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: 5274Z

Calculation Name: 5E0N-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E0N

Chain ID: X

ChEMBL ID:

UniProt ID: A0QX16

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2365026.410585
FMO2-HF: Nuclear repulsion 2283553.142258
FMO2-HF: Total energy -81473.268326
FMO2-MP2: Total energy -81706.565677


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(X:5:THR)


Summations of interaction energy for fragment #1(X:5:THR)
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.
-2.3050.1340.339-1.169-1.609-0.002
Interaction energy analysis for fragmet #1(X:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.007
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].
3X7PHE00.0690.0293.341-3.449-1.7040.012-0.883-0.874-0.001
4X8VAL00.0010.0115.8440.0140.0140.0000.0000.0000.000
5X9LEU0-0.059-0.0174.1740.7610.9010.000-0.034-0.1050.000
6X10LEU00.0220.0057.813-0.603-0.6030.0000.0000.0000.000
7X11ASP-1-0.814-0.88311.2481.4981.4980.0000.0000.0000.000
8X12ARG10.8400.90313.219-0.922-0.9220.0000.0000.0000.000
9X13SER0-0.024-0.02915.509-0.112-0.1120.0000.0000.0000.000
10X14ARG10.7650.85617.978-0.644-0.6440.0000.0000.0000.000
11X15PRO00.0370.00920.8720.0140.0140.0000.0000.0000.000
12X16GLY0-0.010-0.01023.538-0.028-0.0280.0000.0000.0000.000
13X17VAL00.0040.01019.161-0.036-0.0360.0000.0000.0000.000
14X18ALA00.0200.02216.7690.0760.0760.0000.0000.0000.000
15X19LEU0-0.0120.00713.295-0.096-0.0960.0000.0000.0000.000
16X20VAL00.011-0.00612.1160.2180.2180.0000.0000.0000.000
17X21THR00.003-0.0018.643-0.162-0.1620.0000.0000.0000.000
18X22LEU0-0.009-0.0068.5800.1860.1860.0000.0000.0000.000
19X23ASN0-0.043-0.0502.5180.5951.1460.328-0.246-0.633-0.001
20X24ARG10.7820.8654.9320.5350.538-0.001-0.0060.0030.000
21X25PRO00.0230.0285.9660.2560.2560.0000.0000.0000.000
22X26GLU-1-0.878-0.9516.553-2.255-2.2550.0000.0000.0000.000
23X27ARG10.9210.95610.1811.0501.0500.0000.0000.0000.000
24X28MET0-0.012-0.00712.1780.1020.1020.0000.0000.0000.000
25X29ASN00.0020.0039.423-0.055-0.0550.0000.0000.0000.000
26X30SER0-0.0080.03011.4550.0790.0790.0000.0000.0000.000
27X31MET0-0.0200.00413.085-0.062-0.0620.0000.0000.0000.000
28X32ALA0-0.005-0.00212.9220.0330.0330.0000.0000.0000.000
29X33PHE00.0810.01614.2880.0340.0340.0000.0000.0000.000
30X34ASP-1-0.781-0.8629.992-1.006-1.0060.0000.0000.0000.000
31X35VAL0-0.036-0.0189.374-0.065-0.0650.0000.0000.0000.000
32X36MET00.006-0.00511.2680.1930.1930.0000.0000.0000.000
33X37VAL00.0400.03014.5620.0810.0810.0000.0000.0000.000
34X38PRO00.0240.01710.2290.0750.0750.0000.0000.0000.000
35X39LEU0-0.033-0.00412.7910.1460.1460.0000.0000.0000.000
36X40LEU00.000-0.00413.8070.0530.0530.0000.0000.0000.000
37X41GLU-1-0.912-0.96014.8580.2170.2170.0000.0000.0000.000
38X42LEU00.0060.01112.1100.0470.0470.0000.0000.0000.000
39X43LEU0-0.036-0.02815.6060.0020.0020.0000.0000.0000.000
40X44GLY0-0.010-0.00918.422-0.023-0.0230.0000.0000.0000.000
41X45ASP-1-0.898-0.95317.3020.4870.4870.0000.0000.0000.000
42X46LEU0-0.034-0.02816.257-0.011-0.0110.0000.0000.0000.000
43X47ARG10.8680.94920.148-0.255-0.2550.0000.0000.0000.000
44X48HIS0-0.001-0.00423.017-0.065-0.0650.0000.0000.0000.000
45X49ASP-1-0.780-0.83820.6480.5500.5500.0000.0000.0000.000
46X50ASN0-0.009-0.03023.432-0.013-0.0130.0000.0000.0000.000
47X51SER0-0.099-0.06222.651-0.001-0.0010.0000.0000.0000.000
48X52VAL0-0.038-0.01119.7850.0120.0120.0000.0000.0000.000
49X53ARG10.8210.89422.929-0.309-0.3090.0000.0000.0000.000
50X54VAL0-0.028-0.01522.643-0.036-0.0360.0000.0000.0000.000
51X55VAL00.0280.01817.6520.0570.0570.0000.0000.0000.000
52X56ILE0-0.0050.01317.363-0.058-0.0580.0000.0000.0000.000
53X57LEU00.0050.00514.0610.0940.0940.0000.0000.0000.000
54X58THR0-0.004-0.02012.709-0.075-0.0750.0000.0000.0000.000
55X59GLY00.0100.02211.4930.0390.0390.0000.0000.0000.000
56X60ALA00.0140.0117.7360.0640.0640.0000.0000.0000.000
57X61GLY0-0.026-0.0189.652-0.194-0.1940.0000.0000.0000.000
58X62ARG10.9930.97911.5630.3560.3560.0000.0000.0000.000
59X63GLY00.0410.02113.7520.0240.0240.0000.0000.0000.000
60X64PHE0-0.0440.01513.6790.0120.0120.0000.0000.0000.000
61X65SER00.001-0.04213.921-0.005-0.0050.0000.0000.0000.000
62X66SER00.0130.01015.5490.0340.0340.0000.0000.0000.000
63X67GLY0-0.031-0.00216.955-0.019-0.0190.0000.0000.0000.000
64X92MET00.001-0.00523.196-0.005-0.0050.0000.0000.0000.000
65X93GLU-1-0.848-0.94022.657-0.126-0.1260.0000.0000.0000.000
66X94VAL00.0520.02918.2180.0150.0150.0000.0000.0000.000
67X95LEU00.0020.00519.7700.0320.0320.0000.0000.0000.000
68X96ASP-1-0.801-0.90321.2120.0090.0090.0000.0000.0000.000
69X97ASN0-0.070-0.04522.1300.0340.0340.0000.0000.0000.000
70X98VAL00.0080.00317.6240.0340.0340.0000.0000.0000.000
71X99ILE00.0050.00120.6050.0340.0340.0000.0000.0000.000
72X100LEU0-0.005-0.01123.3490.0210.0210.0000.0000.0000.000
73X101ALA0-0.047-0.03021.1640.0130.0130.0000.0000.0000.000
74X102LEU00.0090.00418.9200.0290.0290.0000.0000.0000.000
75X103ARG10.8360.91022.611-0.069-0.0690.0000.0000.0000.000
76X104ARG10.9160.95624.257-0.130-0.1300.0000.0000.0000.000
77X105LEU0-0.074-0.00520.6020.0040.0040.0000.0000.0000.000
78X106HIS0-0.009-0.00625.281-0.027-0.0270.0000.0000.0000.000
79X107GLN0-0.038-0.02623.459-0.034-0.0340.0000.0000.0000.000
80X108PRO0-0.0080.00025.079-0.009-0.0090.0000.0000.0000.000
81X109VAL00.005-0.00919.9300.0390.0390.0000.0000.0000.000
82X110ILE0-0.017-0.01921.487-0.035-0.0350.0000.0000.0000.000
83X111ALA00.0140.00019.3530.0430.0430.0000.0000.0000.000
84X112ALA00.023-0.00217.463-0.023-0.0230.0000.0000.0000.000
85X113VAL0-0.0040.00017.5210.0090.0090.0000.0000.0000.000
86X114ASN00.0960.02313.9560.0060.0060.0000.0000.0000.000
87X115GLY00.0550.02217.772-0.015-0.0150.0000.0000.0000.000
88X116ALA0-0.029-0.00418.2140.0090.0090.0000.0000.0000.000
89X117ALA00.0280.02118.086-0.007-0.0070.0000.0000.0000.000
90X118ILE0-0.001-0.00419.8450.0050.0050.0000.0000.0000.000
91X119GLY00.0150.01420.757-0.018-0.0180.0000.0000.0000.000
92X120GLY00.0470.00320.6280.0220.0220.0000.0000.0000.000
93X121GLY00.014-0.00118.5680.0250.0250.0000.0000.0000.000
94X122LEU00.0030.00319.3720.0380.0380.0000.0000.0000.000
95X123CYS0-0.046-0.02022.7830.0280.0280.0000.0000.0000.000
96X124LEU00.0160.00916.2120.0210.0210.0000.0000.0000.000
97X125ALA00.0110.00420.7360.0340.0340.0000.0000.0000.000
98X126LEU0-0.041-0.01921.7800.0190.0190.0000.0000.0000.000
99X127ALA00.0080.01522.6280.0030.0030.0000.0000.0000.000
100X128CYS0-0.096-0.02420.8320.0300.0300.0000.0000.0000.000
101X129ASP-1-0.726-0.84823.5030.1760.1760.0000.0000.0000.000
102X130VAL0-0.029-0.01625.012-0.014-0.0140.0000.0000.0000.000
103X131ARG10.8760.95223.437-0.091-0.0910.0000.0000.0000.000
104X132ILE0-0.004-0.00723.022-0.010-0.0100.0000.0000.0000.000
105X133ALA0-0.0110.00322.3390.0090.0090.0000.0000.0000.000
106X134ALA00.0230.02120.6450.0090.0090.0000.0000.0000.000
107X135HIS0-0.008-0.00422.641-0.014-0.0140.0000.0000.0000.000
108X136ASN0-0.066-0.04918.795-0.034-0.0340.0000.0000.0000.000
109X137ALA0-0.105-0.02921.369-0.024-0.0240.0000.0000.0000.000
110X138TYR0-0.025-0.01521.631-0.014-0.0140.0000.0000.0000.000
111X139PHE0-0.022-0.01622.846-0.003-0.0030.0000.0000.0000.000
112X140ARG10.8710.91324.4520.1090.1090.0000.0000.0000.000
113X141ALA00.0380.03124.947-0.005-0.0050.0000.0000.0000.000
114X142ALA00.000-0.01924.525-0.007-0.0070.0000.0000.0000.000
115X143GLY00.0600.02225.3550.0050.0050.0000.0000.0000.000
116X144ILE0-0.055-0.03325.259-0.009-0.0090.0000.0000.0000.000
117X145ASN00.0130.01627.7040.0160.0160.0000.0000.0000.000
118X146ASN0-0.037-0.02029.744-0.010-0.0100.0000.0000.0000.000
119X147GLY00.0370.02430.3090.0060.0060.0000.0000.0000.000
120X148LEU00.0030.00730.3130.0000.0000.0000.0000.0000.000
121X149THR00.0320.01925.9480.0000.0000.0000.0000.0000.000
122X150ALA00.0240.00024.8820.0130.0130.0000.0000.0000.000
123X151SER00.011-0.00423.6220.0150.0150.0000.0000.0000.000
124X152GLU-1-0.933-0.96425.433-0.057-0.0570.0000.0000.0000.000
125X153LEU00.0310.01928.8470.0110.0110.0000.0000.0000.000
126X154GLY00.0220.00427.5340.0100.0100.0000.0000.0000.000
127X155LEU00.008-0.00925.7660.0110.0110.0000.0000.0000.000
128X156SER0-0.051-0.02229.0200.0080.0080.0000.0000.0000.000
129X157TYR0-0.062-0.05331.7310.0010.0010.0000.0000.0000.000
130X158LEU00.003-0.01627.3810.0060.0060.0000.0000.0000.000
131X159LEU00.0240.02129.3240.0070.0070.0000.0000.0000.000
132X160PRO0-0.024-0.03131.5620.0040.0040.0000.0000.0000.000
133X161ARG10.8580.93933.933-0.029-0.0290.0000.0000.0000.000
134X162ALA0-0.0280.01031.2160.0060.0060.0000.0000.0000.000
135X163ILE00.0060.00932.2210.0020.0020.0000.0000.0000.000
136X164GLY00.0080.01335.076-0.003-0.0030.0000.0000.0000.000
137X165THR00.023-0.01737.247-0.003-0.0030.0000.0000.0000.000
138X166SER0-0.012-0.00238.819-0.003-0.0030.0000.0000.0000.000
139X167ARG11.0161.00635.742-0.028-0.0280.0000.0000.0000.000
140X168ALA00.0300.02933.949-0.005-0.0050.0000.0000.0000.000
141X169PHE00.018-0.00334.527-0.006-0.0060.0000.0000.0000.000
142X170GLU-1-0.831-0.88936.497-0.024-0.0240.0000.0000.0000.000
143X171ILE00.0030.02230.774-0.007-0.0070.0000.0000.0000.000
144X172MET0-0.060-0.04030.585-0.005-0.0050.0000.0000.0000.000
145X173LEU0-0.035-0.01032.850-0.008-0.0080.0000.0000.0000.000
146X174THR0-0.064-0.04534.876-0.006-0.0060.0000.0000.0000.000
147X175GLY0-0.0060.01130.886-0.007-0.0070.0000.0000.0000.000
148X176ARG10.7050.80630.1430.0070.0070.0000.0000.0000.000
149X177ASP-1-0.823-0.88626.401-0.086-0.0860.0000.0000.0000.000
150X178VAL0-0.018-0.01127.9260.0060.0060.0000.0000.0000.000
151X179ASP-1-0.818-0.91227.4320.0130.0130.0000.0000.0000.000
152X180ALA00.0800.02525.5480.0060.0060.0000.0000.0000.000
153X181ALA00.0100.01227.5040.0120.0120.0000.0000.0000.000
154X182GLU-1-0.853-0.91331.0580.0040.0040.0000.0000.0000.000
155X183ALA0-0.002-0.00828.1620.0020.0020.0000.0000.0000.000
156X184GLU-1-0.958-0.97730.0350.0780.0780.0000.0000.0000.000
157X185ARG10.9641.00631.334-0.027-0.0270.0000.0000.0000.000
158X186ILE0-0.124-0.07432.150-0.001-0.0010.0000.0000.0000.000
159X187GLY00.0270.02732.915-0.002-0.0020.0000.0000.0000.000
160X188LEU0-0.047-0.01427.4970.0020.0020.0000.0000.0000.000
161X189VAL0-0.068-0.04425.2980.0090.0090.0000.0000.0000.000
162X190SER0-0.013-0.01228.032-0.002-0.0020.0000.0000.0000.000
163X191ARG10.9010.95128.091-0.173-0.1730.0000.0000.0000.000
164X192THR00.0350.00326.5190.0080.0080.0000.0000.0000.000
165X193VAL0-0.069-0.02224.089-0.004-0.0040.0000.0000.0000.000
166X194PRO00.0610.02025.065-0.009-0.0090.0000.0000.0000.000
167X195ASP-1-0.794-0.91320.2850.1090.1090.0000.0000.0000.000
168X196ASP-1-0.951-0.96920.4280.2220.2220.0000.0000.0000.000
169X197ASP-1-0.892-0.94621.7620.2280.2280.0000.0000.0000.000
170X198LEU0-0.053-0.01618.4950.0190.0190.0000.0000.0000.000
171X199LEU00.0500.01014.9020.0090.0090.0000.0000.0000.000
172X200GLU-1-0.728-0.82819.4380.4850.4850.0000.0000.0000.000
173X201THR0-0.0020.01622.411-0.019-0.0190.0000.0000.0000.000
174X202CYS0-0.054-0.02320.661-0.016-0.0160.0000.0000.0000.000
175X203PHE00.021-0.01317.0150.0010.0010.0000.0000.0000.000
176X204GLU-1-0.896-0.93622.7460.2080.2080.0000.0000.0000.000
177X205MET0-0.009-0.00625.700-0.016-0.0160.0000.0000.0000.000
178X206ALA00.022-0.00223.263-0.011-0.0110.0000.0000.0000.000
179X207GLN00.0240.01625.3490.0160.0160.0000.0000.0000.000
180X208ARG10.9410.97027.386-0.186-0.1860.0000.0000.0000.000
181X209MET0-0.005-0.00827.219-0.006-0.0060.0000.0000.0000.000
182X210ARG10.8780.93825.491-0.357-0.3570.0000.0000.0000.000
183X211GLY0-0.0260.00429.402-0.004-0.0040.0000.0000.0000.000
184X212PHE0-0.0080.01332.567-0.015-0.0150.0000.0000.0000.000
185X213SER00.0370.01632.7720.0170.0170.0000.0000.0000.000
186X214ARG10.8450.88629.347-0.228-0.2280.0000.0000.0000.000
187X215PRO00.0450.00632.0320.0000.0000.0000.0000.0000.000
188X216GLY00.0120.02434.665-0.009-0.0090.0000.0000.0000.000
189X217ILE0-0.002-0.00829.414-0.007-0.0070.0000.0000.0000.000
190X218GLU-1-0.780-0.85031.0980.1830.1830.0000.0000.0000.000
191X219LEU00.0210.01132.074-0.008-0.0080.0000.0000.0000.000
192X220THR0-0.036-0.00233.665-0.011-0.0110.0000.0000.0000.000
193X221LYS10.8040.90125.218-0.221-0.2210.0000.0000.0000.000
194X222ARG10.9810.97431.835-0.127-0.1270.0000.0000.0000.000
195X223THR0-0.021-0.00833.579-0.010-0.0100.0000.0000.0000.000
196X224LEU00.0080.01233.049-0.009-0.0090.0000.0000.0000.000
197X225TRP0-0.045-0.03727.101-0.018-0.0180.0000.0000.0000.000
198X226SER0-0.063-0.05733.187-0.010-0.0100.0000.0000.0000.000
199X227GLY00.0480.01636.273-0.007-0.0070.0000.0000.0000.000
200X228LEU0-0.076-0.03332.809-0.007-0.0070.0000.0000.0000.000
201X229ASP-1-0.814-0.87134.7540.0510.0510.0000.0000.0000.000
202X230ALA0-0.0420.00937.995-0.004-0.0040.0000.0000.0000.000
203X231ALA00.0130.00741.299-0.003-0.0030.0000.0000.0000.000
204X232SER0-0.013-0.01944.409-0.002-0.0020.0000.0000.0000.000
205X233LEU00.0410.01845.6840.0030.0030.0000.0000.0000.000
206X234GLU-1-0.913-0.96646.9340.0430.0430.0000.0000.0000.000
207X235GLY00.0330.01747.1370.0020.0020.0000.0000.0000.000
208X236HIS0-0.065-0.02639.2800.0010.0010.0000.0000.0000.000
209X237MET0-0.044-0.03544.2700.0030.0030.0000.0000.0000.000
210X238GLN0-0.082-0.02646.5750.0010.0010.0000.0000.0000.000
211X239ALA0-0.0100.01742.2100.0000.0000.0000.0000.0000.000
212X240GLU-1-1.004-0.99941.7910.0710.0710.0000.0000.0000.000