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

tag_button

FMODB ID: 2LL5R

Calculation Name: 5EY6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EY6

Chain ID: A

ChEMBL ID:

UniProt ID: B9GQ64

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2600784.983156
FMO2-HF: Nuclear repulsion 2516045.125387
FMO2-HF: Total energy -84739.857769
FMO2-MP2: Total energy -84989.53242


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:4:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-5.873-0.1470.891-2.483-4.132-0.005
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.003
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].
3A6LYS10.9230.9533.209-3.260-0.5980.061-1.382-1.3410.002
4A7VAL00.0320.0165.7190.1550.1550.0000.0000.0000.000
5A8TYR0-0.043-0.0428.4440.0160.0160.0000.0000.0000.000
6A9GLY00.0380.00111.4840.0100.0100.0000.0000.0000.000
7A10PRO0-0.026-0.00613.101-0.018-0.0180.0000.0000.0000.000
8A11PRO00.1290.03513.0280.0040.0040.0000.0000.0000.000
9A12LEU00.0100.02915.3350.0040.0040.0000.0000.0000.000
10A13SER00.0090.02617.4450.0070.0070.0000.0000.0000.000
11A14THR00.0820.03018.115-0.010-0.0100.0000.0000.0000.000
12A15ALA00.0150.00618.505-0.005-0.0050.0000.0000.0000.000
13A16VAL0-0.006-0.01412.805-0.009-0.0090.0000.0000.0000.000
14A17SER00.0290.01813.919-0.018-0.0180.0000.0000.0000.000
15A18ARG10.8780.93815.4000.0570.0570.0000.0000.0000.000
16A19VAL00.0100.00610.4860.0000.0000.0000.0000.0000.000
17A20LEU0-0.023-0.0149.561-0.020-0.0200.0000.0000.0000.000
18A21VAL00.0550.02211.616-0.007-0.0070.0000.0000.0000.000
19A22THR00.018-0.00113.3600.0130.0130.0000.0000.0000.000
20A23LEU0-0.012-0.0127.1760.0010.0010.0000.0000.0000.000
21A24LEU0-0.069-0.03010.2870.0110.0110.0000.0000.0000.000
22A25GLU-1-0.750-0.81611.741-0.062-0.0620.0000.0000.0000.000
23A26LYS10.7880.91311.4990.0880.0880.0000.0000.0000.000
24A27ASP-1-0.911-0.94910.656-0.087-0.0870.0000.0000.0000.000
25A28VAL0-0.018-0.0025.4680.0100.0100.0000.0000.0000.000
26A29PRO0-0.009-0.0082.845-0.621-0.0820.098-0.169-0.4670.000
27A30PHE0-0.004-0.0112.549-1.1190.0740.508-0.705-0.996-0.003
28A31GLN00.0060.0063.221-1.1110.2030.224-0.218-1.319-0.004
29A32ILE00.001-0.0074.2710.0070.0250.000-0.009-0.0090.000
30A33ILE0-0.046-0.0176.8600.0520.0520.0000.0000.0000.000
31A34PRO00.0150.0049.7260.0060.0060.0000.0000.0000.000
32A35VAL00.0300.00613.4030.0140.0140.0000.0000.0000.000
33A36ASP-1-0.812-0.88316.225-0.032-0.0320.0000.0000.0000.000
34A37MET0-0.017-0.02919.4690.0050.0050.0000.0000.0000.000
35A38SER0-0.079-0.06322.1020.0050.0050.0000.0000.0000.000
36A39LYS10.9310.96221.5150.0170.0170.0000.0000.0000.000
37A40GLY0-0.0060.00324.0090.0040.0040.0000.0000.0000.000
38A41GLU-1-0.892-0.94417.712-0.013-0.0130.0000.0000.0000.000
39A42HIS0-0.0030.00519.3990.0030.0030.0000.0000.0000.000
40A43LYS10.9180.95420.4190.0090.0090.0000.0000.0000.000
41A44LYS10.9661.00118.115-0.012-0.0120.0000.0000.0000.000
42A45PRO00.0390.00720.8590.0000.0000.0000.0000.0000.000
43A46ASP-1-0.903-0.95616.9890.0620.0620.0000.0000.0000.000
44A47TYR0-0.065-0.04214.4850.0020.0020.0000.0000.0000.000
45A48LEU00.008-0.00617.579-0.004-0.0040.0000.0000.0000.000
46A49LYS10.8930.95418.336-0.050-0.0500.0000.0000.0000.000
47A50ILE0-0.0070.01013.1900.0040.0040.0000.0000.0000.000
48A51GLN00.0250.00617.020-0.005-0.0050.0000.0000.0000.000
49A52PRO00.0330.03218.8180.0000.0000.0000.0000.0000.000
50A53PHE0-0.009-0.00422.0310.0010.0010.0000.0000.0000.000
51A54GLY0-0.027-0.00921.478-0.001-0.0010.0000.0000.0000.000
52A55GLN0-0.052-0.02320.711-0.004-0.0040.0000.0000.0000.000
53A56VAL0-0.0060.03116.103-0.001-0.0010.0000.0000.0000.000
54A57PRO0-0.014-0.01913.1410.0060.0060.0000.0000.0000.000
55A58ALA00.0090.00013.2690.0190.0190.0000.0000.0000.000
56A59PHE00.0200.0007.999-0.050-0.0500.0000.0000.0000.000
57A60GLN00.0180.0138.5850.1060.1060.0000.0000.0000.000
58A61ASP-1-0.734-0.8536.096-0.241-0.2410.0000.0000.0000.000
59A62GLU-1-0.916-0.9576.1650.2660.2660.0000.0000.0000.000
60A63SER0-0.062-0.0357.867-0.057-0.0570.0000.0000.0000.000
61A64ILE0-0.027-0.00110.838-0.018-0.0180.0000.0000.0000.000
62A65SER0-0.030-0.02111.0760.0100.0100.0000.0000.0000.000
63A66LEU0-0.027-0.00313.1910.0000.0000.0000.0000.0000.000
64A67PHE00.0430.00114.510-0.013-0.0130.0000.0000.0000.000
65A68GLU-1-0.881-0.94516.950-0.039-0.0390.0000.0000.0000.000
66A69SER00.0160.01516.046-0.005-0.0050.0000.0000.0000.000
67A70ARG10.9010.92216.5680.0350.0350.0000.0000.0000.000
68A71SER00.0050.00618.5210.0000.0000.0000.0000.0000.000
69A72ILE0-0.0210.00512.087-0.002-0.0020.0000.0000.0000.000
70A73CYS0-0.051-0.00713.771-0.016-0.0160.0000.0000.0000.000
71A74ARG10.9650.98715.3390.0380.0380.0000.0000.0000.000
72A75TYR0-0.030-0.01310.0950.0100.0100.0000.0000.0000.000
73A76VAL0-0.020-0.0129.849-0.002-0.0020.0000.0000.0000.000
74A77CYS0-0.041-0.02412.1200.0040.0040.0000.0000.0000.000
75A78GLU-1-0.965-0.96515.045-0.022-0.0220.0000.0000.0000.000
76A79LYS10.8830.9558.5560.0390.0390.0000.0000.0000.000
77A80TYR0-0.012-0.0216.5120.0010.0010.0000.0000.0000.000
78A81ALA00.0510.03012.165-0.001-0.0010.0000.0000.0000.000
79A82ASP-1-0.977-0.98614.262-0.045-0.0450.0000.0000.0000.000
80A83ARG10.8460.9169.6400.0880.0880.0000.0000.0000.000
81A84GLY0-0.009-0.01013.706-0.002-0.0020.0000.0000.0000.000
82A85ASP-1-0.830-0.92315.012-0.047-0.0470.0000.0000.0000.000
83A86LYS10.8830.93817.5300.0360.0360.0000.0000.0000.000
84A87GLY00.0770.05318.9980.0020.0020.0000.0000.0000.000
85A88LEU0-0.0140.01416.4970.0010.0010.0000.0000.0000.000
86A89TYR0-0.052-0.07718.942-0.001-0.0010.0000.0000.0000.000
87A90GLY0-0.0020.00021.0480.0030.0030.0000.0000.0000.000
88A91THR0-0.054-0.04521.909-0.001-0.0010.0000.0000.0000.000
89A92ASN00.000-0.00623.8390.0030.0030.0000.0000.0000.000
90A93PRO00.006-0.02426.217-0.002-0.0020.0000.0000.0000.000
91A94LEU00.0250.02227.5460.0000.0000.0000.0000.0000.000
92A95GLU-1-0.797-0.86826.432-0.028-0.0280.0000.0000.0000.000
93A96ARG10.9730.99622.1070.0260.0260.0000.0000.0000.000
94A97ALA00.008-0.00325.391-0.002-0.0020.0000.0000.0000.000
95A98SER0-0.007-0.00428.2770.0000.0000.0000.0000.0000.000
96A99ILE0-0.0070.00323.5260.0000.0000.0000.0000.0000.000
97A100ASP-1-0.843-0.92524.808-0.033-0.0330.0000.0000.0000.000
98A101GLN0-0.017-0.00426.3380.0000.0000.0000.0000.0000.000
99A102TRP00.0370.01028.5080.0000.0000.0000.0000.0000.000
100A103VAL0-0.029-0.00722.985-0.002-0.0020.0000.0000.0000.000
101A104GLU-1-0.946-0.97225.958-0.028-0.0280.0000.0000.0000.000
102A105ALA0-0.0030.00728.3460.0010.0010.0000.0000.0000.000
103A106GLU-1-0.735-0.84524.394-0.043-0.0430.0000.0000.0000.000
104A107GLY0-0.012-0.00226.7000.0000.0000.0000.0000.0000.000
105A108GLN0-0.034-0.01927.2560.0030.0030.0000.0000.0000.000
106A109SER0-0.061-0.02730.9340.0020.0020.0000.0000.0000.000
107A110PHE00.0310.01427.0110.0010.0010.0000.0000.0000.000
108A111GLY00.0040.03027.8720.0000.0000.0000.0000.0000.000
109A112PRO0-0.027-0.01728.5190.0000.0000.0000.0000.0000.000
110A113SER00.0030.00830.9980.0000.0000.0000.0000.0000.000
111A114SER00.025-0.00629.126-0.001-0.0010.0000.0000.0000.000
112A115GLY00.0280.01028.179-0.001-0.0010.0000.0000.0000.000
113A116ALA0-0.040-0.01628.9870.0000.0000.0000.0000.0000.000
114A117LEU0-0.001-0.00832.1920.0010.0010.0000.0000.0000.000
115A118VAL00.0330.02326.2740.0000.0000.0000.0000.0000.000
116A119PHE0-0.010-0.00729.0690.0000.0000.0000.0000.0000.000
117A120GLN00.042-0.00230.2320.0010.0010.0000.0000.0000.000
118A121LEU0-0.018-0.00432.8980.0010.0010.0000.0000.0000.000
119A122ALA00.0040.01628.7270.0000.0000.0000.0000.0000.000
120A123PHE0-0.127-0.06523.459-0.002-0.0020.0000.0000.0000.000
121A124ALA0-0.0210.00229.3690.0010.0010.0000.0000.0000.000
122A125PRO00.0340.01932.5650.0010.0010.0000.0000.0000.000
123A126ARG10.9430.96626.4170.0340.0340.0000.0000.0000.000
124A127MET0-0.042-0.01331.028-0.001-0.0010.0000.0000.0000.000
125A128ASN00.0150.00733.0230.0000.0000.0000.0000.0000.000
126A129ILE0-0.0070.00833.1830.0010.0010.0000.0000.0000.000
127A130PRO0-0.055-0.02036.947-0.001-0.0010.0000.0000.0000.000
128A131GLN00.0110.00537.0970.0010.0010.0000.0000.0000.000
129A132ASP-1-0.841-0.93738.768-0.012-0.0120.0000.0000.0000.000
130A133GLN00.0450.02640.054-0.001-0.0010.0000.0000.0000.000
131A134GLY0-0.038-0.00742.5730.0000.0000.0000.0000.0000.000
132A135VAL00.022-0.01236.1930.0000.0000.0000.0000.0000.000
133A136ILE0-0.0050.00737.329-0.001-0.0010.0000.0000.0000.000
134A137LYS10.9560.98638.8770.0120.0120.0000.0000.0000.000
135A138GLN00.003-0.00340.364-0.001-0.0010.0000.0000.0000.000
136A139ASN0-0.062-0.05935.5270.0000.0000.0000.0000.0000.000
137A140GLU-1-0.790-0.87336.897-0.019-0.0190.0000.0000.0000.000
138A141GLU-1-0.945-0.96738.454-0.014-0.0140.0000.0000.0000.000
139A142LYS10.8800.93437.4680.0160.0160.0000.0000.0000.000
140A143LEU00.0370.02432.5670.0000.0000.0000.0000.0000.000
141A144GLY00.0190.00536.138-0.001-0.0010.0000.0000.0000.000
142A145LYS10.9500.97738.8880.0140.0140.0000.0000.0000.000
143A146VAL0-0.010-0.00133.3270.0000.0000.0000.0000.0000.000
144A147LEU0-0.003-0.01232.7470.0000.0000.0000.0000.0000.000
145A148ASP-1-0.855-0.92636.338-0.017-0.0170.0000.0000.0000.000
146A149ILE0-0.066-0.02537.0040.0000.0000.0000.0000.0000.000
147A150TYR0-0.040-0.06829.8570.0010.0010.0000.0000.0000.000
148A151GLU-1-0.755-0.86535.684-0.021-0.0210.0000.0000.0000.000
149A152GLN0-0.025-0.00738.2600.0000.0000.0000.0000.0000.000
150A153ARG10.9020.95333.0450.0230.0230.0000.0000.0000.000
151A154LEU0-0.045-0.02731.8840.0000.0000.0000.0000.0000.000
152A155GLY00.0380.01235.9300.0000.0000.0000.0000.0000.000
153A156GLU-1-1.025-1.00338.510-0.015-0.0150.0000.0000.0000.000
154A157SER0-0.054-0.02733.0490.0000.0000.0000.0000.0000.000
155A158ARG10.7770.88930.7960.0290.0290.0000.0000.0000.000
156A159PHE0-0.001-0.01127.555-0.002-0.0020.0000.0000.0000.000
157A160LEU00.0080.00928.2460.0020.0020.0000.0000.0000.000
158A161ALA0-0.0020.00227.8860.0020.0020.0000.0000.0000.000
159A162GLY0-0.0010.00429.9580.0020.0020.0000.0000.0000.000
160A163ASP-1-0.881-0.94831.107-0.024-0.0240.0000.0000.0000.000
161A164GLU-1-0.954-0.97824.030-0.038-0.0380.0000.0000.0000.000
162A165PHE0-0.027-0.00720.108-0.001-0.0010.0000.0000.0000.000
163A166THR00.0410.01422.485-0.002-0.0020.0000.0000.0000.000
164A167PHE00.006-0.03217.283-0.002-0.0020.0000.0000.0000.000
165A168ALA00.0150.00821.417-0.001-0.0010.0000.0000.0000.000
166A169ASP-1-0.732-0.86124.553-0.037-0.0370.0000.0000.0000.000
167A170LEU00.0150.01816.8860.0000.0000.0000.0000.0000.000
168A171SER0-0.056-0.03721.023-0.006-0.0060.0000.0000.0000.000
169A172HIS00.0300.02422.0080.0040.0040.0000.0000.0000.000
170A173LEU0-0.0170.00820.4480.0020.0020.0000.0000.0000.000
171A174PRO0-0.037-0.01219.4540.0020.0020.0000.0000.0000.000
172A175ASN0-0.037-0.03822.006-0.001-0.0010.0000.0000.0000.000
173A176GLY00.0540.02825.5710.0030.0030.0000.0000.0000.000
174A177ASP-1-0.841-0.93123.758-0.048-0.0480.0000.0000.0000.000
175A178TYR0-0.074-0.07121.7080.0020.0020.0000.0000.0000.000
176A179LEU0-0.0180.00126.8650.0030.0030.0000.0000.0000.000
177A180VAL0-0.0080.01929.1960.0030.0030.0000.0000.0000.000
178A181ASN0-0.028-0.01126.3800.0040.0040.0000.0000.0000.000
179A182ALA0-0.076-0.03328.0790.0000.0000.0000.0000.0000.000
180A183THR0-0.077-0.05630.1700.0020.0020.0000.0000.0000.000
181A184ASP-1-0.883-0.94233.384-0.020-0.0200.0000.0000.0000.000
182A185LYS10.8890.92134.5460.0200.0200.0000.0000.0000.000
183A186GLY00.0570.03233.695-0.001-0.0010.0000.0000.0000.000
184A187HIS00.0100.01034.6440.0000.0000.0000.0000.0000.000
185A188LEU0-0.058-0.00535.1390.0010.0010.0000.0000.0000.000
186A189PHE00.0330.00030.3820.0000.0000.0000.0000.0000.000
187A190THR00.0040.00134.8940.0000.0000.0000.0000.0000.000
188A191SER0-0.100-0.06137.1500.0010.0010.0000.0000.0000.000
189A192ARG10.8090.92137.5450.0210.0210.0000.0000.0000.000
190A193GLU-1-0.876-0.92837.831-0.019-0.0190.0000.0000.0000.000
191A194ASN0-0.043-0.03737.061-0.001-0.0010.0000.0000.0000.000
192A195VAL0-0.041-0.02833.007-0.002-0.0020.0000.0000.0000.000
193A196GLY00.0310.02033.031-0.002-0.0020.0000.0000.0000.000
194A197ARG10.8150.91533.2480.0230.0230.0000.0000.0000.000
195A198TRP0-0.033-0.02727.699-0.002-0.0020.0000.0000.0000.000
196A199TRP00.0300.00925.430-0.003-0.0030.0000.0000.0000.000
197A200ASN0-0.0120.00728.275-0.003-0.0030.0000.0000.0000.000
198A201GLU-1-0.816-0.87328.204-0.033-0.0330.0000.0000.0000.000
199A202ILE0-0.046-0.02424.358-0.003-0.0030.0000.0000.0000.000
200A203SER0-0.105-0.07523.387-0.005-0.0050.0000.0000.0000.000
201A204ASP-1-0.856-0.91724.095-0.043-0.0430.0000.0000.0000.000
202A205ARG10.8470.92019.8770.0570.0570.0000.0000.0000.000
203A206GLU-1-0.857-0.96018.845-0.058-0.0580.0000.0000.0000.000
204A207SER0-0.095-0.07215.588-0.005-0.0050.0000.0000.0000.000
205A208TRP00.022-0.01116.120-0.013-0.0130.0000.0000.0000.000
206A209LYS10.8790.94518.5010.0460.0460.0000.0000.0000.000
207A210LYS10.9530.97911.6880.1160.1160.0000.0000.0000.000
208A211VAL0-0.007-0.00213.946-0.007-0.0070.0000.0000.0000.000
209A212ILE0-0.029-0.01415.8420.0000.0000.0000.0000.0000.000
210A213GLU-1-0.861-0.93817.528-0.055-0.0550.0000.0000.0000.000
211A214MET0-0.070-0.03710.545-0.001-0.0010.0000.0000.0000.000
212A215ARG10.8220.91315.4100.0710.0710.0000.0000.0000.000
213A216LYS10.8550.95117.9690.0570.0570.0000.0000.0000.000
214A217SER0-0.0260.00416.0890.0080.0080.0000.0000.0000.000
215A218GLY0-0.030-0.01515.768-0.013-0.0130.0000.0000.0000.000