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: 8991Y

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2224879.953781
FMO2-HF: Nuclear repulsion 2146549.94351
FMO2-HF: Total energy -78330.010271
FMO2-MP2: Total energy -78555.712483


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.
-7.927-3.9130.254-1.546-2.722-0.002
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 : 0.009 / q_NPA : -0.005
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].
3A12THR00.008-0.0022.954-2.3730.4470.215-1.237-1.798-0.002
4A13LEU0-0.034-0.0154.6070.3330.355-0.001-0.005-0.0160.000
5A14PHE00.0120.0237.5810.1370.1370.0000.0000.0000.000
6A15SER00.021-0.03410.5390.1050.1050.0000.0000.0000.000
7A16ASN00.031-0.01713.5930.0480.0480.0000.0000.0000.000
8A17LYS10.8660.91917.0230.2750.2750.0000.0000.0000.000
9A18ASP-1-0.878-0.92818.637-0.226-0.2260.0000.0000.0000.000
10A19ASP-1-0.761-0.86818.949-0.391-0.3910.0000.0000.0000.000
11A20ILE0-0.009-0.00820.142-0.016-0.0160.0000.0000.0000.000
12A21TYR0-0.058-0.05519.656-0.002-0.0020.0000.0000.0000.000
13A22CYS0-0.071-0.00616.100-0.074-0.0740.0000.0000.0000.000
14A23HIS0-0.0160.00716.484-0.023-0.0230.0000.0000.0000.000
15A24GLN00.0170.00118.652-0.026-0.0260.0000.0000.0000.000
16A25VAL00.0130.00613.1820.0100.0100.0000.0000.0000.000
17A26LYS10.8840.95113.5010.5410.5410.0000.0000.0000.000
18A27ILE0-0.0020.00615.3750.0350.0350.0000.0000.0000.000
19A28VAL00.0060.00015.9650.0320.0320.0000.0000.0000.000
20A29LEU0-0.020-0.01910.2950.0200.0200.0000.0000.0000.000
21A30ALA00.0090.02013.6460.0530.0530.0000.0000.0000.000
22A31GLU-1-0.838-0.87215.710-0.107-0.1070.0000.0000.0000.000
23A32LYS10.7110.84814.0170.2960.2960.0000.0000.0000.000
24A33GLY0-0.0130.01014.1640.0400.0400.0000.0000.0000.000
25A34VAL0-0.064-0.0269.0380.0830.0830.0000.0000.0000.000
26A35LEU0-0.018-0.0167.023-0.062-0.0620.0000.0000.0000.000
27A36TYR0-0.022-0.0225.562-0.222-0.2220.0000.0000.0000.000
28A37GLU-1-0.885-0.9164.247-2.143-1.8380.000-0.032-0.2730.000
29A38ASN0-0.010-0.0255.923-0.316-0.3160.0000.0000.0000.000
30A39ALA00.0140.0097.9430.1370.1370.0000.0000.0000.000
31A40GLU-1-0.845-0.9319.736-0.465-0.4650.0000.0000.0000.000
32A41VAL00.0160.00213.1120.0060.0060.0000.0000.0000.000
33A42ASP-1-0.841-0.91515.469-0.258-0.2580.0000.0000.0000.000
34A43LEU0-0.008-0.01918.797-0.017-0.0170.0000.0000.0000.000
35A44GLN0-0.096-0.05320.7370.0080.0080.0000.0000.0000.000
36A45ALA0-0.054-0.02621.1650.0230.0230.0000.0000.0000.000
37A46LEU0-0.0130.01217.373-0.024-0.0240.0000.0000.0000.000
38A47PRO0-0.0050.00613.4980.0350.0350.0000.0000.0000.000
39A48GLU-1-0.888-0.96615.507-0.395-0.3950.0000.0000.0000.000
40A49ASP-1-0.867-0.94510.036-0.896-0.8960.0000.0000.0000.000
41A50LEU0-0.032-0.00311.182-0.137-0.1370.0000.0000.0000.000
42A51MET0-0.028-0.00612.485-0.016-0.0160.0000.0000.0000.000
43A52GLU-1-0.982-0.98813.303-0.485-0.4850.0000.0000.0000.000
44A53LEU0-0.070-0.0248.120-0.050-0.0500.0000.0000.0000.000
45A54ASN0-0.032-0.03512.3800.0840.0840.0000.0000.0000.000
46A55PRO00.0500.03114.8990.0440.0440.0000.0000.0000.000
47A56TYR0-0.076-0.03718.2870.0550.0550.0000.0000.0000.000
48A57GLY00.0100.00316.8200.0310.0310.0000.0000.0000.000
49A58THR0-0.029-0.00316.8900.0430.0430.0000.0000.0000.000
50A59VAL0-0.0220.00313.905-0.088-0.0880.0000.0000.0000.000
51A60PRO0-0.018-0.02713.6960.0680.0680.0000.0000.0000.000
52A61THR0-0.024-0.02410.3310.0780.0780.0000.0000.0000.000
53A62LEU0-0.048-0.0218.185-0.077-0.0770.0000.0000.0000.000
54A63VAL00.0320.0145.0810.3370.3370.0000.0000.0000.000
55A64ASP-1-0.760-0.8815.071-3.321-3.289-0.001-0.017-0.0130.000
56A65ARG10.8760.9333.0921.4152.1190.041-0.233-0.5130.000
57A66ASP-1-0.897-0.9494.065-0.919-0.7880.000-0.022-0.1090.000
58A67LEU0-0.062-0.0097.4750.2630.2630.0000.0000.0000.000
59A68VAL00.0460.0258.977-0.388-0.3880.0000.0000.0000.000
60A69LEU0-0.043-0.01910.8990.2490.2490.0000.0000.0000.000
61A70PHE00.0620.02412.641-0.066-0.0660.0000.0000.0000.000
62A71ASN00.0210.00115.3130.0660.0660.0000.0000.0000.000
63A72SER00.0460.00717.134-0.030-0.0300.0000.0000.0000.000
64A73ARG10.9871.00018.2160.3210.3210.0000.0000.0000.000
65A74ILE0-0.031-0.01717.1540.0250.0250.0000.0000.0000.000
66A75ILE00.0050.01713.111-0.008-0.0080.0000.0000.0000.000
67A76MET00.0050.00615.529-0.005-0.0050.0000.0000.0000.000
68A77GLU-1-0.832-0.88217.760-0.250-0.2500.0000.0000.0000.000
69A78TYR0-0.004-0.0189.3270.1350.1350.0000.0000.0000.000
70A79LEU0-0.017-0.00911.4150.0160.0160.0000.0000.0000.000
71A80ASP-1-0.839-0.92414.464-0.190-0.1900.0000.0000.0000.000
72A81GLU-1-0.998-0.99617.236-0.245-0.2450.0000.0000.0000.000
73A82ARG10.8110.9147.5630.7740.7740.0000.0000.0000.000
74A83PHE0-0.028-0.0208.4700.0680.0680.0000.0000.0000.000
75A84PRO00.0200.01814.5730.0140.0140.0000.0000.0000.000
76A85HIS0-0.038-0.00718.056-0.001-0.0010.0000.0000.0000.000
77A86PRO00.0560.02417.851-0.004-0.0040.0000.0000.0000.000
78A87PRO00.0150.01820.653-0.028-0.0280.0000.0000.0000.000
79A88LEU00.0350.02219.4990.0060.0060.0000.0000.0000.000
80A89MET0-0.021-0.00723.175-0.003-0.0030.0000.0000.0000.000
81A90GLN00.0170.00825.4600.0200.0200.0000.0000.0000.000
82A91VAL00.0530.01827.396-0.010-0.0100.0000.0000.0000.000
83A92TYR0-0.016-0.01129.122-0.002-0.0020.0000.0000.0000.000
84A93PRO00.0530.01531.053-0.007-0.0070.0000.0000.0000.000
85A94VAL00.0080.00432.099-0.007-0.0070.0000.0000.0000.000
86A95SER0-0.020-0.02132.155-0.002-0.0020.0000.0000.0000.000
87A96ARG10.9921.00723.4260.1830.1830.0000.0000.0000.000
88A97ALA0-0.0170.00129.664-0.013-0.0130.0000.0000.0000.000
89A98LYS10.9400.95931.9070.0970.0970.0000.0000.0000.000
90A99ASP-1-0.806-0.89029.033-0.149-0.1490.0000.0000.0000.000
91A100ARG10.8120.85824.1500.2270.2270.0000.0000.0000.000
92A101LEU0-0.039-0.00529.393-0.007-0.0070.0000.0000.0000.000
93A102LEU0-0.015-0.02131.8320.0010.0010.0000.0000.0000.000
94A103MET0-0.0020.01625.803-0.005-0.0050.0000.0000.0000.000
95A104LEU0-0.0070.00528.793-0.007-0.0070.0000.0000.0000.000
96A105ARG10.8880.92830.0070.1340.1340.0000.0000.0000.000
97A106ILE0-0.036-0.00129.0680.0030.0030.0000.0000.0000.000
98A107GLU-1-0.881-0.92625.863-0.256-0.2560.0000.0000.0000.000
99A108GLN0-0.047-0.02629.054-0.003-0.0030.0000.0000.0000.000
100A109ASP-1-0.855-0.92231.912-0.138-0.1380.0000.0000.0000.000
101A110TRP0-0.050-0.03432.1050.0050.0050.0000.0000.0000.000
102A111TYR00.024-0.00924.626-0.002-0.0020.0000.0000.0000.000
103A112PRO00.0220.02530.186-0.002-0.0020.0000.0000.0000.000
104A113THR0-0.015-0.00932.1890.0030.0030.0000.0000.0000.000
105A114LEU00.0150.00128.1630.0080.0080.0000.0000.0000.000
106A115ALA00.0600.03629.2310.0020.0020.0000.0000.0000.000
107A116LYS10.9460.98830.5830.1250.1250.0000.0000.0000.000
108A117ALA0-0.065-0.05233.5300.0070.0070.0000.0000.0000.000
109A118GLU-1-0.833-0.89127.993-0.207-0.2070.0000.0000.0000.000
110A119ASN0-0.070-0.04728.546-0.003-0.0030.0000.0000.0000.000
111A120GLY0-0.0160.02032.4350.0030.0030.0000.0000.0000.000
112A121THR0-0.017-0.05436.1840.0040.0040.0000.0000.0000.000
113A122GLU-1-0.811-0.90938.295-0.115-0.1150.0000.0000.0000.000
114A123LYS10.8520.93040.7140.0890.0890.0000.0000.0000.000
115A124GLU-1-0.819-0.88038.638-0.121-0.1210.0000.0000.0000.000
116A125LYS10.9220.95634.4740.1310.1310.0000.0000.0000.000
117A126THR00.003-0.01238.2170.0010.0010.0000.0000.0000.000
118A127SER0-0.085-0.02741.0970.0020.0020.0000.0000.0000.000
119A128ALA00.0160.00136.6260.0020.0020.0000.0000.0000.000
120A129LEU00.0480.02335.4400.0000.0000.0000.0000.0000.000
121A130LYS10.8180.90638.4160.0830.0830.0000.0000.0000.000
122A131GLN0-0.041-0.02738.8410.0040.0040.0000.0000.0000.000
123A132LEU00.0540.02633.7150.0020.0020.0000.0000.0000.000
124A133LYS10.8890.94737.8610.0860.0860.0000.0000.0000.000
125A134GLU-1-0.889-0.93639.625-0.076-0.0760.0000.0000.0000.000
126A135GLU-1-0.851-0.92337.583-0.120-0.1200.0000.0000.0000.000
127A136LEU0-0.016-0.01034.6560.0020.0020.0000.0000.0000.000
128A137LEU0-0.034-0.03138.7850.0040.0040.0000.0000.0000.000
129A138GLY0-0.0040.00942.1030.0040.0040.0000.0000.0000.000
130A139ILE0-0.018-0.00836.7030.0030.0030.0000.0000.0000.000
131A140ALA0-0.0020.02140.6540.0000.0000.0000.0000.0000.000
132A141PRO0-0.040-0.04041.6150.0010.0010.0000.0000.0000.000
133A142ILE00.0210.00737.5150.0030.0030.0000.0000.0000.000
134A143PHE0-0.009-0.00733.8160.0010.0010.0000.0000.0000.000
135A144GLN0-0.059-0.03638.3640.0050.0050.0000.0000.0000.000
136A145GLN0-0.044-0.00639.6230.0000.0000.0000.0000.0000.000
137A146MET0-0.0310.00636.1430.0040.0040.0000.0000.0000.000
138A147PRO0-0.0310.01534.057-0.003-0.0030.0000.0000.0000.000
139A148TYR00.0510.02429.174-0.006-0.0060.0000.0000.0000.000
140A149PHE00.012-0.00331.3860.0060.0060.0000.0000.0000.000
141A150MET0-0.089-0.04932.574-0.008-0.0080.0000.0000.0000.000
142A151ASN0-0.012-0.00731.3970.0060.0060.0000.0000.0000.000
143A152GLU-1-0.872-0.95733.449-0.069-0.0690.0000.0000.0000.000
144A153GLU-1-0.940-0.97128.585-0.074-0.0740.0000.0000.0000.000
145A154PHE0-0.044-0.01722.570-0.006-0.0060.0000.0000.0000.000
146A155GLY00.0530.01924.7280.0000.0000.0000.0000.0000.000
147A156LEU00.001-0.02720.535-0.006-0.0060.0000.0000.0000.000
148A157VAL00.0230.00124.346-0.010-0.0100.0000.0000.0000.000
149A158ASP-1-0.714-0.83926.433-0.149-0.1490.0000.0000.0000.000
150A159CYS0-0.046-0.00621.749-0.004-0.0040.0000.0000.0000.000
151A160TYR00.0220.01023.477-0.024-0.0240.0000.0000.0000.000
152A161VAL00.0100.01225.9010.0040.0040.0000.0000.0000.000
153A162ALA0-0.011-0.00825.6210.0050.0050.0000.0000.0000.000
154A163PRO00.0570.01922.9310.0130.0130.0000.0000.0000.000
155A164LEU00.0120.01725.2980.0050.0050.0000.0000.0000.000
156A165LEU0-0.006-0.01928.5150.0120.0120.0000.0000.0000.000
157A166TRP00.0190.01824.2300.0230.0230.0000.0000.0000.000
158A167LYS10.8120.88024.7850.2470.2470.0000.0000.0000.000
159A168LEU00.000-0.00228.7050.0100.0100.0000.0000.0000.000
160A169LYS10.9300.97730.7620.1160.1160.0000.0000.0000.000
161A170HIS0-0.058-0.02927.4900.0160.0160.0000.0000.0000.000
162A171LEU0-0.0170.00131.1290.0010.0010.0000.0000.0000.000
163A172GLY0-0.022-0.00533.7350.0060.0060.0000.0000.0000.000
164A173VAL0-0.059-0.01935.9250.0080.0080.0000.0000.0000.000
165A174GLU-1-0.897-0.93537.035-0.074-0.0740.0000.0000.0000.000
166A175PHE0-0.031-0.02335.7560.0040.0040.0000.0000.0000.000
167A176THR00.003-0.01641.0010.0030.0030.0000.0000.0000.000
168A177GLY00.0530.03444.677-0.002-0.0020.0000.0000.0000.000
169A178THR00.0290.00646.1650.0000.0000.0000.0000.0000.000
170A179GLY00.0330.01444.451-0.003-0.0030.0000.0000.0000.000
171A180SER00.005-0.01941.671-0.003-0.0030.0000.0000.0000.000
172A181LYS10.9350.96740.9000.0550.0550.0000.0000.0000.000
173A182ALA0-0.031-0.00940.5090.0010.0010.0000.0000.0000.000
174A183ILE00.0450.02836.349-0.002-0.0020.0000.0000.0000.000
175A184LYS10.9240.96736.0060.0680.0680.0000.0000.0000.000
176A185ALA00.0520.03435.949-0.002-0.0020.0000.0000.0000.000
177A186TYR0-0.081-0.06929.948-0.002-0.0020.0000.0000.0000.000
178A187MET0-0.020-0.01031.773-0.003-0.0030.0000.0000.0000.000
179A188GLU-1-0.945-0.97831.121-0.074-0.0740.0000.0000.0000.000
180A189ARG10.8620.94831.1720.0840.0840.0000.0000.0000.000
181A190VAL00.0300.00827.426-0.001-0.0010.0000.0000.0000.000
182A191PHE0-0.078-0.04226.655-0.005-0.0050.0000.0000.0000.000
183A192THR0-0.059-0.04926.6160.0000.0000.0000.0000.0000.000
184A193ARG10.8730.93723.3730.1420.1420.0000.0000.0000.000
185A194ASP-1-0.873-0.94521.459-0.065-0.0650.0000.0000.0000.000
186A195SER0-0.071-0.06419.305-0.006-0.0060.0000.0000.0000.000
187A196PHE00.0610.02119.668-0.033-0.0330.0000.0000.0000.000
188A197LEU0-0.0120.00821.549-0.015-0.0150.0000.0000.0000.000
189A198GLN0-0.008-0.01316.390-0.017-0.0170.0000.0000.0000.000
190A199SER0-0.081-0.04217.040-0.027-0.0270.0000.0000.0000.000
191A200VAL0-0.055-0.02218.126-0.029-0.0290.0000.0000.0000.000
192A201GLY0-0.032-0.00417.8650.0010.0010.0000.0000.0000.000