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: 7K7QK

Calculation Name: 4L2H-A-Xray547

Preferred Name: Poly(ADP-ribose) glycohydrolase

Target Type: SINGLE PROTEIN

Ligand Name: [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl[hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate

Ligand 3-letter code: AR6

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4L2H

Chain ID: A

ChEMBL ID: CHEMBL4105712

UniProt ID: I6L8L7

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 436
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -8726908.168055
FMO2-HF: Nuclear repulsion 8546260.343887
FMO2-HF: Total energy -180647.824168
FMO2-MP2: Total energy -181171.200701


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
-66.526-60.24820.152-12.329-14.10.089
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.008
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].
3A16GLN0-0.013-0.0273.0902.4805.0320.171-1.161-1.562-0.003
94A107LYS10.8850.9592.433-34.764-31.8452.091-2.191-2.8190.025
95A108ASN0-0.029-0.0163.1031.6682.3730.023-0.176-0.552-0.001
96A109GLN0-0.068-0.0351.773-32.782-32.96317.811-8.994-8.6360.067
97A110ILE00.0480.0333.587-4.145-3.9760.0570.195-0.4200.001
98A111PRO0-0.050-0.0045.4583.1173.231-0.001-0.002-0.1110.000
4A17PHE00.0540.0475.7850.1470.1470.0000.0000.0000.000
5A18PRO0-0.0050.0008.8870.6920.6920.0000.0000.0000.000
6A19LEU00.0000.00311.7860.3230.3230.0000.0000.0000.000
7A20PRO00.0420.01114.256-0.163-0.1630.0000.0000.0000.000
8A21GLN0-0.022-0.01216.310-0.097-0.0970.0000.0000.0000.000
9A22LYS10.8700.9439.9193.3233.3230.0000.0000.0000.000
10A23ASN00.0160.02015.233-0.107-0.1070.0000.0000.0000.000
11A24SER0-0.018-0.02718.3890.1740.1740.0000.0000.0000.000
12A25GLU-1-0.806-0.90020.449-0.964-0.9640.0000.0000.0000.000
13A26LEU00.0060.01021.4900.0830.0830.0000.0000.0000.000
14A27TRP0-0.002-0.00420.5110.1190.1190.0000.0000.0000.000
15A28ILE00.0000.00622.6330.1050.1050.0000.0000.0000.000
16A29ILE00.0270.01526.0330.0690.0690.0000.0000.0000.000
17A30GLN0-0.005-0.01121.2670.0550.0550.0000.0000.0000.000
18A31LYS10.9700.99024.4610.1600.1600.0000.0000.0000.000
19A32LYS10.8320.90726.0850.2010.2010.0000.0000.0000.000
20A33THR00.002-0.01028.5990.0340.0340.0000.0000.0000.000
21A34LEU0-0.009-0.01023.9030.0350.0350.0000.0000.0000.000
22A35GLN0-0.001-0.00528.5530.0290.0290.0000.0000.0000.000
23A36ASP-1-0.807-0.89030.636-0.083-0.0830.0000.0000.0000.000
24A37LEU00.0330.02630.7080.0180.0180.0000.0000.0000.000
25A38SER0-0.052-0.02430.3070.0290.0290.0000.0000.0000.000
26A39SER0-0.075-0.06032.4580.0160.0160.0000.0000.0000.000
27A40GLY0-0.025-0.01635.3840.0080.0080.0000.0000.0000.000
28A41LYS10.9270.98037.0720.0720.0720.0000.0000.0000.000
29A42GLN0-0.009-0.00835.130-0.022-0.0220.0000.0000.0000.000
30A43LYS10.8840.95736.6590.0160.0160.0000.0000.0000.000
31A44LEU0-0.040-0.02034.099-0.018-0.0180.0000.0000.0000.000
32A45ASP-1-0.793-0.88138.827-0.097-0.0970.0000.0000.0000.000
33A46SER0-0.004-0.00840.643-0.001-0.0010.0000.0000.0000.000
34A47PHE00.0290.02134.247-0.008-0.0080.0000.0000.0000.000
35A48GLN00.0600.02036.948-0.003-0.0030.0000.0000.0000.000
36A49SER0-0.0070.00437.410-0.020-0.0200.0000.0000.0000.000
37A50LEU00.0170.00731.395-0.011-0.0110.0000.0000.0000.000
38A51GLU-1-0.871-0.96332.769-0.254-0.2540.0000.0000.0000.000
39A52SER0-0.034-0.02832.729-0.039-0.0390.0000.0000.0000.000
40A53ILE0-0.0010.00030.194-0.031-0.0310.0000.0000.0000.000
41A54LEU00.0050.00827.614-0.032-0.0320.0000.0000.0000.000
42A55GLU-1-0.773-0.83128.011-0.516-0.5160.0000.0000.0000.000
43A56ILE00.0110.00828.907-0.060-0.0600.0000.0000.0000.000
44A57LEU0-0.006-0.00225.236-0.055-0.0550.0000.0000.0000.000
45A58ARG10.8870.95023.9270.4470.4470.0000.0000.0000.000
46A59ASP-1-0.892-0.93624.279-0.906-0.9060.0000.0000.0000.000
47A60SER0-0.087-0.06226.279-0.077-0.0770.0000.0000.0000.000
48A61LYS10.8030.88326.9090.7630.7630.0000.0000.0000.000
49A62ASN00.0230.01331.2530.0380.0380.0000.0000.0000.000
50A63GLN00.0160.02033.160-0.016-0.0160.0000.0000.0000.000
51A64ASN00.034-0.00134.4190.0170.0170.0000.0000.0000.000
52A65ASP-1-0.840-0.90934.624-0.270-0.2700.0000.0000.0000.000
53A66GLU-1-0.837-0.91435.802-0.287-0.2870.0000.0000.0000.000
54A67LYS10.7400.85830.1050.4670.4670.0000.0000.0000.000
55A68TYR0-0.019-0.04029.163-0.016-0.0160.0000.0000.0000.000
56A69PHE00.0260.03033.0210.0340.0340.0000.0000.0000.000
57A70ASN0-0.001-0.01332.3180.0500.0500.0000.0000.0000.000
58A71LEU00.0030.00030.3290.0260.0260.0000.0000.0000.000
59A72LYS10.8530.91933.1890.1630.1630.0000.0000.0000.000
60A73ALA00.0180.00336.7860.0180.0180.0000.0000.0000.000
61A74VAL0-0.033-0.00333.9380.0180.0180.0000.0000.0000.000
62A75PHE00.0280.01936.6870.0170.0170.0000.0000.0000.000
63A76GLU-1-0.852-0.92538.172-0.078-0.0780.0000.0000.0000.000
64A77GLN0-0.071-0.03438.7880.0190.0190.0000.0000.0000.000
65A78LEU0-0.067-0.00837.3710.0160.0160.0000.0000.0000.000
66A79ASP-1-0.831-0.90241.7740.0400.0400.0000.0000.0000.000
67A80LYS10.9570.96343.5410.0250.0250.0000.0000.0000.000
68A81GLU-1-0.853-0.91444.4890.0230.0230.0000.0000.0000.000
69A82GLU-1-0.777-0.87037.5660.0900.0900.0000.0000.0000.000
70A83GLN0-0.051-0.03739.508-0.004-0.0040.0000.0000.0000.000
71A84THR00.0250.00139.947-0.012-0.0120.0000.0000.0000.000
72A85TYR00.0120.01234.818-0.001-0.0010.0000.0000.0000.000
73A86PHE0-0.039-0.02632.513-0.001-0.0010.0000.0000.0000.000
74A87LEU00.0070.00035.220-0.006-0.0060.0000.0000.0000.000
75A88GLU-1-0.912-0.96436.7110.0000.0000.0000.0000.0000.000
76A89GLN0-0.036-0.03336.4120.0060.0060.0000.0000.0000.000
77A90PHE0-0.006-0.00129.2820.0120.0120.0000.0000.0000.000
78A91ILE00.0310.02030.5950.0100.0100.0000.0000.0000.000
79A92PRO0-0.0080.00430.2280.0010.0010.0000.0000.0000.000
80A93LYS11.0041.00630.560-0.159-0.1590.0000.0000.0000.000
81A94ILE00.0360.02026.3210.0330.0330.0000.0000.0000.000
82A95CYS0-0.064-0.03525.696-0.016-0.0160.0000.0000.0000.000
83A96GLN0-0.037-0.02426.2050.0040.0040.0000.0000.0000.000
84A97LEU0-0.022-0.00623.9120.0400.0400.0000.0000.0000.000
85A98VAL00.010-0.00620.8760.0500.0500.0000.0000.0000.000
86A99LEU0-0.067-0.02821.6460.0030.0030.0000.0000.0000.000
87A100LYS10.8480.94822.902-0.506-0.5060.0000.0000.0000.000
88A101ILE0-0.054-0.01016.5100.1410.1410.0000.0000.0000.000
89A102LYS10.9510.96217.947-0.750-0.7500.0000.0000.0000.000
90A103LYS10.8360.92412.357-2.078-2.0780.0000.0000.0000.000
91A104LYS10.9820.97212.4980.0280.0280.0000.0000.0000.000
92A105GLN00.0280.0197.168-1.132-1.1320.0000.0000.0000.000
93A106LEU0-0.0020.0128.1710.8850.8850.0000.0000.0000.000
99A112LYS10.9450.9576.663-4.985-4.9850.0000.0000.0000.000
100A113GLU-1-0.821-0.9209.5901.2681.2680.0000.0000.0000.000
101A114SER0-0.014-0.00613.3810.0850.0850.0000.0000.0000.000
102A115LYS10.8580.94310.492-3.277-3.2770.0000.0000.0000.000
103A116ILE00.0630.02411.499-0.343-0.3430.0000.0000.0000.000
104A117TYR0-0.062-0.0326.1523.2663.2660.0000.0000.0000.000
105A118GLU-1-0.872-0.9388.4892.0562.0560.0000.0000.0000.000
106A119ALA0-0.025-0.0099.1771.0561.0560.0000.0000.0000.000
107A120ALA00.0070.00410.855-0.723-0.7230.0000.0000.0000.000
108A121PHE0-0.018-0.01511.2530.1500.1500.0000.0000.0000.000
109A122SER00.0240.01616.399-0.075-0.0750.0000.0000.0000.000
110A123ARG10.8230.89019.721-0.899-0.8990.0000.0000.0000.000
111A124GLU-1-0.809-0.90522.2050.6140.6140.0000.0000.0000.000
112A125GLU-1-0.828-0.88616.8061.5701.5700.0000.0000.0000.000
113A126ILE0-0.030-0.00916.792-0.093-0.0930.0000.0000.0000.000
114A127SER00.006-0.00719.116-0.147-0.1470.0000.0000.0000.000
115A128TYR00.0620.02719.103-0.115-0.1150.0000.0000.0000.000
116A129TYR00.0450.01814.534-0.045-0.0450.0000.0000.0000.000
117A130VAL00.0380.01718.157-0.144-0.1440.0000.0000.0000.000
118A131SER00.0170.00020.947-0.090-0.0900.0000.0000.0000.000
119A132CYS0-0.086-0.04418.574-0.080-0.0800.0000.0000.0000.000
120A133MET0-0.083-0.03316.841-0.096-0.0960.0000.0000.0000.000
121A134PHE00.0560.01921.071-0.063-0.0630.0000.0000.0000.000
122A135LEU00.0190.01123.832-0.028-0.0280.0000.0000.0000.000
123A136CYS0-0.096-0.02022.501-0.053-0.0530.0000.0000.0000.000
124A137ILE00.0190.00119.740-0.086-0.0860.0000.0000.0000.000
125A138LEU0-0.030-0.01015.245-0.069-0.0690.0000.0000.0000.000
126A139LYS10.9060.93316.3651.1211.1210.0000.0000.0000.000
127A140ASP-1-0.773-0.84511.640-3.950-3.9500.0000.0000.0000.000
128A141GLN00.0450.01314.6710.1780.1780.0000.0000.0000.000
129A142ASP-1-0.917-0.95114.024-2.776-2.7760.0000.0000.0000.000
130A143ARG10.8350.8967.3426.4386.4380.0000.0000.0000.000
131A144LYS10.8970.96414.9012.0712.0710.0000.0000.0000.000
132A145ILE00.0180.02613.9290.2050.2050.0000.0000.0000.000
133A146TYR0-0.008-0.01015.830-0.083-0.0830.0000.0000.0000.000
134A147LYS10.9370.96012.9411.1891.1890.0000.0000.0000.000
135A148ASP-1-0.726-0.82916.760-0.511-0.5110.0000.0000.0000.000
136A149PHE00.0480.01220.125-0.039-0.0390.0000.0000.0000.000
137A150ARG10.8250.88420.9320.7690.7690.0000.0000.0000.000
138A151LEU0-0.043-0.01124.5070.0060.0060.0000.0000.0000.000
139A152ILE0-0.021-0.00424.3470.0290.0290.0000.0000.0000.000
140A153TYR00.009-0.04127.2370.0360.0360.0000.0000.0000.000
141A154LEU0-0.0060.02229.1730.0140.0140.0000.0000.0000.000
142A155LYS10.8560.94030.9850.2660.2660.0000.0000.0000.000
143A156ASP-1-0.840-0.92032.474-0.352-0.3520.0000.0000.0000.000
144A157LEU00.0360.01934.5650.0220.0220.0000.0000.0000.000
145A158VAL0-0.011-0.00235.9850.0270.0270.0000.0000.0000.000
146A159GLN00.0700.02636.930-0.008-0.0080.0000.0000.0000.000
147A160GLN00.0360.00736.9480.0060.0060.0000.0000.0000.000
148A161ILE0-0.029-0.01131.7380.0190.0190.0000.0000.0000.000
149A162ASN00.0580.03933.260-0.013-0.0130.0000.0000.0000.000
150A163ILE00.0180.02434.7430.0120.0120.0000.0000.0000.000
151A164ARG10.8370.89731.2160.1490.1490.0000.0000.0000.000
152A165ARG10.7700.87129.3930.3280.3280.0000.0000.0000.000
153A166GLN00.011-0.01030.9020.0300.0300.0000.0000.0000.000
154A167GLU-1-0.777-0.87733.2350.0440.0440.0000.0000.0000.000
155A168LYS10.8010.89325.6610.1510.1510.0000.0000.0000.000
156A169ILE0-0.0210.00328.9540.0280.0280.0000.0000.0000.000
157A170LYS10.8250.89530.1510.0130.0130.0000.0000.0000.000
158A171CYS0-0.068-0.01729.2930.0280.0280.0000.0000.0000.000
159A172PHE00.005-0.02124.2230.0410.0410.0000.0000.0000.000
160A173TYR0-0.027-0.03127.5920.0280.0280.0000.0000.0000.000
161A174GLU-1-0.769-0.86030.3410.2390.2390.0000.0000.0000.000
162A175TYR0-0.019-0.01823.2250.0190.0190.0000.0000.0000.000
163A176LEU0-0.007-0.01024.4280.0330.0330.0000.0000.0000.000
164A177LYS10.8240.91128.165-0.111-0.1110.0000.0000.0000.000
165A178GLN0-0.032-0.02230.0020.0450.0450.0000.0000.0000.000
166A179ALA0-0.022-0.02026.0600.0290.0290.0000.0000.0000.000
167A180LEU0-0.085-0.04128.1390.0210.0210.0000.0000.0000.000
168A181ASP-1-0.917-0.93730.3180.2590.2590.0000.0000.0000.000
169A182PHE0-0.073-0.02724.8810.0310.0310.0000.0000.0000.000
170A183SER00.0240.01530.6050.0050.0050.0000.0000.0000.000
171A184GLU-1-0.819-0.92028.8370.7010.7010.0000.0000.0000.000
172A185LYS10.9120.95728.796-0.632-0.6320.0000.0000.0000.000
173A186GLU-1-0.774-0.84328.0780.6280.6280.0000.0000.0000.000
174A187SER0-0.035-0.03425.8360.0660.0660.0000.0000.0000.000
175A188LYS10.8530.91024.063-0.668-0.6680.0000.0000.0000.000
176A189GLU-1-0.827-0.88623.9720.8720.8720.0000.0000.0000.000
177A190VAL0-0.019-0.01418.5750.0130.0130.0000.0000.0000.000
178A191VAL0-0.032-0.00717.853-0.105-0.1050.0000.0000.0000.000
179A192ILE0-0.013-0.01214.8820.1860.1860.0000.0000.0000.000
180A193PHE00.0100.01112.611-0.334-0.3340.0000.0000.0000.000
181A194GLN0-0.029-0.03912.5580.3750.3750.0000.0000.0000.000
182A195ARG10.7420.8288.810-2.012-2.0120.0000.0000.0000.000
183A196ILE00.011-0.00611.4610.9450.9450.0000.0000.0000.000
184A197ASN00.0460.02911.833-0.605-0.6050.0000.0000.0000.000
185A198CYS0-0.057-0.03013.7870.0870.0870.0000.0000.0000.000
186A199GLY00.0160.00916.461-0.141-0.1410.0000.0000.0000.000
187A200GLN0-0.009-0.01218.034-0.190-0.1900.0000.0000.0000.000
188A201LEU0-0.017-0.00220.2890.0260.0260.0000.0000.0000.000
189A202GLU-1-0.837-0.88022.5160.6280.6280.0000.0000.0000.000
190A203ASP-1-0.818-0.90726.2300.2570.2570.0000.0000.0000.000
191A204TYR00.0720.01428.7590.0450.0450.0000.0000.0000.000
192A205GLU-1-0.821-0.92132.0380.2200.2200.0000.0000.0000.000
193A206ASN0-0.041-0.01828.0320.0400.0400.0000.0000.0000.000
194A207TRP0-0.008-0.02526.8430.0420.0420.0000.0000.0000.000
195A208VAL00.0170.02231.8740.0160.0160.0000.0000.0000.000
196A209ASP-1-0.848-0.90333.9840.4060.4060.0000.0000.0000.000
197A210LYS10.8600.93729.031-0.550-0.5500.0000.0000.0000.000
198A211LEU0-0.001-0.00733.0230.0260.0260.0000.0000.0000.000
199A212LYS10.8530.92835.491-0.381-0.3810.0000.0000.0000.000
200A213ALA0-0.017-0.00537.691-0.020-0.0200.0000.0000.0000.000
201A214ILE0-0.050-0.00433.8500.0090.0090.0000.0000.0000.000
202A215LYS10.8520.92637.500-0.358-0.3580.0000.0000.0000.000
203A216LEU00.0120.01937.6170.0310.0310.0000.0000.0000.000
204A217LYS10.8460.93035.417-0.527-0.5270.0000.0000.0000.000
205A218ASN0-0.035-0.02338.950-0.028-0.0280.0000.0000.0000.000
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