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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: N977Q

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1654967.278395
FMO2-HF: Nuclear repulsion 1585368.696529
FMO2-HF: Total energy -69598.581866
FMO2-MP2: Total energy -69801.08608


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.
-17.317-11.2432.859-3.457-5.4760.03
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 : -0.915 / q_NPA : -0.962
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].
3D3GLN00.0390.0312.801-4.840-1.8880.110-1.261-1.8020.005
4D4MET00.0040.0125.609-2.862-2.8620.0000.0000.0000.000
5D5THR0-0.011-0.0148.609-0.406-0.4060.0000.0000.0000.000
6D6GLN0-0.001-0.04311.6190.2170.2170.0000.0000.0000.000
7D7SER0-0.0460.01514.370-0.176-0.1760.0000.0000.0000.000
8D8PRO00.0280.00417.959-0.046-0.0460.0000.0000.0000.000
9D9SER00.0700.02618.1670.0700.0700.0000.0000.0000.000
10D10SER00.0010.00619.7760.0350.0350.0000.0000.0000.000
11D11LEU0-0.025-0.01323.2680.0140.0140.0000.0000.0000.000
12D12SER0-0.023-0.01725.7990.0610.0610.0000.0000.0000.000
13D13ALA0-0.022-0.01329.501-0.071-0.0710.0000.0000.0000.000
14D14SER00.007-0.00331.363-0.133-0.1330.0000.0000.0000.000
15D15LEU00.008-0.00333.8940.1530.1530.0000.0000.0000.000
16D16GLY00.0020.00034.905-0.203-0.2030.0000.0000.0000.000
17D17GLU-1-0.876-0.89931.6929.2399.2390.0000.0000.0000.000
18D18ARG10.9760.99629.003-9.859-9.8590.0000.0000.0000.000
19D19VAL0-0.030-0.01526.222-0.017-0.0170.0000.0000.0000.000
20D20SER0-0.002-0.03923.480-0.119-0.1190.0000.0000.0000.000
21D21LEU0-0.0240.01219.209-0.009-0.0090.0000.0000.0000.000
22D22THR0-0.011-0.01817.174-0.224-0.2240.0000.0000.0000.000
23D23CYS0-0.054-0.00812.3130.5800.5800.0000.0000.0000.000
24D24ARG10.9010.94713.140-17.933-17.9330.0000.0000.0000.000
25D25ALA0-0.009-0.0039.4711.4041.4040.0000.0000.0000.000
26D26SER0-0.076-0.0355.595-1.983-1.9830.0000.0000.0000.000
27D27GLN00.0250.0215.4842.6962.6960.0000.0000.0000.000
28D28ASP-1-0.825-0.9188.68218.91818.9180.0000.0000.0000.000
29D29ILE00.005-0.0028.4471.4551.4550.0000.0000.0000.000
30D30GLY0-0.005-0.00110.953-0.634-0.6340.0000.0000.0000.000
31D31GLY0-0.0050.00414.512-0.942-0.9420.0000.0000.0000.000
32D32ASN0-0.056-0.01912.303-1.589-1.5890.0000.0000.0000.000
33D33LEU0-0.005-0.01811.8541.9061.9060.0000.0000.0000.000
34D34TYR0-0.005-0.00413.487-2.065-2.0650.0000.0000.0000.000
35D35TRP00.001-0.00114.9021.0251.0250.0000.0000.0000.000
36D36LEU0-0.006-0.00714.831-0.638-0.6380.0000.0000.0000.000
37D37GLN00.0110.00218.3520.0150.0150.0000.0000.0000.000
38D38GLN0-0.033-0.03519.4920.5430.5430.0000.0000.0000.000
39D39GLY00.0410.02021.924-0.254-0.2540.0000.0000.0000.000
40D40PRO00.0390.00224.9640.3450.3450.0000.0000.0000.000
41D41ASP-1-0.879-0.90127.47810.90810.9080.0000.0000.0000.000
42D42GLY00.0060.01723.5960.0880.0880.0000.0000.0000.000
43D43THR0-0.049-0.06122.5380.8160.8160.0000.0000.0000.000
44D44ILE0-0.008-0.00217.4610.0120.0120.0000.0000.0000.000
45D45LYS10.9320.97721.485-11.645-11.6450.0000.0000.0000.000
46D46ARG10.7970.86618.208-14.658-14.6580.0000.0000.0000.000
47D47LEU0-0.045-0.01820.528-0.711-0.7110.0000.0000.0000.000
48D48ILE00.015-0.00219.603-0.543-0.5430.0000.0000.0000.000
49D49TYR0-0.004-0.00318.3291.0111.0110.0000.0000.0000.000
50D50ALA00.0450.01717.946-0.648-0.6480.0000.0000.0000.000
51D51THR0-0.011-0.00317.385-0.483-0.4830.0000.0000.0000.000
52D52SER0-0.030-0.03718.828-0.087-0.0870.0000.0000.0000.000
53D53SER0-0.070-0.00722.005-0.824-0.8240.0000.0000.0000.000
54D54LEU00.0010.01222.8560.4860.4860.0000.0000.0000.000
55D55ASP-1-0.769-0.85522.18913.44913.4490.0000.0000.0000.000
56D56SER0-0.014-0.01725.487-0.475-0.4750.0000.0000.0000.000
57D57GLY00.011-0.00228.7530.1150.1150.0000.0000.0000.000
58D58VAL0-0.062-0.00625.239-0.067-0.0670.0000.0000.0000.000
59D59PRO00.0340.01728.470-0.150-0.1500.0000.0000.0000.000
60D60LYS10.9790.96529.397-9.122-9.1220.0000.0000.0000.000
61D61ARG10.6910.81329.832-9.638-9.6380.0000.0000.0000.000
62D62PHE0-0.0070.01524.7210.1740.1740.0000.0000.0000.000
63D63SER0-0.022-0.01525.519-0.156-0.1560.0000.0000.0000.000
64D64GLY00.0620.02321.9090.3450.3450.0000.0000.0000.000
65D65SER0-0.053-0.02521.423-0.525-0.5250.0000.0000.0000.000
66D66ARG10.8720.90815.316-16.503-16.5030.0000.0000.0000.000
67D67SER0-0.0040.00820.100-0.806-0.8060.0000.0000.0000.000
68D68GLY00.0390.02418.9450.2220.2220.0000.0000.0000.000
69D69SER00.0100.00613.687-0.093-0.0930.0000.0000.0000.000
70D70ASP-1-0.840-0.89814.59317.33817.3380.0000.0000.0000.000
71D71TYR00.0250.00213.713-1.014-1.0140.0000.0000.0000.000
72D72SER00.0390.00717.3550.2300.2300.0000.0000.0000.000
73D73LEU0-0.0250.01719.861-0.219-0.2190.0000.0000.0000.000
74D74THR0-0.019-0.01121.449-0.246-0.2460.0000.0000.0000.000
75D75ILE00.0170.02524.960-0.051-0.0510.0000.0000.0000.000
76D76SER0-0.049-0.04627.731-0.162-0.1620.0000.0000.0000.000
77D77SER00.0430.00131.052-0.279-0.2790.0000.0000.0000.000
78D78LEU0-0.0490.00028.2520.0170.0170.0000.0000.0000.000
79D79GLU-1-0.805-0.89031.9418.4888.4880.0000.0000.0000.000
80D80SER00.023-0.02132.1300.2490.2490.0000.0000.0000.000
81D81GLU-1-0.868-0.91131.2809.6669.6660.0000.0000.0000.000
82D82ASP-1-0.752-0.84328.12810.61310.6130.0000.0000.0000.000
83D83PHE0-0.0210.00427.0130.4640.4640.0000.0000.0000.000
84D84VAL0-0.049-0.02724.136-0.094-0.0940.0000.0000.0000.000
85D85ASP-1-0.847-0.91820.09513.61713.6170.0000.0000.0000.000
86D86TYR0-0.039-0.04219.280-0.053-0.0530.0000.0000.0000.000
87D87TYR00.0310.03613.9240.5840.5840.0000.0000.0000.000
88D89LEU0-0.006-0.0049.3251.1181.1180.0000.0000.0000.000
89D90GLN00.0200.0105.300-5.911-5.9110.0000.0000.0000.000
90D91TYR00.003-0.0258.9681.7211.7210.0000.0000.0000.000
91D92SER0-0.0350.0128.492-1.733-1.7330.0000.0000.0000.000
92D93SER0-0.045-0.0415.637-0.816-0.8160.0000.0000.0000.000
93D94SER00.011-0.0035.8870.9960.9960.0000.0000.0000.000
94D95PRO0-0.0050.0382.689-11.635-9.2152.589-2.014-2.9950.025
95D96TRP00.0270.0084.8480.6190.667-0.001-0.005-0.0410.000
96D97THR0-0.033-0.0272.7340.0600.7140.161-0.177-0.6380.000
97D98PHE00.014-0.0106.083-3.765-3.7650.0000.0000.0000.000
98D99GLY0-0.0030.0008.5641.5721.5720.0000.0000.0000.000
99D100GLY0-0.034-0.03311.068-0.038-0.0380.0000.0000.0000.000
100D101GLY00.0190.01512.996-0.583-0.5830.0000.0000.0000.000
101D102THR0-0.086-0.05316.0510.0120.0120.0000.0000.0000.000
102D103LYS10.9030.96719.521-11.801-11.8010.0000.0000.0000.000
103D104LEU0-0.027-0.01422.792-0.258-0.2580.0000.0000.0000.000
104D105GLU-1-0.789-0.82225.9219.9129.9120.0000.0000.0000.000
105D106ILE0-0.017-0.01329.097-0.060-0.0600.0000.0000.0000.000
106D107LYS10.8350.89932.687-9.190-9.1900.0000.0000.0000.000
107D108ARG10.7990.88934.276-7.851-7.8510.0000.0000.0000.000
108D109ALA0-0.004-0.00137.7290.0390.0390.0000.0000.0000.000
109D110ASP-1-0.820-0.89038.2228.1348.1340.0000.0000.0000.000
110D111ALA0-0.021-0.01840.190-0.214-0.2140.0000.0000.0000.000
111D112ALA00.0200.01440.8480.1750.1750.0000.0000.0000.000
112D113PRO0-0.0250.00440.898-0.041-0.0410.0000.0000.0000.000
113D114THR00.0060.00142.775-0.232-0.2320.0000.0000.0000.000
114D115VAL0-0.035-0.02443.5900.0960.0960.0000.0000.0000.000
115D116SER0-0.027-0.01445.735-0.252-0.2520.0000.0000.0000.000
116D117ILE0-0.021-0.00646.3140.1400.1400.0000.0000.0000.000
117D118PHE0-0.017-0.01246.857-0.169-0.1690.0000.0000.0000.000
118D119PRO00.001-0.00248.5660.1280.1280.0000.0000.0000.000
119D120PRO00.0120.01048.8540.0020.0020.0000.0000.0000.000
120D121SER00.0130.01850.195-0.173-0.1730.0000.0000.0000.000
121D122SER00.0370.00152.1700.0520.0520.0000.0000.0000.000
122D123GLU-1-0.862-0.94252.8275.7975.7970.0000.0000.0000.000
123D124GLN0-0.018-0.00445.535-0.017-0.0170.0000.0000.0000.000
124D125LEU00.001-0.01250.7650.0150.0150.0000.0000.0000.000
125D126THR0-0.040-0.01253.159-0.002-0.0020.0000.0000.0000.000
126D127SER0-0.037-0.01850.346-0.024-0.0240.0000.0000.0000.000
127D128GLY0-0.0180.00451.0080.0740.0740.0000.0000.0000.000
128D129GLY0-0.034-0.00447.6420.0680.0680.0000.0000.0000.000
129D130ALA0-0.021-0.03047.257-0.123-0.1230.0000.0000.0000.000
130D131SER0-0.042-0.00543.8650.1500.1500.0000.0000.0000.000
131D132VAL00.0060.01144.916-0.112-0.1120.0000.0000.0000.000
132D133VAL00.0230.00742.1730.1940.1940.0000.0000.0000.000
133D134CYS0-0.028-0.01642.702-0.240-0.2400.0000.0000.0000.000
134D135PHE00.0000.01041.6650.1880.1880.0000.0000.0000.000
135D136LEU0-0.004-0.01538.753-0.191-0.1910.0000.0000.0000.000
136D137ASN00.047-0.00139.8650.3480.3480.0000.0000.0000.000
137D138ASN00.0290.00740.365-0.299-0.2990.0000.0000.0000.000
138D139PHE0-0.0320.00035.055-0.163-0.1630.0000.0000.0000.000
139D140TYR00.043-0.01232.4100.1050.1050.0000.0000.0000.000
140D141PRO0-0.020-0.00932.943-0.239-0.2390.0000.0000.0000.000
141D142LYS10.9540.96026.795-11.103-11.1030.0000.0000.0000.000
142D143ASP-1-0.895-0.92729.29210.50210.5020.0000.0000.0000.000
143D144ILE0-0.019-0.00532.250-0.345-0.3450.0000.0000.0000.000
144D145ASN0-0.032-0.00933.9730.3470.3470.0000.0000.0000.000
145D146VAL00.0410.01635.875-0.271-0.2710.0000.0000.0000.000
146D147LYS10.9660.99237.203-8.110-8.1100.0000.0000.0000.000
147D159VAL00.0050.00236.065-0.104-0.1040.0000.0000.0000.000
148D160LEU0-0.059-0.03333.3660.3060.3060.0000.0000.0000.000
149D161ASN00.012-0.01032.887-0.505-0.5050.0000.0000.0000.000
150D162SER0-0.0060.00632.7600.3590.3590.0000.0000.0000.000
151D163TRP00.020-0.01429.476-0.230-0.2300.0000.0000.0000.000
152D164THR00.0130.01332.1650.1330.1330.0000.0000.0000.000
153D165ASP-1-0.923-0.95730.1169.9439.9430.0000.0000.0000.000
154D166GLN0-0.059-0.04631.417-0.067-0.0670.0000.0000.0000.000
155D167ASP-1-0.861-0.92633.3588.1508.1500.0000.0000.0000.000
156D168SER0-0.015-0.01936.323-0.074-0.0740.0000.0000.0000.000
157D169LYS10.9240.96937.195-7.345-7.3450.0000.0000.0000.000
158D170ASP-1-0.784-0.88940.2937.5207.5200.0000.0000.0000.000
159D171SER00.0130.02936.078-0.097-0.0970.0000.0000.0000.000
160D172THR0-0.099-0.04636.2210.1750.1750.0000.0000.0000.000
161D173TYR0-0.016-0.03930.4160.2340.2340.0000.0000.0000.000
162D174SER00.0560.02835.985-0.361-0.3610.0000.0000.0000.000
163D175MET0-0.060-0.00834.3700.2810.2810.0000.0000.0000.000
164D176SER00.0270.02136.832-0.369-0.3690.0000.0000.0000.000
165D177SER0-0.0130.00137.1200.2420.2420.0000.0000.0000.000
166D178THR0-0.017-0.01738.634-0.311-0.3110.0000.0000.0000.000
167D179LEU00.0290.02039.4910.1330.1330.0000.0000.0000.000
168D196ALA0-0.004-0.00640.6220.0220.0220.0000.0000.0000.000
169D197THR0-0.051-0.02738.383-0.144-0.1440.0000.0000.0000.000
170D198HIS00.0610.03336.6870.0210.0210.0000.0000.0000.000
171D199LYS10.8880.92436.361-8.424-8.4240.0000.0000.0000.000
172D200THR0-0.013-0.02638.807-0.174-0.1740.0000.0000.0000.000
173D201SER0-0.062-0.01642.205-0.252-0.2520.0000.0000.0000.000
174D202THR00.0090.00942.8080.0880.0880.0000.0000.0000.000
175D203SER0-0.014-0.01344.0890.0400.0400.0000.0000.0000.000
176D204PRO0-0.031-0.02942.6790.0060.0060.0000.0000.0000.000
177D205ILE00.0340.03243.922-0.189-0.1890.0000.0000.0000.000
178D206VAL00.0020.00145.4040.1210.1210.0000.0000.0000.000
179D207LYS10.9270.96147.269-6.425-6.4250.0000.0000.0000.000
180D208SER0-0.012-0.01747.9800.1370.1370.0000.0000.0000.000
181D209PHE00.0390.03449.526-0.073-0.0730.0000.0000.0000.000