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: GVQL1

Calculation Name: 1K3Y-A-Xray547

Preferred Name: Glutathione S-transferase A1

Target Type: SINGLE PROTEIN

Ligand Name: s-hexylglutathione

Ligand 3-letter code: GTX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K3Y

Chain ID: A

ChEMBL ID: CHEMBL3409

UniProt ID: P08263

Base Structure: X-ray

Registration Date: 2025-10-05

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2796844.019235
FMO2-HF: Nuclear repulsion 2707904.944939
FMO2-HF: Total energy -88939.074296
FMO2-MP2: Total energy -89199.341654


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
41.15443.0840-1.088-0.842-0.005
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.904
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].
3A4LYS10.8560.9383.28923.16125.0120.001-1.083-0.770-0.005
60A61ASP-1-0.797-0.8584.434-44.894-44.815-0.001-0.005-0.0720.000
4A5PRO0-0.004-0.0016.1350.3290.3290.0000.0000.0000.000
5A6LYS10.8820.9517.74029.44829.4480.0000.0000.0000.000
6A7LEU0-0.002-0.00410.8250.6360.6360.0000.0000.0000.000
7A8HIS0-0.021-0.03312.4362.0852.0850.0000.0000.0000.000
8A9TYR00.039-0.00116.9600.6480.6480.0000.0000.0000.000
9A10PHE00.0720.06320.403-0.215-0.2150.0000.0000.0000.000
10A11ASN0-0.034-0.02422.914-0.670-0.6700.0000.0000.0000.000
11A12ALA00.0340.02124.2020.5400.5400.0000.0000.0000.000
12A13ARG10.7500.85323.84110.51310.5130.0000.0000.0000.000
13A14GLY00.0280.01023.838-0.552-0.5520.0000.0000.0000.000
14A15ARG10.8150.85623.71811.40411.4040.0000.0000.0000.000
15A16MET00.0110.01716.944-0.722-0.7220.0000.0000.0000.000
16A17GLU-1-0.729-0.85619.581-14.736-14.7360.0000.0000.0000.000
17A18SER00.0460.03420.851-0.683-0.6830.0000.0000.0000.000
18A19THR0-0.027-0.02815.071-0.238-0.2380.0000.0000.0000.000
19A20ARG10.7280.84416.34914.37814.3780.0000.0000.0000.000
20A21TRP00.0080.00317.652-0.478-0.4780.0000.0000.0000.000
21A22LEU0-0.037-0.01316.435-0.183-0.1830.0000.0000.0000.000
22A23LEU0-0.013-0.00711.098-0.619-0.6190.0000.0000.0000.000
23A24ALA00.0290.02214.525-0.599-0.5990.0000.0000.0000.000
24A25ALA00.002-0.00716.6420.1730.1730.0000.0000.0000.000
25A26ALA0-0.018-0.00414.1820.5190.5190.0000.0000.0000.000
26A27GLY0-0.025-0.01214.263-0.643-0.6430.0000.0000.0000.000
27A28VAL0-0.064-0.0218.879-1.359-1.3590.0000.0000.0000.000
28A29GLU-1-0.883-0.9429.647-26.226-26.2260.0000.0000.0000.000
29A30PHE0-0.036-0.0299.407-2.984-2.9840.0000.0000.0000.000
30A31GLU-1-0.843-0.92410.195-28.545-28.5450.0000.0000.0000.000
31A32GLU-1-0.769-0.87312.487-16.848-16.8480.0000.0000.0000.000
32A33LYS10.9190.96515.44517.67617.6760.0000.0000.0000.000
33A34PHE0-0.037-0.02917.2200.3550.3550.0000.0000.0000.000
34A35ILE0-0.011-0.00220.5850.2120.2120.0000.0000.0000.000
35A36LYS10.8170.88622.90912.35412.3540.0000.0000.0000.000
36A37SER0-0.0020.00626.2840.5300.5300.0000.0000.0000.000
37A38ALA00.0520.02226.815-0.410-0.4100.0000.0000.0000.000
38A39GLU-1-0.860-0.94027.444-10.547-10.5470.0000.0000.0000.000
39A40ASP-1-0.825-0.90722.900-13.237-13.2370.0000.0000.0000.000
40A41LEU0-0.037-0.01922.522-0.756-0.7560.0000.0000.0000.000
41A42ASP-1-0.777-0.86323.555-11.232-11.2320.0000.0000.0000.000
42A43LYS10.7790.88019.76314.72014.7200.0000.0000.0000.000
43A44LEU0-0.016-0.01317.332-0.594-0.5940.0000.0000.0000.000
44A45ARG10.8150.89320.09311.27111.2710.0000.0000.0000.000
45A46ASN0-0.001-0.00422.6420.0210.0210.0000.0000.0000.000
46A47ASP-1-0.842-0.88717.932-15.407-15.4070.0000.0000.0000.000
47A48GLY00.0050.00518.482-0.638-0.6380.0000.0000.0000.000
48A49TYR0-0.053-0.03814.331-0.875-0.8750.0000.0000.0000.000
49A50LEU0-0.0110.00216.952-0.759-0.7590.0000.0000.0000.000
50A51MET00.0170.01719.2680.5250.5250.0000.0000.0000.000
51A52PHE00.004-0.01921.0520.4940.4940.0000.0000.0000.000
52A53GLN00.0220.01623.2890.3810.3810.0000.0000.0000.000
53A54GLN00.0030.00623.0750.1350.1350.0000.0000.0000.000
54A55VAL00.0270.02519.413-0.730-0.7300.0000.0000.0000.000
55A56PRO0-0.050-0.04518.8680.6730.6730.0000.0000.0000.000
56A57MET0-0.0260.01014.222-0.319-0.3190.0000.0000.0000.000
57A58VAL0-0.008-0.01010.9610.0410.0410.0000.0000.0000.000
58A59GLU-1-0.801-0.8738.584-26.668-26.6680.0000.0000.0000.000
59A60ILE00.009-0.0146.607-1.643-1.6430.0000.0000.0000.000
61A62GLY00.0320.0255.0122.5142.5140.0000.0000.0000.000
62A63MET0-0.045-0.0035.7555.3495.3490.0000.0000.0000.000
63A64LYS10.8750.9299.46023.11223.1120.0000.0000.0000.000
64A65LEU00.0070.01312.2341.4731.4730.0000.0000.0000.000
65A66VAL00.0330.00614.7250.0900.0900.0000.0000.0000.000
66A67GLN00.0400.01218.2210.0060.0060.0000.0000.0000.000
67A68THR00.0250.01019.438-0.466-0.4660.0000.0000.0000.000
68A69ARG10.8760.90319.62211.15811.1580.0000.0000.0000.000
69A70ALA00.0200.02218.260-0.277-0.2770.0000.0000.0000.000
70A71ILE0-0.012-0.00214.444-0.895-0.8950.0000.0000.0000.000
71A72LEU0-0.007-0.00215.193-1.066-1.0660.0000.0000.0000.000
72A73ASN00.0160.01617.394-0.112-0.1120.0000.0000.0000.000
73A74TYR0-0.035-0.0408.8211.3741.3740.0000.0000.0000.000
74A75ILE00.0230.00511.712-0.998-0.9980.0000.0000.0000.000
75A76ALA00.007-0.00513.567-0.302-0.3020.0000.0000.0000.000
76A77SER0-0.065-0.02715.4900.5020.5020.0000.0000.0000.000
77A78LYS10.8420.9166.43340.76640.7660.0000.0000.0000.000
78A79TYR00.008-0.0058.421-2.222-2.2220.0000.0000.0000.000
79A80ASN0-0.032-0.01014.1271.3761.3760.0000.0000.0000.000
80A81LEU00.0020.01416.8811.0831.0830.0000.0000.0000.000
81A82TYR0-0.075-0.08418.9490.5000.5000.0000.0000.0000.000
82A83GLY00.0300.01621.1520.5450.5450.0000.0000.0000.000
83A84LYS10.8480.91222.51910.42210.4220.0000.0000.0000.000
84A85ASP-1-0.839-0.91924.386-11.060-11.0600.0000.0000.0000.000
85A86ILE00.013-0.00726.366-0.203-0.2030.0000.0000.0000.000
86A87LYS10.9490.97728.0159.3079.3070.0000.0000.0000.000
87A88GLU-1-0.799-0.89626.851-11.549-11.5490.0000.0000.0000.000
88A89ARG10.9770.99622.32913.29813.2980.0000.0000.0000.000
89A90ALA00.0170.01426.4270.0290.0290.0000.0000.0000.000
90A91LEU0-0.031-0.01329.8320.2020.2020.0000.0000.0000.000
91A92ILE00.001-0.00123.8600.0010.0010.0000.0000.0000.000
92A93ASP-1-0.811-0.89524.926-12.765-12.7650.0000.0000.0000.000
93A94MET0-0.029-0.01127.4050.2620.2620.0000.0000.0000.000
94A95TYR0-0.027-0.02629.1650.3330.3330.0000.0000.0000.000
95A96ILE00.008-0.00723.8420.0700.0700.0000.0000.0000.000
96A97GLU-1-0.800-0.85626.660-11.721-11.7210.0000.0000.0000.000
97A98GLY00.0130.01829.5370.2110.2110.0000.0000.0000.000
98A99ILE0-0.052-0.03627.9210.2110.2110.0000.0000.0000.000
99A100ALA0-0.0070.00027.4840.0090.0090.0000.0000.0000.000
100A101ASP-1-0.891-0.93629.217-9.395-9.3950.0000.0000.0000.000
101A102LEU0-0.034-0.02532.9050.1770.1770.0000.0000.0000.000
102A103GLY00.0270.00629.9300.1090.1090.0000.0000.0000.000
103A104GLU-1-0.762-0.84029.754-10.706-10.7060.0000.0000.0000.000
104A105MET0-0.086-0.04931.8270.2400.2400.0000.0000.0000.000
105A106ILE0-0.017-0.01033.1400.2330.2330.0000.0000.0000.000
106A107LEU0-0.047-0.01928.1200.0530.0530.0000.0000.0000.000
107A108LEU00.010-0.00532.0040.0060.0060.0000.0000.0000.000
108A109LEU0-0.0200.01034.7080.2590.2590.0000.0000.0000.000
109A110PRO0-0.047-0.03234.6660.2450.2450.0000.0000.0000.000
110A111VAL0-0.009-0.00334.8970.0140.0140.0000.0000.0000.000
111A112CYS0-0.061-0.00937.7950.1200.1200.0000.0000.0000.000
112A113PRO00.0540.02740.8510.0050.0050.0000.0000.0000.000
113A114PRO00.001-0.01744.1950.0230.0230.0000.0000.0000.000
114A115GLU-1-0.904-0.95445.897-6.222-6.2220.0000.0000.0000.000
115A116GLU-1-0.930-0.95445.021-7.054-7.0540.0000.0000.0000.000
116A117LYS10.8550.92042.2257.2337.2330.0000.0000.0000.000
117A118ASP-1-0.803-0.89343.951-6.955-6.9550.0000.0000.0000.000
118A119ALA00.0270.00946.305-0.039-0.0390.0000.0000.0000.000
119A120LYS10.9000.94540.5197.6877.6870.0000.0000.0000.000
120A121LEU00.0290.01540.810-0.179-0.1790.0000.0000.0000.000
121A122ALA00.003-0.00142.836-0.075-0.0750.0000.0000.0000.000
122A123LEU0-0.012-0.01543.085-0.038-0.0380.0000.0000.0000.000
123A124ILE00.0080.00738.006-0.084-0.0840.0000.0000.0000.000
124A125LYS10.8590.91240.8117.2637.2630.0000.0000.0000.000
125A126GLU-1-0.839-0.89742.794-7.137-7.1370.0000.0000.0000.000
126A127LYS10.9000.94940.3077.3867.3860.0000.0000.0000.000
127A128ILE00.0090.01337.616-0.111-0.1110.0000.0000.0000.000
128A129LYS10.9700.98639.9066.8476.8470.0000.0000.0000.000
129A130ASN0-0.021-0.03343.0770.0770.0770.0000.0000.0000.000
130A131ARG10.9030.95839.4337.8067.8060.0000.0000.0000.000
131A132TYR00.000-0.01035.5280.0620.0620.0000.0000.0000.000
132A133PHE00.0090.00335.200-0.190-0.1900.0000.0000.0000.000
133A134PRO00.0190.00838.651-0.060-0.0600.0000.0000.0000.000
134A135ALA0-0.0240.00237.5280.0300.0300.0000.0000.0000.000
135A136PHE00.0190.00332.655-0.060-0.0600.0000.0000.0000.000
136A137GLU-1-0.759-0.87636.111-8.203-8.2030.0000.0000.0000.000
137A138LYS10.9400.96738.8157.6007.6000.0000.0000.0000.000
138A139VAL0-0.0140.00433.4810.0700.0700.0000.0000.0000.000
139A140LEU00.0080.02033.0180.0040.0040.0000.0000.0000.000
140A141LYS10.9470.96536.7347.1917.1910.0000.0000.0000.000
141A142SER0-0.128-0.06437.8760.1410.1410.0000.0000.0000.000
142A143HIS0-0.008-0.01233.3540.3060.3060.0000.0000.0000.000
143A144GLY00.0060.01438.2960.0470.0470.0000.0000.0000.000
144A145GLN0-0.031-0.01433.009-0.271-0.2710.0000.0000.0000.000
145A146ASP-1-0.863-0.94631.260-9.533-9.5330.0000.0000.0000.000
146A147TYR0-0.026-0.01426.301-0.253-0.2530.0000.0000.0000.000
147A148LEU0-0.001-0.01028.6420.3360.3360.0000.0000.0000.000
148A149VAL0-0.001-0.00627.7890.3430.3430.0000.0000.0000.000
149A150GLY00.0320.01628.124-0.250-0.2500.0000.0000.0000.000
150A151ASN0-0.026-0.00528.760-0.102-0.1020.0000.0000.0000.000
151A152LYS10.9080.95223.01913.19113.1910.0000.0000.0000.000
152A153LEU00.0140.01420.9310.1020.1020.0000.0000.0000.000
153A154SER0-0.021-0.02322.330-0.476-0.4760.0000.0000.0000.000
154A155ARG10.8960.92320.35514.81914.8190.0000.0000.0000.000
155A156ALA00.0100.01522.0430.2210.2210.0000.0000.0000.000
156A157ASP-1-0.770-0.87125.446-11.451-11.4510.0000.0000.0000.000
157A158ILE0-0.017-0.00120.9330.2750.2750.0000.0000.0000.000
158A159HIS00.0490.01120.556-0.018-0.0180.0000.0000.0000.000
159A160LEU00.0160.02225.3150.3880.3880.0000.0000.0000.000
160A161VAL0-0.012-0.01827.4230.3750.3750.0000.0000.0000.000
161A162GLU-1-0.800-0.88624.006-13.024-13.0240.0000.0000.0000.000
162A163LEU00.0010.00127.2340.3260.3260.0000.0000.0000.000
163A164LEU0-0.036-0.02430.2490.4130.4130.0000.0000.0000.000
164A165TYR0-0.043-0.03929.0210.3790.3790.0000.0000.0000.000
165A166TYR0-0.041-0.04825.4440.2590.2590.0000.0000.0000.000
166A167VAL0-0.003-0.00732.3720.3010.3010.0000.0000.0000.000
167A168GLU-1-0.891-0.93934.544-8.941-8.9410.0000.0000.0000.000
168A169GLU-1-0.799-0.87031.744-10.030-10.0300.0000.0000.0000.000
169A170LEU0-0.0370.00536.1900.2200.2200.0000.0000.0000.000
170A171ASP-1-0.779-0.87638.365-7.086-7.0860.0000.0000.0000.000
171A172SER00.0370.03139.6370.0150.0150.0000.0000.0000.000
172A173SER0-0.053-0.04440.6080.0470.0470.0000.0000.0000.000
173A174LEU0-0.0070.00640.3230.1040.1040.0000.0000.0000.000
174A175ILE00.0260.00736.1970.0240.0240.0000.0000.0000.000
175A176SER0-0.040-0.03240.2450.0580.0580.0000.0000.0000.000
176A177SER0-0.020-0.02443.4730.0550.0550.0000.0000.0000.000
177A178PHE0-0.0060.01239.7580.0830.0830.0000.0000.0000.000
178A179PRO00.0090.00439.800-0.204-0.2040.0000.0000.0000.000
179A180LEU00.0110.00037.603-0.171-0.1710.0000.0000.0000.000
180A181LEU00.0040.00734.561-0.316-0.3160.0000.0000.0000.000
181A182LYS10.8640.94034.8917.4097.4090.0000.0000.0000.000
182A183ALA00.0090.01635.661-0.183-0.1830.0000.0000.0000.000
183A184LEU00.0080.00929.708-0.227-0.2270.0000.0000.0000.000
184A185LYS10.8560.92430.9029.1679.1670.0000.0000.0000.000
185A186THR0-0.021-0.00330.844-0.298-0.2980.0000.0000.0000.000
186A187ARG10.8340.92730.2279.4909.4900.0000.0000.0000.000
187A188ILE00.0140.00325.332-0.364-0.3640.0000.0000.0000.000
188A189SER00.008-0.01226.109-0.530-0.5300.0000.0000.0000.000
189A190ASN0-0.042-0.02327.715-0.131-0.1310.0000.0000.0000.000
190A191LEU00.0190.03623.169-0.055-0.0550.0000.0000.0000.000
191A192PRO00.011-0.00521.639-0.176-0.1760.0000.0000.0000.000
192A193THR0-0.033-0.01117.6420.3340.3340.0000.0000.0000.000
193A194VAL00.0360.02120.003-0.250-0.2500.0000.0000.0000.000
194A195LYS10.8750.93722.57311.35911.3590.0000.0000.0000.000
195A196LYS10.9700.98217.64516.64516.6450.0000.0000.0000.000
196A197PHE00.0370.01319.501-0.095-0.0950.0000.0000.0000.000
197A198LEU0-0.0140.00521.9900.2980.2980.0000.0000.0000.000
198A199GLN0-0.0190.00424.7240.1050.1050.0000.0000.0000.000
199A200PRO00.0230.00125.081-0.361-0.3610.0000.0000.0000.000
200A201GLY00.0060.00724.008-0.144-0.1440.0000.0000.0000.000
201A202SER0-0.043-0.00820.554-0.853-0.8530.0000.0000.0000.000
202A203PRO00.006-0.01116.8600.4290.4290.0000.0000.0000.000
203A204ARG10.8480.94119.88412.14212.1420.0000.0000.0000.000
204A205LYS10.7940.88720.29615.36415.3640.0000.0000.0000.000
205A206PRO00.0190.00925.3090.2100.2100.0000.0000.0000.000
206A207PRO0-0.004-0.01628.704-0.245-0.2450.0000.0000.0000.000
207A208MET0-0.0400.00130.134-0.168-0.1680.0000.0000.0000.000
208A209ASP-1-0.833-0.91131.593-9.135-9.1350.0000.0000.0000.000
209A210GLU-1-0.836-0.94834.372-8.351-8.3510.0000.0000.0000.000
210A211LYS10.9190.96235.0608.4058.4050.0000.0000.0000.000
211A212SER0-0.0180.00029.361-0.203-0.2030.0000.0000.0000.000
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