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: PZNNN

Calculation Name: 4PQD-A-Xray29

Preferred Name: Beta amyloid A4 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4PQD

Chain ID: A

ChEMBL ID: CHEMBL2487

UniProt ID: P05067

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1006449.128352
FMO2-HF: Nuclear repulsion 955900.628913
FMO2-HF: Total energy -50548.499438
FMO2-MP2: Total energy -50687.180663


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:22:THR)


Summations of interaction energy for fragment #1(A:22:THR)
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.
-10.912-9.9948.762-4.571-5.110.008
Interaction energy analysis for fragmet #1(A:22:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.034
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].
3A24GLY00.0100.0083.624-0.7970.630-0.008-0.510-0.9090.001
4A25ASN0-0.002-0.0246.3420.1330.1330.0000.0000.0000.000
5A26ALA00.0420.0189.551-0.012-0.0120.0000.0000.0000.000
6A27GLY00.0390.03111.820-0.003-0.0030.0000.0000.0000.000
7A28LEU0-0.020-0.0049.6400.0020.0020.0000.0000.0000.000
8A29LEU0-0.056-0.00612.791-0.004-0.0040.0000.0000.0000.000
9A30ALA0-0.021-0.00515.6190.0080.0080.0000.0000.0000.000
10A31GLU-1-0.804-0.87919.3460.0440.0440.0000.0000.0000.000
11A32PRO00.0030.01920.986-0.005-0.0050.0000.0000.0000.000
12A33GLN00.0380.02023.7260.0010.0010.0000.0000.0000.000
13A34ILE00.0280.01427.311-0.002-0.0020.0000.0000.0000.000
14A35ALA0-0.001-0.00430.5310.0010.0010.0000.0000.0000.000
15A36MET0-0.0200.01233.339-0.001-0.0010.0000.0000.0000.000
16A37PHE00.0430.01636.9350.0000.0000.0000.0000.0000.000
17A62CYS0-0.006-0.00439.3330.0000.0000.0000.0000.0000.000
18A39GLY00.0230.01943.0160.0000.0000.0000.0000.0000.000
19A40ARG10.8420.92239.217-0.009-0.0090.0000.0000.0000.000
20A41LEU0-0.057-0.00336.5010.0010.0010.0000.0000.0000.000
21A42ASN00.0810.04334.318-0.001-0.0010.0000.0000.0000.000
22A43MET0-0.0590.03731.246-0.001-0.0010.0000.0000.0000.000
23A44HIS00.0430.02425.7570.0010.0010.0000.0000.0000.000
24A45MET0-0.0300.02422.669-0.003-0.0030.0000.0000.0000.000
25A46ASN00.0270.03221.0190.0010.0010.0000.0000.0000.000
26A47VAL00.0490.01517.197-0.003-0.0030.0000.0000.0000.000
27A48GLN00.0200.02115.4910.0070.0070.0000.0000.0000.000
28A49ASN0-0.035-0.01816.913-0.006-0.0060.0000.0000.0000.000
29A50GLY00.0980.06319.4010.0020.0020.0000.0000.0000.000
30A51LYS10.8730.94221.305-0.002-0.0020.0000.0000.0000.000
31A52TRP00.009-0.00124.6860.0000.0000.0000.0000.0000.000
32A53ASP-1-0.722-0.82725.8660.0010.0010.0000.0000.0000.000
33A54SER00.032-0.02228.8370.0020.0020.0000.0000.0000.000
34A55ASP-1-0.690-0.81230.9700.0120.0120.0000.0000.0000.000
35A56PRO00.0600.03929.080-0.002-0.0020.0000.0000.0000.000
36A57SER00.0090.02031.544-0.001-0.0010.0000.0000.0000.000
37A58GLY0-0.012-0.00334.959-0.001-0.0010.0000.0000.0000.000
38A59THR0-0.099-0.07536.7710.0000.0000.0000.0000.0000.000
39A60LYS10.9691.00636.086-0.013-0.0130.0000.0000.0000.000
40A61THR0-0.040-0.01837.7540.0000.0000.0000.0000.0000.000
41A63ILE0-0.044-0.02436.626-0.001-0.0010.0000.0000.0000.000
42A64ASP-1-0.900-0.95240.4620.0140.0140.0000.0000.0000.000
43A65THR00.0260.01441.3690.0000.0000.0000.0000.0000.000
44A66LYS10.9730.98435.907-0.025-0.0250.0000.0000.0000.000
45A67GLU-1-0.863-0.93837.1270.0200.0200.0000.0000.0000.000
46A68GLY00.0630.03437.3450.0010.0010.0000.0000.0000.000
47A69ILE00.003-0.00433.7520.0000.0000.0000.0000.0000.000
48A70LEU0-0.0250.00031.5490.0010.0010.0000.0000.0000.000
49A71GLN00.0130.01532.4250.0000.0000.0000.0000.0000.000
50A72TYR0-0.020-0.04032.3720.0000.0000.0000.0000.0000.000
51A117CYS0-0.069-0.03626.166-0.002-0.0020.0000.0000.0000.000
52A74GLN0-0.0030.00628.387-0.002-0.0020.0000.0000.0000.000
53A75GLU-1-0.885-0.93128.9970.0160.0160.0000.0000.0000.000
54A76VAL0-0.027-0.01726.720-0.001-0.0010.0000.0000.0000.000
55A77TYR0-0.004-0.02923.259-0.001-0.0010.0000.0000.0000.000
56A78PRO00.0730.04625.3110.0050.0050.0000.0000.0000.000
57A79GLU-1-0.825-0.89321.0590.0390.0390.0000.0000.0000.000
58A80LEU0-0.021-0.01519.6060.0080.0080.0000.0000.0000.000
59A81GLN00.0750.09222.6100.0070.0070.0000.0000.0000.000
60A82ILE0-0.010-0.00124.5940.0010.0010.0000.0000.0000.000
61A83THR00.0200.02227.136-0.003-0.0030.0000.0000.0000.000
62A84ASN00.0560.02829.651-0.005-0.0050.0000.0000.0000.000
63A85VAL00.0160.02230.0260.0010.0010.0000.0000.0000.000
64A86VAL0-0.0040.00630.442-0.001-0.0010.0000.0000.0000.000
65A87GLU-1-0.842-0.89331.9130.0200.0200.0000.0000.0000.000
66A88ALA0-0.0080.00130.0770.0020.0020.0000.0000.0000.000
67A89ASN00.0330.00229.695-0.002-0.0020.0000.0000.0000.000
68A90GLN0-0.0070.03030.283-0.003-0.0030.0000.0000.0000.000
69A91PRO00.0280.03232.6140.0000.0000.0000.0000.0000.000
70A92VAL00.0120.00329.6560.0000.0000.0000.0000.0000.000
71A93THR00.017-0.00232.614-0.001-0.0010.0000.0000.0000.000
72A94ILE0-0.0300.00831.1210.0000.0000.0000.0000.0000.000
73A95GLN00.012-0.01032.588-0.001-0.0010.0000.0000.0000.000
74A96ASN0-0.018-0.02031.3570.0000.0000.0000.0000.0000.000
75A97TRP00.0490.04234.883-0.001-0.0010.0000.0000.0000.000
76A105CYS0-0.0440.00236.1300.0000.0000.0000.0000.0000.000
77A99LYS10.9060.95638.403-0.005-0.0050.0000.0000.0000.000
78A100ARG11.0000.97739.832-0.007-0.0070.0000.0000.0000.000
79A101GLY0-0.028-0.01239.256-0.001-0.0010.0000.0000.0000.000
80A102ARG10.8950.93133.183-0.005-0.0050.0000.0000.0000.000
81A103LYS10.9200.96637.294-0.004-0.0040.0000.0000.0000.000
82A104GLN00.016-0.01540.2160.0010.0010.0000.0000.0000.000
83A106LYS10.9380.97238.539-0.006-0.0060.0000.0000.0000.000
84A107THR00.0740.04335.6460.0000.0000.0000.0000.0000.000
85A108HIS0-0.034-0.01137.2800.0000.0000.0000.0000.0000.000
86A109PRO00.0330.02936.5780.0000.0000.0000.0000.0000.000
87A110HIS0-0.076-0.01637.112-0.001-0.0010.0000.0000.0000.000
88A111PHE0-0.007-0.00136.3770.0000.0000.0000.0000.0000.000
89A112VAL00.0140.01734.818-0.001-0.0010.0000.0000.0000.000
90A113ILE00.0330.01334.9420.0010.0010.0000.0000.0000.000
91A114PRO0-0.0250.01330.597-0.001-0.0010.0000.0000.0000.000
92A115TYR00.023-0.01732.0170.0010.0010.0000.0000.0000.000
93A116ARG10.8180.89525.179-0.039-0.0390.0000.0000.0000.000
94A118LEU0-0.016-0.01425.5710.0030.0030.0000.0000.0000.000
95A119VAL00.0540.01621.276-0.003-0.0030.0000.0000.0000.000
96A120GLY0-0.029-0.00324.452-0.001-0.0010.0000.0000.0000.000
97A121GLU-1-0.947-0.97523.6100.0910.0910.0000.0000.0000.000
98A122PHE0-0.042-0.03025.191-0.006-0.0060.0000.0000.0000.000
99A123VAL00.0100.00626.4270.0060.0060.0000.0000.0000.000
100A124SER0-0.069-0.04028.979-0.003-0.0030.0000.0000.0000.000
101A125ASP-1-0.903-0.94531.7350.0380.0380.0000.0000.0000.000
102A126ALA-1-0.983-0.98735.4050.0280.0280.0000.0000.0000.000
103A201HOH0-0.003-0.01231.4580.0000.0000.0000.0000.0000.000
104A202HOH0-0.043-0.02832.8560.0000.0000.0000.0000.0000.000
105A203HOH00.001-0.01138.0520.0000.0000.0000.0000.0000.000
106A204HOH00.0060.00526.5390.0000.0000.0000.0000.0000.000
107A205HOH00.001-0.00535.5610.0000.0000.0000.0000.0000.000
108A206HOH0-0.009-0.03135.0320.0000.0000.0000.0000.0000.000
109A207HOH0-0.038-0.02838.7200.0000.0000.0000.0000.0000.000
110A208HOH0-0.056-0.03819.584-0.001-0.0010.0000.0000.0000.000
111A209HOH00.016-0.00421.2310.0020.0020.0000.0000.0000.000
112A210HOH0-0.007-0.01225.6970.0010.0010.0000.0000.0000.000
113A211HOH0-0.028-0.01934.9290.0000.0000.0000.0000.0000.000
114A212HOH0-0.046-0.03636.9070.0000.0000.0000.0000.0000.000
115A213HOH0-0.004-0.00730.3510.0000.0000.0000.0000.0000.000
116A214HOH0-0.047-0.02334.417-0.001-0.0010.0000.0000.0000.000
117A215HOH0-0.038-0.02833.5870.0000.0000.0000.0000.0000.000
118A216HOH00.0110.00121.4230.0000.0000.0000.0000.0000.000
119A217HOH00.0580.06940.6330.0000.0000.0000.0000.0000.000
120A218HOH00.0090.00336.5190.0010.0010.0000.0000.0000.000
121A219HOH0-0.012-0.02323.015-0.001-0.0010.0000.0000.0000.000
122A220HOH0-0.030-0.01544.3700.0000.0000.0000.0000.0000.000
123A221HOH0-0.042-0.06841.0750.0000.0000.0000.0000.0000.000
124A222HOH00.0010.02739.3470.0000.0000.0000.0000.0000.000
125A223HOH0-0.049-0.02522.134-0.002-0.0020.0000.0000.0000.000
126A224HOH00.0380.02326.815-0.001-0.0010.0000.0000.0000.000
127A225HOH0-0.068-0.04537.3130.0000.0000.0000.0000.0000.000
128A226HOH0-0.047-0.03736.4550.0000.0000.0000.0000.0000.000
129A227HOH00.0180.02724.6290.0000.0000.0000.0000.0000.000
130A228HOH00.0150.01427.5020.0000.0000.0000.0000.0000.000
131A229HOH0-0.028-0.03938.1720.0000.0000.0000.0000.0000.000
132A230HOH00.0210.01919.6510.0030.0030.0000.0000.0000.000
133A231HOH0-0.010-0.01833.0410.0000.0000.0000.0000.0000.000
134A234HOH0-0.041-0.02626.242-0.001-0.0010.0000.0000.0000.000
135A235HOH0-0.013-0.00541.8030.0000.0000.0000.0000.0000.000
136A236HOH0-0.008-0.00934.4620.0000.0000.0000.0000.0000.000
137A237HOH00.002-0.00230.3220.0010.0010.0000.0000.0000.000
138A238HOH0-0.008-0.00321.5160.0010.0010.0000.0000.0000.000
139A239HOH00.007-0.00630.1800.0000.0000.0000.0000.0000.000
140A241HOH0-0.015-0.02043.1810.0000.0000.0000.0000.0000.000
141A242HOH00.0270.01728.185-0.001-0.0010.0000.0000.0000.000
142A243HOH00.0370.02143.7820.0000.0000.0000.0000.0000.000
143A244HOH0-0.018-0.01428.9340.0010.0010.0000.0000.0000.000
144A245HOH0-0.034-0.02229.8010.0000.0000.0000.0000.0000.000
145A247HOH0-0.014-0.01330.388-0.001-0.0010.0000.0000.0000.000
146A248HOH0-0.039-0.02616.8830.0020.0020.0000.0000.0000.000
147A249HOH0-0.016-0.01742.5560.0000.0000.0000.0000.0000.000
148A250HOH0-0.060-0.04832.1850.0000.0000.0000.0000.0000.000
149A251HOH00.0160.01342.3480.0000.0000.0000.0000.0000.000
150A252HOH0-0.017-0.01325.229-0.001-0.0010.0000.0000.0000.000
151A253HOH0-0.014-0.01226.2000.0000.0000.0000.0000.0000.000
152A255HOH0-0.028-0.01734.3250.0000.0000.0000.0000.0000.000
153A256HOH00.0210.01839.3100.0000.0000.0000.0000.0000.000
154A257HOH0-0.030-0.03334.4830.0000.0000.0000.0000.0000.000
155A258HOH0-0.024-0.02331.0680.0010.0010.0000.0000.0000.000
156A259HOH0-0.020-0.01129.0650.0000.0000.0000.0000.0000.000
157A260HOH0-0.037-0.02722.5160.0010.0010.0000.0000.0000.000
158A261HOH00.014-0.00538.4370.0000.0000.0000.0000.0000.000
159A262HOH0-0.026-0.01137.6470.0000.0000.0000.0000.0000.000
160A263HOH00.0120.01033.4770.0000.0000.0000.0000.0000.000
161A264HOH0-0.060-0.04814.455-0.008-0.0080.0000.0000.0000.000
162A266HOH00.0310.02238.2710.0000.0000.0000.0000.0000.000
163A267HOH00.0030.00229.202-0.001-0.0010.0000.0000.0000.000
164A270HOH0-0.031-0.03329.9680.0000.0000.0000.0000.0000.000
165A271HOH0-0.036-0.0262.069-5.671-6.5764.886-1.986-1.9950.014
166A272HOH0-0.083-0.06425.3010.0000.0000.0000.0000.0000.000
167A273HOH00.0070.01933.5820.0000.0000.0000.0000.0000.000
168A276HOH00.0060.01328.3260.0000.0000.0000.0000.0000.000
169A279HOH0-0.047-0.02824.6280.0000.0000.0000.0000.0000.000
170A280HOH00.0300.01827.595-0.001-0.0010.0000.0000.0000.000
171A281HOH00.0020.01924.756-0.001-0.0010.0000.0000.0000.000
172A287HOH00.0270.0188.324-0.021-0.0210.0000.0000.0000.000
173A290HOH00.0460.03238.6630.0000.0000.0000.0000.0000.000
174A294HOH00.0320.02129.8570.0000.0000.0000.0000.0000.000
175A299HOH0-0.024-0.02033.3150.0000.0000.0000.0000.0000.000
176A302HOH0-0.002-0.00834.7210.0000.0000.0000.0000.0000.000
177A303HOH00.0380.02828.3970.0000.0000.0000.0000.0000.000
178A309HOH0-0.025-0.00622.571-0.001-0.0010.0000.0000.0000.000
179A313HOH0-0.052-0.04523.331-0.003-0.0030.0000.0000.0000.000
180A315HOH0-0.061-0.05141.8590.0000.0000.0000.0000.0000.000
181A316HOH0-0.033-0.02333.859-0.001-0.0010.0000.0000.0000.000
182A318HOH00.0350.02142.2450.0000.0000.0000.0000.0000.000
183A319HOH0-0.0010.0082.118-4.734-4.3383.884-2.075-2.206-0.007
184A320HOH0-0.011-0.01927.986-0.001-0.0010.0000.0000.0000.000
185A321HOH0-0.043-0.02317.1130.0020.0020.0000.0000.0000.000
186A322HOH00.0300.02840.6000.0000.0000.0000.0000.0000.000
187A323HOH0-0.036-0.04335.5400.0000.0000.0000.0000.0000.000
188A327HOH0-0.043-0.03519.2920.0000.0000.0000.0000.0000.000
189A329HOH00.0140.01243.1390.0000.0000.0000.0000.0000.000
190A330HOH0-0.050-0.03240.5040.0000.0000.0000.0000.0000.000
191A331HOH0-0.065-0.09124.3020.0000.0000.0000.0000.0000.000
192A333HOH0-0.002-0.00140.4610.0000.0000.0000.0000.0000.000
193A334HOH00.0470.03443.3900.0000.0000.0000.0000.0000.000
194A336HOH0-0.020-0.01444.7880.0000.0000.0000.0000.0000.000
195A346HOH00.0170.01320.9520.0010.0010.0000.0000.0000.000
196A349HOH00.001-0.01043.3280.0000.0000.0000.0000.0000.000
197A350HOH0-0.047-0.04623.1490.0030.0030.0000.0000.0000.000
198A355HOH0-0.018-0.03024.7890.0000.0000.0000.0000.0000.000
199A356HOH00.0360.03322.486-0.001-0.0010.0000.0000.0000.000