537-0.627-0.6270.0000.0000.0000.000
52D52THR00.0710.04720.7500.6860.6860.0000.0000.0000.000
53D53THR0-0.035-0.02118.366-0.020-0.0200.0000.0000.0000.000
54D54ALA0-0.0110.00420.858-0.059-0.0590.0000.0000.0000.000
55D55GLY0-0.033-0.00923.758-0.349-0.3490.0000.0000.0000.000
56D56ASP-1-0.889-0.94224.98110.22810.2280.0000.0000.0000.000
57D57THR0-0.063-0.03725.4350.3660.3660.0000.0000.0000.000
58D58TYR00.0120.00725.881-0.407-0.4070.0000.0000.0000.000
59D59TYR00.0100.00026.8710.4720.4720.0000.0000.0000.000
60D60PRO00.0090.03827.887-0.380-0.3800.0000.0000.0000.000
61D61GLY0-0.004-0.02330.880-0.112-0.1120.0000.0000.0000.000
62D62SER0-0.0140.00230.825-0.201-0.2010.0000.0000.0000.000
63D63VAL00.013-0.01729.609-0.261-0.2610.0000.0000.0000.000
64D64LYS10.9300.98032.232-8.499-8.4990.0000.0000.0000.000
65D65GLY0-0.032-0.00833.413-0.054-0.0540.0000.0000.0000.000
66D66ARG10.9020.95833.529-8.244-8.2440.0000.0000.0000.000
67D67PHE00.0380.01527.4460.1250.1250.0000.0000.0000.000
68D68THR00.0210.00828.325-0.059-0.0590.0000.0000.0000.000
69D69THR00.0300.01022.2900.0730.0730.0000.0000.0000.000
70D70SER0-0.0130.00123.073-0.298-0.2980.0000.0000.0000.000
71D71ARG10.8370.91116.480-14.808-14.8080.0000.0000.0000.000
72D72GLU-1-0.927-0.95518.87211.48411.4840.0000.0000.0000.000
73D73ASN00.042-0.00317.0010.7710.7710.0000.0000.0000.000
74D74ALA00.0100.02816.4500.5750.5750.0000.0000.0000.000
75D75LYS10.9310.95116.439-12.818-12.8180.0000.0000.0000.000
76D76ASN0-0.008-0.00111.8240.9390.9390.0000.0000.0000.000
77D77SER00.0100.02113.2810.7780.7780.0000.0000.0000.000
78D78LEU00.0060.00915.667-0.636-0.6360.0000.0000.0000.000
79D79TYR0-0.036-0.04218.0100.2060.2060.0000.0000.0000.000
80D80LEU0-0.0030.00820.947-0.199-0.1990.0000.0000.0000.000
81D81GLN0-0.022-0.00323.7290.1390.1390.0000.0000.0000.000
82D82MET00.0100.01226.363-0.079-0.0790.0000.0000.0000.000
83D83ASN00.0410.00429.174-0.028-0.0280.0000.0000.0000.000
84D84SER0-0.029-0.03132.807-0.005-0.0050.0000.0000.0000.000
85D85LEU0-0.0080.01529.901-0.148-0.1480.0000.0000.0000.000
86D86ARG10.9070.95333.512-9.165-9.1650.0000.0000.0000.000
87D87ALA00.016-0.00534.9800.1250.1250.0000.0000.0000.000
88D88GLY00.025-0.00734.2250.1320.1320.0000.0000.0000.000
89D89ASP-1-0.835-0.91530.8489.6169.6160.0000.0000.0000.000
90D90THR0-0.0160.01029.5250.3140.3140.0000.0000.0000.000
91D91GLY00.0370.01826.746-0.027-0.0270.0000.0000.0000.000
92D92VAL0-0.026-0.00820.177-0.046-0.0460.0000.0000.0000.000
93D93TYR0-0.021-0.02221.561-0.089-0.0890.0000.0000.0000.000
94D94TYR0-0.012-0.00416.213-0.183-0.1830.0000.0000.0000.000
95D96THR00.002-0.01013.7451.1251.1250.0000.0000.0000.000
96D97ARG10.9410.9827.553-28.223-28.2230.0000.0000.0000.000
97D98GLY0-0.011-0.00413.4751.0141.0140.0000.0000.0000.000
98D99VAL0-0.0110.00016.037-0.522-0.5220.0000.0000.0000.000
99D100ARG10.9170.95914.897-16.484-16.4840.0000.0000.0000.000
100D101GLU-1-0.874-0.94116.64513.46913.4690.0000.0000.0000.000
101D102VAL00.0350.00819.846-0.526-0.5260.0000.0000.0000.000
102D103GLY0-0.050-0.00921.6060.2470.2470.0000.0000.0000.000
103D104ALA0-0.007-0.00216.962-0.010-0.0100.0000.0000.0000.000
104D105THR0-0.023-0.02417.6620.2710.2710.0000.0000.0000.000
105D106GLY0-0.030-0.01117.813-0.829-0.8290.0000.0000.0000.000
106D107ASP-1-0.890-0.93113.78119.75719.7570.0000.0000.0000.000
107D108ASP-1-0.856-0.90810.82626.10226.1020.0000.0000.0000.000
108D109PRO00.006-0.01011.682-1.852-1.8520.0000.0000.0000.000
109D110PHE0-0.030-0.01014.4740.2110.2110.0000.0000.0000.000
110D111TYR0-0.004-0.00911.8030.1090.1090.0000.0000.0000.000
111D112TYR00.0230.00617.5510.1740.1740.0000.0000.0000.000
112D113GLY0-0.015-0.01117.346-0.413-0.4130.0000.0000.0000.000
113D114MET0-0.034-0.01114.9510.3830.3830.0000.0000.0000.000
114D115TYR0-0.008-0.0026.427-1.870-1.8700.0000.0000.0000.000
115D116VAL0-0.0020.0036.9770.7960.7960.0000.0000.0000.000
116D117TRP00.0290.0059.568-3.153-3.1530.0000.0000.0000.000
117D118GLY00.0520.03810.3211.9791.9790.0000.0000.0000.000
118D119GLN0-0.009-0.01911.9840.4420.4420.0000.0000.0000.000
119D120GLY00.0380.03014.312-0.985-0.9850.0000.0000.0000.000
120D121THR0-0.061-0.05217.5650.0210.0210.0000.0000.0000.000
121D122THR0-0.057-0.01620.359-0.229-0.2290.0000.0000.0000.000
122D123VAL00.0310.01523.993-0.241-0.2410.0000.0000.0000.000
123D124THR0-0.037-0.03226.808-0.125-0.1250.0000.0000.0000.000
124D125VAL00.0000.01330.625-0.058-0.0580.0000.0000.0000.000
125D126SER0-0.074-0.05833.994-0.166-0.1660.0000.0000.0000.000
126D127GLY00.0330.00636.829-0.031-0.0310.0000.0000.0000.000
127D128ALA0-0.019-0.01740.195-0.193-0.1930.0000.0000.0000.000
128D129SER00.0170.00336.103-0.035-0.0350.0000.0000.0000.000
129D130THR0-0.035-0.00735.581-0.118-0.1180.0000.0000.0000.000
130D131LYS10.9570.98938.026-7.246-7.2460.0000.0000.0000.000
131D132GLY00.0610.03539.6030.1790.1790.0000.0000.0000.000
132D133PRO0-0.008-0.01238.884-0.080-0.0800.0000.0000.0000.000
133D134SER0-0.0040.01641.381-0.134-0.1340.0000.0000.0000.000
134D135VAL00.004-0.01542.1850.0480.0480.0000.0000.0000.000
135D136PHE0-0.025-0.01245.207-0.126-0.1260.0000.0000.0000.000
136D137PRO0-0.041-0.02647.3940.0330.0330.0000.0000.0000.000
137D138LEU00.0230.01448.658-0.089-0.0890.0000.0000.0000.000
138D139ALA0-0.005-0.00851.5930.0170.0170.0000.0000.0000.000
139D140PRO00.0370.00555.0180.0220.0220.0000.0000.0000.000
140D141SER0-0.0130.01057.532-0.083-0.0830.0000.0000.0000.000
141D142SER00.0400.02054.315-0.018-0.0180.0000.0000.0000.000
142D143LYS10.9460.98155.531-5.816-5.8160.0000.0000.0000.000
143D144SER0-0.051-0.04256.309-0.078-0.0780.0000.0000.0000.000
144D145THR00.0220.01954.8740.1220.1220.0000.0000.0000.000
145D146SER0-0.033-0.02954.380-0.138-0.1380.0000.0000.0000.000
146D147GLY00.0420.02951.6510.0850.0850.0000.0000.0000.000
147D148GLY00.0200.01350.3920.1180.1180.0000.0000.0000.000
148D149THR0-0.053-0.04350.6120.0520.0520.0000.0000.0000.000
149D150ALA00.0460.03449.236-0.097-0.0970.0000.0000.0000.000
150D151ALA0-0.011-0.01846.6310.1730.1730.0000.0000.0000.000
151D152LEU0-0.0130.00846.886-0.132-0.1320.0000.0000.0000.000
152D153GLY00.0090.00644.7720.1470.1470.0000.0000.0000.000
153D154CYS0-0.060-0.02642.8280.0250.0250.0000.0000.0000.000
154D155LEU00.0270.02043.6940.0850.0850.0000.0000.0000.000
155D156VAL0-0.0110.00338.862-0.105-0.1050.0000.0000.0000.000
156D157LYS10.9520.96041.007-6.647-6.6470.0000.0000.0000.000
157D158ASP-1-0.849-0.94242.5286.8996.8990.0000.0000.0000.000
158D159TYR00.0240.01634.6470.0580.0580.0000.0000.0000.000
159D160PHE00.0090.02135.2780.1410.1410.0000.0000.0000.000
160D161PRO0-0.032-0.01932.219-0.180-0.1800.0000.0000.0000.000
161D162GLU-1-0.846-0.92730.5479.8839.8830.0000.0000.0000.000
162D163PRO0-0.058-0.04128.0620.1620.1620.0000.0000.0000.000
163D164VAL0-0.001-0.01131.180-0.187-0.1870.0000.0000.0000.000
164D165THR0-0.054-0.02130.9750.1580.1580.0000.0000.0000.000
165D166VAL00.0540.02333.351-0.296-0.2960.0000.0000.0000.000
166D167SER0-0.043-0.01934.8990.2310.2310.0000.0000.0000.000
167D168TRP00.0920.04437.343-0.301-0.3010.0000.0000.0000.000
168D169ASN00.016-0.01939.8780.0490.0490.0000.0000.0000.000
169D170SER0-0.029-0.01937.8010.0310.0310.0000.0000.0000.000
170D171GLY00.0010.02735.3370.1990.1990.0000.0000.0000.000
171D172ALA00.0270.01836.2060.0510.0510.0000.0000.0000.000
172D173LEU0-0.022-0.01338.788-0.015-0.0150.0000.0000.0000.000
173D174THR00.0130.00334.6410.2370.2370.0000.0000.0000.000
174D175SER0-0.033-0.02735.7660.1540.1540.0000.0000.0000.000
175D176GLY00.0370.01738.395-0.161-0.1610.0000.0000.0000.000
176D177VAL0-0.037-0.00636.921-0.147-0.1470.0000.0000.0000.000
177D178HIS00.0270.01936.4340.3270.3270.0000.0000.0000.000
178D179THR0-0.024-0.01733.026-0.268-0.2680.0000.0000.0000.000
179D180PHE0-0.007-0.01234.1820.2610.2610.0000.0000.0000.000
180D181PRO00.0130.00132.0880.0290.0290.0000.0000.0000.000
181D182ALA0-0.025-0.00433.290-0.322-0.3220.0000.0000.0000.000
182D183VAL00.0230.01134.3100.1790.1790.0000.0000.0000.000
183D184LEU0-0.071-0.00836.379-0.177-0.1770.0000.0000.0000.000
184D185GLN0-0.0310.00738.2210.0160.0160.0000.0000.0000.000
185D186SER00.005-0.01641.6480.0850.0850.0000.0000.0000.000
186D187SER0-0.024-0.01944.019-0.098-0.0980.0000.0000.0000.000
187D188GLY00.0010.00040.194-0.034-0.0340.0000.0000.0000.000
188D189LEU0-0.023-0.00739.532-0.057-0.0570.0000.0000.0000.000
189D190TYR00.0360.01532.609-0.121-0.1210.0000.0000.0000.000
190D191SER0-0.042-0.02537.979-0.201-0.2010.0000.0000.0000.000
191D192LEU00.0280.03234.8790.0480.0480.0000.0000.0000.000
192D193SER00.0230.00638.636-0.206-0.2060.0000.0000.0000.000
193D194SER0-0.034-0.02938.4870.2180.2180.0000.0000.0000.000
194D195VAL00.0160.01540.088-0.203-0.2030.0000.0000.0000.000
195D196VAL00.0460.01440.8420.2240.2240.0000.0000.0000.000
196D197THR0-0.022-0.00442.973-0.131-0.1310.0000.0000.0000.000
197D198VAL0-0.0170.00345.2480.0760.0760.0000.0000.0000.000
198D199PRO00.035-0.00148.038-0.057-0.0570.0000.0000.0000.000
199D200SER00.0240.00850.212-0.038-0.0380.0000.0000.0000.000
200D201SER00.004-0.00153.868-0.107-0.1070.0000.0000.0000.000
201D202SER0-0.013-0.00451.368-0.042-0.0420.0000.0000.0000.000
202D203LEU00.0320.02252.3750.0920.0920.0000.0000.0000.000
203D204GLY00.0050.01354.1880.0060.0060.0000.0000.0000.000
204D205THR0-0.032-0.04052.2030.0880.0880.0000.0000.0000.000
205D206GLN00.0140.01748.006-0.089-0.0890.0000.0000.0000.000
206D207THR0-0.0050.01249.7290.0360.0360.0000.0000.0000.000
207D208TYR00.0550.03545.0820.1090.1090.0000.0000.0000.000
208D209ILE0-0.052-0.03442.868-0.113-0.1130.0000.0000.0000.000
209D211ASN0-0.018-0.00739.499-0.026-0.0260.0000.0000.0000.000
210D212VAL00.0050.00238.0880.1740.1740.0000.0000.0000.000
211D213ASN0-0.003-0.00832.841-0.326-0.3260.0000.0000.0000.000
212D214HIS00.0840.06434.7280.1680.1680.0000.0000.0000.000
213D215LYS10.9870.98926.978-10.851-10.8510.0000.0000.0000.000
214D216PRO0-0.045-0.02131.814-0.038-0.0380.0000.0000.0000.000
215D217SER00.001-0.02733.474-0.148-0.1480.0000.0000.0000.000
216D218ASN0-0.044-0.01634.153-0.133-0.1330.0000.0000.0000.000
217D219THR00.0180.02937.074-0.239-0.2390.0000.0000.0000.000
218D220LYS10.9270.95135.342-8.215-8.2150.0000.0000.0000.000
219D221VAL0-0.0020.01140.504-0.202-0.2020.0000.0000.0000.000
220D222ASP-1-0.826-0.92242.5667.4767.4760.0000.0000.0000.000
221D223LYS10.9030.95845.084-6.330-6.3300.0000.0000.0000.000
222D224ARG10.9610.98346.751-6.119-6.1190.0000.0000.0000.000
223D225VAL0-0.001-0.00546.716-0.094-0.0940.0000.0000.0000.000
224D226GLU-1-0.954-0.97649.5025.9115.9110.0000.0000.0000.000
225D227PRO0-0.047-0.00152.971-0.012-0.0120.0000.0000.0000.000