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: LGKJ9

Calculation Name: 6E3A-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a | [[(2~{r},3~{s},4~{r},5~{r})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{r},3~{s},4~{r},5~{r})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate

Ligand 3-letter code: COA | HQG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6E3A

Chain ID: A

ChEMBL ID:

UniProt ID: A3DJX6

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1976104.814527
FMO2-HF: Nuclear repulsion 1904120.457124
FMO2-HF: Total energy -71984.357403
FMO2-MP2: Total energy -72198.63361


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
77.9980.0340.007-0.757-1.293-0.002
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.881 / q_NPA : 0.929
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].
3A5ASP-1-0.802-0.8863.520-31.235-29.5220.009-0.734-0.987-0.002
4A6TYR00.062-0.0104.4862.2212.431-0.001-0.008-0.2010.000
49A51LYS10.8810.9474.46246.16746.288-0.001-0.015-0.1050.000
5A7SER0-0.0090.0087.8643.7793.7790.0000.0000.0000.000
6A8LYS10.8340.8899.58631.34631.3460.0000.0000.0000.000
7A9LEU00.0510.0409.3221.7381.7380.0000.0000.0000.000
8A10SER00.0380.00811.2692.4832.4830.0000.0000.0000.000
9A11LYS10.8830.94513.57421.32221.3220.0000.0000.0000.000
10A12GLU-1-0.785-0.85314.359-18.867-18.8670.0000.0000.0000.000
11A13VAL00.0680.02214.7201.1141.1140.0000.0000.0000.000
12A14ALA0-0.055-0.01617.1211.0951.0950.0000.0000.0000.000
13A15TYR0-0.013-0.01419.2151.0771.0770.0000.0000.0000.000
14A16ALA00.0570.02619.7540.7840.7840.0000.0000.0000.000
15A17LEU00.0040.00119.8950.6220.6220.0000.0000.0000.000
16A18ARG10.7900.90321.25314.01714.0170.0000.0000.0000.000
17A19HIS0-0.053-0.05023.1750.2180.2180.0000.0000.0000.000
18A20ALA00.0620.03124.8530.4960.4960.0000.0000.0000.000
19A21PRO00.0120.02524.603-0.361-0.3610.0000.0000.0000.000
20A22TRP00.0820.02625.444-0.209-0.2090.0000.0000.0000.000
21A23GLU-1-0.968-0.96924.333-11.907-11.9070.0000.0000.0000.000
22A24TYR0-0.094-0.06618.414-0.294-0.2940.0000.0000.0000.000
23A25GLY00.0280.03123.167-0.252-0.2520.0000.0000.0000.000
24A26LEU0-0.084-0.03821.2870.0850.0850.0000.0000.0000.000
25A27GLU-1-0.916-0.96425.971-9.464-9.4640.0000.0000.0000.000
26A28LEU0-0.094-0.03925.073-0.292-0.2920.0000.0000.0000.000
27A29ASP-1-0.734-0.87428.635-10.155-10.1550.0000.0000.0000.000
28A30ALA00.0330.00331.160-0.130-0.1300.0000.0000.0000.000
29A31GLU-1-0.913-0.95330.863-9.438-9.4380.0000.0000.0000.000
30A32GLY0-0.033-0.02327.817-0.279-0.2790.0000.0000.0000.000
31A33TRP0-0.044-0.03524.346-0.828-0.8280.0000.0000.0000.000
32A34VAL00.0220.01822.3280.4240.4240.0000.0000.0000.000
33A35ASP-1-0.795-0.90923.199-13.492-13.4920.0000.0000.0000.000
34A36ILE0-0.002-0.00916.958-0.453-0.4530.0000.0000.0000.000
35A37ASN00.002-0.00218.618-1.545-1.5450.0000.0000.0000.000
36A38GLN00.0040.00219.987-0.425-0.4250.0000.0000.0000.000
37A39LEU00.0090.01317.291-0.366-0.3660.0000.0000.0000.000
38A40LEU0-0.038-0.03413.638-1.017-1.0170.0000.0000.0000.000
39A41SER00.0100.00916.260-0.837-0.8370.0000.0000.0000.000
40A42SER00.027-0.00618.450-0.405-0.4050.0000.0000.0000.000
41A43LEU0-0.069-0.03813.548-0.668-0.6680.0000.0000.0000.000
42A44HIS10.7830.89412.41220.90320.9030.0000.0000.0000.000
43A45GLU-1-0.810-0.88815.487-15.210-15.2100.0000.0000.0000.000
44A46CYS0-0.080-0.03314.619-0.511-0.5110.0000.0000.0000.000
45A47GLU-1-0.809-0.89911.866-24.372-24.3720.0000.0000.0000.000
46A48LYS10.8870.9469.37721.12621.1260.0000.0000.0000.000
47A49TRP0-0.080-0.0807.547-6.773-6.7730.0000.0000.0000.000
48A50LYS10.9110.95710.49620.10520.1050.0000.0000.0000.000
50A52VAL0-0.059-0.0078.344-1.917-1.9170.0000.0000.0000.000
51A53SER00.015-0.0259.2943.4863.4860.0000.0000.0000.000
52A54GLU-1-0.791-0.92811.333-16.835-16.8350.0000.0000.0000.000
53A55HIS00.0300.0189.1021.7811.7810.0000.0000.0000.000
54A56ASP-1-0.798-0.8656.911-37.174-37.1740.0000.0000.0000.000
55A57LEU00.005-0.0019.707-0.195-0.1950.0000.0000.0000.000
56A58HIS00.0200.00913.0400.9060.9060.0000.0000.0000.000
57A59VAL0-0.0060.0018.0450.5530.5530.0000.0000.0000.000
58A60MET0-0.070-0.02610.477-0.070-0.0700.0000.0000.0000.000
59A61ILE0-0.059-0.02511.2840.9970.9970.0000.0000.0000.000
60A62GLU-1-0.812-0.88412.384-20.986-20.9860.0000.0000.0000.000
61A63LYS10.8010.8788.74823.94323.9430.0000.0000.0000.000
62A64SER0-0.056-0.02912.011-0.361-0.3610.0000.0000.0000.000
63A65ASP-1-0.826-0.90314.487-15.588-15.5880.0000.0000.0000.000
64A66LYS10.8700.93416.95914.99414.9940.0000.0000.0000.000
65A67LYS11.0111.03918.44011.74311.7430.0000.0000.0000.000
66A68ARG10.7940.88116.58717.48517.4850.0000.0000.0000.000
67A69TYR00.007-0.02015.9960.8300.8300.0000.0000.0000.000
68A70GLU-1-0.845-0.91820.284-11.958-11.9580.0000.0000.0000.000
69A71ILE00.0230.00916.7640.0730.0730.0000.0000.0000.000
70A72SER0-0.013-0.00821.3500.2060.2060.0000.0000.0000.000
71A73ASN00.0080.00624.450-0.057-0.0570.0000.0000.0000.000
72A74GLY00.0740.04922.1560.2670.2670.0000.0000.0000.000
73A75LYS10.8570.94322.77510.96310.9630.0000.0000.0000.000
74A76ILE0-0.005-0.01017.792-0.326-0.3260.0000.0000.0000.000
75A77ARG10.8410.94522.02211.39811.3980.0000.0000.0000.000
76A78ALA0-0.020-0.00822.099-0.584-0.5840.0000.0000.0000.000
77A79LEU0-0.016-0.00223.1500.5240.5240.0000.0000.0000.000
78A80TYR00.004-0.01121.9660.4500.4500.0000.0000.0000.000
79A81GLY00.0050.00224.790-0.586-0.5860.0000.0000.0000.000
80A82HIS00.0370.03226.3430.0720.0720.0000.0000.0000.000
81A83SER0-0.007-0.00428.0690.1400.1400.0000.0000.0000.000
82A84ILE0-0.0060.03028.5550.1850.1850.0000.0000.0000.000
83A85PRO00.0320.01231.2630.1410.1410.0000.0000.0000.000
84A86GLN00.0430.03733.9260.2990.2990.0000.0000.0000.000
85A87ARG10.8270.89633.5517.9917.9910.0000.0000.0000.000
86A88ILE00.0090.01029.6340.0890.0890.0000.0000.0000.000
87A89ILE00.0070.00833.0240.1960.1960.0000.0000.0000.000
88A90LYS10.8400.92128.83010.06110.0610.0000.0000.0000.000
89A91GLU-1-0.803-0.89134.067-8.614-8.6140.0000.0000.0000.000
90A92GLN00.000-0.01135.878-0.021-0.0210.0000.0000.0000.000
91A93LYS10.8390.91234.0648.8738.8730.0000.0000.0000.000
92A94CYS0-0.0040.01738.9770.0670.0670.0000.0000.0000.000
93A95PRO0-0.041-0.01538.546-0.196-0.1960.0000.0000.0000.000
94A96PRO00.022-0.00236.4500.1750.1750.0000.0000.0000.000
95A97GLU-1-0.925-0.96339.778-6.848-6.8480.0000.0000.0000.000
96A98VAL0-0.020-0.01638.3730.0730.0730.0000.0000.0000.000
97A99LEU0-0.0260.00034.517-0.228-0.2280.0000.0000.0000.000
98A100TYR00.0470.02033.5390.1300.1300.0000.0000.0000.000
99A101HIS0-0.036-0.03532.885-0.243-0.2430.0000.0000.0000.000
100A102GLY00.0140.03331.8150.2240.2240.0000.0000.0000.000
101A103THR0-0.004-0.01631.705-0.306-0.3060.0000.0000.0000.000
102A104ALA0-0.009-0.00932.536-0.042-0.0420.0000.0000.0000.000
103A105ARG10.9110.91234.1968.7958.7950.0000.0000.0000.000
104A106ARG10.8670.92831.2339.6089.6080.0000.0000.0000.000
105A107PHE0-0.021-0.01632.7920.0080.0080.0000.0000.0000.000
106A108VAL00.0330.02238.4750.1300.1300.0000.0000.0000.000
107A109LYS10.9600.99840.6116.7276.7270.0000.0000.0000.000
108A110SER00.0320.00141.0850.1120.1120.0000.0000.0000.000
109A111ILE0-0.019-0.00537.1300.0180.0180.0000.0000.0000.000
110A112LYS10.9440.99141.7136.9966.9960.0000.0000.0000.000
111A113GLU-1-0.918-0.95345.076-6.552-6.5520.0000.0000.0000.000
112A114LYS10.9320.96743.4137.1947.1940.0000.0000.0000.000
113A115GLY00.0620.04143.137-0.011-0.0110.0000.0000.0000.000
114A116LEU0-0.063-0.02236.232-0.142-0.1420.0000.0000.0000.000
115A117GLN00.0230.00238.1840.0060.0060.0000.0000.0000.000
116A118PRO00.0380.00935.092-0.206-0.2060.0000.0000.0000.000
117A119GLN0-0.062-0.03233.893-0.227-0.2270.0000.0000.0000.000
118A120GLY00.0210.02431.9660.0880.0880.0000.0000.0000.000
119A121ARG10.7380.86425.18811.07211.0720.0000.0000.0000.000
120A122GLN00.0270.00731.7390.2550.2550.0000.0000.0000.000
121A123TYR0-0.022-0.01932.3570.3110.3110.0000.0000.0000.000
122A124VAL0-0.0160.00733.076-0.279-0.2790.0000.0000.0000.000
123A125HIS0-0.031-0.03227.880-0.524-0.5240.0000.0000.0000.000
124A126LEU00.0020.01131.7010.1380.1380.0000.0000.0000.000
125A127SER0-0.049-0.03729.484-0.476-0.4760.0000.0000.0000.000
126A128ALA00.0480.02930.4020.2960.2960.0000.0000.0000.000
127A129ASP-1-0.786-0.85128.522-10.237-10.2370.0000.0000.0000.000
128A130VAL00.0760.02731.081-0.181-0.1810.0000.0000.0000.000
129A131GLU-1-0.822-0.88926.397-10.747-10.7470.0000.0000.0000.000
130A132THR0-0.095-0.10625.597-0.547-0.5470.0000.0000.0000.000
131A133ALA00.0140.01227.269-0.220-0.2200.0000.0000.0000.000
132A134LEU00.0270.00729.611-0.088-0.0880.0000.0000.0000.000
133A135GLN0-0.044-0.04024.134-0.352-0.3520.0000.0000.0000.000
134A136VAL0-0.068-0.02025.497-0.487-0.4870.0000.0000.0000.000
135A137GLY00.0510.03627.234-0.083-0.0830.0000.0000.0000.000
136A138LYS10.9360.95325.87710.79710.7970.0000.0000.0000.000
137A139ARG10.8230.91523.10011.86911.8690.0000.0000.0000.000
138A140ARG10.9050.96425.62010.37010.3700.0000.0000.0000.000
139A141ASP-1-0.742-0.85128.966-8.729-8.7290.0000.0000.0000.000
140A142ILE00.0760.04728.448-0.151-0.1510.0000.0000.0000.000
141A143LYS10.8970.94830.5598.3928.3920.0000.0000.0000.000
142A144PRO0-0.044-0.00430.2440.2280.2280.0000.0000.0000.000
143A145VAL00.011-0.00233.2900.1280.1280.0000.0000.0000.000
144A146LEU00.0040.00133.987-0.223-0.2230.0000.0000.0000.000
145A147LEU0-0.024-0.00336.1480.2010.2010.0000.0000.0000.000
146A148ILE00.008-0.00337.235-0.257-0.2570.0000.0000.0000.000
147A149VAL0-0.0020.00138.4420.1910.1910.0000.0000.0000.000
148A150ASN00.0650.03340.761-0.218-0.2180.0000.0000.0000.000
149A151ALA0-0.007-0.01139.5630.1020.1020.0000.0000.0000.000
150A152LEU00.0370.02541.6390.0480.0480.0000.0000.0000.000
151A153GLU-1-0.814-0.89344.242-6.327-6.3270.0000.0000.0000.000
152A154ALA00.0340.01043.2950.0840.0840.0000.0000.0000.000
153A155TRP0-0.011-0.01142.7360.0580.0580.0000.0000.0000.000
154A156SER0-0.079-0.04144.9740.1100.1100.0000.0000.0000.000
155A157GLU-1-0.788-0.84748.229-6.047-6.0470.0000.0000.0000.000
156A158GLY00.0350.03347.6350.0360.0360.0000.0000.0000.000
157A159ILE0-0.086-0.04541.559-0.112-0.1120.0000.0000.0000.000
158A160LYS10.8720.94640.6847.1097.1090.0000.0000.0000.000
159A161PHE00.044-0.00437.390-0.186-0.1860.0000.0000.0000.000
160A162TYR0-0.045-0.05634.6100.1070.1070.0000.0000.0000.000
161A163LEU00.0120.01430.392-0.164-0.1640.0000.0000.0000.000
162A164GLY00.0140.00728.990-0.149-0.1490.0000.0000.0000.000
163A165ASN0-0.080-0.06323.965-0.082-0.0820.0000.0000.0000.000
164A166ASP-1-0.838-0.91527.537-10.444-10.4440.0000.0000.0000.000
165A167LYS10.8970.95123.67312.06112.0610.0000.0000.0000.000
166A168VAL0-0.078-0.02925.2630.1240.1240.0000.0000.0000.000
167A169TRP00.0780.04228.4350.0780.0780.0000.0000.0000.000
168A170LEU0-0.031-0.02029.695-0.174-0.1740.0000.0000.0000.000
169A171ALA00.0380.02533.2690.2100.2100.0000.0000.0000.000
170A172ASP-1-0.743-0.83936.492-8.085-8.0850.0000.0000.0000.000
171A173ALA0-0.016-0.02339.198-0.073-0.0730.0000.0000.0000.000
172A174ILE00.0110.01238.0390.1290.1290.0000.0000.0000.000
173A175PRO00.0190.00542.074-0.043-0.0430.0000.0000.0000.000
174A176SER00.023-0.03044.798-0.053-0.0530.0000.0000.0000.000
175A177LYS10.8120.90745.8296.1676.1670.0000.0000.0000.000
176A178TYR0-0.023-0.03144.155-0.013-0.0130.0000.0000.0000.000
177A179ILE0-0.076-0.03340.732-0.187-0.1870.0000.0000.0000.000
178A180ARG10.9500.98042.9687.1827.1820.0000.0000.0000.000
179A181PHE0-0.041-0.06341.632-0.268-0.2680.0000.0000.0000.000
180A182GLU-2-1.878-1.91842.958-13.718-13.7180.0000.0000.0000.000