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: MV2KZ

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 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 -2210464.681506
FMO2-HF: Nuclear repulsion 2126027.23615
FMO2-HF: Total energy -84437.445356
FMO2-MP2: Total energy -84682.78341


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.
-27.046-24.7530.025-1.022-1.2950.006
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 : -0.906 / q_NPA : -0.958
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].
3D3GLN0-0.004-0.0053.856-1.938-0.241-0.009-0.835-0.8530.005
4D4LEU00.0070.0006.326-1.819-1.8190.0000.0000.0000.000
5D5VAL0-0.013-0.0078.789-0.450-0.4500.0000.0000.0000.000
6D6GLU-1-0.802-0.92111.37016.08116.0810.0000.0000.0000.000
7D7SER0-0.003-0.01215.132-0.257-0.2570.0000.0000.0000.000
8D8GLY00.0510.01317.898-0.195-0.1950.0000.0000.0000.000
9D9GLY0-0.0130.00221.679-0.143-0.1430.0000.0000.0000.000
10D10GLY00.0220.01124.4000.2940.2940.0000.0000.0000.000
11D11LEU0-0.052-0.02227.019-0.190-0.1900.0000.0000.0000.000
12D12VAL00.0350.01730.249-0.011-0.0110.0000.0000.0000.000
13D13GLN00.0320.00932.8190.0140.0140.0000.0000.0000.000
14D14PRO00.0100.00935.6970.1800.1800.0000.0000.0000.000
15D15GLY00.0450.03236.599-0.228-0.2280.0000.0000.0000.000
16D16GLY0-0.033-0.01334.879-0.093-0.0930.0000.0000.0000.000
17D17SER0-0.041-0.03931.8510.0810.0810.0000.0000.0000.000
18D18LEU0-0.0040.00826.067-0.065-0.0650.0000.0000.0000.000
19D19ARG10.8820.94523.169-11.228-11.2280.0000.0000.0000.000
20D20LEU0-0.0140.01020.6100.0430.0430.0000.0000.0000.000
21D21SER0-0.019-0.02217.974-0.271-0.2710.0000.0000.0000.000
22D22CYS0-0.048-0.00714.2340.0030.0030.0000.0000.0000.000
23D23ALA00.0310.03111.516-0.035-0.0350.0000.0000.0000.000
24D24ALA00.0280.0169.3220.8010.8010.0000.0000.0000.000
25D25SER0-0.008-0.0144.601-1.492-1.354-0.001-0.008-0.1280.000
26D26GLY00.0420.0123.4111.1941.4190.036-0.175-0.0860.001
27D27PHE0-0.0070.0024.1252.5122.745-0.001-0.004-0.2280.000
28D28THR00.0490.0277.220-1.196-1.1960.0000.0000.0000.000
29D29PHE00.0600.02210.952-0.609-0.6090.0000.0000.0000.000
30D30ASN0-0.022-0.03312.7790.3530.3530.0000.0000.0000.000
31D31ILE00.0340.02513.158-0.934-0.9340.0000.0000.0000.000
32D32TYR0-0.066-0.08210.7700.3540.3540.0000.0000.0000.000
33D33ASP-1-0.846-0.89915.53313.74513.7450.0000.0000.0000.000
34D34MET0-0.063-0.03212.8181.2121.2120.0000.0000.0000.000
35D35HIS0-0.021-0.03817.122-0.433-0.4330.0000.0000.0000.000
36D36TRP00.0230.01418.3690.6430.6430.0000.0000.0000.000
37D37VAL0-0.007-0.00719.635-0.712-0.7120.0000.0000.0000.000
38D38ARG10.8070.88020.922-10.071-10.0710.0000.0000.0000.000
39D39GLN00.0220.00922.110-0.488-0.4880.0000.0000.0000.000
40D40ALA00.0170.01524.350-0.009-0.0090.0000.0000.0000.000
41D41PRO0-0.016-0.02126.9960.2260.2260.0000.0000.0000.000
42D42GLY0-0.0210.01228.5760.0620.0620.0000.0000.0000.000
43D43LYS10.9540.96526.448-11.193-11.1930.0000.0000.0000.000
44D44GLY0-0.0050.00026.498-0.330-0.3300.0000.0000.0000.000
45D45LEU0-0.0040.00220.594-0.063-0.0630.0000.0000.0000.000
46D46GLU-1-0.777-0.86024.4879.9969.9960.0000.0000.0000.000
47D47TRP00.0060.00423.2960.0860.0860.0000.0000.0000.000
48D48VAL0-0.016-0.01924.198-0.499-0.4990.0000.0000.0000.000
49D49SER0-0.016-0.03323.818-0.304-0.3040.0000.0000.0000.000
50D50SER0-0.007-0.00322.1230.6810.6810.0000.0000.0000.000
51D51ILE0-0.039-0.00520.756-0.622-0.6220.0000.0000.0000.000
52D52THR00.0500.02120.8810.6880.6880.0000.0000.0000.000
53D53THR0-0.036-0.04718.326-0.035-0.0350.0000.0000.0000.000
54D54ALA0-0.026-0.00520.881-0.074-0.0740.0000.0000.0000.000
55D55GLY0-0.032-0.00723.784-0.361-0.3610.0000.0000.0000.000
56D56ASP-1-0.858-0.91325.00010.39610.3960.0000.0000.0000.000
57D57THR0-0.068-0.04125.6430.3290.3290.0000.0000.0000.000
58D58TYR00.0090.00826.040-0.585-0.5850.0000.0000.0000.000
59D59TYR00.016-0.00227.0480.4670.4670.0000.0000.0000.000
60D60PRO00.0120.04128.140-0.362-0.3620.0000.0000.0000.000
61D61GLY0-0.005-0.02631.081-0.113-0.1130.0000.0000.0000.000
62D62SER0-0.029-0.01630.946-0.205-0.2050.0000.0000.0000.000
63D63VAL00.0400.00129.026-0.265-0.2650.0000.0000.0000.000
64D64LYS10.9200.97632.258-8.484-8.4840.0000.0000.0000.000
65D65GLY0-0.026-0.00433.606-0.053-0.0530.0000.0000.0000.000
66D66ARG10.8940.93933.417-8.162-8.1620.0000.0000.0000.000
67D67PHE00.0450.02027.2730.0980.0980.0000.0000.0000.000
68D68THR00.0180.00928.296-0.034-0.0340.0000.0000.0000.000
69D69THR00.0180.02522.2680.2980.2980.0000.0000.0000.000
70D70SER0-0.007-0.00323.052-0.317-0.3170.0000.0000.0000.000
71D71ARG10.8110.89016.461-14.884-14.8840.0000.0000.0000.000
72D72GLU-1-0.916-0.95618.92411.66411.6640.0000.0000.0000.000
73D73ASN00.045-0.00116.9860.9200.9200.0000.0000.0000.000
74D74ALA00.0120.03016.4520.6200.6200.0000.0000.0000.000
75D75LYS10.9310.95116.429-12.700-12.7000.0000.0000.0000.000
76D76ASN0-0.011-0.00111.7971.1131.1130.0000.0000.0000.000
77D77SER00.0030.01813.2590.6970.6970.0000.0000.0000.000
78D78LEU00.0010.01615.646-0.635-0.6350.0000.0000.0000.000
79D79TYR0-0.029-0.04317.9840.1320.1320.0000.0000.0000.000
80D80LEU00.0020.01020.922-0.231-0.2310.0000.0000.0000.000
81D81GLN0-0.0120.00723.7020.1210.1210.0000.0000.0000.000
82D82MET00.0060.00926.112-0.065-0.0650.0000.0000.0000.000
83D83ASN00.0370.00029.148-0.058-0.0580.0000.0000.0000.000
84D84SER0-0.014-0.02232.781-0.001-0.0010.0000.0000.0000.000
85D85LEU00.0050.02729.914-0.151-0.1510.0000.0000.0000.000
86D86ARG10.7960.86532.989-9.086-9.0860.0000.0000.0000.000
87D87ALA00.012-0.00634.9530.1180.1180.0000.0000.0000.000
88D88GLY00.029-0.00134.1420.1260.1260.0000.0000.0000.000
89D89ASP-1-0.776-0.84030.7459.4819.4810.0000.0000.0000.000
90D90THR00.0070.02229.4470.2960.2960.0000.0000.0000.000
91D91GLY00.0340.01326.673-0.024-0.0240.0000.0000.0000.000
92D92VAL0-0.029-0.00820.134-0.046-0.0460.0000.0000.0000.000
93D93TYR0-0.037-0.04321.478-0.049-0.0490.0000.0000.0000.000
94D94TYR0-0.0040.00016.384-0.081-0.0810.0000.0000.0000.000
95D96THR0-0.010-0.01913.8770.6730.6730.0000.0000.0000.000
96D97ARG10.9010.9579.803-26.049-26.0490.0000.0000.0000.000
97D98GLY00.0030.00113.6421.0441.0440.0000.0000.0000.000
98D99VAL0-0.021-0.00316.187-0.532-0.5320.0000.0000.0000.000
99D100ARG10.9080.95614.639-16.674-16.6740.0000.0000.0000.000
100D101GLU-1-0.847-0.89716.69813.49913.4990.0000.0000.0000.000
101D102VAL00.0270.00319.889-0.525-0.5250.0000.0000.0000.000
102D103GLY0-0.048-0.00721.6040.2600.2600.0000.0000.0000.000
103D104ALA0-0.005-0.00417.001-0.008-0.0080.0000.0000.0000.000
104D105THR0-0.023-0.02117.6650.2750.2750.0000.0000.0000.000
105D106GLY0-0.042-0.01717.746-0.842-0.8420.0000.0000.0000.000
106D107ASP-1-0.858-0.92113.78419.36819.3680.0000.0000.0000.000
107D108ASP-1-0.844-0.87110.59427.34927.3490.0000.0000.0000.000
108D109PRO0-0.012-0.01711.640-1.851-1.8510.0000.0000.0000.000
109D110PHE0-0.034-0.00214.5070.2290.2290.0000.0000.0000.000
110D111TYR00.0250.01011.287-0.288-0.2880.0000.0000.0000.000
111D112TYR00.0280.00717.6580.2020.2020.0000.0000.0000.000
112D113GLY0-0.010-0.00817.504-0.423-0.4230.0000.0000.0000.000
113D114MET0-0.047-0.01615.1080.4110.4110.0000.0000.0000.000
114D115TYR0-0.023-0.0056.303-2.147-2.1470.0000.0000.0000.000
115D116VAL00.0070.0037.3600.5410.5410.0000.0000.0000.000
116D117TRP00.0350.0039.787-3.064-3.0640.0000.0000.0000.000
117D118GLY00.0530.04110.2221.7781.7780.0000.0000.0000.000
118D119GLN0-0.036-0.01912.0870.4870.4870.0000.0000.0000.000
119D120GLY00.0340.03014.271-0.910-0.9100.0000.0000.0000.000
120D121THR0-0.055-0.04717.4310.0170.0170.0000.0000.0000.000
121D122THR0-0.053-0.01220.299-0.161-0.1610.0000.0000.0000.000
122D123VAL00.0150.00323.834-0.223-0.2230.0000.0000.0000.000
123D124THR0-0.010-0.02026.784-0.015-0.0150.0000.0000.0000.000
124D125VAL0-0.0030.01030.571-0.069-0.0690.0000.0000.0000.000
125D126SER0-0.074-0.05333.971-0.168-0.1680.0000.0000.0000.000
126D127GLY00.0280.00536.808-0.032-0.0320.0000.0000.0000.000
127D128ALA0-0.019-0.01840.154-0.188-0.1880.0000.0000.0000.000
128D129SER00.0130.01336.280-0.020-0.0200.0000.0000.0000.000
129D130THR0-0.033-0.00735.702-0.104-0.1040.0000.0000.0000.000
130D131LYS10.9310.97537.966-7.167-7.1670.0000.0000.0000.000
131D132GLY00.0720.03939.3440.1630.1630.0000.0000.0000.000
132D133PRO0-0.018-0.01138.528-0.089-0.0890.0000.0000.0000.000
133D134SER00.0040.01640.956-0.127-0.1270.0000.0000.0000.000
134D135VAL0-0.004-0.01641.8680.0420.0420.0000.0000.0000.000
135D136PHE0-0.024-0.01244.790-0.123-0.1230.0000.0000.0000.000
136D137PRO0-0.047-0.03046.6140.0230.0230.0000.0000.0000.000
137D138LEU00.0290.02648.414-0.086-0.0860.0000.0000.0000.000
138D139ALA0-0.001-0.00951.4370.0190.0190.0000.0000.0000.000
139D140PRO00.0270.00054.7850.0190.0190.0000.0000.0000.000
140D141SER0-0.0180.01357.326-0.083-0.0830.0000.0000.0000.000
141D142SER00.0280.01054.186-0.015-0.0150.0000.0000.0000.000
142D143LYS10.9450.98155.602-5.770-5.7700.0000.0000.0000.000
143D144SER0-0.009-0.02156.329-0.139-0.1390.0000.0000.0000.000
144D145THR0-0.0220.00254.8950.1220.1220.0000.0000.0000.000
145D146SER0-0.028-0.03154.407-0.130-0.1300.0000.0000.0000.000
146D147GLY00.0460.03051.8060.0820.0820.0000.0000.0000.000
147D148GLY00.0200.01350.5490.1140.1140.0000.0000.0000.000
148D149THR0-0.051-0.04250.7120.0520.0520.0000.0000.0000.000
149D150ALA00.0420.03649.269-0.096-0.0960.0000.0000.0000.000
150D151ALA0-0.012-0.02246.6500.1680.1680.0000.0000.0000.000
151D152LEU0-0.0130.00946.908-0.128-0.1280.0000.0000.0000.000
152D153GLY00.0070.00144.7840.1440.1440.0000.0000.0000.000
153D154CYS0-0.080-0.03542.4220.0320.0320.0000.0000.0000.000
154D155LEU00.0380.01843.5780.0870.0870.0000.0000.0000.000
155D156VAL0-0.0150.00838.527-0.104-0.1040.0000.0000.0000.000
156D157LYS10.8640.91140.804-6.642-6.6420.0000.0000.0000.000
157D158ASP-1-0.828-0.91642.2726.7936.7930.0000.0000.0000.000
158D159TYR00.0420.02533.851-0.023-0.0230.0000.0000.0000.000
159D160PHE00.0100.01935.1330.1460.1460.0000.0000.0000.000
160D161PRO0-0.0030.00132.011-0.171-0.1710.0000.0000.0000.000
161D162GLU-1-0.813-0.90730.3019.6989.6980.0000.0000.0000.000
162D163PRO0-0.062-0.03927.7330.1330.1330.0000.0000.0000.000
163D164VAL00.016-0.00430.748-0.157-0.1570.0000.0000.0000.000
164D165THR0-0.043-0.01730.6120.1250.1250.0000.0000.0000.000
165D166VAL00.0400.01732.887-0.287-0.2870.0000.0000.0000.000
166D167SER0-0.059-0.03534.5290.2850.2850.0000.0000.0000.000
167D168TRP00.0680.03136.899-0.292-0.2920.0000.0000.0000.000
168D169ASN00.010-0.01739.4810.0640.0640.0000.0000.0000.000
169D170SER0-0.003-0.00237.1400.0120.0120.0000.0000.0000.000
170D171GLY0-0.0130.02034.8240.1980.1980.0000.0000.0000.000
171D172ALA00.0240.01735.7270.0500.0500.0000.0000.0000.000
172D173LEU0-0.026-0.01438.423-0.021-0.0210.0000.0000.0000.000
173D174THR00.0180.00734.6270.2240.2240.0000.0000.0000.000
174D175SER0-0.036-0.02735.8220.1500.1500.0000.0000.0000.000
175D176GLY00.0410.01838.456-0.155-0.1550.0000.0000.0000.000
176D177VAL0-0.032-0.00536.840-0.148-0.1480.0000.0000.0000.000
177D178HIS00.0170.01436.6170.3140.3140.0000.0000.0000.000
178D179THR0-0.024-0.01533.031-0.252-0.2520.0000.0000.0000.000
179D180PHE0-0.004-0.00934.1860.2540.2540.0000.0000.0000.000
180D181PRO00.0120.00032.1170.0250.0250.0000.0000.0000.000
181D182ALA0-0.015-0.00133.228-0.295-0.2950.0000.0000.0000.000
182D183VAL00.0120.00534.2830.1760.1760.0000.0000.0000.000
183D184LEU0-0.059-0.01336.235-0.184-0.1840.0000.0000.0000.000
184D185GLN00.0070.02738.184-0.107-0.1070.0000.0000.0000.000
185D186SER00.003-0.01441.6050.0840.0840.0000.0000.0000.000
186D187SER0-0.018-0.01643.976-0.095-0.0950.0000.0000.0000.000
187D188GLY00.0010.00240.058-0.034-0.0340.0000.0000.0000.000
188D189LEU0-0.032-0.02339.254-0.066-0.0660.0000.0000.0000.000
189D190TYR0-0.008-0.00431.781-0.173-0.1730.0000.0000.0000.000
190D191SER0-0.052-0.02937.841-0.217-0.2170.0000.0000.0000.000
191D192LEU00.0150.02834.9300.0220.0220.0000.0000.0000.000
192D193SER00.0350.01238.625-0.198-0.1980.0000.0000.0000.000
193D194SER0-0.022-0.02338.4900.2180.2180.0000.0000.0000.000
194D195VAL00.0200.01240.097-0.197-0.1970.0000.0000.0000.000
195D196VAL00.0410.01140.8650.2200.2200.0000.0000.0000.000
196D197THR0-0.020-0.00343.002-0.128-0.1280.0000.0000.0000.000
197D198VAL0-0.0010.01045.2750.0860.0860.0000.0000.0000.000
198D199PRO00.020-0.00747.922-0.058-0.0580.0000.0000.0000.000
199D200SER00.0160.00950.256-0.028-0.0280.0000.0000.0000.000
200D201SER00.0190.00753.936-0.083-0.0830.0000.0000.0000.000
201D202SER0-0.016-0.00651.214-0.045-0.0450.0000.0000.0000.000
202D203LEU00.0280.02052.2360.0910.0910.0000.0000.0000.000
203D204GLY00.0280.02553.9560.0090.0090.0000.0000.0000.000
204D205THR0-0.037-0.04552.0600.0900.0900.0000.0000.0000.000
205D206GLN00.0140.01847.632-0.025-0.0250.0000.0000.0000.000
206D207THR0-0.027-0.00149.3470.0270.0270.0000.0000.0000.000
207D208TYR00.0490.02944.8350.1140.1140.0000.0000.0000.000
208D209ILE0-0.038-0.03142.500-0.114-0.1140.0000.0000.0000.000
209D211ASN00.0150.00438.7550.0330.0330.0000.0000.0000.000
210D212VAL00.0020.00137.6350.1670.1670.0000.0000.0000.000
211D213ASN00.007-0.00132.118-0.317-0.3170.0000.0000.0000.000
212D214HIS00.0400.01334.2540.0960.0960.0000.0000.0000.000
213D215LYS10.9900.99226.629-10.582-10.5820.0000.0000.0000.000
214D216PRO0-0.053-0.02531.502-0.021-0.0210.0000.0000.0000.000
215D217SER00.0250.00633.326-0.033-0.0330.0000.0000.0000.000
216D218ASN0-0.067-0.02333.728-0.131-0.1310.0000.0000.0000.000
217D219THR00.0220.02436.878-0.148-0.1480.0000.0000.0000.000
218D220LYS10.9360.95734.987-8.132-8.1320.0000.0000.0000.000
219D221VAL0-0.0040.00940.064-0.196-0.1960.0000.0000.0000.000
220D222ASP-1-0.806-0.90341.9577.4287.4280.0000.0000.0000.000
221D223LYS10.9000.95744.464-6.276-6.2760.0000.0000.0000.000
222D224ARG10.9650.97946.284-6.068-6.0680.0000.0000.0000.000
223D225VAL00.0030.00046.588-0.093-0.0930.0000.0000.0000.000
224D226GLU-1-0.928-0.96849.2105.8525.8520.0000.0000.0000.000
225D227PRO0-0.053-0.00352.694-0.074-0.0740.0000.0000.0000.000