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: QY45Y

Calculation Name: 4XXD-A-Xray372

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4XXD

Chain ID: A

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2233624.559055
FMO2-HF: Nuclear repulsion 2149805.02929
FMO2-HF: Total energy -83819.529765
FMO2-MP2: Total energy -84065.296047


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(A:1:ASP)


Summations of interaction energy for fragment #1(A: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.
-102.035-94.5163.372-4.438-6.4510.046
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.846 / q_NPA : -0.946
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].
3A3VAL00.0150.0133.131-4.195-1.6450.029-1.090-1.4880.004
4A4MET0-0.038-0.0055.142-9.207-9.089-0.001-0.013-0.1040.000
5A5THR0-0.006-0.0128.170-0.677-0.6770.0000.0000.0000.000
6A6GLN0-0.003-0.02611.226-0.088-0.0880.0000.0000.0000.000
7A7SER0-0.0190.00714.083-0.547-0.5470.0000.0000.0000.000
8A8PRO00.0560.02617.614-0.171-0.1710.0000.0000.0000.000
9A9LEU00.0540.01815.0690.5590.5590.0000.0000.0000.000
10A10SER0-0.035-0.01018.696-0.069-0.0690.0000.0000.0000.000
11A11LEU00.0090.00122.306-0.051-0.0510.0000.0000.0000.000
12A12PRO00.0140.02424.770-0.144-0.1440.0000.0000.0000.000
13A13VAL0-0.004-0.01128.028-0.155-0.1550.0000.0000.0000.000
14A14THR0-0.0080.00330.397-0.020-0.0200.0000.0000.0000.000
15A15LEU00.0360.01133.4810.1250.1250.0000.0000.0000.000
16A16GLY0-0.031-0.01534.638-0.226-0.2260.0000.0000.0000.000
17A17GLN0-0.030-0.00532.922-0.023-0.0230.0000.0000.0000.000
18A18PRO00.0420.03030.3490.2060.2060.0000.0000.0000.000
19A19ALA00.0080.00026.1840.0170.0170.0000.0000.0000.000
20A20SER0-0.066-0.05223.9070.0300.0300.0000.0000.0000.000
21A21ILE0-0.0010.01917.901-0.046-0.0460.0000.0000.0000.000
22A22SER0-0.0060.01518.2660.3250.3250.0000.0000.0000.000
23A23CYS00.0360.02112.1001.1541.1540.0000.0000.0000.000
24A24ARG10.8380.90912.474-21.747-21.7470.0000.0000.0000.000
25A25SER00.013-0.0119.6233.5533.5530.0000.0000.0000.000
26A26SER00.0230.0015.808-2.320-2.3200.0000.0000.0000.000
27A27GLN00.0170.0175.428-0.439-0.4390.0000.0000.0000.000
28A27SER00.0180.0109.805-0.189-0.1890.0000.0000.0000.000
29A27LEU00.0310.0208.9832.0242.0240.0000.0000.0000.000
30A27ILE0-0.042-0.00412.331-0.461-0.4610.0000.0000.0000.000
31A27TYR00.0310.02113.4000.3160.3160.0000.0000.0000.000
32A27SER00.016-0.00615.781-0.745-0.7450.0000.0000.0000.000
33A28ASP-1-0.772-0.85918.52616.05816.0580.0000.0000.0000.000
34A29GLY00.0060.01019.875-0.719-0.7190.0000.0000.0000.000
35A30ASN0-0.090-0.05418.869-0.337-0.3370.0000.0000.0000.000
36A31ALA00.0290.01515.6460.8970.8970.0000.0000.0000.000
37A32TYR0-0.070-0.05912.925-0.966-0.9660.0000.0000.0000.000
38A33LEU00.0050.01112.1682.1762.1760.0000.0000.0000.000
39A34HIS10.7960.87412.350-25.752-25.7520.0000.0000.0000.000
40A35TRP00.0420.01614.6381.4861.4860.0000.0000.0000.000
41A36PHE00.0230.00414.816-0.779-0.7790.0000.0000.0000.000
42A37LEU00.0140.01017.9240.1650.1650.0000.0000.0000.000
43A38GLN0-0.021-0.00818.1480.5300.5300.0000.0000.0000.000
44A39LYS10.8690.94420.729-11.558-11.5580.0000.0000.0000.000
45A40PRO00.0530.00523.6970.3520.3520.0000.0000.0000.000
46A41GLY00.0030.00225.063-0.273-0.2730.0000.0000.0000.000
47A42GLN0-0.0060.02224.004-0.298-0.2980.0000.0000.0000.000
48A43SER00.0590.02020.6670.4780.4780.0000.0000.0000.000
49A44PRO0-0.010-0.00416.411-0.598-0.5980.0000.0000.0000.000
50A45ARG10.8740.94019.332-12.562-12.5620.0000.0000.0000.000
51A46LEU0-0.0030.00517.7620.4270.4270.0000.0000.0000.000
52A47LEU0-0.014-0.00419.958-0.832-0.8320.0000.0000.0000.000
53A48ILE0-0.012-0.00919.581-0.705-0.7050.0000.0000.0000.000
54A49TYR00.0330.01218.2211.3011.3010.0000.0000.0000.000
55A50LYS10.9050.98017.393-15.198-15.1980.0000.0000.0000.000
56A51VAL00.0270.03417.141-1.107-1.1070.0000.0000.0000.000
57A52SER0-0.014-0.01419.033-0.047-0.0470.0000.0000.0000.000
58A53ASN0-0.051-0.01922.120-1.080-1.0800.0000.0000.0000.000
59A54ARG10.9680.98722.530-10.395-10.3950.0000.0000.0000.000
60A55PHE00.009-0.00722.673-0.254-0.2540.0000.0000.0000.000
61A56SER00.019-0.00224.729-0.604-0.6040.0000.0000.0000.000
62A57GLY00.002-0.00127.5460.2370.2370.0000.0000.0000.000
63A58VAL0-0.057-0.00524.732-0.148-0.1480.0000.0000.0000.000
64A59PRO00.003-0.00528.085-0.168-0.1680.0000.0000.0000.000
65A60ASP-1-0.871-0.94129.09210.13310.1330.0000.0000.0000.000
66A61ARG10.7390.84829.141-10.405-10.4050.0000.0000.0000.000
67A62PHE0-0.0130.00424.8390.2390.2390.0000.0000.0000.000
68A63SER00.0240.00825.462-0.057-0.0570.0000.0000.0000.000
69A64GLY00.0410.02421.7130.4590.4590.0000.0000.0000.000
70A65SER0-0.051-0.03721.209-0.976-0.9760.0000.0000.0000.000
71A66GLY00.0550.02219.1080.6880.6880.0000.0000.0000.000
72A67SER0-0.0070.00218.924-0.698-0.6980.0000.0000.0000.000
73A68GLY00.0300.01915.885-0.035-0.0350.0000.0000.0000.000
74A69THR00.006-0.02812.2431.4951.4950.0000.0000.0000.000
75A70ASP-1-0.791-0.83814.04319.93519.9350.0000.0000.0000.000
76A71PHE00.017-0.00913.862-0.969-0.9690.0000.0000.0000.000
77A72THR0-0.074-0.04417.734-0.252-0.2520.0000.0000.0000.000
78A73LEU0-0.0050.01919.488-0.114-0.1140.0000.0000.0000.000
79A74LYS10.9140.94320.973-13.150-13.1500.0000.0000.0000.000
80A75ILE00.0080.00123.6840.0450.0450.0000.0000.0000.000
81A76SER00.004-0.01127.369-0.194-0.1940.0000.0000.0000.000
82A77ARG10.8590.91730.935-9.187-9.1870.0000.0000.0000.000
83A78VAL00.0010.02128.4880.2040.2040.0000.0000.0000.000
84A79GLU-1-0.819-0.90230.9368.8668.8660.0000.0000.0000.000
85A80ALA00.0270.00331.3000.3010.3010.0000.0000.0000.000
86A81GLU-1-0.818-0.90130.50810.73510.7350.0000.0000.0000.000
87A82ASP-1-0.775-0.86527.26111.57811.5780.0000.0000.0000.000
88A83VAL0-0.0010.01525.9760.5850.5850.0000.0000.0000.000
89A84GLY00.012-0.00623.646-0.041-0.0410.0000.0000.0000.000
90A85VAL0-0.032-0.00417.268-0.106-0.1060.0000.0000.0000.000
91A86TYR00.010-0.00518.4960.2840.2840.0000.0000.0000.000
92A87TYR00.0080.00812.9940.5090.5090.0000.0000.0000.000
93A88CYS0-0.076-0.03911.686-0.394-0.3940.0000.0000.0000.000
94A89SER00.006-0.0129.8901.3591.3590.0000.0000.0000.000
95A90GLN00.026-0.0015.456-8.632-8.6320.0000.0000.0000.000
96A91SER0-0.021-0.0178.4042.1432.1430.0000.0000.0000.000
97A92THR0-0.046-0.0289.679-2.305-2.3050.0000.0000.0000.000
98A93HIS0-0.031-0.0206.259-1.822-1.8220.0000.0000.0000.000
99A94VAL0-0.0170.0116.538-0.738-0.7380.0000.0000.0000.000
100A95PRO00.0360.0132.550-7.238-4.8361.968-1.735-2.6350.023
101A96TRP0-0.021-0.0174.8701.2571.281-0.001-0.002-0.0210.000
102A97THR0-0.030-0.0062.829-8.691-6.2851.378-1.598-2.1850.019
103A98PHE00.024-0.0215.601-8.977-8.958-0.0010.000-0.0180.000
104A99GLY00.0110.0157.2323.4983.4980.0000.0000.0000.000
105A100GLN00.0190.0029.9030.5950.5950.0000.0000.0000.000
106A101GLY00.0020.02011.695-1.206-1.2060.0000.0000.0000.000
107A102THR0-0.047-0.04614.8250.0870.0870.0000.0000.0000.000
108A103LYS10.8350.91018.213-13.050-13.0500.0000.0000.0000.000
109A104VAL0-0.006-0.00421.334-0.178-0.1780.0000.0000.0000.000
110A105GLU-1-0.810-0.88524.50010.56110.5610.0000.0000.0000.000
111A106ILE00.0200.00927.912-0.118-0.1180.0000.0000.0000.000
112A107LYS10.9090.96631.395-9.167-9.1670.0000.0000.0000.000
113A108ARG10.8280.90133.252-8.590-8.5900.0000.0000.0000.000
114A109THR0-0.019-0.01436.6590.0460.0460.0000.0000.0000.000
115A110VAL00.0180.01639.4710.1300.1300.0000.0000.0000.000
116A111ALA0-0.023-0.01340.694-0.173-0.1730.0000.0000.0000.000
117A112ALA00.0600.02741.3960.1700.1700.0000.0000.0000.000
118A113PRO0-0.0150.00541.364-0.012-0.0120.0000.0000.0000.000
119A114SER00.0100.00343.151-0.247-0.2470.0000.0000.0000.000
120A115VAL0-0.022-0.00444.4480.0960.0960.0000.0000.0000.000
121A116PHE0-0.004-0.00445.420-0.232-0.2320.0000.0000.0000.000
122A117ILE00.002-0.01146.0730.1540.1540.0000.0000.0000.000
123A118PHE0-0.002-0.00345.182-0.111-0.1110.0000.0000.0000.000
124A119PRO00.0180.01048.1270.1190.1190.0000.0000.0000.000
125A120PRO0-0.0200.00648.5760.0770.0770.0000.0000.0000.000
126A121SER00.000-0.02249.625-0.092-0.0920.0000.0000.0000.000
127A122ASP-1-0.843-0.93151.6085.7735.7730.0000.0000.0000.000
128A123GLU-1-0.857-0.92250.9536.2136.2130.0000.0000.0000.000
129A124GLN00.006-0.00845.162-0.011-0.0110.0000.0000.0000.000
130A125LEU00.0260.01749.9080.0030.0030.0000.0000.0000.000
131A126LYS10.9040.95350.805-6.361-6.3610.0000.0000.0000.000
132A127SER0-0.077-0.03749.023-0.035-0.0350.0000.0000.0000.000
133A128GLY00.0130.00749.4840.1180.1180.0000.0000.0000.000
134A129THR0-0.042-0.01445.1700.0790.0790.0000.0000.0000.000
135A130ALA00.0040.00547.669-0.105-0.1050.0000.0000.0000.000
136A131SER0-0.016-0.00443.3230.0950.0950.0000.0000.0000.000
137A132VAL0-0.0120.01445.501-0.080-0.0800.0000.0000.0000.000
138A133VAL0-0.0020.00341.8950.1780.1780.0000.0000.0000.000
139A134CYS0-0.042-0.02542.715-0.163-0.1630.0000.0000.0000.000
140A135LEU0-0.0230.00240.3070.2200.2200.0000.0000.0000.000
141A136LEU00.0170.00639.368-0.215-0.2150.0000.0000.0000.000
142A137ASN00.009-0.01539.7490.3290.3290.0000.0000.0000.000
143A138ASN0-0.027-0.02639.348-0.189-0.1890.0000.0000.0000.000
144A139PHE0-0.0090.01236.336-0.174-0.1740.0000.0000.0000.000
145A140TYR0-0.025-0.03532.1250.1860.1860.0000.0000.0000.000
146A141PRO00.0230.00434.346-0.260-0.2600.0000.0000.0000.000
147A142ARG10.9550.96329.227-10.841-10.8410.0000.0000.0000.000
148A143GLU-1-0.874-0.92930.94310.07310.0730.0000.0000.0000.000
149A144ALA00.0050.02334.551-0.278-0.2780.0000.0000.0000.000
150A145LYS10.7570.85935.278-8.569-8.5690.0000.0000.0000.000
151A146VAL00.0570.01839.203-0.193-0.1930.0000.0000.0000.000
152A147GLN00.0030.00341.201-0.028-0.0280.0000.0000.0000.000
153A148TRP00.0170.00841.537-0.259-0.2590.0000.0000.0000.000
154A149LYS10.8660.91145.542-6.510-6.5100.0000.0000.0000.000
155A150VAL00.0110.00249.044-0.037-0.0370.0000.0000.0000.000
156A151ASP-1-0.780-0.89151.6845.6565.6560.0000.0000.0000.000
157A152ASN0-0.037-0.02253.2190.0090.0090.0000.0000.0000.000
158A153ALA00.0130.02751.3810.0770.0770.0000.0000.0000.000
159A154LEU0-0.011-0.00144.6310.0580.0580.0000.0000.0000.000
160A155GLN0-0.037-0.01045.0330.0160.0160.0000.0000.0000.000
161A156SER00.008-0.00841.4230.0810.0810.0000.0000.0000.000
162A157GLY0-0.0100.00638.461-0.073-0.0730.0000.0000.0000.000
163A158ASN00.0170.00239.1960.2330.2330.0000.0000.0000.000
164A159SER00.0120.00239.488-0.184-0.1840.0000.0000.0000.000
165A160GLN0-0.031-0.00234.3320.1460.1460.0000.0000.0000.000
166A161GLU-1-0.862-0.92333.9758.6928.6920.0000.0000.0000.000
167A162SER0-0.019-0.00132.3390.4040.4040.0000.0000.0000.000
168A163VAL00.002-0.01030.964-0.311-0.3110.0000.0000.0000.000
169A164THR0-0.020-0.00330.7610.2250.2250.0000.0000.0000.000
170A165GLU-1-0.820-0.90225.46512.43412.4340.0000.0000.0000.000
171A166GLN0-0.018-0.00329.264-0.056-0.0560.0000.0000.0000.000
172A167ASP-1-0.716-0.84130.8089.1919.1910.0000.0000.0000.000
173A168SER0-0.044-0.02931.0750.1630.1630.0000.0000.0000.000
174A169LYS10.8110.89033.432-9.087-9.0870.0000.0000.0000.000
175A170ASP-1-0.764-0.84637.2668.1398.1390.0000.0000.0000.000
176A171SER0-0.061-0.02733.557-0.092-0.0920.0000.0000.0000.000
177A172THR0-0.095-0.05634.9500.1060.1060.0000.0000.0000.000
178A173TYR0-0.034-0.03829.6260.4100.4100.0000.0000.0000.000
179A174SER00.0380.01634.918-0.426-0.4260.0000.0000.0000.000
180A175LEU0-0.0320.00435.1040.2950.2950.0000.0000.0000.000
181A176SER00.0080.00736.477-0.347-0.3470.0000.0000.0000.000
182A177SER00.0580.02137.0810.1830.1830.0000.0000.0000.000
183A178THR0-0.022-0.02439.378-0.185-0.1850.0000.0000.0000.000
184A179LEU00.0080.02440.5350.1650.1650.0000.0000.0000.000
185A180THR00.001-0.01441.640-0.096-0.0960.0000.0000.0000.000
186A181LEU0-0.031-0.00943.8680.0120.0120.0000.0000.0000.000
187A182SER00.030-0.01446.927-0.039-0.0390.0000.0000.0000.000
188A183LYS10.8600.90749.143-5.838-5.8380.0000.0000.0000.000
189A184ALA00.0170.00952.484-0.098-0.0980.0000.0000.0000.000
190A185ASP-1-0.831-0.88849.5976.3446.3440.0000.0000.0000.000
191A186TYR00.0010.00250.958-0.046-0.0460.0000.0000.0000.000
192A187GLU-1-0.758-0.88852.6075.6195.6190.0000.0000.0000.000
193A188LYS10.8650.94855.186-5.603-5.6030.0000.0000.0000.000
194A189HIS10.8460.93152.523-6.055-6.0550.0000.0000.0000.000
195A190LYS10.8980.94456.420-5.336-5.3360.0000.0000.0000.000
196A191VAL0-0.010-0.01354.5750.0050.0050.0000.0000.0000.000
197A192TYR00.000-0.00750.0370.1350.1350.0000.0000.0000.000
198A193ALA00.009-0.00750.441-0.057-0.0570.0000.0000.0000.000
199A194CYS0-0.0220.00345.2210.1120.1120.0000.0000.0000.000
200A195GLU-1-0.852-0.90146.4806.4736.4730.0000.0000.0000.000
201A196VAL00.012-0.00342.2480.1980.1980.0000.0000.0000.000
202A197THR00.0120.00642.321-0.200-0.2000.0000.0000.0000.000
203A198HIS00.006-0.02038.0820.0050.0050.0000.0000.0000.000
204A199GLN00.0260.01138.076-0.113-0.1130.0000.0000.0000.000
205A200GLY0-0.003-0.00541.584-0.113-0.1130.0000.0000.0000.000
206A201LEU0-0.059-0.02743.885-0.150-0.1500.0000.0000.0000.000
207A202SER00.0140.00946.4970.0510.0510.0000.0000.0000.000
208A203SER0-0.008-0.00949.070-0.123-0.1230.0000.0000.0000.000
209A204PRO00.0030.00547.2500.0490.0490.0000.0000.0000.000
210A205VAL0-0.0150.00247.265-0.163-0.1630.0000.0000.0000.000
211A206THR00.0180.00647.8490.1370.1370.0000.0000.0000.000
212A207LYS10.8260.91648.964-6.512-6.5120.0000.0000.0000.000
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