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: 2RRZR

Calculation Name: 4E9J-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4E9J

Chain ID: A

ChEMBL ID:

UniProt ID: P35818

Base Structure: X-ray

Registration Date: 2025-10-04

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 222
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2385247.748611
FMO2-HF: Nuclear repulsion 2301612.99387
FMO2-HF: Total energy -83634.754741
FMO2-MP2: Total energy -83882.667426


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:41:ALA)


Summations of interaction energy for fragment #1(A:41: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.
-174.072-169.5638.742-6.993-6.258-0.061
Interaction energy analysis for fragmet #1(A:41:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.924
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].
3A43VAL0-0.004-0.0013.5710.0451.3850.013-0.583-0.7700.000
15A55ILE00.000-0.0093.644-6.397-6.1900.001-0.078-0.1300.000
16A56ASN00.003-0.0074.7628.9629.084-0.001-0.008-0.1130.000
17A57LEU00.0190.0322.446-6.707-6.0180.322-0.308-0.703-0.004
18A58LYS10.8780.9284.71536.87336.909-0.001-0.006-0.0290.000
24A64GLU-1-0.875-0.9254.037-58.327-58.115-0.001-0.075-0.1360.000
28A68GLN0-0.049-0.0412.105-22.255-20.5268.411-5.918-4.221-0.057
29A69ILE0-0.026-0.0085.2150.8800.873-0.001-0.0020.0090.000
31A71GLU-1-0.957-0.9624.425-44.382-44.201-0.001-0.015-0.1650.000
4A44PRO0-0.031-0.0145.8693.6123.6120.0000.0000.0000.000
5A45ALA0-0.026-0.0119.0740.3070.3070.0000.0000.0000.000
6A46GLY00.0170.00912.4371.8071.8070.0000.0000.0000.000
7A47ASN0-0.014-0.01514.070-1.154-1.1540.0000.0000.0000.000
8A48GLN00.0080.01216.3590.4910.4910.0000.0000.0000.000
9A49GLN0-0.048-0.02620.0640.4220.4220.0000.0000.0000.000
10A50GLU-1-0.759-0.88616.415-18.080-18.0800.0000.0000.0000.000
11A51ALA0-0.056-0.00312.654-0.181-0.1810.0000.0000.0000.000
12A52HIS0-0.029-0.03013.0340.2660.2660.0000.0000.0000.000
13A53TRP00.0490.0126.792-0.141-0.1410.0000.0000.0000.000
14A54THR0-0.0120.0078.6221.5481.5480.0000.0000.0000.000
19A59ASP-1-0.771-0.8598.000-25.791-25.7910.0000.0000.0000.000
20A60ALA00.0550.0526.3921.5211.5210.0000.0000.0000.000
21A61ASP-1-0.823-0.9148.416-21.214-21.2140.0000.0000.0000.000
22A62ILE0-0.007-0.0129.082-3.287-3.2870.0000.0000.0000.000
23A63ARG10.7970.87810.50918.26918.2690.0000.0000.0000.000
25A65PHE0-0.014-0.0225.954-3.999-3.9990.0000.0000.0000.000
26A66ILE0-0.012-0.0117.0090.0650.0650.0000.0000.0000.000
27A67ASP-1-0.876-0.9337.787-27.521-27.5210.0000.0000.0000.000
30A70SER0-0.035-0.0168.1961.8861.8860.0000.0000.0000.000
32A72ILE0-0.069-0.0325.2771.5391.5390.0000.0000.0000.000
33A73THR0-0.069-0.0728.6133.1393.1390.0000.0000.0000.000
34A74GLY0-0.0170.00711.8691.7601.7600.0000.0000.0000.000
35A75GLU-1-0.894-0.93913.793-15.439-15.4390.0000.0000.0000.000
36A76THR0-0.068-0.02313.633-1.644-1.6440.0000.0000.0000.000
37A77PHE00.0380.00812.2331.3391.3390.0000.0000.0000.000
38A78VAL0-0.0010.01016.401-0.256-0.2560.0000.0000.0000.000
39A79VAL00.0400.01414.1780.2980.2980.0000.0000.0000.000
40A80ASP-1-0.757-0.84117.657-12.728-12.7280.0000.0000.0000.000
41A81PRO00.0220.00019.935-0.599-0.5990.0000.0000.0000.000
42A82ARG10.8210.89121.43412.10512.1050.0000.0000.0000.000
43A83VAL00.0040.02516.0180.2400.2400.0000.0000.0000.000
44A84LYS10.8870.93316.36214.26314.2630.0000.0000.0000.000
45A85GLY00.0650.02815.4600.8970.8970.0000.0000.0000.000
46A86GLN0-0.022-0.00312.013-0.440-0.4400.0000.0000.0000.000
47A87VAL0-0.016-0.0148.0551.1391.1390.0000.0000.0000.000
48A88SER00.0120.0218.553-3.776-3.7760.0000.0000.0000.000
49A89VAL0-0.006-0.0046.6742.6072.6070.0000.0000.0000.000
50A90VAL0-0.041-0.0176.899-4.926-4.9260.0000.0000.0000.000
51A91SER00.008-0.0158.9303.9233.9230.0000.0000.0000.000
52A92LYS10.8760.91510.28217.19417.1940.0000.0000.0000.000
53A93ALA00.0120.02612.6510.7690.7690.0000.0000.0000.000
54A94GLN0-0.010-0.00212.528-2.492-2.4920.0000.0000.0000.000
55A95LEU0-0.038-0.01410.8791.6081.6080.0000.0000.0000.000
56A96SER00.0370.00412.811-1.343-1.3430.0000.0000.0000.000
57A97LEU00.0600.03112.742-1.216-1.2160.0000.0000.0000.000
58A98SER0-0.033-0.02614.099-0.083-0.0830.0000.0000.0000.000
59A99GLU-1-0.798-0.84915.069-17.499-17.4990.0000.0000.0000.000
60A100VAL0-0.0040.0028.930-0.434-0.4340.0000.0000.0000.000
61A101TYR00.0610.02711.526-0.730-0.7300.0000.0000.0000.000
62A102GLN0-0.020-0.02513.7651.0051.0050.0000.0000.0000.000
63A103LEU00.0030.0019.4630.4410.4410.0000.0000.0000.000
64A104PHE00.0220.00811.151-0.210-0.2100.0000.0000.0000.000
65A105LEU0-0.0050.00712.4500.7400.7400.0000.0000.0000.000
66A106SER0-0.008-0.01715.1200.7390.7390.0000.0000.0000.000
67A107VAL0-0.0290.01010.3850.9280.9280.0000.0000.0000.000
68A108MET0-0.019-0.00712.3650.9120.9120.0000.0000.0000.000
69A109SER0-0.0070.00215.9760.9740.9740.0000.0000.0000.000
70A110THR0-0.049-0.03415.7350.8520.8520.0000.0000.0000.000
71A111HIS0-0.015-0.00413.9771.0761.0760.0000.0000.0000.000
72A112GLY00.0010.02317.8700.3930.3930.0000.0000.0000.000
73A113PHE0-0.012-0.01616.6730.6560.6560.0000.0000.0000.000
74A114THR0-0.015-0.01319.702-0.205-0.2050.0000.0000.0000.000
75A115VAL00.0160.00517.351-0.345-0.3450.0000.0000.0000.000
76A116VAL0-0.024-0.00220.3310.6460.6460.0000.0000.0000.000
77A117ALA00.0430.02422.619-0.461-0.4610.0000.0000.0000.000
78A118GLN0-0.037-0.03724.5960.2590.2590.0000.0000.0000.000
79A119GLY0-0.039-0.02125.243-0.279-0.2790.0000.0000.0000.000
80A120ASP-1-0.948-0.97426.325-11.457-11.4570.0000.0000.0000.000
81A121GLN00.0430.02419.242-0.926-0.9260.0000.0000.0000.000
82A122ALA00.0470.04018.7400.4730.4730.0000.0000.0000.000
83A123ARG10.8460.90619.75412.84112.8410.0000.0000.0000.000
84A124ILE00.0320.02414.5100.3620.3620.0000.0000.0000.000
85A125VAL0-0.032-0.03218.6920.2410.2410.0000.0000.0000.000
86A126PRO0-0.031-0.02821.163-0.361-0.3610.0000.0000.0000.000
87A127ASN0-0.020-0.00322.9300.7230.7230.0000.0000.0000.000
88A128ALA-1-0.954-0.96224.943-11.377-11.3770.0000.0000.0000.000
89A140ALA10.8520.92121.37813.21513.2150.0000.0000.0000.000
90A141PRO00.0350.02020.6450.3830.3830.0000.0000.0000.000
91A142ASP-1-0.915-0.95718.192-17.208-17.2080.0000.0000.0000.000
92A143ARG0-0.065-0.02613.1040.5470.5470.0000.0000.0000.000
93A144LEU0-0.048-0.02915.1091.1011.1010.0000.0000.0000.000
94A145GLU-1-0.802-0.86911.396-24.734-24.7340.0000.0000.0000.000
95A146THR0-0.018-0.02411.6641.5151.5150.0000.0000.0000.000
96A147ARG10.7800.85711.45517.58117.5810.0000.0000.0000.000
97A148VAL00.0100.00812.4411.5631.5630.0000.0000.0000.000
98A149ILE0-0.062-0.03714.774-0.248-0.2480.0000.0000.0000.000
99A150GLN0-0.047-0.03618.0350.1960.1960.0000.0000.0000.000
100A151VAL0-0.022-0.00319.7530.2650.2650.0000.0000.0000.000
101A152GLN0-0.070-0.03423.159-0.555-0.5550.0000.0000.0000.000
102A153GLN0-0.056-0.03325.8910.1360.1360.0000.0000.0000.000
103A154SER0-0.014-0.02228.5590.5020.5020.0000.0000.0000.000
104A155PRO00.0220.02627.655-0.528-0.5280.0000.0000.0000.000
105A156VAL00.0340.02622.8470.2660.2660.0000.0000.0000.000
106A157SER0-0.011-0.01626.152-0.045-0.0450.0000.0000.0000.000
107A158GLU-1-0.895-0.95528.587-9.412-9.4120.0000.0000.0000.000
108A159LEU00.0130.00326.2290.2220.2220.0000.0000.0000.000
109A160ILE00.0000.00523.9290.0900.0900.0000.0000.0000.000
110A161PRO0-0.058-0.04027.5790.0030.0030.0000.0000.0000.000
111A162LEU0-0.0170.00130.5470.2100.2100.0000.0000.0000.000
112A163ILE00.0360.01624.0740.0630.0630.0000.0000.0000.000
113A164ARG10.9560.99025.48911.57111.5710.0000.0000.0000.000
114A165PRO0-0.057-0.03228.104-0.026-0.0260.0000.0000.0000.000
115A166LEU0-0.026-0.00626.6420.1120.1120.0000.0000.0000.000
116A167VAL0-0.0020.01622.691-0.343-0.3430.0000.0000.0000.000
117A168PRO0-0.0080.01023.6130.5310.5310.0000.0000.0000.000
118A169GLN00.010-0.02625.087-0.484-0.4840.0000.0000.0000.000
119A170TYR0-0.072-0.05921.1140.3880.3880.0000.0000.0000.000
120A171GLY00.0270.02920.713-0.630-0.6300.0000.0000.0000.000
121A172HIS00.0020.01218.4450.1390.1390.0000.0000.0000.000
122A173LEU0-0.015-0.01620.354-0.157-0.1570.0000.0000.0000.000
123A174ALA0-0.0050.00619.7310.7560.7560.0000.0000.0000.000
124A175ALA0-0.004-0.01321.016-0.209-0.2090.0000.0000.0000.000
125A176VAL00.0330.02617.1950.0180.0180.0000.0000.0000.000
126A177PRO0-0.014-0.02520.6270.0090.0090.0000.0000.0000.000
127A178SER0-0.054-0.04219.9600.4740.4740.0000.0000.0000.000
128A179ALA00.0450.03518.4600.2020.2020.0000.0000.0000.000
129A180ASN0-0.002-0.01820.4980.0720.0720.0000.0000.0000.000
130A181ALA00.0160.00218.169-0.027-0.0270.0000.0000.0000.000
131A182LEU0-0.021-0.01119.7360.5230.5230.0000.0000.0000.000
132A183ILE00.0270.01315.072-1.066-1.0660.0000.0000.0000.000
133A184ILE0-0.011-0.01016.8111.1621.1620.0000.0000.0000.000
134A185SER0-0.005-0.01316.083-1.696-1.6960.0000.0000.0000.000
135A186ASP-1-0.775-0.85716.994-12.967-12.9670.0000.0000.0000.000
136A187ARG00.022-0.02016.966-0.919-0.9190.0000.0000.0000.000
137A188SER00.030-0.02114.1950.6380.6380.0000.0000.0000.000
138A189ALA0-0.019-0.01317.0630.2080.2080.0000.0000.0000.000
139A190ASN0-0.041-0.02220.6321.0681.0680.0000.0000.0000.000
140A191ILE00.0020.00515.6390.5740.5740.0000.0000.0000.000
141A192ALA0-0.008-0.00319.6080.2750.2750.0000.0000.0000.000
142A193ARG10.8900.94520.76712.68912.6890.0000.0000.0000.000
143A194ILE0-0.008-0.00622.0550.4790.4790.0000.0000.0000.000
144A195GLU-1-0.787-0.87818.131-17.388-17.3880.0000.0000.0000.000
145A196ASP-1-0.866-0.92522.153-11.534-11.5340.0000.0000.0000.000
146A197VAL00.0270.01725.3240.4590.4590.0000.0000.0000.000
147A198ILE0-0.026-0.00722.1270.3680.3680.0000.0000.0000.000
148A199ARG10.9020.94624.81212.15612.1560.0000.0000.0000.000
149A200GLN0-0.019-0.01126.5160.2300.2300.0000.0000.0000.000
150A201LEU0-0.020-0.02129.1120.3990.3990.0000.0000.0000.000
151A202ASP-1-0.751-0.84327.222-11.381-11.3810.0000.0000.0000.000
152A203GLN0-0.0070.01229.5170.0700.0700.0000.0000.0000.000
153A204LYS0-0.067-0.01932.3150.4990.4990.0000.0000.0000.000
154A205GLY00.011-0.00534.374-0.131-0.1310.0000.0000.0000.000
155A206SER0-0.020-0.01236.6270.1360.1360.0000.0000.0000.000
156A207HIS10.8770.91732.4349.7469.7460.0000.0000.0000.000
157A208ASP-1-0.836-0.90235.598-8.069-8.0690.0000.0000.0000.000
158A209TYR0-0.044-0.03635.2820.0460.0460.0000.0000.0000.000
159A210SER0-0.020-0.00139.3190.0820.0820.0000.0000.0000.000
160A211VAL0-0.027-0.01839.070-0.177-0.1770.0000.0000.0000.000
161A212ILE0-0.0060.00241.7110.2010.2010.0000.0000.0000.000
162A213ASN0-0.015-0.02241.929-0.326-0.3260.0000.0000.0000.000
163A214LEU0-0.0290.01243.0890.1460.1460.0000.0000.0000.000
164A215ARG10.8810.93545.7486.0226.0220.0000.0000.0000.000
165A216TYR0-0.032-0.03348.5770.0720.0720.0000.0000.0000.000
166A217GLY00.0360.03247.6850.0030.0030.0000.0000.0000.000
167A218TRP0-0.001-0.00339.091-0.208-0.2080.0000.0000.0000.000
168A219VAL00.007-0.00938.886-0.012-0.0120.0000.0000.0000.000
169A220MET0-0.037-0.01436.117-0.126-0.1260.0000.0000.0000.000
170A221ASP-1-0.815-0.90440.622-7.167-7.1670.0000.0000.0000.000
171A222ALA00.0060.00143.7650.0720.0720.0000.0000.0000.000
172A223ALA00.016-0.00539.3630.0400.0400.0000.0000.0000.000
173A224GLU-1-0.962-0.97141.500-7.540-7.5400.0000.0000.0000.000
174A225VAL00.005-0.00242.3600.0850.0850.0000.0000.0000.000
175A226LEU0-0.0040.00043.4710.1070.1070.0000.0000.0000.000
176A227ASN00.0290.00538.5750.1000.1000.0000.0000.0000.000
177A228ASN00.0090.01142.5850.0020.0020.0000.0000.0000.000
178A229ALA00.0100.00745.3140.1090.1090.0000.0000.0000.000
179A230MET0-0.048-0.02141.7190.1490.1490.0000.0000.0000.000
180A231SER0-0.019-0.01442.8240.0160.0160.0000.0000.0000.000
181A232ARG10.8990.96445.0106.7616.7610.0000.0000.0000.000
182A233GLY00.0220.02348.2000.1590.1590.0000.0000.0000.000
183A234GLN0-0.034-0.02550.0490.0820.0820.0000.0000.0000.000
184A235ALA00.0300.02148.2050.1290.1290.0000.0000.0000.000
185A236LYS10.8710.92250.0235.8975.8970.0000.0000.0000.000
186A237GLY00.008-0.00251.3960.0470.0470.0000.0000.0000.000
187A238ALA00.0090.00446.687-0.053-0.0530.0000.0000.0000.000
188A239ALA0-0.003-0.00345.646-0.174-0.1740.0000.0000.0000.000
189A240GLY00.0210.00642.4210.0480.0480.0000.0000.0000.000
190A241ALA0-0.052-0.01941.518-0.163-0.1630.0000.0000.0000.000
191A242GLN00.007-0.01034.769-0.198-0.1980.0000.0000.0000.000
192A243VAL00.0010.00439.0090.0720.0720.0000.0000.0000.000
193A244ILE00.0110.01732.263-0.156-0.1560.0000.0000.0000.000
194A245ALA00.0300.01135.2810.2420.2420.0000.0000.0000.000
195A246ASP-1-0.798-0.88634.088-9.731-9.7310.0000.0000.0000.000
196A247ALA00.0580.01235.1730.2070.2070.0000.0000.0000.000
197A248ARG10.8060.89829.34410.44110.4410.0000.0000.0000.000
198A249THR0-0.026-0.01735.6630.1190.1190.0000.0000.0000.000
199A250ASN0-0.018-0.00838.6910.0610.0610.0000.0000.0000.000
200A251ARG10.9000.95435.0088.9348.9340.0000.0000.0000.000
201A252LEU0-0.015-0.00638.807-0.221-0.2210.0000.0000.0000.000
202A253ILE0-0.014-0.00734.6680.1080.1080.0000.0000.0000.000
203A254ILE0-0.007-0.00438.437-0.061-0.0610.0000.0000.0000.000
204A255LEU00.0620.02234.9030.0310.0310.0000.0000.0000.000
205A256GLY00.0580.01539.3410.1830.1830.0000.0000.0000.000
206A257PRO00.0160.02241.226-0.001-0.0010.0000.0000.0000.000
207A258PRO00.0330.00843.5420.0930.0930.0000.0000.0000.000
208A259GLN00.0360.00945.9810.0080.0080.0000.0000.0000.000
209A260ALA00.0200.02745.3660.0880.0880.0000.0000.0000.000
210A261ARG10.8330.92641.5307.6857.6850.0000.0000.0000.000
211A262ALA00.0280.00944.9050.0160.0160.0000.0000.0000.000
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