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: RQZN8

Calculation Name: 1Y1A-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glutathione | calcium ion

Ligand 3-letter code: GSH | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Y1A

Chain ID: A

ChEMBL ID:

UniProt ID: Q99828

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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1872862.634625
FMO2-HF: Nuclear repulsion 1799619.020634
FMO2-HF: Total energy -73243.61399
FMO2-MP2: Total energy -73458.62432


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:9:SER)


Summations of interaction energy for fragment #1(A:9:SER)
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.
-271.482-263.5491.591-4.043-5.482-0.034
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.902
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].
3A11GLU-1-0.836-0.9252.628-84.389-79.2790.544-2.756-2.898-0.027
4A12LEU00.0200.0102.3552.9814.3610.834-0.799-1.415-0.006
5A13LEU0-0.033-0.0203.5807.2807.7320.009-0.107-0.354-0.001
37A45VAL00.0590.0242.703-0.1250.8660.204-0.381-0.8150.000
6A14ALA00.0170.0126.0825.7135.7130.0000.0000.0000.000
7A15GLU-1-0.893-0.9457.620-32.063-32.0630.0000.0000.0000.000
8A16TYR00.032-0.0037.9823.3363.3360.0000.0000.0000.000
9A17GLN0-0.034-0.00410.4260.2800.2800.0000.0000.0000.000
10A18ASP-1-0.910-0.97212.295-21.774-21.7740.0000.0000.0000.000
11A19LEU0-0.099-0.03013.5181.4951.4950.0000.0000.0000.000
12A20THR00.009-0.01814.1611.1501.1500.0000.0000.0000.000
13A21PHE0-0.008-0.01516.4151.2721.2720.0000.0000.0000.000
14A22LEU00.0190.03414.6500.6800.6800.0000.0000.0000.000
15A23THR0-0.022-0.05414.657-1.278-1.2780.0000.0000.0000.000
16A24LYS10.9480.9559.69622.61622.6160.0000.0000.0000.000
17A25GLN00.0220.01710.327-2.393-2.3930.0000.0000.0000.000
18A26GLU-1-0.717-0.82512.694-17.897-17.8970.0000.0000.0000.000
19A27ILE00.0610.0458.415-0.110-0.1100.0000.0000.0000.000
20A28LEU0-0.017-0.0146.412-1.160-1.1600.0000.0000.0000.000
21A29LEU0-0.064-0.0279.6690.4610.4610.0000.0000.0000.000
22A30ALA00.0440.02112.7190.6220.6220.0000.0000.0000.000
23A31HIS0-0.001-0.0146.595-0.224-0.2240.0000.0000.0000.000
24A32ARG10.9420.9719.49625.15225.1520.0000.0000.0000.000
25A33ARG10.8140.87111.59116.25316.2530.0000.0000.0000.000
26A34PHE0-0.0060.01212.0900.9710.9710.0000.0000.0000.000
27A35CYS0-0.045-0.0409.9540.1410.1410.0000.0000.0000.000
28A36GLU-1-0.896-0.93712.692-17.105-17.1050.0000.0000.0000.000
29A37LEU0-0.046-0.01115.9991.1271.1270.0000.0000.0000.000
30A38LEU00.0010.01813.1930.5840.5840.0000.0000.0000.000
31A39PRO00.001-0.00317.0330.4450.4450.0000.0000.0000.000
32A40GLN00.031-0.00515.878-1.039-1.0390.0000.0000.0000.000
33A41GLU-1-0.971-0.98314.626-16.157-16.1570.0000.0000.0000.000
34A42GLN00.0100.01912.826-1.321-1.3210.0000.0000.0000.000
35A43ARG10.8350.89910.53416.60616.6060.0000.0000.0000.000
36A44SER0-0.0450.0037.445-3.353-3.3530.0000.0000.0000.000
38A46GLU-1-0.892-0.9465.457-36.424-36.4240.0000.0000.0000.000
39A47SER0-0.059-0.0426.4472.9552.9550.0000.0000.0000.000
40A48SER0-0.024-0.0228.0981.3081.3080.0000.0000.0000.000
41A49LEU0-0.005-0.0024.9831.6371.6370.0000.0000.0000.000
42A50ARG10.9340.9829.09027.64227.6420.0000.0000.0000.000
43A51ALA0-0.060-0.01111.9551.9151.9150.0000.0000.0000.000
44A52GLN0-0.038-0.05214.402-0.646-0.6460.0000.0000.0000.000
45A53VAL0-0.0070.01516.6820.4270.4270.0000.0000.0000.000
46A54PRO00.0110.01019.2750.3080.3080.0000.0000.0000.000
47A55PHE00.0430.00023.1190.0230.0230.0000.0000.0000.000
48A56GLU-1-0.948-0.95525.474-11.237-11.2370.0000.0000.0000.000
49A57GLN00.0200.01021.3680.6840.6840.0000.0000.0000.000
50A58ILE0-0.0170.00520.324-0.268-0.2680.0000.0000.0000.000
51A59LEU0-0.013-0.02624.0730.2960.2960.0000.0000.0000.000
52A60SER0-0.080-0.04925.9870.2350.2350.0000.0000.0000.000
53A61LEU00.0040.02120.508-0.025-0.0250.0000.0000.0000.000
54A62PRO0-0.010-0.01923.0610.4170.4170.0000.0000.0000.000
55A63GLU-1-0.729-0.81922.078-12.968-12.9680.0000.0000.0000.000
56A64LEU00.0340.03825.3080.3330.3330.0000.0000.0000.000
57A65LYS10.9430.99127.8589.7759.7750.0000.0000.0000.000
58A66ALA0-0.027-0.02830.3960.3500.3500.0000.0000.0000.000
59A67ASN00.0370.02730.1370.1440.1440.0000.0000.0000.000
60A68PRO0-0.004-0.00332.848-0.004-0.0040.0000.0000.0000.000
61A69PHE0-0.009-0.00333.707-0.157-0.1570.0000.0000.0000.000
62A70LYS10.8960.94929.7389.4499.4490.0000.0000.0000.000
63A71GLU-1-0.771-0.91029.431-9.602-9.6020.0000.0000.0000.000
64A72ARG10.8520.94531.0119.2399.2390.0000.0000.0000.000
65A73ILE00.0230.01726.543-0.110-0.1100.0000.0000.0000.000
66A74CYS0-0.022-0.00925.844-0.385-0.3850.0000.0000.0000.000
67A75ARG10.8940.91925.7909.2759.2750.0000.0000.0000.000
68A76VAL0-0.090-0.03327.7200.1110.1110.0000.0000.0000.000
69A77PHE00.0550.02222.3490.1150.1150.0000.0000.0000.000
70A78SER0-0.043-0.02822.224-0.542-0.5420.0000.0000.0000.000
71A79THR00.024-0.00319.9750.6530.6530.0000.0000.0000.000
72A80SER0-0.050-0.02321.1050.0810.0810.0000.0000.0000.000
73A81PRO00.005-0.00123.0130.2690.2690.0000.0000.0000.000
74A82ALA0-0.049-0.02925.7830.3800.3800.0000.0000.0000.000
75A83LYS10.9060.95219.94414.77814.7780.0000.0000.0000.000
76A84ASP-1-0.858-0.92724.927-10.893-10.8930.0000.0000.0000.000
77A85SER0-0.052-0.03220.962-0.272-0.2720.0000.0000.0000.000
78A86LEU0-0.0330.01519.4390.2410.2410.0000.0000.0000.000
79A87SER00.018-0.01115.658-0.923-0.9230.0000.0000.0000.000
80A88PHE00.027-0.0029.5020.1910.1910.0000.0000.0000.000
81A89GLU-1-0.855-0.93313.776-19.389-19.3890.0000.0000.0000.000
82A90ASP-1-0.724-0.82115.160-15.054-15.0540.0000.0000.0000.000
83A91PHE0-0.051-0.02914.9580.9350.9350.0000.0000.0000.000
84A92LEU00.0100.01311.9320.3560.3560.0000.0000.0000.000
85A93ASP-1-0.848-0.90416.298-14.988-14.9880.0000.0000.0000.000
86A94LEU0-0.082-0.05119.8320.8410.8410.0000.0000.0000.000
87A95LEU0-0.046-0.04416.5530.6470.6470.0000.0000.0000.000
88A96SER00.011-0.00718.7760.3540.3540.0000.0000.0000.000
89A97VAL0-0.078-0.01821.1170.5810.5810.0000.0000.0000.000
90A98PHE0-0.080-0.05123.6860.7260.7260.0000.0000.0000.000
91A99SER0-0.019-0.02221.1430.2650.2650.0000.0000.0000.000
92A100ASP-1-0.903-0.93922.457-11.844-11.8440.0000.0000.0000.000
93A101THR0-0.141-0.08718.460-0.520-0.5200.0000.0000.0000.000
94A102ALA0-0.004-0.00717.600-1.118-1.1180.0000.0000.0000.000
95A103THR0-0.034-0.02219.1211.0301.0300.0000.0000.0000.000
96A104PRO0-0.0050.00819.454-0.149-0.1490.0000.0000.0000.000
97A105ASP-1-0.789-0.86420.319-12.382-12.3820.0000.0000.0000.000
98A106ILE00.0010.00021.483-0.421-0.4210.0000.0000.0000.000
99A107LYS10.9190.95822.73210.74910.7490.0000.0000.0000.000
100A108SER00.018-0.02921.8110.0780.0780.0000.0000.0000.000
101A109HIS0-0.0360.00615.5060.1130.1130.0000.0000.0000.000
102A110TYR0-0.014-0.01719.934-0.507-0.5070.0000.0000.0000.000
103A111ALA0-0.0070.00222.1230.1410.1410.0000.0000.0000.000
104A112PHE0-0.024-0.00117.2060.2620.2620.0000.0000.0000.000
105A113ARG10.9590.95516.48918.59418.5940.0000.0000.0000.000
106A114ILE0-0.065-0.00520.0200.1850.1850.0000.0000.0000.000
107A115PHE0-0.044-0.03723.1530.6030.6030.0000.0000.0000.000
108A116ASP-1-0.809-0.90416.986-18.666-18.6660.0000.0000.0000.000
109A117PHE0-0.051-0.03720.1290.1090.1090.0000.0000.0000.000
110A118ASP-1-0.968-0.97018.632-14.777-14.7770.0000.0000.0000.000
111A119ASP-1-0.990-0.97614.982-19.306-19.3060.0000.0000.0000.000
112A120ASP-1-0.930-0.94613.820-20.916-20.9160.0000.0000.0000.000
113A121GLY0-0.081-0.05513.190-2.319-2.3190.0000.0000.0000.000
114A122THR0-0.165-0.10514.6610.3530.3530.0000.0000.0000.000
115A123LEU00.0260.02617.9240.5100.5100.0000.0000.0000.000
116A124ASN00.0910.03221.2051.0371.0370.0000.0000.0000.000
117A125ARG10.8380.87623.24411.21411.2140.0000.0000.0000.000
118A126GLU-1-0.881-0.92525.665-10.696-10.6960.0000.0000.0000.000
119A127ASP-1-0.777-0.87522.349-13.837-13.8370.0000.0000.0000.000
120A128LEU0-0.011-0.01825.0680.4110.4110.0000.0000.0000.000
121A129SER0-0.071-0.04327.8270.5810.5810.0000.0000.0000.000
122A130ARG10.8750.93825.39012.52012.5200.0000.0000.0000.000
123A131LEU00.0130.01927.0560.2640.2640.0000.0000.0000.000
124A132VAL0-0.002-0.00829.9740.3520.3520.0000.0000.0000.000
125A133ASN0-0.067-0.03533.1290.5600.5600.0000.0000.0000.000
126A134CYS0-0.046-0.00132.2980.1410.1410.0000.0000.0000.000
127A135LEU0-0.039-0.01535.0260.2160.2160.0000.0000.0000.000
128A136THR0-0.087-0.04037.5970.0060.0060.0000.0000.0000.000
129A137GLY00.000-0.00441.292-0.028-0.0280.0000.0000.0000.000
130A138GLU-1-0.939-0.96643.277-6.778-6.7780.0000.0000.0000.000
131A139GLY00.001-0.00246.1130.0310.0310.0000.0000.0000.000
132A140GLU-1-0.942-0.97345.547-6.902-6.9020.0000.0000.0000.000
133A141ASP-1-0.932-0.96244.452-7.245-7.2450.0000.0000.0000.000
134A142THR0-0.104-0.05144.6760.0850.0850.0000.0000.0000.000
135A143ARG10.9230.94140.5647.6597.6590.0000.0000.0000.000
136A144LEU00.0410.04036.6800.1990.1990.0000.0000.0000.000
137A145SER0-0.046-0.04840.698-0.019-0.0190.0000.0000.0000.000
138A146ALA00.042-0.00538.290-0.172-0.1720.0000.0000.0000.000
139A147SER0-0.074-0.03038.130-0.154-0.1540.0000.0000.0000.000
140A148GLU-1-0.769-0.85539.164-7.762-7.7620.0000.0000.0000.000
141A149MET00.0190.02134.393-0.209-0.2090.0000.0000.0000.000
142A150LYS10.8550.90634.5568.6248.6240.0000.0000.0000.000
143A151GLN0-0.035-0.02234.394-0.105-0.1050.0000.0000.0000.000
144A152LEU00.0380.01634.623-0.120-0.1200.0000.0000.0000.000
145A153ILE00.0080.00529.084-0.251-0.2510.0000.0000.0000.000
146A154ASP-1-0.796-0.87430.359-9.856-9.8560.0000.0000.0000.000
147A155ASN0-0.015-0.00531.792-0.090-0.0900.0000.0000.0000.000
148A156ILE00.0070.01027.482-0.106-0.1060.0000.0000.0000.000
149A157LEU00.0120.00725.840-0.235-0.2350.0000.0000.0000.000
150A158GLU-1-0.918-0.95727.931-10.214-10.2140.0000.0000.0000.000
151A159GLU-1-0.928-0.96529.951-10.117-10.1170.0000.0000.0000.000
152A160SER0-0.056-0.03125.652-0.077-0.0770.0000.0000.0000.000
153A161ASP-1-0.787-0.87922.995-13.786-13.7860.0000.0000.0000.000
154A162ILE0-0.083-0.04321.7190.4520.4520.0000.0000.0000.000
155A163ASP-1-0.961-0.98417.981-16.647-16.6470.0000.0000.0000.000
156A164ARG10.7260.85820.92511.58311.5830.0000.0000.0000.000
157A165ASP-1-0.872-0.89518.185-16.180-16.1800.0000.0000.0000.000
158A166GLY0-0.041-0.01621.2180.1530.1530.0000.0000.0000.000
159A167THR0-0.156-0.10319.7230.2530.2530.0000.0000.0000.000
160A168ILE0-0.0080.00421.8390.4490.4490.0000.0000.0000.000
161A169ASN00.0700.02216.443-0.863-0.8630.0000.0000.0000.000
162A170LEU00.0230.00015.9490.6240.6240.0000.0000.0000.000
163A171SER0-0.032-0.02817.3800.5620.5620.0000.0000.0000.000
164A172GLU-1-0.835-0.89419.192-14.415-14.4150.0000.0000.0000.000
165A173PHE00.0300.01021.5070.7540.7540.0000.0000.0000.000
166A174GLN00.0270.01019.8740.0680.0680.0000.0000.0000.000
167A175HIS10.8250.91123.70011.98011.9800.0000.0000.0000.000
168A176VAL00.0000.02025.7910.5500.5500.0000.0000.0000.000
169A177ILE00.0260.00426.0690.5560.5560.0000.0000.0000.000
170A178SER0-0.075-0.03727.8720.4750.4750.0000.0000.0000.000
171A179ARG10.9220.95229.3299.6409.6400.0000.0000.0000.000
172A180SER00.0340.01931.5360.4340.4340.0000.0000.0000.000
173A181PRO0-0.020-0.01932.370-0.198-0.1980.0000.0000.0000.000
174A182ASP-1-0.879-0.92433.500-8.954-8.9540.0000.0000.0000.000
175A183PHE00.0330.03327.879-0.055-0.0550.0000.0000.0000.000
176A184ALA0-0.046-0.04030.247-0.108-0.1080.0000.0000.0000.000
177A185SER0-0.063-0.04731.446-0.076-0.0760.0000.0000.0000.000
178A186SER0-0.079-0.04834.3960.2120.2120.0000.0000.0000.000
179A187PHE00.0180.00628.8540.0280.0280.0000.0000.0000.000
180A188LYS10.9120.97732.1528.2838.2830.0000.0000.0000.000
181A189ILE00.0080.00229.751-0.142-0.1420.0000.0000.0000.000
182A190VAL0-0.059-0.02833.6410.3410.3410.0000.0000.0000.000
183A191LEU-1-0.929-0.96035.482-9.010-9.0100.0000.0000.0000.000