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: YZ3J2

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2370553.402012
FMO2-HF: Nuclear repulsion 2289079.798833
FMO2-HF: Total energy -81473.603179
FMO2-MP2: Total energy -81706.902414


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.
0.1981.930.027-0.672-1.0860
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 : 0.021 / q_NPA : 0.012
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].
3X7PHE00.0700.0303.883-1.0170.210-0.013-0.541-0.6720.001
4X8VAL00.0040.0146.299-0.042-0.0420.0000.0000.0000.000
5X9LEU0-0.067-0.0254.3710.9491.057-0.001-0.028-0.0790.000
6X10LEU00.0220.0028.116-0.647-0.6470.0000.0000.0000.000
7X11ASP-1-0.799-0.86611.3121.5941.5940.0000.0000.0000.000
8X12ARG10.8000.87513.470-0.966-0.9660.0000.0000.0000.000
9X13SER0-0.024-0.03015.685-0.120-0.1200.0000.0000.0000.000
10X14ARG10.7550.85618.280-0.736-0.7360.0000.0000.0000.000
11X15PRO00.0250.01121.1430.0080.0080.0000.0000.0000.000
12X16GLY00.002-0.01023.825-0.035-0.0350.0000.0000.0000.000
13X17VAL0-0.0120.00019.819-0.039-0.0390.0000.0000.0000.000
14X18ALA00.0270.01717.1230.0660.0660.0000.0000.0000.000
15X19LEU0-0.0090.00913.551-0.099-0.0990.0000.0000.0000.000
16X20VAL00.0240.00612.6040.2430.2430.0000.0000.0000.000
17X21THR0-0.009-0.0098.867-0.152-0.1520.0000.0000.0000.000
18X22LEU00.0170.0109.0370.2540.2540.0000.0000.0000.000
19X23ASN0-0.054-0.0512.8940.0000.3970.041-0.103-0.335-0.001
20X24ARG10.8140.8835.3620.4760.4760.0000.0000.0000.000
21X25PRO00.0270.0346.4130.1670.1670.0000.0000.0000.000
22X26GLU-1-0.871-0.9557.524-1.561-1.5610.0000.0000.0000.000
23X27ARG10.9110.95510.3700.8570.8570.0000.0000.0000.000
24X28MET0-0.0080.00112.4080.0970.0970.0000.0000.0000.000
25X29ASN00.007-0.0079.7490.0090.0090.0000.0000.0000.000
26X30SER0-0.0210.02011.8990.0500.0500.0000.0000.0000.000
27X31MET0-0.0180.00313.365-0.049-0.0490.0000.0000.0000.000
28X32ALA00.0170.01113.5770.0220.0220.0000.0000.0000.000
29X33PHE00.0740.02714.7260.0430.0430.0000.0000.0000.000
30X34ASP-1-0.792-0.87110.736-0.768-0.7680.0000.0000.0000.000
31X35VAL0-0.044-0.02510.088-0.047-0.0470.0000.0000.0000.000
32X36MET00.010-0.00311.8520.1800.1800.0000.0000.0000.000
33X37VAL00.0220.02615.1980.0650.0650.0000.0000.0000.000
34X38PRO00.0290.01410.6810.0720.0720.0000.0000.0000.000
35X39LEU0-0.032-0.00813.0850.1510.1510.0000.0000.0000.000
36X40LEU0-0.006-0.00214.3870.0390.0390.0000.0000.0000.000
37X41GLU-1-0.903-0.95814.8130.2760.2760.0000.0000.0000.000
38X42LEU0-0.015-0.00112.2710.0340.0340.0000.0000.0000.000
39X43LEU0-0.033-0.03115.9030.0010.0010.0000.0000.0000.000
40X44GLY00.0030.00518.875-0.034-0.0340.0000.0000.0000.000
41X45ASP-1-0.832-0.92018.2290.4460.4460.0000.0000.0000.000
42X46LEU0-0.036-0.02416.439-0.003-0.0030.0000.0000.0000.000
43X47ARG10.8450.93820.344-0.304-0.3040.0000.0000.0000.000
44X48HIS0-0.018-0.01022.518-0.075-0.0750.0000.0000.0000.000
45X49ASP-1-0.734-0.82820.5640.5960.5960.0000.0000.0000.000
46X50ASN00.011-0.00923.111-0.007-0.0070.0000.0000.0000.000
47X51SER0-0.111-0.06622.969-0.010-0.0100.0000.0000.0000.000
48X52VAL0-0.058-0.01820.0820.0270.0270.0000.0000.0000.000
49X53ARG10.8410.90423.265-0.341-0.3410.0000.0000.0000.000
50X54VAL0-0.028-0.01523.281-0.038-0.0380.0000.0000.0000.000
51X55VAL00.0180.00918.1260.0570.0570.0000.0000.0000.000
52X56ILE0-0.0070.00617.659-0.060-0.0600.0000.0000.0000.000
53X57LEU0-0.001-0.00114.4790.0970.0970.0000.0000.0000.000
54X58THR00.000-0.01812.852-0.080-0.0800.0000.0000.0000.000
55X59GLY00.0030.01411.7850.0480.0480.0000.0000.0000.000
56X60ALA00.0110.0057.9330.0530.0530.0000.0000.0000.000
57X61GLY0-0.024-0.0179.917-0.200-0.2000.0000.0000.0000.000
58X62ARG10.9810.97812.0910.2490.2490.0000.0000.0000.000
59X63GLY00.0540.02414.141-0.007-0.0070.0000.0000.0000.000
60X64PHE0-0.0370.02514.0630.0210.0210.0000.0000.0000.000
61X65SER00.002-0.04114.4560.0040.0040.0000.0000.0000.000
62X66SER00.0250.01715.9080.0220.0220.0000.0000.0000.000
63X67GLY0-0.053-0.01817.454-0.037-0.0370.0000.0000.0000.000
64X92MET00.014-0.00523.504-0.009-0.0090.0000.0000.0000.000
65X93GLU-1-0.814-0.92722.948-0.047-0.0470.0000.0000.0000.000
66X94VAL00.0010.00418.9090.0040.0040.0000.0000.0000.000
67X95LEU00.0110.01320.1910.0340.0340.0000.0000.0000.000
68X96ASP-1-0.801-0.89621.8490.0610.0610.0000.0000.0000.000
69X97ASN0-0.064-0.04222.8430.0330.0330.0000.0000.0000.000
70X98VAL00.0090.00218.1940.0330.0330.0000.0000.0000.000
71X99ILE00.0120.00221.0670.0350.0350.0000.0000.0000.000
72X100LEU00.0170.00123.8990.0180.0180.0000.0000.0000.000
73X101ALA0-0.062-0.01321.3830.0080.0080.0000.0000.0000.000
74X102LEU00.0320.01119.4190.0260.0260.0000.0000.0000.000
75X103ARG10.8300.90723.051-0.110-0.1100.0000.0000.0000.000
76X104ARG10.8610.91524.675-0.176-0.1760.0000.0000.0000.000
77X105LEU0-0.0480.00220.9600.0040.0040.0000.0000.0000.000
78X106HIS0-0.020-0.01025.530-0.032-0.0320.0000.0000.0000.000
79X107GLN0-0.037-0.02423.776-0.037-0.0370.0000.0000.0000.000
80X108PRO0-0.004-0.00425.493-0.008-0.0080.0000.0000.0000.000
81X109VAL0-0.010-0.01220.1890.0430.0430.0000.0000.0000.000
82X110ILE0-0.012-0.00921.858-0.037-0.0370.0000.0000.0000.000
83X111ALA00.024-0.00319.6900.0520.0520.0000.0000.0000.000
84X112ALA00.0480.01817.777-0.038-0.0380.0000.0000.0000.000
85X113VAL0-0.014-0.00517.7960.0290.0290.0000.0000.0000.000
86X114ASN00.0670.00914.169-0.009-0.0090.0000.0000.0000.000
87X115GLY00.0430.01317.935-0.020-0.0200.0000.0000.0000.000
88X116ALA0-0.0070.00918.3570.0060.0060.0000.0000.0000.000
89X117ALA00.0150.00418.4390.0120.0120.0000.0000.0000.000
90X118ILE00.0040.00420.290-0.004-0.0040.0000.0000.0000.000
91X119GLY00.0170.01121.279-0.010-0.0100.0000.0000.0000.000
92X120GLY00.0510.01221.1730.0190.0190.0000.0000.0000.000
93X121GLY00.016-0.00119.0660.0280.0280.0000.0000.0000.000
94X122LEU0-0.0050.00519.8130.0380.0380.0000.0000.0000.000
95X123CYS0-0.061-0.01923.2810.0240.0240.0000.0000.0000.000
96X124LEU00.0160.00216.7730.0190.0190.0000.0000.0000.000
97X125ALA00.0110.00621.2820.0340.0340.0000.0000.0000.000
98X126LEU0-0.039-0.02022.2070.0160.0160.0000.0000.0000.000
99X127ALA00.0070.01123.2270.0020.0020.0000.0000.0000.000
100X128CYS0-0.060-0.00321.1830.0330.0330.0000.0000.0000.000
101X129ASP-1-0.744-0.84123.8590.2290.2290.0000.0000.0000.000
102X130VAL0-0.021-0.01625.428-0.019-0.0190.0000.0000.0000.000
103X131ARG10.8320.91723.790-0.148-0.1480.0000.0000.0000.000
104X132ILE0-0.014-0.01323.200-0.013-0.0130.0000.0000.0000.000
105X133ALA0-0.0170.00122.6370.0130.0130.0000.0000.0000.000
106X134ALA00.0310.02320.6610.0060.0060.0000.0000.0000.000
107X135HIS00.0240.01222.700-0.014-0.0140.0000.0000.0000.000
108X136ASN0-0.073-0.05418.696-0.043-0.0430.0000.0000.0000.000
109X137ALA0-0.098-0.02821.831-0.018-0.0180.0000.0000.0000.000
110X138TYR0-0.016-0.01221.443-0.020-0.0200.0000.0000.0000.000
111X139PHE0-0.012-0.01123.1760.0020.0020.0000.0000.0000.000
112X140ARG10.8610.90124.9290.0470.0470.0000.0000.0000.000
113X141ALA00.0230.02525.581-0.001-0.0010.0000.0000.0000.000
114X142ALA00.009-0.01824.969-0.009-0.0090.0000.0000.0000.000
115X143GLY00.0420.00925.2180.0060.0060.0000.0000.0000.000
116X144ILE0-0.031-0.00525.601-0.010-0.0100.0000.0000.0000.000
117X145ASN00.0060.00628.1640.0120.0120.0000.0000.0000.000
118X146ASN0-0.020-0.01730.438-0.012-0.0120.0000.0000.0000.000
119X147GLY00.0250.01130.6580.0040.0040.0000.0000.0000.000
120X148LEU00.0070.02029.9580.0010.0010.0000.0000.0000.000
121X149THR00.0180.01126.187-0.003-0.0030.0000.0000.0000.000
122X150ALA00.008-0.00225.4100.0100.0100.0000.0000.0000.000
123X151SER00.005-0.00323.9030.0180.0180.0000.0000.0000.000
124X152GLU-1-0.907-0.95625.692-0.020-0.0200.0000.0000.0000.000
125X153LEU00.0230.01429.2010.0090.0090.0000.0000.0000.000
126X154GLY00.0370.01527.9320.0080.0080.0000.0000.0000.000
127X155LEU0-0.007-0.01526.2420.0100.0100.0000.0000.0000.000
128X156SER0-0.039-0.03629.4670.0050.0050.0000.0000.0000.000
129X157TYR0-0.065-0.05732.017-0.002-0.0020.0000.0000.0000.000
130X158LEU0-0.002-0.00527.8360.0050.0050.0000.0000.0000.000
131X159LEU00.0370.02729.6090.0060.0060.0000.0000.0000.000
132X160PRO0-0.024-0.03331.9590.0030.0030.0000.0000.0000.000
133X161ARG10.7820.89434.051-0.067-0.0670.0000.0000.0000.000
134X162ALA0-0.0110.01931.4760.0060.0060.0000.0000.0000.000
135X163ILE0-0.016-0.00132.4190.0020.0020.0000.0000.0000.000
136X164GLY00.0350.02535.283-0.005-0.0050.0000.0000.0000.000
137X165THR00.013-0.01637.621-0.002-0.0020.0000.0000.0000.000
138X166SER00.0010.00238.893-0.002-0.0020.0000.0000.0000.000
139X167ARG10.9841.00236.038-0.060-0.0600.0000.0000.0000.000
140X168ALA00.0410.02434.195-0.004-0.0040.0000.0000.0000.000
141X169PHE0-0.005-0.01034.732-0.006-0.0060.0000.0000.0000.000
142X170GLU-1-0.811-0.86536.6280.0110.0110.0000.0000.0000.000
143X171ILE00.0170.02730.944-0.006-0.0060.0000.0000.0000.000
144X172MET0-0.062-0.04131.151-0.004-0.0040.0000.0000.0000.000
145X173LEU0-0.034-0.01833.240-0.008-0.0080.0000.0000.0000.000
146X174THR0-0.054-0.04534.974-0.005-0.0050.0000.0000.0000.000
147X175GLY0-0.0090.01031.012-0.007-0.0070.0000.0000.0000.000
148X176ARG10.6740.78530.063-0.026-0.0260.0000.0000.0000.000
149X177ASP-1-0.828-0.88526.681-0.025-0.0250.0000.0000.0000.000
150X178VAL00.0030.00928.3340.0020.0020.0000.0000.0000.000
151X179ASP-1-0.760-0.89627.8200.0610.0610.0000.0000.0000.000
152X180ALA00.0580.03125.8820.0070.0070.0000.0000.0000.000
153X181ALA00.0180.01627.5970.0130.0130.0000.0000.0000.000
154X182GLU-1-0.870-0.91031.0090.0330.0330.0000.0000.0000.000
155X183ALA00.007-0.01728.1700.0010.0010.0000.0000.0000.000
156X184GLU-1-0.925-0.96230.1380.1080.1080.0000.0000.0000.000
157X185ARG10.8760.95831.666-0.062-0.0620.0000.0000.0000.000
158X186ILE0-0.102-0.05432.119-0.007-0.0070.0000.0000.0000.000
159X187GLY00.0200.01133.630-0.004-0.0040.0000.0000.0000.000
160X188LEU0-0.048-0.00427.4910.0060.0060.0000.0000.0000.000
161X189VAL0-0.038-0.03425.5680.0140.0140.0000.0000.0000.000
162X190SER0-0.002-0.00528.353-0.005-0.0050.0000.0000.0000.000
163X191ARG10.8290.89628.229-0.227-0.2270.0000.0000.0000.000
164X192THR00.011-0.00526.6270.0160.0160.0000.0000.0000.000
165X193VAL0-0.081-0.02224.384-0.006-0.0060.0000.0000.0000.000
166X194PRO00.0550.01625.441-0.006-0.0060.0000.0000.0000.000
167X195ASP-1-0.828-0.92320.5280.1720.1720.0000.0000.0000.000
168X196ASP-1-0.941-0.96720.5300.2850.2850.0000.0000.0000.000
169X197ASP-1-0.870-0.93521.5460.2750.2750.0000.0000.0000.000
170X198LEU0-0.043-0.00218.6730.0190.0190.0000.0000.0000.000
171X199LEU00.0370.00815.2110.0120.0120.0000.0000.0000.000
172X200GLU-1-0.723-0.83019.6390.5490.5490.0000.0000.0000.000
173X201THR00.0090.00722.666-0.026-0.0260.0000.0000.0000.000
174X202CYS0-0.060-0.02320.831-0.021-0.0210.0000.0000.0000.000
175X203PHE00.017-0.01117.3620.0010.0010.0000.0000.0000.000
176X204GLU-1-0.853-0.89923.2220.2360.2360.0000.0000.0000.000
177X205MET0-0.012-0.00225.919-0.015-0.0150.0000.0000.0000.000
178X206ALA00.0360.00623.594-0.013-0.0130.0000.0000.0000.000
179X207GLN00.0260.01625.6760.0160.0160.0000.0000.0000.000
180X208ARG10.9260.96227.838-0.215-0.2150.0000.0000.0000.000
181X209MET0-0.005-0.00827.615-0.007-0.0070.0000.0000.0000.000
182X210ARG10.8780.93925.855-0.391-0.3910.0000.0000.0000.000
183X211GLY0-0.0210.00429.576-0.006-0.0060.0000.0000.0000.000
184X212PHE00.0100.02033.010-0.016-0.0160.0000.0000.0000.000
185X213SER00.0340.01433.0250.0180.0180.0000.0000.0000.000
186X214ARG10.8340.88629.530-0.258-0.2580.0000.0000.0000.000
187X215PRO00.0630.01732.5110.0010.0010.0000.0000.0000.000
188X216GLY00.0260.02935.280-0.008-0.0080.0000.0000.0000.000
189X217ILE0-0.0030.00829.642-0.006-0.0060.0000.0000.0000.000
190X218GLU-1-0.792-0.86431.5180.2140.2140.0000.0000.0000.000
191X219LEU00.0060.00032.489-0.008-0.0080.0000.0000.0000.000
192X220THR0-0.030-0.01133.944-0.012-0.0120.0000.0000.0000.000
193X221LYS10.7740.87725.609-0.274-0.2740.0000.0000.0000.000
194X222ARG10.9750.97632.192-0.159-0.1590.0000.0000.0000.000
195X223THR0-0.0110.00034.112-0.011-0.0110.0000.0000.0000.000
196X224LEU00.0140.00633.588-0.009-0.0090.0000.0000.0000.000
197X225TRP0-0.042-0.04327.415-0.019-0.0190.0000.0000.0000.000
198X226SER0-0.043-0.03833.616-0.011-0.0110.0000.0000.0000.000
199X227GLY00.0450.02536.809-0.008-0.0080.0000.0000.0000.000
200X228LEU0-0.060-0.02332.999-0.008-0.0080.0000.0000.0000.000
201X229ASP-1-0.758-0.84235.1270.0820.0820.0000.0000.0000.000
202X230ALA0-0.0300.00638.477-0.004-0.0040.0000.0000.0000.000
203X231ALA00.002-0.00141.812-0.003-0.0030.0000.0000.0000.000
204X232SER0-0.002-0.00744.927-0.003-0.0030.0000.0000.0000.000
205X233LEU00.0370.01845.9650.0030.0030.0000.0000.0000.000
206X234GLU-1-0.896-0.94647.0130.0560.0560.0000.0000.0000.000
207X235GLY00.0430.01947.3550.0020.0020.0000.0000.0000.000
208X236HIS0-0.083-0.04739.4300.0000.0000.0000.0000.0000.000
209X237MET0-0.061-0.04344.5330.0040.0040.0000.0000.0000.000
210X238GLN0-0.066-0.02846.9690.0000.0000.0000.0000.0000.000
211X239ALA0-0.0380.00642.823-0.001-0.0010.0000.0000.0000.000
212X240GLU-1-1.002-0.99542.5640.0940.0940.0000.0000.0000.000