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: 394ML

Calculation Name: 4XHJ-C-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4XHJ

Chain ID: C

ChEMBL ID:

UniProt ID: Q775J3

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2114624.719083
FMO2-HF: Nuclear repulsion 2033209.464682
FMO2-HF: Total energy -81415.254401
FMO2-MP2: Total energy -81653.380824


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:ASP)


Summations of interaction energy for fragment #1(C: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.
-82.152-90.32525.617-11.312-6.130.079
Interaction energy analysis for fragmet #1(C:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.873 / q_NPA : -0.913
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].
3C3GLN00.0250.0203.812-0.7551.175-0.019-0.872-1.0380.006
4C4MET0-0.0040.0025.966-2.072-2.0720.0000.0000.0000.000
5C5THR0-0.037-0.0299.211-1.191-1.1910.0000.0000.0000.000
6C6GLN00.0390.00012.6330.7080.7080.0000.0000.0000.000
7C7SER0-0.0500.00715.862-0.497-0.4970.0000.0000.0000.000
8C8PRO00.1020.03319.411-0.019-0.0190.0000.0000.0000.000
9C9SER00.0120.02118.9640.2610.2610.0000.0000.0000.000
10C10PHE0-0.011-0.02020.4640.2290.2290.0000.0000.0000.000
11C11LEU0-0.0070.00323.955-0.206-0.2060.0000.0000.0000.000
12C12SER00.0270.00926.951-0.094-0.0940.0000.0000.0000.000
13C13ALA0-0.026-0.00130.347-0.090-0.0900.0000.0000.0000.000
14C14SER00.0160.01532.664-0.122-0.1220.0000.0000.0000.000
15C15VAL0-0.046-0.03435.2480.0850.0850.0000.0000.0000.000
16C16GLY0-0.026-0.01236.118-0.240-0.2400.0000.0000.0000.000
17C17ASP-1-0.841-0.90733.8258.7018.7010.0000.0000.0000.000
18C18ARG10.9650.97130.538-9.277-9.2770.0000.0000.0000.000
19C19VAL0-0.0230.00426.1710.0440.0440.0000.0000.0000.000
20C20THR00.001-0.01524.6220.0110.0110.0000.0000.0000.000
21C21ILE0-0.039-0.00719.6860.0170.0170.0000.0000.0000.000
22C22THR00.0290.02118.3570.2500.2500.0000.0000.0000.000
23C23CYS0-0.042-0.01313.9660.5620.5620.0000.0000.0000.000
24C24ARG10.8620.92113.880-17.364-17.3640.0000.0000.0000.000
25C25ALA00.0590.0439.3681.3951.3950.0000.0000.0000.000
26C26SER0-0.024-0.0196.599-0.767-0.7670.0000.0000.0000.000
27C27GLN0-0.007-0.0096.8280.2830.2830.0000.0000.0000.000
28C28GLY0-0.023-0.0139.9680.1540.1540.0000.0000.0000.000
29C29LEU00.0240.0137.9491.4671.4670.0000.0000.0000.000
30C30ASP-1-0.921-0.96411.59316.64516.6450.0000.0000.0000.000
31C31ASN0-0.006-0.01115.211-0.477-0.4770.0000.0000.0000.000
32C32PHE0-0.042-0.01912.505-0.622-0.6220.0000.0000.0000.000
33C33LEU0-0.009-0.01212.2581.6361.6360.0000.0000.0000.000
34C34ALA00.0070.02114.336-1.096-1.0960.0000.0000.0000.000
35C35TRP00.0230.00716.0060.6700.6700.0000.0000.0000.000
36C36TYR0-0.031-0.04115.080-1.457-1.4570.0000.0000.0000.000
37C37GLN0-0.024-0.02819.698-0.309-0.3090.0000.0000.0000.000
38C38GLN00.0100.00220.0310.2960.2960.0000.0000.0000.000
39C39LYS10.8820.93622.725-10.872-10.8720.0000.0000.0000.000
40C40PRO00.0730.02825.3610.3660.3660.0000.0000.0000.000
41C41GLY0-0.0070.00725.961-0.388-0.3880.0000.0000.0000.000
42C42LYS10.9150.96026.461-10.403-10.4030.0000.0000.0000.000
43C43ALA00.0230.01222.8480.4470.4470.0000.0000.0000.000
44C44PRO00.001-0.00918.556-0.491-0.4910.0000.0000.0000.000
45C45LYS10.9610.99421.342-11.592-11.5920.0000.0000.0000.000
46C46LEU0-0.0100.00018.8620.0960.0960.0000.0000.0000.000
47C47LEU0-0.036-0.02121.464-0.805-0.8050.0000.0000.0000.000
48C48ILE0-0.014-0.02020.640-0.629-0.6290.0000.0000.0000.000
49C49TYR00.0160.01919.0840.5940.5940.0000.0000.0000.000
50C50ALA00.0340.03417.8770.9290.9290.0000.0000.0000.000
51C51ALA00.0520.02417.796-0.183-0.1830.0000.0000.0000.000
52C52SER0-0.010-0.01919.149-0.262-0.2620.0000.0000.0000.000
53C53THR0-0.025-0.00122.336-0.440-0.4400.0000.0000.0000.000
54C54LEU00.0030.01423.4230.3950.3950.0000.0000.0000.000
55C55GLN00.0610.01924.184-0.538-0.5380.0000.0000.0000.000
56C56ARG10.8980.94526.063-10.930-10.9300.0000.0000.0000.000
57C57GLY00.0310.01229.2960.1420.1420.0000.0000.0000.000
58C58VAL0-0.088-0.03025.975-0.146-0.1460.0000.0000.0000.000
59C59PRO00.0170.00429.364-0.165-0.1650.0000.0000.0000.000
60C60SER00.0450.00730.2540.2260.2260.0000.0000.0000.000
61C61ARG10.7210.83531.479-9.641-9.6410.0000.0000.0000.000
62C62PHE0-0.0190.00926.1430.1010.1010.0000.0000.0000.000
63C63GLY00.0500.02026.582-0.190-0.1900.0000.0000.0000.000
64C64GLY00.0050.00222.6950.3190.3190.0000.0000.0000.000
65C65SER0-0.020-0.01022.257-0.447-0.4470.0000.0000.0000.000
66C66GLY00.0440.00919.4790.3830.3830.0000.0000.0000.000
67C67SER00.0110.00817.920-0.251-0.2510.0000.0000.0000.000
68C68GLY00.0340.03015.296-0.015-0.0150.0000.0000.0000.000
69C69THR0-0.008-0.00712.1670.7810.7810.0000.0000.0000.000
70C70GLU-1-0.866-0.91314.12115.37315.3730.0000.0000.0000.000
71C71PHE00.0230.00713.435-0.671-0.6710.0000.0000.0000.000
72C72THR00.0260.00818.0630.0360.0360.0000.0000.0000.000
73C73LEU0-0.0480.00021.097-0.279-0.2790.0000.0000.0000.000
74C74THR0-0.043-0.02722.606-0.285-0.2850.0000.0000.0000.000
75C75ILE0-0.005-0.00126.302-0.077-0.0770.0000.0000.0000.000
76C76SER0-0.032-0.03528.865-0.263-0.2630.0000.0000.0000.000
77C77SER00.0310.01332.198-0.282-0.2820.0000.0000.0000.000
78C78LEU0-0.0240.00430.1630.1080.1080.0000.0000.0000.000
79C79GLN00.003-0.01032.941-0.557-0.5570.0000.0000.0000.000
80C80PRO00.0520.02133.2060.3000.3000.0000.0000.0000.000
81C81GLU-1-0.850-0.90032.3719.4939.4930.0000.0000.0000.000
82C82ASP-1-0.795-0.87829.19010.54110.5410.0000.0000.0000.000
83C83PHE0-0.0090.02828.1140.4630.4630.0000.0000.0000.000
84C84ALA0-0.033-0.01924.6750.0250.0250.0000.0000.0000.000
85C85THR0-0.0060.00120.233-0.225-0.2250.0000.0000.0000.000
86C86TYR0-0.014-0.02020.3330.1370.1370.0000.0000.0000.000
87C87TYR00.0170.03315.0180.2350.2350.0000.0000.0000.000
88C89GLN00.0080.00310.819-0.436-0.4360.0000.0000.0000.000
89C90GLN00.0460.0154.468-3.449-3.369-0.001-0.003-0.0750.000
90C91LEU0-0.013-0.0159.6730.1390.1390.0000.0000.0000.000
91C92ASN0-0.049-0.02610.329-0.270-0.2700.0000.0000.0000.000
92C93SER00.0550.0365.145-0.183-0.1830.0000.0000.0000.000
93C94TYR00.004-0.0056.854-2.135-2.1350.0000.0000.0000.000
94C95SER0-0.047-0.0451.556-26.986-37.58325.634-10.347-4.6900.073
95C96LEU0-0.049-0.0084.529-2.526-2.425-0.001-0.028-0.0720.000
96C97THR00.011-0.0023.678-2.688-2.3750.004-0.062-0.2550.000
97C98PHE00.006-0.0086.967-3.795-3.7950.0000.0000.0000.000
98C99GLY0-0.004-0.0049.5621.0041.0040.0000.0000.0000.000
99C100PRO0-0.031-0.03311.672-0.507-0.5070.0000.0000.0000.000
100C101GLY00.0060.00813.656-0.792-0.7920.0000.0000.0000.000
101C102THR0-0.068-0.04316.8090.0060.0060.0000.0000.0000.000
102C103LYS10.9350.96320.224-13.601-13.6010.0000.0000.0000.000
103C104VAL00.0040.00323.293-0.173-0.1730.0000.0000.0000.000
104C105GLU-1-0.871-0.93726.4119.8179.8170.0000.0000.0000.000
105C106ILE0-0.047-0.03129.868-0.031-0.0310.0000.0000.0000.000
106C107LYS10.9310.96633.216-9.255-9.2550.0000.0000.0000.000
107C108ARG10.8390.91236.195-7.516-7.5160.0000.0000.0000.000
108C109ARG10.9590.97539.680-7.641-7.6410.0000.0000.0000.000
109C110THR00.0110.01142.634-0.089-0.0890.0000.0000.0000.000
110C111VAL00.0190.01343.3300.1790.1790.0000.0000.0000.000
111C112ALA0-0.028-0.00544.141-0.152-0.1520.0000.0000.0000.000
112C113ALA00.0670.02245.4600.1120.1120.0000.0000.0000.000
113C114PRO00.0030.01545.5610.0130.0130.0000.0000.0000.000
114C115SER0-0.0020.00447.153-0.210-0.2100.0000.0000.0000.000
115C116VAL00.0140.00948.6240.0930.0930.0000.0000.0000.000
116C117PHE0-0.018-0.00249.559-0.199-0.1990.0000.0000.0000.000
117C118ILE00.016-0.00750.1870.0970.0970.0000.0000.0000.000
118C119PHE00.0060.00348.654-0.095-0.0950.0000.0000.0000.000
119C120PRO0-0.019-0.01452.4640.0450.0450.0000.0000.0000.000
120C121PRO0-0.0020.00553.819-0.024-0.0240.0000.0000.0000.000
121C122SER00.0730.02953.4210.1210.1210.0000.0000.0000.000
122C123ASP-1-0.870-0.93454.9455.4335.4330.0000.0000.0000.000
123C124GLU-1-0.885-0.93753.4735.8195.8190.0000.0000.0000.000
124C125GLN00.0280.04348.8530.0090.0090.0000.0000.0000.000
125C126LEU00.0190.04053.4710.0050.0050.0000.0000.0000.000
126C127LYS10.8240.90056.515-5.507-5.5070.0000.0000.0000.000
127C128SER0-0.070-0.05052.6280.0280.0280.0000.0000.0000.000
128C129GLY00.0080.01053.5580.0740.0740.0000.0000.0000.000
129C130THR0-0.076-0.03749.5670.0940.0940.0000.0000.0000.000
130C131ALA00.0410.02452.312-0.059-0.0590.0000.0000.0000.000
131C132SER0-0.038-0.05648.0300.1040.1040.0000.0000.0000.000
132C133VAL0-0.0370.00550.120-0.056-0.0560.0000.0000.0000.000
133C134VAL00.0250.01645.4830.0700.0700.0000.0000.0000.000
134C135CYS0-0.047-0.01546.798-0.040-0.0400.0000.0000.0000.000
135C136LEU0-0.018-0.00844.0780.1660.1660.0000.0000.0000.000
136C137LEU00.0130.00343.469-0.173-0.1730.0000.0000.0000.000
137C138ASN0-0.002-0.01543.0030.0760.0760.0000.0000.0000.000
138C139ASN00.018-0.01342.116-0.112-0.1120.0000.0000.0000.000
139C140PHE0-0.0350.00040.264-0.146-0.1460.0000.0000.0000.000
140C141TYR00.0540.03736.4240.1820.1820.0000.0000.0000.000
141C142PRO00.007-0.01939.341-0.190-0.1900.0000.0000.0000.000
142C143ARG11.0020.99933.124-9.032-9.0320.0000.0000.0000.000
143C144GLU-1-0.927-0.96837.3608.1608.1600.0000.0000.0000.000
144C145ALA00.0400.01240.472-0.195-0.1950.0000.0000.0000.000
145C146LYS10.7850.89040.018-7.532-7.5320.0000.0000.0000.000
146C147VAL00.0340.01244.165-0.152-0.1520.0000.0000.0000.000
147C148GLN0-0.025-0.00946.2740.0320.0320.0000.0000.0000.000
148C149TRP00.011-0.01146.945-0.128-0.1280.0000.0000.0000.000
149C150LYS10.8460.91251.810-5.693-5.6930.0000.0000.0000.000
150C151VAL0-0.032-0.00252.866-0.083-0.0830.0000.0000.0000.000
151C152ASP-1-0.855-0.92451.5126.2016.2010.0000.0000.0000.000
152C153ASN0-0.041-0.02247.1460.1260.1260.0000.0000.0000.000
153C154ALA00.0570.01946.7860.0510.0510.0000.0000.0000.000
154C155LEU00.020-0.01440.6200.0230.0230.0000.0000.0000.000
155C156GLN0-0.0080.00943.981-0.032-0.0320.0000.0000.0000.000
156C157SER00.020-0.00546.621-0.066-0.0660.0000.0000.0000.000
157C158GLY00.0260.02343.1360.0290.0290.0000.0000.0000.000
158C159ASN00.0530.03643.3050.1280.1280.0000.0000.0000.000
159C160SER0-0.032-0.01339.3080.0360.0360.0000.0000.0000.000
160C161GLN0-0.078-0.02838.9250.3710.3710.0000.0000.0000.000
161C162GLU-1-0.841-0.92037.9567.6647.6640.0000.0000.0000.000
162C163SER0-0.045-0.00736.1030.3700.3700.0000.0000.0000.000
163C164VAL0-0.029-0.03234.588-0.219-0.2190.0000.0000.0000.000
164C165THR0-0.012-0.00134.0280.1850.1850.0000.0000.0000.000
165C166GLU-1-0.904-0.96428.41510.80210.8020.0000.0000.0000.000
166C167GLN0-0.016-0.01232.367-0.005-0.0050.0000.0000.0000.000
167C168ASP-1-0.740-0.85033.8298.4538.4530.0000.0000.0000.000
168C169SER0-0.057-0.02833.598-0.080-0.0800.0000.0000.0000.000
169C170LYS10.8120.88335.350-8.431-8.4310.0000.0000.0000.000
170C171ASP-1-0.774-0.86538.8917.6627.6620.0000.0000.0000.000
171C172SER0-0.013-0.00636.238-0.123-0.1230.0000.0000.0000.000
172C173THR0-0.132-0.07237.5950.0480.0480.0000.0000.0000.000
173C174TYR0-0.023-0.03133.2990.1520.1520.0000.0000.0000.000
174C175SER00.0370.02838.194-0.354-0.3540.0000.0000.0000.000
175C176LEU0-0.031-0.00538.5880.2370.2370.0000.0000.0000.000
176C177SER00.006-0.00540.172-0.165-0.1650.0000.0000.0000.000
177C178SER00.0020.01641.0050.1220.1220.0000.0000.0000.000
178C179THR0-0.001-0.01642.505-0.199-0.1990.0000.0000.0000.000
179C180LEU00.0150.03044.6270.0470.0470.0000.0000.0000.000
180C181THR00.005-0.00545.429-0.020-0.0200.0000.0000.0000.000
181C182LEU00.0230.01647.8610.0370.0370.0000.0000.0000.000
182C183SER0-0.014-0.01248.523-0.044-0.0440.0000.0000.0000.000
183C184LYS10.9350.94450.567-6.286-6.2860.0000.0000.0000.000
184C185ALA0-0.0120.00753.689-0.107-0.1070.0000.0000.0000.000
185C186ASP-1-0.806-0.88353.8305.7835.7830.0000.0000.0000.000
186C187TYR0-0.039-0.04054.662-0.082-0.0820.0000.0000.0000.000
187C188GLU-1-0.735-0.83956.0545.0905.0900.0000.0000.0000.000
188C189LYS10.7800.88453.042-6.027-6.0270.0000.0000.0000.000
189C190HIS00.0190.00557.214-0.052-0.0520.0000.0000.0000.000
190C191LYS10.8170.88759.324-5.050-5.0500.0000.0000.0000.000
191C192VAL0-0.044-0.01958.838-0.053-0.0530.0000.0000.0000.000
192C193TYR00.0280.02053.0770.1120.1120.0000.0000.0000.000
193C194ALA0-0.005-0.02154.332-0.074-0.0740.0000.0000.0000.000
194C196GLU-1-0.873-0.93350.6165.8055.8050.0000.0000.0000.000
195C197VAL00.0610.03446.6380.1510.1510.0000.0000.0000.000
196C198THR0-0.014-0.00446.982-0.077-0.0770.0000.0000.0000.000
197C199HIS00.0370.00443.102-0.011-0.0110.0000.0000.0000.000
198C200GLN00.0200.00643.079-0.133-0.1330.0000.0000.0000.000
199C201GLY0-0.0040.00247.428-0.073-0.0730.0000.0000.0000.000
200C202LEU0-0.063-0.03248.715-0.098-0.0980.0000.0000.0000.000
201C203SER0-0.009-0.00151.7380.0080.0080.0000.0000.0000.000
202C204SER00.0260.01254.532-0.045-0.0450.0000.0000.0000.000
203C205PRO0-0.010-0.01651.5690.0360.0360.0000.0000.0000.000
204C206VAL0-0.0050.02452.665-0.111-0.1110.0000.0000.0000.000
205C207THR0-0.012-0.00852.9150.0930.0930.0000.0000.0000.000
206C208LYS10.8600.93953.718-5.995-5.9950.0000.0000.0000.000
207C209SER00.021-0.01354.5620.1170.1170.0000.0000.0000.000
208C210PHE0-0.026-0.01555.901-0.070-0.0700.0000.0000.0000.000
209C211ASN00.0310.01457.9610.0640.0640.0000.0000.0000.000
210C212ARG10.9971.01560.571-5.322-5.3220.0000.0000.0000.000