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: 4QKZN

Calculation Name: 1IM5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IM5

Chain ID: A

ChEMBL ID:

UniProt ID: O58727

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1964006.893862
FMO2-HF: Nuclear repulsion 1893739.223752
FMO2-HF: Total energy -70267.67011
FMO2-MP2: Total energy -70473.148533


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-97.71-88.1616.274-11.269-14.554-0.12
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.900
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].
3A4GLU-1-0.879-0.9312.997-35.558-33.4250.029-0.915-1.247-0.001
4A5ALA00.0320.0102.747-13.026-11.0400.398-1.129-1.255-0.014
43A44GLY00.0090.0224.682-2.620-2.485-0.001-0.027-0.1070.000
44A45ALA0-0.057-0.0312.383-19.140-16.2423.219-2.711-3.406-0.027
45A46LEU0-0.004-0.0042.338-0.9990.4662.132-0.580-3.017-0.012
46A47ILE00.0130.0083.3515.4765.5350.0400.085-0.1840.000
117A118ASN0-0.038-0.0232.703-6.190-4.5770.481-0.792-1.301-0.005
118A119GLY0-0.009-0.0011.798-39.317-40.9289.928-4.976-3.341-0.060
119A120VAL0-0.076-0.0233.112-0.3880.3180.049-0.208-0.548-0.001
120A121LYS10.8410.8964.91440.90241.068-0.001-0.016-0.1480.000
5A6LEU0-0.0270.0055.4604.4344.4340.0000.0000.0000.000
6A7ILE0-0.008-0.0208.711-0.749-0.7490.0000.0000.0000.000
7A8VAL00.022-0.00511.6251.4441.4440.0000.0000.0000.000
8A9VAL0-0.012-0.01714.4620.1350.1350.0000.0000.0000.000
9A10ASP-1-0.713-0.83317.393-14.228-14.2280.0000.0000.0000.000
10A11MET00.0080.03718.5260.8310.8310.0000.0000.0000.000
11A12GLN0-0.040-0.04720.508-0.198-0.1980.0000.0000.0000.000
12A13ARG10.8500.90223.22011.46411.4640.0000.0000.0000.000
13A14ASP-1-0.771-0.90126.618-9.913-9.9130.0000.0000.0000.000
14A15PHE0-0.030-0.00724.2040.3580.3580.0000.0000.0000.000
15A16MET00.0070.02623.779-0.063-0.0630.0000.0000.0000.000
16A17PRO0-0.040-0.02628.0190.3470.3470.0000.0000.0000.000
17A18GLY0-0.0060.00031.569-0.018-0.0180.0000.0000.0000.000
18A19GLY0-0.0190.01330.6520.1100.1100.0000.0000.0000.000
19A20ALA0-0.019-0.02231.6820.2350.2350.0000.0000.0000.000
20A21LEU0-0.085-0.05329.7500.2860.2860.0000.0000.0000.000
21A22PRO0-0.0460.00630.113-0.340-0.3400.0000.0000.0000.000
22A23VAL00.022-0.00126.5570.2060.2060.0000.0000.0000.000
23A24PRO0-0.007-0.00929.5140.0010.0010.0000.0000.0000.000
24A25GLU-1-0.907-0.97929.751-9.934-9.9340.0000.0000.0000.000
25A26GLY00.0240.01726.184-0.277-0.2770.0000.0000.0000.000
26A27ASP-1-0.823-0.94524.891-10.867-10.8670.0000.0000.0000.000
27A28LYS10.8810.94725.4809.4229.4220.0000.0000.0000.000
28A29ILE0-0.0070.01320.893-0.120-0.1200.0000.0000.0000.000
29A30ILE00.0110.02020.889-0.712-0.7120.0000.0000.0000.000
30A31PRO0-0.018-0.01020.087-0.686-0.6860.0000.0000.0000.000
31A32LYS10.8620.93318.34614.39214.3920.0000.0000.0000.000
32A33VAL00.0430.01515.917-1.034-1.0340.0000.0000.0000.000
33A34ASN00.0390.00815.286-1.675-1.6750.0000.0000.0000.000
34A35GLU-1-0.903-0.92415.558-16.057-16.0570.0000.0000.0000.000
35A36TYR0-0.031-0.04412.670-1.200-1.2000.0000.0000.0000.000
36A37ILE00.0120.00511.062-2.137-2.1370.0000.0000.0000.000
37A38ARG10.8910.95410.66214.58614.5860.0000.0000.0000.000
38A39LYS10.8960.92811.26316.25816.2580.0000.0000.0000.000
39A40PHE0-0.037-0.0356.349-0.841-0.8410.0000.0000.0000.000
40A41LYS10.9891.0076.70618.00318.0030.0000.0000.0000.000
41A42GLU-1-0.970-0.9907.810-21.434-21.4340.0000.0000.0000.000
42A43LYS10.8640.9496.47629.15229.1520.0000.0000.0000.000
47A48VAL0-0.0090.0017.1140.1340.1340.0000.0000.0000.000
48A49ALA00.0230.0209.9881.0201.0200.0000.0000.0000.000
49A50THR0-0.051-0.05313.686-0.106-0.1060.0000.0000.0000.000
50A51ARG10.9010.95416.30315.29215.2920.0000.0000.0000.000
51A52ASP-1-0.746-0.83919.883-12.462-12.4620.0000.0000.0000.000
52A53TRP00.011-0.00222.2060.0390.0390.0000.0000.0000.000
53A54HIS10.8730.94324.23511.44011.4400.0000.0000.0000.000
54A55PRO00.0160.03127.6780.0240.0240.0000.0000.0000.000
55A56GLU-1-0.734-0.85530.603-8.998-8.9980.0000.0000.0000.000
56A57ASN0-0.065-0.04734.0440.0020.0020.0000.0000.0000.000
57A58HIS00.0240.03228.6960.2150.2150.0000.0000.0000.000
58A59ILE0-0.004-0.00431.6390.2170.2170.0000.0000.0000.000
59A60SER0-0.034-0.02530.5490.1910.1910.0000.0000.0000.000
60A61PHE0-0.016-0.01330.6340.0830.0830.0000.0000.0000.000
61A62ARG10.9060.94735.1738.5148.5140.0000.0000.0000.000
62A63GLU-1-0.890-0.93537.383-8.220-8.2200.0000.0000.0000.000
63A64ARG10.7680.87235.2268.8378.8370.0000.0000.0000.000
64A65GLY0-0.013-0.00139.5710.0170.0170.0000.0000.0000.000
65A66GLY00.0120.02635.819-0.020-0.0200.0000.0000.0000.000
66A67PRO00.005-0.01933.8310.1520.1520.0000.0000.0000.000
67A68TRP0-0.0080.01030.3670.2620.2620.0000.0000.0000.000
68A69PRO00.0060.01333.6750.2260.2260.0000.0000.0000.000
69A70ARG10.8390.88633.3278.7598.7590.0000.0000.0000.000
70A71HIS10.8110.89927.49410.72610.7260.0000.0000.0000.000
71A72CYS0-0.061-0.03124.966-0.026-0.0260.0000.0000.0000.000
72A73VAL0-0.0180.01527.058-0.272-0.2720.0000.0000.0000.000
73A74GLN0-0.033-0.02126.2350.1480.1480.0000.0000.0000.000
74A75ASN0-0.026-0.02926.6810.0180.0180.0000.0000.0000.000
75A76THR0-0.031-0.01328.1820.3750.3750.0000.0000.0000.000
76A77PRO00.0550.00928.042-0.343-0.3430.0000.0000.0000.000
77A78GLY00.0280.02728.204-0.163-0.1630.0000.0000.0000.000
78A79ALA0-0.009-0.00425.150-0.306-0.3060.0000.0000.0000.000
79A80GLU-1-0.838-0.89123.408-11.904-11.9040.0000.0000.0000.000
80A81PHE0-0.004-0.01217.1990.1190.1190.0000.0000.0000.000
81A82VAL0-0.045-0.02521.1810.4480.4480.0000.0000.0000.000
82A83VAL0-0.015-0.01317.0010.1320.1320.0000.0000.0000.000
83A84ASP-1-0.897-0.94717.223-14.699-14.6990.0000.0000.0000.000
84A85LEU0-0.051-0.03112.707-1.141-1.1410.0000.0000.0000.000
85A86PRO0-0.034-0.0099.9271.1021.1020.0000.0000.0000.000
86A87GLU-1-0.914-0.96912.358-18.029-18.0290.0000.0000.0000.000
87A88ASP-1-0.938-0.9647.769-30.309-30.3090.0000.0000.0000.000
88A89ALA0-0.052-0.0158.197-3.140-3.1400.0000.0000.0000.000
89A90VAL0-0.012-0.0217.8221.6851.6850.0000.0000.0000.000
90A91ILE00.0090.00310.6890.7030.7030.0000.0000.0000.000
91A92ILE0-0.039-0.01612.0000.6060.6060.0000.0000.0000.000
92A93SER0-0.002-0.01015.3250.9050.9050.0000.0000.0000.000
93A94LYS10.8020.90619.15714.21114.2110.0000.0000.0000.000
94A95ALA00.008-0.00221.0970.4280.4280.0000.0000.0000.000
95A96THR00.0130.00722.8930.4710.4710.0000.0000.0000.000
96A97GLU-1-0.812-0.88825.710-11.011-11.0110.0000.0000.0000.000
97A98PRO00.015-0.01228.528-0.058-0.0580.0000.0000.0000.000
98A99ASP-1-0.806-0.89431.623-8.940-8.9400.0000.0000.0000.000
99A100LYS10.8300.90626.80811.36211.3620.0000.0000.0000.000
100A101GLU-1-0.831-0.92827.203-11.275-11.2750.0000.0000.0000.000
101A102ALA0-0.036-0.01722.142-0.195-0.1950.0000.0000.0000.000
102A103TYR00.0140.00823.403-0.029-0.0290.0000.0000.0000.000
103A104SER0-0.019-0.05818.706-0.857-0.8570.0000.0000.0000.000
104A105GLY00.016-0.00615.8600.1840.1840.0000.0000.0000.000
105A106PHE0-0.047-0.03012.184-1.054-1.0540.0000.0000.0000.000
106A107GLU-1-0.840-0.91216.940-12.836-12.8360.0000.0000.0000.000
107A108GLY0-0.0160.00120.6840.2510.2510.0000.0000.0000.000
108A109THR0-0.030-0.03015.872-0.379-0.3790.0000.0000.0000.000
109A110ASP-1-0.866-0.93314.288-18.369-18.3690.0000.0000.0000.000
110A111LEU00.0060.0179.921-1.929-1.9290.0000.0000.0000.000
111A112ALA00.0230.00210.355-2.553-2.5530.0000.0000.0000.000
112A113LYS10.9060.94211.14318.66718.6670.0000.0000.0000.000
113A114ILE00.0430.0267.470-2.091-2.0910.0000.0000.0000.000
114A115LEU00.0180.0186.022-5.184-5.1840.0000.0000.0000.000
115A116ARG10.8590.9235.69216.80416.8040.0000.0000.0000.000
116A117GLY0-0.0100.0046.871-1.803-1.8030.0000.0000.0000.000
121A122ARG10.8370.9186.23240.16940.1690.0000.0000.0000.000
122A123VAL00.003-0.0107.073-3.998-3.9980.0000.0000.0000.000
123A124TYR00.0130.0068.2292.1642.1640.0000.0000.0000.000
124A125ILE0-0.0130.00711.065-0.673-0.6730.0000.0000.0000.000
125A126CYS0-0.038-0.00713.9620.9220.9220.0000.0000.0000.000
126A127GLY00.0370.01616.306-0.442-0.4420.0000.0000.0000.000
127A128VAL0-0.003-0.00519.1500.5710.5710.0000.0000.0000.000
128A129ALA00.0320.01421.955-0.276-0.2760.0000.0000.0000.000
129A130THR0-0.009-0.03522.755-0.464-0.4640.0000.0000.0000.000
130A131GLU-1-0.732-0.88923.477-11.467-11.4670.0000.0000.0000.000
131A132TYR0-0.029-0.00925.3710.2220.2220.0000.0000.0000.000
132A133CYS0-0.001-0.00220.994-0.089-0.0890.0000.0000.0000.000
133A134VAL0-0.0250.02918.735-0.862-0.8620.0000.0000.0000.000
134A135ARG10.8810.90219.30711.11811.1180.0000.0000.0000.000
135A136ALA0-0.009-0.00121.064-0.294-0.2940.0000.0000.0000.000
136A137THR00.020-0.00914.948-0.518-0.5180.0000.0000.0000.000
137A138ALA00.003-0.00216.297-1.123-1.1230.0000.0000.0000.000
138A139LEU0-0.012-0.01517.604-0.384-0.3840.0000.0000.0000.000
139A140ASP-1-0.776-0.85317.701-15.008-15.0080.0000.0000.0000.000
140A141ALA0-0.012-0.00813.395-0.641-0.6410.0000.0000.0000.000
141A142LEU0-0.006-0.00114.846-0.798-0.7980.0000.0000.0000.000
142A143LYS10.8200.91017.33814.17014.1700.0000.0000.0000.000
143A144HIS0-0.014-0.00613.883-0.254-0.2540.0000.0000.0000.000
144A145GLY00.0190.02014.218-1.099-1.0990.0000.0000.0000.000
145A146PHE0-0.060-0.0188.893-0.765-0.7650.0000.0000.0000.000
146A147GLU-1-0.874-0.93611.622-20.201-20.2010.0000.0000.0000.000
147A148VAL0-0.018-0.00511.654-1.724-1.7240.0000.0000.0000.000
148A149TYR0-0.045-0.04311.6291.9561.9560.0000.0000.0000.000
149A150LEU0-0.017-0.00514.285-0.553-0.5530.0000.0000.0000.000
150A151LEU00.0150.00412.4090.4350.4350.0000.0000.0000.000
151A152ARG10.9610.97216.69612.53612.5360.0000.0000.0000.000
152A153ASP-1-0.808-0.89219.166-14.446-14.4460.0000.0000.0000.000
153A154ALA0-0.014-0.01117.3530.2140.2140.0000.0000.0000.000
154A155VAL00.0040.00718.957-0.529-0.5290.0000.0000.0000.000
155A156LYS10.8930.96321.33611.27611.2760.0000.0000.0000.000
156A157GLY00.008-0.00224.868-0.380-0.3800.0000.0000.0000.000
157A158ILE0-0.044-0.03227.2720.2160.2160.0000.0000.0000.000
158A159LYS10.8860.93330.8649.3789.3780.0000.0000.0000.000
159A160PRO00.0660.03931.641-0.198-0.1980.0000.0000.0000.000
160A161GLU-1-0.843-0.91432.009-8.691-8.6910.0000.0000.0000.000
161A162ASP-1-0.870-0.93131.182-9.356-9.3560.0000.0000.0000.000
162A163GLU-1-0.889-0.95627.499-11.269-11.2690.0000.0000.0000.000
163A164GLU-1-0.926-0.96827.658-9.725-9.7250.0000.0000.0000.000
164A165ARG10.8820.93528.8868.7328.7320.0000.0000.0000.000
165A166ALA00.0080.01825.588-0.224-0.2240.0000.0000.0000.000
166A167LEU0-0.019-0.02322.577-0.581-0.5810.0000.0000.0000.000
167A168GLU-1-0.948-0.96024.841-10.240-10.2400.0000.0000.0000.000
168A169GLU-1-0.778-0.85326.211-11.771-11.7710.0000.0000.0000.000
169A170MET0-0.0050.00321.142-0.574-0.5740.0000.0000.0000.000
170A171LYS10.9720.98822.31211.46911.4690.0000.0000.0000.000
171A172SER0-0.088-0.04923.696-0.083-0.0830.0000.0000.0000.000
172A173ARG10.8720.93022.91212.50812.5080.0000.0000.0000.000
173A174GLY00.0280.02121.318-0.476-0.4760.0000.0000.0000.000
174A175ILE0-0.033-0.00817.084-0.940-0.9400.0000.0000.0000.000
175A176LYS10.8560.92916.16118.26918.2690.0000.0000.0000.000
176A177ILE0-0.022-0.00617.044-0.712-0.7120.0000.0000.0000.000
177A178VAL0-0.034-0.01614.8320.4550.4550.0000.0000.0000.000
178A179GLN0-0.028-0.02317.2290.3360.3360.0000.0000.0000.000
179A180PHE-1-0.842-0.89511.533-17.387-17.3870.0000.0000.0000.000