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: ZGR2N

Calculation Name: 2HJ9-C-Xray549

Preferred Name: Autoinducer 2-binding periplasmic protein luxP

Target Type: SINGLE PROTEIN

Ligand Name: 3a-methyl-5,6-dihydro-furo[2,3-d][1,3,2]dioxaborole-2,2,6,6a-tetraol

Ligand 3-letter code: AI2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HJ9

Chain ID: C

ChEMBL ID: CHEMBL6100

UniProt ID: P54300

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -2570284.045621
FMO2-HF: Nuclear repulsion 2484469.274788
FMO2-HF: Total energy -85814.770832
FMO2-MP2: Total energy -86068.391437


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(C:52:SER)


Summations of interaction energy for fragment #1(C:52: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.
-166.682-166.45216.044-8.255-8.019-0.079
Interaction energy analysis for fragmet #1(C:52:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.893
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].
3C54GLN00.1000.0413.6530.2461.7510.001-0.572-0.9340.000
4C55GLN00.0420.0221.793-39.750-41.70616.042-7.412-6.674-0.078
5C56THR00.0430.0243.5652.7933.4740.001-0.271-0.411-0.001
6C57SER0-0.006-0.0115.7046.0286.0280.0000.0000.0000.000
7C58ALA00.011-0.0077.6043.1333.1330.0000.0000.0000.000
8C59LEU0-0.0480.0007.4642.4122.4120.0000.0000.0000.000
9C60ILE00.0510.0209.6012.6322.6320.0000.0000.0000.000
10C61HIS0-0.013-0.00411.7642.2902.2900.0000.0000.0000.000
11C62ASN0-0.018-0.01311.3272.8532.8530.0000.0000.0000.000
12C63ILE0-0.0080.02812.3901.3071.3070.0000.0000.0000.000
13C64PHE00.0180.00815.7661.4201.4200.0000.0000.0000.000
14C65ASP-1-0.836-0.92417.212-16.306-16.3060.0000.0000.0000.000
15C66SER0-0.057-0.04617.6331.0891.0890.0000.0000.0000.000
16C67HIS00.0400.03219.9750.4840.4840.0000.0000.0000.000
17C68PHE00.0500.00621.6330.8140.8140.0000.0000.0000.000
18C69ALA0-0.0100.00422.9400.6720.6720.0000.0000.0000.000
19C70ALA0-0.0040.01324.1380.5910.5910.0000.0000.0000.000
20C71ILE00.0440.01926.0040.5800.5800.0000.0000.0000.000
21C72GLN0-0.075-0.04527.2580.0950.0950.0000.0000.0000.000
22C73ILE0-0.007-0.00526.5600.4890.4890.0000.0000.0000.000
23C74HIS00.003-0.00530.0990.6410.6410.0000.0000.0000.000
24C75HIS0-0.0180.00331.9590.1120.1120.0000.0000.0000.000
25C76ASP-1-0.781-0.86431.985-9.493-9.4930.0000.0000.0000.000
26C77SER0-0.041-0.00234.2160.4130.4130.0000.0000.0000.000
27C78ASN00.0560.00935.3740.4820.4820.0000.0000.0000.000
28C79SER0-0.050-0.03237.1200.2930.2930.0000.0000.0000.000
29C80LYS10.8440.90937.3098.6348.6340.0000.0000.0000.000
30C81SER0-0.029-0.01041.5960.2640.2640.0000.0000.0000.000
31C82GLU-1-0.941-0.97343.564-6.567-6.5670.0000.0000.0000.000
32C83VAL00.0440.03345.8330.0740.0740.0000.0000.0000.000
33C84ILE0-0.026-0.01741.3130.0410.0410.0000.0000.0000.000
34C85ARG10.8910.95445.6126.8906.8900.0000.0000.0000.000
35C86ASP-1-0.834-0.93047.728-6.303-6.3030.0000.0000.0000.000
36C87PHE0-0.0060.01148.4340.1340.1340.0000.0000.0000.000
37C88TYR0-0.028-0.03445.5880.0510.0510.0000.0000.0000.000
38C89THR0-0.033-0.01051.4310.1170.1170.0000.0000.0000.000
39C90ASP-1-0.888-0.96353.915-5.776-5.7760.0000.0000.0000.000
40C91ARG10.7360.86752.6205.9735.9730.0000.0000.0000.000
41C92ASP-1-0.850-0.91353.105-6.060-6.0600.0000.0000.0000.000
42C93THR00.037-0.00650.278-0.192-0.1920.0000.0000.0000.000
43C94ASP-1-0.926-0.94349.441-6.261-6.2610.0000.0000.0000.000
44C95VAL0-0.023-0.02449.508-0.158-0.1580.0000.0000.0000.000
45C96LEU0-0.0020.00444.842-0.167-0.1670.0000.0000.0000.000
46C97ASN0-0.001-0.01045.200-0.320-0.3200.0000.0000.0000.000
47C98PHE0-0.031-0.01244.751-0.179-0.1790.0000.0000.0000.000
48C99PHE00.0210.01040.872-0.142-0.1420.0000.0000.0000.000
49C100PHE00.019-0.00939.672-0.222-0.2220.0000.0000.0000.000
50C101LEU00.0130.01540.044-0.197-0.1970.0000.0000.0000.000
51C102SER0-0.026-0.01140.908-0.171-0.1710.0000.0000.0000.000
52C103ILE0-0.0020.00137.113-0.165-0.1650.0000.0000.0000.000
53C104ASP-1-0.756-0.84735.803-9.024-9.0240.0000.0000.0000.000
54C105GLN0-0.057-0.01935.656-0.206-0.2060.0000.0000.0000.000
55C106SER0-0.088-0.05036.347-0.023-0.0230.0000.0000.0000.000
56C107ASP-1-0.848-0.91830.063-11.023-11.0230.0000.0000.0000.000
57C108PRO00.0220.00631.405-0.143-0.1430.0000.0000.0000.000
58C109SER0-0.059-0.02026.471-0.186-0.1860.0000.0000.0000.000
59C110HIS0-0.108-0.08325.662-1.052-1.0520.0000.0000.0000.000
60C111THR0-0.0070.02529.2070.2020.2020.0000.0000.0000.000
61C112PRO0-0.093-0.03030.760-0.333-0.3330.0000.0000.0000.000
62C113GLU-1-0.775-0.88729.421-10.870-10.8700.0000.0000.0000.000
63C114PHE0-0.033-0.02133.2140.2800.2800.0000.0000.0000.000
64C115ARG10.7710.84935.6138.4218.4210.0000.0000.0000.000
65C116PHE0-0.001-0.00338.1070.1650.1650.0000.0000.0000.000
66C117LEU0-0.0090.01140.905-0.171-0.1710.0000.0000.0000.000
67C118THR00.002-0.00743.0630.0350.0350.0000.0000.0000.000
68C119ASP-1-0.721-0.83145.452-6.429-6.4290.0000.0000.0000.000
69C120HIS0-0.034-0.04046.513-0.200-0.2000.0000.0000.0000.000
70C121LYS10.7790.87548.5386.2036.2030.0000.0000.0000.000
71C122GLY00.0430.01546.895-0.019-0.0190.0000.0000.0000.000
72C123ILE0-0.013-0.00543.410-0.006-0.0060.0000.0000.0000.000
73C124ILE0-0.071-0.02946.7370.1620.1620.0000.0000.0000.000
74C125TRP00.0060.00341.6780.0250.0250.0000.0000.0000.000
75C126ASP-1-0.864-0.94642.579-7.485-7.4850.0000.0000.0000.000
76C127ASP-1-0.756-0.87938.776-8.222-8.2220.0000.0000.0000.000
77C128GLY0-0.0150.00942.4640.0240.0240.0000.0000.0000.000
78C129ASN0-0.047-0.03737.7730.0620.0620.0000.0000.0000.000
79C130ALA0-0.005-0.01038.097-0.139-0.1390.0000.0000.0000.000
80C131HIS00.0080.00438.948-0.166-0.1660.0000.0000.0000.000
81C132PHE0-0.043-0.00434.8570.0210.0210.0000.0000.0000.000
82C133TYR00.0240.00332.819-0.079-0.0790.0000.0000.0000.000
83C134GLY0-0.006-0.01136.469-0.169-0.1690.0000.0000.0000.000
84C135VAL0-0.055-0.03536.5320.1070.1070.0000.0000.0000.000
85C136ASN00.0470.02439.7350.0640.0640.0000.0000.0000.000
86C137ASP-1-0.791-0.91242.937-7.020-7.0200.0000.0000.0000.000
87C138LEU0-0.006-0.00144.741-0.052-0.0520.0000.0000.0000.000
88C139ILE0-0.050-0.00938.813-0.097-0.0970.0000.0000.0000.000
89C140LEU00.0560.04339.471-0.232-0.2320.0000.0000.0000.000
90C141ASP-1-0.843-0.92641.148-7.184-7.1840.0000.0000.0000.000
91C142SER0-0.169-0.09739.947-0.119-0.1190.0000.0000.0000.000
92C143LEU0-0.036-0.02735.268-0.202-0.2020.0000.0000.0000.000
93C144ALA00.0180.00437.981-0.154-0.1540.0000.0000.0000.000
94C145ASN0-0.033-0.02040.3110.0240.0240.0000.0000.0000.000
95C146ARG10.8840.96334.2789.0379.0370.0000.0000.0000.000
96C147VAL0-0.0110.00134.185-0.173-0.1730.0000.0000.0000.000
97C148SER00.0270.01136.4810.0960.0960.0000.0000.0000.000
98C149PHE0-0.040-0.02835.1670.2430.2430.0000.0000.0000.000
99C150SER00.0560.01235.824-0.075-0.0750.0000.0000.0000.000
100C151ASN0-0.017-0.00932.640-0.079-0.0790.0000.0000.0000.000
101C152ASN0-0.0110.00129.703-0.474-0.4740.0000.0000.0000.000
102C153TRP0-0.002-0.00525.8770.3090.3090.0000.0000.0000.000
103C154TYR00.0030.00528.136-0.193-0.1930.0000.0000.0000.000
104C155TYR0-0.033-0.05026.148-0.131-0.1310.0000.0000.0000.000
105C156ILE0-0.045-0.02828.2710.3560.3560.0000.0000.0000.000
106C157ASN0-0.053-0.03229.4260.0710.0710.0000.0000.0000.000
107C158VAL00.0120.00431.6360.2840.2840.0000.0000.0000.000
108C159MET0-0.029-0.00934.743-0.234-0.2340.0000.0000.0000.000
109C160THR00.0260.00736.6310.1920.1920.0000.0000.0000.000
110C161SER0-0.019-0.01939.027-0.077-0.0770.0000.0000.0000.000
111C162ILE0-0.0040.00837.1500.0870.0870.0000.0000.0000.000
112C163GLY00.0300.02135.310-0.282-0.2820.0000.0000.0000.000
113C164SER0-0.017-0.01032.2130.0210.0210.0000.0000.0000.000
114C165ARG10.8280.92931.6169.3419.3410.0000.0000.0000.000
115C166HIS10.8190.88227.37011.17311.1730.0000.0000.0000.000
116C167MET0-0.0010.00528.736-0.058-0.0580.0000.0000.0000.000
117C168LEU00.0060.01724.121-0.168-0.1680.0000.0000.0000.000
118C169VAL0-0.004-0.00228.4100.2100.2100.0000.0000.0000.000
119C170ARG10.7870.88029.8559.9879.9870.0000.0000.0000.000
120C171ARG10.8830.95932.9618.3158.3150.0000.0000.0000.000
121C172VAL0-0.0010.00035.130-0.173-0.1730.0000.0000.0000.000
122C173PRO0-0.050-0.01637.5840.1530.1530.0000.0000.0000.000
123C174ILE00.0110.00741.133-0.124-0.1240.0000.0000.0000.000
124C175LEU0-0.023-0.01842.6140.1120.1120.0000.0000.0000.000
125C176ASP-1-0.721-0.83045.560-6.272-6.2720.0000.0000.0000.000
126C177PRO0-0.076-0.05946.1040.0140.0140.0000.0000.0000.000
127C178SER0-0.099-0.05748.2580.0710.0710.0000.0000.0000.000
128C179THR0-0.018-0.01751.3860.0520.0520.0000.0000.0000.000
129C180GLY0-0.036-0.01147.9190.0160.0160.0000.0000.0000.000
130C181GLU-1-0.958-0.97347.949-6.247-6.2470.0000.0000.0000.000
131C182VAL0-0.042-0.02944.390-0.127-0.1270.0000.0000.0000.000
132C183LEU00.0240.02646.8560.0800.0800.0000.0000.0000.000
133C184GLY00.0110.00345.9970.1100.1100.0000.0000.0000.000
134C185PHE0-0.063-0.02040.559-0.171-0.1710.0000.0000.0000.000
135C186SER00.0650.04339.2500.0170.0170.0000.0000.0000.000
136C187PHE0-0.007-0.02237.013-0.266-0.2660.0000.0000.0000.000
137C188ASN00.0570.02432.5620.3380.3380.0000.0000.0000.000
138C189ALA0-0.023-0.01532.425-0.206-0.2060.0000.0000.0000.000
139C190VAL00.0310.01826.5650.0650.0650.0000.0000.0000.000
140C191VAL0-0.045-0.02629.230-0.082-0.0820.0000.0000.0000.000
141C192LEU00.009-0.00123.531-0.337-0.3370.0000.0000.0000.000
142C193ASP-1-0.795-0.88125.575-11.423-11.4230.0000.0000.0000.000
143C194ASN0-0.042-0.04426.3520.0710.0710.0000.0000.0000.000
144C195ASN0-0.020-0.00124.736-0.158-0.1580.0000.0000.0000.000
145C196PHE00.0480.00923.943-0.622-0.6220.0000.0000.0000.000
146C197ALA00.0270.02123.313-0.536-0.5360.0000.0000.0000.000
147C198LEU0-0.0030.00520.181-0.550-0.5500.0000.0000.0000.000
148C199MET0-0.064-0.02518.520-1.052-1.0520.0000.0000.0000.000
149C200GLU-1-0.818-0.93218.395-16.536-16.5360.0000.0000.0000.000
150C201LYS10.8930.96618.58814.14014.1400.0000.0000.0000.000
151C202LEU0-0.016-0.01715.368-1.112-1.1120.0000.0000.0000.000
152C203LYS10.8580.96213.90714.98414.9840.0000.0000.0000.000
153C204SER00.0100.00314.056-1.188-1.1880.0000.0000.0000.000
154C205GLU-1-0.962-0.98914.686-18.227-18.2270.0000.0000.0000.000
155C206SER0-0.069-0.0749.833-1.804-1.8040.0000.0000.0000.000
156C207ASN0-0.088-0.0389.528-2.030-2.0300.0000.0000.0000.000
157C208VAL0-0.026-0.0048.618-1.832-1.8320.0000.0000.0000.000
158C209ASP0-0.062-0.06410.9412.3412.3410.0000.0000.0000.000
159C210ASN00.0190.02313.3491.8491.8490.0000.0000.0000.000
160C211VAL00.0430.01513.607-1.825-1.8250.0000.0000.0000.000
161C212VAL0-0.023-0.02415.9081.4221.4220.0000.0000.0000.000
162C213LEU00.0040.02117.506-0.914-0.9140.0000.0000.0000.000
163C214VAL0-0.022-0.02319.3830.8920.8920.0000.0000.0000.000
164C215ALA00.0430.03321.790-0.307-0.3070.0000.0000.0000.000
165C216ASN0-0.020-0.02423.3350.0820.0820.0000.0000.0000.000
166C217SER0-0.008-0.01521.754-0.510-0.5100.0000.0000.0000.000
167C218VAL0-0.044-0.01023.2850.2820.2820.0000.0000.0000.000
168C219PRO0-0.021-0.01322.855-0.290-0.2900.0000.0000.0000.000
169C220LEU0-0.020-0.00923.5910.6170.6170.0000.0000.0000.000
170C221ALA00.0520.03222.7750.5010.5010.0000.0000.0000.000
171C222ASN0-0.049-0.04020.381-0.725-0.7250.0000.0000.0000.000
172C223SER00.0650.03318.1990.1790.1790.0000.0000.0000.000
173C224LEU0-0.087-0.03719.228-0.347-0.3470.0000.0000.0000.000
174C225ILE0-0.020-0.00421.1850.5570.5570.0000.0000.0000.000
175C226GLY0-0.070-0.03823.4820.6500.6500.0000.0000.0000.000
176C227ASP-1-0.958-0.98122.933-13.133-13.1330.0000.0000.0000.000
177C228GLU-1-0.769-0.86318.993-15.037-15.0370.0000.0000.0000.000
178C229PRO0-0.066-0.05218.6300.3660.3660.0000.0000.0000.000
179C230TYR0-0.0020.02115.4050.3750.3750.0000.0000.0000.000
180C231ASN00.0680.02420.560-0.178-0.1780.0000.0000.0000.000
181C232VAL00.0700.00820.929-0.570-0.5700.0000.0000.0000.000
182C233ALA0-0.026-0.01121.428-0.309-0.3090.0000.0000.0000.000
183C234ASP-1-0.783-0.87120.284-13.666-13.6660.0000.0000.0000.000
184C235VAL00.0790.04915.822-0.452-0.4520.0000.0000.0000.000
185C236LEU0-0.0140.00617.333-0.689-0.6890.0000.0000.0000.000
186C237GLN00.0640.04519.421-0.467-0.4670.0000.0000.0000.000
187C238ARG11.0081.00618.37815.44115.4410.0000.0000.0000.000
188C239LYS10.7840.85221.83112.56312.5630.0000.0000.0000.000
189C240SER00.0080.04821.0640.4760.4760.0000.0000.0000.000
190C241SER0-0.029-0.03823.6270.0530.0530.0000.0000.0000.000
191C242ASP-1-0.727-0.88218.593-16.144-16.1440.0000.0000.0000.000
192C243LYS10.7580.88416.41317.11117.1110.0000.0000.0000.000
193C244ARG10.7210.83718.56713.77513.7750.0000.0000.0000.000
194C245LEU00.0170.00416.018-0.921-0.9210.0000.0000.0000.000
195C246ASP-1-0.644-0.80414.132-20.508-20.5080.0000.0000.0000.000
196C247LYS10.8350.91412.51418.06018.0600.0000.0000.0000.000
197C248LEU0-0.134-0.06411.141-0.703-0.7030.0000.0000.0000.000
198C249LEU0-0.047-0.0117.419-3.714-3.7140.0000.0000.0000.000
199C250VAL0-0.0230.0078.168-3.047-3.0470.0000.0000.0000.000
200C251ILE0-0.090-0.0505.110-6.287-6.2870.0000.0000.0000.000
201C252GLU-1-0.868-0.9179.570-17.402-17.4020.0000.0000.0000.000
202C253THR0-0.024-0.01110.931-3.109-3.1090.0000.0000.0000.000
203C254PRO00.0200.01313.0101.0941.0940.0000.0000.0000.000
204C255ILE00.0080.01515.750-0.696-0.6960.0000.0000.0000.000
205C256VAL0-0.037-0.00917.3021.0521.0520.0000.0000.0000.000
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207C258ASN0-0.026-0.01423.2010.2690.2690.0000.0000.0000.000
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