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: 6N2KZ

Calculation Name: 5LSK-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSK

Chain ID: D

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1104833.169844
FMO2-HF: Nuclear repulsion 1031514.689461
FMO2-HF: Total energy -73318.480383
FMO2-MP2: Total energy -73528.896324


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(D:116:GLY)


Summations of interaction energy for fragment #1(D:116:GLY)
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.
-0.2721.5790.059-0.719-1.1920.001
Interaction energy analysis for fragmet #1(D:116:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.004
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].
3D118THR00.0400.0143.156-1.1900.2480.053-0.638-0.8530.001
4D119GLU-1-0.856-0.9073.669-0.548-0.1350.006-0.081-0.3390.000
5D120LEU0-0.013-0.0045.5860.4930.4930.0000.0000.0000.000
6D121SER0-0.0470.0007.8980.2910.2910.0000.0000.0000.000
7D122ARG10.8380.8987.7780.6160.6160.0000.0000.0000.000
8D123SER0-0.016-0.0169.0590.0150.0150.0000.0000.0000.000
9D124ILE0-0.015-0.01311.5330.0520.0520.0000.0000.0000.000
10D125SER0-0.041-0.02615.2200.0200.0200.0000.0000.0000.000
11D126VAL00.0460.01418.0020.0080.0080.0000.0000.0000.000
12D127ASP-1-0.911-0.94919.422-0.091-0.0910.0000.0000.0000.000
13D128LEU0-0.034-0.00820.9000.0110.0110.0000.0000.0000.000
14D129ALA0-0.018-0.01323.6370.0010.0010.0000.0000.0000.000
15D130GLU-1-0.766-0.85919.444-0.104-0.1040.0000.0000.0000.000
16D131SER0-0.010-0.00820.838-0.008-0.0080.0000.0000.0000.000
17D132LYS10.8800.92422.0580.0910.0910.0000.0000.0000.000
18D133ARG10.8610.91714.9640.1370.1370.0000.0000.0000.000
19D134LEU00.0150.01317.364-0.031-0.0310.0000.0000.0000.000
20D135GLY00.0610.02318.179-0.008-0.0080.0000.0000.0000.000
21D136CYS0-0.035-0.02717.316-0.012-0.0120.0000.0000.0000.000
22D137LEU0-0.0100.01211.646-0.058-0.0580.0000.0000.0000.000
23D138LEU0-0.0010.00714.345-0.027-0.0270.0000.0000.0000.000
24D139LEU00.0300.00916.366-0.010-0.0100.0000.0000.0000.000
25D140SER0-0.014-0.02012.216-0.029-0.0290.0000.0000.0000.000
26D141SER0-0.004-0.00111.671-0.093-0.0930.0000.0000.0000.000
27D142PHE0-0.028-0.00512.7460.0150.0150.0000.0000.0000.000
28D143GLN00.0400.01414.0690.0290.0290.0000.0000.0000.000
29D144PHE0-0.0060.0064.967-0.073-0.0730.0000.0000.0000.000
30D145SER0-0.050-0.03810.3450.0400.0400.0000.0000.0000.000
31D146ILE00.008-0.00112.3120.0300.0300.0000.0000.0000.000
32D147GLN0-0.002-0.01411.2030.0570.0570.0000.0000.0000.000
33D148LYS10.8510.9387.4440.1340.1340.0000.0000.0000.000
34D149LEU0-0.006-0.00210.8030.0730.0730.0000.0000.0000.000
35D150GLU-1-0.786-0.87714.301-0.213-0.2130.0000.0000.0000.000
36D151PRO0-0.096-0.04411.4800.0240.0240.0000.0000.0000.000
37D152PHE0-0.032-0.01912.6840.0290.0290.0000.0000.0000.000
38D153LEU00.0450.02717.3980.0130.0130.0000.0000.0000.000
39D154ARG10.8820.94820.6600.0130.0130.0000.0000.0000.000
40D155ASP-1-0.875-0.93123.850-0.032-0.0320.0000.0000.0000.000
41D156THR00.0410.02125.498-0.005-0.0050.0000.0000.0000.000
42D157LYS10.8570.87926.5920.0520.0520.0000.0000.0000.000
43D158GLY0-0.0040.01829.996-0.001-0.0010.0000.0000.0000.000
44D159PHE00.0810.04827.1500.0010.0010.0000.0000.0000.000
45D160SER00.0120.00726.204-0.001-0.0010.0000.0000.0000.000
46D161LEU0-0.0070.00619.9930.0010.0010.0000.0000.0000.000
47D162GLU-1-0.942-0.98723.554-0.110-0.1100.0000.0000.0000.000
48D163SER0-0.0040.00726.0230.0000.0000.0000.0000.0000.000
49D164PHE00.0030.00819.2080.0030.0030.0000.0000.0000.000
50D165ARG10.8960.91818.7530.2010.2010.0000.0000.0000.000
51D166ALA00.0370.03923.257-0.004-0.0040.0000.0000.0000.000
52D167LYS10.9450.97924.7240.0730.0730.0000.0000.0000.000
53D168ALA00.0420.02719.8960.0000.0000.0000.0000.0000.000
54D169SER00.051-0.00221.928-0.014-0.0140.0000.0000.0000.000
55D170SER0-0.072-0.02123.3820.0060.0060.0000.0000.0000.000
56D171LEU00.0540.01222.4150.0000.0000.0000.0000.0000.000
57D172SER0-0.068-0.02720.449-0.006-0.0060.0000.0000.0000.000
58D173GLU-1-0.890-0.95722.229-0.146-0.1460.0000.0000.0000.000
59D174GLU-1-0.978-0.98525.168-0.064-0.0640.0000.0000.0000.000
60D175LEU0-0.027-0.01219.8690.0060.0060.0000.0000.0000.000
61D176LYS10.8590.91622.6580.1430.1430.0000.0000.0000.000
62D177HIS00.0090.00224.0280.0020.0020.0000.0000.0000.000
63D178PHE0-0.036-0.01225.4280.0100.0100.0000.0000.0000.000
64D179ALA0-0.022-0.01922.8660.0080.0080.0000.0000.0000.000
65D180ASP-1-0.822-0.90224.899-0.117-0.1170.0000.0000.0000.000
66D181GLY0-0.023-0.00127.2520.0070.0070.0000.0000.0000.000
67D182LEU00.001-0.01528.1350.0070.0070.0000.0000.0000.000
68D183GLU-1-0.806-0.88425.541-0.086-0.0860.0000.0000.0000.000
69D184THR0-0.101-0.05427.8500.0060.0060.0000.0000.0000.000
70D185ASP-1-0.892-0.93531.553-0.023-0.0230.0000.0000.0000.000
71D186GLY00.037-0.00331.1640.0040.0040.0000.0000.0000.000
72D187THR0-0.016-0.01728.0930.0040.0040.0000.0000.0000.000
73D188LEU0-0.0260.01222.8840.0040.0040.0000.0000.0000.000
74D189GLN0-0.021-0.01925.4320.0070.0070.0000.0000.0000.000
75D190LYS10.9190.96227.4900.0190.0190.0000.0000.0000.000
76D191CYS0-0.057-0.02722.3070.0080.0080.0000.0000.0000.000
77D192PHE0-0.056-0.02321.4550.0040.0040.0000.0000.0000.000
78D193GLU-1-0.962-0.95326.0040.0130.0130.0000.0000.0000.000
79D203SER00.0450.00936.4230.0010.0010.0000.0000.0000.000
80D204LEU00.0350.02135.7860.0010.0010.0000.0000.0000.000
81D205GLU-1-0.897-0.95731.7580.0460.0460.0000.0000.0000.000
82D206ALA00.0140.01335.6540.0020.0020.0000.0000.0000.000
83D207SER00.0510.02537.9700.0010.0010.0000.0000.0000.000
84D208VAL0-0.042-0.02336.4930.0010.0010.0000.0000.0000.000
85D209ALA0-0.022-0.01136.3020.0020.0020.0000.0000.0000.000
86D210GLU-1-0.888-0.95038.1440.0300.0300.0000.0000.0000.000
87D211MET0-0.037-0.01241.6790.0000.0000.0000.0000.0000.000
88D212LYS10.9150.93734.394-0.066-0.0660.0000.0000.0000.000
89D213GLU-1-0.901-0.93939.7900.0470.0470.0000.0000.0000.000
90D214TYR0-0.017-0.02142.091-0.001-0.0010.0000.0000.0000.000
91D215ILE0-0.0120.00842.720-0.001-0.0010.0000.0000.0000.000
92D216THR00.0300.01841.125-0.001-0.0010.0000.0000.0000.000
93D217LYS10.9560.99244.503-0.033-0.0330.0000.0000.0000.000
94D218PHE00.013-0.00347.127-0.001-0.0010.0000.0000.0000.000
95D219SER0-0.070-0.03746.3700.0000.0000.0000.0000.0000.000
96D220LEU00.0220.00945.6660.0000.0000.0000.0000.0000.000
97D221GLU-1-0.885-0.92849.2660.0270.0270.0000.0000.0000.000
98D222ARG10.9430.97348.612-0.040-0.0400.0000.0000.0000.000
99D223GLN00.0170.01149.1520.0000.0000.0000.0000.0000.000
100D224THR0-0.035-0.02852.843-0.001-0.0010.0000.0000.0000.000
101D225TRP0-0.065-0.04255.062-0.002-0.0020.0000.0000.0000.000
102D226ASP-1-0.916-0.95255.1930.0320.0320.0000.0000.0000.000
103D227GLN0-0.034-0.02055.1080.0000.0000.0000.0000.0000.000
104D228LEU0-0.011-0.00658.046-0.001-0.0010.0000.0000.0000.000
105D229LEU0-0.0050.00460.489-0.001-0.0010.0000.0000.0000.000
106D230LEU00.015-0.01059.078-0.001-0.0010.0000.0000.0000.000
107D231HIS0-0.0410.00061.8800.0000.0000.0000.0000.0000.000
108D232TYR00.0380.00763.594-0.001-0.0010.0000.0000.0000.000
109D233GLN0-0.025-0.00265.1800.0000.0000.0000.0000.0000.000
110D234GLN0-0.025-0.02262.7370.0000.0000.0000.0000.0000.000
111D235GLU-1-0.905-0.94867.6180.0200.0200.0000.0000.0000.000
112D236ALA00.0110.00569.313-0.001-0.0010.0000.0000.0000.000
113D237LYS10.8990.93570.488-0.021-0.0210.0000.0000.0000.000
114D238GLU-1-0.824-0.89170.4130.0200.0200.0000.0000.0000.000
115D239ILE00.0160.00072.428-0.001-0.0010.0000.0000.0000.000
116D240LEU0-0.070-0.03275.023-0.001-0.0010.0000.0000.0000.000
117D241SER0-0.062-0.03275.1470.0000.0000.0000.0000.0000.000
118D242ARG10.8570.93073.604-0.019-0.0190.0000.0000.0000.000
119D243GLY0-0.037-0.02277.5610.0000.0000.0000.0000.0000.000
120D244SER0-0.021-0.00180.779-0.001-0.0010.0000.0000.0000.000
121D245THR0-0.031-0.00777.8690.0000.0000.0000.0000.0000.000
122D258THR0-0.003-0.01591.6380.0000.0000.0000.0000.0000.000
123D259TYR00.0150.00984.9970.0000.0000.0000.0000.0000.000
124D260LEU00.0100.00382.3930.0000.0000.0000.0000.0000.000
125D261GLY00.0360.01285.2040.0000.0000.0000.0000.0000.000
126D262SER0-0.035-0.01086.2220.0000.0000.0000.0000.0000.000
127D263SER00.0690.02889.3290.0000.0000.0000.0000.0000.000
128D264GLN00.0200.00391.2430.0000.0000.0000.0000.0000.000
129D265ASN0-0.039-0.01890.1530.0000.0000.0000.0000.0000.000
130D266GLU-1-0.872-0.93092.7080.0090.0090.0000.0000.0000.000
131D267VAL00.009-0.00395.2710.0000.0000.0000.0000.0000.000
132D268LEU0-0.076-0.04594.0530.0000.0000.0000.0000.0000.000
133D269ASN0-0.038-0.02092.2110.0000.0000.0000.0000.0000.000
134D270THR0-0.0370.00796.5700.0000.0000.0000.0000.0000.000
135D271LYS10.9550.983100.083-0.009-0.0090.0000.0000.0000.000
136D272PRO00.0060.009101.8680.0000.0000.0000.0000.0000.000
137D273ASP-1-0.795-0.895105.0570.0080.0080.0000.0000.0000.000
138D274TYR00.0450.007104.9930.0000.0000.0000.0000.0000.000
139D275GLN00.0220.009106.9720.0000.0000.0000.0000.0000.000
140D276LYS10.8690.923107.169-0.008-0.0080.0000.0000.0000.000
141D277ILE00.0070.006110.4090.0000.0000.0000.0000.0000.000
142D278LEU00.0130.002112.2990.0000.0000.0000.0000.0000.000
143D279GLN00.0190.006109.9450.0000.0000.0000.0000.0000.000
144D280ASN0-0.026-0.024113.2080.0000.0000.0000.0000.0000.000
145D281GLN00.0240.007116.3760.0000.0000.0000.0000.0000.000
146D282SER0-0.007-0.005117.8530.0000.0000.0000.0000.0000.000
147D283LYS10.9400.989115.247-0.007-0.0070.0000.0000.0000.000
148D284VAL0-0.046-0.015120.3180.0000.0000.0000.0000.0000.000
149D285PHE0-0.019-0.022122.3440.0000.0000.0000.0000.0000.000
150D286ASP-1-0.829-0.899122.2260.0060.0060.0000.0000.0000.000
151D287CYS0-0.069-0.046124.2040.0000.0000.0000.0000.0000.000
152D288MET0-0.028-0.014126.0810.0000.0000.0000.0000.0000.000
153D289GLU-1-0.923-0.957128.2050.0060.0060.0000.0000.0000.000
154D290LEU00.0100.011126.7330.0000.0000.0000.0000.0000.000
155D291VAL00.0050.001129.5920.0000.0000.0000.0000.0000.000
156D292MET0-0.059-0.021132.0600.0000.0000.0000.0000.0000.000
157D293ASP-1-0.873-0.943133.6600.0050.0050.0000.0000.0000.000
158D294GLU-1-0.983-0.985133.2760.0050.0050.0000.0000.0000.000
159D295LEU0-0.020-0.007136.0700.0000.0000.0000.0000.0000.000
160D296GLN0-0.024-0.029138.1620.0000.0000.0000.0000.0000.000
161D297GLY00.0250.014139.1510.0000.0000.0000.0000.0000.000
162D298SER0-0.034-0.028139.4690.0000.0000.0000.0000.0000.000
163D299VAL0-0.026-0.010142.0810.0000.0000.0000.0000.0000.000
164D300LYS10.9450.974143.840-0.005-0.0050.0000.0000.0000.000
165D301GLN0-0.0130.004143.9530.0000.0000.0000.0000.0000.000
166D302LEU0-0.016-0.002145.9610.0000.0000.0000.0000.0000.000
167D303GLN0-0.042-0.041148.0990.0000.0000.0000.0000.0000.000
168D304ALA00.0150.005149.5630.0000.0000.0000.0000.0000.000
169D305PHE00.0310.023150.8570.0000.0000.0000.0000.0000.000
170D306MET0-0.0160.010150.9020.0000.0000.0000.0000.0000.000
171D307ASP-1-0.856-0.920153.9780.0040.0040.0000.0000.0000.000
172D308GLU-1-0.958-0.980154.5900.0040.0040.0000.0000.0000.000
173D309SER0-0.035-0.045155.8630.0000.0000.0000.0000.0000.000
174D310THR0-0.031-0.011158.2100.0000.0000.0000.0000.0000.000
175D311GLN0-0.029-0.006159.9170.0000.0000.0000.0000.0000.000
176D312CYS0-0.019-0.021160.9140.0000.0000.0000.0000.0000.000
177D313PHE00.007-0.009160.3700.0000.0000.0000.0000.0000.000
178D314GLN00.0450.041164.3140.0000.0000.0000.0000.0000.000
179D315LYS10.7840.891164.713-0.003-0.0030.0000.0000.0000.000
180D316VAL0-0.0030.003167.5550.0000.0000.0000.0000.0000.000
181D317SER0-0.048-0.007169.9830.0000.0000.0000.0000.0000.000