FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: QLQLY

Calculation Name: 5LNK-J-Other547

Preferred Name:

Target Type:

Ligand Name: cardiolipin | nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | 1,2-diacyl-sn-glycero-3-phosphocholine | 1,2-distearoyl-sn-glycerophosphoethanolamine | flavin mononucleotide | s-[2-({n-[(2s)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate | 4'-phosphopantetheine | iron/sulfur cluster | fe2/s2 (inorganic) cluster | zinc ion

Ligand 3-letter code: CDL | NDP | PC1 | 3PE | FMN | ZMP | PNS | SF4 | FES | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LNK

Chain ID: J

ChEMBL ID:

UniProt ID: Q02377

Base Structure: ElectronMicroscopy

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1430655.305106
FMO2-HF: Nuclear repulsion 1362338.323424
FMO2-HF: Total energy -68316.981682
FMO2-MP2: Total energy -68509.896153


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-98.771-96.224-0.02-1.13-1.398-0.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / 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].
3A3THR00.0280.0133.8003.9156.462-0.020-1.130-1.398-0.004
4A4TYR0-0.001-0.0155.7972.0292.0290.0000.0000.0000.000
5A5ILE0-0.020-0.0077.7212.2992.2990.0000.0000.0000.000
6A6VAL00.0860.0369.4471.8051.8050.0000.0000.0000.000
7A7PHE00.0330.03212.1681.6551.6550.0000.0000.0000.000
8A8ILE00.006-0.0089.3891.0051.0050.0000.0000.0000.000
9A9LEU0-0.026-0.00812.8031.5311.5310.0000.0000.0000.000
10A10SER00.0550.02015.1481.5151.5150.0000.0000.0000.000
11A11ILE0-0.034-0.00715.7581.1301.1300.0000.0000.0000.000
12A12ILE0-0.017-0.01714.1361.0101.0100.0000.0000.0000.000
13A13PHE0-0.0090.00418.1450.9540.9540.0000.0000.0000.000
14A14VAL00.0320.02920.8190.8230.8230.0000.0000.0000.000
15A15MET0-0.026-0.02519.5200.7830.7830.0000.0000.0000.000
16A16GLY0-0.0170.00922.1060.5330.5330.0000.0000.0000.000
17A17PHE00.028-0.00223.7450.5560.5560.0000.0000.0000.000
18A18VAL0-0.020-0.00325.1230.5100.5100.0000.0000.0000.000
19A19GLY0-0.013-0.01625.8750.3970.3970.0000.0000.0000.000
20A20PHE0-0.069-0.03527.2400.2350.2350.0000.0000.0000.000
21A21SER00.0000.00229.5500.3030.3030.0000.0000.0000.000
22A22SER0-0.044-0.00532.4070.2540.2540.0000.0000.0000.000
23A23LYS00.0350.03430.996-0.235-0.2350.0000.0000.0000.000
24A24PRO0-0.032-0.02336.453-0.004-0.0040.0000.0000.0000.000
25A25SER00.0170.01537.7330.1440.1440.0000.0000.0000.000
26A26PRO00.0310.00936.391-0.276-0.2760.0000.0000.0000.000
27A27ILE0-0.0080.01335.485-0.212-0.2120.0000.0000.0000.000
28A28TYR-1-0.917-0.97931.543-9.635-9.6350.0000.0000.0000.000
29A29GLY00.016-0.00231.085-0.374-0.3740.0000.0000.0000.000
30A30GLY00.0310.01131.597-0.248-0.2480.0000.0000.0000.000
31A31LEU0-0.003-0.00428.173-0.351-0.3510.0000.0000.0000.000
32A32GLY00.0150.00026.600-0.502-0.5020.0000.0000.0000.000
33A33LEU0-0.0070.00926.258-0.464-0.4640.0000.0000.0000.000
34A34ILE0-0.003-0.00726.330-0.385-0.3850.0000.0000.0000.000
35A35VAL0-0.0170.00921.311-0.573-0.5730.0000.0000.0000.000
36A36SER00.0160.00021.995-0.683-0.6830.0000.0000.0000.000
37A37GLY00.001-0.00122.682-0.338-0.3380.0000.0000.0000.000
38A38GLY00.0160.00221.843-0.213-0.2130.0000.0000.0000.000
39A39VAL0-0.035-0.02317.201-0.840-0.8400.0000.0000.0000.000
40A40GLY00.0320.01818.263-0.752-0.7520.0000.0000.0000.000
41A41CYS0-0.057-0.01720.088-0.050-0.0500.0000.0000.0000.000
42A42GLY00.0280.01616.211-0.358-0.3580.0000.0000.0000.000
43A43ILE0-0.027-0.01115.325-1.168-1.1680.0000.0000.0000.000
44A44VAL0-0.0060.00316.687-0.368-0.3680.0000.0000.0000.000
45A45LEU0-0.028-0.01016.8050.0190.0190.0000.0000.0000.000
46A46ASN0-0.072-0.03911.732-1.438-1.4380.0000.0000.0000.000
47A47PHE0-0.037-0.01613.997-0.737-0.7370.0000.0000.0000.000
48A48GLY00.0240.02416.4050.5750.5750.0000.0000.0000.000
49A49GLY00.0390.04017.9120.7420.7420.0000.0000.0000.000
50A50SER0-0.069-0.05220.5450.5230.5230.0000.0000.0000.000
51A51PHE00.005-0.01421.5130.2230.2230.0000.0000.0000.000
52A52LEU00.0380.01224.3410.3270.3270.0000.0000.0000.000
53A53GLY00.0360.00921.6210.1810.1810.0000.0000.0000.000
54A54LEU00.007-0.00322.5520.0730.0730.0000.0000.0000.000
55A55MET0-0.0080.00224.6710.4190.4190.0000.0000.0000.000
56A56VAL0-0.024-0.01524.3110.3930.3930.0000.0000.0000.000
57A57PHE00.021-0.01322.6170.1270.1270.0000.0000.0000.000
58A58LEU0-0.0330.00425.7230.2260.2260.0000.0000.0000.000
59A59ILE0-0.001-0.01629.2880.3210.3210.0000.0000.0000.000
60A60TYR00.0060.00527.9510.3620.3620.0000.0000.0000.000
61A61LEU0-0.002-0.00124.2090.1900.1900.0000.0000.0000.000
62A62GLY00.0450.02428.9290.1810.1810.0000.0000.0000.000
63A63GLY0-0.012-0.00931.6000.2320.2320.0000.0000.0000.000
64A64MET0-0.033-0.01532.8590.2880.2880.0000.0000.0000.000
65A65MET0-0.013-0.00329.8230.1900.1900.0000.0000.0000.000
66A66VAL00.0140.02233.0410.1500.1500.0000.0000.0000.000
67A67VAL00.0180.01735.1850.2620.2620.0000.0000.0000.000
68A68PHE00.0060.00735.5030.2220.2220.0000.0000.0000.000
69A69GLY00.0220.02036.0860.1580.1580.0000.0000.0000.000
70A70TYR0-0.020-0.00836.9030.1820.1820.0000.0000.0000.000
71A71THR0-0.028-0.03740.0940.1930.1930.0000.0000.0000.000
72A72THR0-0.044-0.02538.4470.1830.1830.0000.0000.0000.000
73A73ALA00.002-0.00839.7980.1410.1410.0000.0000.0000.000
74A74MET0-0.056-0.01341.6890.1740.1740.0000.0000.0000.000
75A75ALA0-0.048-0.02144.5460.1830.1830.0000.0000.0000.000
76A76THR0-0.072-0.03842.9610.1420.1420.0000.0000.0000.000
77A77GLU-1-0.923-0.94743.601-6.814-6.8140.0000.0000.0000.000
78A78GLN0-0.042-0.03838.0080.0830.0830.0000.0000.0000.000
79A79TYR00.0310.02242.702-0.085-0.0850.0000.0000.0000.000
80A80PRO0-0.052-0.02943.421-0.092-0.0920.0000.0000.0000.000
81A81GLU-1-0.869-0.92736.732-8.635-8.6350.0000.0000.0000.000
82A82VAL0-0.007-0.00938.194-0.033-0.0330.0000.0000.0000.000
83A83TRP00.002-0.00233.467-0.151-0.1510.0000.0000.0000.000
84A84VAL00.0080.00936.0620.0860.0860.0000.0000.0000.000
85A85SER00.0460.01137.9160.0690.0690.0000.0000.0000.000
86A86ASN00.031-0.00637.120-0.284-0.2840.0000.0000.0000.000
87A87LYS10.9210.94528.94410.59410.5940.0000.0000.0000.000
88A88VAL0-0.0140.01032.912-0.276-0.2760.0000.0000.0000.000
89A89VAL00.0470.02133.897-0.201-0.2010.0000.0000.0000.000
90A90LEU0-0.0060.02730.012-0.166-0.1660.0000.0000.0000.000
91A91GLY00.0340.01129.379-0.402-0.4020.0000.0000.0000.000
92A92THR0-0.051-0.04129.328-0.178-0.1780.0000.0000.0000.000
93A93PHE00.0260.02729.327-0.117-0.1170.0000.0000.0000.000
94A94ILE00.0370.02323.226-0.375-0.3750.0000.0000.0000.000
95A95THR0-0.027-0.02625.350-0.367-0.3670.0000.0000.0000.000
96A96GLY0-0.033-0.01426.980-0.216-0.2160.0000.0000.0000.000
97A97LEU00.0200.01124.363-0.141-0.1410.0000.0000.0000.000
98A98LEU0-0.0060.01020.330-0.602-0.6020.0000.0000.0000.000
99A99MET0-0.037-0.03122.811-0.393-0.3930.0000.0000.0000.000
100A100GLU-1-0.887-0.94525.083-11.377-11.3770.0000.0000.0000.000
101A101PHE00.004-0.00519.681-0.358-0.3580.0000.0000.0000.000
102A102LEU0-0.013-0.01218.768-0.671-0.6710.0000.0000.0000.000
103A103MET0-0.024-0.01221.168-0.196-0.1960.0000.0000.0000.000
104A104VAL0-0.001-0.00721.421-0.216-0.2160.0000.0000.0000.000
105A105TYR00.0100.01312.660-0.569-0.5690.0000.0000.0000.000
106A106TYR0-0.048-0.00818.621-0.632-0.6320.0000.0000.0000.000
107A107VAL0-0.085-0.05020.854-0.008-0.0080.0000.0000.0000.000
108A108LEU00.0220.00816.7690.3530.3530.0000.0000.0000.000
109A109LYS10.9170.95820.35812.99012.9900.0000.0000.0000.000
110A110ASP-1-0.881-0.92821.418-11.756-11.7560.0000.0000.0000.000
111A111LYS0-0.016-0.00222.966-0.370-0.3700.0000.0000.0000.000
112A112GLU0-0.046-0.03622.7390.6830.6830.0000.0000.0000.000
113A113VAL0-0.039-0.02625.933-0.185-0.1850.0000.0000.0000.000
114A114GLU-1-0.713-0.84628.287-10.176-10.1760.0000.0000.0000.000
115A115ILE0-0.091-0.06730.4670.1780.1780.0000.0000.0000.000
116A116VAL0-0.060-0.01734.2080.3390.3390.0000.0000.0000.000
117A117PHE0-0.021-0.00929.2380.2780.2780.0000.0000.0000.000
118A118LYS0-0.018-0.01331.6720.0600.0600.0000.0000.0000.000
119A119PHE0-0.028-0.03228.084-0.201-0.2010.0000.0000.0000.000
120A120ASN0-0.036-0.01522.9990.1800.1800.0000.0000.0000.000
121A121GLY00.005-0.00524.790-0.018-0.0180.0000.0000.0000.000
122A122MET0-0.114-0.03320.829-0.631-0.6310.0000.0000.0000.000
123A123GLY00.0840.03818.4430.4880.4880.0000.0000.0000.000
124A124ASP-1-0.904-0.93011.743-26.958-26.9580.0000.0000.0000.000
125A125TRP0-0.020-0.02612.719-0.130-0.1300.0000.0000.0000.000
126A126VAL0-0.032-0.00311.9330.6190.6190.0000.0000.0000.000
127A127ILE0-0.035-0.01114.417-0.376-0.3760.0000.0000.0000.000
128A128TYR0-0.013-0.02712.195-0.198-0.1980.0000.0000.0000.000
129A129ASP-1-0.854-0.92716.965-14.153-14.1530.0000.0000.0000.000
130A130THR0-0.073-0.03817.606-0.649-0.6490.0000.0000.0000.000
131A131GLY0-0.033-0.00120.1040.4850.4850.0000.0000.0000.000
132A132ASP-1-0.901-0.94222.046-12.135-12.1350.0000.0000.0000.000
133A133SER00.0500.01923.7440.5020.5020.0000.0000.0000.000
134A134GLY0-0.001-0.00726.506-0.139-0.1390.0000.0000.0000.000
135A135PHE0-0.076-0.05426.7730.3530.3530.0000.0000.0000.000
136A136PHE0-0.0210.00527.5550.3860.3860.0000.0000.0000.000
137A137SER00.000-0.00825.317-0.284-0.2840.0000.0000.0000.000
138A138GLU-1-0.878-0.92424.323-12.563-12.5630.0000.0000.0000.000
139A139GLU-1-0.833-0.91723.073-12.762-12.7620.0000.0000.0000.000
140A140ALA0-0.016-0.02327.3800.4360.4360.0000.0000.0000.000
141A141MET00.0170.01529.8160.3780.3780.0000.0000.0000.000
142A142GLY00.0570.02630.8400.3380.3380.0000.0000.0000.000
143A143ILE0-0.041-0.02129.8250.2940.2940.0000.0000.0000.000
144A144ALA00.007-0.00633.6270.2990.2990.0000.0000.0000.000
145A145ALA00.0110.00935.3480.2870.2870.0000.0000.0000.000
146A146LEU0-0.0160.00136.0300.2310.2310.0000.0000.0000.000
147A147TYR0-0.029-0.01936.7660.3010.3010.0000.0000.0000.000
148A148SER0-0.021-0.00239.8380.1440.1440.0000.0000.0000.000
149A149TYR0-0.020-0.02238.8670.2700.2700.0000.0000.0000.000
150A150GLY00.0090.02540.4400.1070.1070.0000.0000.0000.000
151A151THR00.001-0.00641.3100.0270.0270.0000.0000.0000.000
152A152TRP00.0450.01044.9340.0870.0870.0000.0000.0000.000
153A153LEU00.0290.01838.2140.0480.0480.0000.0000.0000.000
154A154VAL00.0420.02440.655-0.036-0.0360.0000.0000.0000.000
155A155ILE0-0.0240.00443.0340.0820.0820.0000.0000.0000.000
156A156VAL0-0.009-0.00943.8770.0600.0600.0000.0000.0000.000
157A157THR0-0.027-0.02140.0080.0160.0160.0000.0000.0000.000
158A158GLY00.0600.04043.2090.0160.0160.0000.0000.0000.000
159A159TRP0-0.009-0.00645.1090.1000.1000.0000.0000.0000.000
160A160SER0-0.054-0.04044.1080.0240.0240.0000.0000.0000.000
161A161LEU00.0230.00540.8810.0070.0070.0000.0000.0000.000
162A162LEU0-0.0200.00045.2150.0560.0560.0000.0000.0000.000
163A163ILE00.004-0.01048.7990.1100.1100.0000.0000.0000.000
164A164GLY00.0230.01146.4260.0630.0630.0000.0000.0000.000
165A165VAL0-0.022-0.01147.1400.0290.0290.0000.0000.0000.000
166A166VAL0-0.003-0.00148.9550.0730.0730.0000.0000.0000.000
167A167VAL00.0040.00749.9260.0830.0830.0000.0000.0000.000
168A168ILE0-0.017-0.01045.3010.0280.0280.0000.0000.0000.000
169A169MET00.003-0.00249.8220.0450.0450.0000.0000.0000.000
170A170GLU-1-0.913-0.94552.739-5.471-5.4710.0000.0000.0000.000
171A171ILE0-0.052-0.02550.5640.0810.0810.0000.0000.0000.000
172A172THR0-0.124-0.07150.8510.0010.0010.0000.0000.0000.000
173A173ARG10.8780.93753.7855.4575.4570.0000.0000.0000.000
174A174GLY0-0.0020.00957.1410.0360.0360.0000.0000.0000.000
175A175ASN-1-0.960-0.96858.270-5.129-5.1290.0000.0000.0000.000