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

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FMODB ID: 3JQ9L

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 OptAll
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 -3068931.627884
FMO2-HF: Nuclear repulsion 2974311.032057
FMO2-HF: Total energy -94620.595826
FMO2-MP2: Total energy -94898.5899


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.
-0.443.0750.083-1.156-2.4410
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 : 0.024 / q_NPA : -0.005
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].
3A4GLN00.0280.0063.864-1.5020.2940.000-0.730-1.0660.002
4A5ALA00.0090.0083.059-0.7200.1750.083-0.308-0.669-0.002
5A6GLU-1-0.782-0.8884.4592.5833.102-0.001-0.070-0.4480.000
6A7GLU-1-0.846-0.8976.3340.2370.2370.0000.0000.0000.000
7A8PHE0-0.001-0.0047.584-0.013-0.0130.0000.0000.0000.000
8A9LYS10.8530.9238.221-1.077-1.0770.0000.0000.0000.000
9A10LYS10.8340.9028.997-0.616-0.6160.0000.0000.0000.000
10A11TYR0-0.052-0.03312.093-0.063-0.0630.0000.0000.0000.000
11A12LEU0-0.009-0.01011.682-0.035-0.0350.0000.0000.0000.000
12A13GLU-1-0.820-0.88513.1530.6670.6670.0000.0000.0000.000
13A14THR0-0.082-0.03816.007-0.035-0.0350.0000.0000.0000.000
14A15ASN0-0.033-0.01917.762-0.026-0.0260.0000.0000.0000.000
15A16GLY00.0040.00819.514-0.015-0.0150.0000.0000.0000.000
16A17ILE0-0.0190.00217.1400.0010.0010.0000.0000.0000.000
17A18LYS10.9620.97016.430-0.205-0.2050.0000.0000.0000.000
18A19PRO0-0.0110.00013.876-0.028-0.0280.0000.0000.0000.000
19A20LYS10.8040.88815.958-0.267-0.2670.0000.0000.0000.000
20A21GLN00.0210.02416.1600.0790.0790.0000.0000.0000.000
21A22PHE00.0050.00817.164-0.051-0.0510.0000.0000.0000.000
22A23HIS0-0.032-0.03418.9720.0200.0200.0000.0000.0000.000
23A24LYS10.7880.87521.193-0.156-0.1560.0000.0000.0000.000
24A25LYS10.8490.91022.336-0.113-0.1130.0000.0000.0000.000
25A26GLU-1-0.798-0.85521.8350.1980.1980.0000.0000.0000.000
26A27LEU0-0.016-0.01722.0770.0050.0050.0000.0000.0000.000
27A28ILE0-0.035-0.02016.4400.0030.0030.0000.0000.0000.000
28A29PHE00.0170.00418.084-0.001-0.0010.0000.0000.0000.000
29A30ASN0-0.054-0.05722.936-0.006-0.0060.0000.0000.0000.000
30A31GLN00.0540.03325.8720.0010.0010.0000.0000.0000.000
31A32TRP0-0.028-0.02228.145-0.004-0.0040.0000.0000.0000.000
32A33ASP-1-0.857-0.90329.2100.0820.0820.0000.0000.0000.000
33A34PRO0-0.034-0.00526.8210.0080.0080.0000.0000.0000.000
34A35GLN0-0.014-0.02125.640-0.007-0.0070.0000.0000.0000.000
35A36GLU-1-0.833-0.91323.4780.0930.0930.0000.0000.0000.000
36A37TYR0-0.0030.00119.4490.0080.0080.0000.0000.0000.000
37A38CYS0-0.020-0.00614.407-0.014-0.0140.0000.0000.0000.000
38A39ILE0-0.0280.00113.9190.0220.0220.0000.0000.0000.000
39A40PHE00.0160.0006.368-0.006-0.0060.0000.0000.0000.000
40A41LEU00.0000.00810.5910.0760.0760.0000.0000.0000.000
41A42TYR0-0.031-0.0416.219-0.260-0.2600.0000.0000.0000.000
42A43ASP-1-0.846-0.9357.1201.4931.4930.0000.0000.0000.000
43A44GLY00.0180.0179.692-0.213-0.2130.0000.0000.0000.000
44A45ILE0-0.073-0.05211.752-0.013-0.0130.0000.0000.0000.000
45A46THR00.0210.00714.464-0.010-0.0100.0000.0000.0000.000
46A47LYS10.8050.89416.485-0.102-0.1020.0000.0000.0000.000
47A48LEU00.0240.03118.2690.0080.0080.0000.0000.0000.000
48A49THR0-0.040-0.03320.020-0.011-0.0110.0000.0000.0000.000
49A50SER00.0660.02923.8490.0030.0030.0000.0000.0000.000
50A51ILE0-0.072-0.03327.228-0.004-0.0040.0000.0000.0000.000
51A52SER00.0070.00830.8260.0010.0010.0000.0000.0000.000
52A53GLU-1-0.790-0.89433.9100.0350.0350.0000.0000.0000.000
53A54ASN0-0.061-0.01737.2040.0010.0010.0000.0000.0000.000
54A55GLY00.0160.00635.523-0.001-0.0010.0000.0000.0000.000
55A56THR0-0.081-0.05133.8170.0020.0020.0000.0000.0000.000
56A57ILE00.0060.00727.9930.0020.0020.0000.0000.0000.000
57A58MET0-0.053-0.01525.354-0.006-0.0060.0000.0000.0000.000
58A59ASN0-0.003-0.02422.3820.0110.0110.0000.0000.0000.000
59A60LEU00.0160.01221.241-0.008-0.0080.0000.0000.0000.000
60A61GLN00.0090.01014.701-0.012-0.0120.0000.0000.0000.000
61A62TYR0-0.021-0.02215.7990.0130.0130.0000.0000.0000.000
62A63TYR0-0.030-0.02411.948-0.022-0.0220.0000.0000.0000.000
63A64LYS10.8830.9409.200-0.050-0.0500.0000.0000.0000.000
64A65GLY00.0090.0477.863-0.145-0.1450.0000.0000.0000.000
65A66ALA0-0.050-0.0283.752-0.1580.0840.002-0.044-0.2000.000
66A67PHE0-0.052-0.0475.298-0.633-0.6330.0000.0000.0000.000
67A68VAL00.0170.0037.7990.1150.1150.0000.0000.0000.000
68A69ILE0-0.038-0.01710.651-0.014-0.0140.0000.0000.0000.000
69A70MET0-0.017-0.00214.3380.0200.0200.0000.0000.0000.000
70A71SER00.000-0.00717.163-0.007-0.0070.0000.0000.0000.000
71A72GLY00.0730.02020.633-0.007-0.0070.0000.0000.0000.000
72A73PHE0-0.026-0.01321.0820.0040.0040.0000.0000.0000.000
73A74ILE0-0.003-0.01118.6440.0020.0020.0000.0000.0000.000
74A75ASP-1-0.877-0.92922.2450.0750.0750.0000.0000.0000.000
75A76THR0-0.024-0.02225.734-0.002-0.0020.0000.0000.0000.000
76A77GLU-1-0.876-0.91625.4520.0860.0860.0000.0000.0000.000
77A78THR00.0270.00526.369-0.001-0.0010.0000.0000.0000.000
78A79SER0-0.016-0.01125.0900.0010.0010.0000.0000.0000.000
79A80VAL0-0.077-0.03121.001-0.005-0.0050.0000.0000.0000.000
80A81GLY0-0.022-0.01024.332-0.006-0.0060.0000.0000.0000.000
81A82TYR0-0.032-0.00425.6150.0040.0040.0000.0000.0000.000
82A83TYR00.002-0.00722.966-0.005-0.0050.0000.0000.0000.000
83A84ASN0-0.011-0.01423.6370.0060.0060.0000.0000.0000.000
84A85LEU0-0.0230.00115.874-0.007-0.0070.0000.0000.0000.000
85A86GLU-1-0.813-0.90120.3890.1180.1180.0000.0000.0000.000
86A87VAL00.0210.00517.3960.0040.0040.0000.0000.0000.000
87A88ILE0-0.038-0.02918.346-0.021-0.0210.0000.0000.0000.000
88A89SER0-0.016-0.01416.023-0.021-0.0210.0000.0000.0000.000
89A90GLU-1-0.814-0.91518.1820.1670.1670.0000.0000.0000.000
90A91GLN0-0.019-0.00716.9520.0040.0040.0000.0000.0000.000
91A92ALA00.0010.02614.2730.0200.0200.0000.0000.0000.000
92A93THR0-0.007-0.01012.035-0.027-0.0270.0000.0000.0000.000
93A94ALA0-0.018-0.01211.8690.0880.0880.0000.0000.0000.000
94A95TYR0-0.033-0.04210.6160.0180.0180.0000.0000.0000.000
95A96VAL0-0.002-0.00514.642-0.025-0.0250.0000.0000.0000.000
96A97ILE00.0010.01313.975-0.007-0.0070.0000.0000.0000.000
97A98LYS10.8770.92418.281-0.160-0.1600.0000.0000.0000.000
98A99ILE0-0.010-0.00120.4640.0020.0020.0000.0000.0000.000
99A100ASN00.013-0.01022.0290.0070.0070.0000.0000.0000.000
100A101GLU-1-0.811-0.88521.2230.1510.1510.0000.0000.0000.000
101A102LEU0-0.002-0.01115.3590.0040.0040.0000.0000.0000.000
102A103LYS10.9110.94818.837-0.076-0.0760.0000.0000.0000.000
103A104GLU-1-0.840-0.88921.3750.1020.1020.0000.0000.0000.000
104A105LEU0-0.006-0.00417.1850.0020.0020.0000.0000.0000.000
105A106LEU0-0.0040.00414.0410.0070.0070.0000.0000.0000.000
106A107SER0-0.033-0.02917.090-0.002-0.0020.0000.0000.0000.000
107A108LYS10.8070.90918.715-0.116-0.1160.0000.0000.0000.000
108A109ASN00.0360.03613.536-0.015-0.0150.0000.0000.0000.000
109A110LEU00.0820.03515.2320.0130.0130.0000.0000.0000.000
110A111THR0-0.035-0.03011.9960.0160.0160.0000.0000.0000.000
111A112HIS0-0.036-0.02710.4630.0440.0440.0000.0000.0000.000
112A113PHE00.0380.02711.645-0.004-0.0040.0000.0000.0000.000
113A114PHE00.006-0.00812.241-0.006-0.0060.0000.0000.0000.000
114A115TYR0-0.0180.0094.4750.0100.073-0.001-0.004-0.0580.000
115A116VAL00.0520.0309.007-0.030-0.0300.0000.0000.0000.000
116A117PHE0-0.0050.00511.184-0.016-0.0160.0000.0000.0000.000
117A118GLN00.0120.0008.6980.0120.0120.0000.0000.0000.000
118A119THR0-0.035-0.0317.075-0.022-0.0220.0000.0000.0000.000
119A120LEU00.0520.0239.600-0.026-0.0260.0000.0000.0000.000
120A121GLN00.0140.00513.0750.0110.0110.0000.0000.0000.000
121A122LYS10.8550.9396.914-0.400-0.4000.0000.0000.0000.000
122A123GLN00.0680.04412.367-0.026-0.0260.0000.0000.0000.000
123A124VAL00.0120.01614.363-0.007-0.0070.0000.0000.0000.000
124A125SER0-0.005-0.02314.945-0.012-0.0120.0000.0000.0000.000
125A126TYR0-0.0130.00514.263-0.006-0.0060.0000.0000.0000.000
126A127SER0-0.007-0.02816.330-0.002-0.0020.0000.0000.0000.000
127A128LEU0-0.021-0.01119.411-0.002-0.0020.0000.0000.0000.000
128A129ALA00.0030.00518.564-0.003-0.0030.0000.0000.0000.000
129A130LYS10.8480.91419.619-0.016-0.0160.0000.0000.0000.000
130A131PHE0-0.0050.00121.3820.0000.0000.0000.0000.0000.000
131A132ASN0-0.0180.00224.051-0.004-0.0040.0000.0000.0000.000
132A133ASP-1-0.717-0.86422.657-0.035-0.0350.0000.0000.0000.000
133A134PHE0-0.067-0.04122.6310.0010.0010.0000.0000.0000.000
134A135SER0-0.035-0.01627.0540.0030.0030.0000.0000.0000.000
135A136ILE0-0.040-0.00729.4210.0010.0010.0000.0000.0000.000
136A137ASN00.0170.01528.9800.0010.0010.0000.0000.0000.000
137A138GLY00.0550.03731.7860.0000.0000.0000.0000.0000.000
138A139LYS10.8390.90630.399-0.012-0.0120.0000.0000.0000.000
139A140LEU00.0140.01530.3390.0010.0010.0000.0000.0000.000
140A141GLY00.1050.03728.583-0.003-0.0030.0000.0000.0000.000
141A142SER0-0.038-0.02226.278-0.002-0.0020.0000.0000.0000.000
142A143ILE0-0.036-0.01325.3640.0000.0000.0000.0000.0000.000
143A144CYS0-0.057-0.02925.381-0.003-0.0030.0000.0000.0000.000
144A145GLY00.0950.03522.748-0.008-0.0080.0000.0000.0000.000
145A146GLN00.0140.00418.960-0.001-0.0010.0000.0000.0000.000
146A147LEU00.013-0.00320.572-0.001-0.0010.0000.0000.0000.000
147A148LEU00.0010.02918.571-0.008-0.0080.0000.0000.0000.000
148A149ILE0-0.015-0.01115.702-0.016-0.0160.0000.0000.0000.000
149A150LEU0-0.048-0.02315.876-0.013-0.0130.0000.0000.0000.000
150A151THR0-0.015-0.03116.9640.0030.0030.0000.0000.0000.000
151A152TYR0-0.041-0.03013.710-0.024-0.0240.0000.0000.0000.000
152A153VAL0-0.035-0.01010.971-0.046-0.0460.0000.0000.0000.000
153A154TYR0-0.009-0.02412.1660.0340.0340.0000.0000.0000.000
154A155GLY00.0080.02614.8180.0210.0210.0000.0000.0000.000
155A156LYS10.9080.95313.986-0.038-0.0380.0000.0000.0000.000
156A157GLU-1-0.879-0.93917.297-0.168-0.1680.0000.0000.0000.000
157A158THR0-0.075-0.04920.0070.0090.0090.0000.0000.0000.000
158A159PRO00.018-0.00723.0730.0000.0000.0000.0000.0000.000
159A160ASP-1-0.820-0.88626.298-0.042-0.0420.0000.0000.0000.000
160A161GLY00.0040.00525.4980.0110.0110.0000.0000.0000.000
161A162ILE00.0000.00919.262-0.003-0.0030.0000.0000.0000.000
162A163LYS10.9220.97120.7560.0490.0490.0000.0000.0000.000
163A164ILE00.0240.00418.927-0.007-0.0070.0000.0000.0000.000
164A165THR0-0.076-0.04816.6720.0110.0110.0000.0000.0000.000
165A166LEU0-0.014-0.01417.1260.0240.0240.0000.0000.0000.000
166A167ASP-1-0.829-0.89820.1600.0900.0900.0000.0000.0000.000
167A168ASN00.0070.00323.113-0.022-0.0220.0000.0000.0000.000
168A169LEU0-0.020-0.00221.7210.0000.0000.0000.0000.0000.000
169A170THR00.0350.01124.780-0.011-0.0110.0000.0000.0000.000
170A171MET00.006-0.01127.875-0.002-0.0020.0000.0000.0000.000
171A172GLN00.0120.01030.249-0.005-0.0050.0000.0000.0000.000
172A173GLU-1-0.728-0.83024.8700.0660.0660.0000.0000.0000.000
173A174LEU00.0010.01824.307-0.002-0.0020.0000.0000.0000.000
174A175GLY00.0240.02226.561-0.004-0.0040.0000.0000.0000.000
175A176TYR00.0550.02226.685-0.004-0.0040.0000.0000.0000.000
176A177SER0-0.031-0.01022.9940.0030.0030.0000.0000.0000.000
177A178SER0-0.011-0.02724.462-0.005-0.0050.0000.0000.0000.000
178A179GLY00.0690.05527.255-0.003-0.0030.0000.0000.0000.000
179A180ILE0-0.111-0.06230.042-0.003-0.0030.0000.0000.0000.000
180A181ALA00.0680.02832.2630.0020.0020.0000.0000.0000.000
181A182HIS00.0420.03834.5050.0020.0020.0000.0000.0000.000
182A183SER00.0650.01133.195-0.004-0.0040.0000.0000.0000.000
183A184SER00.0020.00434.405-0.003-0.0030.0000.0000.0000.000
184A185ALA0-0.001-0.00535.877-0.003-0.0030.0000.0000.0000.000
185A186VAL00.0230.01629.986-0.003-0.0030.0000.0000.0000.000
186A187SER00.0330.01633.081-0.004-0.0040.0000.0000.0000.000
187A188ARG10.9650.99634.807-0.005-0.0050.0000.0000.0000.000
188A189ILE0-0.0030.00431.489-0.003-0.0030.0000.0000.0000.000
189A190ILE00.0360.00928.589-0.004-0.0040.0000.0000.0000.000
190A191SER0-0.019-0.02832.437-0.003-0.0030.0000.0000.0000.000
191A192LYS10.8690.95435.1080.0190.0190.0000.0000.0000.000
192A193LEU00.0160.00729.060-0.002-0.0020.0000.0000.0000.000
193A194LYS10.9260.96432.6610.0040.0040.0000.0000.0000.000
194A195GLN0-0.040-0.01034.109-0.004-0.0040.0000.0000.0000.000
195A196GLU-1-0.793-0.88334.593-0.028-0.0280.0000.0000.0000.000
196A197LYS10.8680.93133.4850.0270.0270.0000.0000.0000.000
197A198VAL0-0.0030.01128.109-0.005-0.0050.0000.0000.0000.000
198A199ILE00.005-0.00326.727-0.006-0.0060.0000.0000.0000.000
199A200VAL0-0.010-0.00228.5350.0040.0040.0000.0000.0000.000
200A201TYR0-0.049-0.03127.8780.0000.0000.0000.0000.0000.000
201A202LYS10.8460.91928.9410.0390.0390.0000.0000.0000.000
202A203ASN00.015-0.00628.550-0.001-0.0010.0000.0000.0000.000
203A204SER00.0210.01328.6660.0030.0030.0000.0000.0000.000
204A205CYS0-0.0040.03023.0570.0010.0010.0000.0000.0000.000
205A206PHE00.027-0.00624.101-0.007-0.0070.0000.0000.0000.000
206A207TYR0-0.0060.00023.678-0.006-0.0060.0000.0000.0000.000
207A208VAL00.0080.00622.7980.0040.0040.0000.0000.0000.000
208A209GLN0-0.003-0.01624.977-0.003-0.0030.0000.0000.0000.000
209A210ASN00.0090.01427.327-0.008-0.0080.0000.0000.0000.000
210A211LEU00.0780.03319.9210.0090.0090.0000.0000.0000.000
211A212ASP-1-0.772-0.89224.437-0.099-0.0990.0000.0000.0000.000
212A213TYR0-0.118-0.09826.2720.0070.0070.0000.0000.0000.000
213A214LEU0-0.033-0.02023.4150.0060.0060.0000.0000.0000.000
214A215LYS10.8560.92620.9640.1330.1330.0000.0000.0000.000
215A216ARG10.8940.96024.4930.0610.0610.0000.0000.0000.000
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