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: XVQN1

Calculation Name: 2C4J-D-Xray17

Preferred Name: Glutathione S-transferase Mu 2

Target Type: SINGLE PROTEIN

Ligand Name: l-gamma-glutamyl-s-[(2s)-2-hydroxy-2-phenylethyl]-l-cysteinylglycine

ligand 3-letter code: GSO

PDB ID: 2C4J

Chain ID: D

ChEMBL ID: CHEMBL4589

UniProt ID: P28161

Base Structure: X-ray

Registration Date: 2018-06-01

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 232
LigandCharge GSO=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2967578.272542
FMO2-HF: Nuclear repulsion 2872808.951587
FMO2-HF: Total energy -94769.320955
FMO2-MP2: Total energy -95041.952325


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(D:1:ACE)


Summations of interaction energy for fragment #1(D:1:ACE)
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.
-0.3360.174-0.001-0.261-0.2480
Interaction energy analysis for fragmet #1(D:1:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.019
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].
3D3MET0-0.010-0.0073.8420.7521.262-0.001-0.261-0.2480.000
4D4THR0-0.018-0.0106.6960.0900.0900.0000.0000.0000.000
5D5LEU0-0.045-0.0148.8280.0960.0960.0000.0000.0000.000
6D6GLY00.0160.01412.5590.0440.0440.0000.0000.0000.000
7D7TYR00.003-0.01614.9780.0140.0140.0000.0000.0000.000
8D8TRP00.0250.01918.5990.0130.0130.0000.0000.0000.000
9D9ASN0-0.015-0.01320.879-0.030-0.0300.0000.0000.0000.000
10D10ILE0-0.0010.00622.1950.0120.0120.0000.0000.0000.000
11D11ARG10.7880.91222.7790.1080.1080.0000.0000.0000.000
12D12GLY0-0.037-0.02323.518-0.014-0.0140.0000.0000.0000.000
13D13LEU00.008-0.02623.228-0.004-0.0040.0000.0000.0000.000
14D14ALA00.0120.01818.887-0.012-0.0120.0000.0000.0000.000
15D15HIS00.0090.01919.956-0.035-0.0350.0000.0000.0000.000
16D16SER00.0430.00121.467-0.010-0.0100.0000.0000.0000.000
17D17ILE0-0.008-0.00216.217-0.008-0.0080.0000.0000.0000.000
18D18ARG10.8540.91416.6510.2060.2060.0000.0000.0000.000
19D19LEU00.0170.01317.462-0.024-0.0240.0000.0000.0000.000
20D20LEU0-0.0030.01017.823-0.004-0.0040.0000.0000.0000.000
21D21LEU0-0.035-0.01611.916-0.022-0.0220.0000.0000.0000.000
22D22GLU-1-0.754-0.82914.602-0.421-0.4210.0000.0000.0000.000
23D23TYR0-0.017-0.00216.6760.0140.0140.0000.0000.0000.000
24D24THR0-0.040-0.02915.171-0.013-0.0130.0000.0000.0000.000
25D25ASP-1-0.886-0.93114.149-0.369-0.3690.0000.0000.0000.000
26D26SER0-0.056-0.03110.710-0.112-0.1120.0000.0000.0000.000
27D27SER0-0.019-0.0095.6160.0980.0980.0000.0000.0000.000
28D28TYR0-0.100-0.0977.177-0.508-0.5080.0000.0000.0000.000
29D29GLU-1-0.865-0.9077.121-0.171-0.1710.0000.0000.0000.000
30D30GLU-1-0.867-0.9509.471-0.326-0.3260.0000.0000.0000.000
31D31LYS10.8590.93312.5930.1260.1260.0000.0000.0000.000
32D32LYS10.9450.96714.1100.2060.2060.0000.0000.0000.000
33D33TYR0-0.039-0.05616.0670.0170.0170.0000.0000.0000.000
34D34THR00.000-0.01520.186-0.002-0.0020.0000.0000.0000.000
35D35MET0-0.045-0.01223.6590.0040.0040.0000.0000.0000.000
36D36GLY00.0250.00726.9150.0000.0000.0000.0000.0000.000
37D37ASP-1-0.857-0.94730.133-0.047-0.0470.0000.0000.0000.000
38D38ALA0-0.0140.01533.4920.0010.0010.0000.0000.0000.000
39D39PRO0-0.017-0.02236.3070.0010.0010.0000.0000.0000.000
40D40ASP-1-0.853-0.93234.208-0.025-0.0250.0000.0000.0000.000
41D41TYR0-0.082-0.04431.084-0.002-0.0020.0000.0000.0000.000
42D42ASP-1-0.875-0.94228.983-0.028-0.0280.0000.0000.0000.000
43D43ARG10.9430.97325.5520.0440.0440.0000.0000.0000.000
44D44SER00.0340.02024.907-0.002-0.0020.0000.0000.0000.000
45D45GLN00.0460.01418.035-0.005-0.0050.0000.0000.0000.000
46D46TRP00.0570.02117.8660.0010.0010.0000.0000.0000.000
47D47LEU0-0.024-0.02421.264-0.001-0.0010.0000.0000.0000.000
48D48ASN0-0.0180.00820.2760.0080.0080.0000.0000.0000.000
49D49GLU-1-0.787-0.85715.775-0.044-0.0440.0000.0000.0000.000
50D50LYS10.9230.98518.3900.0650.0650.0000.0000.0000.000
51D51PHE00.005-0.01619.722-0.011-0.0110.0000.0000.0000.000
52D52LYS10.8830.94417.875-0.008-0.0080.0000.0000.0000.000
53D53LEU00.0220.01613.0610.0190.0190.0000.0000.0000.000
54D54GLY0-0.014-0.00214.068-0.019-0.0190.0000.0000.0000.000
55D55LEU0-0.039-0.01314.886-0.014-0.0140.0000.0000.0000.000
56D56ASP-1-0.858-0.92317.798-0.077-0.0770.0000.0000.0000.000
57D57PHE0-0.014-0.01120.9520.0130.0130.0000.0000.0000.000
58D58PRO0-0.041-0.01820.058-0.014-0.0140.0000.0000.0000.000
59D59ASN0-0.026-0.02919.9100.0110.0110.0000.0000.0000.000
60D60LEU0-0.0410.01518.305-0.016-0.0160.0000.0000.0000.000
61D61PRO0-0.012-0.01417.8120.0170.0170.0000.0000.0000.000
62D62TYR0-0.028-0.03312.1680.0190.0190.0000.0000.0000.000
63D63LEU00.013-0.00211.161-0.021-0.0210.0000.0000.0000.000
64D64ILE0-0.048-0.0147.9470.1020.1020.0000.0000.0000.000
65D65ASP-1-0.736-0.8597.283-1.627-1.6270.0000.0000.0000.000
66D66GLY00.0720.0376.4570.2040.2040.0000.0000.0000.000
67D67THR0-0.033-0.0317.5550.0640.0640.0000.0000.0000.000
68D68HIS0-0.0080.01310.8380.1120.1120.0000.0000.0000.000
69D69LYS10.8980.9469.8630.0460.0460.0000.0000.0000.000
70D70ILE00.0130.01813.7100.0400.0400.0000.0000.0000.000
71D71THR0-0.012-0.00916.022-0.016-0.0160.0000.0000.0000.000
72D72GLN00.0470.01818.858-0.002-0.0020.0000.0000.0000.000
73D73SER00.0620.01720.452-0.016-0.0160.0000.0000.0000.000
74D74ASN00.0820.03520.965-0.028-0.0280.0000.0000.0000.000
75D75ALA0-0.0030.00820.387-0.006-0.0060.0000.0000.0000.000
76D76ILE0-0.043-0.02115.483-0.021-0.0210.0000.0000.0000.000
77D77LEU00.0150.00617.305-0.037-0.0370.0000.0000.0000.000
78D78ARG10.8120.87019.4320.1340.1340.0000.0000.0000.000
79D79TYR0-0.118-0.07610.7600.0650.0650.0000.0000.0000.000
80D80ILE00.0170.00013.867-0.019-0.0190.0000.0000.0000.000
81D81ALA00.0290.00816.026-0.001-0.0010.0000.0000.0000.000
82D82ARG10.9530.96418.6590.2350.2350.0000.0000.0000.000
83D83LYS10.8620.9649.1460.9350.9350.0000.0000.0000.000
84D84HIS0-0.005-0.00213.2390.0510.0510.0000.0000.0000.000
85D85ASN0-0.0030.01318.0810.0220.0220.0000.0000.0000.000
86D86LEU0-0.010-0.00619.7490.0170.0170.0000.0000.0000.000
87D87CYS0-0.021-0.01722.454-0.005-0.0050.0000.0000.0000.000
88D88GLY00.0180.00025.1890.0060.0060.0000.0000.0000.000
89D89GLU-1-0.903-0.93727.821-0.128-0.1280.0000.0000.0000.000
90D90SER0-0.0090.00130.0560.0070.0070.0000.0000.0000.000
91D91GLU-1-0.837-0.93133.234-0.081-0.0810.0000.0000.0000.000
92D92LYS10.9030.94735.1370.0670.0670.0000.0000.0000.000
93D93GLU-1-0.870-0.94331.796-0.101-0.1010.0000.0000.0000.000
94D94GLN00.0330.01429.726-0.007-0.0070.0000.0000.0000.000
95D95ILE00.0260.03031.854-0.001-0.0010.0000.0000.0000.000
96D96ARG10.8960.94134.5030.0770.0770.0000.0000.0000.000
97D97GLU-1-0.829-0.90527.150-0.149-0.1490.0000.0000.0000.000
98D98ASP-1-0.819-0.90330.049-0.115-0.1150.0000.0000.0000.000
99D99ILE0-0.055-0.02331.6380.0010.0010.0000.0000.0000.000
100D100LEU0-0.005-0.00731.9160.0010.0010.0000.0000.0000.000
101D101GLU-1-0.817-0.87426.336-0.145-0.1450.0000.0000.0000.000
102D102ASN0-0.080-0.05629.872-0.001-0.0010.0000.0000.0000.000
103D103GLN00.0450.03732.2690.0030.0030.0000.0000.0000.000
104D104PHE00.024-0.00930.7970.0020.0020.0000.0000.0000.000
105D105MET0-0.026-0.00126.625-0.001-0.0010.0000.0000.0000.000
106D106ASP-1-0.873-0.93131.174-0.076-0.0760.0000.0000.0000.000
107D107SER0-0.038-0.01534.3830.0040.0040.0000.0000.0000.000
108D108ARG10.8270.90826.6810.1410.1410.0000.0000.0000.000
109D109MET0-0.049-0.03829.7600.0030.0030.0000.0000.0000.000
110D110GLN00.0040.00933.6450.0050.0050.0000.0000.0000.000
111D111LEU00.0210.02633.8890.0030.0030.0000.0000.0000.000
112D112ALA0-0.012-0.01831.8960.0030.0030.0000.0000.0000.000
113D113LYS10.9620.97233.9110.0570.0570.0000.0000.0000.000
114D114LEU00.0050.01736.5750.0030.0030.0000.0000.0000.000
115D115CYS0-0.030-0.00835.2120.0030.0030.0000.0000.0000.000
116D116TYR0-0.030-0.00529.747-0.001-0.0010.0000.0000.0000.000
117D117ASP-1-0.882-0.92236.490-0.043-0.0430.0000.0000.0000.000
118D118PRO00.011-0.00540.1280.0000.0000.0000.0000.0000.000
119D119ASP-1-0.961-0.96642.466-0.034-0.0340.0000.0000.0000.000
120D120PHE00.006-0.01540.0810.0000.0000.0000.0000.0000.000
121D121GLU-1-0.910-0.97943.097-0.044-0.0440.0000.0000.0000.000
122D122LYS10.8830.94045.9730.0320.0320.0000.0000.0000.000
123D123LEU00.0220.01743.6330.0010.0010.0000.0000.0000.000
124D124LYS10.9340.98942.2980.0490.0490.0000.0000.0000.000
125D125PRO00.0070.00044.780-0.002-0.0020.0000.0000.0000.000
126D126GLU-1-0.921-0.95446.087-0.045-0.0450.0000.0000.0000.000
127D127TYR0-0.023-0.03637.913-0.002-0.0020.0000.0000.0000.000
128D128LEU00.007-0.01643.054-0.002-0.0020.0000.0000.0000.000
129D129GLN0-0.065-0.03345.1370.0010.0010.0000.0000.0000.000
130D130ALA00.0080.01244.0060.0010.0010.0000.0000.0000.000
131D131LEU0-0.026-0.00239.436-0.002-0.0020.0000.0000.0000.000
132D132PRO00.0310.00542.530-0.003-0.0030.0000.0000.0000.000
133D133GLU-1-0.881-0.94244.489-0.052-0.0520.0000.0000.0000.000
134D134MET0-0.0260.00638.233-0.003-0.0030.0000.0000.0000.000
135D135LEU00.001-0.00738.283-0.003-0.0030.0000.0000.0000.000
136D136LYS10.9690.99240.8100.0480.0480.0000.0000.0000.000
137D137LEU0-0.010-0.00441.435-0.001-0.0010.0000.0000.0000.000
138D138TYR00.000-0.02035.566-0.003-0.0030.0000.0000.0000.000
139D139SER0-0.029-0.02738.784-0.001-0.0010.0000.0000.0000.000
140D140GLN0-0.044-0.03940.7310.0000.0000.0000.0000.0000.000
141D141PHE0-0.058-0.02135.5230.0010.0010.0000.0000.0000.000
142D142LEU0-0.0040.02135.021-0.001-0.0010.0000.0000.0000.000
143D143GLY00.0250.02038.2580.0010.0010.0000.0000.0000.000
144D144LYS10.9460.95440.6790.0530.0530.0000.0000.0000.000
145D145GLN0-0.0200.02436.3170.0000.0000.0000.0000.0000.000
146D146PRO00.0050.03133.4900.0000.0000.0000.0000.0000.000
147D147TRP00.0260.00629.315-0.007-0.0070.0000.0000.0000.000
148D148PHE0-0.003-0.02731.5360.0080.0080.0000.0000.0000.000
149D149LEU0-0.052-0.02229.5070.0070.0070.0000.0000.0000.000
150D150GLY00.0190.01932.9200.0040.0040.0000.0000.0000.000
151D151ASP-1-0.900-0.96633.718-0.086-0.0860.0000.0000.0000.000
152D152LYS10.7830.90125.3120.1490.1490.0000.0000.0000.000
153D153ILE0-0.0140.01025.1030.0000.0000.0000.0000.0000.000
154D154THR0-0.017-0.02124.979-0.008-0.0080.0000.0000.0000.000
155D155PHE00.0610.00822.331-0.004-0.0040.0000.0000.0000.000
156D156VAL00.0060.01123.947-0.001-0.0010.0000.0000.0000.000
157D157ASP-1-0.709-0.86026.947-0.126-0.1260.0000.0000.0000.000
158D158PHE00.0360.00921.6340.0010.0010.0000.0000.0000.000
159D159ILE0-0.046-0.00925.1470.0010.0010.0000.0000.0000.000
160D160ALA00.0040.00426.8730.0080.0080.0000.0000.0000.000
161D161TYR0-0.067-0.05126.5590.0040.0040.0000.0000.0000.000
162D162ASP-1-0.730-0.85226.222-0.139-0.1390.0000.0000.0000.000
163D163VAL0-0.038-0.01828.3120.0090.0090.0000.0000.0000.000
164D164LEU00.0110.00431.4200.0090.0090.0000.0000.0000.000
165D165GLU-1-0.802-0.88530.585-0.102-0.1020.0000.0000.0000.000
166D166ARG10.7900.87926.6470.1280.1280.0000.0000.0000.000
167D167ASN00.0030.00332.7210.0100.0100.0000.0000.0000.000
168D168GLN00.0180.01835.5960.0080.0080.0000.0000.0000.000
169D169VAL0-0.069-0.03032.7310.0040.0040.0000.0000.0000.000
170D170PHE0-0.055-0.04136.0820.0050.0050.0000.0000.0000.000
171D171GLU-1-0.920-0.96438.060-0.048-0.0480.0000.0000.0000.000
172D172PRO0-0.006-0.00840.170-0.001-0.0010.0000.0000.0000.000
173D173SER00.0260.02441.213-0.002-0.0020.0000.0000.0000.000
174D174CYS0-0.040-0.00439.924-0.001-0.0010.0000.0000.0000.000
175D175LEU00.019-0.00836.7020.0000.0000.0000.0000.0000.000
176D176ASP-1-0.918-0.95641.410-0.054-0.0540.0000.0000.0000.000
177D177ALA0-0.058-0.02644.6430.0010.0010.0000.0000.0000.000
178D178PHE0-0.029-0.01541.5550.0010.0010.0000.0000.0000.000
179D179PRO00.0520.01641.336-0.004-0.0040.0000.0000.0000.000
180D180ASN00.0280.01839.710-0.002-0.0020.0000.0000.0000.000
181D181LEU00.0030.00936.699-0.005-0.0050.0000.0000.0000.000
182D182LYS10.9290.97336.2910.0560.0560.0000.0000.0000.000
183D183ASP-1-0.913-0.95636.564-0.074-0.0740.0000.0000.0000.000
184D184PHE0-0.060-0.01929.981-0.005-0.0050.0000.0000.0000.000
185D185ILE00.0100.00232.014-0.008-0.0080.0000.0000.0000.000
186D186SER0-0.0070.00131.600-0.005-0.0050.0000.0000.0000.000
187D187ARG10.8350.91331.1840.0940.0940.0000.0000.0000.000
188D188PHE0-0.010-0.01624.011-0.008-0.0080.0000.0000.0000.000
189D189GLU-1-0.854-0.92227.346-0.123-0.1230.0000.0000.0000.000
190D190GLY0-0.026-0.00428.138-0.002-0.0020.0000.0000.0000.000
191D191LEU0-0.040-0.00525.1660.0000.0000.0000.0000.0000.000
192D192GLU-1-0.918-0.95624.162-0.146-0.1460.0000.0000.0000.000
193D193LYS10.9170.95317.6090.2660.2660.0000.0000.0000.000
194D194ILE0-0.0030.01321.167-0.015-0.0150.0000.0000.0000.000
195D195SER00.0600.05423.3340.0060.0060.0000.0000.0000.000
196D196ALA0-0.026-0.02421.5070.0070.0070.0000.0000.0000.000
197D197TYR00.0170.01418.0070.0100.0100.0000.0000.0000.000
198D198MET0-0.018-0.00421.1190.0040.0040.0000.0000.0000.000
199D199LYS10.8830.95524.0510.1230.1230.0000.0000.0000.000
200D200SER0-0.069-0.02819.4750.0020.0020.0000.0000.0000.000
201D201SER0-0.029-0.03318.469-0.003-0.0030.0000.0000.0000.000
202D202ARG10.8330.88714.7700.3170.3170.0000.0000.0000.000
203D203PHE00.0100.02918.854-0.010-0.0100.0000.0000.0000.000
204D204LEU0-0.019-0.01420.5580.0140.0140.0000.0000.0000.000
205D205PRO0-0.027-0.00323.2950.0000.0000.0000.0000.0000.000
206D206ARG10.9470.97426.6410.0980.0980.0000.0000.0000.000
207D207PRO00.0640.03226.688-0.005-0.0050.0000.0000.0000.000
208D208VAL00.0230.01327.514-0.011-0.0110.0000.0000.0000.000
209D209PHE0-0.016-0.02728.317-0.012-0.0120.0000.0000.0000.000
210D210SER0-0.011-0.02227.9980.0020.0020.0000.0000.0000.000
211D211LYS10.8920.93428.4790.0660.0660.0000.0000.0000.000
212D212MET0-0.031-0.02031.6810.0030.0030.0000.0000.0000.000
213D213ALA0-0.0460.00533.1560.0020.0020.0000.0000.0000.000
214D214VAL00.009-0.00534.8110.0020.0020.0000.0000.0000.000
215D215TRP00.0420.03133.9880.0000.0000.0000.0000.0000.000
216D216GLY00.008-0.00333.762-0.004-0.0040.0000.0000.0000.000
217D217ASN0-0.009-0.01032.024-0.006-0.0060.0000.0000.0000.000
218D218LYS00.0190.01832.046-0.023-0.0230.0000.0000.0000.000
219C1219GSO-1-1.000-1.00057.956-0.017-0.0170.0000.0000.0000.000
220D1219GSO-1-0.872-0.92937.274-0.061-0.0610.0000.0000.0000.000
221A2156HOH0-0.048-0.04540.7470.0020.0020.0000.0000.0000.000
222A2157HOH0-0.016-0.01937.803-0.001-0.0010.0000.0000.0000.000
223A2166HOH0-0.029-0.02932.8100.0000.0000.0000.0000.0000.000
224A2197HOH0-0.003-0.00635.8220.0000.0000.0000.0000.0000.000
225A2206HOH00.010-0.01726.5250.0030.0030.0000.0000.0000.000
226D2040HOH00.0010.01035.854-0.002-0.0020.0000.0000.0000.000
227D2053HOH0-0.009-0.01524.6650.0060.0060.0000.0000.0000.000
228D2092HOH0-0.038-0.01945.502-0.001-0.0010.0000.0000.0000.000
229D2112HOH0-0.032-0.01650.7390.0010.0010.0000.0000.0000.000
230D2273HOH0-0.055-0.03740.2330.0010.0010.0000.0000.0000.000
231D2274HOH0-0.029-0.01937.001-0.001-0.0010.0000.0000.0000.000
232D2275HOH00.0270.02049.7250.0000.0000.0000.0000.0000.000