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: RQK78

Calculation Name: 1IRU-L-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IRU

Chain ID: L

ChEMBL ID:

UniProt ID: Q3T0X5

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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2263507.171178
FMO2-HF: Nuclear repulsion 2184849.631673
FMO2-HF: Total energy -78657.539505
FMO2-MP2: Total energy -78884.354368


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:1:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-95.826-85.60336.921-21.24-25.899-0.183
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.725 / q_NPA : 0.868
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].
3A3THR00.0120.0082.6165.9967.7010.593-0.558-1.740-0.004
4A4LEU0-0.009-0.0034.7410.4210.417-0.001-0.0040.0090.000
16A16ALA00.006-0.0074.511-2.627-2.582-0.001-0.004-0.0400.000
17A17ASP-1-0.671-0.8072.277-75.144-72.2573.674-3.426-3.135-0.041
18A18SER00.000-0.0135.070-0.471-0.376-0.001-0.003-0.0910.000
19A19ARG10.8150.9124.49443.94744.039-0.001-0.009-0.0820.000
20A20ALA0-0.009-0.0054.048-5.722-5.3670.002-0.051-0.3050.000
33A33LYS10.7850.8701.90852.82250.2759.905-3.141-4.2160.032
45A45MET0-0.0010.0104.5930.3370.466-0.001-0.025-0.1030.000
46A46ALA00.010-0.0072.409-11.734-9.9521.457-1.254-1.984-0.012
47A47GLY00.0410.0363.2706.9346.7360.0250.356-0.184-0.001
48A48GLY00.028-0.0034.815-3.451-3.391-0.001-0.001-0.0570.000
129A129GLY00.0280.0132.653-7.638-6.6420.297-0.583-0.710-0.003
130A130SER0-0.033-0.0281.995-6.777-6.5895.425-2.647-2.965-0.032
131A131GLY00.0270.0103.43010.69211.0970.001-0.127-0.2780.000
132A132SER0-0.031-0.0195.1038.8788.992-0.001-0.007-0.1060.000
167A167ASP-1-0.721-0.8232.123-106.546-104.5553.293-2.919-2.365-0.039
168A168ALA00.0580.0325.021-3.390-3.344-0.001-0.001-0.0430.000
169A169TYR0-0.055-0.0182.8333.6214.7450.299-0.575-0.848-0.003
170A170SER0-0.070-0.0591.941-39.756-38.95411.909-6.242-6.470-0.079
171A171GLY00.013-0.0143.2609.99210.1480.049-0.019-0.186-0.001
5A5ALA00.0190.0058.3340.7630.7630.0000.0000.0000.000
6A6PHE00.0360.01111.6050.1510.1510.0000.0000.0000.000
7A7LYS10.8430.95115.16014.10814.1080.0000.0000.0000.000
8A8PHE00.004-0.00518.7190.0030.0030.0000.0000.0000.000
9A9ARG10.8710.92321.80510.72510.7250.0000.0000.0000.000
10A10HIS00.0000.01023.4850.4340.4340.0000.0000.0000.000
11A11GLY00.0110.01321.750-0.048-0.0480.0000.0000.0000.000
12A12VAL0-0.056-0.03415.450-0.150-0.1500.0000.0000.0000.000
13A13ILE0-0.0080.01513.7930.1470.1470.0000.0000.0000.000
14A14VAL00.017-0.0079.767-0.675-0.6750.0000.0000.0000.000
15A15ALA00.0160.0089.4251.0521.0520.0000.0000.0000.000
21A21THR0-0.043-0.0285.2360.5570.5570.0000.0000.0000.000
22A22ALA00.0190.0207.5400.1260.1260.0000.0000.0000.000
23A23GLY00.0270.0109.9111.9651.9650.0000.0000.0000.000
24A24ALA00.0320.0068.549-3.561-3.5610.0000.0000.0000.000
25A25TYR00.0020.01910.392-0.282-0.2820.0000.0000.0000.000
26A26ILE00.023-0.0078.046-2.388-2.3880.0000.0000.0000.000
27A27ALA00.0360.0229.6111.9721.9720.0000.0000.0000.000
28A28SER00.0060.0019.1971.4941.4940.0000.0000.0000.000
29A29GLN00.0590.0238.682-5.397-5.3970.0000.0000.0000.000
30A30THR00.0290.0389.8090.4550.4550.0000.0000.0000.000
31A31VAL0-0.022-0.0036.3991.6321.6320.0000.0000.0000.000
32A32LYS10.9080.9337.94316.90816.9080.0000.0000.0000.000
34A34VAL00.0050.0216.315-1.035-1.0350.0000.0000.0000.000
35A35ILE0-0.020-0.0088.6711.3001.3000.0000.0000.0000.000
36A36GLU-1-0.757-0.84811.471-16.239-16.2390.0000.0000.0000.000
37A37ILE0-0.072-0.01813.6030.8520.8520.0000.0000.0000.000
38A38ASN0-0.002-0.01116.5770.9980.9980.0000.0000.0000.000
39A39PRO00.0170.01719.394-0.444-0.4440.0000.0000.0000.000
40A40TYR00.0300.00321.5370.0460.0460.0000.0000.0000.000
41A41LEU0-0.046-0.03317.5520.0680.0680.0000.0000.0000.000
42A42LEU00.0140.01713.138-0.037-0.0370.0000.0000.0000.000
43A43GLY00.0410.02211.5960.6070.6070.0000.0000.0000.000
44A44THR0-0.071-0.0306.399-0.792-0.7920.0000.0000.0000.000
49A49ALA00.0370.0006.1561.2041.2040.0000.0000.0000.000
50A50ALA00.0040.0117.3261.7131.7130.0000.0000.0000.000
51A51ASP-1-0.792-0.89010.222-20.466-20.4660.0000.0000.0000.000
52A52CYS0-0.040-0.0067.2720.8240.8240.0000.0000.0000.000
53A53SER0-0.008-0.0229.7211.5881.5880.0000.0000.0000.000
54A54PHE0-0.044-0.01311.7261.5161.5160.0000.0000.0000.000
55A55TRP00.0640.01613.6431.4511.4510.0000.0000.0000.000
56A56GLU-1-0.717-0.86010.520-21.371-21.3710.0000.0000.0000.000
57A57ARG10.9550.98814.42515.31015.3100.0000.0000.0000.000
58A58LEU0-0.029-0.01516.8930.9700.9700.0000.0000.0000.000
59A59LEU00.0140.01016.1940.8520.8520.0000.0000.0000.000
60A60ALA00.0420.03417.9890.6840.6840.0000.0000.0000.000
61A61ARG10.9390.97319.72911.82911.8290.0000.0000.0000.000
62A62GLN0-0.001-0.00522.1450.5260.5260.0000.0000.0000.000
63A63CYS0-0.047-0.02720.8490.3610.3610.0000.0000.0000.000
64A64ARG10.9300.96023.61710.48510.4850.0000.0000.0000.000
65A65ILE0-0.014-0.01625.8260.4730.4730.0000.0000.0000.000
66A66TYR00.005-0.00126.5670.3280.3280.0000.0000.0000.000
67A67GLU-1-0.859-0.91327.360-10.166-10.1660.0000.0000.0000.000
68A68LEU0-0.065-0.03829.2190.3360.3360.0000.0000.0000.000
69A69ARG10.9010.95631.3619.3279.3270.0000.0000.0000.000
70A70ASN0-0.045-0.02630.6830.4290.4290.0000.0000.0000.000
71A71LYS10.9330.97633.0388.0208.0200.0000.0000.0000.000
72A72GLU-1-0.806-0.88130.773-8.966-8.9660.0000.0000.0000.000
73A73ARG10.8790.93525.61910.86210.8620.0000.0000.0000.000
74A74ILE0-0.024-0.00722.9050.1390.1390.0000.0000.0000.000
75A75SER0-0.007-0.00124.130-0.306-0.3060.0000.0000.0000.000
76A76VAL00.0580.02418.533-0.195-0.1950.0000.0000.0000.000
77A77ALA0-0.0320.00420.203-0.486-0.4860.0000.0000.0000.000
78A78ALA00.0040.00222.143-0.175-0.1750.0000.0000.0000.000
79A79ALA00.0440.01719.369-0.105-0.1050.0000.0000.0000.000
80A80SER00.0370.00117.247-0.263-0.2630.0000.0000.0000.000
81A81LYS10.8800.94418.19911.92711.9270.0000.0000.0000.000
82A82LEU0-0.011-0.01420.9340.1470.1470.0000.0000.0000.000
83A83LEU00.0120.00913.0750.1860.1860.0000.0000.0000.000
84A84ALA00.0510.01917.436-0.181-0.1810.0000.0000.0000.000
85A85ASN0-0.034-0.01418.3000.0290.0290.0000.0000.0000.000
86A86MET0-0.036-0.00518.1300.3440.3440.0000.0000.0000.000
87A87VAL00.0330.01814.7470.1240.1240.0000.0000.0000.000
88A88TYR00.0000.00417.864-0.149-0.1490.0000.0000.0000.000
89A89GLN0-0.054-0.02820.2860.1370.1370.0000.0000.0000.000
90A90TYR00.003-0.00718.4790.4630.4630.0000.0000.0000.000
91A91LYS10.8540.92918.34215.11415.1140.0000.0000.0000.000
92A92GLY0-0.003-0.00118.4910.6880.6880.0000.0000.0000.000
93A93MET0-0.065-0.03119.4640.1900.1900.0000.0000.0000.000
94A94GLY00.0070.00615.860-0.040-0.0400.0000.0000.0000.000
95A95LEU0-0.0250.00813.764-1.039-1.0390.0000.0000.0000.000
96A96SER0-0.0090.0038.757-1.193-1.1930.0000.0000.0000.000
97A97MET0-0.011-0.0178.266-1.005-1.0050.0000.0000.0000.000
98A98GLY00.0560.0357.1231.9521.9520.0000.0000.0000.000
99A99THR0-0.091-0.0646.520-3.182-3.1820.0000.0000.0000.000
100A100MET00.0060.0146.9462.0812.0810.0000.0000.0000.000
101A101ILE0-0.0100.00910.8890.3560.3560.0000.0000.0000.000
102A102CYS0-0.039-0.02712.8350.5180.5180.0000.0000.0000.000
103A103GLY00.037-0.00715.8640.1520.1520.0000.0000.0000.000
104A104TRP0-0.027-0.00719.514-0.395-0.3950.0000.0000.0000.000
105A105ASP-1-0.757-0.85523.041-11.613-11.6130.0000.0000.0000.000
106A106LYS10.8740.92125.5999.3589.3580.0000.0000.0000.000
107A107ARG10.8120.88325.99010.93410.9340.0000.0000.0000.000
108A108GLY00.0730.06226.190-0.012-0.0120.0000.0000.0000.000
109A109PRO00.0140.01221.268-0.278-0.2780.0000.0000.0000.000
110A110GLY0-0.019-0.01320.3510.0740.0740.0000.0000.0000.000
111A111LEU00.0200.00213.076-0.427-0.4270.0000.0000.0000.000
112A112TYR0-0.017-0.01815.5331.0441.0440.0000.0000.0000.000
113A113TYR0-0.030-0.0088.671-1.311-1.3110.0000.0000.0000.000
114A114VAL0-0.037-0.04711.9331.8241.8240.0000.0000.0000.000
115A115ASP-1-0.751-0.83611.407-24.343-24.3430.0000.0000.0000.000
116A116SER0-0.040-0.04011.9830.9300.9300.0000.0000.0000.000
117A117GLU-1-0.848-0.91213.797-17.025-17.0250.0000.0000.0000.000
118A118GLY00.0130.00115.8811.1161.1160.0000.0000.0000.000
119A119ASN0-0.078-0.03615.0831.7061.7060.0000.0000.0000.000
120A120ARG10.8680.92015.84512.92512.9250.0000.0000.0000.000
121A121ILE0-0.0130.00615.5511.0391.0390.0000.0000.0000.000
122A122SER0-0.062-0.03916.697-0.516-0.5160.0000.0000.0000.000
123A123GLY00.0530.01517.0970.1710.1710.0000.0000.0000.000
124A124ALA0-0.022-0.00117.9880.1590.1590.0000.0000.0000.000
125A125THR00.0280.00214.535-0.068-0.0680.0000.0000.0000.000
126A126PHE00.0110.00610.7150.4710.4710.0000.0000.0000.000
127A127SER0-0.006-0.0246.916-1.449-1.4490.0000.0000.0000.000
128A128VAL00.0360.0105.0211.4781.4780.0000.0000.0000.000
133A133VAL00.0300.0127.2854.1144.1140.0000.0000.0000.000
134A134TYR00.003-0.0017.2462.6992.6990.0000.0000.0000.000
135A135ALA00.0060.0138.6782.4402.4400.0000.0000.0000.000
136A136TYR00.0410.00410.0482.5752.5750.0000.0000.0000.000
137A137GLY00.0140.02312.7081.7881.7880.0000.0000.0000.000
138A138VAL0-0.031-0.02013.3861.5771.5770.0000.0000.0000.000
139A139MET0-0.0290.01112.3330.9110.9110.0000.0000.0000.000
140A140ASP-1-0.844-0.94615.327-17.811-17.8110.0000.0000.0000.000
141A141ARG10.7740.88817.72916.16316.1630.0000.0000.0000.000
142A142GLY00.0690.02219.8780.0710.0710.0000.0000.0000.000
143A143TYR0-0.053-0.03817.7580.5890.5890.0000.0000.0000.000
144A144SER00.0270.01319.7710.5780.5780.0000.0000.0000.000
145A145TYR00.0270.02322.152-0.257-0.2570.0000.0000.0000.000
146A146ASP-1-0.844-0.92423.630-10.707-10.7070.0000.0000.0000.000
147A147LEU0-0.0400.00320.3740.2690.2690.0000.0000.0000.000
148A148GLU-1-0.911-0.96524.380-10.690-10.6900.0000.0000.0000.000
149A149VAL0-0.008-0.01522.105-0.580-0.5800.0000.0000.0000.000
150A150GLU-1-0.824-0.92421.273-13.696-13.6960.0000.0000.0000.000
151A151GLN00.0310.02121.309-0.783-0.7830.0000.0000.0000.000
152A152ALA0-0.019-0.00318.980-0.777-0.7770.0000.0000.0000.000
153A153TYR0-0.026-0.04817.035-1.283-1.2830.0000.0000.0000.000
154A154ASP-1-0.888-0.94716.357-16.308-16.3080.0000.0000.0000.000
155A155LEU0-0.093-0.02816.021-0.908-0.9080.0000.0000.0000.000
156A156ALA0-0.006-0.00412.762-1.392-1.3920.0000.0000.0000.000
157A157ARG10.9060.93711.93715.05315.0530.0000.0000.0000.000
158A158ARG10.9700.99912.43815.44415.4440.0000.0000.0000.000
159A159ALA00.005-0.00411.457-1.010-1.0100.0000.0000.0000.000
160A160ILE0-0.047-0.0186.408-3.227-3.2270.0000.0000.0000.000
161A161TYR00.0550.0408.331-3.539-3.5390.0000.0000.0000.000
162A162GLN00.017-0.00210.164-0.515-0.5150.0000.0000.0000.000
163A163ALA0-0.0150.0066.3310.0930.0930.0000.0000.0000.000
164A164THR0-0.112-0.0775.899-3.269-3.2690.0000.0000.0000.000
165A165TYR0-0.0010.0217.0191.2821.2820.0000.0000.0000.000
166A166ARG10.9130.9548.36924.60024.6000.0000.0000.0000.000
172A172GLY0-0.030-0.0046.634-1.043-1.0430.0000.0000.0000.000
173A173ALA00.0200.0109.1202.1062.1060.0000.0000.0000.000
174A174VAL0-0.023-0.0078.724-3.146-3.1460.0000.0000.0000.000
175A175ASN0-0.053-0.0278.8753.8723.8720.0000.0000.0000.000
176A176LEU00.0190.01410.050-1.671-1.6710.0000.0000.0000.000
177A177TYR0-0.021-0.03511.9871.0711.0710.0000.0000.0000.000
178A178HIS0-0.0010.00814.572-0.506-0.5060.0000.0000.0000.000
179A179VAL0-0.036-0.01816.6290.5280.5280.0000.0000.0000.000
180A180ARG10.8820.92319.25511.98911.9890.0000.0000.0000.000
181A181GLU-1-0.866-0.92623.075-10.256-10.2560.0000.0000.0000.000
182A182ASP-1-0.817-0.89525.924-11.062-11.0620.0000.0000.0000.000
183A183GLY00.024-0.00522.9290.1040.1040.0000.0000.0000.000
184A184TRP0-0.063-0.02617.802-0.272-0.2720.0000.0000.0000.000
185A185ILE0-0.0070.00119.2780.3970.3970.0000.0000.0000.000
186A186ARG10.8480.90114.87115.78115.7810.0000.0000.0000.000
187A187VAL0-0.045-0.00716.3530.6260.6260.0000.0000.0000.000
188A188SER0-0.033-0.04015.7240.5080.5080.0000.0000.0000.000
189A189SER0-0.054-0.05413.426-0.960-0.9600.0000.0000.0000.000
190A190ASP-1-0.733-0.82013.951-17.045-17.0450.0000.0000.0000.000
191A191ASN00.0080.00912.948-2.709-2.7090.0000.0000.0000.000
192A192VAL00.023-0.0059.2580.3640.3640.0000.0000.0000.000
193A193ALA0-0.019-0.00612.6370.5330.5330.0000.0000.0000.000
194A194ASP-1-0.815-0.92416.100-16.301-16.3010.0000.0000.0000.000
195A195LEU0-0.069-0.03712.7840.4350.4350.0000.0000.0000.000
196A196HIS0-0.006-0.00215.9301.0421.0420.0000.0000.0000.000
197A197GLU-1-0.953-0.97717.445-13.417-13.4170.0000.0000.0000.000
198A198LYS10.9320.97219.26315.69515.6950.0000.0000.0000.000
199A199TYR0-0.110-0.07516.1170.1100.1100.0000.0000.0000.000
200A200SER0-0.097-0.05019.8410.0450.0450.0000.0000.0000.000
201A201GLY-1-0.910-0.91621.919-11.976-11.9760.0000.0000.0000.000