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: N8Y3Q

Calculation Name: 6DKF-A-Other547

Preferred Name: ATP-dependent Clp protease proteolytic subunit

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6DKF

Chain ID: A

ChEMBL ID: CHEMBL1932910

UniProt ID: Q2G036

Base Structure: ElectronMicroscopy

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1727219.541681
FMO2-HF: Nuclear repulsion 1660436.284425
FMO2-HF: Total energy -66783.257256
FMO2-MP2: Total energy -66977.402806


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:20:ILE)


Summations of interaction energy for fragment #1(A:20:ILE)
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.
-82.158-79.2770.026-0.997-1.909-0.002
Interaction energy analysis for fragmet #1(A:20:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.918
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].
3A22SER00.0450.0373.6056.0218.2660.028-0.902-1.370-0.002
4A23ARG10.9470.9634.21641.53041.920-0.001-0.076-0.3130.000
5A24LEU00.0010.0094.5662.9523.198-0.001-0.019-0.2260.000
6A25LEU00.0660.0396.5642.9802.9800.0000.0000.0000.000
7A26LYS10.9190.9588.89127.81427.8140.0000.0000.0000.000
8A27ASP-1-0.948-0.9809.924-21.288-21.2880.0000.0000.0000.000
9A28ARG10.8300.90311.58518.22018.2200.0000.0000.0000.000
10A29ILE0-0.0080.0108.4380.8310.8310.0000.0000.0000.000
11A30ILE0-0.064-0.0329.232-3.301-3.3010.0000.0000.0000.000
12A31MET0-0.043-0.0267.628-0.481-0.4810.0000.0000.0000.000
13A32LEU00.0110.0099.828-0.836-0.8360.0000.0000.0000.000
14A33GLY00.0170.00410.1820.9810.9810.0000.0000.0000.000
15A34SER00.003-0.00511.1680.2350.2350.0000.0000.0000.000
16A35GLN0-0.0090.01413.6261.1511.1510.0000.0000.0000.000
17A36ILE0-0.023-0.00615.760-0.972-0.9720.0000.0000.0000.000
18A37ASP-1-0.841-0.94217.254-14.272-14.2720.0000.0000.0000.000
19A38ASP-1-0.896-0.94917.884-14.878-14.8780.0000.0000.0000.000
20A39ASN0-0.029-0.00714.541-1.183-1.1830.0000.0000.0000.000
21A40VAL0-0.024-0.01411.921-1.046-1.0460.0000.0000.0000.000
22A41ALA00.0450.02014.116-0.797-0.7970.0000.0000.0000.000
23A42ASN00.0120.00416.846-0.444-0.4440.0000.0000.0000.000
24A43SER0-0.041-0.02710.399-0.822-0.8220.0000.0000.0000.000
25A44ILE0-0.005-0.00612.297-0.950-0.9500.0000.0000.0000.000
26A45VAL00.0670.03613.5040.0410.0410.0000.0000.0000.000
27A46SER0-0.040-0.00814.6740.2770.2770.0000.0000.0000.000
28A47GLN00.015-0.0018.594-0.246-0.2460.0000.0000.0000.000
29A48LEU00.0280.02013.569-0.114-0.1140.0000.0000.0000.000
30A49LEU00.0370.02316.3280.5920.5920.0000.0000.0000.000
31A50PHE0-0.061-0.03611.0570.1370.1370.0000.0000.0000.000
32A51LEU0-0.001-0.00713.1850.1660.1660.0000.0000.0000.000
33A52GLN00.0280.01016.4030.3770.3770.0000.0000.0000.000
34A53ALA0-0.073-0.03518.7020.6750.6750.0000.0000.0000.000
35A54GLN0-0.116-0.04513.928-0.591-0.5910.0000.0000.0000.000
36A55ASP-1-0.821-0.92317.959-13.943-13.9430.0000.0000.0000.000
37A56SER00.0210.01720.513-0.233-0.2330.0000.0000.0000.000
38A57GLU-1-0.937-0.95922.845-11.030-11.0300.0000.0000.0000.000
39A58LYS0-0.061-0.02614.8690.2670.2670.0000.0000.0000.000
40A59ASP-1-0.801-0.88318.407-15.149-15.1490.0000.0000.0000.000
41A60ILE0-0.032-0.00214.646-1.006-1.0060.0000.0000.0000.000
42A61TYR00.0520.03211.8630.7050.7050.0000.0000.0000.000
43A62LEU00.028-0.00412.792-1.928-1.9280.0000.0000.0000.000
44A63TYR0-0.032-0.0169.4861.1881.1880.0000.0000.0000.000
45A64ILE0-0.045-0.00112.690-1.023-1.0230.0000.0000.0000.000
46A65ASN0-0.045-0.02412.7450.0480.0480.0000.0000.0000.000
47A66SER0-0.002-0.02414.123-0.455-0.4550.0000.0000.0000.000
48A67PRO00.010-0.01916.7860.6490.6490.0000.0000.0000.000
49A68GLY00.0550.05619.0700.7430.7430.0000.0000.0000.000
50A69GLY0-0.013-0.02319.595-0.686-0.6860.0000.0000.0000.000
51A70SER0-0.022-0.00721.4380.7080.7080.0000.0000.0000.000
52A71VAL00.0810.03022.635-0.403-0.4030.0000.0000.0000.000
53A72THR0-0.016-0.00525.291-0.127-0.1270.0000.0000.0000.000
54A73ALA00.0210.01320.170-0.079-0.0790.0000.0000.0000.000
55A74GLY00.052-0.01721.099-0.475-0.4750.0000.0000.0000.000
56A75PHE00.0120.00122.192-0.107-0.1070.0000.0000.0000.000
57A76ALA0-0.0110.01221.8650.0230.0230.0000.0000.0000.000
58A77ILE0-0.0010.00016.396-0.317-0.3170.0000.0000.0000.000
59A78TYR00.0140.00420.0880.0400.0400.0000.0000.0000.000
60A79ASP-1-0.900-0.95022.822-11.437-11.4370.0000.0000.0000.000
61A80THR0-0.018-0.03320.718-0.198-0.1980.0000.0000.0000.000
62A81ILE0-0.062-0.03019.336-0.438-0.4380.0000.0000.0000.000
63A82GLN0-0.0260.00021.9470.1470.1470.0000.0000.0000.000
64A83HIS0-0.087-0.04825.0800.4340.4340.0000.0000.0000.000
65A84ILE0-0.050-0.00520.2560.1810.1810.0000.0000.0000.000
66A85LYS10.8510.92224.39512.14312.1430.0000.0000.0000.000
67A86PRO0-0.082-0.04820.0220.1690.1690.0000.0000.0000.000
68A87ASP-1-0.747-0.85721.915-12.813-12.8130.0000.0000.0000.000
69A88VAL00.0310.00717.855-0.681-0.6810.0000.0000.0000.000
70A89GLN0-0.038-0.01517.4160.1100.1100.0000.0000.0000.000
71A90THR0-0.012-0.02217.411-0.860-0.8600.0000.0000.0000.000
72A91ILE00.0080.01414.5880.5140.5140.0000.0000.0000.000
73A92CYS0-0.0050.00316.107-0.985-0.9850.0000.0000.0000.000
74A93ILE0-0.006-0.01312.1510.3230.3230.0000.0000.0000.000
75A94GLY0-0.0060.00515.922-0.369-0.3690.0000.0000.0000.000
76A95MET00.0120.01517.3150.8750.8750.0000.0000.0000.000
77A96ALA00.0300.01217.858-0.941-0.9410.0000.0000.0000.000
78A97ALA00.0430.02020.1680.6410.6410.0000.0000.0000.000
79A98SER00.0640.04222.064-0.584-0.5840.0000.0000.0000.000
80A99MET0-0.0640.00920.695-0.328-0.3280.0000.0000.0000.000
81A100GLY00.062-0.00319.510-0.251-0.2510.0000.0000.0000.000
82A101SER0-0.016-0.00220.169-0.082-0.0820.0000.0000.0000.000
83A102PHE00.0160.00123.1790.1020.1020.0000.0000.0000.000
84A103LEU0-0.002-0.01316.9100.0210.0210.0000.0000.0000.000
85A104LEU0-0.029-0.00619.125-0.197-0.1970.0000.0000.0000.000
86A105ALA00.0610.03221.2290.0620.0620.0000.0000.0000.000
87A106ALA0-0.030-0.00822.5420.3930.3930.0000.0000.0000.000
88A107GLY00.0060.00922.112-0.028-0.0280.0000.0000.0000.000
89A108ALA00.0140.02222.7230.6150.6150.0000.0000.0000.000
90A109LYS10.8500.93024.7769.7499.7490.0000.0000.0000.000
91A110GLY0-0.025-0.01127.416-0.004-0.0040.0000.0000.0000.000
92A111LYS10.7200.85520.53113.94113.9410.0000.0000.0000.000
93A112ARG0-0.0160.03621.625-0.523-0.5230.0000.0000.0000.000
94A113PHE0-0.005-0.01117.5760.3880.3880.0000.0000.0000.000
95A114ALA00.005-0.00619.473-0.468-0.4680.0000.0000.0000.000
96A115LEU00.0310.01915.7230.4620.4620.0000.0000.0000.000
97A116PRO00.0450.00719.4400.2030.2030.0000.0000.0000.000
98A117ASN0-0.093-0.04720.2290.4940.4940.0000.0000.0000.000
99A118ALA0-0.051-0.01119.643-0.088-0.0880.0000.0000.0000.000
100A119GLU00.0000.00121.0470.5200.5200.0000.0000.0000.000
101A120VAL0-0.068-0.03221.805-0.663-0.6630.0000.0000.0000.000
102A121MET0-0.0060.00724.2150.2810.2810.0000.0000.0000.000
103A122ILE00.0360.00825.916-0.439-0.4390.0000.0000.0000.000
104A123HIS0-0.0180.01128.194-0.013-0.0130.0000.0000.0000.000
105A124GLN00.005-0.00927.883-0.318-0.3180.0000.0000.0000.000
106A125PRO0-0.010-0.00128.0430.3280.3280.0000.0000.0000.000
107A126LEU0-0.011-0.01030.222-0.180-0.1800.0000.0000.0000.000
108A127GLY00.0250.00930.3330.1660.1660.0000.0000.0000.000
109A128GLY0-0.030-0.00826.768-0.252-0.2520.0000.0000.0000.000
110A129ALA00.0450.01925.2180.3480.3480.0000.0000.0000.000
111A130GLN0-0.036-0.02123.817-0.182-0.1820.0000.0000.0000.000
112A131GLY0-0.017-0.00526.5310.1430.1430.0000.0000.0000.000
113A132GLN0-0.089-0.05727.8700.2040.2040.0000.0000.0000.000
114A133ALA00.0660.05230.9830.0640.0640.0000.0000.0000.000
115A134THR0-0.007-0.01132.1240.3680.3680.0000.0000.0000.000
116A135GLU-1-0.842-0.93935.206-8.043-8.0430.0000.0000.0000.000
117A136ILE0-0.026-0.01734.5160.0460.0460.0000.0000.0000.000
118A137GLU-1-0.882-0.93229.491-10.260-10.2600.0000.0000.0000.000
119A138ILE00.0450.02533.100-0.104-0.1040.0000.0000.0000.000
120A139ALA0-0.036-0.01135.1170.0730.0730.0000.0000.0000.000
121A140ALA00.007-0.00432.8870.0760.0760.0000.0000.0000.000
122A141ASN00.0190.01631.329-0.131-0.1310.0000.0000.0000.000
123A142HIS0-0.0120.00033.181-0.111-0.1110.0000.0000.0000.000
124A143ILE0-0.053-0.02236.3550.1350.1350.0000.0000.0000.000
125A144LEU0-0.053-0.02429.9080.0320.0320.0000.0000.0000.000
126A145LYS00.0150.02434.319-0.027-0.0270.0000.0000.0000.000
127A146THR0-0.009-0.03129.793-0.018-0.0180.0000.0000.0000.000
128A147ARG10.8250.90231.8458.4118.4110.0000.0000.0000.000
129A148GLU00.009-0.00933.3720.0510.0510.0000.0000.0000.000
130A149LYS0-0.027-0.01130.1380.1000.1000.0000.0000.0000.000
131A150LEU00.0030.00327.790-0.080-0.0800.0000.0000.0000.000
132A151ASN0-0.018-0.03430.9240.0520.0520.0000.0000.0000.000
133A152ARG10.8380.91433.9748.6178.6170.0000.0000.0000.000
134A153ILE0-0.026-0.00228.1220.0300.0300.0000.0000.0000.000
135A154LEU00.0430.01928.070-0.140-0.1400.0000.0000.0000.000
136A155SER0-0.0290.00230.9950.0530.0530.0000.0000.0000.000
137A156GLU-1-0.865-0.92733.080-8.800-8.8000.0000.0000.0000.000
138A157ARG10.6850.81625.31911.39211.3920.0000.0000.0000.000
139A158THR0-0.005-0.02030.7580.1740.1740.0000.0000.0000.000
140A159GLY0-0.028-0.00832.7650.1290.1290.0000.0000.0000.000
141A160GLN0-0.031-0.02035.6340.3430.3430.0000.0000.0000.000
142A161SER-1-0.809-0.89037.656-7.454-7.4540.0000.0000.0000.000
143A162ILE0-0.033-0.02838.222-0.159-0.1590.0000.0000.0000.000
144A163GLU-1-0.919-0.96538.855-7.013-7.0130.0000.0000.0000.000
145A164LYS0-0.022-0.00637.4460.0490.0490.0000.0000.0000.000
146A165ILE00.0180.03132.259-0.109-0.1090.0000.0000.0000.000
147A166GLN0-0.0460.00435.276-0.124-0.1240.0000.0000.0000.000
148A167LYS0-0.012-0.00337.566-0.016-0.0160.0000.0000.0000.000
149A168ASP-1-0.838-0.92132.021-9.280-9.2800.0000.0000.0000.000
150A169THR0-0.030-0.04531.281-0.119-0.1190.0000.0000.0000.000
151A170ASP-1-0.897-0.92633.095-8.153-8.1530.0000.0000.0000.000
152A171ARG10.8700.94234.3878.4068.4060.0000.0000.0000.000
153A172ASP-1-0.932-0.96530.557-9.946-9.9460.0000.0000.0000.000
154A173ASN0-0.029-0.04730.7390.3380.3380.0000.0000.0000.000
155A174PHE0-0.081-0.03825.450-0.436-0.4360.0000.0000.0000.000
156A175LEU00.0500.06027.8240.1760.1760.0000.0000.0000.000
157A176THR0-0.035-0.04826.471-0.542-0.5420.0000.0000.0000.000
158A177ALA00.0270.00223.6940.0630.0630.0000.0000.0000.000
159A178GLU-1-0.957-0.97925.594-9.174-9.1740.0000.0000.0000.000
160A179GLU-1-0.794-0.88728.952-9.261-9.2610.0000.0000.0000.000
161A180ALA00.006-0.01026.7570.1410.1410.0000.0000.0000.000
162A181LYS10.8430.91128.4099.9039.9030.0000.0000.0000.000
163A182GLU-1-0.996-0.98829.833-8.059-8.0590.0000.0000.0000.000
164A183TYR-1-0.876-0.94331.366-8.923-8.9230.0000.0000.0000.000
165A184GLY00.005-0.00631.676-0.136-0.1360.0000.0000.0000.000
166A185LEU00.0100.00326.212-0.266-0.2660.0000.0000.0000.000
167A186ILE0-0.059-0.02023.593-0.275-0.2750.0000.0000.0000.000
168A187ASP-1-0.756-0.87525.701-10.568-10.5680.0000.0000.0000.000
169A188GLU-1-0.962-0.99424.332-11.081-11.0810.0000.0000.0000.000
170A189VAL00.0330.02223.463-0.482-0.4820.0000.0000.0000.000
171A190MET0-0.025-0.00518.7010.0340.0340.0000.0000.0000.000
172A191VAL0-0.042-0.02522.343-0.034-0.0340.0000.0000.0000.000
173A192PRO-1-0.936-0.97020.296-12.894-12.8940.0000.0000.0000.000