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: R9K48

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2226164.8641
FMO2-HF: Nuclear repulsion 2142345.896331
FMO2-HF: Total energy -83818.967768
FMO2-MP2: Total energy -84064.565414


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.
-85.651-79.2562.792-3.714-5.4740.041
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 : -0.916 / q_NPA : -0.975
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].
3A3VAL00.0420.0353.3171.0502.810-0.001-0.637-1.1230.003
4A4MET0-0.045-0.0115.629-7.247-7.2470.0000.0000.0000.000
5A5THR0-0.011-0.0028.832-0.777-0.7770.0000.0000.0000.000
6A6GLN00.000-0.02911.8180.1410.1410.0000.0000.0000.000
7A7SER0-0.0340.00014.647-0.626-0.6260.0000.0000.0000.000
8A8PRO00.0400.02018.316-0.151-0.1510.0000.0000.0000.000
9A9LEU00.0630.02115.4050.3340.3340.0000.0000.0000.000
10A10SER0-0.024-0.00819.163-0.037-0.0370.0000.0000.0000.000
11A11LEU00.004-0.01522.779-0.083-0.0830.0000.0000.0000.000
12A12PRO00.0280.04324.961-0.168-0.1680.0000.0000.0000.000
13A13VAL0-0.017-0.01928.091-0.095-0.0950.0000.0000.0000.000
14A14THR00.0030.01130.710-0.047-0.0470.0000.0000.0000.000
15A15LEU00.0410.01333.6560.1440.1440.0000.0000.0000.000
16A16GLY0-0.045-0.03034.794-0.216-0.2160.0000.0000.0000.000
17A17GLN0-0.030-0.00133.464-0.013-0.0130.0000.0000.0000.000
18A18PRO00.0380.03330.4040.2220.2220.0000.0000.0000.000
19A19ALA00.003-0.00126.1510.0360.0360.0000.0000.0000.000
20A20SER0-0.041-0.03424.2330.0710.0710.0000.0000.0000.000
21A21ILE0-0.0200.00318.1750.0770.0770.0000.0000.0000.000
22A22SER0-0.0110.00118.6300.4770.4770.0000.0000.0000.000
23A23CYS00.0270.01012.5591.0621.0620.0000.0000.0000.000
24A24ARG10.8300.90612.786-20.232-20.2320.0000.0000.0000.000
25A25SER00.0330.0019.6993.0983.0980.0000.0000.0000.000
26A26SER00.0140.0065.620-1.207-1.2070.0000.0000.0000.000
27A27GLN00.0120.0075.3860.4640.4640.0000.0000.0000.000
28A27SER00.0160.0149.507-0.571-0.5710.0000.0000.0000.000
29A27LEU00.0460.0149.0522.0232.0230.0000.0000.0000.000
30A27ILE0-0.042-0.01211.997-0.237-0.2370.0000.0000.0000.000
31A27TYR00.0490.03612.9350.1110.1110.0000.0000.0000.000
32A27SER00.020-0.00515.382-0.706-0.7060.0000.0000.0000.000
33A28ASP-1-0.780-0.86518.23915.90615.9060.0000.0000.0000.000
34A29GLY00.0090.01419.304-0.750-0.7500.0000.0000.0000.000
35A30ASN0-0.103-0.06118.824-0.347-0.3470.0000.0000.0000.000
36A31ALA00.0360.01615.3490.9230.9230.0000.0000.0000.000
37A32TYR0-0.097-0.07113.074-0.968-0.9680.0000.0000.0000.000
38A33LEU0-0.016-0.00812.5961.8271.8270.0000.0000.0000.000
39A34HIS10.8280.90313.273-24.269-24.2690.0000.0000.0000.000
40A35TRP00.0250.00314.9831.3001.3000.0000.0000.0000.000
41A36PHE00.000-0.01014.552-0.790-0.7900.0000.0000.0000.000
42A37LEU00.0160.01417.9560.1550.1550.0000.0000.0000.000
43A38GLN0-0.0030.00218.2100.5780.5780.0000.0000.0000.000
44A39LYS10.8900.95220.965-11.567-11.5670.0000.0000.0000.000
45A40PRO00.0560.00423.8010.3500.3500.0000.0000.0000.000
46A41GLY00.0030.00224.933-0.332-0.3320.0000.0000.0000.000
47A42GLN00.0020.02124.285-0.134-0.1340.0000.0000.0000.000
48A43SER00.0530.01721.0910.4780.4780.0000.0000.0000.000
49A44PRO0-0.018-0.00616.665-0.536-0.5360.0000.0000.0000.000
50A45ARG10.8940.94619.491-12.416-12.4160.0000.0000.0000.000
51A46LEU0-0.0160.01117.9050.3290.3290.0000.0000.0000.000
52A47LEU0-0.012-0.00220.287-0.815-0.8150.0000.0000.0000.000
53A48ILE00.027-0.00120.046-0.624-0.6240.0000.0000.0000.000
54A49TYR00.0350.00518.7071.1441.1440.0000.0000.0000.000
55A50LYS10.8960.97117.862-14.909-14.9090.0000.0000.0000.000
56A51VAL00.0400.03817.595-0.831-0.8310.0000.0000.0000.000
57A52SER00.004-0.01319.676-0.119-0.1190.0000.0000.0000.000
58A53ASN0-0.065-0.00722.924-1.008-1.0080.0000.0000.0000.000
59A54ARG10.9781.00223.269-10.220-10.2200.0000.0000.0000.000
60A55PHE00.0340.00323.225-0.212-0.2120.0000.0000.0000.000
61A56SER0-0.002-0.01025.340-0.555-0.5550.0000.0000.0000.000
62A57GLY00.0080.00327.9590.2160.2160.0000.0000.0000.000
63A58VAL0-0.073-0.01024.826-0.107-0.1070.0000.0000.0000.000
64A59PRO0-0.007-0.01728.058-0.133-0.1330.0000.0000.0000.000
65A60ASP-1-0.908-0.95229.13510.00210.0020.0000.0000.0000.000
66A61ARG10.7200.83129.534-10.271-10.2710.0000.0000.0000.000
67A62PHE00.0050.00724.9230.2160.2160.0000.0000.0000.000
68A63SER00.0130.00525.615-0.066-0.0660.0000.0000.0000.000
69A64GLY00.0300.02722.1250.4170.4170.0000.0000.0000.000
70A65SER0-0.049-0.03521.883-0.794-0.7940.0000.0000.0000.000
71A66GLY00.0640.02919.5990.6370.6370.0000.0000.0000.000
72A67SER0-0.018-0.00818.653-0.538-0.5380.0000.0000.0000.000
73A68GLY00.0090.01015.730-0.192-0.1920.0000.0000.0000.000
74A69THR00.002-0.01512.2551.1121.1120.0000.0000.0000.000
75A70ASP-1-0.791-0.85914.05318.91318.9130.0000.0000.0000.000
76A71PHE00.0270.00113.767-0.759-0.7590.0000.0000.0000.000
77A72THR0-0.061-0.03417.955-0.332-0.3320.0000.0000.0000.000
78A73LEU00.0030.02219.917-0.167-0.1670.0000.0000.0000.000
79A74LYS10.9230.94921.546-12.639-12.6390.0000.0000.0000.000
80A75ILE00.0170.00724.1370.0360.0360.0000.0000.0000.000
81A76SER0-0.016-0.02127.698-0.259-0.2590.0000.0000.0000.000
82A77ARG10.8690.92231.424-8.982-8.9820.0000.0000.0000.000
83A78VAL00.0020.00728.8400.1440.1440.0000.0000.0000.000
84A79GLU-1-0.809-0.88331.2548.7838.7830.0000.0000.0000.000
85A80ALA00.0490.01131.3890.2900.2900.0000.0000.0000.000
86A81GLU-1-0.863-0.91530.95010.20910.2090.0000.0000.0000.000
87A82ASP-1-0.781-0.86627.37911.42911.4290.0000.0000.0000.000
88A83VAL0-0.0070.02026.0840.5820.5820.0000.0000.0000.000
89A84GLY00.000-0.01623.806-0.085-0.0850.0000.0000.0000.000
90A85VAL0-0.033-0.01217.440-0.100-0.1000.0000.0000.0000.000
91A86TYR0-0.020-0.02518.6620.3360.3360.0000.0000.0000.000
92A87TYR00.0140.00713.0800.5960.5960.0000.0000.0000.000
93A88CYS0-0.055-0.00912.324-0.279-0.2790.0000.0000.0000.000
94A89SER00.013-0.01610.1251.2691.2690.0000.0000.0000.000
95A90GLN00.0360.0236.043-7.658-7.6580.0000.0000.0000.000
96A91SER00.014-0.0129.0821.7891.7890.0000.0000.0000.000
97A92THR0-0.054-0.0199.555-2.006-2.0060.0000.0000.0000.000
98A93HIS0-0.033-0.0315.814-1.656-1.6560.0000.0000.0000.000
99A94VAL0-0.0130.0196.7190.7820.7820.0000.0000.0000.000
100A95PRO00.0210.0102.504-8.381-5.6682.226-1.986-2.9530.026
101A96TRP0-0.013-0.0124.9761.9251.942-0.001-0.002-0.0140.000
102A97THR0-0.024-0.0072.791-6.278-4.3730.568-1.089-1.3840.012
103A98PHE0-0.004-0.0335.917-7.381-7.3810.0000.0000.0000.000
104A99GLY00.0340.0267.5883.0423.0420.0000.0000.0000.000
105A100GLN00.0360.00710.3260.5710.5710.0000.0000.0000.000
106A101GLY00.0000.01612.180-0.882-0.8820.0000.0000.0000.000
107A102THR0-0.064-0.04515.231-0.136-0.1360.0000.0000.0000.000
108A103LYS10.8500.91318.707-12.853-12.8530.0000.0000.0000.000
109A104VAL00.0060.01521.767-0.245-0.2450.0000.0000.0000.000
110A105GLU-1-0.836-0.90724.73710.34310.3430.0000.0000.0000.000
111A106ILE00.0120.00328.147-0.104-0.1040.0000.0000.0000.000
112A107LYS10.9130.96731.708-8.901-8.9010.0000.0000.0000.000
113A108ARG10.8350.89533.848-8.374-8.3740.0000.0000.0000.000
114A109THR0-0.004-0.00537.3540.0210.0210.0000.0000.0000.000
115A110VAL00.0230.01840.2820.1170.1170.0000.0000.0000.000
116A111ALA0-0.023-0.00540.961-0.186-0.1860.0000.0000.0000.000
117A112ALA00.0410.01241.8410.1520.1520.0000.0000.0000.000
118A113PRO0-0.0040.01541.726-0.013-0.0130.0000.0000.0000.000
119A114SER0-0.034-0.01343.547-0.240-0.2400.0000.0000.0000.000
120A115VAL0-0.009-0.00844.8970.1240.1240.0000.0000.0000.000
121A116PHE0-0.017-0.01845.860-0.209-0.2090.0000.0000.0000.000
122A117ILE0-0.0050.00846.4250.1630.1630.0000.0000.0000.000
123A118PHE0-0.009-0.00645.709-0.115-0.1150.0000.0000.0000.000
124A119PRO00.0010.00148.5960.1010.1010.0000.0000.0000.000
125A120PRO0-0.027-0.00549.1070.0550.0550.0000.0000.0000.000
126A121SER0-0.009-0.01949.797-0.090-0.0900.0000.0000.0000.000
127A122ASP-1-0.856-0.93751.6405.7225.7220.0000.0000.0000.000
128A123GLU-1-0.895-0.95151.4366.1876.1870.0000.0000.0000.000
129A124GLN0-0.009-0.01145.398-0.047-0.0470.0000.0000.0000.000
130A125LEU00.0370.02050.2230.0300.0300.0000.0000.0000.000
131A126LYS10.9530.98950.855-6.330-6.3300.0000.0000.0000.000
132A127SER0-0.098-0.06248.831-0.035-0.0350.0000.0000.0000.000
133A128GLY00.0120.01549.9630.0810.0810.0000.0000.0000.000
134A129THR0-0.066-0.03945.0970.1070.1070.0000.0000.0000.000
135A130ALA0-0.0100.00448.041-0.086-0.0860.0000.0000.0000.000
136A131SER0-0.0150.00243.6830.1020.1020.0000.0000.0000.000
137A132VAL00.0100.01345.663-0.102-0.1020.0000.0000.0000.000
138A133VAL00.0010.01742.0120.1690.1690.0000.0000.0000.000
139A134CYS0-0.049-0.03242.928-0.166-0.1660.0000.0000.0000.000
140A135LEU0-0.013-0.00940.8890.2140.2140.0000.0000.0000.000
141A136LEU00.0200.00839.867-0.201-0.2010.0000.0000.0000.000
142A137ASN0-0.007-0.02340.1260.3090.3090.0000.0000.0000.000
143A138ASN00.004-0.01239.629-0.168-0.1680.0000.0000.0000.000
144A139PHE0-0.0080.00936.982-0.149-0.1490.0000.0000.0000.000
145A140TYR0-0.020-0.03132.3800.1410.1410.0000.0000.0000.000
146A141PRO00.000-0.00734.732-0.253-0.2530.0000.0000.0000.000
147A142ARG10.9770.97729.601-10.659-10.6590.0000.0000.0000.000
148A143GLU-1-0.903-0.94831.4459.8659.8650.0000.0000.0000.000
149A144ALA00.0360.01635.026-0.267-0.2670.0000.0000.0000.000
150A145LYS10.7510.87835.895-8.478-8.4780.0000.0000.0000.000
151A146VAL00.0660.02739.623-0.170-0.1700.0000.0000.0000.000
152A147GLN0-0.014-0.01141.286-0.016-0.0160.0000.0000.0000.000
153A148TRP00.0400.02842.021-0.230-0.2300.0000.0000.0000.000
154A149LYS10.8750.91745.956-6.411-6.4110.0000.0000.0000.000
155A150VAL00.0170.00949.236-0.045-0.0450.0000.0000.0000.000
156A151ASP-1-0.789-0.90151.8605.6235.6230.0000.0000.0000.000
157A152ASN0-0.054-0.03553.4860.0160.0160.0000.0000.0000.000
158A153ALA00.0250.03451.7620.0600.0600.0000.0000.0000.000
159A154LEU0-0.014-0.00844.9430.0560.0560.0000.0000.0000.000
160A155GLN0-0.042-0.01145.1290.0300.0300.0000.0000.0000.000
161A156SER0-0.006-0.01441.7060.0890.0890.0000.0000.0000.000
162A157GLY00.0080.00338.824-0.074-0.0740.0000.0000.0000.000
163A158ASN00.0160.01139.8450.1820.1820.0000.0000.0000.000
164A159SER00.001-0.00239.363-0.187-0.1870.0000.0000.0000.000
165A160GLN0-0.027-0.00234.1330.0900.0900.0000.0000.0000.000
166A161GLU-1-0.862-0.93034.1368.6478.6470.0000.0000.0000.000
167A162SER0-0.033-0.01232.6860.4050.4050.0000.0000.0000.000
168A163VAL00.006-0.00831.277-0.290-0.2900.0000.0000.0000.000
169A164THR00.0030.01331.1200.2320.2320.0000.0000.0000.000
170A165GLU-1-0.855-0.92425.79812.19712.1970.0000.0000.0000.000
171A166GLN00.0060.00829.388-0.013-0.0130.0000.0000.0000.000
172A167ASP-1-0.781-0.88031.0389.0949.0940.0000.0000.0000.000
173A168SER0-0.071-0.05131.4660.1340.1340.0000.0000.0000.000
174A169LYS10.8860.94833.584-9.026-9.0260.0000.0000.0000.000
175A170ASP-1-0.766-0.85237.3868.1058.1050.0000.0000.0000.000
176A171SER0-0.034-0.01434.049-0.123-0.1230.0000.0000.0000.000
177A172THR0-0.094-0.05635.1090.1080.1080.0000.0000.0000.000
178A173TYR0-0.047-0.04330.3230.3720.3720.0000.0000.0000.000
179A174SER00.0530.02335.273-0.400-0.4000.0000.0000.0000.000
180A175LEU0-0.054-0.01435.3410.2720.2720.0000.0000.0000.000
181A176SER00.0180.01036.818-0.326-0.3260.0000.0000.0000.000
182A177SER00.0490.03037.3180.2080.2080.0000.0000.0000.000
183A178THR00.015-0.00239.322-0.262-0.2620.0000.0000.0000.000
184A179LEU0-0.018-0.00740.7710.1370.1370.0000.0000.0000.000
185A180THR00.001-0.00541.377-0.114-0.1140.0000.0000.0000.000
186A181LEU0-0.011-0.00643.845-0.004-0.0040.0000.0000.0000.000
187A182SER00.037-0.00547.165-0.058-0.0580.0000.0000.0000.000
188A183LYS10.9000.93149.232-5.818-5.8180.0000.0000.0000.000
189A184ALA00.0210.00752.561-0.099-0.0990.0000.0000.0000.000
190A185ASP-1-0.856-0.89250.2206.2736.2730.0000.0000.0000.000
191A186TYR0-0.004-0.00651.087-0.052-0.0520.0000.0000.0000.000
192A187GLU-1-0.760-0.88252.8085.5925.5920.0000.0000.0000.000
193A188LYS10.9030.96355.686-5.609-5.6090.0000.0000.0000.000
194A189HIS10.8350.92853.099-6.027-6.0270.0000.0000.0000.000
195A190LYS10.9070.96256.706-5.264-5.2640.0000.0000.0000.000
196A191VAL0-0.003-0.01154.5970.0290.0290.0000.0000.0000.000
197A192TYR00.0120.00050.2250.1400.1400.0000.0000.0000.000
198A193ALA0-0.004-0.01250.635-0.033-0.0330.0000.0000.0000.000
199A194CYS0-0.0100.01745.4420.0980.0980.0000.0000.0000.000
200A195GLU-1-0.865-0.91846.7296.4326.4320.0000.0000.0000.000
201A196VAL00.014-0.00742.8490.2110.2110.0000.0000.0000.000
202A197THR0-0.011-0.00342.481-0.177-0.1770.0000.0000.0000.000
203A198HIS00.010-0.01238.5930.0110.0110.0000.0000.0000.000
204A199GLN00.0220.00738.471-0.136-0.1360.0000.0000.0000.000
205A200GLY00.004-0.00842.292-0.123-0.1230.0000.0000.0000.000
206A201LEU0-0.066-0.01944.326-0.147-0.1470.0000.0000.0000.000
207A202SER00.0100.00747.0440.0670.0670.0000.0000.0000.000
208A203SER00.0150.00649.753-0.081-0.0810.0000.0000.0000.000
209A204PRO00.005-0.00347.6100.0560.0560.0000.0000.0000.000
210A205VAL0-0.0160.00747.707-0.163-0.1630.0000.0000.0000.000
211A206THR00.0330.01348.3160.1460.1460.0000.0000.0000.000
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