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: 6GGRZ

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2603487.986193
FMO2-HF: Nuclear repulsion 2518747.153164
FMO2-HF: Total energy -84740.833028
FMO2-MP2: Total energy -84990.578447


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.
-5.959-0.7340.933-2.249-3.908-0.006
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 : -0.012 / 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].
3A6LYS10.9170.9553.200-3.464-1.0700.062-1.214-1.2410.001
4A7VAL00.0350.0165.6850.0720.0720.0000.0000.0000.000
5A8TYR0-0.039-0.0388.4320.0540.0540.0000.0000.0000.000
6A9GLY00.038-0.00111.452-0.011-0.0110.0000.0000.0000.000
7A10PRO0-0.035-0.01013.083-0.013-0.0130.0000.0000.0000.000
8A11PRO00.1240.03213.021-0.003-0.0030.0000.0000.0000.000
9A12LEU00.0000.02515.343-0.001-0.0010.0000.0000.0000.000
10A13SER00.0220.02417.4430.0020.0020.0000.0000.0000.000
11A14THR00.0750.03918.131-0.011-0.0110.0000.0000.0000.000
12A15ALA00.0380.01818.523-0.009-0.0090.0000.0000.0000.000
13A16VAL0-0.016-0.01712.809-0.013-0.0130.0000.0000.0000.000
14A17SER00.0230.00613.945-0.023-0.0230.0000.0000.0000.000
15A18ARG10.8650.93215.4430.0620.0620.0000.0000.0000.000
16A19VAL00.0160.01310.536-0.009-0.0090.0000.0000.0000.000
17A20LEU0-0.031-0.0129.584-0.031-0.0310.0000.0000.0000.000
18A21VAL00.0600.02111.670-0.020-0.0200.0000.0000.0000.000
19A22THR00.0190.00613.3780.0070.0070.0000.0000.0000.000
20A23LEU0-0.008-0.0097.205-0.008-0.0080.0000.0000.0000.000
21A24LEU0-0.069-0.02810.062-0.010-0.0100.0000.0000.0000.000
22A25GLU-1-0.743-0.80011.600-0.114-0.1140.0000.0000.0000.000
23A26LYS10.7660.89511.6150.1720.1720.0000.0000.0000.000
24A27ASP-1-0.888-0.92610.312-0.251-0.2510.0000.0000.0000.000
25A28VAL0-0.0080.0055.474-0.021-0.0210.0000.0000.0000.000
26A29PRO0-0.012-0.0102.661-0.675-0.0750.184-0.198-0.5870.000
27A30PHE00.004-0.0072.605-1.2180.0690.531-0.746-1.072-0.004
28A31GLN00.0050.0043.147-0.4280.4990.156-0.082-1.000-0.003
29A32ILE00.008-0.0034.2440.0060.0230.000-0.009-0.0080.000
30A33ILE0-0.033-0.0117.2330.0810.0810.0000.0000.0000.000
31A34PRO00.0140.00610.009-0.022-0.0220.0000.0000.0000.000
32A35VAL00.0340.00713.5770.0190.0190.0000.0000.0000.000
33A36ASP-1-0.776-0.84916.3820.0040.0040.0000.0000.0000.000
34A37MET0-0.009-0.01919.6680.0020.0020.0000.0000.0000.000
35A38SER0-0.073-0.05822.1210.0010.0010.0000.0000.0000.000
36A39LYS10.8780.92321.999-0.023-0.0230.0000.0000.0000.000
37A40GLY00.0010.00424.3630.0040.0040.0000.0000.0000.000
38A41GLU-1-0.833-0.90018.2000.0660.0660.0000.0000.0000.000
39A42HIS00.0090.00719.5790.0110.0110.0000.0000.0000.000
40A43LYS10.9190.95220.597-0.016-0.0160.0000.0000.0000.000
41A44LYS10.8930.94918.764-0.073-0.0730.0000.0000.0000.000
42A45PRO00.0580.01421.3810.0010.0010.0000.0000.0000.000
43A46ASP-1-0.865-0.92717.7090.1100.1100.0000.0000.0000.000
44A47TYR0-0.043-0.03114.5160.0050.0050.0000.0000.0000.000
45A48LEU00.005-0.00618.098-0.008-0.0080.0000.0000.0000.000
46A49LYS10.8110.90118.836-0.099-0.0990.0000.0000.0000.000
47A50ILE0-0.0120.00413.223-0.001-0.0010.0000.0000.0000.000
48A51GLN0-0.005-0.01417.079-0.013-0.0130.0000.0000.0000.000
49A52PRO00.0360.03618.7860.0030.0030.0000.0000.0000.000
50A53PHE0-0.0120.00022.0370.0010.0010.0000.0000.0000.000
51A54GLY0-0.021-0.01121.442-0.001-0.0010.0000.0000.0000.000
52A55GLN0-0.067-0.02720.677-0.005-0.0050.0000.0000.0000.000
53A56VAL00.0030.03516.2160.0040.0040.0000.0000.0000.000
54A57PRO00.007-0.00613.1320.0020.0020.0000.0000.0000.000
55A58ALA00.007-0.00513.2700.0130.0130.0000.0000.0000.000
56A59PHE00.0200.0058.040-0.034-0.0340.0000.0000.0000.000
57A60GLN00.0260.0178.5690.1310.1310.0000.0000.0000.000
58A61ASP-1-0.721-0.8276.112-0.453-0.4530.0000.0000.0000.000
59A62GLU-1-0.862-0.8975.980-0.051-0.0510.0000.0000.0000.000
60A63SER0-0.043-0.0327.6770.0310.0310.0000.0000.0000.000
61A64ILE0-0.044-0.00910.7890.0130.0130.0000.0000.0000.000
62A65SER0-0.025-0.01611.0760.0120.0120.0000.0000.0000.000
63A66LEU0-0.021-0.00313.193-0.001-0.0010.0000.0000.0000.000
64A67PHE00.034-0.00814.499-0.004-0.0040.0000.0000.0000.000
65A68GLU-1-0.842-0.93816.944-0.058-0.0580.0000.0000.0000.000
66A69SER0-0.0090.01416.062-0.011-0.0110.0000.0000.0000.000
67A70ARG10.8960.90316.6000.0400.0400.0000.0000.0000.000
68A71SER0-0.0030.00418.512-0.005-0.0050.0000.0000.0000.000
69A72ILE0-0.0240.00112.121-0.008-0.0080.0000.0000.0000.000
70A73CYS0-0.049-0.01513.789-0.027-0.0270.0000.0000.0000.000
71A74ARG10.8220.89915.3670.0550.0550.0000.0000.0000.000
72A75TYR0-0.032-0.03610.0350.0170.0170.0000.0000.0000.000
73A76VAL0-0.025-0.0149.816-0.015-0.0150.0000.0000.0000.000
74A77CYS0-0.048-0.02712.134-0.006-0.0060.0000.0000.0000.000
75A78GLU-1-0.917-0.94115.063-0.074-0.0740.0000.0000.0000.000
76A79LYS10.8110.8918.3510.2790.2790.0000.0000.0000.000
77A80TYR0-0.009-0.0196.595-0.024-0.0240.0000.0000.0000.000
78A81ALA00.0440.02912.1700.0030.0030.0000.0000.0000.000
79A82ASP-1-0.958-0.97414.179-0.144-0.1440.0000.0000.0000.000
80A83ARG10.8520.9089.6030.2600.2600.0000.0000.0000.000
81A84GLY0-0.002-0.00713.7260.0040.0040.0000.0000.0000.000
82A85ASP-1-0.811-0.90615.007-0.089-0.0890.0000.0000.0000.000
83A86LYS10.8550.92017.5630.1070.1070.0000.0000.0000.000
84A87GLY00.0850.05719.0240.0030.0030.0000.0000.0000.000
85A88LEU0-0.0120.01516.5130.0040.0040.0000.0000.0000.000
86A89TYR0-0.034-0.08018.7790.0030.0030.0000.0000.0000.000
87A90GLY00.0080.00121.0730.0050.0050.0000.0000.0000.000
88A91THR0-0.061-0.05121.925-0.005-0.0050.0000.0000.0000.000
89A92ASN0-0.047-0.03323.8520.0050.0050.0000.0000.0000.000
90A93PRO00.036-0.00226.227-0.002-0.0020.0000.0000.0000.000
91A94LEU00.0270.02127.5510.0010.0010.0000.0000.0000.000
92A95GLU-1-0.752-0.83326.447-0.058-0.0580.0000.0000.0000.000
93A96ARG10.8790.94521.5270.0750.0750.0000.0000.0000.000
94A97ALA00.0150.00425.407-0.001-0.0010.0000.0000.0000.000
95A98SER0-0.029-0.02728.2930.0020.0020.0000.0000.0000.000
96A99ILE00.0020.00523.4960.0010.0010.0000.0000.0000.000
97A100ASP-1-0.810-0.87924.307-0.059-0.0590.0000.0000.0000.000
98A101GLN0-0.020-0.00726.3620.0030.0030.0000.0000.0000.000
99A102TRP00.0300.00428.6390.0020.0020.0000.0000.0000.000
100A103VAL0-0.0190.00223.0170.0000.0000.0000.0000.0000.000
101A104GLU-1-0.837-0.92026.009-0.045-0.0450.0000.0000.0000.000
102A105ALA00.0020.01128.3900.0030.0030.0000.0000.0000.000
103A106GLU-1-0.728-0.81524.266-0.055-0.0550.0000.0000.0000.000
104A107GLY0-0.008-0.00826.7410.0020.0020.0000.0000.0000.000
105A108GLN0-0.050-0.02127.2910.0050.0050.0000.0000.0000.000
106A109SER0-0.058-0.02630.9660.0030.0030.0000.0000.0000.000
107A110PHE00.0370.01527.0980.0020.0020.0000.0000.0000.000
108A111GLY00.0090.03527.9060.0010.0010.0000.0000.0000.000
109A112PRO0-0.016-0.01228.5500.0010.0010.0000.0000.0000.000
110A113SER0-0.0090.00431.0210.0010.0010.0000.0000.0000.000
111A114SER00.043-0.00529.1880.0000.0000.0000.0000.0000.000
112A115GLY00.0280.01228.1990.0000.0000.0000.0000.0000.000
113A116ALA0-0.050-0.02329.0080.0020.0020.0000.0000.0000.000
114A117LEU0-0.012-0.00832.2070.0020.0020.0000.0000.0000.000
115A118VAL00.0450.02526.2580.0010.0010.0000.0000.0000.000
116A119PHE0-0.014-0.00829.1490.0010.0010.0000.0000.0000.000
117A120GLN00.0370.00030.2400.0020.0020.0000.0000.0000.000
118A121LEU0-0.0100.00232.8900.0020.0020.0000.0000.0000.000
119A122ALA00.0130.02028.7730.0000.0000.0000.0000.0000.000
120A123PHE0-0.139-0.07423.4760.0000.0000.0000.0000.0000.000
121A124ALA0-0.0170.00629.3710.0020.0020.0000.0000.0000.000
122A125PRO00.0360.02032.5640.0020.0020.0000.0000.0000.000
123A126ARG10.9420.96827.4030.0220.0220.0000.0000.0000.000
124A127MET0-0.039-0.01531.1340.0000.0000.0000.0000.0000.000
125A128ASN00.0030.00633.0050.0000.0000.0000.0000.0000.000
126A129ILE0-0.0060.00633.1490.0010.0010.0000.0000.0000.000
127A130PRO0-0.052-0.02036.936-0.001-0.0010.0000.0000.0000.000
128A131GLN00.0250.00936.8940.0000.0000.0000.0000.0000.000
129A132ASP-1-0.839-0.92538.769-0.009-0.0090.0000.0000.0000.000
130A133GLN00.0370.02140.064-0.002-0.0020.0000.0000.0000.000
131A134GLY0-0.034-0.00742.5840.0000.0000.0000.0000.0000.000
132A135VAL0-0.013-0.03636.214-0.001-0.0010.0000.0000.0000.000
133A136ILE0-0.0020.00037.279-0.001-0.0010.0000.0000.0000.000
134A137LYS10.8480.91438.8940.0130.0130.0000.0000.0000.000
135A138GLN00.0330.01240.345-0.001-0.0010.0000.0000.0000.000
136A139ASN0-0.035-0.03335.545-0.001-0.0010.0000.0000.0000.000
137A140GLU-1-0.766-0.86536.927-0.021-0.0210.0000.0000.0000.000
138A141GLU-1-0.834-0.89438.484-0.016-0.0160.0000.0000.0000.000
139A142LYS10.8120.90237.5710.0170.0170.0000.0000.0000.000
140A143LEU00.0330.02232.519-0.001-0.0010.0000.0000.0000.000
141A144GLY00.0150.00836.176-0.001-0.0010.0000.0000.0000.000
142A145LYS10.8880.93838.9310.0190.0190.0000.0000.0000.000
143A146VAL0-0.0050.00333.3760.0000.0000.0000.0000.0000.000
144A147LEU00.001-0.00832.790-0.001-0.0010.0000.0000.0000.000
145A148ASP-1-0.799-0.88236.389-0.022-0.0220.0000.0000.0000.000
146A149ILE0-0.042-0.01337.1060.0000.0000.0000.0000.0000.000
147A150TYR0-0.030-0.05329.9900.0000.0000.0000.0000.0000.000
148A151GLU-1-0.766-0.86435.743-0.030-0.0300.0000.0000.0000.000
149A152GLN0-0.056-0.02738.3210.0010.0010.0000.0000.0000.000
150A153ARG10.8770.94433.1730.0370.0370.0000.0000.0000.000
151A154LEU0-0.042-0.02331.884-0.001-0.0010.0000.0000.0000.000
152A155GLY00.0380.02835.998-0.001-0.0010.0000.0000.0000.000
153A156GLU-1-0.981-0.97638.543-0.027-0.0270.0000.0000.0000.000
154A157SER0-0.067-0.04033.1320.0000.0000.0000.0000.0000.000
155A158ARG10.8200.90930.2530.0490.0490.0000.0000.0000.000
156A159PHE00.001-0.00827.696-0.002-0.0020.0000.0000.0000.000
157A160LEU00.0050.01328.2810.0030.0030.0000.0000.0000.000
158A161ALA0-0.005-0.00327.8970.0030.0030.0000.0000.0000.000
159A162GLY0-0.0040.00229.9950.0010.0010.0000.0000.0000.000
160A163ASP-1-0.854-0.93031.142-0.041-0.0410.0000.0000.0000.000
161A164GLU-1-0.975-0.98524.544-0.072-0.0720.0000.0000.0000.000
162A165PHE0-0.019-0.00619.9740.0000.0000.0000.0000.0000.000
163A166THR00.0130.00122.535-0.004-0.0040.0000.0000.0000.000
164A167PHE00.018-0.02617.5280.0000.0000.0000.0000.0000.000
165A168ALA00.0210.01121.4830.0020.0020.0000.0000.0000.000
166A169ASP-1-0.734-0.85824.607-0.057-0.0570.0000.0000.0000.000
167A170LEU00.0120.01717.0260.0020.0020.0000.0000.0000.000
168A171SER0-0.047-0.03721.073-0.004-0.0040.0000.0000.0000.000
169A172HIS00.0300.01422.0590.0080.0080.0000.0000.0000.000
170A173LEU0-0.0210.00720.3690.0040.0040.0000.0000.0000.000
171A174PRO0-0.028-0.00819.4390.0040.0040.0000.0000.0000.000
172A175ASN0-0.043-0.04222.0440.0010.0010.0000.0000.0000.000
173A176GLY00.0560.02925.6050.0040.0040.0000.0000.0000.000
174A177ASP-1-0.819-0.90823.784-0.053-0.0530.0000.0000.0000.000
175A178TYR0-0.073-0.07121.5310.0030.0030.0000.0000.0000.000
176A179LEU0-0.0170.00126.8950.0030.0030.0000.0000.0000.000
177A180VAL0-0.0080.01029.2720.0030.0030.0000.0000.0000.000
178A181ASN0-0.043-0.02026.0290.0040.0040.0000.0000.0000.000
179A182ALA0-0.078-0.03928.1190.0010.0010.0000.0000.0000.000
180A183THR0-0.070-0.04530.1940.0030.0030.0000.0000.0000.000
181A184ASP-1-0.860-0.93033.410-0.020-0.0200.0000.0000.0000.000
182A185LYS10.8590.91134.6550.0200.0200.0000.0000.0000.000
183A186GLY00.0620.03333.738-0.001-0.0010.0000.0000.0000.000
184A187HIS00.0160.01334.686-0.001-0.0010.0000.0000.0000.000
185A188LEU0-0.073-0.00635.2370.0000.0000.0000.0000.0000.000
186A189PHE00.0360.00130.600-0.001-0.0010.0000.0000.0000.000
187A190THR00.0110.00334.9450.0000.0000.0000.0000.0000.000
188A191SER0-0.100-0.06337.2030.0010.0010.0000.0000.0000.000
189A192ARG10.7830.89037.6880.0260.0260.0000.0000.0000.000
190A193GLU-1-0.889-0.93637.891-0.027-0.0270.0000.0000.0000.000
191A194ASN0-0.023-0.04437.130-0.002-0.0020.0000.0000.0000.000
192A195VAL0-0.024-0.02133.120-0.003-0.0030.0000.0000.0000.000
193A196GLY00.0280.02033.092-0.003-0.0030.0000.0000.0000.000
194A197ARG10.7760.89533.3110.0360.0360.0000.0000.0000.000
195A198TRP0-0.019-0.02427.905-0.002-0.0020.0000.0000.0000.000
196A199TRP00.0220.00625.186-0.005-0.0050.0000.0000.0000.000
197A200ASN0-0.021-0.00428.337-0.003-0.0030.0000.0000.0000.000
198A201GLU-1-0.824-0.88728.135-0.051-0.0510.0000.0000.0000.000
199A202ILE0-0.045-0.02224.445-0.005-0.0050.0000.0000.0000.000
200A203SER0-0.102-0.06623.453-0.006-0.0060.0000.0000.0000.000
201A204ASP-1-0.839-0.90724.156-0.060-0.0600.0000.0000.0000.000
202A205ARG10.8220.88619.1960.0940.0940.0000.0000.0000.000
203A206GLU-1-0.828-0.93118.578-0.081-0.0810.0000.0000.0000.000
204A207SER0-0.113-0.07815.663-0.003-0.0030.0000.0000.0000.000
205A208TRP00.029-0.01616.182-0.012-0.0120.0000.0000.0000.000
206A209LYS10.8240.90218.5540.0700.0700.0000.0000.0000.000
207A210LYS10.9570.97911.5200.1780.1780.0000.0000.0000.000
208A211VAL00.000-0.00313.876-0.001-0.0010.0000.0000.0000.000
209A212ILE0-0.034-0.01315.8850.0070.0070.0000.0000.0000.000
210A213GLU-1-0.798-0.89017.551-0.050-0.0500.0000.0000.0000.000
211A214MET0-0.076-0.03810.6330.0000.0000.0000.0000.0000.000
212A215ARG10.8300.92215.4320.0750.0750.0000.0000.0000.000
213A216LYS10.7970.90217.9820.0600.0600.0000.0000.0000.000
214A217SER0-0.035-0.00316.0130.0090.0090.0000.0000.0000.000
215A218GLY0-0.024-0.01015.765-0.003-0.0030.0000.0000.0000.000