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: 8G48Y

Calculation Name: 1JJT-A-Xray547

Preferred Name: Beta-lactamase

Target Type: SINGLE PROTEIN

Ligand Name: 2,3-bis-benzo[1,3]dioxol-5-ylmethyl-succinic acid | acetate ion

Ligand 3-letter code: BDS | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JJT

Chain ID: A

ChEMBL ID: CHEMBL1293244

UniProt ID: Q79MP6

Base Structure: X-ray

Registration Date: 2025-10-03

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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2670974.568711
FMO2-HF: Nuclear repulsion 2587803.969525
FMO2-HF: Total energy -83170.599185
FMO2-MP2: Total energy -83420.541853


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:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
5.256.694-0.016-0.675-0.753-0.001
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.903
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].
3A5PRO00.0120.0073.8571.5953.039-0.016-0.675-0.753-0.001
4A6ASP-1-0.834-0.9136.562-32.608-32.6080.0000.0000.0000.000
5A7LEU0-0.080-0.0367.8421.8741.8740.0000.0000.0000.000
6A8LYS10.8340.91211.23319.49219.4920.0000.0000.0000.000
7A9ILE00.013-0.00514.1170.4190.4190.0000.0000.0000.000
8A10GLU-1-0.829-0.89117.401-16.417-16.4170.0000.0000.0000.000
9A11LYS10.8430.92520.38010.61410.6140.0000.0000.0000.000
10A12LEU0-0.0170.00024.2220.0080.0080.0000.0000.0000.000
11A13ASP-1-0.780-0.89126.113-9.184-9.1840.0000.0000.0000.000
12A14GLU-1-0.851-0.93928.858-9.821-9.8210.0000.0000.0000.000
13A15GLY0-0.0140.00329.9910.0930.0930.0000.0000.0000.000
14A16VAL0-0.039-0.01526.849-0.186-0.1860.0000.0000.0000.000
15A17TYR00.0510.01722.227-0.018-0.0180.0000.0000.0000.000
16A18VAL00.0010.00219.3130.1390.1390.0000.0000.0000.000
17A19HIS0-0.041-0.00917.088-1.021-1.0210.0000.0000.0000.000
18A20THR00.018-0.00414.1070.7720.7720.0000.0000.0000.000
19A21SER00.0260.02611.230-0.855-0.8550.0000.0000.0000.000
20A22PHE00.007-0.0258.4912.0652.0650.0000.0000.0000.000
21A23GLU-1-0.864-0.9247.742-38.011-38.0110.0000.0000.0000.000
22A24GLU-1-0.920-0.9536.991-31.374-31.3740.0000.0000.0000.000
23A25VAL0-0.040-0.0268.9301.6961.6960.0000.0000.0000.000
24A26ASN00.016-0.01012.6000.5340.5340.0000.0000.0000.000
25A27GLY00.0110.00714.214-0.876-0.8760.0000.0000.0000.000
26A28TRP0-0.068-0.03715.4150.8850.8850.0000.0000.0000.000
27A29GLY00.0370.05011.5160.0660.0660.0000.0000.0000.000
28A30VAL00.013-0.0087.463-0.144-0.1440.0000.0000.0000.000
29A31VAL0-0.0200.00010.2562.3392.3390.0000.0000.0000.000
30A32PRO00.0210.01112.588-1.081-1.0810.0000.0000.0000.000
31A33LYS10.7360.85414.24717.77517.7750.0000.0000.0000.000
32A34HIS10.7880.87915.79616.07216.0720.0000.0000.0000.000
33A35GLY00.0390.01718.5530.3110.3110.0000.0000.0000.000
34A36LEU0-0.044-0.01520.6340.0390.0390.0000.0000.0000.000
35A37VAL0-0.0170.00321.137-0.181-0.1810.0000.0000.0000.000
36A38VAL0-0.007-0.00223.9650.2160.2160.0000.0000.0000.000
37A39LEU0-0.007-0.00226.170-0.008-0.0080.0000.0000.0000.000
38A40VAL0-0.021-0.01929.5380.3050.3050.0000.0000.0000.000
39A41ASN0-0.027-0.01833.0580.0990.0990.0000.0000.0000.000
40A42ALA00.0580.03131.992-0.142-0.1420.0000.0000.0000.000
41A43GLU-1-0.864-0.92830.607-9.233-9.2330.0000.0000.0000.000
42A44ALA00.0210.00825.571-0.037-0.0370.0000.0000.0000.000
43A45TYR0-0.039-0.03827.0310.0430.0430.0000.0000.0000.000
44A46LEU00.004-0.00120.407-0.191-0.1910.0000.0000.0000.000
45A47ILE0-0.013-0.01423.5470.4020.4020.0000.0000.0000.000
46A48ASP-1-0.672-0.78920.331-14.343-14.3430.0000.0000.0000.000
47A49THR0-0.0120.00317.4840.2740.2740.0000.0000.0000.000
48A50PRO0-0.025-0.01713.547-0.151-0.1510.0000.0000.0000.000
49A51PHE00.0100.01311.5760.9640.9640.0000.0000.0000.000
50A52THR00.0530.0349.0891.0241.0240.0000.0000.0000.000
51A53ALA00.0810.04512.4090.8790.8790.0000.0000.0000.000
52A54LYS10.9951.0018.29528.68228.6820.0000.0000.0000.000
53A55ASP-1-0.826-0.9359.259-28.242-28.2420.0000.0000.0000.000
54A56THR0-0.013-0.02512.0491.5741.5740.0000.0000.0000.000
55A57GLU-1-0.892-0.94014.462-16.927-16.9270.0000.0000.0000.000
56A58LYS10.8360.9307.96529.14829.1480.0000.0000.0000.000
57A59LEU0-0.009-0.00114.3950.8490.8490.0000.0000.0000.000
58A60VAL0-0.016-0.01416.8650.9280.9280.0000.0000.0000.000
59A61THR0-0.011-0.01817.1160.8970.8970.0000.0000.0000.000
60A62TRP00.0350.02316.6620.8720.8720.0000.0000.0000.000
61A63PHE0-0.017-0.02019.0300.5830.5830.0000.0000.0000.000
62A64VAL00.0080.00222.2770.6210.6210.0000.0000.0000.000
63A65GLU-1-0.969-0.98319.270-13.653-13.6530.0000.0000.0000.000
64A66ARG10.8630.93919.54213.72213.7220.0000.0000.0000.000
65A67GLY00.0050.01125.5470.3800.3800.0000.0000.0000.000
66A68TYR0-0.049-0.01825.9910.2650.2650.0000.0000.0000.000
67A69LYS10.9690.98326.1809.1059.1050.0000.0000.0000.000
68A70ILE0-0.004-0.00623.0830.1710.1710.0000.0000.0000.000
69A71LYS10.8810.95126.6679.3209.3200.0000.0000.0000.000
70A72GLY00.0210.01027.0870.2700.2700.0000.0000.0000.000
71A73SER0-0.028-0.00723.365-0.110-0.1100.0000.0000.0000.000
72A74ILE0-0.016-0.00525.4680.4610.4610.0000.0000.0000.000
73A75SER0-0.005-0.01822.544-0.297-0.2970.0000.0000.0000.000
74A76SER0-0.054-0.05223.9050.3920.3920.0000.0000.0000.000
75A77HIS10.8130.91521.59114.18714.1870.0000.0000.0000.000
76A78PHE00.0560.01824.144-0.501-0.5010.0000.0000.0000.000
77A79HIS0-0.012-0.00720.246-0.740-0.7400.0000.0000.0000.000
78A80SER00.0820.02616.5970.3890.3890.0000.0000.0000.000
79A81ASP-1-0.809-0.90016.394-16.620-16.6200.0000.0000.0000.000
80A82SER0-0.052-0.06117.4150.0010.0010.0000.0000.0000.000
81A83THR00.0130.01419.6640.1910.1910.0000.0000.0000.000
82A84GLY00.0260.02716.2390.3640.3640.0000.0000.0000.000
83A85GLY00.0060.00016.560-0.621-0.6210.0000.0000.0000.000
84A86ILE0-0.040-0.02817.8970.4030.4030.0000.0000.0000.000
85A87GLU-1-0.916-0.95019.637-14.241-14.2410.0000.0000.0000.000
86A88TRP0-0.005-0.00617.2680.6010.6010.0000.0000.0000.000
87A89LEU00.0150.00519.7280.4350.4350.0000.0000.0000.000
88A90ASN00.0810.06622.3290.6100.6100.0000.0000.0000.000
89A91SER0-0.053-0.02521.5730.2940.2940.0000.0000.0000.000
90A92ARG10.8510.92219.43914.43514.4350.0000.0000.0000.000
91A93SER0-0.022-0.00924.5700.4370.4370.0000.0000.0000.000
92A94ILE0-0.042-0.01123.0940.3000.3000.0000.0000.0000.000
93A95PRO0-0.0060.00026.520-0.201-0.2010.0000.0000.0000.000
94A96THR00.0190.00424.225-0.223-0.2230.0000.0000.0000.000
95A97TYR00.007-0.00127.1800.4860.4860.0000.0000.0000.000
96A98ALA00.0230.00427.711-0.454-0.4540.0000.0000.0000.000
97A99SER00.0280.01129.5050.4420.4420.0000.0000.0000.000
98A100GLU-1-0.797-0.90631.839-8.464-8.4640.0000.0000.0000.000
99A101LEU00.0050.01132.531-0.129-0.1290.0000.0000.0000.000
100A102THR0-0.031-0.03827.182-0.073-0.0730.0000.0000.0000.000
101A103ASN00.0500.02028.527-0.745-0.7450.0000.0000.0000.000
102A104GLU-1-0.842-0.90830.178-9.308-9.3080.0000.0000.0000.000
103A105LEU0-0.064-0.02728.145-0.055-0.0550.0000.0000.0000.000
104A106LEU0-0.018-0.01223.561-0.282-0.2820.0000.0000.0000.000
105A107LYS10.8420.91326.5779.1899.1890.0000.0000.0000.000
106A108LYS10.9160.96229.24410.38910.3890.0000.0000.0000.000
107A109ASP-1-0.906-0.94422.757-13.584-13.5840.0000.0000.0000.000
108A110GLY00.0070.01424.341-0.454-0.4540.0000.0000.0000.000
109A111LYS10.8060.89719.66614.56814.5680.0000.0000.0000.000
110A112VAL00.003-0.00123.1040.5990.5990.0000.0000.0000.000
111A113GLN00.0260.01424.7790.0560.0560.0000.0000.0000.000
112A114ALA0-0.028-0.01726.957-0.206-0.2060.0000.0000.0000.000
113A115THR0-0.020-0.01827.8100.4000.4000.0000.0000.0000.000
114A116ASN0-0.060-0.02830.1960.2320.2320.0000.0000.0000.000
115A117SER00.0440.01331.345-0.399-0.3990.0000.0000.0000.000
116A118PHE0-0.030-0.00931.0190.2530.2530.0000.0000.0000.000
117A119SER00.029-0.00435.672-0.117-0.1170.0000.0000.0000.000
118A120GLY0-0.028-0.00538.3800.0880.0880.0000.0000.0000.000
119A121VAL0-0.017-0.01738.062-0.188-0.1880.0000.0000.0000.000
120A122ASN00.009-0.00637.970-0.228-0.2280.0000.0000.0000.000
121A123TYR00.0570.04733.6690.2830.2830.0000.0000.0000.000
122A124TRP0-0.021-0.01935.713-0.254-0.2540.0000.0000.0000.000
123A125LEU00.0080.02429.9910.1100.1100.0000.0000.0000.000
124A126VAL00.0410.02233.1850.0630.0630.0000.0000.0000.000
125A127LYS11.0000.99735.9377.0727.0720.0000.0000.0000.000
126A128ASN0-0.044-0.03539.269-0.011-0.0110.0000.0000.0000.000
127A129LYS10.8550.92334.7968.3828.3820.0000.0000.0000.000
128A130ILE00.005-0.00330.125-0.236-0.2360.0000.0000.0000.000
129A131GLU-1-0.790-0.86833.869-8.126-8.1260.0000.0000.0000.000
130A132VAL0-0.005-0.00131.300-0.330-0.3300.0000.0000.0000.000
131A133PHE0-0.003-0.01433.3390.3320.3320.0000.0000.0000.000
132A134TYR00.012-0.00133.635-0.151-0.1510.0000.0000.0000.000
133A135PRO0-0.048-0.02133.4410.2870.2870.0000.0000.0000.000
134A136GLY00.0380.02136.0610.2620.2620.0000.0000.0000.000
135A137PRO0-0.009-0.01433.682-0.274-0.2740.0000.0000.0000.000
136A138GLY00.0240.00231.8190.2430.2430.0000.0000.0000.000
137A139HIS0-0.0370.00223.0140.1050.1050.0000.0000.0000.000
138A140THR00.000-0.02226.118-0.257-0.2570.0000.0000.0000.000
139A141PRO00.023-0.00529.0590.3010.3010.0000.0000.0000.000
140A142ASP-1-0.720-0.82228.432-11.028-11.0280.0000.0000.0000.000
141A143ASN0-0.048-0.01328.504-0.201-0.2010.0000.0000.0000.000
142A144VAL0-0.0120.00029.2710.4510.4510.0000.0000.0000.000
143A145VAL0-0.051-0.01528.909-0.427-0.4270.0000.0000.0000.000
144A146VAL00.008-0.00528.3720.2300.2300.0000.0000.0000.000
145A147TRP0-0.026-0.00730.583-0.184-0.1840.0000.0000.0000.000
146A148LEU00.0500.03428.8890.1150.1150.0000.0000.0000.000
147A149PRO0-0.027-0.01833.5120.0570.0570.0000.0000.0000.000
148A150GLU-1-0.836-0.91235.772-8.394-8.3940.0000.0000.0000.000
149A151ARG10.8410.91032.4429.1279.1270.0000.0000.0000.000
150A152LYS10.9160.97534.6277.7887.7880.0000.0000.0000.000
151A153ILE00.0320.02128.760-0.065-0.0650.0000.0000.0000.000
152A154LEU00.005-0.00130.9680.0940.0940.0000.0000.0000.000
153A155PHE00.0240.01522.361-0.210-0.2100.0000.0000.0000.000
154A156GLY00.0280.00027.5660.2650.2650.0000.0000.0000.000
155A157GLY00.0690.03524.2980.1100.1100.0000.0000.0000.000
156A158CYS0-0.054-0.01821.724-0.370-0.3700.0000.0000.0000.000
157A159PHE00.0130.01224.5980.1340.1340.0000.0000.0000.000
158A160ILE0-0.045-0.01827.0560.2710.2710.0000.0000.0000.000
159A161LYS10.8300.92023.27712.27012.2700.0000.0000.0000.000
160A162PRO00.0310.01626.4010.2760.2760.0000.0000.0000.000
161A163TYR00.0340.00125.8250.4470.4470.0000.0000.0000.000
162A164GLY00.0520.03727.2370.0040.0040.0000.0000.0000.000
163A165LEU0-0.006-0.00826.127-0.445-0.4450.0000.0000.0000.000
164A166GLY00.0240.02023.134-0.241-0.2410.0000.0000.0000.000
165A167ASN00.0100.00420.8160.6110.6110.0000.0000.0000.000
166A168LEU00.029-0.00922.8750.3040.3040.0000.0000.0000.000
167A169GLY0-0.0080.01124.7350.3930.3930.0000.0000.0000.000
168A170ASP-1-0.835-0.90325.417-11.867-11.8670.0000.0000.0000.000
169A171ALA0-0.024-0.01128.1270.2940.2940.0000.0000.0000.000
170A172ASN00.000-0.00729.7630.3700.3700.0000.0000.0000.000
171A173ILE00.0440.00631.0850.1270.1270.0000.0000.0000.000
172A174GLU-1-0.799-0.88634.229-8.188-8.1880.0000.0000.0000.000
173A175ALA0-0.029-0.00336.6810.2290.2290.0000.0000.0000.000
174A176TRP0-0.0060.02127.5050.0690.0690.0000.0000.0000.000
175A177PRO00.0300.00635.2290.0280.0280.0000.0000.0000.000
176A178LYS10.9230.95837.8887.5727.5720.0000.0000.0000.000
177A179SER00.027-0.00835.6990.2200.2200.0000.0000.0000.000
178A180ALA00.0250.01035.020-0.009-0.0090.0000.0000.0000.000
179A181LYS10.9190.96836.5877.6807.6800.0000.0000.0000.000
180A182LEU0-0.0040.01439.5630.1600.1600.0000.0000.0000.000
181A183LEU00.0120.00832.5020.0770.0770.0000.0000.0000.000
182A184LYS10.9440.96937.1637.8267.8260.0000.0000.0000.000
183A185SER0-0.046-0.02538.5390.1460.1460.0000.0000.0000.000
184A186LYS10.7640.88838.4658.2678.2670.0000.0000.0000.000
185A187TYR0-0.004-0.02935.9640.0100.0100.0000.0000.0000.000
186A188GLY00.0420.03137.358-0.171-0.1710.0000.0000.0000.000
187A189LYS10.8710.92639.7787.3987.3980.0000.0000.0000.000
188A190ALA00.0030.00334.2170.0380.0380.0000.0000.0000.000
189A191LYS10.8520.93832.2539.7119.7110.0000.0000.0000.000
190A192LEU0-0.013-0.01529.024-0.092-0.0920.0000.0000.0000.000
191A193VAL0-0.011-0.00629.0250.1420.1420.0000.0000.0000.000
192A194VAL00.0390.01223.779-0.223-0.2230.0000.0000.0000.000
193A195PRO0-0.030-0.00923.6040.1390.1390.0000.0000.0000.000
194A196SER00.0510.00320.447-0.419-0.4190.0000.0000.0000.000
195A197HIS10.7840.87716.98816.55916.5590.0000.0000.0000.000
196A198SER0-0.002-0.00220.1900.2630.2630.0000.0000.0000.000
197A199GLU-1-0.800-0.88519.667-16.367-16.3670.0000.0000.0000.000
198A200VAL0-0.033-0.02122.8710.4310.4310.0000.0000.0000.000
199A201GLY00.0500.03125.9250.0570.0570.0000.0000.0000.000
200A202ASP-1-0.771-0.86229.470-9.316-9.3160.0000.0000.0000.000
201A203ALA00.038-0.00132.746-0.180-0.1800.0000.0000.0000.000
202A204SER0-0.035-0.03833.9300.1850.1850.0000.0000.0000.000
203A205LEU00.0010.00128.009-0.008-0.0080.0000.0000.0000.000
204A206LEU0-0.0120.00931.932-0.131-0.1310.0000.0000.0000.000
205A207LYS10.8060.90334.2928.8278.8270.0000.0000.0000.000
206A208LEU00.0370.02531.5050.0740.0740.0000.0000.0000.000
207A209THR0-0.006-0.00730.709-0.224-0.2240.0000.0000.0000.000
208A210LEU0-0.037-0.01332.3610.0740.0740.0000.0000.0000.000
209A211GLU-1-0.841-0.92235.625-8.583-8.5830.0000.0000.0000.000
210A212GLN00.001-0.00430.5030.1720.1720.0000.0000.0000.000
211A213ALA0-0.0190.00133.200-0.022-0.0220.0000.0000.0000.000
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