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: 8566Y

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1654514.04013
FMO2-HF: Nuclear repulsion 1584916.05247
FMO2-HF: Total energy -69597.98766
FMO2-MP2: Total energy -69800.503153


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.
-15.82-10.122.39-2.96-5.1290.023
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 : -0.926 / q_NPA : -0.968
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].
3D3GLN00.0190.0112.714-5.241-2.3130.247-1.259-1.9170.005
4D4MET00.0070.0145.745-2.822-2.8220.0000.0000.0000.000
5D5THR0-0.014-0.0188.685-0.391-0.3910.0000.0000.0000.000
6D6GLN00.005-0.03811.7460.2290.2290.0000.0000.0000.000
7D7SER0-0.0630.00714.468-0.519-0.5190.0000.0000.0000.000
8D8PRO00.0460.01518.073-0.050-0.0500.0000.0000.0000.000
9D9SER00.0730.02718.3670.0800.0800.0000.0000.0000.000
10D10SER0-0.044-0.01019.903-0.106-0.1060.0000.0000.0000.000
11D11LEU00.0240.00423.3800.0320.0320.0000.0000.0000.000
12D12SER0-0.0090.00925.897-0.104-0.1040.0000.0000.0000.000
13D13ALA00.0050.00629.597-0.064-0.0640.0000.0000.0000.000
14D14SER0-0.003-0.00331.438-0.146-0.1460.0000.0000.0000.000
15D15LEU00.007-0.00333.9400.1510.1510.0000.0000.0000.000
16D16GLY0-0.007-0.00634.938-0.201-0.2010.0000.0000.0000.000
17D17GLU-1-0.935-0.96031.5969.2989.2980.0000.0000.0000.000
18D18ARG10.9760.99729.078-9.821-9.8210.0000.0000.0000.000
19D19VAL0-0.0020.00026.3080.0080.0080.0000.0000.0000.000
20D20SER0-0.040-0.04823.502-0.019-0.0190.0000.0000.0000.000
21D21LEU0-0.0070.02619.282-0.049-0.0490.0000.0000.0000.000
22D22THR00.009-0.00717.176-0.217-0.2170.0000.0000.0000.000
23D23CYS0-0.068-0.01012.3960.4670.4670.0000.0000.0000.000
24D24ARG10.9500.99013.195-17.723-17.7230.0000.0000.0000.000
25D25ALA0-0.007-0.0029.3571.3731.3730.0000.0000.0000.000
26D26SER0-0.077-0.0215.335-1.780-1.7800.0000.0000.0000.000
27D27GLN00.0340.0275.1762.0812.075-0.001-0.0060.0140.000
28D28ASP-1-0.846-0.9408.65118.71418.7140.0000.0000.0000.000
29D29ILE0-0.004-0.0118.4151.4171.4170.0000.0000.0000.000
30D30GLY0-0.010-0.00710.925-0.616-0.6160.0000.0000.0000.000
31D31GLY0-0.020-0.00514.486-0.947-0.9470.0000.0000.0000.000
32D32ASN0-0.039-0.00712.333-1.769-1.7690.0000.0000.0000.000
33D33LEU00.001-0.01211.8351.8601.8600.0000.0000.0000.000
34D34TYR0-0.005-0.00913.672-1.349-1.3490.0000.0000.0000.000
35D35TRP00.0060.00214.8291.0671.0670.0000.0000.0000.000
36D36LEU0-0.004-0.00514.768-0.611-0.6110.0000.0000.0000.000
37D37GLN00.0160.00618.2920.0490.0490.0000.0000.0000.000
38D38GLN0-0.038-0.03519.7920.4650.4650.0000.0000.0000.000
39D39GLY00.0330.01621.903-0.253-0.2530.0000.0000.0000.000
40D40PRO00.0440.00624.9600.3510.3510.0000.0000.0000.000
41D41ASP-1-0.901-0.94227.48710.78110.7810.0000.0000.0000.000
42D42GLY0-0.0010.01723.5870.1010.1010.0000.0000.0000.000
43D43THR0-0.045-0.03722.5810.8110.8110.0000.0000.0000.000
44D44ILE00.0230.01217.5040.0010.0010.0000.0000.0000.000
45D45LYS10.9250.98021.418-11.514-11.5140.0000.0000.0000.000
46D46ARG10.8110.87918.205-14.636-14.6360.0000.0000.0000.000
47D47LEU0-0.052-0.01920.441-0.693-0.6930.0000.0000.0000.000
48D48ILE00.015-0.00219.390-0.515-0.5150.0000.0000.0000.000
49D49TYR0-0.007-0.00518.2070.9420.9420.0000.0000.0000.000
50D50ALA00.0600.02417.794-0.623-0.6230.0000.0000.0000.000
51D51THR0-0.031-0.01417.366-0.502-0.5020.0000.0000.0000.000
52D52SER0-0.058-0.04818.735-0.381-0.3810.0000.0000.0000.000
53D53SER0-0.0490.00121.883-0.735-0.7350.0000.0000.0000.000
54D54LEU00.0050.00922.7390.4910.4910.0000.0000.0000.000
55D55ASP-1-0.763-0.86322.10413.37213.3720.0000.0000.0000.000
56D56SER0-0.017-0.02025.360-0.468-0.4680.0000.0000.0000.000
57D57GLY00.0110.00128.6330.1110.1110.0000.0000.0000.000
58D58VAL0-0.0440.00025.136-0.069-0.0690.0000.0000.0000.000
59D59PRO00.0130.00828.379-0.160-0.1600.0000.0000.0000.000
60D60LYS10.9890.96929.329-9.010-9.0100.0000.0000.0000.000
61D61ARG10.7560.87629.714-9.551-9.5510.0000.0000.0000.000
62D62PHE0-0.0100.01424.7430.1490.1490.0000.0000.0000.000
63D63SER0-0.024-0.01625.473-0.171-0.1710.0000.0000.0000.000
64D64GLY00.0660.03221.8510.3450.3450.0000.0000.0000.000
65D65SER0-0.044-0.01921.407-0.456-0.4560.0000.0000.0000.000
66D66ARG10.9170.94415.847-16.102-16.1020.0000.0000.0000.000
67D67SER0-0.009-0.00320.096-0.817-0.8170.0000.0000.0000.000
68D68GLY00.0260.02718.9360.2240.2240.0000.0000.0000.000
69D69SER0-0.002-0.00813.449-0.093-0.0930.0000.0000.0000.000
70D70ASP-1-0.867-0.92814.59317.05617.0560.0000.0000.0000.000
71D71TYR00.012-0.00213.987-0.946-0.9460.0000.0000.0000.000
72D72SER00.0350.00717.3520.2310.2310.0000.0000.0000.000
73D73LEU0-0.0270.01419.917-0.187-0.1870.0000.0000.0000.000
74D74THR0-0.035-0.03221.439-0.107-0.1070.0000.0000.0000.000
75D75ILE00.0130.01725.047-0.066-0.0660.0000.0000.0000.000
76D76SER0-0.051-0.05027.727-0.159-0.1590.0000.0000.0000.000
77D77SER00.0510.00831.048-0.258-0.2580.0000.0000.0000.000
78D78LEU0-0.052-0.00628.2990.0220.0220.0000.0000.0000.000
79D79GLU-1-0.865-0.93131.9418.3768.3760.0000.0000.0000.000
80D80SER00.008-0.02832.1380.2450.2450.0000.0000.0000.000
81D81GLU-1-0.875-0.92331.4579.4849.4840.0000.0000.0000.000
82D82ASP-1-0.747-0.84928.16210.49810.4980.0000.0000.0000.000
83D83PHE0-0.037-0.00427.0280.4480.4480.0000.0000.0000.000
84D84VAL0-0.024-0.00724.156-0.090-0.0900.0000.0000.0000.000
85D85ASP-1-0.856-0.92620.06613.73013.7300.0000.0000.0000.000
86D86TYR0-0.045-0.05119.292-0.068-0.0680.0000.0000.0000.000
87D87TYR00.0300.04413.9440.5950.5950.0000.0000.0000.000
88D89LEU0-0.007-0.0079.1821.0541.0540.0000.0000.0000.000
89D90GLN00.0200.0135.085-5.509-5.5090.0000.0000.0000.000
90D91TYR00.008-0.0128.8071.4991.4990.0000.0000.0000.000
91D92SER0-0.0400.0058.466-1.715-1.7150.0000.0000.0000.000
92D93SER0-0.043-0.0415.577-0.687-0.6870.0000.0000.0000.000
93D94SER00.013-0.0025.8750.7210.7210.0000.0000.0000.000
94D95PRO00.0050.0392.652-9.908-7.6771.980-1.540-2.6710.018
95D96TRP00.0300.0094.6330.3370.370-0.001-0.007-0.0240.000
96D97THR0-0.035-0.0302.820-0.0090.5050.165-0.148-0.5310.000
97D98PHE00.015-0.0076.004-3.522-3.5220.0000.0000.0000.000
98D99GLY0-0.009-0.0068.6181.5541.5540.0000.0000.0000.000
99D100GLY0-0.029-0.03111.125-0.020-0.0200.0000.0000.0000.000
100D101GLY00.0270.01813.102-0.574-0.5740.0000.0000.0000.000
101D102THR0-0.079-0.05616.121-0.003-0.0030.0000.0000.0000.000
102D103LYS10.9150.96419.596-11.583-11.5830.0000.0000.0000.000
103D104LEU0-0.027-0.01622.866-0.264-0.2640.0000.0000.0000.000
104D105GLU-1-0.910-0.93925.9859.9929.9920.0000.0000.0000.000
105D106ILE0-0.004-0.00629.176-0.058-0.0580.0000.0000.0000.000
106D107LYS10.9020.94832.787-8.950-8.9500.0000.0000.0000.000
107D108ARG10.8580.92834.368-7.845-7.8450.0000.0000.0000.000
108D109ALA0-0.010-0.00437.8260.0370.0370.0000.0000.0000.000
109D110ASP-1-0.809-0.90238.2338.1538.1530.0000.0000.0000.000
110D111ALA0-0.033-0.02540.307-0.215-0.2150.0000.0000.0000.000
111D112ALA00.0290.01940.9210.1770.1770.0000.0000.0000.000
112D113PRO0-0.0380.00140.900-0.046-0.0460.0000.0000.0000.000
113D114THR00.009-0.00142.800-0.231-0.2310.0000.0000.0000.000
114D115VAL0-0.030-0.01943.4200.0990.0990.0000.0000.0000.000
115D116SER0-0.030-0.01845.689-0.252-0.2520.0000.0000.0000.000
116D117ILE0-0.023-0.00446.2390.1370.1370.0000.0000.0000.000
117D118PHE0-0.019-0.01346.832-0.169-0.1690.0000.0000.0000.000
118D119PRO0-0.002-0.00248.4370.1280.1280.0000.0000.0000.000
119D120PRO00.0180.01148.682-0.001-0.0010.0000.0000.0000.000
120D121SER00.0210.02150.068-0.174-0.1740.0000.0000.0000.000
121D122SER00.030-0.00352.0490.0510.0510.0000.0000.0000.000
122D123GLU-1-0.867-0.94852.4355.8305.8300.0000.0000.0000.000
123D124GLN0-0.032-0.00245.342-0.004-0.0040.0000.0000.0000.000
124D125LEU0-0.006-0.01950.6210.0130.0130.0000.0000.0000.000
125D126THR0-0.051-0.01652.991-0.003-0.0030.0000.0000.0000.000
126D127SER0-0.021-0.01150.175-0.025-0.0250.0000.0000.0000.000
127D128GLY0-0.0180.00550.8240.0750.0750.0000.0000.0000.000
128D129GLY0-0.032-0.00347.4540.0700.0700.0000.0000.0000.000
129D130ALA0-0.014-0.02947.064-0.125-0.1250.0000.0000.0000.000
130D131SER0-0.0280.00343.6250.1430.1430.0000.0000.0000.000
131D132VAL0-0.0050.00544.822-0.116-0.1160.0000.0000.0000.000
132D133VAL00.0320.01642.2010.1880.1880.0000.0000.0000.000
133D134CYS0-0.020-0.01442.668-0.238-0.2380.0000.0000.0000.000
134D135PHE0-0.0080.00241.2600.2010.2010.0000.0000.0000.000
135D136LEU0-0.013-0.01838.525-0.185-0.1850.0000.0000.0000.000
136D137ASN00.0670.00439.9270.3750.3750.0000.0000.0000.000
137D138ASN00.0300.01440.527-0.276-0.2760.0000.0000.0000.000
138D139PHE0-0.039-0.00535.060-0.166-0.1660.0000.0000.0000.000
139D140TYR00.0520.01732.8730.1270.1270.0000.0000.0000.000
140D141PRO0-0.0010.00033.053-0.238-0.2380.0000.0000.0000.000
141D142LYS11.0251.00426.443-11.313-11.3130.0000.0000.0000.000
142D143ASP-1-0.937-0.95129.45710.44110.4410.0000.0000.0000.000
143D144ILE0-0.033-0.01932.148-0.357-0.3570.0000.0000.0000.000
144D145ASN0-0.0330.00033.8880.2700.2700.0000.0000.0000.000
145D146VAL00.0500.01335.803-0.264-0.2640.0000.0000.0000.000
146D147LYS10.9640.99337.593-8.016-8.0160.0000.0000.0000.000
147D159VAL0-0.033-0.03036.072-0.070-0.0700.0000.0000.0000.000
148D160LEU0-0.034-0.00633.0870.3110.3110.0000.0000.0000.000
149D161ASN00.025-0.00532.795-0.537-0.5370.0000.0000.0000.000
150D162SER0-0.0160.00432.6460.3520.3520.0000.0000.0000.000
151D163TRP00.023-0.01328.778-0.237-0.2370.0000.0000.0000.000
152D164THR00.0180.01932.2620.1490.1490.0000.0000.0000.000
153D165ASP-1-0.924-0.95930.1349.9679.9670.0000.0000.0000.000
154D166GLN0-0.086-0.06031.497-0.050-0.0500.0000.0000.0000.000
155D167ASP-1-0.857-0.91933.4358.2308.2300.0000.0000.0000.000
156D168SER0-0.014-0.02036.371-0.078-0.0780.0000.0000.0000.000
157D169LYS10.9360.97837.239-7.266-7.2660.0000.0000.0000.000
158D170ASP-1-0.850-0.93140.2467.5877.5870.0000.0000.0000.000
159D171SER0-0.0010.00336.294-0.090-0.0900.0000.0000.0000.000
160D172THR0-0.098-0.04336.3120.1580.1580.0000.0000.0000.000
161D173TYR00.0240.00931.0020.3080.3080.0000.0000.0000.000
162D174SER00.0590.03236.093-0.359-0.3590.0000.0000.0000.000
163D175MET0-0.057-0.00234.3440.2840.2840.0000.0000.0000.000
164D176SER0-0.0040.00736.834-0.330-0.3300.0000.0000.0000.000
165D177SER00.0030.01037.0180.2180.2180.0000.0000.0000.000
166D178THR0-0.008-0.01638.489-0.300-0.3000.0000.0000.0000.000
167D179LEU00.0300.01939.3200.1360.1360.0000.0000.0000.000
168D196ALA00.0450.02640.5300.0210.0210.0000.0000.0000.000
169D197THR0-0.109-0.06438.401-0.200-0.2000.0000.0000.0000.000
170D198HIS00.0600.03036.7500.0240.0240.0000.0000.0000.000
171D199LYS10.8930.94036.379-8.419-8.4190.0000.0000.0000.000
172D200THR0-0.029-0.03838.714-0.179-0.1790.0000.0000.0000.000
173D201SER0-0.052-0.00742.108-0.255-0.2550.0000.0000.0000.000
174D202THR00.0040.00742.7300.0910.0910.0000.0000.0000.000
175D203SER0-0.024-0.02044.0280.0320.0320.0000.0000.0000.000
176D204PRO0-0.019-0.02042.578-0.007-0.0070.0000.0000.0000.000
177D205ILE00.0440.03744.167-0.189-0.1890.0000.0000.0000.000
178D206VAL0-0.009-0.00645.3260.1190.1190.0000.0000.0000.000
179D207LYS10.9380.96647.248-6.385-6.3850.0000.0000.0000.000
180D208SER0-0.010-0.01747.9070.1340.1340.0000.0000.0000.000
181D209PHE00.0350.03449.444-0.081-0.0810.0000.0000.0000.000