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: PK283

Calculation Name: 1OA2-C-Xray31

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 1OA2

Chain ID: C

ChEMBL ID:

UniProt ID: O00095

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2579064.759632
FMO2-HF: Nuclear repulsion 2494536.927683
FMO2-HF: Total energy -84527.831949
FMO2-MP2: Total energy -84775.291261


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(C:1:PCA)


Summations of interaction energy for fragment #1(C:1:PCA)
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.
-18.503-8.8437.395-6.928-10.126-0.042
Interaction energy analysis for fragmet #1(C:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.013
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].
3C3SER00.0010.0043.836-1.0731.454-0.020-1.375-1.1330.003
4C32CYS0-0.056-0.0215.9990.1540.1540.0000.0000.0000.000
5C5ASP-1-0.870-0.9099.059-1.025-1.0250.0000.0000.0000.000
6C6GLN0-0.018-0.00810.971-0.052-0.0520.0000.0000.0000.000
7C7TRP0-0.001-0.01512.7970.0280.0280.0000.0000.0000.000
8C8ALA00.0050.0187.0160.0990.0990.0000.0000.0000.000
9C9THR0-0.032-0.0277.8940.1910.1910.0000.0000.0000.000
10C10PHE00.0280.0222.751-4.353-2.1762.903-1.532-3.548-0.020
11C11THR00.0090.0005.3160.0310.054-0.001-0.001-0.0210.000
12C12GLY00.0240.0077.0780.6330.6330.0000.0000.0000.000
13C13ASN0-0.052-0.0298.354-0.376-0.3760.0000.0000.0000.000
14C14GLY00.0130.01411.572-0.147-0.1470.0000.0000.0000.000
15C15TYR00.0210.0219.958-0.289-0.2890.0000.0000.0000.000
16C16THR0-0.013-0.0239.1620.3830.3830.0000.0000.0000.000
17C17VAL00.0170.0146.877-0.174-0.1740.0000.0000.0000.000
18C18SER0-0.029-0.0218.094-0.202-0.2020.0000.0000.0000.000
19C19ASN00.009-0.0269.7030.0150.0150.0000.0000.0000.000
20C20ASN0-0.037-0.02711.2540.0930.0930.0000.0000.0000.000
21C21LEU0-0.0020.00413.4510.0780.0780.0000.0000.0000.000
22C22TRP00.025-0.00416.3100.0030.0030.0000.0000.0000.000
23C23GLY00.0240.02019.4170.0250.0250.0000.0000.0000.000
24C24ALA00.0120.00118.5300.0090.0090.0000.0000.0000.000
25C25SER0-0.036-0.02620.6140.0040.0040.0000.0000.0000.000
26C26ALA0-0.033-0.00623.8500.0230.0230.0000.0000.0000.000
27C27GLY0-0.036-0.03524.3850.0210.0210.0000.0000.0000.000
28C28SER0-0.0290.00322.916-0.013-0.0130.0000.0000.0000.000
29C29GLY00.022-0.00320.3240.0170.0170.0000.0000.0000.000
30C30PHE0-0.011-0.00713.3570.0100.0100.0000.0000.0000.000
31C31GLY00.0620.01713.8890.0770.0770.0000.0000.0000.000
32C33VAL00.0260.0216.5720.3070.3070.0000.0000.0000.000
33C34THR00.021-0.0203.648-1.223-0.8710.001-0.126-0.2260.000
34C35VAL0-0.019-0.0082.566-0.6241.6251.943-1.437-2.7550.012
35C36VAL0-0.005-0.0012.141-10.490-8.3522.571-2.453-2.256-0.037
36C37SER00.007-0.0174.8661.3761.480-0.001-0.003-0.0990.000
37C38LEU00.0060.0165.097-0.434-0.344-0.001-0.001-0.0880.000
38C39SER0-0.035-0.0127.737-0.464-0.4640.0000.0000.0000.000
39C40GLY0-0.011-0.00410.740-0.185-0.1850.0000.0000.0000.000
40C41GLY00.0360.01512.395-0.195-0.1950.0000.0000.0000.000
41C42ALA0-0.064-0.0289.3210.3620.3620.0000.0000.0000.000
42C43SER0-0.044-0.0288.478-0.417-0.4170.0000.0000.0000.000
43C44TRP0-0.049-0.0376.6810.2810.2810.0000.0000.0000.000
44C45HIS0-0.018-0.0197.3230.0480.0480.0000.0000.0000.000
45C46ALA00.0090.0168.597-0.399-0.3990.0000.0000.0000.000
46C47ASP-1-0.793-0.86410.482-1.222-1.2220.0000.0000.0000.000
47C48TRP0-0.004-0.01113.101-0.042-0.0420.0000.0000.0000.000
48C49GLN00.017-0.00416.1210.0950.0950.0000.0000.0000.000
49C50TRP00.0030.01916.975-0.008-0.0080.0000.0000.0000.000
50C51SER0-0.0020.00122.0580.0390.0390.0000.0000.0000.000
51C52GLY00.0340.01625.571-0.006-0.0060.0000.0000.0000.000
52C53GLY00.0840.04227.204-0.009-0.0090.0000.0000.0000.000
53C54GLN00.0070.00728.236-0.014-0.0140.0000.0000.0000.000
54C55ASN00.012-0.00329.495-0.005-0.0050.0000.0000.0000.000
55C56ASN0-0.026-0.01527.2590.0120.0120.0000.0000.0000.000
56C57VAL00.0400.03522.117-0.021-0.0210.0000.0000.0000.000
57C58LYS10.7840.88420.6070.2890.2890.0000.0000.0000.000
58C59SER0-0.066-0.02016.586-0.057-0.0570.0000.0000.0000.000
59C60TYR00.016-0.00317.2170.0440.0440.0000.0000.0000.000
60C61GLN00.0140.03512.1160.1680.1680.0000.0000.0000.000
61C62ASN0-0.060-0.04913.0140.1760.1760.0000.0000.0000.000
62C63SER00.0430.03611.066-0.001-0.0010.0000.0000.0000.000
63C64GLN00.005-0.00912.415-0.102-0.1020.0000.0000.0000.000
64C65ILE0-0.0090.01013.2960.1660.1660.0000.0000.0000.000
65C66ALA00.0010.00915.673-0.093-0.0930.0000.0000.0000.000
66C67ILE0-0.015-0.00317.094-0.007-0.0070.0000.0000.0000.000
67C68PRO0-0.002-0.00819.811-0.043-0.0430.0000.0000.0000.000
68C69GLN00.0280.02222.134-0.016-0.0160.0000.0000.0000.000
69C70LYS10.8850.95621.908-0.189-0.1890.0000.0000.0000.000
70C71ARG10.8500.92327.052-0.221-0.2210.0000.0000.0000.000
71C72THR00.0390.02129.545-0.001-0.0010.0000.0000.0000.000
72C73VAL00.0960.04030.2040.0120.0120.0000.0000.0000.000
73C74ASN0-0.064-0.06431.7280.0100.0100.0000.0000.0000.000
74C75SER0-0.059-0.00731.9090.0050.0050.0000.0000.0000.000
75C76ILE0-0.036-0.00327.4750.0110.0110.0000.0000.0000.000
76C77SER0-0.030-0.02729.967-0.012-0.0120.0000.0000.0000.000
77C78SER0-0.011-0.00627.740-0.002-0.0020.0000.0000.0000.000
78C79MET0-0.044-0.01724.4300.0090.0090.0000.0000.0000.000
79C80PRO00.0250.03223.256-0.018-0.0180.0000.0000.0000.000
80C81THR0-0.0110.00519.4390.0170.0170.0000.0000.0000.000
81C82THR0-0.036-0.02019.056-0.029-0.0290.0000.0000.0000.000
82C83ALA00.0360.00617.6690.0400.0400.0000.0000.0000.000
83C84SER0-0.043-0.00816.895-0.048-0.0480.0000.0000.0000.000
84C85TRP0-0.032-0.01315.891-0.018-0.0180.0000.0000.0000.000
85C86SER00.006-0.00316.5450.0000.0000.0000.0000.0000.000
86C87TYR00.004-0.02716.807-0.063-0.0630.0000.0000.0000.000
87C88SER0-0.0430.00617.1600.0250.0250.0000.0000.0000.000
88C89GLY00.0690.00518.934-0.047-0.0470.0000.0000.0000.000
89C90SER0-0.050-0.01420.9380.0440.0440.0000.0000.0000.000
90C91ASN0-0.014-0.02224.2070.0030.0030.0000.0000.0000.000
91C92ILE0-0.0120.00721.114-0.004-0.0040.0000.0000.0000.000
92C93ARG10.8080.90424.1750.2190.2190.0000.0000.0000.000
93C94ALA00.0510.02020.962-0.021-0.0210.0000.0000.0000.000
94C95ASN0-0.0280.00422.0250.0080.0080.0000.0000.0000.000
95C96VAL00.0140.01818.376-0.037-0.0370.0000.0000.0000.000
96C97ALA00.019-0.00119.9930.0280.0280.0000.0000.0000.000
97C98TYR00.007-0.03120.072-0.016-0.0160.0000.0000.0000.000
98C99ASH0-0.080-0.09021.068-0.029-0.0290.0000.0000.0000.000
99C100LEU0-0.012-0.00521.7090.0320.0320.0000.0000.0000.000
100C101PHE00.0360.04022.902-0.014-0.0140.0000.0000.0000.000
101C102THR0-0.010-0.02126.4320.0210.0210.0000.0000.0000.000
102C103ALA00.0180.00929.265-0.015-0.0150.0000.0000.0000.000
103C104ALA00.0260.01631.6700.0120.0120.0000.0000.0000.000
104C105ASN0-0.0120.00132.3500.0130.0130.0000.0000.0000.000
105C106PRO00.0160.00730.0750.0000.0000.0000.0000.0000.000
106C107ASN0-0.034-0.03728.3470.0180.0180.0000.0000.0000.000
107C108HIS0-0.085-0.03627.695-0.013-0.0130.0000.0000.0000.000
108C109VAL00.0110.01325.2060.0120.0120.0000.0000.0000.000
109C110THR00.015-0.00720.335-0.010-0.0100.0000.0000.0000.000
110C111TYR0-0.0150.00222.0880.0020.0020.0000.0000.0000.000
111C112SER00.0270.01523.254-0.014-0.0140.0000.0000.0000.000
112C113GLY00.0250.00126.8460.0160.0160.0000.0000.0000.000
113C114ASP-1-0.795-0.88529.5880.0200.0200.0000.0000.0000.000
114C115TYR0-0.071-0.04931.465-0.006-0.0060.0000.0000.0000.000
115C116GLU-1-0.776-0.84725.959-0.036-0.0360.0000.0000.0000.000
116C117LEU0-0.056-0.02527.416-0.005-0.0050.0000.0000.0000.000
117C118MET00.0180.02824.2500.0050.0050.0000.0000.0000.000
118C119ILE0-0.015-0.00424.8780.0010.0010.0000.0000.0000.000
119C120TRP0-0.006-0.02224.069-0.007-0.0070.0000.0000.0000.000
120C121LEU00.0160.00520.9410.0040.0040.0000.0000.0000.000
121C122GLY00.0280.01223.154-0.001-0.0010.0000.0000.0000.000
122C123LYS10.8750.93824.0890.0790.0790.0000.0000.0000.000
123C124TYR0-0.029-0.00222.9210.0100.0100.0000.0000.0000.000
124C125GLY00.0670.02426.135-0.012-0.0120.0000.0000.0000.000
125C126ASP-1-0.934-0.95928.925-0.135-0.1350.0000.0000.0000.000
126C127ILE00.0110.02925.7230.0060.0060.0000.0000.0000.000
127C128GLY0-0.027-0.04430.0490.0110.0110.0000.0000.0000.000
128C129PRO0-0.012-0.00329.978-0.009-0.0090.0000.0000.0000.000
129C130ILE00.0450.03830.135-0.002-0.0020.0000.0000.0000.000
130C131GLY0-0.004-0.00232.9830.0080.0080.0000.0000.0000.000
131C132SER0-0.021-0.00136.603-0.004-0.0040.0000.0000.0000.000
132C133SER00.007-0.00137.7310.0070.0070.0000.0000.0000.000
133C134GLN0-0.062-0.05438.3970.0010.0010.0000.0000.0000.000
134C135GLY0-0.0040.01639.6430.0040.0040.0000.0000.0000.000
135C136THR0-0.017-0.01837.514-0.002-0.0020.0000.0000.0000.000
136C137VAL0-0.0220.00935.2650.0030.0030.0000.0000.0000.000
137C138ASN00.0440.02336.092-0.005-0.0050.0000.0000.0000.000
138C139VAL0-0.001-0.00431.8250.0040.0040.0000.0000.0000.000
139C140GLY00.0230.01131.4170.0010.0010.0000.0000.0000.000
140C141GLY0-0.033-0.00631.8320.0030.0030.0000.0000.0000.000
141C142GLN00.0580.02728.3890.0120.0120.0000.0000.0000.000
142C143SER0-0.042-0.04032.9300.0030.0030.0000.0000.0000.000
143C144TRP0-0.051-0.02727.078-0.007-0.0070.0000.0000.0000.000
144C145THR00.000-0.00533.2800.0030.0030.0000.0000.0000.000
145C146LEU00.0000.01233.407-0.002-0.0020.0000.0000.0000.000
146C147TYR0-0.028-0.02133.247-0.004-0.0040.0000.0000.0000.000
147C148TYR00.000-0.02834.5440.0040.0040.0000.0000.0000.000
148C149GLY00.0320.01035.838-0.005-0.0050.0000.0000.0000.000
149C150TYR0-0.0350.00335.7830.0060.0060.0000.0000.0000.000
150C151ASN00.0010.00929.981-0.011-0.0110.0000.0000.0000.000
151C152GLY00.0250.01133.6720.0020.0020.0000.0000.0000.000
152C153ALA0-0.003-0.02235.7060.0040.0040.0000.0000.0000.000
153C154MET0-0.0390.02128.7120.0090.0090.0000.0000.0000.000
154C155GLN00.0190.02934.020-0.005-0.0050.0000.0000.0000.000
155C156VAL00.0370.01029.9780.0070.0070.0000.0000.0000.000
156C157TYR00.013-0.00431.607-0.003-0.0030.0000.0000.0000.000
157C158SER00.0100.00829.4570.0010.0010.0000.0000.0000.000
158C159PHE0-0.0040.00029.563-0.003-0.0030.0000.0000.0000.000
159C160VAL0-0.011-0.01328.7410.0000.0000.0000.0000.0000.000
160C161ALA00.0080.01227.8500.0060.0060.0000.0000.0000.000
161C162GLN0-0.018-0.02029.676-0.008-0.0080.0000.0000.0000.000
162C163THR0-0.0050.00130.206-0.005-0.0050.0000.0000.0000.000
163C164ASN00.0190.00524.6280.0010.0010.0000.0000.0000.000
164C165THR0-0.006-0.00125.0170.0080.0080.0000.0000.0000.000
165C166THR00.0340.00821.3590.0060.0060.0000.0000.0000.000
166C167ASN0-0.025-0.00420.577-0.009-0.0090.0000.0000.0000.000
167C168TYR00.0230.00921.830-0.007-0.0070.0000.0000.0000.000
168C169SER00.009-0.00122.3970.0400.0400.0000.0000.0000.000
169C170GLY00.0270.02024.628-0.025-0.0250.0000.0000.0000.000
170C171ASP-1-0.783-0.90125.3900.2120.2120.0000.0000.0000.000
171C172VAL00.0380.01223.912-0.024-0.0240.0000.0000.0000.000
172C173LYS10.8540.95226.956-0.149-0.1490.0000.0000.0000.000
173C174ASN0-0.023-0.01729.861-0.014-0.0140.0000.0000.0000.000
174C175PHE00.0080.00528.208-0.011-0.0110.0000.0000.0000.000
175C176PHE00.0250.00527.261-0.010-0.0100.0000.0000.0000.000
176C177ASN00.011-0.00632.362-0.008-0.0080.0000.0000.0000.000
177C178TYR00.0510.04334.689-0.007-0.0070.0000.0000.0000.000
178C179LEU0-0.008-0.01232.755-0.008-0.0080.0000.0000.0000.000
179C180ARG10.8120.88836.499-0.086-0.0860.0000.0000.0000.000
180C181ASP-1-0.888-0.92138.3300.0650.0650.0000.0000.0000.000
181C182ASN0-0.058-0.02739.687-0.007-0.0070.0000.0000.0000.000
182C183LYS10.8810.94338.358-0.019-0.0190.0000.0000.0000.000
183C184GLY00.0250.03140.769-0.003-0.0030.0000.0000.0000.000
184C185TYR0-0.023-0.00931.9920.0040.0040.0000.0000.0000.000
185C186ASN00.0720.01938.2020.0090.0090.0000.0000.0000.000
186C187ALA00.0410.00735.0220.0030.0030.0000.0000.0000.000
187C188ALA0-0.078-0.03535.1730.0090.0090.0000.0000.0000.000
188C189GLY00.020-0.00337.0060.0040.0040.0000.0000.0000.000
189C190GLN0-0.0090.01932.531-0.002-0.0020.0000.0000.0000.000
190C191TYR0-0.021-0.01329.3260.0150.0150.0000.0000.0000.000
191C192VAL00.0080.00324.402-0.013-0.0130.0000.0000.0000.000
192C193LEU0-0.043-0.02424.7350.0230.0230.0000.0000.0000.000
193C194SER00.011-0.00520.4290.0160.0160.0000.0000.0000.000
194C195TYR00.018-0.01719.526-0.018-0.0180.0000.0000.0000.000
195C196GLN0-0.017-0.00816.3260.0430.0430.0000.0000.0000.000
196C197PHE00.0170.01615.321-0.025-0.0250.0000.0000.0000.000
197C198GLY00.0530.01815.3130.0080.0080.0000.0000.0000.000
198C199THR0-0.056-0.00415.5680.0090.0090.0000.0000.0000.000
199C200GLU-1-0.799-0.90018.007-0.184-0.1840.0000.0000.0000.000
200C201PRO0-0.046-0.00618.2150.0320.0320.0000.0000.0000.000
201C202PHE00.0140.00121.3610.0040.0040.0000.0000.0000.000
202C203THR00.0080.00024.412-0.005-0.0050.0000.0000.0000.000
203C204GLY00.0280.02523.9540.0150.0150.0000.0000.0000.000
204C205SER0-0.023-0.02219.926-0.034-0.0340.0000.0000.0000.000
205C206GLY00.007-0.01118.3400.0660.0660.0000.0000.0000.000
206C207THR00.0130.00112.717-0.041-0.0410.0000.0000.0000.000
207C208LEU0-0.067-0.01114.1720.1080.1080.0000.0000.0000.000
208C209ASN00.0400.00311.470-0.211-0.2110.0000.0000.0000.000
209C210VAL0-0.018-0.01311.4380.1020.1020.0000.0000.0000.000
210C211ALA00.0170.00511.2390.0600.0600.0000.0000.0000.000
211C212SER0-0.017-0.00712.5440.1680.1680.0000.0000.0000.000
212C213TRP00.0490.03113.539-0.096-0.0960.0000.0000.0000.000
213C214THR00.0180.02414.0730.1410.1410.0000.0000.0000.000
214C215ALA00.0130.01216.626-0.092-0.0920.0000.0000.0000.000
215C216SER0-0.0020.00218.1480.0630.0630.0000.0000.0000.000
216C217ILE00.006-0.00820.705-0.046-0.0460.0000.0000.0000.000
217C218ASN-1-0.791-0.88423.6990.2590.2590.0000.0000.0000.000
218C301NAG00.0270.01961.547-0.001-0.0010.0000.0000.0000.000
219D301NAG00.0630.05766.0500.0000.0000.0000.0000.0000.000
220C2111HOH00.0290.02060.5710.0000.0000.0000.0000.0000.000
221C2112HOH0-0.032-0.02561.2670.0000.0000.0000.0000.0000.000
222D2056HOH0-0.034-0.03372.6090.0000.0000.0000.0000.0000.000
223D2057HOH0-0.051-0.03665.9970.0000.0000.0000.0000.0000.000
224D2058HOH00.0260.01864.1180.0000.0000.0000.0000.0000.000
225D2059HOH0-0.028-0.02168.9360.0000.0000.0000.0000.0000.000