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: G55M1

Calculation Name: 3LYK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYK

Chain ID: A

ChEMBL ID:

UniProt ID: P45207

Base Structure: X-ray

Registration Date: 2023-09-21

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2222403.854038
FMO2-HF: Nuclear repulsion 2144074.915191
FMO2-HF: Total energy -78328.938848
FMO2-MP2: Total energy -78554.652103


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:10:VAL)


Summations of interaction energy for fragment #1(A:10:VAL)
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.
-9.508-5.8290.304-1.281-2.702-0.004
Interaction energy analysis for fragmet #1(A:10:VAL)
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 : -0.030
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].
3A12THR00.0250.0243.081-2.657-0.1900.259-1.017-1.708-0.004
4A13LEU0-0.033-0.0184.7630.4340.465-0.001-0.005-0.0260.000
5A14PHE00.0140.0227.0210.0890.0890.0000.0000.0000.000
6A15SER00.062-0.01710.5940.1510.1510.0000.0000.0000.000
7A16ASN0-0.009-0.01313.7360.0280.0280.0000.0000.0000.000
8A17LYS10.9160.94317.0970.2720.2720.0000.0000.0000.000
9A18ASP-1-0.923-0.95118.491-0.195-0.1950.0000.0000.0000.000
10A19ASP-1-0.850-0.93019.103-0.281-0.2810.0000.0000.0000.000
11A20ILE00.001-0.01120.158-0.003-0.0030.0000.0000.0000.000
12A21TYR0-0.057-0.04419.5900.0160.0160.0000.0000.0000.000
13A22CYS0-0.0330.02415.875-0.038-0.0380.0000.0000.0000.000
14A23HIS0-0.0180.00216.426-0.005-0.0050.0000.0000.0000.000
15A24GLN00.0260.01118.4780.0020.0020.0000.0000.0000.000
16A25VAL00.0090.00513.2250.0350.0350.0000.0000.0000.000
17A26LYS10.9310.97413.4080.4350.4350.0000.0000.0000.000
18A27ILE0-0.0090.00315.1100.0530.0530.0000.0000.0000.000
19A28VAL00.0070.00316.0240.0450.0450.0000.0000.0000.000
20A29LEU0-0.015-0.01710.2220.0640.0640.0000.0000.0000.000
21A30ALA00.0090.02313.6180.0950.0950.0000.0000.0000.000
22A31GLU-1-0.856-0.89715.6830.1400.1400.0000.0000.0000.000
23A32LYS10.7050.84813.922-0.154-0.1540.0000.0000.0000.000
24A33GLY0-0.0170.00614.1410.0870.0870.0000.0000.0000.000
25A34VAL0-0.054-0.0249.0270.1410.1410.0000.0000.0000.000
26A35LEU0-0.023-0.0176.951-0.183-0.1830.0000.0000.0000.000
27A36TYR0-0.023-0.0205.4390.1840.1840.0000.0000.0000.000
28A37GLU-1-0.913-0.9484.054-2.692-2.3900.000-0.031-0.2720.000
29A38ASN0-0.012-0.0225.816-0.201-0.2010.0000.0000.0000.000
30A39ALA00.0220.0108.1350.0690.0690.0000.0000.0000.000
31A40GLU-1-0.867-0.9429.728-0.391-0.3910.0000.0000.0000.000
32A41VAL00.006-0.00213.090-0.017-0.0170.0000.0000.0000.000
33A42ASP-1-0.880-0.94015.623-0.278-0.2780.0000.0000.0000.000
34A43LEU00.007-0.01918.862-0.019-0.0190.0000.0000.0000.000
35A44GLN0-0.071-0.03620.7780.0140.0140.0000.0000.0000.000
36A45ALA0-0.054-0.02121.1700.0210.0210.0000.0000.0000.000
37A46LEU0-0.0180.00517.316-0.033-0.0330.0000.0000.0000.000
38A47PRO00.0000.01313.4860.0340.0340.0000.0000.0000.000
39A48GLU-1-0.892-0.96815.331-0.506-0.5060.0000.0000.0000.000
40A49ASP-1-0.865-0.9469.671-1.200-1.2000.0000.0000.0000.000
41A50LEU0-0.038-0.00510.862-0.125-0.1250.0000.0000.0000.000
42A51MET0-0.032-0.00712.2420.0240.0240.0000.0000.0000.000
43A52GLU-1-0.975-0.98512.947-0.663-0.6630.0000.0000.0000.000
44A53LEU0-0.059-0.0207.661-0.027-0.0270.0000.0000.0000.000
45A54ASN0-0.032-0.02611.8870.1330.1330.0000.0000.0000.000
46A55PRO00.0490.02914.4690.0390.0390.0000.0000.0000.000
47A56TYR0-0.084-0.04417.8410.0530.0530.0000.0000.0000.000
48A57GLY00.0100.00416.5600.0310.0310.0000.0000.0000.000
49A58THR0-0.052-0.01816.7970.0190.0190.0000.0000.0000.000
50A59VAL00.0170.02314.214-0.084-0.0840.0000.0000.0000.000
51A60PRO0-0.024-0.03313.7380.0670.0670.0000.0000.0000.000
52A61THR00.002-0.0179.8610.0920.0920.0000.0000.0000.000
53A62LEU0-0.062-0.0287.992-0.111-0.1110.0000.0000.0000.000
54A63VAL00.0270.0134.6020.2050.326-0.001-0.008-0.1120.000
55A64ASP-1-0.792-0.9054.744-0.293-0.243-0.001-0.017-0.0310.000
56A65ARG10.8790.9352.942-0.898-0.2900.048-0.188-0.4680.000
57A66ASP-1-0.899-0.9513.879-1.190-1.0900.000-0.015-0.0850.000
58A67LEU0-0.076-0.0137.3780.0710.0710.0000.0000.0000.000
59A68VAL00.0490.0288.532-0.303-0.3030.0000.0000.0000.000
60A69LEU0-0.050-0.02810.3620.2270.2270.0000.0000.0000.000
61A70PHE00.0750.03612.316-0.083-0.0830.0000.0000.0000.000
62A71ASN00.010-0.00215.0010.0860.0860.0000.0000.0000.000
63A72SER00.0480.00317.007-0.001-0.0010.0000.0000.0000.000
64A73ARG10.9850.99918.0880.1680.1680.0000.0000.0000.000
65A74ILE0-0.025-0.01516.5350.0390.0390.0000.0000.0000.000
66A75ILE00.0040.01713.0230.0350.0350.0000.0000.0000.000
67A76MET00.0030.00415.3260.0540.0540.0000.0000.0000.000
68A77GLU-1-0.802-0.86317.6780.0130.0130.0000.0000.0000.000
69A78TYR0-0.002-0.0169.4790.0640.0640.0000.0000.0000.000
70A79LEU0-0.019-0.01011.4010.0880.0880.0000.0000.0000.000
71A80ASP-1-0.845-0.93114.9000.1830.1830.0000.0000.0000.000
72A81GLU-1-0.992-0.99017.6360.0790.0790.0000.0000.0000.000
73A82ARG10.8590.9398.639-0.866-0.8660.0000.0000.0000.000
74A83PHE0-0.026-0.0169.3320.1380.1380.0000.0000.0000.000
75A84PRO00.0160.01815.345-0.057-0.0570.0000.0000.0000.000
76A85HIS0-0.043-0.00818.704-0.054-0.0540.0000.0000.0000.000
77A86PRO00.0490.02218.1450.0400.0400.0000.0000.0000.000
78A87PRO00.0200.02120.868-0.006-0.0060.0000.0000.0000.000
79A88LEU00.0440.02619.406-0.019-0.0190.0000.0000.0000.000
80A89MET0-0.031-0.01123.327-0.031-0.0310.0000.0000.0000.000
81A90GLN00.0050.00225.8210.0210.0210.0000.0000.0000.000
82A91VAL00.0540.01428.0770.0000.0000.0000.0000.0000.000
83A92TYR0-0.026-0.01929.846-0.003-0.0030.0000.0000.0000.000
84A93PRO00.0470.01531.517-0.006-0.0060.0000.0000.0000.000
85A94VAL00.0150.00932.571-0.007-0.0070.0000.0000.0000.000
86A95SER00.0220.00032.671-0.008-0.0080.0000.0000.0000.000
87A96ARG10.9881.01124.412-0.050-0.0500.0000.0000.0000.000
88A97ALA0-0.0220.00430.069-0.011-0.0110.0000.0000.0000.000
89A98LYS10.9430.95532.254-0.008-0.0080.0000.0000.0000.000
90A99ASP-1-0.816-0.89829.209-0.003-0.0030.0000.0000.0000.000
91A100ARG10.7750.83924.6760.0140.0140.0000.0000.0000.000
92A101LEU0-0.037-0.00629.247-0.011-0.0110.0000.0000.0000.000
93A102LEU0-0.018-0.02731.783-0.006-0.0060.0000.0000.0000.000
94A103MET0-0.0090.01325.841-0.008-0.0080.0000.0000.0000.000
95A104LEU0-0.0070.00428.743-0.010-0.0100.0000.0000.0000.000
96A105ARG10.9690.97529.8710.0410.0410.0000.0000.0000.000
97A106ILE0-0.0280.00529.111-0.002-0.0020.0000.0000.0000.000
98A107GLU-1-0.885-0.93225.808-0.157-0.1570.0000.0000.0000.000
99A108GLN0-0.018-0.00729.000-0.009-0.0090.0000.0000.0000.000
100A109ASP-1-0.920-0.96731.810-0.072-0.0720.0000.0000.0000.000
101A110TRP0-0.077-0.04832.1060.0030.0030.0000.0000.0000.000
102A111TYR00.009-0.03124.752-0.003-0.0030.0000.0000.0000.000
103A112PRO00.0220.02630.205-0.007-0.0070.0000.0000.0000.000
104A113THR0-0.016-0.01132.177-0.002-0.0020.0000.0000.0000.000
105A114LEU0-0.013-0.00728.2390.0050.0050.0000.0000.0000.000
106A115ALA00.0860.04829.273-0.002-0.0020.0000.0000.0000.000
107A116LYS10.9150.97230.6530.0860.0860.0000.0000.0000.000
108A117ALA0-0.049-0.05233.9280.0030.0030.0000.0000.0000.000
109A118GLU-1-0.875-0.92627.774-0.155-0.1550.0000.0000.0000.000
110A119ASN0-0.019-0.01628.420-0.003-0.0030.0000.0000.0000.000
111A120GLY0-0.0030.01732.5420.0010.0010.0000.0000.0000.000
112A121THR0-0.016-0.02536.2800.0020.0020.0000.0000.0000.000
113A122GLU-1-0.848-0.93838.506-0.093-0.0930.0000.0000.0000.000
114A123LYS10.9090.97340.7790.0700.0700.0000.0000.0000.000
115A124GLU-1-0.890-0.94038.573-0.098-0.0980.0000.0000.0000.000
116A125LYS10.9570.99034.2100.1200.1200.0000.0000.0000.000
117A126THR0-0.027-0.03638.2820.0030.0030.0000.0000.0000.000
118A127SER0-0.106-0.04541.1000.0040.0040.0000.0000.0000.000
119A128ALA00.0380.01236.7170.0040.0040.0000.0000.0000.000
120A129LEU00.0470.02135.3030.0030.0030.0000.0000.0000.000
121A130LYS10.8980.95838.3940.0530.0530.0000.0000.0000.000
122A131GLN0-0.016-0.00939.3890.0020.0020.0000.0000.0000.000
123A132LEU00.0670.03533.8100.0040.0040.0000.0000.0000.000
124A133LYS10.8900.96137.8700.0490.0490.0000.0000.0000.000
125A134GLU-1-0.979-0.99039.536-0.035-0.0350.0000.0000.0000.000
126A135GLU-1-0.864-0.93638.233-0.060-0.0600.0000.0000.0000.000
127A136LEU0-0.042-0.02134.5020.0040.0040.0000.0000.0000.000
128A137LEU0-0.037-0.03338.7040.0050.0050.0000.0000.0000.000
129A138GLY00.0060.01741.9700.0040.0040.0000.0000.0000.000
130A139ILE0-0.022-0.01036.7770.0040.0040.0000.0000.0000.000
131A140ALA0-0.0070.02040.5360.0030.0030.0000.0000.0000.000
132A141PRO0-0.029-0.04141.4090.0030.0030.0000.0000.0000.000
133A142ILE00.0280.00937.2370.0040.0040.0000.0000.0000.000
134A143PHE0-0.016-0.01333.6850.0030.0030.0000.0000.0000.000
135A144GLN0-0.097-0.04338.1430.0050.0050.0000.0000.0000.000
136A145GLN0-0.052-0.00839.6550.0000.0000.0000.0000.0000.000
137A146MET0-0.0300.00636.1370.0040.0040.0000.0000.0000.000
138A147PRO0-0.0340.00533.971-0.005-0.0050.0000.0000.0000.000
139A148TYR00.0350.00529.341-0.005-0.0050.0000.0000.0000.000
140A149PHE00.009-0.00631.349-0.002-0.0020.0000.0000.0000.000
141A150MET0-0.095-0.04932.542-0.003-0.0030.0000.0000.0000.000
142A151ASN00.0200.00930.9020.0080.0080.0000.0000.0000.000
143A152GLU-1-0.886-0.96233.4180.0320.0320.0000.0000.0000.000
144A153GLU-1-0.948-0.96928.5900.0770.0770.0000.0000.0000.000
145A154PHE0-0.046-0.01922.512-0.010-0.0100.0000.0000.0000.000
146A155GLY00.0530.01524.6970.0150.0150.0000.0000.0000.000
147A156LEU00.005-0.02520.536-0.016-0.0160.0000.0000.0000.000
148A157VAL00.0210.00524.314-0.018-0.0180.0000.0000.0000.000
149A158ASP-1-0.711-0.84226.345-0.014-0.0140.0000.0000.0000.000
150A159CYS0-0.039-0.00321.635-0.005-0.0050.0000.0000.0000.000
151A160TYR00.0240.01623.471-0.023-0.0230.0000.0000.0000.000
152A161VAL00.0130.01325.905-0.009-0.0090.0000.0000.0000.000
153A162ALA0-0.015-0.00325.282-0.005-0.0050.0000.0000.0000.000
154A163PRO00.0500.01522.8350.0010.0010.0000.0000.0000.000
155A164LEU00.0340.02525.132-0.007-0.0070.0000.0000.0000.000
156A165LEU0-0.012-0.02528.4260.0020.0020.0000.0000.0000.000
157A166TRP00.0090.01424.2460.0160.0160.0000.0000.0000.000
158A167LYS10.8950.92724.4870.1830.1830.0000.0000.0000.000
159A168LEU0-0.0070.00028.5250.0030.0030.0000.0000.0000.000
160A169LYS10.9250.97330.5780.0520.0520.0000.0000.0000.000
161A170HIS0-0.061-0.03027.9180.0020.0020.0000.0000.0000.000
162A171LEU0-0.0150.00431.101-0.004-0.0040.0000.0000.0000.000
163A172GLY0-0.020-0.00333.5290.0030.0030.0000.0000.0000.000
164A173VAL0-0.057-0.01535.6900.0070.0070.0000.0000.0000.000
165A174GLU-1-0.919-0.95036.729-0.039-0.0390.0000.0000.0000.000
166A175PHE0-0.034-0.03535.5480.0020.0020.0000.0000.0000.000
167A176THR00.006-0.01240.6970.0030.0030.0000.0000.0000.000
168A177GLY00.0360.02644.359-0.002-0.0020.0000.0000.0000.000
169A178THR00.030-0.00645.8600.0010.0010.0000.0000.0000.000
170A179GLY00.0380.01344.216-0.002-0.0020.0000.0000.0000.000
171A180SER00.0160.00041.3820.0000.0000.0000.0000.0000.000
172A181LYS10.9720.97640.591-0.002-0.0020.0000.0000.0000.000
173A182ALA0-0.0230.00040.1700.0020.0020.0000.0000.0000.000
174A183ILE00.0500.03136.1200.0020.0020.0000.0000.0000.000
175A184LYS10.9280.96735.6910.0210.0210.0000.0000.0000.000
176A185ALA00.0480.02735.7020.0010.0010.0000.0000.0000.000
177A186TYR0-0.072-0.05229.6620.0000.0000.0000.0000.0000.000
178A187MET0-0.022-0.01231.4660.0010.0010.0000.0000.0000.000
179A188GLU-1-0.971-0.98430.886-0.004-0.0040.0000.0000.0000.000
180A189ARG10.8910.97131.127-0.010-0.0100.0000.0000.0000.000
181A190VAL00.0270.00627.0660.0070.0070.0000.0000.0000.000
182A191PHE0-0.067-0.03826.443-0.001-0.0010.0000.0000.0000.000
183A192THR0-0.058-0.04626.4660.0000.0000.0000.0000.0000.000
184A193ARG10.8790.95323.590-0.047-0.0470.0000.0000.0000.000
185A194ASP-1-0.865-0.94021.2940.0870.0870.0000.0000.0000.000
186A195SER0-0.080-0.07219.296-0.020-0.0200.0000.0000.0000.000
187A196PHE00.0610.02319.492-0.032-0.0320.0000.0000.0000.000
188A197LEU0-0.0060.00621.359-0.026-0.0260.0000.0000.0000.000
189A198GLN0-0.001-0.00815.996-0.019-0.0190.0000.0000.0000.000
190A199SER0-0.080-0.04116.815-0.038-0.0380.0000.0000.0000.000
191A200VAL0-0.056-0.01817.904-0.039-0.0390.0000.0000.0000.000
192A201GLY0-0.042-0.01317.761-0.020-0.0200.0000.0000.0000.000