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

tag_button

FMODB ID: 8KZ6Y

Calculation Name: 2A1K-A-Xray549

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A1K

Chain ID: A

ChEMBL ID:

UniProt ID: Q7Y265

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2438498.308721
FMO2-HF: Nuclear repulsion 2351982.073639
FMO2-HF: Total energy -86516.235082
FMO2-MP2: Total energy -86767.475622


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:27:ASP)


Summations of interaction energy for fragment #1(A:27:ASP)
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.
-13.056-8.916-0.011-2.08-2.048-0.003
Interaction energy analysis for fragmet #1(A:27:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.035
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].
3A29GLY00.0960.0633.157-0.7133.196-0.009-2.066-1.833-0.003
4A30GLU-1-0.825-0.8965.1783.4613.630-0.001-0.010-0.1580.000
109A135PHE0-0.058-0.0214.391-1.647-1.585-0.001-0.004-0.0570.000
5A31TRP0-0.0180.0045.477-0.811-0.8110.0000.0000.0000.000
6A32LYS10.8410.8957.766-0.511-0.5110.0000.0000.0000.000
7A33LEU00.0130.02510.230-0.268-0.2680.0000.0000.0000.000
8A34LYS10.8770.94311.0860.6470.6470.0000.0000.0000.000
9A35LEU0-0.027-0.01512.921-0.208-0.2080.0000.0000.0000.000
10A36ASP-1-0.783-0.88816.1650.1930.1930.0000.0000.0000.000
11A37ALA0-0.004-0.01819.0040.1150.1150.0000.0000.0000.000
12A38SER0-0.046-0.01220.9660.0360.0360.0000.0000.0000.000
13A39GLY0-0.0090.00220.0320.0110.0110.0000.0000.0000.000
14A40ASN0-0.038-0.03321.085-0.004-0.0040.0000.0000.0000.000
15A41GLY00.014-0.00417.9780.0480.0480.0000.0000.0000.000
16A42GLN0-0.055-0.03518.1600.0860.0860.0000.0000.0000.000
17A43ALA00.0340.02015.132-0.082-0.0820.0000.0000.0000.000
18A44VAL0-0.048-0.01616.7890.1880.1880.0000.0000.0000.000
19A45ILE00.0060.01214.115-0.250-0.2500.0000.0000.0000.000
20A46ARG10.8450.91016.2451.2241.2240.0000.0000.0000.000
21A47PHE0-0.001-0.01016.643-0.197-0.1970.0000.0000.0000.000
22A48LEU00.0410.02114.8580.0160.0160.0000.0000.0000.000
23A49PRO00.0440.02418.5670.1160.1160.0000.0000.0000.000
24A50ALA0-0.003-0.00219.873-0.085-0.0850.0000.0000.0000.000
25A51LYS10.8130.89215.5001.7321.7320.0000.0000.0000.000
26A52THR0-0.013-0.01920.119-0.035-0.0350.0000.0000.0000.000
27A53ASP-1-0.887-0.94323.744-0.602-0.6020.0000.0000.0000.000
28A54ASP-1-0.945-0.96725.908-0.435-0.4350.0000.0000.0000.000
29A55ALA0-0.042-0.00221.9950.0480.0480.0000.0000.0000.000
30A56LEU00.000-0.01722.6620.0210.0210.0000.0000.0000.000
31A57PRO00.0110.01620.421-0.066-0.0660.0000.0000.0000.000
32A58PHE0-0.020-0.03519.288-0.065-0.0650.0000.0000.0000.000
33A59ALA00.0270.02818.9080.0430.0430.0000.0000.0000.000
34A60ILE0-0.018-0.01820.5370.0360.0360.0000.0000.0000.000
35A61LEU00.0280.00618.1840.0360.0360.0000.0000.0000.000
36A62VAL0-0.0140.00222.1080.0330.0330.0000.0000.0000.000
37A63ASN0-0.030-0.00720.5570.0860.0860.0000.0000.0000.000
38A64HIS10.7820.82023.493-0.701-0.7010.0000.0000.0000.000
39A65GLY00.0740.02523.0560.1140.1140.0000.0000.0000.000
40A66PHE0-0.0170.00823.845-0.053-0.0530.0000.0000.0000.000
41A67LYS10.9460.97925.623-1.034-1.0340.0000.0000.0000.000
42A68LYS10.8610.92227.396-0.655-0.6550.0000.0000.0000.000
43A69ASN00.0220.01229.8970.0330.0330.0000.0000.0000.000
44A70GLY0-0.015-0.01129.1730.0190.0190.0000.0000.0000.000
45A71LYS10.8840.94726.004-0.761-0.7610.0000.0000.0000.000
46A72TRP00.034-0.00222.441-0.073-0.0730.0000.0000.0000.000
47A73TYR00.0170.02024.0860.0500.0500.0000.0000.0000.000
48A74ILE0-0.026-0.02718.516-0.037-0.0370.0000.0000.0000.000
49A75GLU-1-0.781-0.87121.0581.3441.3440.0000.0000.0000.000
50A76THR0-0.011-0.02619.969-0.043-0.0430.0000.0000.0000.000
51A77CYS-1-0.875-0.70022.5960.4640.4640.0000.0000.0000.000
52A78SER00.0530.01826.017-0.014-0.0140.0000.0000.0000.000
53A79SER00.037-0.07427.870-0.053-0.0530.0000.0000.0000.000
54A80THR0-0.072-0.05123.647-0.032-0.0320.0000.0000.0000.000
55A81HIS0-0.0050.00426.023-0.080-0.0800.0000.0000.0000.000
56A82GLY00.0050.00929.123-0.021-0.0210.0000.0000.0000.000
57A83ASP-1-0.762-0.83930.8460.3310.3310.0000.0000.0000.000
58A84TYR0-0.001-0.01631.4260.0550.0550.0000.0000.0000.000
59A85ASP-1-0.897-0.92533.7300.2930.2930.0000.0000.0000.000
60A86SER0-0.051-0.06630.4180.0240.0240.0000.0000.0000.000
61A87CYS0-0.023-0.06428.9950.0720.0720.0000.0000.0000.000
62A88PRO00.0300.01229.692-0.028-0.0280.0000.0000.0000.000
63A89VAL0-0.0070.00728.251-0.019-0.0190.0000.0000.0000.000
64A90CYS0-0.018-0.02330.829-0.022-0.0220.0000.0000.0000.000
65A91GLN0-0.0010.00333.330-0.042-0.0420.0000.0000.0000.000
66A92TYR00.0610.02534.699-0.025-0.0250.0000.0000.0000.000
67A93ILE0-0.023-0.02532.162-0.019-0.0190.0000.0000.0000.000
68A94SER0-0.051-0.01436.524-0.026-0.0260.0000.0000.0000.000
69A95LYS10.9190.94439.131-0.306-0.3060.0000.0000.0000.000
70A96ASN0-0.0220.00038.788-0.021-0.0210.0000.0000.0000.000
71A97ASP-1-0.794-0.88441.6380.2380.2380.0000.0000.0000.000
72A98LEU00.0030.01235.998-0.001-0.0010.0000.0000.0000.000
73A99TYR0-0.043-0.02038.4160.0060.0060.0000.0000.0000.000
74A100ASN0-0.079-0.06439.987-0.014-0.0140.0000.0000.0000.000
75A101THR0-0.0040.00142.6530.0030.0030.0000.0000.0000.000
76A102ASN00.0150.00339.3710.0090.0090.0000.0000.0000.000
77A103LYS10.9720.98538.604-0.225-0.2250.0000.0000.0000.000
78A104THR0-0.0030.00535.8640.0080.0080.0000.0000.0000.000
79A105GLU-1-0.784-0.88034.7650.5620.5620.0000.0000.0000.000
80A106TYR00.0220.01533.8820.0360.0360.0000.0000.0000.000
81A107SER0-0.071-0.05832.9210.0110.0110.0000.0000.0000.000
82A108GLN0-0.041-0.01729.5270.0770.0770.0000.0000.0000.000
83A109LEU00.0180.00628.9980.0500.0500.0000.0000.0000.000
84A110LYS10.8860.97829.848-0.404-0.4040.0000.0000.0000.000
85A111ARG10.9170.94327.731-0.264-0.2640.0000.0000.0000.000
86A112LYS10.8450.93124.381-0.824-0.8240.0000.0000.0000.000
87A113THR00.0230.00824.6340.0240.0240.0000.0000.0000.000
88A114SER0-0.114-0.05519.5530.0520.0520.0000.0000.0000.000
89A115TYR00.0390.01719.9710.0080.0080.0000.0000.0000.000
90A116TRP0-0.015-0.01511.5130.1240.1240.0000.0000.0000.000
91A117ALA00.0510.02415.3220.0250.0250.0000.0000.0000.000
92A118ASN00.0490.03513.382-0.404-0.4040.0000.0000.0000.000
93A119ILE0-0.034-0.03111.3170.3060.3060.0000.0000.0000.000
94A120LEU00.0880.05712.148-0.519-0.5190.0000.0000.0000.000
95A121VAL0-0.038-0.0209.9360.4680.4680.0000.0000.0000.000
96A122VAL0-0.020-0.00612.953-0.105-0.1050.0000.0000.0000.000
97A123LYS10.8290.88316.0831.6491.6490.0000.0000.0000.000
98A124ASP-1-0.776-0.88210.978-2.135-2.1350.0000.0000.0000.000
99A125PRO00.009-0.00314.158-0.106-0.1060.0000.0000.0000.000
100A126GLN00.0120.01313.664-0.015-0.0150.0000.0000.0000.000
101A127ALA0-0.051-0.0239.1820.3150.3150.0000.0000.0000.000
102A128PRO00.0660.03510.734-0.683-0.6830.0000.0000.0000.000
103A129ASP-1-0.880-0.9318.139-4.438-4.4380.0000.0000.0000.000
104A130ASN0-0.087-0.0576.765-3.251-3.2510.0000.0000.0000.000
105A131GLU-1-0.801-0.8969.183-1.782-1.7820.0000.0000.0000.000
106A132GLY0-0.007-0.00412.549-0.203-0.2030.0000.0000.0000.000
107A133LYS10.8550.9377.5767.3417.3410.0000.0000.0000.000
108A134VAL00.0210.01110.0750.4930.4930.0000.0000.0000.000
110A136LYS10.9350.9848.6201.2151.2150.0000.0000.0000.000
111A137TYR00.011-0.0129.648-0.105-0.1050.0000.0000.0000.000
112A138ARG10.8590.92511.479-1.648-1.6480.0000.0000.0000.000
113A139PHE0-0.027-0.00915.0390.0720.0720.0000.0000.0000.000
114A140GLY00.0750.02818.3640.0710.0710.0000.0000.0000.000
115A141LYS10.8900.90521.970-0.145-0.1450.0000.0000.0000.000
116A142LYS10.9050.95224.212-0.150-0.1500.0000.0000.0000.000
117A143ILE00.0000.00919.440-0.028-0.0280.0000.0000.0000.000
118A144TRP00.0430.03523.121-0.055-0.0550.0000.0000.0000.000
119A145ASP-1-0.816-0.90024.484-0.021-0.0210.0000.0000.0000.000
120A146LYS10.7790.89124.6790.1520.1520.0000.0000.0000.000
121A147ILE0-0.0010.00721.055-0.031-0.0310.0000.0000.0000.000
122A148ASN0-0.011-0.01125.638-0.025-0.0250.0000.0000.0000.000
123A149ALA0-0.006-0.01128.853-0.001-0.0010.0000.0000.0000.000
124A150MET0-0.0120.01527.3430.0060.0060.0000.0000.0000.000
125A151ILE00.0040.01329.660-0.011-0.0110.0000.0000.0000.000
126A152ALA0-0.068-0.03531.6650.0130.0130.0000.0000.0000.000
127A153VAL0-0.0210.00234.2030.0180.0180.0000.0000.0000.000
128A154ASP-1-0.839-0.93236.723-0.133-0.1330.0000.0000.0000.000
129A155THR0-0.008-0.01439.195-0.007-0.0070.0000.0000.0000.000
130A156GLU-1-0.983-0.97441.633-0.140-0.1400.0000.0000.0000.000
131A157MET0-0.128-0.06743.5200.0060.0060.0000.0000.0000.000
132A158GLY0-0.0150.00243.306-0.006-0.0060.0000.0000.0000.000
133A159GLU-1-0.930-0.95938.091-0.211-0.2110.0000.0000.0000.000
134A160THR0-0.032-0.02735.520-0.003-0.0030.0000.0000.0000.000
135A161PRO0-0.0100.00733.907-0.013-0.0130.0000.0000.0000.000
136A162VAL0-0.008-0.02428.398-0.029-0.0290.0000.0000.0000.000
137A163ASP-1-0.790-0.87526.100-0.614-0.6140.0000.0000.0000.000
138A164VAL0-0.062-0.04323.463-0.056-0.0560.0000.0000.0000.000
139A165THR0-0.084-0.07221.868-0.088-0.0880.0000.0000.0000.000
140A166CYS00.0620.07622.598-0.113-0.1130.0000.0000.0000.000
141A167PRO00.004-0.00122.018-0.018-0.0180.0000.0000.0000.000
142A168TRP00.001-0.01923.719-0.050-0.0500.0000.0000.0000.000
143A169GLU-1-0.899-0.97727.186-0.524-0.5240.0000.0000.0000.000
144A170GLY00.0150.03625.1770.0550.0550.0000.0000.0000.000
145A171ALA00.008-0.00824.7990.0010.0010.0000.0000.0000.000
146A172ASN0-0.0120.00321.404-0.087-0.0870.0000.0000.0000.000
147A173PHE00.016-0.00219.3440.1490.1490.0000.0000.0000.000
148A174VAL0-0.020-0.01119.771-0.115-0.1150.0000.0000.0000.000
149A175LEU00.0030.00415.8040.1370.1370.0000.0000.0000.000
150A176LYS10.9120.94219.7510.2900.2900.0000.0000.0000.000
151A177VAL0-0.011-0.00218.7670.0510.0510.0000.0000.0000.000
152A178LYS11.0161.01821.547-0.099-0.0990.0000.0000.0000.000
153A179GLN0-0.020-0.01721.3220.0680.0680.0000.0000.0000.000
154A180VAL0-0.018-0.02025.381-0.051-0.0510.0000.0000.0000.000
155A181SER0-0.006-0.01028.1110.0260.0260.0000.0000.0000.000
156A182GLY00.0170.01826.5850.0250.0250.0000.0000.0000.000
157A183PHE0-0.041-0.01324.2480.0920.0920.0000.0000.0000.000
158A184SER00.0370.02019.508-0.068-0.0680.0000.0000.0000.000
159A185ASN0-0.063-0.03422.551-0.049-0.0490.0000.0000.0000.000
160A186TYR00.0760.01817.2330.0390.0390.0000.0000.0000.000
161A187ASP-1-0.858-0.91623.9700.0060.0060.0000.0000.0000.000
162A188GLU-1-0.936-0.97826.101-0.148-0.1480.0000.0000.0000.000
163A189SER0-0.0290.00322.204-0.068-0.0680.0000.0000.0000.000
164A190LYS10.9400.97723.9300.4020.4020.0000.0000.0000.000
165A191PHE00.0570.02722.607-0.067-0.0670.0000.0000.0000.000
166A192LEU0-0.073-0.02724.1030.0470.0470.0000.0000.0000.000
167A193ASN00.0400.00627.0950.0350.0350.0000.0000.0000.000
168A194GLN0-0.024-0.01927.513-0.023-0.0230.0000.0000.0000.000
169A195SER0-0.056-0.03024.6840.0050.0050.0000.0000.0000.000
170A196ALA00.0870.07025.677-0.031-0.0310.0000.0000.0000.000
171A197ILE0-0.039-0.01519.237-0.044-0.0440.0000.0000.0000.000
172A198PRO0-0.040-0.03620.9040.0300.0300.0000.0000.0000.000
173A199ASN0-0.007-0.01421.317-0.035-0.0350.0000.0000.0000.000
174A200ILE00.0000.01321.624-0.050-0.0500.0000.0000.0000.000
175A201ASP-1-0.845-0.91623.759-0.858-0.8580.0000.0000.0000.000
176A202ASP-1-0.857-0.88423.564-1.246-1.2460.0000.0000.0000.000
177A203GLU-1-0.863-0.93223.863-1.051-1.0510.0000.0000.0000.000
178A204SER0-0.077-0.06622.015-0.039-0.0390.0000.0000.0000.000
179A205PHE0-0.029-0.02617.354-0.207-0.2070.0000.0000.0000.000
180A206GLN0-0.016-0.01119.099-0.149-0.1490.0000.0000.0000.000
181A207LYS10.8700.91919.4491.4871.4870.0000.0000.0000.000
182A208GLU-1-0.852-0.91013.746-3.217-3.2170.0000.0000.0000.000
183A209LEU0-0.053-0.02215.312-0.308-0.3080.0000.0000.0000.000
184A210PHE00.021-0.01615.637-0.127-0.1270.0000.0000.0000.000
185A211GLU-1-0.951-0.94314.708-1.743-1.7430.0000.0000.0000.000
186A212GLN0-0.042-0.06010.440-0.588-0.5880.0000.0000.0000.000
187A213MET0-0.0840.01011.248-0.314-0.3140.0000.0000.0000.000
188A214VAL00.009-0.00110.3720.1480.1480.0000.0000.0000.000
189A215ASP-1-0.741-0.84713.456-0.398-0.3980.0000.0000.0000.000
190A216LEU0-0.047-0.03415.2040.1270.1270.0000.0000.0000.000
191A217SER0-0.035-0.03117.7060.2020.2020.0000.0000.0000.000
192A218GLU-1-0.913-0.95814.984-0.210-0.2100.0000.0000.0000.000
193A219MET0-0.072-0.03612.8210.3370.3370.0000.0000.0000.000
194A220THR0-0.071-0.04417.7120.1550.1550.0000.0000.0000.000
195A221SER00.0190.00320.270-0.021-0.0210.0000.0000.0000.000
196A222LYS10.9800.96622.219-0.136-0.1360.0000.0000.0000.000
197A223ASP-1-0.785-0.84618.7560.6190.6190.0000.0000.0000.000
198A224LYS10.7690.89115.930-0.436-0.4360.0000.0000.0000.000
199A225PHE0-0.014-0.01520.1560.0510.0510.0000.0000.0000.000
200A226LYS10.8200.91920.980-1.245-1.2450.0000.0000.0000.000
201A227SER00.003-0.01125.044-0.033-0.0330.0000.0000.0000.000
202A228PHE00.0490.01728.6850.0490.0490.0000.0000.0000.000
203A229GLU-1-0.799-0.89831.1680.5350.5350.0000.0000.0000.000
204A230GLU-1-0.853-0.90323.9351.0501.0500.0000.0000.0000.000
205A231LEU0-0.015-0.00624.8450.0550.0550.0000.0000.0000.000
206A232ASN00.018-0.00428.0510.0210.0210.0000.0000.0000.000
207A233THR0-0.022-0.00829.878-0.018-0.0180.0000.0000.0000.000
208A234LYS10.8560.91522.313-1.239-1.2390.0000.0000.0000.000
209A235PHE0-0.023-0.02528.2110.0240.0240.0000.0000.0000.000
210A236ASN00.0400.01730.211-0.008-0.0080.0000.0000.0000.000
211A237GLN00.0130.00728.379-0.004-0.0040.0000.0000.0000.000
212A238VAL0-0.094-0.04527.0510.0290.0290.0000.0000.0000.000
213A239LEU0-0.003-0.01030.309-0.004-0.0040.0000.0000.0000.000
214A240GLY0-0.071-0.02533.733-0.018-0.0180.0000.0000.0000.000
215A241THR-1-0.934-0.95435.7570.4580.4580.0000.0000.0000.000