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: QLRNY

Calculation Name: 5AAR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5AAR

Chain ID: A

ChEMBL ID:

UniProt ID: Q38998

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1843410.659482
FMO2-HF: Nuclear repulsion 1771198.58527
FMO2-HF: Total energy -72212.074212
FMO2-MP2: Total energy -72420.38944


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:518:LEU)


Summations of interaction energy for fragment #1(A:518:LEU)
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.
-96.747-92.9132.125-1.789-4.17-0.011
Interaction energy analysis for fragmet #1(A:518:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.912
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].
3A520LEU00.0210.0143.468-1.0790.6620.013-0.776-0.977-0.002
7A524PHE0-0.048-0.0162.285-2.793-1.4481.413-0.637-2.122-0.006
11A528ARG10.8030.8862.55038.07238.8200.699-0.376-1.071-0.003
4A521ASN00.0470.0095.6922.8472.8470.0000.0000.0000.000
5A522LEU00.0860.0438.039-0.897-0.8970.0000.0000.0000.000
6A523CYS00.0540.0367.5681.2361.2360.0000.0000.0000.000
8A525ALA00.0250.0185.7100.3560.3560.0000.0000.0000.000
9A526ALA00.0620.0329.1721.0451.0450.0000.0000.0000.000
10A527ILE0-0.034-0.0245.4610.8670.8670.0000.0000.0000.000
12A529GLU-1-0.828-0.8799.350-15.728-15.7280.0000.0000.0000.000
13A530ASP-1-0.874-0.92810.675-20.574-20.5740.0000.0000.0000.000
14A531ASP-1-0.796-0.92612.521-16.018-16.0180.0000.0000.0000.000
15A532LEU0-0.0070.01115.4840.4680.4680.0000.0000.0000.000
16A533LEU0-0.024-0.0208.459-0.195-0.1950.0000.0000.0000.000
17A534LEU00.0120.00412.538-0.545-0.5450.0000.0000.0000.000
18A535HIS00.0120.01113.6830.6340.6340.0000.0000.0000.000
19A536GLN0-0.044-0.03614.551-0.422-0.4220.0000.0000.0000.000
20A537LEU0-0.054-0.0339.3420.0120.0120.0000.0000.0000.000
21A538LEU00.0260.02313.9160.1660.1660.0000.0000.0000.000
22A539LYS10.9010.96016.97513.73313.7330.0000.0000.0000.000
23A540ARG10.8630.93313.50920.72720.7270.0000.0000.0000.000
24A541GLY00.0110.01817.371-0.214-0.2140.0000.0000.0000.000
25A542LEU0-0.078-0.03610.877-0.611-0.6110.0000.0000.0000.000
26A543ASP-1-0.773-0.89015.302-15.291-15.2910.0000.0000.0000.000
27A544PRO0-0.036-0.03615.537-1.324-1.3240.0000.0000.0000.000
28A545ASN0-0.048-0.03816.6130.2680.2680.0000.0000.0000.000
29A546GLU-1-0.953-0.95313.891-18.860-18.8600.0000.0000.0000.000
30A547SER0-0.027-0.02013.290-0.098-0.0980.0000.0000.0000.000
31A548ASP-1-0.904-0.9529.635-24.023-24.0230.0000.0000.0000.000
32A549ASN0-0.044-0.04211.0291.5861.5860.0000.0000.0000.000
33A550ASN0-0.039-0.00812.0941.6231.6230.0000.0000.0000.000
34A551GLY00.0540.03514.7341.1021.1020.0000.0000.0000.000
35A552ARG10.7250.82512.11117.88917.8890.0000.0000.0000.000
36A553THR00.0600.00312.767-1.414-1.4140.0000.0000.0000.000
37A554PRO0-0.010-0.02611.902-0.365-0.3650.0000.0000.0000.000
38A555LEU00.0160.00913.0420.1840.1840.0000.0000.0000.000
39A556HIS00.0670.04414.996-0.243-0.2430.0000.0000.0000.000
40A557ILE0-0.038-0.0149.280-0.022-0.0220.0000.0000.0000.000
41A558ALA0-0.014-0.01813.4000.3080.3080.0000.0000.0000.000
42A559ALA0-0.024-0.01415.4880.5760.5760.0000.0000.0000.000
43A560SER0-0.0190.01115.2480.2410.2410.0000.0000.0000.000
44A561LYS10.8820.93410.95820.70720.7070.0000.0000.0000.000
45A562GLY00.0770.05416.2140.4670.4670.0000.0000.0000.000
46A563THR0-0.093-0.08015.8710.3860.3860.0000.0000.0000.000
47A564LEU00.004-0.01118.270-0.163-0.1630.0000.0000.0000.000
48A565ASN0-0.035-0.02119.0970.4200.4200.0000.0000.0000.000
49A566CYS0-0.0030.00514.590-0.090-0.0900.0000.0000.0000.000
50A567VAL00.0380.02717.491-0.082-0.0820.0000.0000.0000.000
51A568LEU0-0.026-0.01419.8520.2640.2640.0000.0000.0000.000
52A569LEU00.0160.00618.2650.1160.1160.0000.0000.0000.000
53A570LEU0-0.032-0.02415.127-0.156-0.1560.0000.0000.0000.000
54A571LEU0-0.0040.00119.2680.2630.2630.0000.0000.0000.000
55A572GLU-1-0.982-0.97922.901-12.020-12.0200.0000.0000.0000.000
56A573TYR0-0.095-0.05720.0100.1320.1320.0000.0000.0000.000
57A574HIS0-0.012-0.00921.493-0.239-0.2390.0000.0000.0000.000
58A575ALA00.0070.01419.261-0.170-0.1700.0000.0000.0000.000
59A576ASP-1-0.828-0.92420.993-11.642-11.6420.0000.0000.0000.000
60A577PRO0-0.014-0.00622.008-0.439-0.4390.0000.0000.0000.000
61A578ASN0-0.049-0.02624.1310.1480.1480.0000.0000.0000.000
62A579CYS0-0.0190.02918.8770.0410.0410.0000.0000.0000.000
63A580ARG10.8790.91921.23511.03011.0300.0000.0000.0000.000
64A581ASP-1-0.833-0.89917.387-15.373-15.3730.0000.0000.0000.000
65A582ALA0-0.016-0.02318.2520.6890.6890.0000.0000.0000.000
66A583GLU-1-0.955-0.96618.918-13.310-13.3100.0000.0000.0000.000
67A584GLY0-0.055-0.03121.5090.6530.6530.0000.0000.0000.000
68A585SER0-0.009-0.03819.7060.7900.7900.0000.0000.0000.000
69A586VAL00.0410.02721.114-0.348-0.3480.0000.0000.0000.000
70A587PRO00.016-0.00719.3000.1190.1190.0000.0000.0000.000
71A588LEU0-0.009-0.00920.9650.0280.0280.0000.0000.0000.000
72A589TRP00.0680.02322.2740.4570.4570.0000.0000.0000.000
73A590GLU-1-0.797-0.84617.517-15.169-15.1690.0000.0000.0000.000
74A591ALA0-0.012-0.00120.567-0.093-0.0930.0000.0000.0000.000
75A592MET0-0.050-0.00922.5060.2300.2300.0000.0000.0000.000
76A593VAL0-0.046-0.01122.0900.3020.3020.0000.0000.0000.000
77A594GLU-1-0.931-0.96419.306-13.116-13.1160.0000.0000.0000.000
78A595GLY0-0.0040.01922.8140.1210.1210.0000.0000.0000.000
79A596HIS00.0210.02619.3070.7020.7020.0000.0000.0000.000
80A597GLU-1-0.919-0.98924.344-9.878-9.8780.0000.0000.0000.000
81A598LYS10.8420.90825.52710.76910.7690.0000.0000.0000.000
82A599VAL00.0380.02421.1660.1130.1130.0000.0000.0000.000
83A600VAL00.0420.03024.3980.0450.0450.0000.0000.0000.000
84A601LYS10.9050.96126.7879.3719.3710.0000.0000.0000.000
85A602VAL00.0440.03125.0230.0830.0830.0000.0000.0000.000
86A603LEU00.0170.01322.068-0.029-0.0290.0000.0000.0000.000
87A604LEU00.0040.01226.2010.1840.1840.0000.0000.0000.000
88A605GLU-1-0.982-0.99929.676-9.511-9.5110.0000.0000.0000.000
89A606HIS10.7870.88426.79610.76710.7670.0000.0000.0000.000
90A607GLY00.0360.02428.459-0.162-0.1620.0000.0000.0000.000
91A608SER0-0.030-0.02825.095-0.038-0.0380.0000.0000.0000.000
92A609THR0-0.063-0.05227.7280.1970.1970.0000.0000.0000.000
93A610ILE00.007-0.00527.306-0.318-0.3180.0000.0000.0000.000
94A611ASP-1-0.888-0.93629.049-9.277-9.2770.0000.0000.0000.000
95A612ALA00.0140.02827.3580.0160.0160.0000.0000.0000.000
96A613GLY00.0240.01225.939-0.387-0.3870.0000.0000.0000.000
97A614ASP-1-0.926-0.95326.154-9.822-9.8220.0000.0000.0000.000
98A615VAL00.0280.00728.025-0.044-0.0440.0000.0000.0000.000
99A616GLY00.0440.03630.5190.1550.1550.0000.0000.0000.000
100A617HIS00.0330.02522.7690.5810.5810.0000.0000.0000.000
101A618PHE0-0.0350.00624.031-0.058-0.0580.0000.0000.0000.000
102A619ALA00.0290.01227.9380.0350.0350.0000.0000.0000.000
103A620CYS0-0.060-0.03129.6290.2380.2380.0000.0000.0000.000
104A621THR00.016-0.00724.119-0.058-0.0580.0000.0000.0000.000
105A622ALA0-0.031-0.02127.459-0.046-0.0460.0000.0000.0000.000
106A623ALA0-0.025-0.02829.5120.1540.1540.0000.0000.0000.000
107A624GLU-1-0.787-0.86027.162-10.369-10.3690.0000.0000.0000.000
108A625GLN0-0.053-0.01523.5220.1140.1140.0000.0000.0000.000
109A626GLY00.0120.01128.6000.0910.0910.0000.0000.0000.000
110A627ASN00.0010.00227.9720.5540.5540.0000.0000.0000.000
111A628LEU00.0330.00731.529-0.040-0.0400.0000.0000.0000.000
112A629LYS10.9290.95832.7738.7298.7290.0000.0000.0000.000
113A630LEU00.0410.03126.8000.1470.1470.0000.0000.0000.000
114A631LEU00.0310.01431.1740.0120.0120.0000.0000.0000.000
115A632LYS10.8690.94033.7877.6367.6360.0000.0000.0000.000
116A633GLU-1-0.852-0.91429.741-9.629-9.6290.0000.0000.0000.000
117A634ILE0-0.0020.00329.855-0.028-0.0280.0000.0000.0000.000
118A635VAL00.0070.02332.5480.0160.0160.0000.0000.0000.000
119A636LEU0-0.068-0.01735.0220.1180.1180.0000.0000.0000.000
120A637HIS10.7480.83830.2949.2619.2610.0000.0000.0000.000
121A638GLY00.0330.01933.804-0.141-0.1410.0000.0000.0000.000
122A639GLY00.013-0.00333.4730.0230.0230.0000.0000.0000.000
123A640ASP-1-0.799-0.88334.401-7.745-7.7450.0000.0000.0000.000
124A641VAL0-0.001-0.01733.775-0.164-0.1640.0000.0000.0000.000
125A642THR0-0.048-0.03335.759-0.023-0.0230.0000.0000.0000.000
126A643ARG10.8330.92434.5358.3088.3080.0000.0000.0000.000
127A644PRO0-0.021-0.00734.740-0.102-0.1020.0000.0000.0000.000
128A645ARG10.8310.86226.45710.32910.3290.0000.0000.0000.000
129A646ALA00.0200.00030.2060.2860.2860.0000.0000.0000.000
130A647THR00.002-0.00330.5100.1080.1080.0000.0000.0000.000
131A648GLY0-0.047-0.02533.2810.2370.2370.0000.0000.0000.000
132A649THR00.0390.01132.9540.1350.1350.0000.0000.0000.000
133A650SER00.030-0.00434.056-0.176-0.1760.0000.0000.0000.000
134A651ALA00.0900.03834.100-0.051-0.0510.0000.0000.0000.000
135A652LEU00.0100.01135.0300.0140.0140.0000.0000.0000.000
136A653HIS00.0200.01536.443-0.037-0.0370.0000.0000.0000.000
137A654THR00.0030.00531.9540.0020.0020.0000.0000.0000.000
138A655ALA0-0.001-0.00835.2050.0070.0070.0000.0000.0000.000
139A656VAL0-0.049-0.00837.3360.1420.1420.0000.0000.0000.000
140A657CYS0-0.045-0.01435.6960.0820.0820.0000.0000.0000.000
141A658GLU-1-0.935-0.97533.035-8.746-8.7460.0000.0000.0000.000
142A659GLU-1-0.895-0.94436.271-7.063-7.0630.0000.0000.0000.000
143A660ASN0-0.0070.00835.6010.3070.3070.0000.0000.0000.000
144A661ILE00.0670.01939.1600.0310.0310.0000.0000.0000.000
145A662GLU-1-0.905-0.95640.462-7.199-7.1990.0000.0000.0000.000
146A663MET0-0.0320.00133.6340.0120.0120.0000.0000.0000.000
147A664VAL00.0350.00939.2270.0030.0030.0000.0000.0000.000
148A665LYS10.8200.92941.8726.7746.7740.0000.0000.0000.000
149A666TYR00.0580.02137.5620.0650.0650.0000.0000.0000.000
150A667LEU0-0.001-0.01136.7620.0060.0060.0000.0000.0000.000
151A668LEU00.0200.02140.9190.0090.0090.0000.0000.0000.000
152A669GLU-1-0.943-0.97544.394-6.538-6.5380.0000.0000.0000.000
153A670GLN0-0.104-0.05239.702-0.031-0.0310.0000.0000.0000.000
154A671GLY0-0.0020.00742.886-0.045-0.0450.0000.0000.0000.000
155A672ALA0-0.051-0.03640.664-0.031-0.0310.0000.0000.0000.000
156A673ASP-1-0.867-0.93842.377-6.690-6.6900.0000.0000.0000.000
157A674VAL00.0570.01543.147-0.141-0.1410.0000.0000.0000.000
158A675ASN0-0.047-0.03145.4290.0630.0630.0000.0000.0000.000
159A676LYS10.8850.95838.6477.7087.7080.0000.0000.0000.000
160A677GLN0-0.037-0.02941.525-0.092-0.0920.0000.0000.0000.000
161A678ASP-1-0.848-0.91936.681-8.047-8.0470.0000.0000.0000.000
162A679MET0-0.042-0.03733.6030.0550.0550.0000.0000.0000.000
163A680HIS0-0.074-0.03434.2720.1510.1510.0000.0000.0000.000
164A681GLY0-0.0220.00239.5340.1660.1660.0000.0000.0000.000
165A682TRP00.0150.01239.6230.2840.2840.0000.0000.0000.000
166A683THR0-0.035-0.02241.294-0.136-0.1360.0000.0000.0000.000
167A684PRO0-0.012-0.02140.4250.0200.0200.0000.0000.0000.000
168A685ARG10.8970.94442.4586.2176.2170.0000.0000.0000.000
169A686ASP-1-0.812-0.88844.712-6.521-6.5210.0000.0000.0000.000
170A687LEU0-0.018-0.00639.0920.0260.0260.0000.0000.0000.000
171A688ALA00.0610.02943.1920.0270.0270.0000.0000.0000.000
172A689GLU-1-0.923-0.96845.084-5.973-5.9730.0000.0000.0000.000
173A690GLN0-0.096-0.04244.2470.0990.0990.0000.0000.0000.000
174A691GLN0-0.058-0.03740.090-0.040-0.0400.0000.0000.0000.000
175A692GLY0-0.058-0.01644.7570.0400.0400.0000.0000.0000.000
176A693HIS00.0350.01743.8630.2270.2270.0000.0000.0000.000
177A694GLU-1-0.802-0.91147.331-5.776-5.7760.0000.0000.0000.000
178A695ASP-1-0.908-0.93647.783-6.059-6.0590.0000.0000.0000.000
179A696ILE0-0.019-0.00642.7170.0310.0310.0000.0000.0000.000
180A697LYS10.8860.93646.9806.0126.0120.0000.0000.0000.000
181A698ALA0-0.113-0.04249.6660.1000.1000.0000.0000.0000.000
182A699LEU00.023-0.00246.9120.0040.0040.0000.0000.0000.000
183A700PHE0-0.021-0.00843.565-0.067-0.0670.0000.0000.0000.000
184A701ARG10.7230.85149.5165.7365.7360.0000.0000.0000.000
185A702GLU-2-1.881-1.91651.918-11.530-11.5300.0000.0000.0000.000