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: 4Q2VN

Calculation Name: 2A2R-A-Xray547

Preferred Name: Glutathione S-transferase Pi

Target Type: SINGLE PROTEIN

Ligand Name: 2-amino-5-[1-(carboxylatomethylcarbamoyl)-2-nitrososulfanyl-ethyl]amino-5-oxo-pentanoate | 2-(n-morpholino)-ethanesulfonic acid | carbonate ion | calcium ion

Ligand 3-letter code: GSN | MES | CO3 | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A2R

Chain ID: A

ChEMBL ID: CHEMBL3902

UniProt ID: P09211

Base Structure: X-ray

Registration Date: 2025-10-03

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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2456486.215352
FMO2-HF: Nuclear repulsion 2374713.054225
FMO2-HF: Total energy -81773.161127
FMO2-MP2: Total energy -82012.103583


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:0:MET)


Summations of interaction energy for fragment #1(A:0: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.
-57.117-54.6230.316-1.042-1.768-0.005
Interaction energy analysis for fragmet #1(A:0:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.907
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].
3A2PRO00.0070.0273.223-6.923-5.0970.105-0.914-1.016-0.004
30A29LYS10.8750.9382.89935.39336.0610.211-0.128-0.752-0.001
4A3TYR00.0420.0245.9053.1163.1160.0000.0000.0000.000
5A4THR0-0.057-0.0395.551-5.386-5.3860.0000.0000.0000.000
6A5VAL00.0110.0187.7362.4042.4040.0000.0000.0000.000
7A6VAL00.0070.0039.932-0.840-0.8400.0000.0000.0000.000
8A7TYR00.0410.00412.0711.6001.6000.0000.0000.0000.000
9A8PHE00.0400.03414.855-0.410-0.4100.0000.0000.0000.000
10A9PRO0-0.0140.00516.538-0.430-0.4300.0000.0000.0000.000
11A10VAL00.0000.00017.4610.7390.7390.0000.0000.0000.000
12A11ARG10.8730.95118.39211.71611.7160.0000.0000.0000.000
13A12GLY00.0500.01919.590-0.553-0.5530.0000.0000.0000.000
14A13ARG10.7720.83121.17711.71111.7110.0000.0000.0000.000
15A14CYS0-0.015-0.00416.004-0.580-0.5800.0000.0000.0000.000
16A15ALA00.0090.02317.630-0.717-0.7170.0000.0000.0000.000
17A16ALA00.0410.02319.616-0.388-0.3880.0000.0000.0000.000
18A17LEU00.0070.00014.988-0.134-0.1340.0000.0000.0000.000
19A18ARG10.8070.87213.64717.54817.5480.0000.0000.0000.000
20A19MET0-0.0150.00915.991-0.297-0.2970.0000.0000.0000.000
21A20LEU0-0.0260.00717.208-0.045-0.0450.0000.0000.0000.000
22A21LEU00.003-0.00511.870-0.228-0.2280.0000.0000.0000.000
23A22ALA00.0280.02015.273-0.587-0.5870.0000.0000.0000.000
24A23ASP-1-0.809-0.87216.342-13.899-13.8990.0000.0000.0000.000
25A24GLN0-0.020-0.01617.0020.1610.1610.0000.0000.0000.000
26A25GLY0-0.094-0.03615.496-0.479-0.4790.0000.0000.0000.000
27A26GLN0-0.030-0.01612.047-2.735-2.7350.0000.0000.0000.000
28A27SER00.000-0.0036.375-1.204-1.2040.0000.0000.0000.000
29A28TRP0-0.047-0.0547.008-2.110-2.1100.0000.0000.0000.000
31A30GLU-1-0.718-0.8235.879-19.430-19.4300.0000.0000.0000.000
32A31GLU-1-0.900-0.9536.912-29.474-29.4740.0000.0000.0000.000
33A32VAL00.000-0.0059.2701.4941.4940.0000.0000.0000.000
34A33VAL00.0160.00912.4780.3820.3820.0000.0000.0000.000
35A34THR00.0320.00715.3320.6890.6890.0000.0000.0000.000
36A35VAL00.0430.00118.050-0.029-0.0290.0000.0000.0000.000
37A36GLU-1-0.848-0.91721.185-11.026-11.0260.0000.0000.0000.000
38A37THR0-0.017-0.01915.6340.0670.0670.0000.0000.0000.000
39A38TRP0-0.044-0.02518.582-0.235-0.2350.0000.0000.0000.000
40A39GLN0-0.087-0.04820.8370.4730.4730.0000.0000.0000.000
41A40GLU-1-0.902-0.94020.082-11.955-11.9550.0000.0000.0000.000
42A41GLY0-0.0080.00722.5170.1730.1730.0000.0000.0000.000
43A42SER0-0.010-0.00319.490-0.323-0.3230.0000.0000.0000.000
44A43LEU00.0360.01214.502-0.248-0.2480.0000.0000.0000.000
45A44LYS10.8960.95418.01511.23811.2380.0000.0000.0000.000
46A45ALA00.001-0.00920.9970.1220.1220.0000.0000.0000.000
47A46SER0-0.068-0.03417.233-0.259-0.2590.0000.0000.0000.000
48A47CYS0-0.058-0.02417.967-0.808-0.8080.0000.0000.0000.000
49A48LEU00.0040.01119.5790.6220.6220.0000.0000.0000.000
50A49TYR00.016-0.00421.9860.3640.3640.0000.0000.0000.000
51A50GLY00.0250.03023.0640.3780.3780.0000.0000.0000.000
52A51GLN0-0.055-0.04222.0250.1520.1520.0000.0000.0000.000
53A52LEU00.0260.03115.997-0.630-0.6300.0000.0000.0000.000
54A53PRO0-0.048-0.03016.4640.7640.7640.0000.0000.0000.000
55A54LYS10.9280.97512.12221.53321.5330.0000.0000.0000.000
56A55PHE0-0.003-0.01111.664-0.686-0.6860.0000.0000.0000.000
57A56GLN0-0.013-0.0057.8912.9842.9840.0000.0000.0000.000
58A57ASP-1-0.803-0.8989.207-27.483-27.4830.0000.0000.0000.000
59A58GLY00.0270.0096.9521.4421.4420.0000.0000.0000.000
60A59ASP-1-0.948-0.9748.015-23.923-23.9230.0000.0000.0000.000
61A60LEU00.0040.01510.7022.2092.2090.0000.0000.0000.000
62A61THR0-0.033-0.02312.547-1.172-1.1720.0000.0000.0000.000
63A62LEU0-0.043-0.01913.9091.4611.4610.0000.0000.0000.000
64A63TYR00.0560.00815.927-0.516-0.5160.0000.0000.0000.000
65A64GLN00.0250.01418.6750.2780.2780.0000.0000.0000.000
66A65SER00.0740.03519.766-0.291-0.2910.0000.0000.0000.000
67A66ASN0-0.010-0.02220.620-0.480-0.4800.0000.0000.0000.000
68A67THR00.0150.01719.5660.3010.3010.0000.0000.0000.000
69A68ILE0-0.0060.00615.284-0.275-0.2750.0000.0000.0000.000
70A69LEU0-0.0040.00017.840-0.540-0.5400.0000.0000.0000.000
71A70ARG10.7600.86520.11411.30411.3040.0000.0000.0000.000
72A71HIS0-0.095-0.05614.3941.3031.3030.0000.0000.0000.000
73A72LEU00.0310.01113.367-0.174-0.1740.0000.0000.0000.000
74A73GLY00.0200.00317.3680.0550.0550.0000.0000.0000.000
75A74ARG10.8920.96420.46014.11814.1180.0000.0000.0000.000
76A75THR0-0.017-0.01615.5740.5460.5460.0000.0000.0000.000
77A76LEU0-0.004-0.00615.160-0.247-0.2470.0000.0000.0000.000
78A77GLY0-0.0010.01619.1670.4470.4470.0000.0000.0000.000
79A78LEU0-0.060-0.01820.1610.6140.6140.0000.0000.0000.000
80A79TYR0-0.058-0.05723.757-0.051-0.0510.0000.0000.0000.000
81A80GLY00.0510.03426.4180.3950.3950.0000.0000.0000.000
82A81LYS10.8600.93028.7958.7968.7960.0000.0000.0000.000
83A82ASP-1-0.851-0.92131.303-9.131-9.1310.0000.0000.0000.000
84A83GLN00.028-0.00732.1650.0550.0550.0000.0000.0000.000
85A84GLN0-0.0240.00733.4420.1240.1240.0000.0000.0000.000
86A85GLU-1-0.831-0.93632.425-9.613-9.6130.0000.0000.0000.000
87A86ALA00.0050.01029.622-0.134-0.1340.0000.0000.0000.000
88A87ALA00.0210.00730.740-0.136-0.1360.0000.0000.0000.000
89A88LEU0-0.0050.00333.3140.0910.0910.0000.0000.0000.000
90A89VAL00.0100.00127.343-0.017-0.0170.0000.0000.0000.000
91A90ASP-1-0.814-0.88928.159-11.359-11.3590.0000.0000.0000.000
92A91MET0-0.0090.00030.2290.0740.0740.0000.0000.0000.000
93A92VAL0-0.006-0.00130.7520.1140.1140.0000.0000.0000.000
94A93ASN0-0.002-0.00926.021-0.355-0.3550.0000.0000.0000.000
95A94ASP-1-0.842-0.91229.150-10.575-10.5750.0000.0000.0000.000
96A95GLY00.0500.02731.1410.1270.1270.0000.0000.0000.000
97A96VAL0-0.021-0.01528.2180.1360.1360.0000.0000.0000.000
98A97GLU-1-0.760-0.83026.930-11.333-11.3330.0000.0000.0000.000
99A98ASP-1-0.873-0.93929.723-8.810-8.8100.0000.0000.0000.000
100A99LEU0-0.078-0.02532.8860.2620.2620.0000.0000.0000.000
101A100ARG10.8200.89125.11611.87711.8770.0000.0000.0000.000
102A101CYS0-0.018-0.02129.927-0.065-0.0650.0000.0000.0000.000
103A102LYS10.8750.94431.3388.5798.5790.0000.0000.0000.000
104A103TYR00.0380.02928.408-0.007-0.0070.0000.0000.0000.000
105A104ILE0-0.018-0.01526.513-0.006-0.0060.0000.0000.0000.000
106A105SER0-0.0090.00130.4930.0960.0960.0000.0000.0000.000
107A106LEU00.0090.02833.8910.1460.1460.0000.0000.0000.000
108A107ILE0-0.015-0.01029.2570.1290.1290.0000.0000.0000.000
109A108TYR0-0.037-0.02725.748-0.105-0.1050.0000.0000.0000.000
110A109THR0-0.111-0.05831.9970.1300.1300.0000.0000.0000.000
111A110ASN0-0.015-0.01135.4590.2570.2570.0000.0000.0000.000
112A111TYR00.016-0.00534.5800.1600.1600.0000.0000.0000.000
113A112GLU-1-0.808-0.90337.742-7.872-7.8720.0000.0000.0000.000
114A113ALA0-0.0110.00140.9010.1580.1580.0000.0000.0000.000
115A114GLY00.0350.02240.7710.0870.0870.0000.0000.0000.000
116A115LYS10.8590.93837.1698.0508.0500.0000.0000.0000.000
117A116ASP-1-0.856-0.92740.622-6.903-6.9030.0000.0000.0000.000
118A117ASP-1-0.857-0.92944.048-6.593-6.5930.0000.0000.0000.000
119A118TYR0-0.061-0.05634.651-0.013-0.0130.0000.0000.0000.000
120A119VAL00.010-0.00939.338-0.079-0.0790.0000.0000.0000.000
121A120LYS10.8470.92041.4116.6356.6350.0000.0000.0000.000
122A121ALA0-0.024-0.01341.8290.0800.0800.0000.0000.0000.000
123A122LEU0-0.0080.01136.396-0.035-0.0350.0000.0000.0000.000
124A123PRO00.0430.00939.954-0.126-0.1260.0000.0000.0000.000
125A124GLY0-0.013-0.00842.219-0.013-0.0130.0000.0000.0000.000
126A125GLN0-0.054-0.03337.704-0.164-0.1640.0000.0000.0000.000
127A126LEU00.0290.02335.271-0.218-0.2180.0000.0000.0000.000
128A127LYS11.0071.00338.4326.7436.7430.0000.0000.0000.000
129A128PRO0-0.0040.00338.4170.0630.0630.0000.0000.0000.000
130A129PHE00.0340.02033.752-0.028-0.0280.0000.0000.0000.000
131A130GLU-1-0.728-0.85437.281-7.940-7.9400.0000.0000.0000.000
132A131THR0-0.080-0.04739.9550.1700.1700.0000.0000.0000.000
133A132LEU00.0140.01936.2510.0780.0780.0000.0000.0000.000
134A133LEU0-0.0050.00534.761-0.013-0.0130.0000.0000.0000.000
135A134SER0-0.110-0.08138.5750.1340.1340.0000.0000.0000.000
136A135GLN0-0.033-0.02041.2190.0290.0290.0000.0000.0000.000
137A136ASN0-0.025-0.00835.3820.1690.1690.0000.0000.0000.000
138A137GLN00.0410.02338.3450.0410.0410.0000.0000.0000.000
139A138GLY00.0310.01340.419-0.024-0.0240.0000.0000.0000.000
140A139GLY00.0680.03338.1600.0770.0770.0000.0000.0000.000
141A140LYS10.7700.89237.5577.6227.6220.0000.0000.0000.000
142A141THR00.004-0.00134.034-0.134-0.1340.0000.0000.0000.000
143A142PHE0-0.0260.00028.910-0.291-0.2910.0000.0000.0000.000
144A143ILE0-0.0070.00330.6490.3550.3550.0000.0000.0000.000
145A144VAL0-0.031-0.01831.9050.3020.3020.0000.0000.0000.000
146A145GLY00.0520.04732.298-0.279-0.2790.0000.0000.0000.000
147A146ASP-1-0.876-0.94633.484-9.017-9.0170.0000.0000.0000.000
148A147GLN0-0.061-0.03526.9490.1470.1470.0000.0000.0000.000
149A148ILE0-0.052-0.00624.3940.1520.1520.0000.0000.0000.000
150A149SER00.017-0.02825.571-0.336-0.3360.0000.0000.0000.000
151A150PHE00.018-0.02222.153-0.243-0.2430.0000.0000.0000.000
152A151ALA00.0070.01023.519-0.107-0.1070.0000.0000.0000.000
153A152ASP-1-0.729-0.81526.633-10.654-10.6540.0000.0000.0000.000
154A153TYR00.001-0.02322.3250.0740.0740.0000.0000.0000.000
155A154ASN0-0.002-0.02524.495-0.006-0.0060.0000.0000.0000.000
156A155LEU00.0270.01825.5440.2310.2310.0000.0000.0000.000
157A156LEU0-0.004-0.00425.0960.2580.2580.0000.0000.0000.000
158A157ASP-1-0.823-0.90624.095-12.192-12.1920.0000.0000.0000.000
159A158LEU0-0.0060.00926.2510.2620.2620.0000.0000.0000.000
160A159LEU00.0120.00729.2880.3550.3550.0000.0000.0000.000
161A160LEU0-0.010-0.00226.2210.2370.2370.0000.0000.0000.000
162A161ILE0-0.040-0.02226.7410.1740.1740.0000.0000.0000.000
163A162HIS0-0.024-0.00429.6420.4460.4460.0000.0000.0000.000
164A163GLU-1-0.729-0.85733.017-8.133-8.1330.0000.0000.0000.000
165A164VAL0-0.067-0.02329.6570.1350.1350.0000.0000.0000.000
166A165LEU0-0.0430.00032.9410.2180.2180.0000.0000.0000.000
167A166ALA0-0.050-0.05334.9170.2820.2820.0000.0000.0000.000
168A167PRO00.0000.00536.7820.0060.0060.0000.0000.0000.000
169A168GLY00.0530.03238.3020.2220.2220.0000.0000.0000.000
170A169CYS0-0.138-0.05636.9220.0830.0830.0000.0000.0000.000
171A170LEU0-0.018-0.04034.3860.0290.0290.0000.0000.0000.000
172A171ASP-1-0.910-0.94339.095-7.436-7.4360.0000.0000.0000.000
173A172ALA0-0.075-0.03642.5150.1700.1700.0000.0000.0000.000
174A173PHE0-0.082-0.03939.6110.1050.1050.0000.0000.0000.000
175A174PRO00.0700.02739.809-0.227-0.2270.0000.0000.0000.000
176A175LEU0-0.061-0.03039.286-0.155-0.1550.0000.0000.0000.000
177A176LEU00.021-0.00835.093-0.282-0.2820.0000.0000.0000.000
178A177SER00.0040.02035.075-0.370-0.3700.0000.0000.0000.000
179A178ALA0-0.001-0.01135.578-0.230-0.2300.0000.0000.0000.000
180A179TYR0-0.080-0.06030.239-0.238-0.2380.0000.0000.0000.000
181A180VAL00.0540.02030.509-0.402-0.4020.0000.0000.0000.000
182A181GLY00.0020.01930.659-0.348-0.3480.0000.0000.0000.000
183A182ARG10.8110.88931.5179.0649.0640.0000.0000.0000.000
184A183LEU0-0.012-0.01227.508-0.350-0.3500.0000.0000.0000.000
185A184SER00.002-0.02226.838-0.585-0.5850.0000.0000.0000.000
186A185ALA0-0.037-0.01527.448-0.200-0.2000.0000.0000.0000.000
187A186ARG10.8460.92023.63812.81612.8160.0000.0000.0000.000
188A187PRO0-0.005-0.00523.995-0.341-0.3410.0000.0000.0000.000
189A188LYS10.9200.96717.09517.34617.3460.0000.0000.0000.000
190A189LEU00.0420.02420.357-0.482-0.4820.0000.0000.0000.000
191A190LYS10.9630.98922.08711.23611.2360.0000.0000.0000.000
192A191ALA0-0.029-0.01620.3690.1950.1950.0000.0000.0000.000
193A192PHE00.0140.00915.4620.0670.0670.0000.0000.0000.000
194A193LEU00.0110.00919.566-0.007-0.0070.0000.0000.0000.000
195A194ALA0-0.020-0.00522.5990.3880.3880.0000.0000.0000.000
196A195SER0-0.036-0.02318.136-0.158-0.1580.0000.0000.0000.000
197A196PRO00.007-0.02417.8540.1490.1490.0000.0000.0000.000
198A197GLU-1-0.920-0.95113.077-21.109-21.1090.0000.0000.0000.000
199A198TYR00.0100.00916.4980.2230.2230.0000.0000.0000.000
200A199VAL0-0.032-0.02219.3480.5150.5150.0000.0000.0000.000
201A200ASN0-0.014-0.02019.2220.7910.7910.0000.0000.0000.000
202A201LEU0-0.0220.01815.8880.1180.1180.0000.0000.0000.000
203A202PRO00.0250.02420.2540.3590.3590.0000.0000.0000.000
204A203ILE00.0580.01622.565-0.567-0.5670.0000.0000.0000.000
205A204ASN0-0.005-0.02823.860-0.602-0.6020.0000.0000.0000.000
206A205GLY00.007-0.00524.086-0.043-0.0430.0000.0000.0000.000
207A206ASN0-0.044-0.04024.811-0.074-0.0740.0000.0000.0000.000
208A207GLY0-0.0080.00327.6190.3120.3120.0000.0000.0000.000
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