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: LZR89

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2267237.103504
FMO2-HF: Nuclear repulsion 2182415.720493
FMO2-HF: Total energy -84821.383011
FMO2-MP2: Total energy -85068.842434


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.
-41.355-37.170.17-1.818-2.5360.011
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 : -0.922 / q_NPA : -0.959
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].
3C3VAL00.0160.0013.315-0.6821.4900.058-1.052-1.1780.005
4C4MET0-0.053-0.0245.716-3.296-3.2960.0000.0000.0000.000
5C5THR00.0020.0018.896-0.183-0.1830.0000.0000.0000.000
6C6GLN0-0.018-0.04712.056-0.132-0.1320.0000.0000.0000.000
7C7SER0-0.0170.01115.076-0.259-0.2590.0000.0000.0000.000
8C8PRO00.0200.00718.527-0.263-0.2630.0000.0000.0000.000
9C9LEU00.0990.03916.3450.0680.0680.0000.0000.0000.000
10C10SER0-0.023-0.00420.242-0.048-0.0480.0000.0000.0000.000
11C11LEU0-0.012-0.01123.930-0.169-0.1690.0000.0000.0000.000
12C12PRO00.0480.03526.187-0.151-0.1510.0000.0000.0000.000
13C13VAL0-0.004-0.01129.126-0.133-0.1330.0000.0000.0000.000
14C14THR0-0.0050.00131.863-0.054-0.0540.0000.0000.0000.000
15C15LEU00.0610.02735.1810.1130.1130.0000.0000.0000.000
16C16GLY0-0.0020.00836.050-0.208-0.2080.0000.0000.0000.000
17C17GLN0-0.075-0.03334.1160.0040.0040.0000.0000.0000.000
18C18PRO00.0210.02631.4900.1220.1220.0000.0000.0000.000
19C19ALA00.003-0.00727.6020.0120.0120.0000.0000.0000.000
20C20SER0-0.034-0.02524.594-0.070-0.0700.0000.0000.0000.000
21C21ILE0-0.0120.01119.1400.0540.0540.0000.0000.0000.000
22C22SER0-0.033-0.00318.7120.1660.1660.0000.0000.0000.000
23C23CYS0-0.0140.00213.4790.5890.5890.0000.0000.0000.000
24C24LYS10.8310.91613.654-16.422-16.4220.0000.0000.0000.000
25C25SER00.021-0.0109.2070.4120.4120.0000.0000.0000.000
26C26SER00.0080.0175.241-1.492-1.4920.0000.0000.0000.000
27C27GLN00.0380.0174.746-4.095-3.989-0.001-0.003-0.1020.000
28C27SER00.0090.0059.296-0.602-0.6020.0000.0000.0000.000
29C27LEU00.0010.0109.6021.7311.7310.0000.0000.0000.000
30C27LEU0-0.049-0.00612.354-0.779-0.7790.0000.0000.0000.000
31C27TYR00.0230.00613.1361.3731.3730.0000.0000.0000.000
32C27SER00.0210.00415.330-0.488-0.4880.0000.0000.0000.000
33C28ASP-1-0.840-0.90517.93214.40514.4050.0000.0000.0000.000
34C29ALA00.0260.00419.5480.3400.3400.0000.0000.0000.000
35C30LYS10.8320.92219.545-13.870-13.8700.0000.0000.0000.000
36C31THR00.0240.00515.5210.8630.8630.0000.0000.0000.000
37C32TYR0-0.020-0.00914.295-1.247-1.2470.0000.0000.0000.000
38C33LEU00.0160.01613.2131.3901.3900.0000.0000.0000.000
39C34ASN0-0.083-0.04314.865-2.187-2.1870.0000.0000.0000.000
40C35TRP00.0340.00816.2540.9460.9460.0000.0000.0000.000
41C36PHE00.0410.00316.533-0.540-0.5400.0000.0000.0000.000
42C37GLN00.0490.02719.7090.0310.0310.0000.0000.0000.000
43C38GLN0-0.025-0.02821.7940.5320.5320.0000.0000.0000.000
44C39ARG10.8510.94023.573-9.842-9.8420.0000.0000.0000.000
45C40PRO00.0660.01427.0700.1630.1630.0000.0000.0000.000
46C41GLY0-0.0060.00428.284-0.328-0.3280.0000.0000.0000.000
47C42GLN00.0060.02728.023-0.282-0.2820.0000.0000.0000.000
48C43SER00.0260.00525.1640.3470.3470.0000.0000.0000.000
49C44PRO0-0.009-0.00320.601-0.265-0.2650.0000.0000.0000.000
50C45ARG10.8900.96022.890-11.059-11.0590.0000.0000.0000.000
51C46ARG10.7550.84919.657-13.646-13.6460.0000.0000.0000.000
52C47LEU0-0.0290.00221.952-0.520-0.5200.0000.0000.0000.000
53C48ILE00.0420.00720.814-0.444-0.4440.0000.0000.0000.000
54C49TYR00.0270.00819.8730.8080.8080.0000.0000.0000.000
55C50GLN0-0.033-0.03219.259-0.631-0.6310.0000.0000.0000.000
56C51ILE0-0.0280.00918.567-0.549-0.5490.0000.0000.0000.000
57C52SER0-0.007-0.02220.387-0.133-0.1330.0000.0000.0000.000
58C53ARG10.8960.96823.583-12.009-12.0090.0000.0000.0000.000
59C54LEU00.0400.03324.4800.4780.4780.0000.0000.0000.000
60C55ASP-1-0.774-0.85423.51812.71512.7150.0000.0000.0000.000
61C56PRO0-0.003-0.00626.823-0.337-0.3370.0000.0000.0000.000
62C57GLY00.014-0.00429.7400.1410.1410.0000.0000.0000.000
63C58VAL0-0.108-0.04026.637-0.082-0.0820.0000.0000.0000.000
64C59PRO00.0190.02129.925-0.123-0.1230.0000.0000.0000.000
65C60ASP-1-0.854-0.95730.8409.0229.0220.0000.0000.0000.000
66C61ARG10.6860.82631.566-9.030-9.0300.0000.0000.0000.000
67C62PHE0-0.0120.01125.8030.2520.2520.0000.0000.0000.000
68C63SER00.0240.00726.921-0.115-0.1150.0000.0000.0000.000
69C64GLY00.0200.01723.1850.2700.2700.0000.0000.0000.000
70C65SER0-0.028-0.02222.411-0.606-0.6060.0000.0000.0000.000
71C66GLY00.0530.02320.3260.4590.4590.0000.0000.0000.000
72C67SER0-0.016-0.01518.974-0.344-0.3440.0000.0000.0000.000
73C68GLY00.0640.03015.7530.0820.0820.0000.0000.0000.000
74C69THR00.0580.03211.9341.0221.0220.0000.0000.0000.000
75C70ASP-1-0.854-0.90214.10216.30316.3030.0000.0000.0000.000
76C71PHE00.0320.01214.018-0.880-0.8800.0000.0000.0000.000
77C72THR0-0.054-0.03418.306-0.161-0.1610.0000.0000.0000.000
78C73LEU0-0.0110.01120.963-0.199-0.1990.0000.0000.0000.000
79C74LYS10.9260.94422.576-11.431-11.4310.0000.0000.0000.000
80C75ILE00.0420.02526.0780.0180.0180.0000.0000.0000.000
81C76SER0-0.034-0.02928.931-0.178-0.1780.0000.0000.0000.000
82C77ARG10.9680.96432.314-8.498-8.4980.0000.0000.0000.000
83C78VAL0-0.0070.01930.3480.0490.0490.0000.0000.0000.000
84C79GLU-1-0.841-0.92533.0218.1188.1180.0000.0000.0000.000
85C80ALA00.0440.00333.1400.2560.2560.0000.0000.0000.000
86C81GLU-1-0.890-0.93033.0559.2399.2390.0000.0000.0000.000
87C82ASP-1-0.756-0.86529.12410.10610.1060.0000.0000.0000.000
88C83VAL0-0.0110.02428.0730.4540.4540.0000.0000.0000.000
89C84GLY00.0310.00726.063-0.053-0.0530.0000.0000.0000.000
90C85VAL0-0.051-0.00419.5900.0250.0250.0000.0000.0000.000
91C86TYR0-0.017-0.02320.369-0.001-0.0010.0000.0000.0000.000
92C87TYR00.0400.03315.2180.3730.3730.0000.0000.0000.000
93C89LEU00.0050.00511.8600.8110.8110.0000.0000.0000.000
94C90GLN00.0370.0306.992-3.692-3.6920.0000.0000.0000.000
95C91GLY00.012-0.02010.1861.3811.3810.0000.0000.0000.000
96C92THR0-0.065-0.04110.728-1.277-1.2770.0000.0000.0000.000
97C93HIS0-0.040-0.0266.1760.6310.6310.0000.0000.0000.000
98C94TYR00.0100.0294.719-3.668-3.556-0.001-0.009-0.1010.000
99C95PRO00.0000.0063.1922.9844.7290.115-0.749-1.1110.006
100C96VAL00.037-0.0075.920-0.707-0.7070.0000.0000.0000.000
101C97LEU0-0.020-0.0054.4530.7700.820-0.001-0.005-0.0440.000
102C98PHE0-0.001-0.0128.001-1.963-1.9630.0000.0000.0000.000
103C99GLY0-0.0100.0019.9571.5341.5340.0000.0000.0000.000
104C100GLN00.016-0.02310.804-1.401-1.4010.0000.0000.0000.000
105C101GLY00.0000.01313.696-0.767-0.7670.0000.0000.0000.000
106C102THR0-0.056-0.04016.9660.1430.1430.0000.0000.0000.000
107C103ARG10.8380.90420.143-11.284-11.2840.0000.0000.0000.000
108C104LEU0-0.049-0.02123.329-0.151-0.1510.0000.0000.0000.000
109C105GLU-1-0.777-0.85126.3129.8169.8160.0000.0000.0000.000
110C106ILE00.0320.01229.7720.0100.0100.0000.0000.0000.000
111C107LYS10.8630.94032.348-9.228-9.2280.0000.0000.0000.000
112C108ARG10.8640.93134.850-7.755-7.7550.0000.0000.0000.000
113C109THR00.008-0.00838.1570.1310.1310.0000.0000.0000.000
114C110VAL0-0.0090.00038.3170.0250.0250.0000.0000.0000.000
115C111ALA0-0.0160.00040.358-0.210-0.2100.0000.0000.0000.000
116C112ALA00.0170.01041.1740.1830.1830.0000.0000.0000.000
117C113PRO0-0.0010.00840.926-0.085-0.0850.0000.0000.0000.000
118C114SER0-0.038-0.01043.109-0.208-0.2080.0000.0000.0000.000
119C115VAL0-0.005-0.01044.2490.1000.1000.0000.0000.0000.000
120C116PHE0-0.015-0.01446.015-0.204-0.2040.0000.0000.0000.000
121C117ILE00.0020.01046.4060.1630.1630.0000.0000.0000.000
122C118PHE0-0.017-0.00546.349-0.149-0.1490.0000.0000.0000.000
123C119PRO00.0270.01048.6440.1240.1240.0000.0000.0000.000
124C120PRO0-0.0160.00249.3200.0470.0470.0000.0000.0000.000
125C121SER00.002-0.00950.538-0.098-0.0980.0000.0000.0000.000
126C122ASP-1-0.783-0.90452.7495.5935.5930.0000.0000.0000.000
127C123GLU-1-0.843-0.93153.1815.9295.9290.0000.0000.0000.000
128C124GLN00.0180.01645.712-0.029-0.0290.0000.0000.0000.000
129C125LEU00.0230.02551.1460.0350.0350.0000.0000.0000.000
130C126LYS10.7280.85653.149-5.620-5.6200.0000.0000.0000.000
131C127SER0-0.050-0.03550.2740.0140.0140.0000.0000.0000.000
132C128GLY00.0170.01650.1370.0860.0860.0000.0000.0000.000
133C129THR0-0.053-0.02544.6980.1010.1010.0000.0000.0000.000
134C130ALA00.0090.00647.491-0.136-0.1360.0000.0000.0000.000
135C131SER0-0.0170.00343.5500.1320.1320.0000.0000.0000.000
136C132VAL0-0.029-0.00845.070-0.143-0.1430.0000.0000.0000.000
137C133VAL00.0180.01642.4370.1880.1880.0000.0000.0000.000
138C134CYS0-0.078-0.02442.298-0.087-0.0870.0000.0000.0000.000
139C135LEU0-0.020-0.00541.9200.1840.1840.0000.0000.0000.000
140C136LEU0-0.008-0.01338.888-0.181-0.1810.0000.0000.0000.000
141C137ASN00.024-0.00940.7560.3140.3140.0000.0000.0000.000
142C138ASN00.001-0.01141.021-0.131-0.1310.0000.0000.0000.000
143C139PHE0-0.0100.01535.802-0.145-0.1450.0000.0000.0000.000
144C140TYR0-0.016-0.02832.5120.1490.1490.0000.0000.0000.000
145C141PRO00.014-0.00333.147-0.262-0.2620.0000.0000.0000.000
146C142ARG10.9150.93127.581-10.630-10.6300.0000.0000.0000.000
147C143GLU-1-0.881-0.92229.6659.9929.9920.0000.0000.0000.000
148C144ALA00.001-0.00732.881-0.305-0.3050.0000.0000.0000.000
149C145LYS10.9560.98834.739-7.795-7.7950.0000.0000.0000.000
150C146VAL00.0380.01736.797-0.278-0.2780.0000.0000.0000.000
151C147GLN0-0.047-0.02238.5260.2620.2620.0000.0000.0000.000
152C148TRP00.0350.01940.053-0.317-0.3170.0000.0000.0000.000
153C149LYS10.8180.90843.194-6.752-6.7520.0000.0000.0000.000
154C150VAL00.0450.02346.393-0.057-0.0570.0000.0000.0000.000
155C151ASP-1-0.780-0.88248.9885.8815.8810.0000.0000.0000.000
156C152ASN0-0.052-0.03849.5840.0680.0680.0000.0000.0000.000
157C153ALA00.0480.04847.1500.0570.0570.0000.0000.0000.000
158C154LEU0-0.025-0.02741.8770.0360.0360.0000.0000.0000.000
159C155GLN0-0.044-0.01742.0450.1070.1070.0000.0000.0000.000
160C156SER0-0.014-0.02936.7730.1860.1860.0000.0000.0000.000
161C157GLY00.0180.01535.272-0.066-0.0660.0000.0000.0000.000
162C158ASN00.0010.00336.3450.1760.1760.0000.0000.0000.000
163C159SER00.0160.00837.000-0.205-0.2050.0000.0000.0000.000
164C160GLN0-0.030-0.01233.0000.1250.1250.0000.0000.0000.000
165C161GLU-1-0.881-0.93633.4158.5158.5150.0000.0000.0000.000
166C162SER0-0.033-0.00732.8420.3800.3800.0000.0000.0000.000
167C163VAL0-0.003-0.01431.798-0.284-0.2840.0000.0000.0000.000
168C164THR0-0.0070.00732.5370.1570.1570.0000.0000.0000.000
169C165GLU-1-0.793-0.89728.38710.88310.8830.0000.0000.0000.000
170C166GLN0-0.073-0.03332.192-0.053-0.0530.0000.0000.0000.000
171C167ASP-1-0.776-0.87334.1067.6867.6860.0000.0000.0000.000
172C168SER0-0.029-0.02136.686-0.029-0.0290.0000.0000.0000.000
173C169LYS10.8180.89337.729-7.275-7.2750.0000.0000.0000.000
174C170ASP-1-0.810-0.87740.9907.4277.4270.0000.0000.0000.000
175C171SER00.002-0.00236.5130.0440.0440.0000.0000.0000.000
176C172THR0-0.109-0.06936.9000.1410.1410.0000.0000.0000.000
177C173TYR0-0.018-0.03030.6860.2690.2690.0000.0000.0000.000
178C174SER00.0450.02136.710-0.227-0.2270.0000.0000.0000.000
179C175LEU0-0.037-0.00834.7640.2310.2310.0000.0000.0000.000
180C176SER00.0000.00937.292-0.316-0.3160.0000.0000.0000.000
181C177SER00.034-0.00337.3860.2120.2120.0000.0000.0000.000
182C178THR00.002-0.00638.759-0.307-0.3070.0000.0000.0000.000
183C179LEU0-0.023-0.00139.6370.1930.1930.0000.0000.0000.000
184C180THR00.010-0.00440.765-0.179-0.1790.0000.0000.0000.000
185C181LEU0-0.016-0.00242.8980.0500.0500.0000.0000.0000.000
186C182SER00.0410.00045.734-0.071-0.0710.0000.0000.0000.000
187C183LYS10.8570.89547.870-5.815-5.8150.0000.0000.0000.000
188C184ALA00.0270.01651.384-0.100-0.1000.0000.0000.0000.000
189C185ASP-1-0.825-0.89148.5696.4466.4460.0000.0000.0000.000
190C186TYR00.0070.00050.060-0.078-0.0780.0000.0000.0000.000
191C187GLU-1-0.809-0.91151.4125.6295.6290.0000.0000.0000.000
192C188LYS10.8210.92451.066-6.329-6.3290.0000.0000.0000.000
193C189HIS0-0.056-0.01651.2160.0160.0160.0000.0000.0000.000
194C190LYS10.8360.91854.397-5.409-5.4090.0000.0000.0000.000
195C191VAL0-0.027-0.01952.8950.0250.0250.0000.0000.0000.000
196C192TYR0-0.008-0.00648.4300.1800.1800.0000.0000.0000.000
197C193ALA00.013-0.01548.572-0.084-0.0840.0000.0000.0000.000
198C195GLU-1-0.861-0.93444.0856.7826.7820.0000.0000.0000.000
199C196VAL00.0360.00740.8100.2100.2100.0000.0000.0000.000
200C197THR0-0.044-0.03339.013-0.129-0.1290.0000.0000.0000.000
201C198HIS00.024-0.00137.1800.0070.0070.0000.0000.0000.000
202C199GLN00.0370.01033.976-0.267-0.2670.0000.0000.0000.000
203C200GLY00.0010.00139.190-0.104-0.1040.0000.0000.0000.000
204C201LEU0-0.062-0.01942.333-0.192-0.1920.0000.0000.0000.000
205C202SER00.0130.00543.8530.0570.0570.0000.0000.0000.000
206C203SER0-0.042-0.02946.008-0.033-0.0330.0000.0000.0000.000
207C204PRO00.0090.00643.7310.0150.0150.0000.0000.0000.000
208C205VAL00.0220.03345.321-0.183-0.1830.0000.0000.0000.000
209C206THR0-0.011-0.01046.1100.1580.1580.0000.0000.0000.000
210C207LYS10.8900.96648.187-6.368-6.3680.0000.0000.0000.000
211C208SER00.032-0.00649.3120.0840.0840.0000.0000.0000.000
212C209PHE00.0200.02049.815-0.074-0.0740.0000.0000.0000.000
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