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: 3MNQL

Calculation Name: 1KFU-S-Xray547

Preferred Name: Calpain 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KFU

Chain ID: S

ChEMBL ID: CHEMBL2382

UniProt ID: P17655

Base Structure: X-ray

Registration Date: 2025-10-05

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2007515.74071
FMO2-HF: Nuclear repulsion 1931307.963083
FMO2-HF: Total energy -76207.777626
FMO2-MP2: Total energy -76424.58835


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:785:THR)


Summations of interaction energy for fragment #1(A:785: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.
-191.334-184.5983.301-5.538-4.499-0.065
Interaction energy analysis for fragmet #1(A:785:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.898
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].
3A787TYR00.0360.0173.442-6.497-4.8760.025-0.734-0.912-0.003
27A811ASP-1-0.942-1.0112.224-110.181-105.0663.276-4.804-3.587-0.062
4A788SER0-0.014-0.0024.9526.2666.2660.0000.0000.0000.000
5A789ASN0-0.035-0.0176.5253.4233.4230.0000.0000.0000.000
6A790ILE0-0.002-0.0019.0780.6750.6750.0000.0000.0000.000
7A791GLU-1-0.763-0.88012.202-18.166-18.1660.0000.0000.0000.000
8A792ALA0-0.0210.00715.9101.0941.0940.0000.0000.0000.000
9A793ASN0-0.071-0.04017.6721.0421.0420.0000.0000.0000.000
10A794GLU-1-0.793-0.89315.282-20.889-20.8890.0000.0000.0000.000
11A795SER00.0140.00219.1280.9110.9110.0000.0000.0000.000
12A796GLU-1-0.903-0.95120.301-13.236-13.2360.0000.0000.0000.000
13A797GLU-1-0.789-0.87121.076-13.584-13.5840.0000.0000.0000.000
14A798VAL00.0430.01517.518-0.593-0.5930.0000.0000.0000.000
15A799ARG10.8570.91811.14922.71822.7180.0000.0000.0000.000
16A800GLN0-0.057-0.02616.462-1.049-1.0490.0000.0000.0000.000
17A801PHE00.0140.00817.440-0.737-0.7370.0000.0000.0000.000
18A802ARG10.8510.91711.82221.38721.3870.0000.0000.0000.000
19A803ARG10.8700.9469.45626.56426.5640.0000.0000.0000.000
20A804LEU00.000-0.01213.528-0.804-0.8040.0000.0000.0000.000
21A805PHE00.0360.01313.058-0.127-0.1270.0000.0000.0000.000
22A806ALA00.0100.0009.169-0.969-0.9690.0000.0000.0000.000
23A807GLN0-0.116-0.05710.160-2.674-2.6740.0000.0000.0000.000
24A808LEU0-0.061-0.02112.8671.0891.0890.0000.0000.0000.000
25A809ALA00.0350.02711.1700.4580.4580.0000.0000.0000.000
26A810GLY00.0040.0067.297-2.378-2.3780.0000.0000.0000.000
28A812ASP-1-0.889-0.9225.646-28.886-28.8860.0000.0000.0000.000
29A813MET0-0.155-0.0688.5862.6422.6420.0000.0000.0000.000
30A814GLU-1-0.829-0.89710.928-19.108-19.1080.0000.0000.0000.000
31A815VAL0-0.022-0.01714.221-0.165-0.1650.0000.0000.0000.000
32A816SER00.001-0.02417.2651.0161.0160.0000.0000.0000.000
33A817ALA00.0520.01920.4820.0900.0900.0000.0000.0000.000
34A818THR00.026-0.01223.7750.3600.3600.0000.0000.0000.000
35A819GLU-1-0.807-0.85917.624-17.127-17.1270.0000.0000.0000.000
36A820LEU00.0190.01221.3570.0360.0360.0000.0000.0000.000
37A821MET00.0110.00922.4160.3040.3040.0000.0000.0000.000
38A822ASN0-0.081-0.05023.1380.4590.4590.0000.0000.0000.000
39A823ILE0-0.0120.00618.3080.1710.1710.0000.0000.0000.000
40A824LEU00.0440.02522.6570.1520.1520.0000.0000.0000.000
41A825ASN00.0120.01925.7750.2830.2830.0000.0000.0000.000
42A826LYS10.8260.89324.31812.76512.7650.0000.0000.0000.000
43A827VAL0-0.036-0.00724.2830.2870.2870.0000.0000.0000.000
44A828VAL00.0320.04227.5440.2110.2110.0000.0000.0000.000
45A829THR00.0560.00830.5340.1900.1900.0000.0000.0000.000
46A830ARG10.8650.92626.50811.75111.7510.0000.0000.0000.000
47A831HIS0-0.020-0.00130.6120.2820.2820.0000.0000.0000.000
48A832PRO0-0.007-0.01835.1120.1510.1510.0000.0000.0000.000
49A833ASP-1-0.850-0.91538.336-7.654-7.6540.0000.0000.0000.000
50A834LEU0-0.063-0.02634.4850.0760.0760.0000.0000.0000.000
51A835LYS10.8720.95137.8047.9147.9140.0000.0000.0000.000
52A836THR00.0280.00334.521-0.082-0.0820.0000.0000.0000.000
53A837ASP-1-0.853-0.92936.097-8.198-8.1980.0000.0000.0000.000
54A838GLY0-0.090-0.03232.078-0.238-0.2380.0000.0000.0000.000
55A839PHE00.014-0.00728.4970.1150.1150.0000.0000.0000.000
56A840GLY00.0920.03831.007-0.194-0.1940.0000.0000.0000.000
57A841ILE0-0.002-0.02727.227-0.255-0.2550.0000.0000.0000.000
58A842ASP-1-0.852-0.92329.442-9.824-9.8240.0000.0000.0000.000
59A843THR0-0.014-0.02430.332-0.077-0.0770.0000.0000.0000.000
60A844CYS0-0.053-0.01326.030-0.322-0.3220.0000.0000.0000.000
61A845ARG10.8700.92126.1629.9839.9830.0000.0000.0000.000
62A846SER0-0.003-0.01827.439-0.182-0.1820.0000.0000.0000.000
63A847MET0-0.081-0.03525.773-0.289-0.2890.0000.0000.0000.000
64A848VAL0-0.034-0.00822.182-0.390-0.3900.0000.0000.0000.000
65A849ALA00.0170.00424.201-0.306-0.3060.0000.0000.0000.000
66A850VAL0-0.033-0.02226.6310.0410.0410.0000.0000.0000.000
67A851MET0-0.114-0.05422.8750.2680.2680.0000.0000.0000.000
68A852ASP-1-0.751-0.82721.506-14.786-14.7860.0000.0000.0000.000
69A853SER0-0.028-0.04421.6150.3990.3990.0000.0000.0000.000
70A854ASP-1-0.893-0.91519.568-14.989-14.9890.0000.0000.0000.000
71A855THR0-0.125-0.05722.5320.4350.4350.0000.0000.0000.000
72A856THR00.001-0.01718.500-0.019-0.0190.0000.0000.0000.000
73A857GLY0-0.034-0.00920.911-0.132-0.1320.0000.0000.0000.000
74A858LYS10.7700.85915.39619.33019.3300.0000.0000.0000.000
75A859LEU0-0.0060.00719.3550.2730.2730.0000.0000.0000.000
76A860GLY00.1110.05215.588-0.929-0.9290.0000.0000.0000.000
77A861PHE00.013-0.01513.5490.8440.8440.0000.0000.0000.000
78A862GLU-1-0.809-0.89314.648-19.300-19.3000.0000.0000.0000.000
79A863GLU-1-0.821-0.91617.471-16.348-16.3480.0000.0000.0000.000
80A864PHE0-0.0010.00218.5260.9080.9080.0000.0000.0000.000
81A865LYS10.8040.88616.31719.22619.2260.0000.0000.0000.000
82A866TYR0-0.017-0.00420.8640.7080.7080.0000.0000.0000.000
83A867LEU00.0200.00523.4510.6680.6680.0000.0000.0000.000
84A868TRP0-0.047-0.04923.3040.6470.6470.0000.0000.0000.000
85A869ASN0-0.058-0.03924.8210.6460.6460.0000.0000.0000.000
86A870ASN00.0410.03526.6010.6150.6150.0000.0000.0000.000
87A871ILE00.0220.02826.4990.3950.3950.0000.0000.0000.000
88A872LYS10.8360.91025.09712.83712.8370.0000.0000.0000.000
89A873ARG10.8960.96030.2879.9469.9460.0000.0000.0000.000
90A874TRP00.012-0.01831.4770.1900.1900.0000.0000.0000.000
91A875GLN00.0420.02331.4170.5080.5080.0000.0000.0000.000
92A876ALA0-0.046-0.01334.8360.2250.2250.0000.0000.0000.000
93A877ILE00.0160.01436.7050.1840.1840.0000.0000.0000.000
94A878TYR0-0.022-0.02637.8570.1490.1490.0000.0000.0000.000
95A879LYS10.8460.91335.8679.0629.0620.0000.0000.0000.000
96A880GLN0-0.035-0.01840.8350.1560.1560.0000.0000.0000.000
97A881PHE00.0340.01642.9900.1470.1470.0000.0000.0000.000
98A882ASP-1-0.722-0.83142.517-7.348-7.3480.0000.0000.0000.000
99A883THR0-0.043-0.04143.844-0.099-0.0990.0000.0000.0000.000
100A884ASP-1-0.952-0.97046.021-6.723-6.7230.0000.0000.0000.000
101A885ARG10.7080.86742.4807.6087.6080.0000.0000.0000.000
102A886SER00.0140.00644.7070.0040.0040.0000.0000.0000.000
103A887GLY0-0.040-0.03241.676-0.024-0.0240.0000.0000.0000.000
104A888THR0-0.046-0.03342.115-0.060-0.0600.0000.0000.0000.000
105A889ILE0-0.0010.01641.6920.0820.0820.0000.0000.0000.000
106A890CYS00.012-0.00245.2640.0850.0850.0000.0000.0000.000
107A891SER00.0560.02348.695-0.041-0.0410.0000.0000.0000.000
108A892SER0-0.032-0.03849.563-0.033-0.0330.0000.0000.0000.000
109A893GLU-1-0.919-0.95147.885-6.442-6.4420.0000.0000.0000.000
110A894LEU0-0.003-0.00343.763-0.117-0.1170.0000.0000.0000.000
111A895PRO0-0.049-0.02345.541-0.147-0.1470.0000.0000.0000.000
112A896GLY00.0770.04846.540-0.081-0.0810.0000.0000.0000.000
113A897ALA00.0110.01542.575-0.138-0.1380.0000.0000.0000.000
114A898PHE0-0.018-0.03539.777-0.238-0.2380.0000.0000.0000.000
115A899GLU-1-0.937-0.96642.080-6.844-6.8440.0000.0000.0000.000
116A900ALA00.004-0.00142.280-0.097-0.0970.0000.0000.0000.000
117A901ALA0-0.066-0.03138.111-0.210-0.2100.0000.0000.0000.000
118A902GLY0-0.025-0.00937.490-0.323-0.3230.0000.0000.0000.000
119A903PHE0-0.034-0.02535.406-0.062-0.0620.0000.0000.0000.000
120A904HIS00.0420.02741.4460.0190.0190.0000.0000.0000.000
121A905LEU0-0.042-0.01042.3850.0030.0030.0000.0000.0000.000
122A906ASN0-0.001-0.00746.1070.2300.2300.0000.0000.0000.000
123A907GLU-1-0.845-0.93948.722-5.978-5.9780.0000.0000.0000.000
124A908HIS0-0.007-0.00749.919-0.122-0.1220.0000.0000.0000.000
125A909LEU0-0.0160.00342.277-0.065-0.0650.0000.0000.0000.000
126A910TYR00.0650.03345.373-0.096-0.0960.0000.0000.0000.000
127A911ASN00.0180.00247.030-0.057-0.0570.0000.0000.0000.000
128A912MET0-0.065-0.03844.2470.0470.0470.0000.0000.0000.000
129A913ILE00.0030.00741.515-0.110-0.1100.0000.0000.0000.000
130A914ILE00.0290.01843.716-0.085-0.0850.0000.0000.0000.000
131A915ARG10.9010.94046.1396.5096.5090.0000.0000.0000.000
132A916ARG10.8620.93537.2128.2608.2600.0000.0000.0000.000
133A917TYR00.000-0.00835.909-0.132-0.1320.0000.0000.0000.000
134A918SER0-0.017-0.00441.969-0.113-0.1130.0000.0000.0000.000
135A919ASP-1-0.807-0.89642.783-7.576-7.5760.0000.0000.0000.000
136A920GLU-1-0.941-0.99345.622-6.763-6.7630.0000.0000.0000.000
137A921SER0-0.071-0.02949.1940.0990.0990.0000.0000.0000.000
138A922GLY0-0.009-0.00649.1500.1260.1260.0000.0000.0000.000
139A923ASN0-0.0110.00047.0270.0430.0430.0000.0000.0000.000
140A924MET00.0090.01741.075-0.122-0.1220.0000.0000.0000.000
141A925ASP-1-0.791-0.86038.755-8.315-8.3150.0000.0000.0000.000
142A926PHE00.000-0.03032.570-0.181-0.1810.0000.0000.0000.000
143A927ASP-1-0.816-0.87833.594-9.822-9.8220.0000.0000.0000.000
144A928ASN0-0.013-0.00935.217-0.358-0.3580.0000.0000.0000.000
145A929PHE00.004-0.00137.228-0.097-0.0970.0000.0000.0000.000
146A930ILE0-0.023-0.01431.137-0.117-0.1170.0000.0000.0000.000
147A931SER0-0.014-0.01132.839-0.198-0.1980.0000.0000.0000.000
148A932CYS0-0.048-0.00433.900-0.016-0.0160.0000.0000.0000.000
149A933LEU00.011-0.00234.931-0.029-0.0290.0000.0000.0000.000
150A934VAL0-0.014-0.01229.075-0.133-0.1330.0000.0000.0000.000
151A935ARG10.8790.94631.9859.1559.1550.0000.0000.0000.000
152A936LEU0-0.0150.00133.7450.1090.1090.0000.0000.0000.000
153A937ASP-1-0.822-0.91030.845-10.226-10.2260.0000.0000.0000.000
154A938ALA0-0.0090.00831.072-0.044-0.0440.0000.0000.0000.000
155A939MET0-0.0060.00432.2680.0800.0800.0000.0000.0000.000
156A940PHE0-0.034-0.01535.6750.2140.2140.0000.0000.0000.000
157A941ARG10.8440.90027.89011.04211.0420.0000.0000.0000.000
158A942ALA00.0210.03232.799-0.060-0.0600.0000.0000.0000.000
159A943PHE0-0.017-0.00933.6530.0840.0840.0000.0000.0000.000
160A944LYS10.8560.90435.2778.1438.1430.0000.0000.0000.000
161A945SER0-0.034-0.00731.639-0.166-0.1660.0000.0000.0000.000
162A946LEU0-0.022-0.00933.674-0.023-0.0230.0000.0000.0000.000
163A947ASP-1-0.783-0.87736.518-7.516-7.5160.0000.0000.0000.000
164A948LYS10.8380.91036.3458.1758.1750.0000.0000.0000.000
165A949ASP-1-0.869-0.92637.910-7.843-7.8430.0000.0000.0000.000
166A950GLY0-0.027-0.00540.9870.1480.1480.0000.0000.0000.000
167A951THR0-0.075-0.05342.3940.2070.2070.0000.0000.0000.000
168A952GLY0-0.030-0.01643.6350.1680.1680.0000.0000.0000.000
169A953GLN0-0.089-0.04544.0820.0890.0890.0000.0000.0000.000
170A954ILE00.0260.01539.300-0.158-0.1580.0000.0000.0000.000
171A955GLN0-0.035-0.01842.0990.2490.2490.0000.0000.0000.000
172A956VAL00.0100.00938.464-0.184-0.1840.0000.0000.0000.000
173A957ASN0-0.047-0.03539.4600.3980.3980.0000.0000.0000.000
174A958ILE00.011-0.01040.070-0.127-0.1270.0000.0000.0000.000
175A959GLN0-0.007-0.00535.2910.0970.0970.0000.0000.0000.000
176A960GLU-1-0.757-0.86335.263-8.705-8.7050.0000.0000.0000.000
177A961TRP00.0120.01335.998-0.154-0.1540.0000.0000.0000.000
178A962LEU00.0020.01037.032-0.039-0.0390.0000.0000.0000.000
179A963GLN0-0.016-0.01230.4020.0950.0950.0000.0000.0000.000
180A964LEU00.0130.00632.762-0.197-0.1970.0000.0000.0000.000
181A965THR0-0.053-0.05034.454-0.030-0.0300.0000.0000.0000.000
182A966MET0-0.073-0.04034.2270.1200.1200.0000.0000.0000.000
183A967TYR0-0.109-0.06524.204-0.013-0.0130.0000.0000.0000.000
184A968SER-1-0.776-0.85430.576-10.013-10.0130.0000.0000.0000.000