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: V5LJ1

Calculation Name: 5LSJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q03188

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptH
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 199
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1445391.580208
FMO2-HF: Nuclear repulsion 1362200.863124
FMO2-HF: Total energy -83190.717083
FMO2-MP2: Total energy -83429.005106


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:SER)


Summations of interaction energy for fragment #1(A:2: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.
-3.063-1.170.001-0.899-0.9950.003
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.002
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].
3A4ASP-1-0.785-0.9023.826-4.375-2.4820.001-0.899-0.9950.003
4A5PRO0-0.056-0.0295.5560.8530.8530.0000.0000.0000.000
5A6MET0-0.068-0.0158.4230.3970.3970.0000.0000.0000.000
6A7THR0-0.021-0.01710.8050.2200.2200.0000.0000.0000.000
7A8TYR00.0370.01113.4050.0970.0970.0000.0000.0000.000
8A9GLU-1-0.790-0.88612.662-0.736-0.7360.0000.0000.0000.000
9A10ALA0-0.060-0.02915.2040.1010.1010.0000.0000.0000.000
10A11GLN0-0.059-0.02817.127-0.044-0.0440.0000.0000.0000.000
11A12PHE0-0.008-0.00419.5400.0370.0370.0000.0000.0000.000
12A13PHE0-0.041-0.01617.7420.0390.0390.0000.0000.0000.000
13A14GLY00.0170.01119.8640.0260.0260.0000.0000.0000.000
14A15PHE0-0.071-0.04418.2940.0220.0220.0000.0000.0000.000
15A16THR00.0160.02112.823-0.011-0.0110.0000.0000.0000.000
16A17PRO00.0570.02112.0430.0840.0840.0000.0000.0000.000
17A18GLN00.1010.0348.4790.2010.2010.0000.0000.0000.000
18A19THR00.0310.01112.7830.0810.0810.0000.0000.0000.000
19A20CYS0-0.071-0.02315.6820.0510.0510.0000.0000.0000.000
20A21MET00.0550.02914.0700.0390.0390.0000.0000.0000.000
21A22LEU00.0230.02515.0000.0380.0380.0000.0000.0000.000
22A23ARG10.9280.95016.7460.1010.1010.0000.0000.0000.000
23A24ILE00.006-0.00119.4460.0110.0110.0000.0000.0000.000
24A25TYR0-0.041-0.00817.5530.0080.0080.0000.0000.0000.000
25A26ILE0-0.029-0.02519.6750.0090.0090.0000.0000.0000.000
26A27ALA00.0260.02921.8820.0010.0010.0000.0000.0000.000
27A28PHE0-0.006-0.01522.5690.0000.0000.0000.0000.0000.000
28A29GLN00.0110.00322.0800.0190.0190.0000.0000.0000.000
29A30ASP-1-0.873-0.93724.4170.0710.0710.0000.0000.0000.000
30A31TYR0-0.0070.00027.288-0.005-0.0050.0000.0000.0000.000
31A32LEU0-0.037-0.01026.100-0.001-0.0010.0000.0000.0000.000
32A33PHE0-0.020-0.03525.4460.0030.0030.0000.0000.0000.000
33A34GLU-1-0.916-0.94530.1830.0330.0330.0000.0000.0000.000
34A35VAL0-0.020-0.01331.850-0.002-0.0020.0000.0000.0000.000
35A36MET0-0.024-0.01431.3590.0010.0010.0000.0000.0000.000
36A37GLN00.0210.00534.1760.0040.0040.0000.0000.0000.000
37A38ALA0-0.034-0.00536.071-0.003-0.0030.0000.0000.0000.000
38A39VAL00.003-0.00936.677-0.002-0.0020.0000.0000.0000.000
39A40GLU-1-0.826-0.91737.9310.0660.0660.0000.0000.0000.000
40A41GLN0-0.026-0.03139.773-0.005-0.0050.0000.0000.0000.000
41A42VAL0-0.0180.00441.884-0.003-0.0030.0000.0000.0000.000
42A43ILE0-0.029-0.01840.896-0.002-0.0020.0000.0000.0000.000
43A44LEU00.0130.00343.161-0.001-0.0010.0000.0000.0000.000
44A45LYS10.9160.97045.307-0.042-0.0420.0000.0000.0000.000
45A46LYS10.9330.95947.803-0.033-0.0330.0000.0000.0000.000
46A47LEU0-0.048-0.01646.322-0.001-0.0010.0000.0000.0000.000
47A48ASP-1-0.835-0.91849.4930.0360.0360.0000.0000.0000.000
48A49GLY0-0.158-0.05352.189-0.002-0.0020.0000.0000.0000.000
49A50ILE0-0.061-0.02052.568-0.001-0.0010.0000.0000.0000.000
50A51PRO0-0.037-0.02655.2660.0000.0000.0000.0000.0000.000
51A52ASP-1-0.936-0.96157.7540.0330.0330.0000.0000.0000.000
52A53CYS0-0.081-0.04355.6140.0010.0010.0000.0000.0000.000
53A54ASP-1-0.821-0.92052.1020.0410.0410.0000.0000.0000.000
54A55ILE0-0.058-0.02647.2560.0020.0020.0000.0000.0000.000
55A56SER0-0.025-0.00146.3820.0010.0010.0000.0000.0000.000
56A57PRO00.1120.02344.8600.0020.0020.0000.0000.0000.000
57A58VAL00.003-0.00441.2800.0030.0030.0000.0000.0000.000
58A59GLN0-0.004-0.00240.8700.0030.0030.0000.0000.0000.000
59A60ILE00.0660.02740.5920.0030.0030.0000.0000.0000.000
60A61ARG10.8700.96935.752-0.074-0.0740.0000.0000.0000.000
61A62LYS10.9120.94034.976-0.094-0.0940.0000.0000.0000.000
62A63CYM-1-0.936-0.95135.7970.0780.0780.0000.0000.0000.000
63A64THR00.0540.01034.3050.0030.0030.0000.0000.0000.000
64A65GLU-1-0.917-0.96232.3680.1060.1060.0000.0000.0000.000
65A66LYS10.9460.98831.204-0.086-0.0860.0000.0000.0000.000
66A67PHE0-0.010-0.01531.1450.0070.0070.0000.0000.0000.000
67A68LEU00.0660.01828.4540.0030.0030.0000.0000.0000.000
68A69CYS0-0.045-0.01626.9720.0110.0110.0000.0000.0000.000
69A70PHE0-0.045-0.01826.1210.0130.0130.0000.0000.0000.000
70A71MET0-0.019-0.01326.3020.0050.0050.0000.0000.0000.000
71A72LYS10.9100.96121.027-0.170-0.1700.0000.0000.0000.000
72A73GLY00.0120.02121.9930.0150.0150.0000.0000.0000.000
73A74HIS0-0.020-0.01921.4110.0070.0070.0000.0000.0000.000
74A75PHE0-0.0100.00121.062-0.001-0.0010.0000.0000.0000.000
75A76ASP-1-0.828-0.92017.4890.2200.2200.0000.0000.0000.000
76A77ASN0-0.014-0.01117.341-0.017-0.0170.0000.0000.0000.000
77A78LEU0-0.029-0.03217.610-0.002-0.0020.0000.0000.0000.000
78A79PHE00.0160.02016.211-0.021-0.0210.0000.0000.0000.000
79A80SER00.0380.02513.529-0.001-0.0010.0000.0000.0000.000
80A81LYS10.8850.95114.270-0.169-0.1690.0000.0000.0000.000
81A82MET0-0.027-0.00615.852-0.039-0.0390.0000.0000.0000.000
82A83GLU-1-0.871-0.94311.542-0.017-0.0170.0000.0000.0000.000
83A84GLN00.006-0.00510.642-0.041-0.0410.0000.0000.0000.000
84A85LEU0-0.028-0.02412.658-0.056-0.0560.0000.0000.0000.000
85A86PHE0-0.037-0.02615.732-0.032-0.0320.0000.0000.0000.000
86A87LEU0-0.007-0.0079.675-0.045-0.0450.0000.0000.0000.000
87A88GLN0-0.072-0.02311.477-0.063-0.0630.0000.0000.0000.000
88A89LEU0-0.021-0.02013.839-0.027-0.0270.0000.0000.0000.000
89A90ILE0-0.047-0.01516.6870.0150.0150.0000.0000.0000.000
90A91LEU0-0.045-0.02615.466-0.026-0.0260.0000.0000.0000.000
91A92ARG10.9520.9778.8500.7720.7720.0000.0000.0000.000
92A93ILE00.0000.02315.2480.0670.0670.0000.0000.0000.000
93A94PRO00.006-0.00315.310-0.066-0.0660.0000.0000.0000.000
94A95SER0-0.069-0.02613.749-0.015-0.0150.0000.0000.0000.000
95A96ASN0-0.008-0.02115.8340.0130.0130.0000.0000.0000.000
96A97ILE0-0.041-0.00919.2120.0270.0270.0000.0000.0000.000
97A98LEU00.0360.02719.726-0.038-0.0380.0000.0000.0000.000
98A99LEU0-0.0030.00320.1590.0360.0360.0000.0000.0000.000
99A100PRO0-0.004-0.01823.3640.0090.0090.0000.0000.0000.000
100A101GLU-1-0.885-0.93323.332-0.267-0.2670.0000.0000.0000.000
101A102ASP-1-0.883-0.97222.234-0.316-0.3160.0000.0000.0000.000
102A103LYS11.0571.03524.8960.1680.1680.0000.0000.0000.000
103A104CYS0-0.071-0.03427.526-0.002-0.0020.0000.0000.0000.000
104A105LYS10.8970.94523.6310.2800.2800.0000.0000.0000.000
105A106GLU-1-0.911-0.94624.556-0.216-0.2160.0000.0000.0000.000
106A107THR0-0.032-0.00426.0110.0000.0000.0000.0000.0000.000
107A108PRO0-0.072-0.03924.3690.0110.0110.0000.0000.0000.000
108A109TYR0-0.013-0.00227.2270.0100.0100.0000.0000.0000.000
109A110SER00.0160.01027.941-0.015-0.0150.0000.0000.0000.000
110A111GLU-1-0.919-0.95527.527-0.207-0.2070.0000.0000.0000.000
111A112GLU-1-0.910-0.97329.003-0.183-0.1830.0000.0000.0000.000
112A113ASP-1-0.866-0.93732.339-0.142-0.1420.0000.0000.0000.000
113A114PHE0-0.042-0.01431.9460.0100.0100.0000.0000.0000.000
114A115GLN00.0320.01033.5960.0070.0070.0000.0000.0000.000
115A116HIS0-0.072-0.03235.4070.0120.0120.0000.0000.0000.000
116A117LEU00.0200.01237.1260.0080.0080.0000.0000.0000.000
117A118GLN0-0.003-0.00935.528-0.001-0.0010.0000.0000.0000.000
118A119LYS10.9500.97339.2500.1090.1090.0000.0000.0000.000
119A120GLU-1-0.924-0.95441.472-0.091-0.0910.0000.0000.0000.000
120A121ILE0-0.014-0.01040.3080.0060.0060.0000.0000.0000.000
121A122GLU-1-0.940-0.96443.504-0.079-0.0790.0000.0000.0000.000
122A123GLN0-0.015-0.01945.3780.0050.0050.0000.0000.0000.000
123A124LEU0-0.006-0.00445.8930.0050.0050.0000.0000.0000.000
124A125GLN0-0.026-0.00746.5020.0020.0020.0000.0000.0000.000
125A126GLU-1-0.860-0.93749.670-0.059-0.0590.0000.0000.0000.000
126A127LYS10.9190.96951.2790.0630.0630.0000.0000.0000.000
127A128TYR00.0260.01052.5550.0030.0030.0000.0000.0000.000
128A129LYS10.8580.93652.7000.0630.0630.0000.0000.0000.000
129A130THR0-0.057-0.03955.8080.0030.0030.0000.0000.0000.000
130A131GLU-1-0.848-0.94656.828-0.050-0.0500.0000.0000.0000.000
131A132LEU0-0.0270.00458.4500.0020.0020.0000.0000.0000.000
132A133CYS0-0.060-0.02859.8250.0020.0020.0000.0000.0000.000
133A134THR00.0200.00961.2710.0020.0020.0000.0000.0000.000
134A135LYS10.9811.00562.9940.0440.0440.0000.0000.0000.000
135A136GLN0-0.047-0.03664.7530.0010.0010.0000.0000.0000.000
136A137ALA00.0110.00966.2580.0010.0010.0000.0000.0000.000
137A138LEU00.0320.02066.1990.0010.0010.0000.0000.0000.000
138A139LEU0-0.036-0.01568.9850.0010.0010.0000.0000.0000.000
139A140ALA0-0.025-0.01870.5910.0010.0010.0000.0000.0000.000
140A141GLU-1-0.871-0.92572.059-0.032-0.0320.0000.0000.0000.000
141A142LEU0-0.020-0.01373.5540.0010.0010.0000.0000.0000.000
142A143GLU-1-0.928-0.98175.066-0.029-0.0290.0000.0000.0000.000
143A144GLU-1-0.937-0.96776.496-0.029-0.0290.0000.0000.0000.000
144A145GLN0-0.031-0.00976.5850.0010.0010.0000.0000.0000.000
145A146LYS10.8770.92678.7380.0300.0300.0000.0000.0000.000
146A147ILE0-0.0150.00881.6810.0010.0010.0000.0000.0000.000
147A148VAL00.0270.00682.2170.0010.0010.0000.0000.0000.000
148A149GLN00.0060.01582.2360.0000.0000.0000.0000.0000.000
149A150ALA0-0.009-0.01585.3360.0010.0010.0000.0000.0000.000
150A151LYS10.9460.97987.6040.0220.0220.0000.0000.0000.000
151A152LEU00.0210.00886.9200.0010.0010.0000.0000.0000.000
152A153LYS11.0061.00088.7150.0230.0230.0000.0000.0000.000
153A154GLN00.0040.05491.4430.0000.0000.0000.0000.0000.000
154A155THR0-0.064-0.03692.8500.0010.0010.0000.0000.0000.000
155A156LEU00.0310.00292.0970.0000.0000.0000.0000.0000.000
156A157THR0-0.028-0.04594.9280.0000.0000.0000.0000.0000.000
157A158PHE00.0070.00997.3690.0000.0000.0000.0000.0000.000
158A159PHE0-0.030-0.02498.6730.0000.0000.0000.0000.0000.000
159A160ASP-1-0.894-0.94298.549-0.018-0.0180.0000.0000.0000.000
160A161GLU-1-0.969-0.994100.865-0.017-0.0170.0000.0000.0000.000
161A162LEU0-0.042-0.010103.2180.0000.0000.0000.0000.0000.000
162A163HIS0-0.014-0.016104.3030.0000.0000.0000.0000.0000.000
163A164ASN0-0.056-0.026103.9790.0000.0000.0000.0000.0000.000
164A165VAL00.0090.003107.1280.0000.0000.0000.0000.0000.000
165A166GLY0-0.0130.006108.9080.0000.0000.0000.0000.0000.000
166A167ARG10.9410.955105.6780.0160.0160.0000.0000.0000.000
167A168ASP-1-0.978-0.980110.985-0.014-0.0140.0000.0000.0000.000
168A169HIS0-0.029-0.023113.4590.0000.0000.0000.0000.0000.000
169A170GLY0-0.025-0.001115.5940.0000.0000.0000.0000.0000.000
170A171THR0-0.063-0.023114.1440.0000.0000.0000.0000.0000.000
171A172SER00.0490.022110.1310.0000.0000.0000.0000.0000.000
172A173ASP-1-0.823-0.902108.717-0.015-0.0150.0000.0000.0000.000
173A174PHE00.0280.003110.0750.0000.0000.0000.0000.0000.000
174A175ARG10.9841.000108.3050.0150.0150.0000.0000.0000.000
175A176GLU-1-0.921-0.979111.426-0.014-0.0140.0000.0000.0000.000
176A177SER0-0.0040.000113.9270.0000.0000.0000.0000.0000.000
177A178LEU0-0.028-0.024113.3970.0000.0000.0000.0000.0000.000
178A179VAL0-0.015-0.001114.6900.0000.0000.0000.0000.0000.000
179A180SER00.0050.000116.6650.0000.0000.0000.0000.0000.000
180A181LEU00.0150.017119.1660.0000.0000.0000.0000.0000.000
181A182VAL0-0.005-0.014117.7500.0000.0000.0000.0000.0000.000
182A183GLN0-0.027-0.003119.4880.0000.0000.0000.0000.0000.000
183A184ASN0-0.015-0.029122.3760.0000.0000.0000.0000.0000.000
184A185SER00.0180.024123.6560.0000.0000.0000.0000.0000.000
185A186ARG10.9630.992120.3220.0120.0120.0000.0000.0000.000
186A187LYS10.9380.956126.0000.0110.0110.0000.0000.0000.000
187A188LEU00.0000.013128.5030.0000.0000.0000.0000.0000.000
188A189GLN00.0340.011128.2390.0000.0000.0000.0000.0000.000
189A190ASN0-0.061-0.025130.2020.0000.0000.0000.0000.0000.000
190A191ILE00.0230.001131.9940.0000.0000.0000.0000.0000.000
191A192ARG10.9410.976132.7860.0100.0100.0000.0000.0000.000
192A193ASP-1-0.913-0.949134.080-0.009-0.0090.0000.0000.0000.000
193A194ASN00.012-0.001135.9680.0000.0000.0000.0000.0000.000
194A195VAL0-0.021-0.011138.1500.0000.0000.0000.0000.0000.000
195A196GLU-1-0.967-0.998136.425-0.009-0.0090.0000.0000.0000.000
196A197LYS10.8990.943139.7460.0090.0090.0000.0000.0000.000
197A198GLU-1-0.934-0.948141.679-0.008-0.0080.0000.0000.0000.000
198A199SER0-0.069-0.024143.3080.0000.0000.0000.0000.0000.000
199A200LYS10.8900.958145.1280.0080.0080.0000.0000.0000.000