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: 4925N

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2364323.864442
FMO2-HF: Nuclear repulsion 2282851.089395
FMO2-HF: Total energy -81472.775046
FMO2-MP2: Total energy -81706.093841


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.
-2.989-0.6310.652-1.283-1.727-0.002
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 : 0.001 / q_NPA : -0.015
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].
3X7PHE00.0810.0433.397-3.262-1.6070.011-0.814-0.8520.000
4X8VAL0-0.0010.0105.884-0.114-0.1140.0000.0000.0000.000
5X9LEU0-0.065-0.0214.2250.7140.8510.000-0.038-0.0980.000
6X10LEU00.0230.0067.888-0.561-0.5610.0000.0000.0000.000
7X11ASP-1-0.854-0.90611.3231.3621.3620.0000.0000.0000.000
8X12ARG10.8660.90813.289-0.850-0.8500.0000.0000.0000.000
9X13SER0-0.011-0.00515.638-0.105-0.1050.0000.0000.0000.000
10X14ARG10.7840.87618.041-0.554-0.5540.0000.0000.0000.000
11X15PRO00.0350.01020.9350.0160.0160.0000.0000.0000.000
12X16GLY0-0.010-0.01323.620-0.025-0.0250.0000.0000.0000.000
13X17VAL00.0050.01219.035-0.030-0.0300.0000.0000.0000.000
14X18ALA00.0200.01516.7800.0660.0660.0000.0000.0000.000
15X19LEU0-0.0030.01113.362-0.083-0.0830.0000.0000.0000.000
16X20VAL00.007-0.00912.1550.2000.2000.0000.0000.0000.000
17X21THR00.005-0.0018.550-0.169-0.1690.0000.0000.0000.000
18X22LEU0-0.011-0.0108.6340.2210.2210.0000.0000.0000.000
19X23ASN0-0.045-0.0552.250-0.1970.3740.642-0.427-0.787-0.002
20X24ARG10.8090.8924.9360.2740.269-0.001-0.0040.0100.000
21X25PRO00.0410.0345.8650.2410.2410.0000.0000.0000.000
22X26GLU-1-0.875-0.9365.977-2.162-2.1620.0000.0000.0000.000
23X27ARG10.8960.9359.9930.9260.9260.0000.0000.0000.000
24X28MET0-0.004-0.00412.1470.0990.0990.0000.0000.0000.000
25X29ASN0-0.008-0.0029.451-0.023-0.0230.0000.0000.0000.000
26X30SER0-0.0070.02311.4510.0770.0770.0000.0000.0000.000
27X31MET0-0.027-0.00213.087-0.042-0.0420.0000.0000.0000.000
28X32ALA0-0.015-0.00712.9430.0220.0220.0000.0000.0000.000
29X33PHE00.0780.01414.2610.0420.0420.0000.0000.0000.000
30X34ASP-1-0.794-0.8879.663-0.738-0.7380.0000.0000.0000.000
31X35VAL0-0.020-0.0109.257-0.005-0.0050.0000.0000.0000.000
32X36MET0-0.004-0.00511.2970.1720.1720.0000.0000.0000.000
33X37VAL00.0480.03414.6060.0640.0640.0000.0000.0000.000
34X38PRO00.0200.01210.2280.0690.0690.0000.0000.0000.000
35X39LEU0-0.0260.00112.8480.1160.1160.0000.0000.0000.000
36X40LEU0-0.001-0.00513.8660.0300.0300.0000.0000.0000.000
37X41GLU-1-0.934-0.97014.9130.3390.3390.0000.0000.0000.000
38X42LEU00.0170.02112.1500.0290.0290.0000.0000.0000.000
39X43LEU0-0.041-0.03315.680-0.017-0.0170.0000.0000.0000.000
40X44GLY0-0.021-0.01418.492-0.033-0.0330.0000.0000.0000.000
41X45ASP-1-0.877-0.94116.9190.5390.5390.0000.0000.0000.000
42X46LEU0-0.030-0.02816.411-0.021-0.0210.0000.0000.0000.000
43X47ARG10.9230.97620.226-0.271-0.2710.0000.0000.0000.000
44X48HIS0-0.075-0.04523.114-0.061-0.0610.0000.0000.0000.000
45X49ASP-1-0.790-0.84020.6430.5360.5360.0000.0000.0000.000
46X50ASN0-0.002-0.02323.513-0.008-0.0080.0000.0000.0000.000
47X51SER0-0.115-0.07322.842-0.003-0.0030.0000.0000.0000.000
48X52VAL0-0.035-0.01019.8490.0070.0070.0000.0000.0000.000
49X53ARG10.8160.88923.007-0.299-0.2990.0000.0000.0000.000
50X54VAL0-0.013-0.00622.551-0.033-0.0330.0000.0000.0000.000
51X55VAL00.0280.01917.6830.0520.0520.0000.0000.0000.000
52X56ILE0-0.0020.01317.345-0.054-0.0540.0000.0000.0000.000
53X57LEU00.0070.00414.1230.0900.0900.0000.0000.0000.000
54X58THR0-0.008-0.02212.703-0.078-0.0780.0000.0000.0000.000
55X59GLY00.0100.02111.5160.0550.0550.0000.0000.0000.000
56X60ALA00.0160.0097.7740.0420.0420.0000.0000.0000.000
57X61GLY0-0.031-0.0209.657-0.172-0.1720.0000.0000.0000.000
58X62ARG11.0030.98011.5430.3800.3800.0000.0000.0000.000
59X63GLY00.0150.01513.7260.0230.0230.0000.0000.0000.000
60X64PHE0-0.0320.01713.6780.0140.0140.0000.0000.0000.000
61X65SER0-0.003-0.03913.9330.0060.0060.0000.0000.0000.000
62X66SER00.0000.00415.5400.0250.0250.0000.0000.0000.000
63X67GLY0-0.0100.00616.976-0.017-0.0170.0000.0000.0000.000
64X92MET0-0.031-0.04023.2350.0000.0000.0000.0000.0000.000
65X93GLU-1-0.862-0.93422.631-0.069-0.0690.0000.0000.0000.000
66X94VAL00.0590.04118.2660.0130.0130.0000.0000.0000.000
67X95LEU0-0.013-0.00719.7640.0320.0320.0000.0000.0000.000
68X96ASP-1-0.814-0.92021.2460.0460.0460.0000.0000.0000.000
69X97ASN0-0.022-0.01721.9510.0070.0070.0000.0000.0000.000
70X98VAL00.0090.00417.6860.0310.0310.0000.0000.0000.000
71X99ILE00.0000.00120.6550.0280.0280.0000.0000.0000.000
72X100LEU0-0.014-0.01623.3970.0170.0170.0000.0000.0000.000
73X101ALA0-0.050-0.02621.1870.0090.0090.0000.0000.0000.000
74X102LEU00.0160.00319.0390.0250.0250.0000.0000.0000.000
75X103ARG10.9000.95722.671-0.093-0.0930.0000.0000.0000.000
76X104ARG10.9140.95024.575-0.172-0.1720.0000.0000.0000.000
77X105LEU0-0.075-0.00720.6840.0020.0020.0000.0000.0000.000
78X106HIS00.0020.00525.352-0.030-0.0300.0000.0000.0000.000
79X107GLN0-0.044-0.02923.507-0.032-0.0320.0000.0000.0000.000
80X108PRO0-0.003-0.00325.146-0.006-0.0060.0000.0000.0000.000
81X109VAL00.007-0.00719.9900.0370.0370.0000.0000.0000.000
82X110ILE0-0.006-0.01521.537-0.033-0.0330.0000.0000.0000.000
83X111ALA00.004-0.00819.3960.0410.0410.0000.0000.0000.000
84X112ALA00.0270.00017.452-0.025-0.0250.0000.0000.0000.000
85X113VAL0-0.009-0.00317.5480.0090.0090.0000.0000.0000.000
86X114ASN00.0900.02213.9220.0110.0110.0000.0000.0000.000
87X115GLY00.0520.01317.763-0.019-0.0190.0000.0000.0000.000
88X116ALA0-0.024-0.00318.2660.0110.0110.0000.0000.0000.000
89X117ALA00.0270.02118.085-0.002-0.0020.0000.0000.0000.000
90X118ILE0-0.008-0.00619.8450.0020.0020.0000.0000.0000.000
91X119GLY00.0150.01320.758-0.012-0.0120.0000.0000.0000.000
92X120GLY00.0550.00720.6290.0200.0200.0000.0000.0000.000
93X121GLY00.0220.00418.5840.0260.0260.0000.0000.0000.000
94X122LEU0-0.0020.00319.3860.0340.0340.0000.0000.0000.000
95X123CYS0-0.005-0.00922.8000.0190.0190.0000.0000.0000.000
96X124LEU0-0.0090.00416.1330.0200.0200.0000.0000.0000.000
97X125ALA00.0100.00120.7690.0300.0300.0000.0000.0000.000
98X126LEU0-0.043-0.02321.8130.0150.0150.0000.0000.0000.000
99X127ALA00.0040.01522.6670.0010.0010.0000.0000.0000.000
100X128CYS0-0.097-0.02420.8380.0300.0300.0000.0000.0000.000
101X129ASP-1-0.721-0.84423.5520.1840.1840.0000.0000.0000.000
102X130VAL0-0.021-0.01025.060-0.015-0.0150.0000.0000.0000.000
103X131ARG10.8750.94423.325-0.094-0.0940.0000.0000.0000.000
104X132ILE0-0.007-0.00723.068-0.011-0.0110.0000.0000.0000.000
105X133ALA0-0.0110.00322.3650.0100.0100.0000.0000.0000.000
106X134ALA00.0230.02020.7150.0070.0070.0000.0000.0000.000
107X135HIS0-0.017-0.00922.651-0.009-0.0090.0000.0000.0000.000
108X136ASN0-0.062-0.03418.881-0.027-0.0270.0000.0000.0000.000
109X137ALA0-0.107-0.03221.371-0.021-0.0210.0000.0000.0000.000
110X138TYR0-0.011-0.01321.398-0.013-0.0130.0000.0000.0000.000
111X139PHE0-0.026-0.01822.8450.0000.0000.0000.0000.0000.000
112X140ARG10.8940.93924.1290.0940.0940.0000.0000.0000.000
113X141ALA00.0330.03024.948-0.002-0.0020.0000.0000.0000.000
114X142ALA00.002-0.02124.568-0.008-0.0080.0000.0000.0000.000
115X143GLY00.0650.02825.3500.0070.0070.0000.0000.0000.000
116X144ILE0-0.061-0.03425.309-0.008-0.0080.0000.0000.0000.000
117X145ASN00.0180.01427.7490.0140.0140.0000.0000.0000.000
118X146ASN0-0.038-0.02029.764-0.008-0.0080.0000.0000.0000.000
119X147GLY00.0390.02630.2840.0040.0040.0000.0000.0000.000
120X148LEU0-0.0050.00330.3170.0000.0000.0000.0000.0000.000
121X149THR00.0400.01826.0290.0020.0020.0000.0000.0000.000
122X150ALA00.0310.01224.9190.0090.0090.0000.0000.0000.000
123X151SER00.0160.00223.5880.0120.0120.0000.0000.0000.000
124X152GLU-1-0.943-0.96425.452-0.033-0.0330.0000.0000.0000.000
125X153LEU00.0310.01628.8620.0080.0080.0000.0000.0000.000
126X154GLY00.0190.00827.5620.0080.0080.0000.0000.0000.000
127X155LEU00.007-0.00925.9260.0090.0090.0000.0000.0000.000
128X156SER0-0.042-0.01829.0430.0050.0050.0000.0000.0000.000
129X157TYR0-0.049-0.03031.786-0.001-0.0010.0000.0000.0000.000
130X158LEU00.006-0.01527.3960.0030.0030.0000.0000.0000.000
131X159LEU00.0220.02229.2880.0050.0050.0000.0000.0000.000
132X160PRO0-0.030-0.03131.5870.0030.0030.0000.0000.0000.000
133X161ARG10.8640.93434.055-0.041-0.0410.0000.0000.0000.000
134X162ALA0-0.0250.01531.2130.0050.0050.0000.0000.0000.000
135X163ILE00.0050.00832.1910.0010.0010.0000.0000.0000.000
136X164GLY00.0030.00935.101-0.004-0.0040.0000.0000.0000.000
137X165THR00.016-0.01837.268-0.002-0.0020.0000.0000.0000.000
138X166SER00.001-0.00138.835-0.003-0.0030.0000.0000.0000.000
139X167ARG11.0121.00335.778-0.029-0.0290.0000.0000.0000.000
140X168ALA00.0380.03433.962-0.004-0.0040.0000.0000.0000.000
141X169PHE00.016-0.00434.538-0.005-0.0050.0000.0000.0000.000
142X170GLU-1-0.825-0.88836.241-0.018-0.0180.0000.0000.0000.000
143X171ILE0-0.0020.01530.689-0.006-0.0060.0000.0000.0000.000
144X172MET0-0.060-0.04430.749-0.004-0.0040.0000.0000.0000.000
145X173LEU0-0.034-0.00832.854-0.007-0.0070.0000.0000.0000.000
146X174THR0-0.063-0.03634.854-0.006-0.0060.0000.0000.0000.000
147X175GLY0-0.0030.01230.880-0.007-0.0070.0000.0000.0000.000
148X176ARG10.7130.82630.1300.0020.0020.0000.0000.0000.000
149X177ASP-1-0.845-0.90526.918-0.071-0.0710.0000.0000.0000.000
150X178VAL0-0.028-0.01727.9260.0050.0050.0000.0000.0000.000
151X179ASP-1-0.830-0.92027.4310.0100.0100.0000.0000.0000.000
152X180ALA00.0810.02525.5650.0070.0070.0000.0000.0000.000
153X181ALA00.0010.01027.5080.0110.0110.0000.0000.0000.000
154X182GLU-1-0.860-0.92631.0620.0080.0080.0000.0000.0000.000
155X183ALA00.004-0.00528.2240.0030.0030.0000.0000.0000.000
156X184GLU-1-0.960-0.97930.1220.0740.0740.0000.0000.0000.000
157X185ARG10.9831.01231.352-0.026-0.0260.0000.0000.0000.000
158X186ILE0-0.133-0.07832.1040.0000.0000.0000.0000.0000.000
159X187GLY00.0280.02832.943-0.001-0.0010.0000.0000.0000.000
160X188LEU0-0.042-0.00827.3960.0030.0030.0000.0000.0000.000
161X189VAL0-0.067-0.03525.4550.0110.0110.0000.0000.0000.000
162X190SER0-0.008-0.01028.062-0.003-0.0030.0000.0000.0000.000
163X191ARG10.9700.98328.182-0.140-0.1400.0000.0000.0000.000
164X192THR00.030-0.00226.4900.0090.0090.0000.0000.0000.000
165X193VAL0-0.079-0.02424.138-0.004-0.0040.0000.0000.0000.000
166X194PRO00.0640.01925.075-0.008-0.0080.0000.0000.0000.000
167X195ASP-1-0.779-0.90420.2280.0810.0810.0000.0000.0000.000
168X196ASP-1-0.946-0.96320.4370.1680.1680.0000.0000.0000.000
169X197ASP-1-0.892-0.94821.7760.1900.1900.0000.0000.0000.000
170X198LEU0-0.057-0.01518.3790.0190.0190.0000.0000.0000.000
171X199LEU00.043-0.00114.8480.0120.0120.0000.0000.0000.000
172X200GLU-1-0.755-0.85419.4710.4080.4080.0000.0000.0000.000
173X201THR00.0110.02022.447-0.016-0.0160.0000.0000.0000.000
174X202CYS0-0.058-0.01620.716-0.011-0.0110.0000.0000.0000.000
175X203PHE00.020-0.01217.1960.0090.0090.0000.0000.0000.000
176X204GLU-1-0.949-0.96122.7960.1910.1910.0000.0000.0000.000
177X205MET0-0.012-0.00625.770-0.012-0.0120.0000.0000.0000.000
178X206ALA00.024-0.00323.311-0.008-0.0080.0000.0000.0000.000
179X207GLN00.0140.00225.4070.0170.0170.0000.0000.0000.000
180X208ARG10.9380.97027.445-0.172-0.1720.0000.0000.0000.000
181X209MET0-0.013-0.01327.147-0.005-0.0050.0000.0000.0000.000
182X210ARG10.8860.95225.716-0.329-0.3290.0000.0000.0000.000
183X211GLY0-0.0220.00529.470-0.003-0.0030.0000.0000.0000.000
184X212PHE0-0.0010.02032.626-0.014-0.0140.0000.0000.0000.000
185X213SER00.0380.02132.8430.0160.0160.0000.0000.0000.000
186X214ARG10.9150.93129.686-0.227-0.2270.0000.0000.0000.000
187X215PRO00.026-0.00332.1070.0010.0010.0000.0000.0000.000
188X216GLY00.0170.02334.739-0.008-0.0080.0000.0000.0000.000
189X217ILE00.0200.00029.464-0.007-0.0070.0000.0000.0000.000
190X218GLU-1-0.850-0.89931.1740.1850.1850.0000.0000.0000.000
191X219LEU00.0130.00732.145-0.006-0.0060.0000.0000.0000.000
192X220THR0-0.031-0.00333.814-0.011-0.0110.0000.0000.0000.000
193X221LYS10.8100.91025.190-0.231-0.2310.0000.0000.0000.000
194X222ARG10.9820.97231.898-0.133-0.1330.0000.0000.0000.000
195X223THR0-0.041-0.02133.643-0.010-0.0100.0000.0000.0000.000
196X224LEU00.0150.01332.957-0.008-0.0080.0000.0000.0000.000
197X225TRP0-0.064-0.04427.346-0.017-0.0170.0000.0000.0000.000
198X226SER0-0.074-0.04933.243-0.010-0.0100.0000.0000.0000.000
199X227GLY00.0550.02136.330-0.007-0.0070.0000.0000.0000.000
200X228LEU0-0.072-0.03732.925-0.007-0.0070.0000.0000.0000.000
201X229ASP-1-0.870-0.91735.0650.0660.0660.0000.0000.0000.000
202X230ALA0-0.055-0.00438.044-0.004-0.0040.0000.0000.0000.000
203X231ALA00.0100.00641.351-0.003-0.0030.0000.0000.0000.000
204X232SER0-0.009-0.01644.459-0.003-0.0030.0000.0000.0000.000
205X233LEU00.0370.01645.7370.0030.0030.0000.0000.0000.000
206X234GLU-1-0.926-0.97046.9880.0470.0470.0000.0000.0000.000
207X235GLY00.0300.01547.1930.0020.0020.0000.0000.0000.000
208X236HIS0-0.070-0.03039.4290.0000.0000.0000.0000.0000.000
209X237MET0-0.045-0.03644.3310.0030.0030.0000.0000.0000.000
210X238GLN0-0.065-0.02446.6360.0010.0010.0000.0000.0000.000
211X239ALA00.0140.03442.2830.0000.0000.0000.0000.0000.000
212X240GLU-1-1.023-1.01041.7550.0760.0760.0000.0000.0000.000