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: QK42Y

Calculation Name: 1IRU-I-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: I

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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2343079.964964
FMO2-HF: Nuclear repulsion 2258278.947323
FMO2-HF: Total energy -84801.017641
FMO2-MP2: Total energy -85042.790751


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.
-130.895-124.32839.504-20.523-25.544-0.186
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 : 0.719 / q_NPA : 0.865
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].
3A3ILE0-0.027-0.0042.5133.9065.5411.124-0.664-2.095-0.006
4A4ALA00.0280.0054.5280.7430.740-0.001-0.0070.0110.000
16A16ALA0-0.003-0.0134.492-2.570-2.518-0.001-0.004-0.0460.000
17A17ASP-1-0.666-0.8112.235-75.835-73.4164.479-3.572-3.325-0.043
18A18THR0-0.019-0.0104.813-0.363-0.260-0.001-0.004-0.0980.000
19A19ARG10.8550.9514.62744.95945.053-0.001-0.004-0.0890.000
20A20ALA00.007-0.0044.200-5.640-5.3590.000-0.026-0.2540.000
33A33LYS10.7820.8701.87350.94647.8859.950-2.838-4.0510.030
46A46ALA0-0.020-0.0162.523-7.766-7.0681.642-0.705-1.635-0.003
47A47GLY00.0270.0273.2876.3656.2050.0290.337-0.207-0.001
48A48THR0-0.024-0.0195.108-3.193-3.139-0.0010.000-0.0520.000
128A128GLY00.0160.0012.784-6.979-6.3450.166-0.306-0.494-0.001
129A129SER0-0.047-0.0412.021-5.064-4.7195.211-2.629-2.926-0.032
130A130GLY00.0450.0213.51410.57310.9940.000-0.141-0.2800.000
131A131SER0-0.061-0.0295.1778.1348.244-0.001-0.006-0.1030.000
166A166ASP-1-0.735-0.8112.093-109.039-107.0793.666-3.109-2.517-0.043
167A167LEU00.0340.0174.871-3.899-3.846-0.001-0.002-0.0500.000
168A168GLY00.0080.0113.0455.9466.3580.123-0.182-0.353-0.001
169A169SER0-0.088-0.0681.937-39.814-39.42313.056-6.673-6.774-0.085
170A170GLY00.000-0.0143.20910.97711.1060.0650.012-0.206-0.001
5A5GLY0-0.015-0.0048.1850.6320.6320.0000.0000.0000.000
6A6VAL00.0290.01111.6220.0380.0380.0000.0000.0000.000
7A7VAL0-0.027-0.01915.2790.2840.2840.0000.0000.0000.000
8A8TYR0-0.034-0.01818.8360.1480.1480.0000.0000.0000.000
9A9LYS10.8470.91821.55011.01511.0150.0000.0000.0000.000
10A10ASP-1-0.874-0.92824.481-10.840-10.8400.0000.0000.0000.000
11A11GLY0-0.053-0.05321.8330.2090.2090.0000.0000.0000.000
12A12ILE0-0.053-0.01315.435-0.173-0.1730.0000.0000.0000.000
13A13VAL0-0.0020.01013.7800.3240.3240.0000.0000.0000.000
14A14LEU0-0.005-0.00710.559-0.710-0.7100.0000.0000.0000.000
15A15GLY00.0540.0059.0611.3051.3050.0000.0000.0000.000
21A21THR0-0.029-0.0295.6030.7350.7350.0000.0000.0000.000
22A22GLU-1-0.909-0.9367.535-20.902-20.9020.0000.0000.0000.000
23A23GLY00.003-0.0079.8751.6171.6170.0000.0000.0000.000
24A24MET0-0.013-0.0168.291-4.367-4.3670.0000.0000.0000.000
25A25VAL00.0170.02110.1150.3970.3970.0000.0000.0000.000
26A26VAL0-0.047-0.0348.266-1.728-1.7280.0000.0000.0000.000
27A27ALA00.0300.0279.6442.1572.1570.0000.0000.0000.000
28A28ASP-1-0.813-0.9108.874-22.494-22.4940.0000.0000.0000.000
29A29LYS10.8800.9358.94117.29417.2940.0000.0000.0000.000
30A30ASN00.018-0.00810.116-1.655-1.6550.0000.0000.0000.000
31A31CYS00.0730.0596.7561.5991.5990.0000.0000.0000.000
32A32SER00.002-0.0027.807-1.279-1.2790.0000.0000.0000.000
34A34ILE0-0.029-0.0056.424-0.397-0.3970.0000.0000.0000.000
35A35HIS10.8790.9387.21626.34026.3400.0000.0000.0000.000
36A36PHE00.0590.03211.7270.0450.0450.0000.0000.0000.000
37A37ILE0-0.046-0.01513.663-0.184-0.1840.0000.0000.0000.000
38A38SER00.0380.00616.9630.5740.5740.0000.0000.0000.000
39A39PRO00.016-0.00219.602-0.442-0.4420.0000.0000.0000.000
40A40ASN00.0050.01021.466-0.067-0.0670.0000.0000.0000.000
41A41ILE0-0.021-0.01516.380-0.197-0.1970.0000.0000.0000.000
42A42TYR00.0840.03913.119-0.036-0.0360.0000.0000.0000.000
43A43CYS0-0.020-0.00910.977-0.221-0.2210.0000.0000.0000.000
44A44CYS0-0.0140.0216.1980.3620.3620.0000.0000.0000.000
45A45GLY00.030-0.0065.4801.6281.6280.0000.0000.0000.000
49A49ALA00.0220.0126.7100.8100.8100.0000.0000.0000.000
50A50ALA00.0780.0337.6621.2201.2200.0000.0000.0000.000
51A51ASP-1-0.790-0.89510.562-20.115-20.1150.0000.0000.0000.000
52A52THR0-0.041-0.0055.9940.4140.4140.0000.0000.0000.000
53A53ASP-1-0.893-0.9379.016-22.127-22.1270.0000.0000.0000.000
54A54MET00.000-0.00711.5891.2651.2650.0000.0000.0000.000
55A55THR0-0.060-0.05012.0420.9350.9350.0000.0000.0000.000
56A56THR0-0.001-0.00510.7651.1801.1800.0000.0000.0000.000
57A57GLN00.008-0.00413.7150.3800.3800.0000.0000.0000.000
58A58LEU0-0.0080.01016.5700.8620.8620.0000.0000.0000.000
59A59ILE0-0.038-0.03316.7050.7670.7670.0000.0000.0000.000
60A60SER0-0.027-0.01717.1460.6070.6070.0000.0000.0000.000
61A61SER00.0200.01618.9850.7370.7370.0000.0000.0000.000
62A62ASN00.012-0.00721.6670.8160.8160.0000.0000.0000.000
63A63LEU0-0.032-0.02719.7800.4890.4890.0000.0000.0000.000
64A64GLU-1-0.927-0.93423.123-10.914-10.9140.0000.0000.0000.000
65A65LEU00.007-0.00124.9210.4560.4560.0000.0000.0000.000
66A66HIS0-0.004-0.00426.0760.3800.3800.0000.0000.0000.000
67A67SER0-0.066-0.04326.0790.3560.3560.0000.0000.0000.000
68A68LEU0-0.010-0.00228.4850.3550.3550.0000.0000.0000.000
69A69SER0-0.0210.00730.7320.3900.3900.0000.0000.0000.000
70A70THR0-0.068-0.06030.2480.2290.2290.0000.0000.0000.000
71A71GLY00.0270.01832.6790.2000.2000.0000.0000.0000.000
72A72ARG10.8510.93330.8008.5238.5230.0000.0000.0000.000
73A73LEU00.0530.02725.465-0.149-0.1490.0000.0000.0000.000
74A74PRO00.0090.00422.8010.1170.1170.0000.0000.0000.000
75A75ARG10.9620.99424.0429.8729.8720.0000.0000.0000.000
76A76VAL00.0400.01718.321-0.158-0.1580.0000.0000.0000.000
77A77VAL0-0.032-0.02520.085-0.432-0.4320.0000.0000.0000.000
78A78THR0-0.022-0.00722.3120.0920.0920.0000.0000.0000.000
79A79ALA00.0780.04417.364-0.083-0.0830.0000.0000.0000.000
80A80ASN00.0280.00917.401-1.061-1.0610.0000.0000.0000.000
81A81ARG10.8970.95118.47211.12311.1230.0000.0000.0000.000
82A82MET00.0170.00819.853-0.181-0.1810.0000.0000.0000.000
83A83LEU00.0590.03013.490-0.015-0.0150.0000.0000.0000.000
84A84LYS10.8820.94116.76714.08614.0860.0000.0000.0000.000
85A85GLN0-0.048-0.03017.8770.1620.1620.0000.0000.0000.000
86A86MET0-0.0040.01617.7750.1900.1900.0000.0000.0000.000
87A87LEU00.0170.00412.8140.2500.2500.0000.0000.0000.000
88A88PHE0-0.0040.00216.9430.2300.2300.0000.0000.0000.000
89A89ARG10.9040.95420.00211.90311.9030.0000.0000.0000.000
90A90TYR0-0.004-0.00418.2270.6180.6180.0000.0000.0000.000
91A91ARG10.8980.95619.02213.06413.0640.0000.0000.0000.000
92A92GLY00.0350.02115.4070.0600.0600.0000.0000.0000.000
93A93TYR0-0.048-0.02514.953-0.874-0.8740.0000.0000.0000.000
94A94ILE0-0.0160.01113.229-0.215-0.2150.0000.0000.0000.000
95A95GLY00.0310.01210.872-0.125-0.1250.0000.0000.0000.000
96A96ALA0-0.030-0.0208.369-2.899-2.8990.0000.0000.0000.000
97A97ALA0-0.021-0.0146.6102.0482.0480.0000.0000.0000.000
98A98LEU0-0.006-0.0136.322-3.064-3.0640.0000.0000.0000.000
99A99VAL00.0240.0117.3281.0031.0030.0000.0000.0000.000
100A100LEU0-0.0110.0039.5450.2090.2090.0000.0000.0000.000
101A101GLY00.0400.00712.9540.4150.4150.0000.0000.0000.000
102A102GLY00.0280.01215.125-0.029-0.0290.0000.0000.0000.000
103A103VAL0-0.0140.00918.6310.1920.1920.0000.0000.0000.000
104A104ASP-1-0.752-0.87722.225-11.434-11.4340.0000.0000.0000.000
105A105VAL0-0.013-0.01424.7390.2380.2380.0000.0000.0000.000
106A106THR0-0.052-0.04126.5120.1880.1880.0000.0000.0000.000
107A107GLY00.0390.02425.6450.1800.1800.0000.0000.0000.000
108A108PRO00.0340.03920.840-0.161-0.1610.0000.0000.0000.000
109A109HIS0-0.102-0.05719.9520.3620.3620.0000.0000.0000.000
110A110LEU00.0360.02412.793-0.396-0.3960.0000.0000.0000.000
111A111TYR0-0.017-0.02614.6931.2211.2210.0000.0000.0000.000
112A112SER00.0300.02811.372-0.781-0.7810.0000.0000.0000.000
113A113ILE0-0.029-0.03311.1141.8891.8890.0000.0000.0000.000
114A114TYR00.0190.02210.856-2.782-2.7820.0000.0000.0000.000
115A115PRO00.0380.02010.5671.5491.5490.0000.0000.0000.000
116A116HIS00.008-0.00113.1201.6121.6120.0000.0000.0000.000
117A117GLY00.0160.00715.7371.0901.0900.0000.0000.0000.000
118A118SER0-0.043-0.01916.3520.6650.6650.0000.0000.0000.000
119A119THR0-0.020-0.03415.567-0.351-0.3510.0000.0000.0000.000
120A120ASP-1-0.791-0.86714.824-17.292-17.2920.0000.0000.0000.000
121A121LYS10.8910.94916.03611.95211.9520.0000.0000.0000.000
122A122LEU00.0240.01115.5160.6790.6790.0000.0000.0000.000
123A123PRO00.0080.01017.055-0.355-0.3550.0000.0000.0000.000
124A124TYR0-0.012-0.03414.356-0.041-0.0410.0000.0000.0000.000
125A125VAL0-0.035-0.00710.5730.1520.1520.0000.0000.0000.000
126A126THR00.001-0.0167.689-0.578-0.5780.0000.0000.0000.000
127A127MET0-0.031-0.0115.3851.5461.5460.0000.0000.0000.000
132A132LEU00.0490.0247.3433.8973.8970.0000.0000.0000.000
133A133ALA00.0230.0188.4462.6602.6600.0000.0000.0000.000
134A134ALA00.003-0.0028.4062.3212.3210.0000.0000.0000.000
135A135MET0-0.009-0.00510.3302.5402.5400.0000.0000.0000.000
136A136ALA0-0.0050.00212.5191.8621.8620.0000.0000.0000.000
137A137VAL0-0.0090.00113.6841.3151.3150.0000.0000.0000.000
138A138PHE0-0.035-0.02811.4810.7660.7660.0000.0000.0000.000
139A139GLU-1-0.864-0.93015.980-15.613-15.6130.0000.0000.0000.000
140A140ASP-1-0.928-0.93418.322-14.543-14.5430.0000.0000.0000.000
141A141LYS10.7790.87718.35217.60717.6070.0000.0000.0000.000
142A142PHE00.0160.00618.1050.1020.1020.0000.0000.0000.000
143A143ARG10.8500.91419.92912.62512.6250.0000.0000.0000.000
144A144PRO0-0.013-0.00622.129-0.400-0.4000.0000.0000.0000.000
145A145ASP-1-0.929-0.98224.149-11.029-11.0290.0000.0000.0000.000
146A146MET0-0.0590.00218.6230.1550.1550.0000.0000.0000.000
147A147GLU-1-0.785-0.88723.892-10.841-10.8410.0000.0000.0000.000
148A148GLU-1-0.791-0.89120.838-13.714-13.7140.0000.0000.0000.000
149A149GLU-1-0.823-0.92420.471-14.226-14.2260.0000.0000.0000.000
150A150GLU-1-0.830-0.90420.748-12.842-12.8420.0000.0000.0000.000
151A151ALA00.0470.02018.251-0.565-0.5650.0000.0000.0000.000
152A152LYS10.7510.85916.36512.77212.7720.0000.0000.0000.000
153A153ASN0-0.007-0.00415.895-1.111-1.1110.0000.0000.0000.000
154A154LEU00.0940.07915.882-1.323-1.3230.0000.0000.0000.000
155A155VAL00.005-0.00210.958-1.658-1.6580.0000.0000.0000.000
156A156SER0-0.072-0.04711.529-1.973-1.9730.0000.0000.0000.000
157A157GLU-1-0.825-0.91912.365-19.384-19.3840.0000.0000.0000.000
158A158ALA00.0330.02311.048-1.382-1.3820.0000.0000.0000.000
159A159ILE0-0.066-0.0436.170-3.823-3.8230.0000.0000.0000.000
160A160ALA0-0.006-0.0027.986-3.548-3.5480.0000.0000.0000.000
161A161ALA00.0130.01210.119-0.799-0.7990.0000.0000.0000.000
162A162GLY00.0320.0136.403-0.570-0.5700.0000.0000.0000.000
163A163ILE0-0.098-0.0565.983-4.340-4.3400.0000.0000.0000.000
164A164PHE0-0.048-0.0207.0320.5700.5700.0000.0000.0000.000
165A165ASN0-0.055-0.0258.1843.7903.7900.0000.0000.0000.000
171A171SER0-0.098-0.0476.606-0.181-0.1810.0000.0000.0000.000
172A172ASN00.0140.0059.4471.7311.7310.0000.0000.0000.000
173A173ILE00.0100.0068.449-3.299-3.2990.0000.0000.0000.000
174A174ASP-1-0.797-0.8818.485-22.522-22.5220.0000.0000.0000.000
175A175LEU0-0.011-0.0239.632-1.665-1.6650.0000.0000.0000.000
176A176CYS0-0.100-0.03912.0851.1131.1130.0000.0000.0000.000
177A177VAL00.0070.02414.165-0.410-0.4100.0000.0000.0000.000
178A178ILE0-0.007-0.00416.3140.5080.5080.0000.0000.0000.000
179A179SER00.0540.01819.586-0.033-0.0330.0000.0000.0000.000
180A180LYS10.8480.90923.11110.65310.6530.0000.0000.0000.000
181A181ASN0-0.088-0.03726.0170.2020.2020.0000.0000.0000.000
182A182LYS10.8500.94022.31112.87712.8770.0000.0000.0000.000
183A183LEU0-0.015-0.00717.890-0.412-0.4120.0000.0000.0000.000
184A184ASP-1-0.836-0.90419.310-12.737-12.7370.0000.0000.0000.000
185A185PHE00.028-0.01212.443-0.895-0.8950.0000.0000.0000.000
186A186LEU0-0.023-0.00515.4380.3150.3150.0000.0000.0000.000
187A187ARG10.8540.91110.02821.57621.5760.0000.0000.0000.000
188A188PRO0-0.006-0.01713.226-0.934-0.9340.0000.0000.0000.000
189A189TYR00.0380.04213.5961.3911.3910.0000.0000.0000.000
190A190THR0-0.006-0.01913.4510.5480.5480.0000.0000.0000.000
191A191VAL0-0.040-0.01313.230-1.238-1.2380.0000.0000.0000.000
192A192PRO00.0070.01611.8261.3021.3020.0000.0000.0000.000
193A193ASN0-0.015-0.01010.5940.5840.5840.0000.0000.0000.000
194A194LYS10.9780.97714.07816.24616.2460.0000.0000.0000.000
195A195LYS10.9160.96816.96014.40114.4010.0000.0000.0000.000
196A196GLY00.0570.03118.4120.6320.6320.0000.0000.0000.000
197A197THR00.004-0.00921.4710.0140.0140.0000.0000.0000.000
198A198ARG0-0.029-0.02124.8120.2960.2960.0000.0000.0000.000
199A199LEU00.0360.02126.3410.2900.2900.0000.0000.0000.000
200A200GLY00.0480.03629.6280.3530.3530.0000.0000.0000.000
201A201ARG10.9010.94630.6218.6288.6280.0000.0000.0000.000
202A202TYR00.0530.00628.6360.0160.0160.0000.0000.0000.000
203A203ARG10.8250.91331.9328.8348.8340.0000.0000.0000.000
204A204CYS00.0280.01432.1210.1480.1480.0000.0000.0000.000
205A205GLU-1-0.803-0.89034.436-8.411-8.4110.0000.0000.0000.000
206A206LYS10.9620.96937.9587.1927.1920.0000.0000.0000.000
207A207GLY00.0360.01539.9150.1870.1870.0000.0000.0000.000
208A208THR0-0.056-0.02036.2990.0450.0450.0000.0000.0000.000
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