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: 39GYL

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2265167.626854
FMO2-HF: Nuclear repulsion 2180347.70709
FMO2-HF: Total energy -84819.919764
FMO2-MP2: Total energy -85067.351531


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.
-36.219-32.9250.097-1.435-1.9580.007
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 : -0.921 / q_NPA : -0.954
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].
3C3VAL00.016-0.0073.287-0.5841.6480.065-1.129-1.1690.005
4C4MET0-0.055-0.0335.686-3.228-3.2280.0000.0000.0000.000
5C5THR0-0.010-0.0088.868-0.228-0.2280.0000.0000.0000.000
6C6GLN0-0.060-0.05712.028-0.086-0.0860.0000.0000.0000.000
7C7SER0-0.0240.00115.048-0.258-0.2580.0000.0000.0000.000
8C8PRO00.0260.01318.499-0.239-0.2390.0000.0000.0000.000
9C9LEU00.0890.02916.3580.0680.0680.0000.0000.0000.000
10C10SER0-0.047-0.02520.217-0.125-0.1250.0000.0000.0000.000
11C11LEU0-0.0050.00023.905-0.146-0.1460.0000.0000.0000.000
12C12PRO00.0370.02026.161-0.136-0.1360.0000.0000.0000.000
13C13VAL0-0.032-0.01829.185-0.125-0.1250.0000.0000.0000.000
14C14THR0-0.019-0.01031.837-0.058-0.0580.0000.0000.0000.000
15C15LEU00.0480.02235.1550.1140.1140.0000.0000.0000.000
16C16GLY0-0.0030.00436.035-0.209-0.2090.0000.0000.0000.000
17C17GLN0-0.067-0.03133.9840.0350.0350.0000.0000.0000.000
18C18PRO00.0110.02231.4990.1290.1290.0000.0000.0000.000
19C19ALA00.013-0.00527.5540.0150.0150.0000.0000.0000.000
20C20SER0-0.057-0.03724.5830.0890.0890.0000.0000.0000.000
21C21ILE00.0110.02619.1080.0640.0640.0000.0000.0000.000
22C22SER00.0160.01317.7490.0200.0200.0000.0000.0000.000
23C23CYS0-0.056-0.01213.4060.6110.6110.0000.0000.0000.000
24C24LYS10.8770.95113.621-16.732-16.7320.0000.0000.0000.000
25C25SER00.0270.0039.2760.3870.3870.0000.0000.0000.000
26C26SER00.0160.0255.243-1.841-1.798-0.001-0.006-0.0360.000
27C27GLN00.0360.0144.939-3.614-3.6140.0000.0000.0000.000
28C27SER00.009-0.0029.297-0.622-0.6220.0000.0000.0000.000
29C27LEU00.0040.0189.6811.6521.6520.0000.0000.0000.000
30C27LEU0-0.050-0.01512.339-0.788-0.7880.0000.0000.0000.000
31C27TYR00.0310.00413.2281.3411.3410.0000.0000.0000.000
32C27SER00.0140.00215.319-0.387-0.3870.0000.0000.0000.000
33C28ASP-1-0.869-0.92817.92514.43114.4310.0000.0000.0000.000
34C29ALA0-0.007-0.00219.5380.3380.3380.0000.0000.0000.000
35C30LYS10.8830.94519.579-13.392-13.3920.0000.0000.0000.000
36C31THR00.0310.01415.4370.8350.8350.0000.0000.0000.000
37C32TYR0-0.023-0.00414.293-1.191-1.1910.0000.0000.0000.000
38C33LEU00.0190.01613.2541.3641.3640.0000.0000.0000.000
39C34ASN0-0.077-0.03514.806-2.169-2.1690.0000.0000.0000.000
40C35TRP00.0370.00816.2360.9350.9350.0000.0000.0000.000
41C36PHE00.0390.00316.566-0.535-0.5350.0000.0000.0000.000
42C37GLN00.0370.01419.6930.0560.0560.0000.0000.0000.000
43C38GLN0-0.023-0.03221.7350.5250.5250.0000.0000.0000.000
44C39ARG10.9410.99323.558-9.854-9.8540.0000.0000.0000.000
45C40PRO00.0660.02027.0540.1770.1770.0000.0000.0000.000
46C41GLY00.0030.00928.287-0.328-0.3280.0000.0000.0000.000
47C42GLN0-0.034-0.00327.839-0.459-0.4590.0000.0000.0000.000
48C43SER00.0140.00625.1390.4620.4620.0000.0000.0000.000
49C44PRO0-0.013-0.00720.728-0.283-0.2830.0000.0000.0000.000
50C45ARG10.8990.96922.879-11.044-11.0440.0000.0000.0000.000
51C46ARG10.8130.89319.463-13.643-13.6430.0000.0000.0000.000
52C47LEU0-0.028-0.00121.939-0.508-0.5080.0000.0000.0000.000
53C48ILE00.0430.00820.654-0.437-0.4370.0000.0000.0000.000
54C49TYR00.004-0.00619.8600.7680.7680.0000.0000.0000.000
55C50GLN0-0.039-0.03219.237-0.440-0.4400.0000.0000.0000.000
56C51ILE0-0.0240.01118.586-0.545-0.5450.0000.0000.0000.000
57C52SER0-0.009-0.02420.368-0.137-0.1370.0000.0000.0000.000
58C53ARG10.8930.97023.567-11.994-11.9940.0000.0000.0000.000
59C54LEU00.0290.02824.4650.4820.4820.0000.0000.0000.000
60C55ASP-1-0.774-0.87323.88512.64312.6430.0000.0000.0000.000
61C56PRO0-0.012-0.01326.810-0.332-0.3320.0000.0000.0000.000
62C57GLY00.013-0.00329.7280.1390.1390.0000.0000.0000.000
63C58VAL0-0.106-0.04126.621-0.076-0.0760.0000.0000.0000.000
64C59PRO00.0190.01629.908-0.115-0.1150.0000.0000.0000.000
65C60ASP-1-0.861-0.94930.8218.9888.9880.0000.0000.0000.000
66C61ARG10.7830.89031.565-9.086-9.0860.0000.0000.0000.000
67C62PHE0-0.0150.00925.9840.2530.2530.0000.0000.0000.000
68C63SER00.0090.00726.893-0.116-0.1160.0000.0000.0000.000
69C64GLY00.0160.01123.1630.2700.2700.0000.0000.0000.000
70C65SER0-0.021-0.03322.408-0.529-0.5290.0000.0000.0000.000
71C66GLY00.0360.02020.3020.4590.4590.0000.0000.0000.000
72C67SER0-0.016-0.01518.968-0.396-0.3960.0000.0000.0000.000
73C68GLY00.0530.02515.7490.0880.0880.0000.0000.0000.000
74C69THR00.0390.02312.3290.9250.9250.0000.0000.0000.000
75C70ASP-1-0.878-0.91614.10216.29816.2980.0000.0000.0000.000
76C71PHE00.0230.00314.077-0.894-0.8940.0000.0000.0000.000
77C72THR0-0.033-0.02118.280-0.118-0.1180.0000.0000.0000.000
78C73LEU0-0.0220.00321.002-0.204-0.2040.0000.0000.0000.000
79C74LYS10.9490.95722.551-11.128-11.1280.0000.0000.0000.000
80C75ILE00.0430.03126.1610.0070.0070.0000.0000.0000.000
81C76SER0-0.023-0.03028.906-0.129-0.1290.0000.0000.0000.000
82C77ARG10.9370.94832.290-8.453-8.4530.0000.0000.0000.000
83C78VAL00.0010.02530.3160.0390.0390.0000.0000.0000.000
84C79GLU-1-0.887-0.95232.9978.1108.1100.0000.0000.0000.000
85C80ALA00.039-0.00233.1180.2570.2570.0000.0000.0000.000
86C81GLU-1-0.922-0.95532.8469.2849.2840.0000.0000.0000.000
87C82ASP-1-0.799-0.88829.14010.05410.0540.0000.0000.0000.000
88C83VAL0-0.0190.02728.0520.4670.4670.0000.0000.0000.000
89C84GLY00.0260.00126.044-0.055-0.0550.0000.0000.0000.000
90C85VAL0-0.053-0.00819.5910.0350.0350.0000.0000.0000.000
91C86TYR0-0.018-0.02420.348-0.030-0.0300.0000.0000.0000.000
92C87TYR00.0580.04015.1820.3990.3990.0000.0000.0000.000
93C89LEU00.0050.00211.8140.7650.7650.0000.0000.0000.000
94C90GLN00.0500.0477.122-3.539-3.5390.0000.0000.0000.000
95C91GLY0-0.006-0.02710.1771.3291.3290.0000.0000.0000.000
96C92THR0-0.063-0.04010.630-1.217-1.2170.0000.0000.0000.000
97C93HIS0-0.035-0.0346.2290.1120.1120.0000.0000.0000.000
98C94TYR0-0.0040.0235.4110.2910.2910.0000.0000.0000.000
99C95PRO00.0140.0083.3952.3093.3280.033-0.300-0.7530.002
100C96VAL00.033-0.0075.920-0.676-0.6760.0000.0000.0000.000
101C97LEU0-0.029-0.0134.8510.9220.9220.0000.0000.0000.000
102C98PHE00.003-0.0117.991-2.066-2.0660.0000.0000.0000.000
103C99GLY0-0.0090.0059.9381.5941.5940.0000.0000.0000.000
104C100GLN00.0610.01111.662-0.477-0.4770.0000.0000.0000.000
105C101GLY00.0140.01313.674-0.781-0.7810.0000.0000.0000.000
106C102THR0-0.054-0.03216.9440.1720.1720.0000.0000.0000.000
107C103ARG10.9610.98320.119-11.574-11.5740.0000.0000.0000.000
108C104LEU0-0.035-0.01123.306-0.132-0.1320.0000.0000.0000.000
109C105GLU-1-0.791-0.84226.2899.7399.7390.0000.0000.0000.000
110C106ILE00.0350.01629.7490.0110.0110.0000.0000.0000.000
111C107LYS10.9470.98933.230-8.928-8.9280.0000.0000.0000.000
112C108ARG10.8710.93434.825-7.718-7.7180.0000.0000.0000.000
113C109THR0-0.023-0.02238.1320.1220.1220.0000.0000.0000.000
114C110VAL00.0150.01738.3390.0300.0300.0000.0000.0000.000
115C111ALA0-0.018-0.00340.318-0.211-0.2110.0000.0000.0000.000
116C112ALA00.0200.01141.1290.1830.1830.0000.0000.0000.000
117C113PRO0-0.0070.01240.936-0.079-0.0790.0000.0000.0000.000
118C114SER0-0.032-0.01643.068-0.207-0.2070.0000.0000.0000.000
119C115VAL0-0.003-0.00644.2630.1020.1020.0000.0000.0000.000
120C116PHE0-0.025-0.01845.982-0.204-0.2040.0000.0000.0000.000
121C117ILE0-0.0070.00546.3750.1650.1650.0000.0000.0000.000
122C118PHE0-0.0110.00046.150-0.148-0.1480.0000.0000.0000.000
123C119PRO00.010-0.00348.6210.1270.1270.0000.0000.0000.000
124C120PRO0-0.016-0.00149.3050.0490.0490.0000.0000.0000.000
125C121SER00.0510.03450.520-0.101-0.1010.0000.0000.0000.000
126C122ASP-1-0.835-0.94352.6515.6355.6350.0000.0000.0000.000
127C123GLU-1-0.953-0.99052.9475.8825.8820.0000.0000.0000.000
128C124GLN00.0260.00645.505-0.040-0.0400.0000.0000.0000.000
129C125LEU00.0770.04950.8320.0270.0270.0000.0000.0000.000
130C126LYS10.7680.88352.867-5.711-5.7110.0000.0000.0000.000
131C127SER0-0.018-0.01850.1870.0010.0010.0000.0000.0000.000
132C128GLY00.0120.01649.8760.0840.0840.0000.0000.0000.000
133C129THR0-0.046-0.02044.3170.0910.0910.0000.0000.0000.000
134C130ALA00.0080.00947.272-0.138-0.1380.0000.0000.0000.000
135C131SER0-0.0140.00643.4390.1300.1300.0000.0000.0000.000
136C132VAL0-0.0160.00245.037-0.142-0.1420.0000.0000.0000.000
137C133VAL00.0080.01542.5950.1900.1900.0000.0000.0000.000
138C134CYS0-0.083-0.02942.241-0.087-0.0870.0000.0000.0000.000
139C135LEU0-0.014-0.00341.8480.1860.1860.0000.0000.0000.000
140C136LEU0-0.018-0.01738.694-0.180-0.1800.0000.0000.0000.000
141C137ASN00.031-0.01040.7330.2910.2910.0000.0000.0000.000
142C138ASN00.0210.00241.079-0.011-0.0110.0000.0000.0000.000
143C139PHE0-0.0260.00935.678-0.142-0.1420.0000.0000.0000.000
144C140TYR0-0.013-0.02332.6110.1430.1430.0000.0000.0000.000
145C141PRO00.0260.00033.170-0.262-0.2620.0000.0000.0000.000
146C142ARG10.9860.98426.901-10.736-10.7360.0000.0000.0000.000
147C143GLU-1-0.940-0.95329.7619.9729.9720.0000.0000.0000.000
148C144ALA00.009-0.00632.839-0.308-0.3080.0000.0000.0000.000
149C145LYS10.9690.99634.701-7.968-7.9680.0000.0000.0000.000
150C146VAL00.0410.02036.760-0.271-0.2710.0000.0000.0000.000
151C147GLN0-0.037-0.01338.4950.2690.2690.0000.0000.0000.000
152C148TRP00.0330.01240.097-0.298-0.2980.0000.0000.0000.000
153C149LYS10.8950.95743.167-6.756-6.7560.0000.0000.0000.000
154C150VAL00.0480.02846.367-0.057-0.0570.0000.0000.0000.000
155C151ASP-1-0.782-0.88648.9655.8775.8770.0000.0000.0000.000
156C152ASN0-0.060-0.04449.5840.0760.0760.0000.0000.0000.000
157C153ALA00.0510.05147.0790.0570.0570.0000.0000.0000.000
158C154LEU0-0.019-0.03141.4710.0240.0240.0000.0000.0000.000
159C155GLN0-0.0300.00241.9810.1160.1160.0000.0000.0000.000
160C156SER0-0.023-0.03436.7180.1420.1420.0000.0000.0000.000
161C157GLY00.0150.01535.256-0.068-0.0680.0000.0000.0000.000
162C158ASN0-0.0010.00336.3300.1870.1870.0000.0000.0000.000
163C159SER0-0.007-0.00437.190-0.148-0.1480.0000.0000.0000.000
164C160GLN0-0.010-0.00732.4690.0790.0790.0000.0000.0000.000
165C161GLU-1-0.961-0.98133.0358.8588.8580.0000.0000.0000.000
166C162SER0-0.027-0.00832.8190.3940.3940.0000.0000.0000.000
167C163VAL0-0.001-0.01331.765-0.277-0.2770.0000.0000.0000.000
168C164THR00.0080.02132.5220.1660.1660.0000.0000.0000.000
169C165GLU-1-0.905-0.96728.89610.83910.8390.0000.0000.0000.000
170C166GLN0-0.093-0.05532.184-0.073-0.0730.0000.0000.0000.000
171C167ASP-1-0.856-0.92934.0877.7317.7310.0000.0000.0000.000
172C168SER0-0.029-0.03036.747-0.028-0.0280.0000.0000.0000.000
173C169LYS10.9490.98237.710-7.026-7.0260.0000.0000.0000.000
174C170ASP-1-0.870-0.92641.1417.4467.4460.0000.0000.0000.000
175C171SER0-0.024-0.01336.4210.0310.0310.0000.0000.0000.000
176C172THR0-0.083-0.03736.8780.1990.1990.0000.0000.0000.000
177C173TYR0-0.055-0.07831.2120.2700.2700.0000.0000.0000.000
178C174SER00.0580.02336.691-0.244-0.2440.0000.0000.0000.000
179C175LEU0-0.037-0.01034.8090.2260.2260.0000.0000.0000.000
180C176SER00.0020.01437.262-0.317-0.3170.0000.0000.0000.000
181C177SER00.0710.02937.3600.1980.1980.0000.0000.0000.000
182C178THR00.019-0.00238.740-0.299-0.2990.0000.0000.0000.000
183C179LEU0-0.038-0.00239.6170.1950.1950.0000.0000.0000.000
184C180THR00.021-0.00140.508-0.179-0.1790.0000.0000.0000.000
185C181LEU0-0.007-0.00142.8500.0550.0550.0000.0000.0000.000
186C182SER00.0470.02145.641-0.071-0.0710.0000.0000.0000.000
187C183LYS10.9310.95347.668-5.855-5.8550.0000.0000.0000.000
188C184ALA00.0280.01751.166-0.095-0.0950.0000.0000.0000.000
189C185ASP-1-0.881-0.94747.7666.5086.5080.0000.0000.0000.000
190C186TYR0-0.013-0.01350.031-0.114-0.1140.0000.0000.0000.000
191C187GLU-1-0.931-0.98751.3985.5985.5980.0000.0000.0000.000
192C188LYS10.8810.96451.625-6.247-6.2470.0000.0000.0000.000
193C189HIS0-0.052-0.01450.9060.0180.0180.0000.0000.0000.000
194C190LYS10.9400.96354.379-5.472-5.4720.0000.0000.0000.000
195C191VAL0-0.026-0.01352.3440.0170.0170.0000.0000.0000.000
196C192TYR0-0.023-0.01248.3760.1840.1840.0000.0000.0000.000
197C193ALA00.011-0.01348.490-0.084-0.0840.0000.0000.0000.000
198C195GLU-1-0.942-0.99343.9326.8396.8390.0000.0000.0000.000
199C196VAL00.0340.00740.7180.2130.2130.0000.0000.0000.000
200C197THR0-0.016-0.01438.511-0.160-0.1600.0000.0000.0000.000
201C198HIS00.001-0.02437.0190.0160.0160.0000.0000.0000.000
202C199GLN00.0370.01034.254-0.281-0.2810.0000.0000.0000.000
203C200GLY0-0.012-0.00539.142-0.107-0.1070.0000.0000.0000.000
204C201LEU0-0.067-0.02442.285-0.193-0.1930.0000.0000.0000.000
205C202SER00.0130.00443.8070.1150.1150.0000.0000.0000.000
206C203SER0-0.035-0.02645.969-0.024-0.0240.0000.0000.0000.000
207C204PRO00.0160.02043.9250.0200.0200.0000.0000.0000.000
208C205VAL00.0180.02745.281-0.192-0.1920.0000.0000.0000.000
209C206THR0-0.018-0.01046.0730.1740.1740.0000.0000.0000.000
210C207LYS10.9130.97248.152-6.351-6.3510.0000.0000.0000.000
211C208SER00.033-0.01049.2810.0640.0640.0000.0000.0000.000
212C209PHE00.0040.01450.015-0.066-0.0660.0000.0000.0000.000
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