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: 978J2

Calculation Name: 3L2B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: bis(adenosine)-5'-tetraphosphate

Ligand 3-letter code: B4P

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3L2B

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XIQ9

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 -2588768.155879
FMO2-HF: Nuclear repulsion 2498425.378577
FMO2-HF: Total energy -90342.777302
FMO2-MP2: Total energy -90604.091446


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:65:MET)


Summations of interaction energy for fragment #1(A:65: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.
-115.176-111.4870.568-1.481-2.775-0.008
Interaction energy analysis for fragmet #1(A:65:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.909
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].
3A67LYS10.8860.9502.93241.60845.2230.569-1.473-2.710-0.008
4A68LEU00.0130.0194.9211.4901.564-0.001-0.008-0.0650.000
5A69LYS10.8180.9138.54629.06829.0680.0000.0000.0000.000
6A70VAL00.0420.01911.4560.7760.7760.0000.0000.0000.000
7A71GLU-1-0.889-0.96113.680-21.092-21.0920.0000.0000.0000.000
8A72ASP-1-0.908-0.93510.942-26.089-26.0890.0000.0000.0000.000
9A73LEU0-0.082-0.04013.4370.1670.1670.0000.0000.0000.000
10A74GLU-1-0.949-0.97016.446-13.677-13.6770.0000.0000.0000.000
11A75MET0-0.034-0.01519.0100.1920.1920.0000.0000.0000.000
12A76ASP-1-0.885-0.93622.232-11.296-11.2960.0000.0000.0000.000
13A77LYS10.9080.95023.30412.92812.9280.0000.0000.0000.000
14A78ILE0-0.027-0.01427.8240.4480.4480.0000.0000.0000.000
15A79ALA0-0.012-0.00330.062-0.206-0.2060.0000.0000.0000.000
16A80PRO00.0030.00230.9930.2030.2030.0000.0000.0000.000
17A81LEU0-0.039-0.01933.4070.2460.2460.0000.0000.0000.000
18A82ALA00.0650.04336.311-0.210-0.2100.0000.0000.0000.000
19A83PRO0-0.012-0.01437.7700.0790.0790.0000.0000.0000.000
20A84GLU-1-0.828-0.93239.616-7.578-7.5780.0000.0000.0000.000
21A85VAL0-0.0080.00941.1710.2160.2160.0000.0000.0000.000
22A86SER00.0580.03143.475-0.100-0.1000.0000.0000.0000.000
23A87LEU00.0310.00942.670-0.146-0.1460.0000.0000.0000.000
24A88LYS10.8190.91144.3036.2036.2030.0000.0000.0000.000
25A89MET0-0.048-0.01844.497-0.041-0.0410.0000.0000.0000.000
26A90ALA00.0370.01640.213-0.122-0.1220.0000.0000.0000.000
27A91TRP00.008-0.00640.136-0.207-0.2070.0000.0000.0000.000
28A92ASN0-0.013-0.00241.866-0.019-0.0190.0000.0000.0000.000
29A93ILE00.0460.03137.798-0.086-0.0860.0000.0000.0000.000
30A94MET0-0.040-0.01736.234-0.151-0.1510.0000.0000.0000.000
31A95ARG10.8200.91637.7166.9206.9200.0000.0000.0000.000
32A96ASP-1-0.872-0.93439.813-7.299-7.2990.0000.0000.0000.000
33A97LYS10.8890.94735.1708.4518.4510.0000.0000.0000.000
34A98ASN0-0.042-0.01734.364-0.097-0.0970.0000.0000.0000.000
35A99LEU0-0.0100.00731.841-0.207-0.2070.0000.0000.0000.000
36A100LYS10.8940.92629.9559.9009.9000.0000.0000.0000.000
37A101SER0-0.034-0.04530.5510.1490.1490.0000.0000.0000.000
38A102ILE00.0180.01432.362-0.147-0.1470.0000.0000.0000.000
39A103PRO00.0210.01929.4720.1450.1450.0000.0000.0000.000
40A104VAL0-0.003-0.00131.8370.2420.2420.0000.0000.0000.000
41A105ALA00.0320.00831.805-0.316-0.3160.0000.0000.0000.000
42A106ASP-1-0.776-0.89133.422-9.281-9.2810.0000.0000.0000.000
43A107GLY0-0.002-0.00634.951-0.082-0.0820.0000.0000.0000.000
44A108ASN0-0.078-0.03232.3790.1040.1040.0000.0000.0000.000
45A109ASN0-0.039-0.02429.199-0.185-0.1850.0000.0000.0000.000
46A110HIS0-0.004-0.00129.061-0.569-0.5690.0000.0000.0000.000
47A111LEU0-0.017-0.01126.7190.3480.3480.0000.0000.0000.000
48A112LEU0-0.036-0.01629.7730.0240.0240.0000.0000.0000.000
49A113GLY00.0500.00631.9790.1150.1150.0000.0000.0000.000
50A114MET0-0.051-0.00928.206-0.145-0.1450.0000.0000.0000.000
51A115LEU00.0190.02832.8830.2080.2080.0000.0000.0000.000
52A116SER00.0470.00134.330-0.174-0.1740.0000.0000.0000.000
53A117THR00.0420.01136.2200.1420.1420.0000.0000.0000.000
54A118SER0-0.0350.00136.3770.2240.2240.0000.0000.0000.000
55A119ASN00.0610.04236.4690.0400.0400.0000.0000.0000.000
56A120ILE00.0380.02439.7550.1960.1960.0000.0000.0000.000
57A121THR0-0.042-0.04042.0470.2280.2280.0000.0000.0000.000
58A122ALA0-0.029-0.02441.9280.1710.1710.0000.0000.0000.000
59A123THR0-0.004-0.01043.2920.1150.1150.0000.0000.0000.000
60A124TYR0-0.062-0.02645.7600.1790.1790.0000.0000.0000.000
61A125MET0-0.053-0.03246.8230.1750.1750.0000.0000.0000.000
62A126ASP-1-0.883-0.93348.051-6.234-6.2340.0000.0000.0000.000
63A127ILE0-0.030-0.01849.7490.0450.0450.0000.0000.0000.000
64A128TRP0-0.047-0.01951.6080.2030.2030.0000.0000.0000.000
65A129ASP-1-0.799-0.87651.264-6.058-6.0580.0000.0000.0000.000
66A130SER00.025-0.00453.211-0.058-0.0580.0000.0000.0000.000
67A131ASN0-0.053-0.03054.226-0.036-0.0360.0000.0000.0000.000
68A132ILE00.0370.02049.311-0.058-0.0580.0000.0000.0000.000
69A133LEU00.0040.02550.306-0.117-0.1170.0000.0000.0000.000
70A134ALA0-0.0050.01451.682-0.061-0.0610.0000.0000.0000.000
71A135LYS10.7850.86848.3016.0946.0940.0000.0000.0000.000
72A136SER0-0.025-0.02446.420-0.139-0.1390.0000.0000.0000.000
73A137ALA0-0.014-0.00946.957-0.088-0.0880.0000.0000.0000.000
74A138THR0-0.018-0.01548.861-0.053-0.0530.0000.0000.0000.000
75A139SER00.0510.02148.9100.1540.1540.0000.0000.0000.000
76A140LEU00.0280.00150.8570.0490.0490.0000.0000.0000.000
77A141ASP-1-0.883-0.94250.559-6.161-6.1610.0000.0000.0000.000
78A142ASN0-0.053-0.02646.5140.0240.0240.0000.0000.0000.000
79A143ILE0-0.018-0.00550.6680.0320.0320.0000.0000.0000.000
80A144LEU00.0020.01254.0930.0880.0880.0000.0000.0000.000
81A145ASP-1-0.778-0.89750.082-6.325-6.3250.0000.0000.0000.000
82A146THR0-0.082-0.05050.980-0.004-0.0040.0000.0000.0000.000
83A147LEU0-0.066-0.02952.8250.0700.0700.0000.0000.0000.000
84A148SER0-0.040-0.01155.4440.1200.1200.0000.0000.0000.000
85A149ALA0-0.029-0.01557.0980.1090.1090.0000.0000.0000.000
86A150GLU-1-0.876-0.92558.781-5.419-5.4190.0000.0000.0000.000
87A151ALA00.0170.00960.2030.0480.0480.0000.0000.0000.000
88A152GLN0-0.071-0.04062.1830.0780.0780.0000.0000.0000.000
89A153ASN0-0.039-0.03764.5910.0750.0750.0000.0000.0000.000
90A154ILE00.0280.02158.654-0.048-0.0480.0000.0000.0000.000
91A155ASN0-0.080-0.03561.0420.0110.0110.0000.0000.0000.000
92A156GLU-1-0.845-0.94658.584-5.567-5.5670.0000.0000.0000.000
93A157GLU-1-0.966-0.96757.330-5.621-5.6210.0000.0000.0000.000
94A158ARG10.7970.91257.2025.3745.3740.0000.0000.0000.000
95A159LYS00.0470.02450.479-0.018-0.0180.0000.0000.0000.000
96A160VAL00.0210.02151.464-0.055-0.0550.0000.0000.0000.000
97A161PHE00.0440.00354.1390.1650.1650.0000.0000.0000.000
98A162PRO0-0.030-0.02255.673-0.049-0.0490.0000.0000.0000.000
99A163GLY00.0410.03556.878-0.014-0.0140.0000.0000.0000.000
100A164LYS10.7850.86857.4304.9444.9440.0000.0000.0000.000
101A165VAL00.0260.01856.6640.0680.0680.0000.0000.0000.000
102A166VAL0-0.036-0.02059.6600.0340.0340.0000.0000.0000.000
103A167VAL00.0060.00863.1870.0040.0040.0000.0000.0000.000
104A168ALA00.000-0.00365.3650.0550.0550.0000.0000.0000.000
105A169ALA0-0.041-0.03068.8040.0480.0480.0000.0000.0000.000
106A170MET0-0.0430.00468.4290.0630.0630.0000.0000.0000.000
107A171GLN0-0.061-0.04373.6800.0140.0140.0000.0000.0000.000
108A172ALA00.0510.02175.688-0.046-0.0460.0000.0000.0000.000
109A173GLU-1-0.844-0.93676.250-4.096-4.0960.0000.0000.0000.000
110A174SER00.0380.01675.1280.0130.0130.0000.0000.0000.000
111A175LEU0-0.048-0.01070.907-0.062-0.0620.0000.0000.0000.000
112A176LYS10.8640.92170.9674.1724.1720.0000.0000.0000.000
113A177GLU-1-0.946-0.96172.165-4.305-4.3050.0000.0000.0000.000
114A178PHE0-0.033-0.01868.048-0.050-0.0500.0000.0000.0000.000
115A179ILE0-0.056-0.02765.995-0.105-0.1050.0000.0000.0000.000
116A180SER00.0070.00064.8550.0980.0980.0000.0000.0000.000
117A181GLU-1-0.912-0.95264.937-4.893-4.8930.0000.0000.0000.000
118A182GLY0-0.005-0.01661.783-0.065-0.0650.0000.0000.0000.000
119A183ASP-1-0.785-0.85760.600-5.235-5.2350.0000.0000.0000.000
120A184ILE0-0.015-0.00457.5260.0090.0090.0000.0000.0000.000
121A185ALA00.0090.00861.1220.0080.0080.0000.0000.0000.000
122A186ILE0-0.0010.00559.8030.0180.0180.0000.0000.0000.000
123A187ALA00.0450.01464.2380.0700.0700.0000.0000.0000.000
124A188GLY00.0300.02567.678-0.038-0.0380.0000.0000.0000.000
125A189ASP-1-0.872-0.95970.343-4.398-4.3980.0000.0000.0000.000
126A190ARG10.8470.92573.0324.2164.2160.0000.0000.0000.000
127A191ALA00.0760.03374.402-0.036-0.0360.0000.0000.0000.000
128A192GLU-1-0.872-0.92675.528-4.077-4.0770.0000.0000.0000.000
129A193ILE0-0.010-0.00671.384-0.008-0.0080.0000.0000.0000.000
130A194GLN00.006-0.01770.495-0.027-0.0270.0000.0000.0000.000
131A195ALA00.0180.00771.681-0.045-0.0450.0000.0000.0000.000
132A196GLU-1-0.819-0.89773.423-4.323-4.3230.0000.0000.0000.000
133A197LEU0-0.022-0.02068.005-0.045-0.0450.0000.0000.0000.000
134A198ILE0-0.019-0.00769.067-0.068-0.0680.0000.0000.0000.000
135A199GLU-1-0.976-0.97770.521-4.255-4.2550.0000.0000.0000.000
136A200LEU0-0.049-0.03269.656-0.013-0.0130.0000.0000.0000.000
137A201LYS10.8840.95366.9424.5144.5140.0000.0000.0000.000
138A202VAL00.0170.01564.389-0.082-0.0820.0000.0000.0000.000
139A203SER0-0.083-0.05459.901-0.027-0.0270.0000.0000.0000.000
140A204LEU0-0.020-0.01557.855-0.045-0.0450.0000.0000.0000.000
141A205LEU0-0.0240.00361.6600.0310.0310.0000.0000.0000.000
142A206ILE00.0250.00259.224-0.038-0.0380.0000.0000.0000.000
143A207VAL0-0.0020.00363.4380.0480.0480.0000.0000.0000.000
144A208THR0-0.020-0.02763.845-0.046-0.0460.0000.0000.0000.000
145A209GLY0-0.012-0.01065.3690.0930.0930.0000.0000.0000.000
146A210GLY0-0.009-0.01265.8800.0600.0600.0000.0000.0000.000
147A211HIS10.7780.89966.9924.5994.5990.0000.0000.0000.000
148A212THR00.0370.01668.182-0.027-0.0270.0000.0000.0000.000
149A213PRO00.0240.03068.5170.0820.0820.0000.0000.0000.000
150A214SER00.0360.01271.557-0.008-0.0080.0000.0000.0000.000
151A215LYS10.9880.97473.6874.2184.2180.0000.0000.0000.000
152A216GLU-1-0.960-0.96974.775-4.141-4.1410.0000.0000.0000.000
153A217ILE00.0270.01771.132-0.021-0.0210.0000.0000.0000.000
154A218ILE00.0120.01269.182-0.051-0.0510.0000.0000.0000.000
155A219GLU-1-0.924-0.96770.729-4.468-4.4680.0000.0000.0000.000
156A220LEU0-0.044-0.01672.921-0.013-0.0130.0000.0000.0000.000
157A221ALA00.0330.01767.870-0.021-0.0210.0000.0000.0000.000
158A222LYS10.9420.97968.3534.6174.6170.0000.0000.0000.000
159A223LYS10.9140.96469.2354.2314.2310.0000.0000.0000.000
160A224ASN0-0.082-0.05269.9560.0210.0210.0000.0000.0000.000
161A225ASN0-0.0280.00264.855-0.087-0.0870.0000.0000.0000.000
162A226ILE00.0020.01864.632-0.074-0.0740.0000.0000.0000.000
163A227THR00.0470.02859.4400.0480.0480.0000.0000.0000.000
164A228VAL0-0.035-0.01662.7970.0280.0280.0000.0000.0000.000
165A229ILE00.0400.02058.940-0.033-0.0330.0000.0000.0000.000
166A230THR00.007-0.01162.8530.0900.0900.0000.0000.0000.000
167A231THR0-0.029-0.02459.867-0.058-0.0580.0000.0000.0000.000
168A232PRO00.0020.00160.6860.1100.1100.0000.0000.0000.000
169A233HIS0-0.0040.00557.1270.1360.1360.0000.0000.0000.000
170A234ASP-1-0.768-0.88762.183-4.984-4.9840.0000.0000.0000.000
171A235SER00.0490.01662.627-0.090-0.0900.0000.0000.0000.000
172A236PHE00.0160.02159.366-0.092-0.0920.0000.0000.0000.000
173A237THR0-0.043-0.03957.972-0.130-0.1300.0000.0000.0000.000
174A238ALA00.0200.00257.855-0.110-0.1100.0000.0000.0000.000
175A239SER00.002-0.02557.608-0.094-0.0940.0000.0000.0000.000
176A240ARG10.8720.95354.6425.5535.5530.0000.0000.0000.000
177A241LEU0-0.021-0.00553.295-0.120-0.1200.0000.0000.0000.000
178A242ILE00.0400.02752.646-0.136-0.1360.0000.0000.0000.000
179A243VAL00.0480.03750.348-0.095-0.0950.0000.0000.0000.000
180A244GLN0-0.050-0.03448.209-0.183-0.1830.0000.0000.0000.000
181A245SER0-0.034-0.03548.066-0.115-0.1150.0000.0000.0000.000
182A246LEU00.0100.00646.487-0.055-0.0550.0000.0000.0000.000
183A247PRO00.0140.02443.629-0.060-0.0600.0000.0000.0000.000
184A248VAL0-0.020-0.02239.155-0.059-0.0590.0000.0000.0000.000
185A249ASP-1-0.826-0.92738.899-7.795-7.7950.0000.0000.0000.000
186A250TYR00.0270.01939.815-0.092-0.0920.0000.0000.0000.000
187A251VAL0-0.028-0.01740.776-0.048-0.0480.0000.0000.0000.000
188A252MET0-0.101-0.00935.630-0.107-0.1070.0000.0000.0000.000
189A253THR00.0050.00632.3590.2070.2070.0000.0000.0000.000
190A254LYS10.8470.91933.4908.0328.0320.0000.0000.0000.000
191A255ASP-1-0.862-0.93531.822-9.287-9.2870.0000.0000.0000.000
192A256ASN0-0.091-0.06329.2820.2620.2620.0000.0000.0000.000
193A257LEU00.0110.02727.911-0.174-0.1740.0000.0000.0000.000
194A258VAL0-0.030-0.01222.586-0.235-0.2350.0000.0000.0000.000
195A259ALA00.002-0.00623.5870.1170.1170.0000.0000.0000.000
196A260VAL0-0.035-0.01118.211-0.332-0.3320.0000.0000.0000.000
197A261SER00.0230.01017.0071.0921.0920.0000.0000.0000.000
198A262THR0-0.017-0.01016.912-0.604-0.6040.0000.0000.0000.000
199A263ASP-1-0.891-0.95113.364-20.906-20.9060.0000.0000.0000.000
200A264ASP-1-0.807-0.88212.225-20.151-20.1510.0000.0000.0000.000
201A265LEU0-0.039-0.0397.318-1.994-1.9940.0000.0000.0000.000
202A266VAL00.001-0.01110.0621.5931.5930.0000.0000.0000.000
203A267GLU-1-0.971-0.9976.032-32.959-32.9590.0000.0000.0000.000
204A268ASP-1-0.820-0.9219.740-23.682-23.6820.0000.0000.0000.000
205A269VAL00.0240.01912.5991.6981.6980.0000.0000.0000.000
206A270LYS10.9280.97011.59920.35120.3510.0000.0000.0000.000
207A271VAL0-0.034-0.00813.1491.0721.0720.0000.0000.0000.000
208A272THR00.0590.02115.8711.0981.0980.0000.0000.0000.000
209A273MET00.0110.04017.9010.9110.9110.0000.0000.0000.000
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