Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: JQ3L9

Calculation Name: 5LEJ-A-Xray372

Preferred Name: Listeriolysin regulatory protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5LEJ

Chain ID: A

ChEMBL ID: CHEMBL4295575

UniProt ID: P22262

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3053598.967576
FMO2-HF: Nuclear repulsion 2958978.962174
FMO2-HF: Total energy -94620.005402
FMO2-MP2: Total energy -94897.922974


3D Structure
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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-1.0533.1270.203-1.475-2.9090.001
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.010
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].
3A4GLN00.017-0.0033.646-2.1720.1240.002-0.976-1.3220.004
4A5ALA00.0020.0042.836-1.0670.0320.202-0.398-0.904-0.003
5A6GLU-1-0.789-0.8834.1742.4662.9810.000-0.065-0.4500.000
6A7GLU-1-0.865-0.9066.4120.1240.1240.0000.0000.0000.000
7A8PHE00.007-0.0107.2910.0370.0370.0000.0000.0000.000
8A9LYS10.8780.9398.326-0.788-0.7880.0000.0000.0000.000
9A10LYS10.8680.9119.838-0.258-0.2580.0000.0000.0000.000
10A11TYR0-0.050-0.02711.835-0.034-0.0340.0000.0000.0000.000
11A12LEU00.0320.01311.392-0.017-0.0170.0000.0000.0000.000
12A13GLU-1-0.905-0.91113.4600.5050.5050.0000.0000.0000.000
13A14THR0-0.062-0.03515.934-0.017-0.0170.0000.0000.0000.000
14A15ASN0-0.022-0.02017.973-0.015-0.0150.0000.0000.0000.000
15A16GLY0-0.013-0.00119.878-0.007-0.0070.0000.0000.0000.000
16A17ILE00.0000.01517.202-0.003-0.0030.0000.0000.0000.000
17A18LYS10.9600.97416.753-0.172-0.1720.0000.0000.0000.000
18A19PRO0-0.0060.00314.116-0.022-0.0220.0000.0000.0000.000
19A20LYS10.8500.93016.216-0.210-0.2100.0000.0000.0000.000
20A21GLN0-0.0060.00016.5150.0640.0640.0000.0000.0000.000
21A22PHE00.0050.00517.337-0.047-0.0470.0000.0000.0000.000
22A23HIS0-0.028-0.02718.9880.0230.0230.0000.0000.0000.000
23A24LYS10.8180.89421.301-0.174-0.1740.0000.0000.0000.000
24A25LYS10.9040.95022.212-0.118-0.1180.0000.0000.0000.000
25A26GLU-1-0.803-0.86522.0050.1740.1740.0000.0000.0000.000
26A27LEU0-0.003-0.01421.9180.0080.0080.0000.0000.0000.000
27A28ILE0-0.027-0.00816.6870.0000.0000.0000.0000.0000.000
28A29PHE00.0200.00618.015-0.004-0.0040.0000.0000.0000.000
29A30ASN0-0.045-0.04522.806-0.004-0.0040.0000.0000.0000.000
30A31GLN00.0500.03625.6970.0000.0000.0000.0000.0000.000
31A32TRP0-0.007-0.01327.976-0.003-0.0030.0000.0000.0000.000
32A33ASP-1-0.875-0.92529.4860.0700.0700.0000.0000.0000.000
33A34PRO0-0.056-0.02026.9280.0060.0060.0000.0000.0000.000
34A35GLN0-0.006-0.00625.318-0.006-0.0060.0000.0000.0000.000
35A36GLU-1-0.883-0.93923.2790.0710.0710.0000.0000.0000.000
36A37TYR0-0.036-0.03319.3280.0060.0060.0000.0000.0000.000
37A38CYS0-0.019-0.01114.281-0.011-0.0110.0000.0000.0000.000
38A39ILE0-0.033-0.00713.7260.0170.0170.0000.0000.0000.000
39A40PHE00.0370.0096.305-0.011-0.0110.0000.0000.0000.000
40A41LEU0-0.019-0.01310.3860.0690.0690.0000.0000.0000.000
41A42TYR0-0.050-0.0576.321-0.264-0.2640.0000.0000.0000.000
42A43ASP-1-0.893-0.9527.1891.5011.5010.0000.0000.0000.000
43A44GLY00.0590.0419.654-0.206-0.2060.0000.0000.0000.000
44A45ILE0-0.080-0.05511.536-0.018-0.0180.0000.0000.0000.000
45A46THR00.0170.00514.186-0.015-0.0150.0000.0000.0000.000
46A47LYS10.8220.91016.173-0.102-0.1020.0000.0000.0000.000
47A48LEU00.0230.02318.2660.0060.0060.0000.0000.0000.000
48A49THR0-0.031-0.02420.029-0.009-0.0090.0000.0000.0000.000
49A50SER00.0530.01723.7970.0010.0010.0000.0000.0000.000
50A51ILE0-0.063-0.02627.027-0.002-0.0020.0000.0000.0000.000
51A52SER00.0120.01630.5940.0000.0000.0000.0000.0000.000
52A53GLU-1-0.872-0.93833.4240.0320.0320.0000.0000.0000.000
53A54ASN0-0.020-0.01336.7780.0010.0010.0000.0000.0000.000
54A55GLY00.0240.01235.166-0.001-0.0010.0000.0000.0000.000
55A56THR0-0.078-0.04333.2600.0020.0020.0000.0000.0000.000
56A57ILE00.0150.01427.5820.0010.0010.0000.0000.0000.000
57A58MET0-0.054-0.01325.313-0.005-0.0050.0000.0000.0000.000
58A59ASN0-0.007-0.02522.4600.0090.0090.0000.0000.0000.000
59A60LEU00.0250.01921.143-0.007-0.0070.0000.0000.0000.000
60A61GLN0-0.0010.00414.450-0.011-0.0110.0000.0000.0000.000
61A62TYR0-0.025-0.01315.6320.0120.0120.0000.0000.0000.000
62A63TYR0-0.023-0.02811.779-0.022-0.0220.0000.0000.0000.000
63A64LYS10.8890.9528.408-0.147-0.1470.0000.0000.0000.000
64A65GLY0-0.0090.0417.976-0.173-0.1730.0000.0000.0000.000
65A66ALA0-0.015-0.0243.8860.0300.2240.000-0.031-0.1630.000
66A67PHE0-0.057-0.0485.698-0.414-0.4140.0000.0000.0000.000
67A68VAL00.0120.0057.9230.0830.0830.0000.0000.0000.000
68A69ILE0-0.034-0.01010.783-0.002-0.0020.0000.0000.0000.000
69A70MET0-0.025-0.00614.4280.0140.0140.0000.0000.0000.000
70A71SER00.0270.00817.291-0.004-0.0040.0000.0000.0000.000
71A72GLY00.0780.00820.487-0.003-0.0030.0000.0000.0000.000
72A73PHE0-0.068-0.02920.9580.0010.0010.0000.0000.0000.000
73A74ILE00.016-0.00118.8590.0030.0030.0000.0000.0000.000
74A75ASP-1-0.893-0.93722.4780.0520.0520.0000.0000.0000.000
75A76THR0-0.007-0.01825.8930.0000.0000.0000.0000.0000.000
76A77GLU-1-0.907-0.94725.1830.0630.0630.0000.0000.0000.000
77A78THR00.0210.02126.2800.0010.0010.0000.0000.0000.000
78A79SER00.0360.02424.9950.0010.0010.0000.0000.0000.000
79A80VAL0-0.067-0.01720.902-0.003-0.0030.0000.0000.0000.000
80A81GLY0-0.013-0.01324.257-0.004-0.0040.0000.0000.0000.000
81A82TYR0-0.035-0.00425.0920.0040.0040.0000.0000.0000.000
82A83TYR0-0.001-0.00622.624-0.004-0.0040.0000.0000.0000.000
83A84ASN0-0.003-0.01223.6150.0050.0050.0000.0000.0000.000
84A85LEU0-0.0220.00315.783-0.006-0.0060.0000.0000.0000.000
85A86GLU-1-0.886-0.95220.2600.1210.1210.0000.0000.0000.000
86A87VAL00.0100.00517.4020.0060.0060.0000.0000.0000.000
87A88ILE0-0.013-0.01518.069-0.017-0.0170.0000.0000.0000.000
88A89SER0-0.034-0.01015.805-0.016-0.0160.0000.0000.0000.000
89A90GLU-1-0.815-0.91318.0440.1800.1800.0000.0000.0000.000
90A91GLN0-0.030-0.01916.902-0.013-0.0130.0000.0000.0000.000
91A92ALA00.0000.00714.1200.0480.0480.0000.0000.0000.000
92A93THR0-0.005-0.00512.173-0.034-0.0340.0000.0000.0000.000
93A94ALA0-0.011-0.01412.0690.0520.0520.0000.0000.0000.000
94A95TYR0-0.043-0.04110.7060.0240.0240.0000.0000.0000.000
95A96VAL00.0060.00414.737-0.025-0.0250.0000.0000.0000.000
96A97ILE0-0.0070.00313.774-0.002-0.0020.0000.0000.0000.000
97A98LYS10.8850.92818.214-0.118-0.1180.0000.0000.0000.000
98A99ILE00.0250.01220.1800.0010.0010.0000.0000.0000.000
99A100ASN00.0210.00921.8480.0030.0030.0000.0000.0000.000
100A101GLU-1-0.829-0.89121.3270.1080.1080.0000.0000.0000.000
101A102LEU0-0.005-0.00515.3950.0010.0010.0000.0000.0000.000
102A103LYS10.9160.94018.901-0.054-0.0540.0000.0000.0000.000
103A104GLU-1-0.832-0.89721.3010.0710.0710.0000.0000.0000.000
104A105LEU0-0.016-0.00517.0620.0010.0010.0000.0000.0000.000
105A106LEU0-0.015-0.00914.1410.0030.0030.0000.0000.0000.000
106A107SER0-0.015-0.00817.259-0.002-0.0020.0000.0000.0000.000
107A108LYS10.7860.90718.679-0.077-0.0770.0000.0000.0000.000
108A109ASN00.0510.04213.706-0.007-0.0070.0000.0000.0000.000
109A110LEU00.0880.03315.7400.0060.0060.0000.0000.0000.000
110A111THR0-0.050-0.04212.0690.0140.0140.0000.0000.0000.000
111A112HIS0-0.019-0.0269.9140.0400.0400.0000.0000.0000.000
112A113PHE00.0370.03611.491-0.003-0.0030.0000.0000.0000.000
113A114PHE00.0340.01012.466-0.001-0.0010.0000.0000.0000.000
114A115TYR0-0.0240.0114.496-0.0710.005-0.001-0.005-0.0700.000
115A116VAL00.0530.0179.128-0.011-0.0110.0000.0000.0000.000
116A117PHE0-0.0060.00410.854-0.013-0.0130.0000.0000.0000.000
117A118GLN0-0.008-0.0088.7550.0110.0110.0000.0000.0000.000
118A119THR0-0.044-0.0366.880-0.030-0.0300.0000.0000.0000.000
119A120LEU00.0770.0409.595-0.031-0.0310.0000.0000.0000.000
120A121GLN00.0110.00813.2150.0070.0070.0000.0000.0000.000
121A122LYS10.8470.9286.713-0.424-0.4240.0000.0000.0000.000
122A123GLN00.0560.03612.274-0.026-0.0260.0000.0000.0000.000
123A124VAL00.0140.01114.314-0.006-0.0060.0000.0000.0000.000
124A125SER0-0.013-0.02414.819-0.010-0.0100.0000.0000.0000.000
125A126TYR0-0.0170.00814.144-0.005-0.0050.0000.0000.0000.000
126A127SER00.016-0.01416.213-0.001-0.0010.0000.0000.0000.000
127A128LEU0-0.0110.00319.349-0.002-0.0020.0000.0000.0000.000
128A129ALA00.0300.01618.738-0.002-0.0020.0000.0000.0000.000
129A130LYS10.9020.95219.336-0.016-0.0160.0000.0000.0000.000
130A131PHE0-0.020-0.01221.2520.0010.0010.0000.0000.0000.000
131A132ASN0-0.052-0.01423.799-0.002-0.0020.0000.0000.0000.000
132A133ASP-1-0.722-0.87522.731-0.030-0.0300.0000.0000.0000.000
133A134PHE0-0.096-0.06522.4950.0010.0010.0000.0000.0000.000
134A135SER0-0.016-0.00726.8880.0030.0030.0000.0000.0000.000
135A136ILE0-0.0420.00329.4200.0010.0010.0000.0000.0000.000
136A137ASN00.0200.00329.5340.0000.0000.0000.0000.0000.000
137A138GLY00.0350.02732.1010.0010.0010.0000.0000.0000.000
138A139LYS10.8550.91530.631-0.014-0.0140.0000.0000.0000.000
139A140LEU00.0240.01430.3030.0010.0010.0000.0000.0000.000
140A141GLY00.0880.03328.859-0.002-0.0020.0000.0000.0000.000
141A142SER00.0100.01226.431-0.001-0.0010.0000.0000.0000.000
142A143ILE0-0.050-0.02225.4420.0010.0010.0000.0000.0000.000
143A144CYS0-0.049-0.02325.355-0.001-0.0010.0000.0000.0000.000
144A145GLY00.0840.03922.940-0.005-0.0050.0000.0000.0000.000
145A146GLN00.017-0.00218.817-0.003-0.0030.0000.0000.0000.000
146A147LEU00.005-0.01020.5140.0010.0010.0000.0000.0000.000
147A148LEU0-0.0060.02518.738-0.003-0.0030.0000.0000.0000.000
148A149ILE0-0.012-0.01015.554-0.013-0.0130.0000.0000.0000.000
149A150LEU0-0.057-0.03015.967-0.009-0.0090.0000.0000.0000.000
150A151THR0-0.024-0.03316.5390.0070.0070.0000.0000.0000.000
151A152TYR0-0.036-0.02513.666-0.016-0.0160.0000.0000.0000.000
152A153VAL0-0.055-0.01610.794-0.036-0.0360.0000.0000.0000.000
153A154TYR0-0.022-0.03911.8820.0470.0470.0000.0000.0000.000
154A155GLY00.0340.04114.5640.0200.0200.0000.0000.0000.000
155A156LYS10.8990.94213.545-0.136-0.1360.0000.0000.0000.000
156A157GLU-1-0.883-0.94017.001-0.137-0.1370.0000.0000.0000.000
157A158THR0-0.070-0.04319.8400.0120.0120.0000.0000.0000.000
158A159PRO00.001-0.00222.942-0.003-0.0030.0000.0000.0000.000
159A160ASP-1-0.841-0.89926.581-0.027-0.0270.0000.0000.0000.000
160A161GLY0-0.025-0.03325.3870.0070.0070.0000.0000.0000.000
161A162ILE00.0140.01618.950-0.002-0.0020.0000.0000.0000.000
162A163LYS10.9520.98220.3820.0010.0010.0000.0000.0000.000
163A164ILE00.0320.01118.785-0.001-0.0010.0000.0000.0000.000
164A165THR0-0.073-0.04516.5080.0090.0090.0000.0000.0000.000
165A166LEU0-0.020-0.01917.1180.0280.0280.0000.0000.0000.000
166A167ASP-1-0.889-0.92920.0530.1110.1110.0000.0000.0000.000
167A168ASN00.0380.01622.789-0.022-0.0220.0000.0000.0000.000
168A169LEU00.0080.00121.6900.0000.0000.0000.0000.0000.000
169A170THR00.0270.01224.841-0.011-0.0110.0000.0000.0000.000
170A171MET00.018-0.00327.981-0.003-0.0030.0000.0000.0000.000
171A172GLN0-0.011-0.01030.157-0.005-0.0050.0000.0000.0000.000
172A173GLU-1-0.776-0.86824.8730.0690.0690.0000.0000.0000.000
173A174LEU00.0050.00724.180-0.002-0.0020.0000.0000.0000.000
174A175GLY0-0.003-0.00926.480-0.004-0.0040.0000.0000.0000.000
175A176TYR00.0780.03826.523-0.002-0.0020.0000.0000.0000.000
176A177SER0-0.029-0.00122.9510.0020.0020.0000.0000.0000.000
177A178SER00.0030.00424.745-0.004-0.0040.0000.0000.0000.000
178A179GLY00.0690.04927.320-0.003-0.0030.0000.0000.0000.000
179A180ILE0-0.129-0.06730.082-0.002-0.0020.0000.0000.0000.000
180A181ALA00.0760.03632.0120.0020.0020.0000.0000.0000.000
181A182HIS00.0410.02834.5060.0030.0030.0000.0000.0000.000
182A183SER00.0800.01933.627-0.003-0.0030.0000.0000.0000.000
183A184SER0-0.014-0.00634.795-0.002-0.0020.0000.0000.0000.000
184A185ALA0-0.016-0.01135.758-0.003-0.0030.0000.0000.0000.000
185A186VAL00.0360.02330.093-0.003-0.0030.0000.0000.0000.000
186A187SER00.0370.02033.115-0.003-0.0030.0000.0000.0000.000
187A188ARG10.9730.98834.895-0.010-0.0100.0000.0000.0000.000
188A189ILE00.0040.00531.711-0.003-0.0030.0000.0000.0000.000
189A190ILE00.0490.02028.784-0.003-0.0030.0000.0000.0000.000
190A191SER0-0.039-0.03132.645-0.002-0.0020.0000.0000.0000.000
191A192LYS10.8840.95835.4230.0110.0110.0000.0000.0000.000
192A193LEU00.0270.00929.068-0.002-0.0020.0000.0000.0000.000
193A194LYS10.9040.95332.530-0.007-0.0070.0000.0000.0000.000
194A195GLN0-0.030-0.00933.879-0.003-0.0030.0000.0000.0000.000
195A196GLU-1-0.832-0.89934.413-0.019-0.0190.0000.0000.0000.000
196A197LYS10.8790.94333.5110.0160.0160.0000.0000.0000.000
197A198VAL00.0070.02028.019-0.004-0.0040.0000.0000.0000.000
198A199ILE0-0.002-0.00926.618-0.004-0.0040.0000.0000.0000.000
199A200VAL0-0.017-0.01128.4730.0020.0020.0000.0000.0000.000
200A201TYR0-0.033-0.02427.8450.0010.0010.0000.0000.0000.000
201A202LYS10.8950.95428.8330.0130.0130.0000.0000.0000.000
202A203ASN00.025-0.00128.330-0.001-0.0010.0000.0000.0000.000
203A204SER00.0130.01128.4470.0040.0040.0000.0000.0000.000
204A205CYS00.0020.02523.2810.0040.0040.0000.0000.0000.000
205A206PHE00.017-0.00623.876-0.009-0.0090.0000.0000.0000.000
206A207TYR0-0.027-0.00223.5350.0000.0000.0000.0000.0000.000
207A208VAL00.0120.00022.6640.0020.0020.0000.0000.0000.000
208A209GLN00.000-0.01024.425-0.003-0.0030.0000.0000.0000.000
209A210ASN0-0.0030.00926.921-0.008-0.0080.0000.0000.0000.000
210A211LEU00.0770.03419.6860.0080.0080.0000.0000.0000.000
211A212ASP-1-0.781-0.90324.125-0.084-0.0840.0000.0000.0000.000
212A213TYR0-0.114-0.09226.1810.0050.0050.0000.0000.0000.000
213A214LEU0-0.025-0.02323.1530.0050.0050.0000.0000.0000.000
214A215LYS10.9000.96320.8930.1140.1140.0000.0000.0000.000
215A216ARG10.8860.96124.5690.0470.0470.0000.0000.0000.000
216A217TYR0-0.049-0.02627.3970.0040.0040.0000.0000.0000.000
217A218ALA0-0.020-0.00122.3900.0060.0060.0000.0000.0000.000
218A219PRO00.0200.01922.531-0.008-0.0080.0000.0000.0000.000
219A220LYS10.8220.88921.7990.0240.0240.0000.0000.0000.000
220A221LEU0-0.038-0.02117.968-0.003-0.0030.0000.0000.0000.000
221A222ASP-1-0.777-0.87017.414-0.120-0.1200.0000.0000.0000.000
222A223GLU-1-0.789-0.87217.771-0.052-0.0520.0000.0000.0000.000
223A224TRP0-0.015-0.01210.833-0.012-0.0120.0000.0000.0000.000
224A225PHE0-0.018-0.01712.1220.0040.0040.0000.0000.0000.000
225A226TYR0-0.0120.00612.780-0.022-0.0220.0000.0000.0000.000
226A227LEU0-0.0030.00114.002-0.012-0.0120.0000.0000.0000.000
227A228ALA0-0.0120.00511.0730.0360.0360.0000.0000.0000.000
228A229CYS0-0.105-0.0458.5320.0730.0730.0000.0000.0000.000
229A230PRO00.1280.0639.178-0.076-0.0760.0000.0000.0000.000
230A231ALA0-0.021-0.0117.102-0.067-0.0670.0000.0000.0000.000
231A232THR0-0.057-0.0478.530-0.047-0.0470.0000.0000.0000.000
232A233TRP00.0310.01410.1090.0370.0370.0000.0000.0000.000
233A234GLY00.0290.01312.6250.0330.0330.0000.0000.0000.000
234A235LYS10.8790.9398.0180.6120.6120.0000.0000.0000.000
235A236LEU0-0.0120.00513.9600.0360.0360.0000.0000.0000.000
236A237ASN0-0.038-0.00616.9220.0560.0560.0000.0000.0000.000