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: 97Q42

Calculation Name: 4LKR-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EDM4

Base Structure: X-ray

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 233
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2840591.802525
FMO2-HF: Nuclear repulsion 2750193.492333
FMO2-HF: Total energy -90398.310192
FMO2-MP2: Total energy -90657.905197


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:THR)


Summations of interaction energy for fragment #1(A:2: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.
-155.035-138.70212.089-13.133-15.286-0.102
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.913
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].
3A4HIS10.7920.8803.19558.41161.958-0.004-1.726-1.8170.001
4A5ILE00.0500.0422.6745.7297.6300.699-0.936-1.6650.008
5A6ASN0-0.015-0.0212.128-23.316-21.1932.538-2.441-2.220-0.037
6A7ALA00.0600.0584.6924.0314.123-0.001-0.006-0.0840.000
7A8GLN0-0.016-0.0205.074-6.013-5.962-0.0010.000-0.0490.000
74A75GLU-1-0.773-0.9042.328-82.718-79.7014.487-4.298-3.205-0.042
75A76LEU00.0250.0064.975-1.536-1.404-0.001-0.006-0.1250.000
78A79PHE0-0.070-0.0422.376-16.791-13.1003.461-2.821-4.331-0.036
79A80PHE0-0.028-0.0112.682-2.511-0.7320.911-0.899-1.7900.004
8A9PRO0-0.009-0.0225.2670.8080.8080.0000.0000.0000.000
9A10THR00.0150.0136.7341.1041.1040.0000.0000.0000.000
10A11ASP-1-0.829-0.9048.990-22.822-22.8220.0000.0000.0000.000
11A12PHE0-0.0010.0096.6261.2271.2270.0000.0000.0000.000
12A13ALA0-0.0080.00511.6430.5940.5940.0000.0000.0000.000
13A14GLU-1-0.841-0.91913.760-17.471-17.4710.0000.0000.0000.000
14A15THR00.0010.00515.5060.2230.2230.0000.0000.0000.000
15A16VAL0-0.007-0.00811.406-0.112-0.1120.0000.0000.0000.000
16A17ILE00.0310.01914.8370.3500.3500.0000.0000.0000.000
17A18MET0-0.027-0.02910.819-0.897-0.8970.0000.0000.0000.000
18A19PRO00.0090.03216.1240.6650.6650.0000.0000.0000.000
19A20GLY00.0770.02316.332-0.920-0.9200.0000.0000.0000.000
20A21ASP-1-0.866-0.94216.654-15.054-15.0540.0000.0000.0000.000
21A22PRO00.0370.00614.1820.1560.1560.0000.0000.0000.000
22A23LEU0-0.010-0.00716.1730.0970.0970.0000.0000.0000.000
23A24ARG10.9610.98319.48212.56812.5680.0000.0000.0000.000
24A25ALA0-0.0040.00815.6830.3380.3380.0000.0000.0000.000
25A26LYS10.8630.92517.70613.59913.5990.0000.0000.0000.000
26A27TYR00.0200.01018.8410.3970.3970.0000.0000.0000.000
27A28ILE0-0.001-0.00620.1590.4540.4540.0000.0000.0000.000
28A29ALA0-0.006-0.01218.0500.3110.3110.0000.0000.0000.000
29A30GLU-1-0.867-0.92720.171-12.540-12.5400.0000.0000.0000.000
30A31THR0-0.076-0.03223.2230.5760.5760.0000.0000.0000.000
31A32TYR0-0.050-0.05323.8610.2540.2540.0000.0000.0000.000
32A33LEU0-0.081-0.02418.8450.0310.0310.0000.0000.0000.000
33A34THR0-0.023-0.01022.9510.3890.3890.0000.0000.0000.000
34A35ASP-1-0.913-0.97022.181-12.126-12.1260.0000.0000.0000.000
35A36ALA0-0.024-0.00718.654-0.612-0.6120.0000.0000.0000.000
36A37VAL0-0.012-0.00414.9460.3020.3020.0000.0000.0000.000
37A38GLU-1-0.856-0.92012.561-19.073-19.0730.0000.0000.0000.000
38A39VAL0-0.036-0.0169.646-0.272-0.2720.0000.0000.0000.000
39A40THR0-0.002-0.0096.801-4.538-4.5380.0000.0000.0000.000
40A41ASN00.0210.0028.5850.3900.3900.0000.0000.0000.000
41A42VAL0-0.027-0.0045.4441.6461.6460.0000.0000.0000.000
42A43ARG10.8990.9438.75028.08328.0830.0000.0000.0000.000
43A44ASN00.0350.02311.8620.6750.6750.0000.0000.0000.000
44A45MET0-0.0460.0019.6362.0202.0200.0000.0000.0000.000
45A46LEU0-0.021-0.01410.223-1.654-1.6540.0000.0000.0000.000
46A47GLY00.005-0.01011.0220.4270.4270.0000.0000.0000.000
47A48TYR0-0.012-0.00911.901-0.456-0.4560.0000.0000.0000.000
48A49THR0-0.013-0.02612.647-0.252-0.2520.0000.0000.0000.000
49A50GLY00.0470.04415.2030.2850.2850.0000.0000.0000.000
50A51TYR0-0.035-0.01618.934-0.366-0.3660.0000.0000.0000.000
51A52TYR00.0530.02722.0050.1360.1360.0000.0000.0000.000
52A53GLN0-0.003-0.00924.6570.0180.0180.0000.0000.0000.000
53A54GLY00.0150.01626.7830.1740.1740.0000.0000.0000.000
54A55GLN0-0.032-0.02223.176-0.577-0.5770.0000.0000.0000.000
55A56ARG10.8650.93413.33918.41418.4140.0000.0000.0000.000
56A57ILE0-0.007-0.01018.037-0.177-0.1770.0000.0000.0000.000
57A58SER00.031-0.00413.201-0.274-0.2740.0000.0000.0000.000
58A59VAL0-0.0130.00715.0020.3910.3910.0000.0000.0000.000
59A60MET0-0.009-0.0107.450-1.054-1.0540.0000.0000.0000.000
60A61GLY00.0200.02813.1940.5720.5720.0000.0000.0000.000
61A62HIS0-0.020-0.01011.854-1.228-1.2280.0000.0000.0000.000
62A63GLY00.0200.01313.271-0.635-0.6350.0000.0000.0000.000
63A64MET0-0.019-0.01315.3830.8260.8260.0000.0000.0000.000
64A65GLY00.0630.03517.060-0.545-0.5450.0000.0000.0000.000
65A66ILE00.0290.01916.372-1.393-1.3930.0000.0000.0000.000
66A67SER0-0.025-0.02914.221-1.049-1.0490.0000.0000.0000.000
67A68SER0-0.061-0.02512.204-2.162-2.1620.0000.0000.0000.000
68A69MET0-0.0130.02211.388-1.942-1.9420.0000.0000.0000.000
69A70VAL00.034-0.01411.873-1.422-1.4220.0000.0000.0000.000
70A71LEU0-0.053-0.0046.378-2.044-2.0440.0000.0000.0000.000
71A72TYR0-0.007-0.0177.110-4.720-4.7200.0000.0000.0000.000
72A73GLY00.0680.0307.733-1.288-1.2880.0000.0000.0000.000
73A74HIS00.0010.0056.5991.5131.5130.0000.0000.0000.000
76A77ILE0-0.0050.0057.3530.6800.6800.0000.0000.0000.000
77A78ASN0-0.106-0.0656.4641.8131.8130.0000.0000.0000.000
80A81GLY00.0240.0357.2992.6512.6510.0000.0000.0000.000
81A82VAL0-0.050-0.01810.1112.2222.2220.0000.0000.0000.000
82A83LYS10.8390.90012.10218.27918.2790.0000.0000.0000.000
83A84ARG10.7810.87615.49014.33114.3310.0000.0000.0000.000
84A85ILE00.0020.00211.982-0.735-0.7350.0000.0000.0000.000
85A86ILE0-0.003-0.00316.2330.6770.6770.0000.0000.0000.000
86A87ARG10.7770.88118.52614.02614.0260.0000.0000.0000.000
87A88ILE0-0.008-0.00819.4760.6920.6920.0000.0000.0000.000
88A89GLY00.017-0.00721.505-0.375-0.3750.0000.0000.0000.000
89A90SER0-0.036-0.02723.2580.2910.2910.0000.0000.0000.000
90A91LEU0-0.050-0.01825.993-0.392-0.3920.0000.0000.0000.000
91A92GLY00.0800.04428.7150.2390.2390.0000.0000.0000.000
92A93ALA00.013-0.00831.852-0.074-0.0740.0000.0000.0000.000
93A94THR0-0.020-0.03533.8100.0480.0480.0000.0000.0000.000
94A95GLN0-0.026-0.01936.1400.3370.3370.0000.0000.0000.000
95A96GLN00.0240.00638.993-0.019-0.0190.0000.0000.0000.000
96A97HIS0-0.031-0.00538.6180.0830.0830.0000.0000.0000.000
97A98VAL0-0.038-0.01434.963-0.036-0.0360.0000.0000.0000.000
98A99GLU-1-0.798-0.90538.318-7.227-7.2270.0000.0000.0000.000
99A100MET00.0080.00435.408-0.260-0.2600.0000.0000.0000.000
100A101ARG10.8220.91535.5157.3567.3560.0000.0000.0000.000
101A102ASP-1-0.817-0.87435.041-8.143-8.1430.0000.0000.0000.000
102A103VAL0-0.028-0.02129.330-0.269-0.2690.0000.0000.0000.000
103A104ILE0-0.012-0.00929.7550.1830.1830.0000.0000.0000.000
104A105LEU0-0.010-0.00528.371-0.453-0.4530.0000.0000.0000.000
105A106ALA00.0550.02025.9550.2900.2900.0000.0000.0000.000
106A107GLN00.0260.02727.037-0.294-0.2940.0000.0000.0000.000
107A108ALA0-0.022-0.02127.222-0.263-0.2630.0000.0000.0000.000
108A109ALA00.0050.01524.4480.1510.1510.0000.0000.0000.000
109A110GLY0-0.0070.01426.060-0.164-0.1640.0000.0000.0000.000
110A111THR0-0.021-0.03822.625-0.436-0.4360.0000.0000.0000.000
111A112ASP-1-0.793-0.88425.072-11.686-11.6860.0000.0000.0000.000
112A113SER0-0.0110.00320.441-0.332-0.3320.0000.0000.0000.000
113A114PRO0-0.039-0.02622.010-0.097-0.0970.0000.0000.0000.000
114A115THR0-0.063-0.04817.303-0.278-0.2780.0000.0000.0000.000
115A116ASN00.042-0.00519.140-1.099-1.0990.0000.0000.0000.000
116A117ALA00.0570.03520.802-0.072-0.0720.0000.0000.0000.000
117A118LYS10.9210.96218.35616.29816.2980.0000.0000.0000.000
118A119ARG10.8810.94612.72419.97619.9760.0000.0000.0000.000
119A120SER00.000-0.01219.280-0.202-0.2020.0000.0000.0000.000
120A121SER0-0.032-0.03122.1000.6080.6080.0000.0000.0000.000
121A122GLY0-0.023-0.00623.8830.4490.4490.0000.0000.0000.000
122A123TYR0-0.0200.00025.8090.6210.6210.0000.0000.0000.000
123A124HIS00.0270.01326.164-0.645-0.6450.0000.0000.0000.000
124A125MET0-0.058-0.02025.4490.2540.2540.0000.0000.0000.000
125A126ALA00.0090.01026.270-0.204-0.2040.0000.0000.0000.000
126A127THR0-0.015-0.00522.226-0.393-0.3930.0000.0000.0000.000
127A128SER0-0.053-0.04124.4570.4050.4050.0000.0000.0000.000
128A129ALA00.0450.02723.921-0.527-0.5270.0000.0000.0000.000
129A130THR0-0.001-0.00622.5630.1460.1460.0000.0000.0000.000
130A131PHE00.0280.00724.8590.1120.1120.0000.0000.0000.000
131A132SER00.0180.01025.6710.2230.2230.0000.0000.0000.000
132A133LEU00.0200.01021.8880.2450.2450.0000.0000.0000.000
133A134LEU00.0090.01226.3910.1860.1860.0000.0000.0000.000
134A135HIS00.0110.01028.6380.2300.2300.0000.0000.0000.000
135A136LYS10.8340.93426.31111.35511.3550.0000.0000.0000.000
136A137ALA00.0590.02627.5730.2200.2200.0000.0000.0000.000
137A138TYR00.017-0.00229.6340.2710.2710.0000.0000.0000.000
138A139THR0-0.058-0.04033.0900.3320.3320.0000.0000.0000.000
139A140LYS10.8430.91730.2189.4699.4690.0000.0000.0000.000
140A141ALA00.0060.00632.7640.1070.1070.0000.0000.0000.000
141A142ASN0-0.029-0.01334.1840.2970.2970.0000.0000.0000.000
142A143GLU-1-0.917-0.95835.271-8.422-8.4220.0000.0000.0000.000
143A144LYS10.8020.90031.2519.4299.4290.0000.0000.0000.000
144A145GLY0-0.0190.00636.8460.0770.0770.0000.0000.0000.000
145A146ILE0-0.051-0.02632.3720.0440.0440.0000.0000.0000.000
146A147SER0-0.048-0.03136.3790.1200.1200.0000.0000.0000.000
147A148VAL00.0050.00532.411-0.241-0.2410.0000.0000.0000.000
148A149LYS10.8270.91734.0208.2088.2080.0000.0000.0000.000
149A150VAL0-0.0040.00232.091-0.323-0.3230.0000.0000.0000.000
150A151GLY00.0330.00932.1290.3080.3080.0000.0000.0000.000
151A152ASN0-0.022-0.01230.672-0.471-0.4710.0000.0000.0000.000
152A153VAL00.0330.01526.3090.1890.1890.0000.0000.0000.000
153A154PHE00.0260.00327.687-0.055-0.0550.0000.0000.0000.000
154A155SER0-0.028-0.03122.545-0.068-0.0680.0000.0000.0000.000
155A156GLY00.0490.03324.471-0.118-0.1180.0000.0000.0000.000
156A157ASP-1-0.850-0.94320.766-14.857-14.8570.0000.0000.0000.000
157A158LEU0-0.098-0.03822.991-0.351-0.3510.0000.0000.0000.000
158A159TYR00.013-0.00525.0700.3110.3110.0000.0000.0000.000
159A160TYR0-0.065-0.03626.7770.2320.2320.0000.0000.0000.000
160A161ASP-1-0.822-0.92029.556-10.147-10.1470.0000.0000.0000.000
161A162PRO0-0.070-0.03330.6420.2330.2330.0000.0000.0000.000
162A163ASP-1-0.888-0.93933.588-8.242-8.2420.0000.0000.0000.000
163A164GLU-1-0.951-0.98035.574-7.748-7.7480.0000.0000.0000.000
164A165ASP-1-0.806-0.86538.241-7.640-7.6400.0000.0000.0000.000
165A166MET00.0220.02531.519-0.124-0.1240.0000.0000.0000.000
166A167ILE00.006-0.01033.256-0.097-0.0970.0000.0000.0000.000
167A168PRO00.0330.00736.2620.0310.0310.0000.0000.0000.000
168A169ALA0-0.033-0.01336.1560.1070.1070.0000.0000.0000.000
169A170LEU0-0.028-0.01331.485-0.031-0.0310.0000.0000.0000.000
170A171GLU-1-0.880-0.94635.659-7.418-7.4180.0000.0000.0000.000
171A172ARG10.7340.81438.8887.7757.7750.0000.0000.0000.000
172A173PHE0-0.059-0.02134.5460.0920.0920.0000.0000.0000.000
173A174GLY0-0.017-0.00437.054-0.127-0.1270.0000.0000.0000.000
174A175VAL0-0.065-0.01731.715-0.130-0.1300.0000.0000.0000.000
175A176LEU00.0200.01632.6720.1470.1470.0000.0000.0000.000
176A177GLY00.0450.01431.6350.1470.1470.0000.0000.0000.000
177A178ILE0-0.0160.00728.256-0.222-0.2220.0000.0000.0000.000
178A179ASP-1-0.687-0.83523.087-13.059-13.0590.0000.0000.0000.000
179A180MET00.0040.02321.1960.1040.1040.0000.0000.0000.000
180A181GLU-1-0.829-0.93517.670-15.408-15.4080.0000.0000.0000.000
181A182VAL0-0.029-0.00919.249-0.641-0.6410.0000.0000.0000.000
182A183ALA00.0570.02020.970-0.304-0.3040.0000.0000.0000.000
183A184GLY00.0200.02617.779-0.202-0.2020.0000.0000.0000.000
184A185LEU0-0.004-0.01916.270-0.847-0.8470.0000.0000.0000.000
185A186TYR0-0.012-0.02817.571-0.491-0.4910.0000.0000.0000.000
186A187GLY00.0420.01919.4360.1150.1150.0000.0000.0000.000
187A188LEU0-0.110-0.04811.757-0.420-0.4200.0000.0000.0000.000
188A189ALA00.007-0.00115.864-0.398-0.3980.0000.0000.0000.000
189A190HIS00.0060.00517.4590.5740.5740.0000.0000.0000.000
190A191GLN0-0.0060.01515.292-0.720-0.7200.0000.0000.0000.000
191A192GLN0-0.045-0.03011.855-1.724-1.7240.0000.0000.0000.000
192A193GLY0-0.0040.02215.373-0.235-0.2350.0000.0000.0000.000
193A194ILE0-0.067-0.01813.8780.1010.1010.0000.0000.0000.000
194A195GLU-1-0.826-0.90717.284-12.554-12.5540.0000.0000.0000.000
195A196SER0-0.015-0.02718.195-0.789-0.7890.0000.0000.0000.000
196A197LEU00.0160.00320.1790.7070.7070.0000.0000.0000.000
197A198ALA00.0130.01321.157-0.681-0.6810.0000.0000.0000.000
198A199ILE00.0050.01623.1300.5640.5640.0000.0000.0000.000
199A200LEU0-0.035-0.01724.456-0.503-0.5030.0000.0000.0000.000
200A201THR00.010-0.00226.7910.3960.3960.0000.0000.0000.000
201A202VAL00.0420.01829.342-0.263-0.2630.0000.0000.0000.000
202A203SER0-0.120-0.06529.306-0.035-0.0350.0000.0000.0000.000
203A204ASP-1-0.852-0.90631.394-9.250-9.2500.0000.0000.0000.000
204A205HIS00.0290.00334.325-0.183-0.1830.0000.0000.0000.000
205A206CYS0-0.088-0.02533.5160.0480.0480.0000.0000.0000.000
206A207LEU0-0.048-0.00336.8760.0940.0940.0000.0000.0000.000
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