FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VZ711

Calculation Name: 1XQ8-A-Other549

Preferred Name: Alpha-synuclein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XQ8

Chain ID: A

ChEMBL ID: CHEMBL6152

UniProt ID: P37840

Base Structure: SolutionNMR

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 140
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -624518.62358
FMO2-HF: Nuclear repulsion 573393.564486
FMO2-HF: Total energy -51125.059094
FMO2-MP2: Total energy -51272.491297


3D Structure Molmil
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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
68.20469.623-0.003-0.328-1.0890
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.889
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].
3A3VAL00.0530.0223.5311.8042.904-0.001-0.304-0.7960.000
5A5MET00.0310.0214.0405.2535.401-0.001-0.012-0.1350.000
6A6LYS10.9500.9794.06848.24748.418-0.001-0.012-0.1580.000
4A4PHE00.0530.0206.1863.2393.2390.0000.0000.0000.000
7A7GLY00.0280.0197.2413.6793.6790.0000.0000.0000.000
8A8LEU00.0170.0079.4472.4372.4370.0000.0000.0000.000
9A9SER0-0.006-0.0118.9562.1432.1430.0000.0000.0000.000
10A10LYS10.9640.98510.83122.19622.1960.0000.0000.0000.000
11A11ALA00.0080.00613.0561.6411.6410.0000.0000.0000.000
12A12LYS10.9470.96913.67921.72021.7200.0000.0000.0000.000
13A13GLU-1-0.926-0.95914.960-18.188-18.1880.0000.0000.0000.000
14A14GLY00.0190.00916.7251.0181.0180.0000.0000.0000.000
15A15VAL0-0.017-0.01418.7900.9230.9230.0000.0000.0000.000
16A16VAL0-0.0020.00419.1020.7560.7560.0000.0000.0000.000
17A17ALA00.0610.03421.1840.7120.7120.0000.0000.0000.000
18A18ALA0-0.017-0.00823.0510.6930.6930.0000.0000.0000.000
19A19ALA0-0.0050.01024.3180.6670.6670.0000.0000.0000.000
20A20GLU-1-0.947-0.97124.821-11.886-11.8860.0000.0000.0000.000
21A21LYS10.9850.98927.39610.86510.8650.0000.0000.0000.000
22A22THR0-0.033-0.03228.4810.5030.5030.0000.0000.0000.000
23A23LYS10.9380.96630.03910.53410.5340.0000.0000.0000.000
24A24GLN0-0.030-0.01331.7710.0420.0420.0000.0000.0000.000
25A25GLY00.0300.01633.3560.3060.3060.0000.0000.0000.000
26A26VAL0-0.011-0.02034.2540.3160.3160.0000.0000.0000.000
27A27ALA0-0.0130.00936.3380.2720.2720.0000.0000.0000.000
28A28GLU-1-0.880-0.93937.736-8.094-8.0940.0000.0000.0000.000
29A29ALA0-0.016-0.00839.2450.2630.2630.0000.0000.0000.000
30A30ALA00.0080.02040.6160.2400.2400.0000.0000.0000.000
31A31GLY00.004-0.00142.4780.2120.2120.0000.0000.0000.000
32A32LYS10.9560.96943.8527.1807.1800.0000.0000.0000.000
33A33THR0-0.040-0.04044.0930.1680.1680.0000.0000.0000.000
34A34LYS10.9120.96246.6646.5436.5430.0000.0000.0000.000
35A35GLU-1-0.873-0.92248.770-6.113-6.1130.0000.0000.0000.000
36A36GLY0-0.0030.00349.5810.1200.1200.0000.0000.0000.000
37A37VAL0-0.022-0.01151.0430.0930.0930.0000.0000.0000.000
38A38LEU0-0.049-0.00853.4020.1370.1370.0000.0000.0000.000
39A39TYR00.0180.00555.397-0.037-0.0370.0000.0000.0000.000
40A40VAL00.0100.00154.5070.0460.0460.0000.0000.0000.000
41A41GLY00.0290.01157.677-0.026-0.0260.0000.0000.0000.000
42A42SER00.0150.01557.7080.0310.0310.0000.0000.0000.000
43A43LYS10.8470.91750.7756.1416.1410.0000.0000.0000.000
44A44THR00.0460.01956.343-0.009-0.0090.0000.0000.0000.000
45A45LYS10.9480.95156.8255.4395.4390.0000.0000.0000.000
46A46GLU-1-0.887-0.93456.798-5.259-5.2590.0000.0000.0000.000
47A47GLY00.0570.02856.778-0.049-0.0490.0000.0000.0000.000
48A48VAL0-0.060-0.03251.436-0.119-0.1190.0000.0000.0000.000
49A49VAL00.0000.00252.483-0.127-0.1270.0000.0000.0000.000
50A50HIS00.0710.03653.732-0.039-0.0390.0000.0000.0000.000
51A51GLY00.0080.01651.376-0.078-0.0780.0000.0000.0000.000
52A52VAL0-0.029-0.02948.165-0.133-0.1330.0000.0000.0000.000
53A53ALA00.0090.01349.321-0.107-0.1070.0000.0000.0000.000
54A54THR00.026-0.00249.699-0.047-0.0470.0000.0000.0000.000
55A55VAL0-0.051-0.02744.376-0.117-0.1170.0000.0000.0000.000
56A56ALA0-0.0030.01545.983-0.168-0.1680.0000.0000.0000.000
57A57GLU-1-0.934-0.96047.745-6.197-6.1970.0000.0000.0000.000
58A58LYS11.0080.99444.5116.7296.7290.0000.0000.0000.000
59A59THR0-0.042-0.03241.896-0.226-0.2260.0000.0000.0000.000
60A60LYS10.9250.96542.4196.4556.4550.0000.0000.0000.000
61A61GLU-1-0.874-0.91543.305-7.097-7.0970.0000.0000.0000.000
62A62GLN0-0.036-0.00437.688-0.270-0.2700.0000.0000.0000.000
63A63VAL0-0.005-0.01938.431-0.215-0.2150.0000.0000.0000.000
64A64THR0-0.023-0.02339.112-0.123-0.1230.0000.0000.0000.000
65A65ASN0-0.045-0.02537.171-0.169-0.1690.0000.0000.0000.000
66A66VAL0-0.019-0.01533.157-0.240-0.2400.0000.0000.0000.000
67A67GLY00.0270.01834.437-0.243-0.2430.0000.0000.0000.000
68A68GLY00.0210.00935.738-0.081-0.0810.0000.0000.0000.000
69A69ALA00.0200.01630.772-0.216-0.2160.0000.0000.0000.000
70A70VAL00.0070.00330.677-0.365-0.3650.0000.0000.0000.000
71A71VAL00.0300.03031.305-0.223-0.2230.0000.0000.0000.000
72A72THR0-0.039-0.01629.609-0.224-0.2240.0000.0000.0000.000
73A73GLY00.0220.00726.943-0.349-0.3490.0000.0000.0000.000
74A74VAL00.005-0.00927.052-0.389-0.3890.0000.0000.0000.000
75A75THR0-0.030-0.02229.000-0.029-0.0290.0000.0000.0000.000
76A76ALA00.0100.00624.096-0.155-0.1550.0000.0000.0000.000
77A77VAL0-0.020-0.01524.156-0.469-0.4690.0000.0000.0000.000
78A78ALA00.0100.02225.457-0.193-0.1930.0000.0000.0000.000
79A79GLN0-0.005-0.00625.450-0.319-0.3190.0000.0000.0000.000
80A80LYS10.9790.98817.51816.26116.2610.0000.0000.0000.000
81A81THR0-0.060-0.04222.449-0.455-0.4550.0000.0000.0000.000
82A82VAL0-0.029-0.01725.123-0.023-0.0230.0000.0000.0000.000
83A83GLU-1-0.920-0.95520.595-14.689-14.6890.0000.0000.0000.000
84A84GLY0-0.014-0.00221.239-0.370-0.3700.0000.0000.0000.000
85A85ALA00.0140.00222.293-0.085-0.0850.0000.0000.0000.000
86A86GLY00.0230.01322.4940.2820.2820.0000.0000.0000.000
87A87SER0-0.036-0.01919.453-0.080-0.0800.0000.0000.0000.000
88A88ILE00.0200.00821.3060.1180.1180.0000.0000.0000.000
89A89ALA00.0030.01224.8870.3360.3360.0000.0000.0000.000
90A90ALA0-0.009-0.00421.4280.2720.2720.0000.0000.0000.000
91A91ALA0-0.040-0.01823.2260.1030.1030.0000.0000.0000.000
92A92THR0-0.041-0.02024.3930.4370.4370.0000.0000.0000.000
93A93GLY0-0.032-0.01126.7590.4200.4200.0000.0000.0000.000
94A94PHE0-0.010-0.00825.829-0.414-0.4140.0000.0000.0000.000
95A95VAL0-0.013-0.01121.9830.2090.2090.0000.0000.0000.000
96A96LYS10.9830.99325.3549.6329.6320.0000.0000.0000.000
97A97LYS10.9250.95427.26210.26310.2630.0000.0000.0000.000
98A98ASP-1-0.911-0.94629.536-8.650-8.6500.0000.0000.0000.000
99A99GLN0-0.023-0.02529.394-0.237-0.2370.0000.0000.0000.000
100A100LEU0-0.018-0.00333.8680.1860.1860.0000.0000.0000.000
101A101GLY00.0300.01136.519-0.067-0.0670.0000.0000.0000.000
102A102LYS10.8160.91039.2817.4137.4130.0000.0000.0000.000
103A103ASN00.0210.01140.9170.1310.1310.0000.0000.0000.000
104A104GLU-1-0.891-0.92744.550-6.953-6.9530.0000.0000.0000.000
105A105GLU-1-0.845-0.95546.074-5.998-5.9980.0000.0000.0000.000
106A106GLY0-0.084-0.01349.6970.0060.0060.0000.0000.0000.000
107A107ALA0-0.035-0.03151.2660.0940.0940.0000.0000.0000.000
108A108PRO0-0.043-0.00653.0200.0880.0880.0000.0000.0000.000
109A109GLN00.004-0.00355.9110.0770.0770.0000.0000.0000.000
110A110GLU-1-0.884-0.93459.474-4.994-4.9940.0000.0000.0000.000
111A111GLY0-0.033-0.02762.5510.0620.0620.0000.0000.0000.000
112A112ILE0-0.065-0.04063.363-0.058-0.0580.0000.0000.0000.000
113A113LEU0-0.023-0.00565.3830.0130.0130.0000.0000.0000.000
114A114GLU-1-0.964-0.99464.740-4.811-4.8110.0000.0000.0000.000
115A115ASP-1-0.953-0.98164.398-4.933-4.9330.0000.0000.0000.000
116A116MET0-0.031-0.00665.8930.0110.0110.0000.0000.0000.000
117A117PRO0-0.051-0.02968.7050.0480.0480.0000.0000.0000.000
118A118VAL0-0.0080.01970.1300.0470.0470.0000.0000.0000.000
119A119ASP-1-0.872-0.91872.987-4.196-4.1960.0000.0000.0000.000
120A120PRO0-0.094-0.07073.485-0.003-0.0030.0000.0000.0000.000
121A121ASP-1-0.945-0.96875.279-4.041-4.0410.0000.0000.0000.000
122A122ASN0-0.062-0.05278.695-0.006-0.0060.0000.0000.0000.000
123A123GLU-1-0.993-0.97873.810-4.300-4.3000.0000.0000.0000.000
124A124ALA00.0540.01276.277-0.026-0.0260.0000.0000.0000.000
125A125TYR0-0.093-0.06378.9560.0210.0210.0000.0000.0000.000
126A126GLU-1-0.881-0.93382.824-3.653-3.6530.0000.0000.0000.000
127A127MET00.0000.02179.5580.0110.0110.0000.0000.0000.000
128A128PRO0-0.042-0.03477.507-0.008-0.0080.0000.0000.0000.000
129A129SER0-0.008-0.00779.9010.0170.0170.0000.0000.0000.000
130A130GLU-1-0.991-0.98782.530-3.736-3.7360.0000.0000.0000.000
131A131GLU-1-0.979-0.99884.355-3.614-3.6140.0000.0000.0000.000
132A132GLY00.0330.02287.4230.0500.0500.0000.0000.0000.000
133A133TYR0-0.088-0.04187.5990.0030.0030.0000.0000.0000.000
134A134GLN0-0.067-0.04688.8810.0190.0190.0000.0000.0000.000
135A135ASP-1-0.905-0.93889.045-3.651-3.6510.0000.0000.0000.000
136A136TYR0-0.0070.00890.9180.0030.0030.0000.0000.0000.000
137A137GLU-1-0.975-0.99294.616-3.317-3.3170.0000.0000.0000.000
138A138PRO0-0.104-0.04897.3840.0290.0290.0000.0000.0000.000
139A139GLU-1-0.957-0.99898.594-3.160-3.1600.0000.0000.0000.000
140A140ALA-1-0.967-0.96597.608-3.305-3.3050.0000.0000.0000.000