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: JLRV9

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2113431.47928
FMO2-HF: Nuclear repulsion 2032017.379269
FMO2-HF: Total energy -81414.100011
FMO2-MP2: Total energy -81652.251924


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.
-49.388-44.1670.771-2.479-3.5120.013
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 : -0.930 / q_NPA : -0.969
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].
3C3GLN00.0080.0013.812-2.058-0.107-0.018-0.889-1.0440.006
4C4MET00.0010.0005.917-2.365-2.3650.0000.0000.0000.000
5C5THR0-0.031-0.0219.157-1.023-1.0230.0000.0000.0000.000
6C6GLN00.032-0.00912.5820.7260.7260.0000.0000.0000.000
7C7SER0-0.0560.00615.810-0.478-0.4780.0000.0000.0000.000
8C8PRO00.1020.03419.360-0.024-0.0240.0000.0000.0000.000
9C9SER00.0100.02319.2060.2370.2370.0000.0000.0000.000
10C10PHE00.002-0.01520.4190.2490.2490.0000.0000.0000.000
11C11LEU0-0.0040.00523.910-0.201-0.2010.0000.0000.0000.000
12C12SER00.0130.00626.903-0.105-0.1050.0000.0000.0000.000
13C13ALA0-0.0110.00530.299-0.090-0.0900.0000.0000.0000.000
14C14SER00.0160.01432.613-0.125-0.1250.0000.0000.0000.000
15C15VAL0-0.030-0.02935.1950.0830.0830.0000.0000.0000.000
16C16GLY0-0.034-0.01836.074-0.236-0.2360.0000.0000.0000.000
17C17ASP-1-0.849-0.91133.6638.6598.6590.0000.0000.0000.000
18C18ARG10.9730.97630.620-9.266-9.2660.0000.0000.0000.000
19C19VAL0-0.0230.00126.0860.0440.0440.0000.0000.0000.000
20C20THR0-0.010-0.01624.4840.0620.0620.0000.0000.0000.000
21C21ILE0-0.036-0.00919.6700.0070.0070.0000.0000.0000.000
22C22THR00.0100.01318.1000.1720.1720.0000.0000.0000.000
23C23CYS0-0.041-0.01413.6720.6080.6080.0000.0000.0000.000
24C24ARG10.9360.98113.824-17.350-17.3500.0000.0000.0000.000
25C25ALA00.0690.0459.3111.3651.3650.0000.0000.0000.000
26C26SER0-0.029-0.0206.671-0.205-0.2050.0000.0000.0000.000
27C27GLN00.001-0.0036.1742.2592.2590.0000.0000.0000.000
28C28GLY0-0.031-0.0159.9680.1070.1070.0000.0000.0000.000
29C29LEU00.0290.0168.0681.3021.3020.0000.0000.0000.000
30C30ASP-1-0.952-0.97211.60216.29316.2930.0000.0000.0000.000
31C31ASN00.022-0.00515.222-0.236-0.2360.0000.0000.0000.000
32C32PHE0-0.037-0.02012.399-0.638-0.6380.0000.0000.0000.000
33C33LEU0-0.005-0.00912.3781.5611.5610.0000.0000.0000.000
34C34ALA00.0020.01814.324-1.067-1.0670.0000.0000.0000.000
35C35TRP00.0400.01815.9940.6760.6760.0000.0000.0000.000
36C36TYR0-0.026-0.03714.893-1.474-1.4740.0000.0000.0000.000
37C37GLN00.000-0.01419.649-0.514-0.5140.0000.0000.0000.000
38C38GLN00.0160.00519.6560.0100.0100.0000.0000.0000.000
39C39LYS10.9420.97622.683-10.629-10.6290.0000.0000.0000.000
40C40PRO00.0830.03325.3000.3820.3820.0000.0000.0000.000
41C41GLY0-0.0010.01125.850-0.389-0.3890.0000.0000.0000.000
42C42LYS10.9140.96026.265-10.470-10.4700.0000.0000.0000.000
43C43ALA00.0210.01022.6490.4510.4510.0000.0000.0000.000
44C44PRO0-0.012-0.01318.475-0.489-0.4890.0000.0000.0000.000
45C45LYS10.9650.99721.253-11.522-11.5220.0000.0000.0000.000
46C46LEU0-0.003-0.00218.8780.1260.1260.0000.0000.0000.000
47C47LEU0-0.061-0.03121.462-0.832-0.8320.0000.0000.0000.000
48C48ILE0-0.007-0.00720.575-0.607-0.6070.0000.0000.0000.000
49C49TYR00.0100.00619.0570.5640.5640.0000.0000.0000.000
50C50ALA00.0210.03217.8730.8640.8640.0000.0000.0000.000
51C51ALA00.0580.02517.807-0.177-0.1770.0000.0000.0000.000
52C52SER0-0.016-0.02119.148-0.268-0.2680.0000.0000.0000.000
53C53THR0-0.0070.00922.344-0.433-0.4330.0000.0000.0000.000
54C54LEU0-0.021-0.00423.4170.4350.4350.0000.0000.0000.000
55C55GLN00.0200.00524.252-0.324-0.3240.0000.0000.0000.000
56C56ARG10.9590.97226.055-10.438-10.4380.0000.0000.0000.000
57C57GLY00.0310.01329.3910.1370.1370.0000.0000.0000.000
58C58VAL0-0.085-0.02925.961-0.143-0.1430.0000.0000.0000.000
59C59PRO0-0.002-0.00429.351-0.175-0.1750.0000.0000.0000.000
60C60SER00.0510.00930.2420.1990.1990.0000.0000.0000.000
61C61ARG10.8240.90631.455-9.623-9.6230.0000.0000.0000.000
62C62PHE0-0.0170.01226.1870.0770.0770.0000.0000.0000.000
63C63GLY00.0620.03026.577-0.184-0.1840.0000.0000.0000.000
64C64GLY00.0030.00222.6900.3250.3250.0000.0000.0000.000
65C65SER0-0.017-0.00722.241-0.470-0.4700.0000.0000.0000.000
66C66GLY00.0440.00719.4830.3870.3870.0000.0000.0000.000
67C67SER00.0020.00417.938-0.243-0.2430.0000.0000.0000.000
68C68GLY00.0410.03115.3070.0040.0040.0000.0000.0000.000
69C69THR0-0.025-0.01812.8480.7140.7140.0000.0000.0000.000
70C70GLU-1-0.934-0.96114.12614.89614.8960.0000.0000.0000.000
71C71PHE00.0230.00813.368-0.638-0.6380.0000.0000.0000.000
72C72THR0-0.021-0.00218.060-0.036-0.0360.0000.0000.0000.000
73C73LEU0-0.0020.00521.091-0.246-0.2460.0000.0000.0000.000
74C74THR0-0.036-0.02522.596-0.402-0.4020.0000.0000.0000.000
75C75ILE0-0.0070.00326.273-0.078-0.0780.0000.0000.0000.000
76C76SER0-0.043-0.04528.809-0.257-0.2570.0000.0000.0000.000
77C77SER00.0350.01932.166-0.262-0.2620.0000.0000.0000.000
78C78LEU0-0.026-0.00229.9510.1090.1090.0000.0000.0000.000
79C79GLN00.0340.01032.887-0.490-0.4900.0000.0000.0000.000
80C80PRO00.0380.01733.1550.2900.2900.0000.0000.0000.000
81C81GLU-1-0.972-0.98132.6449.2749.2740.0000.0000.0000.000
82C82ASP-1-0.832-0.91729.15010.44210.4420.0000.0000.0000.000
83C83PHE0-0.0020.03528.0640.4540.4540.0000.0000.0000.000
84C84ALA0-0.028-0.01824.5930.0500.0500.0000.0000.0000.000
85C85THR0-0.0220.00320.7210.1670.1670.0000.0000.0000.000
86C86TYR0-0.018-0.03920.2830.1990.1990.0000.0000.0000.000
87C87TYR00.0010.02914.7250.4430.4430.0000.0000.0000.000
88C89GLN00.0210.00410.955-0.300-0.3000.0000.0000.0000.000
89C90GLN00.0610.0304.387-3.100-3.047-0.001-0.003-0.0480.000
90C91LEU0-0.023-0.0159.6650.2930.2930.0000.0000.0000.000
91C92ASN0-0.044-0.02010.331-0.129-0.1290.0000.0000.0000.000
92C93SER00.0510.0295.4250.1410.1410.0000.0000.0000.000
93C94TYR00.007-0.0027.152-1.920-1.9200.0000.0000.0000.000
94C95SER00.0070.0092.8430.9363.7940.788-1.521-2.1250.007
95C96LEU0-0.061-0.0124.825-1.918-1.887-0.001-0.008-0.0220.000
96C97THR00.0180.0083.683-2.267-1.9390.003-0.058-0.2730.000
97C98PHE00.005-0.0106.922-3.678-3.6780.0000.0000.0000.000
98C99GLY0-0.010-0.0089.5151.0811.0810.0000.0000.0000.000
99C100PRO0-0.032-0.03311.689-0.448-0.4480.0000.0000.0000.000
100C101GLY00.0190.01913.612-0.758-0.7580.0000.0000.0000.000
101C102THR0-0.067-0.04716.7620.0100.0100.0000.0000.0000.000
102C103LYS10.9240.96020.175-13.414-13.4140.0000.0000.0000.000
103C104VAL00.0110.00323.248-0.168-0.1680.0000.0000.0000.000
104C105GLU-1-0.924-0.96526.36310.05010.0500.0000.0000.0000.000
105C106ILE0-0.037-0.02629.822-0.041-0.0410.0000.0000.0000.000
106C107LYS10.9240.95733.277-8.940-8.9400.0000.0000.0000.000
107C108ARG10.9110.96936.147-7.557-7.5570.0000.0000.0000.000
108C109ARG10.9660.97639.632-7.611-7.6110.0000.0000.0000.000
109C110THR0-0.016-0.00342.585-0.082-0.0820.0000.0000.0000.000
110C111VAL00.0210.01143.2840.1720.1720.0000.0000.0000.000
111C112ALA0-0.039-0.01044.144-0.149-0.1490.0000.0000.0000.000
112C113ALA00.0600.01845.4200.1140.1140.0000.0000.0000.000
113C114PRO00.0030.01545.5150.0100.0100.0000.0000.0000.000
114C115SER0-0.0020.00247.117-0.207-0.2070.0000.0000.0000.000
115C116VAL00.0070.00148.5900.0960.0960.0000.0000.0000.000
116C117PHE0-0.057-0.02349.533-0.182-0.1820.0000.0000.0000.000
117C118ILE00.012-0.01250.1590.0900.0900.0000.0000.0000.000
118C119PHE0-0.006-0.00148.170-0.101-0.1010.0000.0000.0000.000
119C120PRO0-0.013-0.01652.4400.0460.0460.0000.0000.0000.000
120C121PRO00.0070.01853.274-0.035-0.0350.0000.0000.0000.000
121C122SER00.0440.00153.2580.1260.1260.0000.0000.0000.000
122C123ASP-1-0.887-0.92354.7465.4865.4860.0000.0000.0000.000
123C124GLU-1-0.917-0.97153.1245.8275.8270.0000.0000.0000.000
124C125GLN00.0220.01648.217-0.002-0.0020.0000.0000.0000.000
125C126LEU00.0430.07953.0930.0030.0030.0000.0000.0000.000
126C127LYS10.8570.92656.218-5.530-5.5300.0000.0000.0000.000
127C128SER0-0.093-0.09852.2200.0180.0180.0000.0000.0000.000
128C129GLY00.0050.00853.1340.0770.0770.0000.0000.0000.000
129C130THR0-0.061-0.03149.3290.1000.1000.0000.0000.0000.000
130C131ALA00.0450.02552.215-0.058-0.0580.0000.0000.0000.000
131C132SER0-0.027-0.01648.0870.1220.1220.0000.0000.0000.000
132C133VAL0-0.0160.01450.069-0.055-0.0550.0000.0000.0000.000
133C134VAL00.0150.01345.6540.0710.0710.0000.0000.0000.000
134C135CYS0-0.031-0.00446.773-0.051-0.0510.0000.0000.0000.000
135C136LEU0-0.010-0.00644.1840.1710.1710.0000.0000.0000.000
136C137LEU00.0130.00543.430-0.174-0.1740.0000.0000.0000.000
137C138ASN00.020-0.00643.0900.1030.1030.0000.0000.0000.000
138C139ASN00.0410.00742.1020.0020.0020.0000.0000.0000.000
139C140PHE0-0.042-0.00740.290-0.145-0.1450.0000.0000.0000.000
140C141TYR00.0390.02736.6610.2170.2170.0000.0000.0000.000
141C142PRO00.003-0.02239.400-0.184-0.1840.0000.0000.0000.000
142C143ARG10.9991.00033.108-9.036-9.0360.0000.0000.0000.000
143C144GLU-1-0.926-0.96737.5618.1378.1370.0000.0000.0000.000
144C145ALA00.0360.01040.437-0.198-0.1980.0000.0000.0000.000
145C146LYS10.8800.95540.342-7.475-7.4750.0000.0000.0000.000
146C147VAL00.0360.01344.209-0.153-0.1530.0000.0000.0000.000
147C148GLN0-0.033-0.01046.2510.0320.0320.0000.0000.0000.000
148C149TRP00.0290.00246.832-0.136-0.1360.0000.0000.0000.000
149C150LYS10.9110.95651.789-5.571-5.5710.0000.0000.0000.000
150C151VAL0-0.0190.00052.754-0.086-0.0860.0000.0000.0000.000
151C152ASP-1-0.862-0.93051.6436.1776.1770.0000.0000.0000.000
152C153ASN0-0.040-0.01747.0840.1120.1120.0000.0000.0000.000
153C154ALA00.0560.01746.7660.0530.0530.0000.0000.0000.000
154C155LEU00.030-0.01040.5050.0170.0170.0000.0000.0000.000
155C156GLN0-0.0110.00743.971-0.044-0.0440.0000.0000.0000.000
156C157SER00.0220.00746.614-0.058-0.0580.0000.0000.0000.000
157C158GLY00.0280.02243.1240.0180.0180.0000.0000.0000.000
158C159ASN00.0590.02043.2890.1240.1240.0000.0000.0000.000
159C160SER0-0.059-0.03039.2450.0520.0520.0000.0000.0000.000
160C161GLN0-0.074-0.01838.9080.3940.3940.0000.0000.0000.000
161C162GLU-1-0.906-0.97137.9327.6707.6700.0000.0000.0000.000
162C163SER0-0.056-0.01236.0790.3770.3770.0000.0000.0000.000
163C164VAL0-0.027-0.03134.492-0.224-0.2240.0000.0000.0000.000
164C165THR0-0.0070.00033.9990.1790.1790.0000.0000.0000.000
165C166GLU-1-0.921-0.97329.00910.71110.7110.0000.0000.0000.000
166C167GLN0-0.012-0.01031.913-0.011-0.0110.0000.0000.0000.000
167C168ASP-1-0.788-0.87533.7898.3778.3770.0000.0000.0000.000
168C169SER0-0.066-0.04933.767-0.034-0.0340.0000.0000.0000.000
169C170LYS10.8580.92835.306-8.396-8.3960.0000.0000.0000.000
170C171ASP-1-0.782-0.84838.8457.6847.6840.0000.0000.0000.000
171C172SER0-0.063-0.03836.576-0.048-0.0480.0000.0000.0000.000
172C173THR0-0.145-0.10537.5510.0490.0490.0000.0000.0000.000
173C174TYR00.021-0.00433.8470.3160.3160.0000.0000.0000.000
174C175SER00.0360.02438.159-0.359-0.3590.0000.0000.0000.000
175C176LEU0-0.044-0.01438.5570.2340.2340.0000.0000.0000.000
176C177SER0-0.002-0.01440.144-0.168-0.1680.0000.0000.0000.000
177C178SER00.0310.04140.9820.1320.1320.0000.0000.0000.000
178C179THR0-0.026-0.02442.331-0.197-0.1970.0000.0000.0000.000
179C180LEU00.0250.03744.6080.0460.0460.0000.0000.0000.000
180C181THR0-0.018-0.02245.108-0.012-0.0120.0000.0000.0000.000
181C182LEU00.0190.01647.8510.0420.0420.0000.0000.0000.000
182C183SER0-0.010-0.01448.097-0.125-0.1250.0000.0000.0000.000
183C184LYS10.9430.95150.495-6.290-6.2900.0000.0000.0000.000
184C185ALA0-0.0120.00853.643-0.107-0.1070.0000.0000.0000.000
185C186ASP-1-0.794-0.87953.9315.7565.7560.0000.0000.0000.000
186C187TYR0-0.052-0.04954.754-0.087-0.0870.0000.0000.0000.000
187C188GLU-1-0.739-0.83956.1845.1045.1040.0000.0000.0000.000
188C189LYS10.7860.88653.124-6.035-6.0350.0000.0000.0000.000
189C190HIS00.004-0.00757.114-0.066-0.0660.0000.0000.0000.000
190C191LYS10.8440.90458.600-5.028-5.0280.0000.0000.0000.000
191C192VAL0-0.062-0.02258.999-0.024-0.0240.0000.0000.0000.000
192C193TYR00.0340.01952.9930.1070.1070.0000.0000.0000.000
193C194ALA0-0.013-0.03054.293-0.079-0.0790.0000.0000.0000.000
194C196GLU-1-0.950-0.98050.6075.8875.8870.0000.0000.0000.000
195C197VAL00.0550.03246.5610.1530.1530.0000.0000.0000.000
196C198THR0-0.013-0.00146.098-0.118-0.1180.0000.0000.0000.000
197C199HIS00.0420.00343.1320.0060.0060.0000.0000.0000.000
198C200GLN00.0210.00443.476-0.108-0.1080.0000.0000.0000.000
199C201GLY0-0.009-0.00147.390-0.073-0.0730.0000.0000.0000.000
200C202LEU0-0.058-0.03348.675-0.098-0.0980.0000.0000.0000.000
201C203SER0-0.007-0.00251.7000.0450.0450.0000.0000.0000.000
202C204SER00.0210.01254.506-0.040-0.0400.0000.0000.0000.000
203C205PRO0-0.004-0.01151.6510.0350.0350.0000.0000.0000.000
204C206VAL0-0.0090.02852.516-0.113-0.1130.0000.0000.0000.000
205C207THR00.010-0.00452.8840.0870.0870.0000.0000.0000.000
206C208LYS10.9350.98753.872-5.943-5.9430.0000.0000.0000.000
207C209SER00.005-0.02054.5350.1150.1150.0000.0000.0000.000
208C210PHE0-0.031-0.01456.304-0.073-0.0730.0000.0000.0000.000
209C211ASN00.0280.01357.9400.0480.0480.0000.0000.0000.000
210C212ARG10.9981.01460.551-5.338-5.3380.0000.0000.0000.000