FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2L42R

Calculation Name: 3ALZ-AB-Other466

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 3ALZ

Chain ID: AB

ChEMBL ID:

UniProt ID: P08362

Base Structure: Homology modeling

Registration Date: 2024-03-27

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization AMBER15:AMBER14SB
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water All crystal waters in PDB.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 572
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12676861.432118
FMO2-HF: Nuclear repulsion 12449374.852954
FMO2-HF: Total energy -227486.579164
FMO2-MP2: Total energy -228138.096123


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
trp6 interaction enegry (frag 6 : frag 1-4,8-20)
"
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.
38.4374751.2554610.38731-9.2223-13.98300.0792


Interactive mode: IFIE and PIEDA for fragment #1(A:151:ACE)


Summations of interaction energy for fragment #1(A:151:ACE)
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.
2.5944.3970.088-0.751-1.1420
Interaction energy analysis for fragmet #1(A:151:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.015
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].
3A153TYR00.0560.0403.3930.2831.4110.012-0.525-0.6150.000
4A154CYS00.006-0.0063.1730.4060.9110.077-0.169-0.4140.000
5A155ALA0-0.004-0.0014.4060.6880.858-0.001-0.057-0.1130.000
6A156ASP-1-0.862-0.9186.283-0.317-0.3170.0000.0000.0000.000
7A157VAL00.0660.0328.3530.2060.2060.0000.0000.0000.000
8A158ALA0-0.033-0.0148.6450.1630.1630.0000.0000.0000.000
9A159ALA0-0.031-0.00610.2990.1380.1380.0000.0000.0000.000
10A160GLU-1-0.915-0.97412.164-0.412-0.4120.0000.0000.0000.000
11A161GLU-1-0.876-0.92513.423-0.179-0.1790.0000.0000.0000.000
12A162LEU0-0.024-0.01714.2870.0570.0570.0000.0000.0000.000
13A163MET0-0.089-0.01816.7730.0430.0430.0000.0000.0000.000
14A164ASN0-0.007-0.02417.1450.0420.0420.0000.0000.0000.000
15A165ALA00.0170.01719.4420.0290.0290.0000.0000.0000.000
16A166LEU0-0.035-0.02621.2910.0200.0200.0000.0000.0000.000
17A167VAL00.014-0.00624.0580.0140.0140.0000.0000.0000.000
18A168ASN0-0.066-0.03324.0100.0190.0190.0000.0000.0000.000
19A169SER0-0.0260.01327.5230.0030.0030.0000.0000.0000.000
20A170THR0-0.071-0.04328.0180.0040.0040.0000.0000.0000.000
21A171LEU00.0050.01428.393-0.004-0.0040.0000.0000.0000.000
22A172LEU00.0560.01622.534-0.003-0.0030.0000.0000.0000.000
23A173GLU-1-0.808-0.89923.570-0.132-0.1320.0000.0000.0000.000
24A174ALA00.0510.02625.5500.0100.0100.0000.0000.0000.000
25A175ARG10.7800.88427.0900.1190.1190.0000.0000.0000.000
26A176ALA00.0870.04528.3860.0090.0090.0000.0000.0000.000
27A177THR00.016-0.00130.1230.0070.0070.0000.0000.0000.000
28A178ASN00.0160.02231.6640.0080.0080.0000.0000.0000.000
29A179GLN0-0.025-0.02131.6050.0090.0090.0000.0000.0000.000
30A180PHE00.0290.02834.3090.0050.0050.0000.0000.0000.000
31A181LEU0-0.032-0.01836.2860.0060.0060.0000.0000.0000.000
32A182ALA0-0.062-0.01337.2280.0030.0030.0000.0000.0000.000
33A183VAL00.0000.01138.3780.0040.0040.0000.0000.0000.000
34A184SER0-0.016-0.01240.0290.0040.0040.0000.0000.0000.000
35A185LYS10.8810.95442.4370.0510.0510.0000.0000.0000.000
36A186GLY00.0440.00144.5350.0010.0010.0000.0000.0000.000
37A187ASN0-0.032-0.00847.4340.0030.0030.0000.0000.0000.000
38A188CYS0-0.044-0.01050.431-0.001-0.0010.0000.0000.0000.000
39A189SER00.012-0.01653.2710.0010.0010.0000.0000.0000.000
40A190GLY00.0340.01656.3110.0010.0010.0000.0000.0000.000
41A191PRO0-0.041-0.01856.158-0.001-0.0010.0000.0000.0000.000
42A192THR0-0.008-0.02252.804-0.001-0.0010.0000.0000.0000.000
43A193THR0-0.037-0.03452.8960.0010.0010.0000.0000.0000.000
44A194ILE00.0060.00747.530-0.001-0.0010.0000.0000.0000.000
45A195ARG10.9110.96246.9250.0460.0460.0000.0000.0000.000
46A196GLY00.0590.01444.879-0.002-0.0020.0000.0000.0000.000
47A197GLN0-0.084-0.05741.2890.0030.0030.0000.0000.0000.000
48A198PHE00.0410.00242.468-0.003-0.0030.0000.0000.0000.000
49A199SER0-0.0060.00238.4690.0010.0010.0000.0000.0000.000
50A200ASN00.0690.02938.4280.0010.0010.0000.0000.0000.000
51A201MET0-0.0120.01336.313-0.003-0.0030.0000.0000.0000.000
52A202SER0-0.037-0.06031.795-0.006-0.0060.0000.0000.0000.000
53A203LEU0-0.014-0.00729.1020.0050.0050.0000.0000.0000.000
54A204SER0-0.021-0.01927.585-0.008-0.0080.0000.0000.0000.000
55A205LEU00.004-0.00525.9310.0090.0090.0000.0000.0000.000
56A206LEU00.0250.02828.7760.0090.0090.0000.0000.0000.000
57A207ASP-1-0.766-0.88630.769-0.083-0.0830.0000.0000.0000.000
58A208LEU0-0.0280.01630.6250.0070.0070.0000.0000.0000.000
59A209TYR0-0.033-0.05528.2660.0090.0090.0000.0000.0000.000
60A210LEU00.0130.00734.2010.0050.0050.0000.0000.0000.000
61A211SER0-0.067-0.04736.2100.0050.0050.0000.0000.0000.000
62A212ARG10.8610.92835.4400.0630.0630.0000.0000.0000.000
63A213GLY00.0150.02338.3590.0030.0030.0000.0000.0000.000
64A214TYR0-0.027-0.00734.9910.0010.0010.0000.0000.0000.000
65A215ASN00.003-0.00437.753-0.003-0.0030.0000.0000.0000.000
66A216VAL0-0.017-0.01733.532-0.003-0.0030.0000.0000.0000.000
67A217SER0-0.0080.00634.4750.0040.0040.0000.0000.0000.000
68A218SER00.0410.02732.111-0.008-0.0080.0000.0000.0000.000
69A219ILE0-0.0250.00931.213-0.007-0.0070.0000.0000.0000.000
70A220VAL0-0.0260.00428.8350.0000.0000.0000.0000.0000.000
71A221THR0-0.011-0.01328.103-0.010-0.0100.0000.0000.0000.000
72A222MET0-0.0150.00725.9740.0080.0080.0000.0000.0000.000
73A223THR00.0600.03026.822-0.008-0.0080.0000.0000.0000.000
74A224SER0-0.070-0.04524.3670.0100.0100.0000.0000.0000.000
75A225GLN00.0230.00420.623-0.027-0.0270.0000.0000.0000.000
76A226GLY00.0410.02323.405-0.010-0.0100.0000.0000.0000.000
77A227MET0-0.0440.00619.415-0.007-0.0070.0000.0000.0000.000
78A228TYR0-0.029-0.03923.9530.0130.0130.0000.0000.0000.000
79A229GLY00.0390.01723.101-0.020-0.0200.0000.0000.0000.000
80A230GLY0-0.006-0.01423.9900.0150.0150.0000.0000.0000.000
81A231THR0-0.069-0.03224.450-0.009-0.0090.0000.0000.0000.000
82A232TYR0-0.003-0.01926.6440.0090.0090.0000.0000.0000.000
83A233LEU0-0.0070.01128.976-0.004-0.0040.0000.0000.0000.000
84A234VAL0-0.003-0.01730.5270.0010.0010.0000.0000.0000.000
85A235GLY00.0260.01433.1800.0010.0010.0000.0000.0000.000
86A236LYS10.8130.88829.2810.0890.0890.0000.0000.0000.000
87A237PRO00.0220.01435.1410.0020.0020.0000.0000.0000.000
88A238ASN0-0.026-0.01135.693-0.003-0.0030.0000.0000.0000.000
89A239LEU0-0.015-0.01133.7240.0010.0010.0000.0000.0000.000
90A240SER00.0610.02136.8900.0000.0000.0000.0000.0000.000
91A241SER0-0.0100.00834.6080.0010.0010.0000.0000.0000.000
92A242LYS10.9270.96330.4170.0570.0570.0000.0000.0000.000
93A243GLY00.0970.04536.1720.0000.0000.0000.0000.0000.000
94A244SER0-0.046-0.03135.554-0.001-0.0010.0000.0000.0000.000
95A245GLU-1-0.958-0.98637.595-0.031-0.0310.0000.0000.0000.000
96A246LEU00.0150.01540.2260.0010.0010.0000.0000.0000.000
97A247SER0-0.071-0.02839.2070.0010.0010.0000.0000.0000.000
98A248GLN00.0270.01841.0490.0010.0010.0000.0000.0000.000
99A249LEU0-0.020-0.02137.716-0.002-0.0020.0000.0000.0000.000
100A250SER0-0.0090.00932.9020.0000.0000.0000.0000.0000.000
101A251MET00.0410.02433.803-0.002-0.0020.0000.0000.0000.000
102A252HIS0-0.040-0.02327.795-0.003-0.0030.0000.0000.0000.000
103A253ARG10.8680.92525.8390.0960.0960.0000.0000.0000.000
104A254VAL0-0.012-0.00625.060-0.006-0.0060.0000.0000.0000.000
105A255PHE0-0.008-0.01121.1620.0030.0030.0000.0000.0000.000
106A256GLU-1-0.713-0.82321.929-0.154-0.1540.0000.0000.0000.000
107A257VAL0-0.008-0.00217.7900.0040.0040.0000.0000.0000.000
108A258GLY00.0530.02121.202-0.006-0.0060.0000.0000.0000.000
109A259VAL0-0.004-0.00221.4130.0010.0010.0000.0000.0000.000
110A260ILE0-0.028-0.00423.9830.0130.0130.0000.0000.0000.000
111A261ARG10.9010.94724.1580.1410.1410.0000.0000.0000.000
112A262ASN00.0580.01528.9230.0080.0080.0000.0000.0000.000
113A263PRO0-0.017-0.01631.4910.0000.0000.0000.0000.0000.000
114A264GLY00.0300.02633.2600.0040.0040.0000.0000.0000.000
115A265LEU0-0.016-0.01235.7280.0040.0040.0000.0000.0000.000
116A266GLY00.0010.01138.3770.0030.0030.0000.0000.0000.000
117A267ALA0-0.024-0.02237.3960.0030.0030.0000.0000.0000.000
118A268PRO0-0.0530.00432.609-0.003-0.0030.0000.0000.0000.000
119A269VAL0-0.012-0.00530.8140.0040.0040.0000.0000.0000.000
120A270PHE0-0.009-0.00228.430-0.008-0.0080.0000.0000.0000.000
121A271HIS00.0370.01523.8970.0140.0140.0000.0000.0000.000
122A272MET00.0180.02922.803-0.014-0.0140.0000.0000.0000.000
123A273THR0-0.055-0.04819.3200.0130.0130.0000.0000.0000.000
124A274ASN0-0.069-0.06415.0080.0060.0060.0000.0000.0000.000
125A275TYR00.0270.01018.9120.0160.0160.0000.0000.0000.000
126A276PHE0-0.027-0.01714.522-0.008-0.0080.0000.0000.0000.000
127A277GLU-1-0.797-0.86020.775-0.097-0.0970.0000.0000.0000.000
128A278GLN0-0.008-0.01121.911-0.001-0.0010.0000.0000.0000.000
129A279PRO0-0.0030.00525.874-0.001-0.0010.0000.0000.0000.000
130A280VAL00.0030.01328.017-0.005-0.0050.0000.0000.0000.000
131A281SER0-0.034-0.01428.0120.0050.0050.0000.0000.0000.000
132A282ASN0-0.010-0.03629.9130.0060.0060.0000.0000.0000.000
133A283ASP-1-0.823-0.88333.214-0.051-0.0510.0000.0000.0000.000
134A284PHE00.016-0.00934.122-0.005-0.0050.0000.0000.0000.000
135A285SER0-0.026-0.02430.067-0.007-0.0070.0000.0000.0000.000
136A286ASN0-0.019-0.00331.943-0.004-0.0040.0000.0000.0000.000
137A287CYS0-0.050-0.03223.4340.0000.0000.0000.0000.0000.000
138A288MET0-0.0360.00025.3520.0060.0060.0000.0000.0000.000
139A289VAL00.0100.00423.714-0.012-0.0120.0000.0000.0000.000
140A290ALA0-0.0030.00621.4860.0130.0130.0000.0000.0000.000
141A291LEU00.0200.01020.898-0.019-0.0190.0000.0000.0000.000
142A292GLY0-0.021-0.01720.0890.0250.0250.0000.0000.0000.000
143A293GLU-1-0.847-0.93815.223-0.310-0.3100.0000.0000.0000.000
144A294LEU00.0460.02015.588-0.047-0.0470.0000.0000.0000.000
145A295LYS10.8260.91512.1780.4840.4840.0000.0000.0000.000
146A296PHE00.0620.01216.2140.0530.0530.0000.0000.0000.000
147A297ALA0-0.018-0.00616.725-0.040-0.0400.0000.0000.0000.000
148A298ALA0-0.009-0.00218.7880.0240.0240.0000.0000.0000.000
149A299LEU0-0.020-0.01120.866-0.008-0.0080.0000.0000.0000.000
150A301HIS0-0.015-0.02926.2700.0000.0000.0000.0000.0000.000
151A302ARG10.8690.92829.0910.0430.0430.0000.0000.0000.000
152A303GLU-1-0.848-0.90632.129-0.037-0.0370.0000.0000.0000.000
153A304ASP-1-0.820-0.88933.801-0.053-0.0530.0000.0000.0000.000
154A305SER0-0.044-0.04836.1390.0000.0000.0000.0000.0000.000
155A306ILE0-0.048-0.01031.0680.0010.0010.0000.0000.0000.000
156A307THR00.0150.00434.4380.0010.0010.0000.0000.0000.000
157A308ILE0-0.025-0.00232.530-0.001-0.0010.0000.0000.0000.000
158A309PRO0-0.047-0.02232.9660.0030.0030.0000.0000.0000.000
159A310TYR00.0340.01935.453-0.001-0.0010.0000.0000.0000.000
160A311GLN00.0260.00036.2910.0020.0020.0000.0000.0000.000
161A312GLY00.0070.00633.000-0.002-0.0020.0000.0000.0000.000
162A313SER0-0.042-0.00433.9070.0030.0030.0000.0000.0000.000
163A314GLY00.0350.01534.152-0.003-0.0030.0000.0000.0000.000
164A315LYS10.9530.97731.1490.0250.0250.0000.0000.0000.000
165A316GLY00.0700.01227.693-0.001-0.0010.0000.0000.0000.000
166A317VAL0-0.032-0.02728.127-0.004-0.0040.0000.0000.0000.000
167A318SER0-0.0130.01424.892-0.002-0.0020.0000.0000.0000.000
168A319PHE00.0540.04324.3010.0010.0010.0000.0000.0000.000
169A320GLN0-0.020-0.01120.7340.0120.0120.0000.0000.0000.000
170A321LEU0-0.0040.00117.396-0.002-0.0020.0000.0000.0000.000
171A322VAL0-0.024-0.02417.280-0.004-0.0040.0000.0000.0000.000
172A323LYS10.8740.9519.3200.8300.8300.0000.0000.0000.000
173A324LEU0-0.029-0.00114.370-0.027-0.0270.0000.0000.0000.000
174A325GLY00.0580.02112.6400.0030.0030.0000.0000.0000.000
175A326VAL00.0270.00913.4900.0530.0530.0000.0000.0000.000
176A327TRP00.0300.02915.0170.0650.0650.0000.0000.0000.000
177A328LYS10.8510.94013.4090.2470.2470.0000.0000.0000.000
178A329SER00.0330.0189.3710.0240.0240.0000.0000.0000.000
179A330PRO0-0.014-0.0265.9710.0090.0090.0000.0000.0000.000
180A331THR00.0180.0076.915-0.058-0.0580.0000.0000.0000.000
181A332ASP-1-0.785-0.8797.915-0.357-0.3570.0000.0000.0000.000
182A333MET0-0.045-0.01610.4650.0100.0100.0000.0000.0000.000
183A334ARG10.9400.97012.8860.1590.1590.0000.0000.0000.000
184A335SER0-0.022-0.00216.1420.0210.0210.0000.0000.0000.000
185A336TRP00.0270.02418.1190.0000.0000.0000.0000.0000.000
186A337VAL0-0.009-0.00618.6540.0070.0070.0000.0000.0000.000
187A338PRO00.0220.02121.755-0.001-0.0010.0000.0000.0000.000
188A339LEU0-0.008-0.00223.826-0.008-0.0080.0000.0000.0000.000
189A340SER0-0.024-0.01625.2660.0090.0090.0000.0000.0000.000
190A341THR0-0.011-0.02026.998-0.002-0.0020.0000.0000.0000.000
191A342ASP-1-0.945-0.96928.215-0.019-0.0190.0000.0000.0000.000
192A343ASP-1-0.789-0.86930.227-0.033-0.0330.0000.0000.0000.000
193A344PRO0-0.009-0.00332.564-0.002-0.0020.0000.0000.0000.000
194A345VAL0-0.0050.00335.3310.0010.0010.0000.0000.0000.000
195A346ILE0-0.013-0.00533.0650.0000.0000.0000.0000.0000.000
196A347ASP-1-0.827-0.89037.172-0.023-0.0230.0000.0000.0000.000
197A348ARG10.8950.92037.0310.0290.0290.0000.0000.0000.000
198A349LEU0-0.0080.00131.283-0.001-0.0010.0000.0000.0000.000
199A350TYR00.0000.00135.7490.0030.0030.0000.0000.0000.000
200A351LEU0-0.050-0.01230.630-0.003-0.0030.0000.0000.0000.000
201A352SER00.0430.01133.5020.0010.0010.0000.0000.0000.000
202A353SER00.0390.01932.087-0.006-0.0060.0000.0000.0000.000
203A354HIS0-0.020-0.00329.3340.0050.0050.0000.0000.0000.000
204A355ARG10.8070.88527.8260.0820.0820.0000.0000.0000.000
205A356GLY00.0510.00925.8580.0090.0090.0000.0000.0000.000
206A357VAL0-0.032-0.01123.109-0.008-0.0080.0000.0000.0000.000
207A358ILE0-0.031-0.00417.0540.0030.0030.0000.0000.0000.000
208A359ALA0-0.046-0.03619.5110.0040.0040.0000.0000.0000.000
209A360ASP-1-0.829-0.90018.079-0.109-0.1090.0000.0000.0000.000
210A361ASN0-0.034-0.01112.321-0.048-0.0480.0000.0000.0000.000
211A362GLN0-0.014-0.01115.0540.0010.0010.0000.0000.0000.000
212A363ALA00.0310.02917.7780.0030.0030.0000.0000.0000.000
213A364LYS10.7840.88720.1220.1300.1300.0000.0000.0000.000
214A365TRP00.004-0.02421.412-0.003-0.0030.0000.0000.0000.000
215A366ALA00.0210.00127.1500.0060.0060.0000.0000.0000.000
216A367VAL00.0140.00430.487-0.003-0.0030.0000.0000.0000.000
217A368PRO00.0200.01133.2310.0030.0030.0000.0000.0000.000
218A369THR0-0.051-0.02734.9850.0000.0000.0000.0000.0000.000
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