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: K3KV3

Calculation Name: 3ALZ-AB-Other371

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: Minimized from PDB(MVH(D505G))

Registration Date: 2023-03-09

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization BaseStructure_original
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 524
LigandResidueName
LigandFragmentNumber 0
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -10851450.182625
FMO2-HF: Nuclear repulsion 10641755.413262
FMO2-HF: Total energy -209694.769363
FMO2-MP2: Total energy -210298.225469


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy (frag 1-415 : frag 416-524)
"
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.
-341.3423-312.8986183.2749-84.9928-126.7258-0.2574


Interactive mode: IFIE and PIEDA for fragment #1(A:188:CYS)


Summations of interaction energy for fragment #1(A:188:CYS)
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.
31.77947.410.616-11.151-15.088-0.015
Interaction energy analysis for fragmet #1(A:188:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.767 / q_NPA : 0.870
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].
3A190GLY00.0520.0163.2885.5099.5000.663-2.026-2.6290.001
4A191PRO00.0050.0033.123-6.185-5.0883.373-1.728-2.742-0.020
5A192THR0-0.0150.0012.837-14.016-8.4652.863-3.624-4.791-0.013
6A193THR00.016-0.0012.122-6.838-5.7933.334-2.038-2.3410.027
7A194ILE0-0.0070.0003.168-1.192-0.2070.399-0.356-1.0280.000
413A604VAL00.0030.0153.614-3.193-0.241-0.016-1.379-1.557-0.010
8A195ARG10.9170.9555.87120.39620.3960.0000.0000.0000.000
9A196GLY00.0710.0237.766-0.686-0.6860.0000.0000.0000.000
10A197GLN0-0.125-0.06211.088-0.429-0.4290.0000.0000.0000.000
11A198PHE00.0570.02113.4450.0860.0860.0000.0000.0000.000
12A199SER0-0.020-0.02217.1510.1440.1440.0000.0000.0000.000
13A200ASN00.0550.02319.912-0.021-0.0210.0000.0000.0000.000
14A201MET0-0.069-0.02220.6990.3690.3690.0000.0000.0000.000
15A202SER00.0020.00224.116-0.185-0.1850.0000.0000.0000.000
16A203LEU0-0.014-0.00326.7900.2460.2460.0000.0000.0000.000
17A204SER0-0.023-0.03728.7780.1160.1160.0000.0000.0000.000
18A205LEU00.0280.01830.5360.0460.0460.0000.0000.0000.000
19A206LEU00.0230.01829.6850.0960.0960.0000.0000.0000.000
20A207ASP-1-0.864-0.95326.423-9.822-9.8220.0000.0000.0000.000
21A208LEU0-0.042-0.01729.7530.0210.0210.0000.0000.0000.000
22A209TYR00.023-0.00832.7610.1650.1650.0000.0000.0000.000
23A210LEU00.0720.04129.3350.0970.0970.0000.0000.0000.000
24A211GLY00.0200.03431.2880.0950.0950.0000.0000.0000.000
25A212ARG10.8000.89531.9497.7287.7280.0000.0000.0000.000
26A213GLY0-0.038-0.00634.7240.1740.1740.0000.0000.0000.000
27A214TYR0-0.082-0.04535.9220.2570.2570.0000.0000.0000.000
28A215ASN00.0320.00536.874-0.299-0.2990.0000.0000.0000.000
29A216VAL0-0.038-0.01834.0810.0880.0880.0000.0000.0000.000
30A217SER00.014-0.00635.432-0.176-0.1760.0000.0000.0000.000
31A218SER00.0450.02335.9400.0830.0830.0000.0000.0000.000
32A219ILE0-0.047-0.02630.5930.0330.0330.0000.0000.0000.000
33A220VAL00.0390.03331.281-0.161-0.1610.0000.0000.0000.000
34A221THR0-0.060-0.09826.9050.1940.1940.0000.0000.0000.000
35A222MET00.0100.01326.076-0.059-0.0590.0000.0000.0000.000
36A223THR0-0.005-0.00121.7430.1730.1730.0000.0000.0000.000
37A224SER00.034-0.00724.832-0.100-0.1000.0000.0000.0000.000
38A225GLN00.0890.04624.457-0.059-0.0590.0000.0000.0000.000
39A226GLY0-0.037-0.00923.172-0.324-0.3240.0000.0000.0000.000
40A227MET0-0.104-0.03424.2180.2640.2640.0000.0000.0000.000
41A228TYR0-0.023-0.06225.775-0.401-0.4010.0000.0000.0000.000
42A229GLY00.0160.00227.5940.3120.3120.0000.0000.0000.000
43A230GLY00.0320.00629.994-0.276-0.2760.0000.0000.0000.000
44A231THR0-0.059-0.01532.2660.2770.2770.0000.0000.0000.000
45A232TYR0-0.017-0.01733.718-0.114-0.1140.0000.0000.0000.000
46A233LEU00.0480.04136.4750.1680.1680.0000.0000.0000.000
47A234VAL0-0.0170.00337.746-0.146-0.1460.0000.0000.0000.000
48A235GLU-1-0.825-0.90440.159-6.390-6.3900.0000.0000.0000.000
49A236LYS10.8180.86442.3986.3636.3630.0000.0000.0000.000
50A237PRO00.0120.00444.1350.1100.1100.0000.0000.0000.000
51A238ASN0-0.038-0.01546.5980.1690.1690.0000.0000.0000.000
52A239LEU00.0960.03848.333-0.029-0.0290.0000.0000.0000.000
53A240SER0-0.096-0.04951.6830.1170.1170.0000.0000.0000.000
54A241SER0-0.002-0.00449.8310.0140.0140.0000.0000.0000.000
55A242LYS10.9191.01049.8715.5015.5010.0000.0000.0000.000
56A243ARG11.1131.06048.5605.3975.3970.0000.0000.0000.000
57A244SER00.3870.48746.3650.0070.0070.0000.0000.0000.000
58A245DGL0-1.146-1.23849.0640.4150.4150.0000.0000.0000.000
59A246LEU-1-0.252-0.32554.676-5.376-5.3760.0000.0000.0000.000
60A247SER0-0.065-0.01753.8460.0260.0260.0000.0000.0000.000
61A248GLN00.021-0.00852.343-0.076-0.0760.0000.0000.0000.000
62A249LEU0-0.0030.02847.4180.0240.0240.0000.0000.0000.000
63A250SER0-0.042-0.03347.264-0.084-0.0840.0000.0000.0000.000
64A251MET00.0730.05241.805-0.067-0.0670.0000.0000.0000.000
65A252TYR0-0.039-0.01143.2000.1310.1310.0000.0000.0000.000
66A253ARG10.9210.96838.3467.1077.1070.0000.0000.0000.000
67A254VAL0-0.059-0.03137.0980.0970.0970.0000.0000.0000.000
68A255PHE00.011-0.00437.046-0.196-0.1960.0000.0000.0000.000
69A256GLU-1-0.715-0.79631.566-8.535-8.5350.0000.0000.0000.000
70A257VAL00.0100.00531.945-0.213-0.2130.0000.0000.0000.000
71A258GLY00.0240.00930.6030.2320.2320.0000.0000.0000.000
72A259VAL0-0.073-0.03626.181-0.181-0.1810.0000.0000.0000.000
73A260ILE0-0.0050.02020.7500.1120.1120.0000.0000.0000.000
74A261ARG10.9140.94023.6059.3409.3400.0000.0000.0000.000
75A262ASN00.0770.02019.921-0.259-0.2590.0000.0000.0000.000
76A263PRO0-0.071-0.02722.1140.0480.0480.0000.0000.0000.000
77A264GLY00.0320.02521.0670.1950.1950.0000.0000.0000.000
78A265LEU0-0.009-0.01721.1400.1450.1450.0000.0000.0000.000
79A266GLY00.0020.01016.930-0.147-0.1470.0000.0000.0000.000
80A267ALA00.007-0.01416.166-0.569-0.5690.0000.0000.0000.000
81A268PRO0-0.0200.01016.7160.4870.4870.0000.0000.0000.000
82A269VAL00.002-0.00219.6840.2640.2640.0000.0000.0000.000
83A270PHE0-0.0060.01721.714-0.060-0.0600.0000.0000.0000.000
84A271HIS00.0190.00125.7660.0010.0010.0000.0000.0000.000
85A272MET00.0100.01029.085-0.048-0.0480.0000.0000.0000.000
86A273THR0-0.129-0.10231.7870.0680.0680.0000.0000.0000.000
87A274ASN0-0.050-0.02834.4350.3660.3660.0000.0000.0000.000
88A275TYR0-0.026-0.03036.081-0.162-0.1620.0000.0000.0000.000
89A276LEU00.0060.03138.3210.1690.1690.0000.0000.0000.000
90A277GLU-1-0.811-0.88340.455-6.768-6.7680.0000.0000.0000.000
91A278GLN00.040-0.01342.7540.0410.0410.0000.0000.0000.000
92A279PRO0-0.0250.02645.256-0.094-0.0940.0000.0000.0000.000
93A280VAL0-0.0100.00944.3220.0130.0130.0000.0000.0000.000
94A281SER0-0.016-0.02447.6710.0740.0740.0000.0000.0000.000
95A282ASN0-0.012-0.02347.463-0.011-0.0110.0000.0000.0000.000
96A283ASP-1-0.881-0.95942.625-6.581-6.5810.0000.0000.0000.000
97A284LEU00.0090.00642.822-0.116-0.1160.0000.0000.0000.000
98A285SER0-0.0280.01143.815-0.100-0.1000.0000.0000.0000.000
99A286ASN00.0370.01337.530-0.247-0.2470.0000.0000.0000.000
100A287CYS0-0.100-0.07137.8200.0700.0700.0000.0000.0000.000
101A288MET00.0240.04236.093-0.196-0.1960.0000.0000.0000.000
102A289VAL00.001-0.01232.2500.1340.1340.0000.0000.0000.000
103A290ALA00.0280.03532.702-0.243-0.2430.0000.0000.0000.000
104A291LEU00.0170.01928.1650.1370.1370.0000.0000.0000.000
105A292GLY00.0220.00330.893-0.174-0.1740.0000.0000.0000.000
106A293GLU-1-0.797-0.89031.857-8.485-8.4850.0000.0000.0000.000
107A294LEU0-0.038-0.02132.3780.2860.2860.0000.0000.0000.000
108A295LYS10.9010.94733.8908.2708.2700.0000.0000.0000.000
109A296LEU00.0190.00633.689-0.277-0.2770.0000.0000.0000.000
110A297ALA0-0.033-0.00635.2330.2640.2640.0000.0000.0000.000
111A298ALA00.016-0.00336.733-0.189-0.1890.0000.0000.0000.000
112A299LEU00.0290.02338.6380.2290.2290.0000.0000.0000.000
113A301HIS00.032-0.01542.4760.1220.1220.0000.0000.0000.000
114A302GLY0-0.0210.00144.015-0.091-0.0910.0000.0000.0000.000
115A303GLU-1-0.852-0.91745.540-6.441-6.4410.0000.0000.0000.000
116A304ASP-1-0.858-0.93641.107-7.262-7.2620.0000.0000.0000.000
117A305SER0-0.107-0.06144.144-0.063-0.0630.0000.0000.0000.000
118A306ILE00.0020.01345.4820.1840.1840.0000.0000.0000.000
119A307THR0-0.008-0.01748.268-0.117-0.1170.0000.0000.0000.000
120A308ILE0-0.0150.00848.3520.0440.0440.0000.0000.0000.000
121A309PRO0-0.039-0.01252.3000.0760.0760.0000.0000.0000.000
122A310TYR00.0570.02256.052-0.026-0.0260.0000.0000.0000.000
123A311GLN00.002-0.00458.9430.0350.0350.0000.0000.0000.000
124A312GLY0-0.0120.00562.0840.0960.0960.0000.0000.0000.000
125A313SER00.038-0.00259.3830.0100.0100.0000.0000.0000.000
126A314GLY0-0.046-0.01161.311-0.008-0.0080.0000.0000.0000.000
127A315LYS10.8830.92758.1825.0205.0200.0000.0000.0000.000
128A316GLY00.0470.04454.9140.0310.0310.0000.0000.0000.000
129A317VAL00.0140.01350.4910.0730.0730.0000.0000.0000.000
130A318SER0-0.022-0.02250.025-0.046-0.0460.0000.0000.0000.000
131A319PHE00.0180.02443.4650.0000.0000.0000.0000.0000.000
132A320GLN0-0.019-0.00845.109-0.006-0.0060.0000.0000.0000.000
133A321LEU0-0.037-0.01641.546-0.157-0.1570.0000.0000.0000.000
134A322VAL0-0.0010.00240.7820.1490.1490.0000.0000.0000.000
135A323LYS10.9310.97740.0106.8986.8980.0000.0000.0000.000
136A324LEU00.014-0.00237.4970.1350.1350.0000.0000.0000.000
137A325GLY00.0190.02937.211-0.205-0.2050.0000.0000.0000.000
138A326VAL0-0.030-0.01531.2440.0070.0070.0000.0000.0000.000
139A327TRP0-0.0190.00232.095-0.082-0.0820.0000.0000.0000.000
140A328LYS11.0261.03037.1706.7746.7740.0000.0000.0000.000
141A329SER0-0.035-0.02540.4280.0300.0300.0000.0000.0000.000
142A330PRO0-0.014-0.01143.263-0.005-0.0050.0000.0000.0000.000
143A331THR0-0.010-0.00142.5150.0530.0530.0000.0000.0000.000
144A332ASP-1-0.819-0.90541.315-7.245-7.2450.0000.0000.0000.000
145A333MET0-0.037-0.01043.7800.1650.1650.0000.0000.0000.000
146A334GLN00.003-0.02244.654-0.118-0.1180.0000.0000.0000.000
147A335SER0-0.025-0.00946.7380.1680.1680.0000.0000.0000.000
148A336TRP00.0570.03847.723-0.135-0.1350.0000.0000.0000.000
149A337VAL0-0.0030.00445.8930.1140.1140.0000.0000.0000.000
150A338PRO00.0520.00848.986-0.056-0.0560.0000.0000.0000.000
151A339LEU00.0160.00946.145-0.119-0.1190.0000.0000.0000.000
152A340SER0-0.073-0.03048.7190.1120.1120.0000.0000.0000.000
153A341THR00.0070.00750.245-0.083-0.0830.0000.0000.0000.000
154A342ASP-1-0.967-0.98851.237-6.121-6.1210.0000.0000.0000.000
155A343ASP-1-0.738-0.89050.618-6.269-6.2690.0000.0000.0000.000
156A344PRO0-0.065-0.00652.788-0.036-0.0360.0000.0000.0000.000
157A345VAL0-0.091-0.03850.1620.0660.0660.0000.0000.0000.000
158A346ILE0-0.057-0.03947.123-0.099-0.0990.0000.0000.0000.000
159A347ASP-1-0.847-0.92749.786-6.042-6.0420.0000.0000.0000.000
160A348ARG10.8620.93347.7016.3326.3320.0000.0000.0000.000
161A349LEU0-0.014-0.00243.692-0.153-0.1530.0000.0000.0000.000
162A350TYR00.009-0.00942.2270.1370.1370.0000.0000.0000.000
163A351LEU0-0.012-0.01939.745-0.240-0.2400.0000.0000.0000.000
164A352SER00.1000.04235.801-0.016-0.0160.0000.0000.0000.000
165A353SER00.0060.02131.7650.0350.0350.0000.0000.0000.000
166A354HIS0-0.017-0.00833.265-0.267-0.2670.0000.0000.0000.000
167A355ARG10.8920.96826.16910.34610.3460.0000.0000.0000.000
168A356GLY00.0300.00231.170-0.199-0.1990.0000.0000.0000.000
169A357VAL0-0.067-0.03229.915-0.233-0.2330.0000.0000.0000.000
170A358ILE0-0.042-0.02832.4260.2870.2870.0000.0000.0000.000
171A359ALA0-0.088-0.04933.542-0.280-0.2800.0000.0000.0000.000
172A360ASP-1-0.951-0.99235.223-7.684-7.6840.0000.0000.0000.000
173A361ASN0-0.044-0.03038.3920.2560.2560.0000.0000.0000.000
174A362GLN00.0580.02738.6020.1370.1370.0000.0000.0000.000
175A363ALA0-0.022-0.00537.051-0.266-0.2660.0000.0000.0000.000
176A364LYS10.8880.95235.7568.4128.4120.0000.0000.0000.000
177A365TRP00.021-0.00534.951-0.163-0.1630.0000.0000.0000.000
178A366ALA00.002-0.00134.6760.1610.1610.0000.0000.0000.000
179A367VAL00.0320.02135.864-0.111-0.1110.0000.0000.0000.000
180A368PRO0-0.002-0.01237.3780.1040.1040.0000.0000.0000.000
181A369THR0-0.002-0.00540.2390.1820.1820.0000.0000.0000.000
182A370THR0-0.0040.01443.800-0.096-0.0960.0000.0000.0000.000
183A371ARG10.9010.95045.3576.8386.8380.0000.0000.0000.000
184A372THR00.0560.04348.792-0.024-0.0240.0000.0000.0000.000
185A373ASP-1-0.842-0.92349.403-6.459-6.4590.0000.0000.0000.000
186A374ASP-1-0.674-0.82647.107-6.542-6.5420.0000.0000.0000.000
187A375LYS10.9710.97848.2455.9445.9440.0000.0000.0000.000
188A376LEU0-0.099-0.06449.9090.1240.1240.0000.0000.0000.000
189A377ARG10.8780.94445.9246.8396.8390.0000.0000.0000.000
190A378MET0-0.0230.00340.697-0.161-0.1610.0000.0000.0000.000
191A379GLU-1-0.843-0.93745.202-6.502-6.5020.0000.0000.0000.000
192A380THR0-0.011-0.00146.0390.0150.0150.0000.0000.0000.000
193A381CYS00.0010.02437.916-0.201-0.2010.0000.0000.0000.000
194A382PHE00.002-0.02242.098-0.142-0.1420.0000.0000.0000.000
195A383GLN00.0170.02042.626-0.196-0.1960.0000.0000.0000.000
196A384GLN0-0.006-0.01042.298-0.143-0.1430.0000.0000.0000.000
197A385ALA00.0530.03438.235-0.068-0.0680.0000.0000.0000.000
198A386CYS0-0.203-0.09439.207-0.035-0.0350.0000.0000.0000.000
199A387LYS10.9580.97541.6486.7106.7100.0000.0000.0000.000
200A388GLY0-0.036-0.00739.3130.0370.0370.0000.0000.0000.000
201A389LYS10.8650.93030.7959.6169.6160.0000.0000.0000.000
202A390ILE0-0.069-0.01535.178-0.081-0.0810.0000.0000.0000.000
203A391GLN00.0420.02137.4450.0760.0760.0000.0000.0000.000
204A392ALA00.0780.01238.8690.0930.0930.0000.0000.0000.000
205A393LEU0-0.088-0.02435.323-0.021-0.0210.0000.0000.0000.000
206A395GLU-1-0.844-0.92842.474-6.902-6.9020.0000.0000.0000.000
207A396ASN0-0.058-0.01743.789-0.035-0.0350.0000.0000.0000.000
208A397PRO00.011-0.00542.428-0.097-0.0970.0000.0000.0000.000
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