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: 94QJ2

Calculation Name: 3U0T-C-Xray372

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3U0T

Chain ID: C

ChEMBL ID: CHEMBL2487

UniProt ID: P05067

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 OptAll
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2272094.634015
FMO2-HF: Nuclear repulsion 2187272.831679
FMO2-HF: Total energy -84821.802336
FMO2-MP2: Total energy -85069.518629


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.
-49.426-44.281.485-2.819-3.8140.018
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 : -0.891 / q_NPA : -0.953
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].
3C3VAL00.0070.0023.0620.4532.7100.180-1.161-1.277-0.001
4C4MET0-0.025-0.0025.435-3.068-3.0680.0000.0000.0000.000
5C5THR00.0000.0028.7750.0950.0950.0000.0000.0000.000
6C6GLN0-0.006-0.03311.8670.0060.0060.0000.0000.0000.000
7C7SER0-0.0340.00315.109-0.388-0.3880.0000.0000.0000.000
8C8PRO00.0530.02218.640-0.195-0.1950.0000.0000.0000.000
9C9LEU00.0710.03016.2420.0890.0890.0000.0000.0000.000
10C10SER0-0.037-0.01120.123-0.116-0.1160.0000.0000.0000.000
11C11LEU0-0.020-0.01323.911-0.121-0.1210.0000.0000.0000.000
12C12PRO00.0730.04526.211-0.160-0.1600.0000.0000.0000.000
13C13VAL0-0.001-0.00429.166-0.134-0.1340.0000.0000.0000.000
14C14THR0-0.0090.00531.827-0.046-0.0460.0000.0000.0000.000
15C15LEU00.0380.01335.5640.0690.0690.0000.0000.0000.000
16C16GLY00.0070.01436.094-0.217-0.2170.0000.0000.0000.000
17C17GLN0-0.057-0.02234.3830.0120.0120.0000.0000.0000.000
18C18PRO00.0190.01831.8260.1540.1540.0000.0000.0000.000
19C19ALA0-0.016-0.01327.8710.0290.0290.0000.0000.0000.000
20C20SER0-0.030-0.02424.746-0.070-0.0700.0000.0000.0000.000
21C21ILE0-0.0100.00919.233-0.009-0.0090.0000.0000.0000.000
22C22SER0-0.034-0.00418.8750.2890.2890.0000.0000.0000.000
23C23CYS0-0.041-0.02013.5420.5400.5400.0000.0000.0000.000
24C24LYS10.8130.90613.575-16.239-16.2390.0000.0000.0000.000
25C25SER00.024-0.0179.1180.3710.3710.0000.0000.0000.000
26C26SER0-0.0160.0065.014-1.635-1.6350.0000.0000.0000.000
27C27GLN00.0460.0254.823-3.546-3.5460.0000.0000.0000.000
28C27SER00.0030.0029.122-0.578-0.5780.0000.0000.0000.000
29C27LEU00.0120.0139.4971.3481.3480.0000.0000.0000.000
30C27LEU0-0.0350.00812.521-0.771-0.7710.0000.0000.0000.000
31C27TYR00.0260.01713.1661.5481.5480.0000.0000.0000.000
32C27SER00.0140.00815.552-0.415-0.4150.0000.0000.0000.000
33C28ASP-1-0.801-0.88917.90414.23414.2340.0000.0000.0000.000
34C29ALA00.0080.01519.5840.4660.4660.0000.0000.0000.000
35C30LYS10.8090.90019.655-14.111-14.1110.0000.0000.0000.000
36C31THR00.0430.01215.6850.6920.6920.0000.0000.0000.000
37C32TYR0-0.046-0.03714.440-1.095-1.0950.0000.0000.0000.000
38C33LEU0-0.0010.00813.5351.0331.0330.0000.0000.0000.000
39C34ASN0-0.070-0.04215.172-2.180-2.1800.0000.0000.0000.000
40C35TRP00.0340.01216.2960.9100.9100.0000.0000.0000.000
41C36PHE00.0450.00716.603-0.526-0.5260.0000.0000.0000.000
42C37GLN00.0430.01720.067-0.054-0.0540.0000.0000.0000.000
43C38GLN0-0.004-0.01022.0580.5660.5660.0000.0000.0000.000
44C39ARG10.8330.90624.042-9.833-9.8330.0000.0000.0000.000
45C40PRO00.0530.00927.4860.1610.1610.0000.0000.0000.000
46C41GLY00.0130.01329.063-0.271-0.2710.0000.0000.0000.000
47C42GLN0-0.0030.01828.245-0.240-0.2400.0000.0000.0000.000
48C43SER00.0440.01325.2700.3190.3190.0000.0000.0000.000
49C44PRO0-0.032-0.01220.695-0.251-0.2510.0000.0000.0000.000
50C45ARG10.8700.94322.911-11.149-11.1490.0000.0000.0000.000
51C46ARG10.7690.86019.794-13.715-13.7150.0000.0000.0000.000
52C47LEU0-0.045-0.01522.065-0.593-0.5930.0000.0000.0000.000
53C48ILE00.0260.01421.140-0.449-0.4490.0000.0000.0000.000
54C49TYR00.0230.01419.7910.8380.8380.0000.0000.0000.000
55C50GLN0-0.012-0.01819.312-0.698-0.6980.0000.0000.0000.000
56C51ILE0-0.0080.01518.436-0.554-0.5540.0000.0000.0000.000
57C52SER0-0.033-0.02720.167-0.130-0.1300.0000.0000.0000.000
58C53ARG10.9020.97123.633-12.058-12.0580.0000.0000.0000.000
59C54LEU00.0500.02124.5380.4750.4750.0000.0000.0000.000
60C55ASP-1-0.777-0.85723.66312.78512.7850.0000.0000.0000.000
61C56PRO0-0.013-0.01526.936-0.369-0.3690.0000.0000.0000.000
62C57GLY00.0280.00929.7900.1400.1400.0000.0000.0000.000
63C58VAL0-0.069-0.01126.9220.0630.0630.0000.0000.0000.000
64C59PRO00.0160.01630.220-0.143-0.1430.0000.0000.0000.000
65C60ASP-1-0.802-0.91931.2638.9198.9190.0000.0000.0000.000
66C61ARG10.6910.82931.698-9.035-9.0350.0000.0000.0000.000
67C62PHE0-0.0030.00725.9110.2280.2280.0000.0000.0000.000
68C63SER00.0190.00726.964-0.163-0.1630.0000.0000.0000.000
69C64GLY00.0380.01823.0790.3060.3060.0000.0000.0000.000
70C65SER0-0.054-0.02322.217-0.591-0.5910.0000.0000.0000.000
71C66GLY00.0750.02220.0070.4620.4620.0000.0000.0000.000
72C67SER0-0.028-0.01519.293-0.474-0.4740.0000.0000.0000.000
73C68GLY00.0660.03415.8560.1150.1150.0000.0000.0000.000
74C69THR00.0530.03312.0871.0301.0300.0000.0000.0000.000
75C70ASP-1-0.839-0.89314.17216.09016.0900.0000.0000.0000.000
76C71PHE00.0630.02613.804-0.910-0.9100.0000.0000.0000.000
77C72THR0-0.080-0.05018.409-0.202-0.2020.0000.0000.0000.000
78C73LEU00.0070.03520.848-0.361-0.3610.0000.0000.0000.000
79C74LYS10.9100.92822.395-11.526-11.5260.0000.0000.0000.000
80C75ILE00.0300.01526.1450.0240.0240.0000.0000.0000.000
81C76SER0-0.013-0.01328.998-0.254-0.2540.0000.0000.0000.000
82C77ARG10.8640.91332.385-8.748-8.7480.0000.0000.0000.000
83C78VAL0-0.0050.01630.1900.1540.1540.0000.0000.0000.000
84C79GLU-1-0.823-0.91532.8198.0608.0600.0000.0000.0000.000
85C80ALA00.016-0.01133.3780.2520.2520.0000.0000.0000.000
86C81GLU-1-0.823-0.87933.5309.2969.2960.0000.0000.0000.000
87C82ASP-1-0.777-0.86529.34110.08210.0820.0000.0000.0000.000
88C83VAL00.0000.02428.4140.4430.4430.0000.0000.0000.000
89C84GLY0-0.003-0.01226.439-0.055-0.0550.0000.0000.0000.000
90C85VAL0-0.056-0.01320.0410.0190.0190.0000.0000.0000.000
91C86TYR0-0.014-0.01720.704-0.003-0.0030.0000.0000.0000.000
92C87TYR00.0260.01715.4520.4260.4260.0000.0000.0000.000
93C89LEU0-0.016-0.01411.9980.6380.6380.0000.0000.0000.000
94C90GLN00.0270.0017.082-4.050-4.0500.0000.0000.0000.000
95C91GLY00.0330.00010.4011.1161.1160.0000.0000.0000.000
96C92THR0-0.081-0.05411.124-1.403-1.4030.0000.0000.0000.000
97C93HIS0-0.036-0.0216.4581.1211.1210.0000.0000.0000.000
98C94TYR00.0150.0314.042-6.560-6.2680.000-0.069-0.2240.000
99C95PRO00.0240.0152.567-0.3822.1811.307-1.586-2.2840.019
100C96VAL00.011-0.0135.582-2.125-2.136-0.0010.0000.0120.000
101C97LEU0-0.021-0.0014.6400.3090.354-0.001-0.003-0.0410.000
102C98PHE00.0240.0028.241-1.907-1.9070.0000.0000.0000.000
103C99GLY00.0060.0019.9381.7471.7470.0000.0000.0000.000
104C100GLN0-0.005-0.03510.323-1.537-1.5370.0000.0000.0000.000
105C101GLY00.0170.02513.737-0.639-0.6390.0000.0000.0000.000
106C102THR0-0.052-0.04517.0410.1570.1570.0000.0000.0000.000
107C103ARG10.7790.85720.396-11.167-11.1670.0000.0000.0000.000
108C104LEU0-0.031-0.01723.633-0.083-0.0830.0000.0000.0000.000
109C105GLU-1-0.747-0.83626.5769.8289.8280.0000.0000.0000.000
110C106ILE00.016-0.00430.1440.0030.0030.0000.0000.0000.000
111C107LYS10.8800.93532.051-9.331-9.3310.0000.0000.0000.000
112C108ARG10.8520.91134.724-7.758-7.7580.0000.0000.0000.000
113C109THR00.0150.00138.2850.1220.1220.0000.0000.0000.000
114C110VAL0-0.0020.01338.7970.0520.0520.0000.0000.0000.000
115C111ALA0-0.013-0.00740.716-0.209-0.2090.0000.0000.0000.000
116C112ALA00.0490.02241.4400.1840.1840.0000.0000.0000.000
117C113PRO0-0.0300.00541.375-0.060-0.0600.0000.0000.0000.000
118C114SER00.0070.00043.342-0.204-0.2040.0000.0000.0000.000
119C115VAL0-0.010-0.00144.2330.0840.0840.0000.0000.0000.000
120C116PHE0-0.022-0.00546.111-0.229-0.2290.0000.0000.0000.000
121C117ILE00.002-0.00346.4250.1680.1680.0000.0000.0000.000
122C118PHE00.000-0.00246.445-0.145-0.1450.0000.0000.0000.000
123C119PRO00.0140.01648.7170.1350.1350.0000.0000.0000.000
124C120PRO0-0.0070.00849.2040.0540.0540.0000.0000.0000.000
125C121SER0-0.020-0.03550.403-0.097-0.0970.0000.0000.0000.000
126C122ASP-1-0.772-0.89552.7945.5695.5690.0000.0000.0000.000
127C123GLU-1-0.813-0.90053.5645.9355.9350.0000.0000.0000.000
128C124GLN00.0420.03546.077-0.036-0.0360.0000.0000.0000.000
129C125LEU00.0100.02251.4980.0410.0410.0000.0000.0000.000
130C126LYS10.7440.85353.620-5.638-5.6380.0000.0000.0000.000
131C127SER0-0.069-0.04650.3030.0220.0220.0000.0000.0000.000
132C128GLY00.0040.00250.3850.1030.1030.0000.0000.0000.000
133C129THR0-0.037-0.01445.1470.1050.1050.0000.0000.0000.000
134C130ALA0-0.002-0.00347.555-0.130-0.1300.0000.0000.0000.000
135C131SER0-0.028-0.01743.7030.1030.1030.0000.0000.0000.000
136C132VAL0-0.0200.00245.393-0.121-0.1210.0000.0000.0000.000
137C133VAL00.0160.00542.9430.1830.1830.0000.0000.0000.000
138C134CYS0-0.072-0.02342.795-0.071-0.0710.0000.0000.0000.000
139C135LEU0-0.0190.00641.7960.2040.2040.0000.0000.0000.000
140C136LEU00.0150.00538.946-0.201-0.2010.0000.0000.0000.000
141C137ASN00.019-0.01140.7790.3260.3260.0000.0000.0000.000
142C138ASN0-0.008-0.01841.207-0.233-0.2330.0000.0000.0000.000
143C139PHE0-0.0070.01535.953-0.145-0.1450.0000.0000.0000.000
144C140TYR0-0.001-0.02432.7000.1460.1460.0000.0000.0000.000
145C141PRO00.0060.00033.482-0.252-0.2520.0000.0000.0000.000
146C142ARG10.8810.91827.922-10.593-10.5930.0000.0000.0000.000
147C143GLU-1-0.868-0.92029.73810.02510.0250.0000.0000.0000.000
148C144ALA0-0.014-0.01132.999-0.292-0.2920.0000.0000.0000.000
149C145LYS10.8670.94834.554-7.554-7.5540.0000.0000.0000.000
150C146VAL00.0450.01936.760-0.301-0.3010.0000.0000.0000.000
151C147GLN0-0.057-0.04138.5140.2550.2550.0000.0000.0000.000
152C148TRP00.0270.01040.162-0.311-0.3110.0000.0000.0000.000
153C149LYS10.8230.90343.228-6.704-6.7040.0000.0000.0000.000
154C150VAL00.0390.01646.458-0.049-0.0490.0000.0000.0000.000
155C151ASP-1-0.779-0.88249.2005.8915.8910.0000.0000.0000.000
156C152ASN0-0.059-0.03849.8040.0410.0410.0000.0000.0000.000
157C153ALA00.0490.04447.4570.0780.0780.0000.0000.0000.000
158C154LEU0-0.013-0.01342.2450.0360.0360.0000.0000.0000.000
159C155GLN0-0.0260.00342.2340.0970.0970.0000.0000.0000.000
160C156SER00.015-0.01637.0090.2010.2010.0000.0000.0000.000
161C157GLY0-0.0250.00735.346-0.078-0.0780.0000.0000.0000.000
162C158ASN00.016-0.00336.3990.2210.2210.0000.0000.0000.000
163C159SER00.0160.00337.406-0.232-0.2320.0000.0000.0000.000
164C160GLN0-0.043-0.01133.6360.1720.1720.0000.0000.0000.000
165C161GLU-1-0.854-0.90934.0968.3518.3510.0000.0000.0000.000
166C162SER0-0.021-0.00232.9870.4040.4040.0000.0000.0000.000
167C163VAL00.007-0.00632.030-0.309-0.3090.0000.0000.0000.000
168C164THR0-0.020-0.00633.0160.1210.1210.0000.0000.0000.000
169C165GLU-1-0.741-0.85428.53910.75810.7580.0000.0000.0000.000
170C166GLN0-0.056-0.02032.352-0.071-0.0710.0000.0000.0000.000
171C167ASP-1-0.760-0.86534.2117.5987.5980.0000.0000.0000.000
172C168SER0-0.016-0.02336.463-0.053-0.0530.0000.0000.0000.000
173C169LYS10.8040.89937.789-7.338-7.3380.0000.0000.0000.000
174C170ASP-1-0.812-0.87540.8317.3387.3380.0000.0000.0000.000
175C171SER0-0.029-0.01236.6170.0280.0280.0000.0000.0000.000
176C172THR0-0.100-0.05436.8250.1750.1750.0000.0000.0000.000
177C173TYR0-0.030-0.03330.8400.2670.2670.0000.0000.0000.000
178C174SER00.0330.01536.936-0.238-0.2380.0000.0000.0000.000
179C175LEU0-0.0290.00734.9980.2250.2250.0000.0000.0000.000
180C176SER0-0.014-0.00337.490-0.321-0.3210.0000.0000.0000.000
181C177SER00.047-0.01637.6520.2060.2060.0000.0000.0000.000
182C178THR0-0.026-0.02839.167-0.264-0.2640.0000.0000.0000.000
183C179LEU00.0010.03039.9500.2070.2070.0000.0000.0000.000
184C180THR0-0.001-0.00541.584-0.165-0.1650.0000.0000.0000.000
185C181LEU0-0.027-0.00643.2360.0770.0770.0000.0000.0000.000
186C182SER00.036-0.00945.948-0.064-0.0640.0000.0000.0000.000
187C183LYS10.8300.89048.414-5.767-5.7670.0000.0000.0000.000
188C184ALA00.0540.02151.857-0.087-0.0870.0000.0000.0000.000
189C185ASP-1-0.836-0.88448.8716.4546.4540.0000.0000.0000.000
190C186TYR00.0330.00950.426-0.056-0.0560.0000.0000.0000.000
191C187GLU-1-0.829-0.91551.7475.5945.5940.0000.0000.0000.000
192C188LYS10.8120.90850.870-6.357-6.3570.0000.0000.0000.000
193C189HIS0-0.043-0.00251.2050.0220.0220.0000.0000.0000.000
194C190LYS10.8080.89454.500-5.439-5.4390.0000.0000.0000.000
195C191VAL0-0.0100.00152.9730.0020.0020.0000.0000.0000.000
196C192TYR00.003-0.00248.8600.1820.1820.0000.0000.0000.000
197C193ALA00.017-0.00848.566-0.097-0.0970.0000.0000.0000.000
198C195GLU-1-0.840-0.92143.9816.7126.7120.0000.0000.0000.000
199C196VAL00.0280.00940.8100.2060.2060.0000.0000.0000.000
200C197THR0-0.025-0.02139.337-0.148-0.1480.0000.0000.0000.000
201C198HIS00.0320.00537.4160.0100.0100.0000.0000.0000.000
202C199GLN00.0470.01633.843-0.250-0.2500.0000.0000.0000.000
203C200GLY0-0.0020.00239.287-0.102-0.1020.0000.0000.0000.000
204C201LEU0-0.067-0.03042.506-0.190-0.1900.0000.0000.0000.000
205C202SER00.0180.00843.9330.0600.0600.0000.0000.0000.000
206C203SER0-0.024-0.01946.073-0.095-0.0950.0000.0000.0000.000
207C204PRO0-0.013-0.00743.8100.0290.0290.0000.0000.0000.000
208C205VAL00.0080.02345.135-0.175-0.1750.0000.0000.0000.000
209C206THR0-0.004-0.00246.0550.1440.1440.0000.0000.0000.000
210C207LYS10.8630.92448.115-6.439-6.4390.0000.0000.0000.000
211C208SER00.023-0.00549.0910.1000.1000.0000.0000.0000.000
212C209PHE00.0120.01149.977-0.072-0.0720.0000.0000.0000.000
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