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: Z6G9N

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2223085.567119
FMO2-HF: Nuclear repulsion 2139267.894716
FMO2-HF: Total energy -83817.672403
FMO2-MP2: Total energy -84063.148167


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.
-75.918-69.390.839-3.151-4.2150.027
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 : -0.898 / q_NPA : -0.962
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].
3A3VAL00.0240.0323.137-1.0510.7240.013-0.707-1.0810.004
4A4MET0-0.030-0.0065.357-5.474-5.369-0.001-0.005-0.0990.000
5A5THR0-0.0060.0008.868-0.572-0.5720.0000.0000.0000.000
6A6GLN00.018-0.01611.5810.2310.2310.0000.0000.0000.000
7A7SER0-0.0470.00014.760-0.534-0.5340.0000.0000.0000.000
8A8PRO00.0460.02318.303-0.147-0.1470.0000.0000.0000.000
9A9LEU00.0600.02115.5430.2990.2990.0000.0000.0000.000
10A10SER0-0.034-0.01119.494-0.056-0.0560.0000.0000.0000.000
11A11LEU00.020-0.01023.213-0.072-0.0720.0000.0000.0000.000
12A12PRO00.0310.03925.426-0.163-0.1630.0000.0000.0000.000
13A13VAL0-0.028-0.02028.802-0.093-0.0930.0000.0000.0000.000
14A14THR00.0030.01331.225-0.048-0.0480.0000.0000.0000.000
15A15LEU00.0430.01134.2580.1370.1370.0000.0000.0000.000
16A16GLY0-0.066-0.04435.527-0.208-0.2080.0000.0000.0000.000
17A17GLN0-0.0200.00033.8230.0550.0550.0000.0000.0000.000
18A18PRO00.0430.03330.8450.2150.2150.0000.0000.0000.000
19A19ALA00.0090.00426.4910.0350.0350.0000.0000.0000.000
20A20SER0-0.043-0.03624.3340.0800.0800.0000.0000.0000.000
21A21ILE0-0.0220.00418.5230.0610.0610.0000.0000.0000.000
22A22SER0-0.0120.00018.2340.4630.4630.0000.0000.0000.000
23A23CYS00.008-0.02412.7080.9450.9450.0000.0000.0000.000
24A24ARG10.9020.95712.627-19.638-19.6380.0000.0000.0000.000
25A25SER00.0360.0069.7802.5932.5930.0000.0000.0000.000
26A26SER00.0210.0075.390-1.350-1.3500.0000.0000.0000.000
27A27GLN00.0000.0055.5971.5121.526-0.001-0.003-0.0100.000
28A27SER0-0.0040.0019.508-0.789-0.7890.0000.0000.0000.000
29A27LEU00.0440.0088.8571.9001.9000.0000.0000.0000.000
30A27ILE0-0.024-0.00211.982-0.237-0.2370.0000.0000.0000.000
31A27TYR00.0310.02812.4870.1580.1580.0000.0000.0000.000
32A27SER00.008-0.01415.374-0.706-0.7060.0000.0000.0000.000
33A28ASP-1-0.795-0.88118.23615.73315.7330.0000.0000.0000.000
34A29GLY00.0010.00819.308-0.730-0.7300.0000.0000.0000.000
35A30ASN0-0.099-0.04618.785-0.429-0.4290.0000.0000.0000.000
36A31ALA00.0330.01715.3300.9190.9190.0000.0000.0000.000
37A32TYR0-0.114-0.07713.058-0.877-0.8770.0000.0000.0000.000
38A33LEU0-0.019-0.00912.7321.6781.6780.0000.0000.0000.000
39A34HIS10.7860.87613.725-22.746-22.7460.0000.0000.0000.000
40A35TRP00.0480.01715.7821.0671.0670.0000.0000.0000.000
41A36PHE0-0.0300.01515.2010.0310.0310.0000.0000.0000.000
42A37LEU00.0200.01418.6690.1480.1480.0000.0000.0000.000
43A38GLN0-0.0040.00618.7090.4800.4800.0000.0000.0000.000
44A39LYS10.9370.99421.618-11.136-11.1360.0000.0000.0000.000
45A40PRO00.0600.00724.3920.3630.3630.0000.0000.0000.000
46A41GLY00.0040.00325.458-0.313-0.3130.0000.0000.0000.000
47A42GLN0-0.050-0.01124.7200.0310.0310.0000.0000.0000.000
48A43SER00.0280.00321.4440.5910.5910.0000.0000.0000.000
49A44PRO00.000-0.00117.108-0.520-0.5200.0000.0000.0000.000
50A45ARG10.9500.97719.985-12.048-12.0480.0000.0000.0000.000
51A46LEU0-0.0180.00718.2900.3060.3060.0000.0000.0000.000
52A47LEU00.0000.00020.908-0.753-0.7530.0000.0000.0000.000
53A48ILE00.0310.00820.776-0.583-0.5830.0000.0000.0000.000
54A49TYR00.039-0.00719.2591.0581.0580.0000.0000.0000.000
55A50LYS10.9400.98218.071-14.683-14.6830.0000.0000.0000.000
56A51VAL00.0410.04417.409-0.731-0.7310.0000.0000.0000.000
57A52SER00.014-0.00519.649-0.113-0.1130.0000.0000.0000.000
58A53ASN0-0.047-0.00222.948-0.920-0.9200.0000.0000.0000.000
59A54ARG11.0021.00823.720-9.943-9.9430.0000.0000.0000.000
60A55PHE00.019-0.00423.787-0.174-0.1740.0000.0000.0000.000
61A56SER0-0.017-0.01425.878-0.541-0.5410.0000.0000.0000.000
62A57GLY00.0080.00328.4530.2070.2070.0000.0000.0000.000
63A58VAL0-0.085-0.01725.403-0.101-0.1010.0000.0000.0000.000
64A59PRO00.001-0.00728.714-0.142-0.1420.0000.0000.0000.000
65A60ASP-1-0.916-0.95729.8999.6759.6750.0000.0000.0000.000
66A61ARG10.8070.90330.385-9.888-9.8880.0000.0000.0000.000
67A62PHE0-0.0160.00025.5190.2040.2040.0000.0000.0000.000
68A63SER00.0150.00726.308-0.063-0.0630.0000.0000.0000.000
69A64GLY00.0230.02222.5480.3800.3800.0000.0000.0000.000
70A65SER0-0.061-0.04022.149-0.704-0.7040.0000.0000.0000.000
71A66GLY00.0600.02519.5890.5830.5830.0000.0000.0000.000
72A67SER0-0.009-0.00418.596-0.483-0.4830.0000.0000.0000.000
73A68GLY00.0080.01015.717-0.156-0.1560.0000.0000.0000.000
74A69THR0-0.0050.00712.2230.7410.7410.0000.0000.0000.000
75A70ASP-1-0.810-0.90014.05317.75517.7550.0000.0000.0000.000
76A71PHE0-0.012-0.02613.581-0.614-0.6140.0000.0000.0000.000
77A72THR0-0.066-0.03517.955-0.340-0.3400.0000.0000.0000.000
78A73LEU00.0110.02320.525-0.148-0.1480.0000.0000.0000.000
79A74LYS10.9580.96922.027-11.942-11.9420.0000.0000.0000.000
80A75ILE00.0070.00424.9440.0190.0190.0000.0000.0000.000
81A76SER0-0.015-0.01628.336-0.256-0.2560.0000.0000.0000.000
82A77ARG10.9660.98232.024-8.781-8.7810.0000.0000.0000.000
83A78VAL0-0.0090.00429.4500.1280.1280.0000.0000.0000.000
84A79GLU-1-0.903-0.95832.1518.6728.6720.0000.0000.0000.000
85A80ALA00.0460.00832.2920.2680.2680.0000.0000.0000.000
86A81GLU-1-0.953-0.97731.7329.6979.6970.0000.0000.0000.000
87A82ASP-1-0.804-0.89128.25710.95810.9580.0000.0000.0000.000
88A83VAL0-0.0100.01926.9610.5550.5550.0000.0000.0000.000
89A84GLY00.016-0.01424.601-0.060-0.0600.0000.0000.0000.000
90A85VAL0-0.040-0.01818.296-0.078-0.0780.0000.0000.0000.000
91A86TYR0-0.019-0.01919.5590.3000.3000.0000.0000.0000.000
92A87TYR00.0200.00413.5660.5360.5360.0000.0000.0000.000
93A88CYS0-0.0690.00212.894-0.167-0.1670.0000.0000.0000.000
94A89SER00.045-0.03810.9221.1451.1450.0000.0000.0000.000
95A90GLN00.0670.0636.370-5.895-5.8950.0000.0000.0000.000
96A91SER00.0180.0139.5181.6421.6420.0000.0000.0000.000
97A92THR0-0.045-0.0279.620-1.801-1.8010.0000.0000.0000.000
98A93HIS0-0.037-0.0315.763-0.877-0.8770.0000.0000.0000.000
99A94VAL0-0.0200.0136.9920.1030.1030.0000.0000.0000.000
100A95PRO00.0290.0122.774-6.854-3.2600.779-1.949-2.4240.020
101A96TRP0-0.028-0.0195.6880.6540.648-0.001-0.0010.0080.000
102A97THR0-0.043-0.0353.378-2.937-1.8910.050-0.486-0.6090.003
103A98PHE00.014-0.0216.489-5.776-5.7760.0000.0000.0000.000
104A99GLY00.0240.0238.5182.2462.2460.0000.0000.0000.000
105A100GLN00.033-0.00411.0640.5050.5050.0000.0000.0000.000
106A101GLY00.0060.02612.852-0.702-0.7020.0000.0000.0000.000
107A102THR0-0.054-0.03916.079-0.077-0.0770.0000.0000.0000.000
108A103LYS10.9550.98119.400-12.476-12.4760.0000.0000.0000.000
109A104VAL00.0070.01822.576-0.221-0.2210.0000.0000.0000.000
110A105GLU-1-0.885-0.94725.52310.14210.1420.0000.0000.0000.000
111A106ILE00.0200.00128.911-0.096-0.0960.0000.0000.0000.000
112A107LYS10.9320.97132.477-8.710-8.7100.0000.0000.0000.000
113A108ARG10.8770.93334.448-8.128-8.1280.0000.0000.0000.000
114A109THR0-0.021-0.01938.0280.0080.0080.0000.0000.0000.000
115A110VAL00.0320.01540.9550.1140.1140.0000.0000.0000.000
116A111ALA0-0.024-0.00841.683-0.176-0.1760.0000.0000.0000.000
117A112ALA00.0330.00942.6080.1480.1480.0000.0000.0000.000
118A113PRO0-0.0090.01142.446-0.014-0.0140.0000.0000.0000.000
119A114SER0-0.030-0.01044.353-0.231-0.2310.0000.0000.0000.000
120A115VAL0-0.006-0.00945.5760.1250.1250.0000.0000.0000.000
121A116PHE0-0.014-0.01546.716-0.199-0.1990.0000.0000.0000.000
122A117ILE0-0.0030.00647.0390.1560.1560.0000.0000.0000.000
123A118PHE0-0.018-0.01145.968-0.114-0.1140.0000.0000.0000.000
124A119PRO00.0070.00449.0750.1020.1020.0000.0000.0000.000
125A120PRO0-0.021-0.00649.4710.0550.0550.0000.0000.0000.000
126A121SER00.0510.03150.099-0.099-0.0990.0000.0000.0000.000
127A122ASP-1-0.869-0.94451.9715.6805.6800.0000.0000.0000.000
128A123GLU-1-0.958-0.99651.7466.0806.0800.0000.0000.0000.000
129A124GLN0-0.008-0.01445.719-0.032-0.0320.0000.0000.0000.000
130A125LEU00.0380.02650.4530.0340.0340.0000.0000.0000.000
131A126LYS10.9470.98751.288-6.249-6.2490.0000.0000.0000.000
132A127SER0-0.133-0.08449.0910.0120.0120.0000.0000.0000.000
133A128GLY00.0340.01750.0770.0790.0790.0000.0000.0000.000
134A129THR0-0.061-0.03645.3110.0910.0910.0000.0000.0000.000
135A130ALA00.0080.01148.329-0.084-0.0840.0000.0000.0000.000
136A131SER0-0.0160.00443.9350.0970.0970.0000.0000.0000.000
137A132VAL00.0130.01746.072-0.101-0.1010.0000.0000.0000.000
138A133VAL00.0080.01642.6170.1600.1600.0000.0000.0000.000
139A134CYS0-0.038-0.03143.469-0.169-0.1690.0000.0000.0000.000
140A135LEU0-0.014-0.00841.6070.2100.2100.0000.0000.0000.000
141A136LEU00.0150.01040.522-0.198-0.1980.0000.0000.0000.000
142A137ASN00.020-0.01840.8320.3540.3540.0000.0000.0000.000
143A138ASN00.0410.01540.414-0.022-0.0220.0000.0000.0000.000
144A139PHE0-0.0280.00737.384-0.148-0.1480.0000.0000.0000.000
145A140TYR0-0.039-0.02932.9670.1590.1590.0000.0000.0000.000
146A141PRO00.000-0.00335.328-0.249-0.2490.0000.0000.0000.000
147A142ARG11.0211.00230.407-10.366-10.3660.0000.0000.0000.000
148A143GLU-1-0.951-0.97331.9559.4859.4850.0000.0000.0000.000
149A144ALA00.0200.00235.601-0.257-0.2570.0000.0000.0000.000
150A145LYS10.8740.94736.683-8.283-8.2830.0000.0000.0000.000
151A146VAL00.0880.04340.093-0.192-0.1920.0000.0000.0000.000
152A147GLN0-0.037-0.02441.928-0.003-0.0030.0000.0000.0000.000
153A148TRP00.0380.03342.575-0.228-0.2280.0000.0000.0000.000
154A149LYS10.8830.93846.536-6.353-6.3530.0000.0000.0000.000
155A150VAL00.0110.01049.744-0.044-0.0440.0000.0000.0000.000
156A151ASP-1-0.810-0.91852.3745.5605.5600.0000.0000.0000.000
157A152ASN0-0.054-0.03554.073-0.003-0.0030.0000.0000.0000.000
158A153ALA00.0260.02852.2310.0600.0600.0000.0000.0000.000
159A154LEU0-0.011-0.01745.2850.0550.0550.0000.0000.0000.000
160A155GLN0-0.0230.00645.5790.0380.0380.0000.0000.0000.000
161A156SER0-0.013-0.02242.1230.0880.0880.0000.0000.0000.000
162A157GLY00.0080.00339.250-0.071-0.0710.0000.0000.0000.000
163A158ASN00.0190.01040.2140.1690.1690.0000.0000.0000.000
164A159SER0-0.015-0.00940.141-0.097-0.0970.0000.0000.0000.000
165A160GLN0-0.0080.00834.3310.0480.0480.0000.0000.0000.000
166A161GLU-1-0.937-0.97734.7838.5388.5380.0000.0000.0000.000
167A162SER0-0.030-0.01233.2430.4160.4160.0000.0000.0000.000
168A163VAL0-0.008-0.01632.023-0.261-0.2610.0000.0000.0000.000
169A164THR00.0120.01731.7490.2300.2300.0000.0000.0000.000
170A165GLU-1-0.955-0.99226.50211.87611.8760.0000.0000.0000.000
171A166GLN00.0050.02030.164-0.035-0.0350.0000.0000.0000.000
172A167ASP-1-0.808-0.89231.8098.8168.8160.0000.0000.0000.000
173A168SER0-0.044-0.04932.1330.1640.1640.0000.0000.0000.000
174A169LYS10.8780.94834.355-8.687-8.6870.0000.0000.0000.000
175A170ASP-1-0.835-0.91438.1707.8887.8880.0000.0000.0000.000
176A171SER0-0.062-0.03534.917-0.111-0.1110.0000.0000.0000.000
177A172THR0-0.071-0.02335.9890.1380.1380.0000.0000.0000.000
178A173TYR0-0.017-0.01931.0360.3920.3920.0000.0000.0000.000
179A174SER00.0540.02336.002-0.381-0.3810.0000.0000.0000.000
180A175LEU0-0.051-0.01335.9150.2600.2600.0000.0000.0000.000
181A176SER00.0100.00437.432-0.316-0.3160.0000.0000.0000.000
182A177SER00.0600.03537.8800.1960.1960.0000.0000.0000.000
183A178THR00.004-0.00839.813-0.256-0.2560.0000.0000.0000.000
184A179LEU0-0.014-0.00341.2070.1370.1370.0000.0000.0000.000
185A180THR0-0.007-0.01041.687-0.089-0.0890.0000.0000.0000.000
186A181LEU00.0020.00044.191-0.003-0.0030.0000.0000.0000.000
187A182SER00.0550.03547.481-0.058-0.0580.0000.0000.0000.000
188A183LYS10.9520.97949.474-5.787-5.7870.0000.0000.0000.000
189A184ALA00.0140.00252.808-0.094-0.0940.0000.0000.0000.000
190A185ASP-1-0.879-0.93450.4926.2176.2170.0000.0000.0000.000
191A186TYR0-0.016-0.00951.407-0.042-0.0420.0000.0000.0000.000
192A187GLU-1-0.826-0.92653.1535.5495.5490.0000.0000.0000.000
193A188LYS10.9160.96956.158-5.599-5.5990.0000.0000.0000.000
194A189HIS10.8500.93953.575-5.965-5.9650.0000.0000.0000.000
195A190LYS10.9521.00357.129-5.163-5.1630.0000.0000.0000.000
196A191VAL00.003-0.00255.1860.0280.0280.0000.0000.0000.000
197A192TYR00.013-0.01050.7750.1390.1390.0000.0000.0000.000
198A193ALA0-0.003-0.01151.233-0.034-0.0340.0000.0000.0000.000
199A194CYS0-0.0090.02246.0650.1020.1020.0000.0000.0000.000
200A195GLU-1-0.908-0.96047.3716.3326.3320.0000.0000.0000.000
201A196VAL00.016-0.00743.6240.2030.2030.0000.0000.0000.000
202A197THR0-0.014-0.00843.199-0.173-0.1730.0000.0000.0000.000
203A198HIS00.0230.00439.4110.0170.0170.0000.0000.0000.000
204A199GLN00.0150.00238.707-0.222-0.2220.0000.0000.0000.000
205A200GLY00.0130.00042.763-0.120-0.1200.0000.0000.0000.000
206A201LEU0-0.067-0.02144.909-0.142-0.1420.0000.0000.0000.000
207A202SER00.0030.00447.5500.0590.0590.0000.0000.0000.000
208A203SER00.0100.00450.225-0.079-0.0790.0000.0000.0000.000
209A204PRO0-0.002-0.00148.1000.0570.0570.0000.0000.0000.000
210A205VAL0-0.0090.00948.427-0.159-0.1590.0000.0000.0000.000
211A206THR00.0280.01149.0370.1430.1430.0000.0000.0000.000
212A207LYS10.8800.95350.079-6.267-6.2670.0000.0000.0000.000
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