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: 6YZLZ

Calculation Name: 3LZ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LZ8

Chain ID: A

ChEMBL ID:

UniProt ID: A6TH30

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptAll
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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1610202.878378
FMO2-HF: Nuclear repulsion 1539245.601153
FMO2-HF: Total energy -70957.277225
FMO2-MP2: Total energy -71168.884152


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:113:ALA)


Summations of interaction energy for fragment #1(A:113:ALA)
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.
3.0184.8572.009-1.664-2.186-0.003
Interaction energy analysis for fragmet #1(A:113:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.018
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].
3A115ARG10.8200.9093.876-0.4550.530-0.010-0.534-0.4410.002
4A116GLY00.0310.0296.9730.2510.2510.0000.0000.0000.000
5A117HIS00.0210.00710.312-0.155-0.1550.0000.0000.0000.000
6A118ASP-1-0.808-0.91413.627-0.092-0.0920.0000.0000.0000.000
7A119LEU0-0.011-0.00116.7150.0210.0210.0000.0000.0000.000
8A120GLU-1-0.802-0.87520.187-0.032-0.0320.0000.0000.0000.000
9A121ILE0-0.021-0.01423.8520.0110.0110.0000.0000.0000.000
10A122GLU-1-0.836-0.90326.8100.0080.0080.0000.0000.0000.000
11A123VAL0-0.058-0.03829.8650.0050.0050.0000.0000.0000.000
12A124ALA00.0650.04432.561-0.004-0.0040.0000.0000.0000.000
13A125VAL0-0.040-0.02035.9210.0020.0020.0000.0000.0000.000
14A126PHE00.0260.01738.598-0.001-0.0010.0000.0000.0000.000
15A127LEU00.0280.01742.340-0.001-0.0010.0000.0000.0000.000
16A128GLU-1-0.804-0.91644.3000.0020.0020.0000.0000.0000.000
17A129GLU-1-0.784-0.85640.5710.0100.0100.0000.0000.0000.000
18A130THR0-0.013-0.01040.508-0.001-0.0010.0000.0000.0000.000
19A131LEU0-0.053-0.01841.984-0.002-0.0020.0000.0000.0000.000
20A132ALA0-0.014-0.01143.108-0.001-0.0010.0000.0000.0000.000
21A133GLU-1-0.856-0.90537.335-0.003-0.0030.0000.0000.0000.000
22A134GLN0-0.037-0.04037.6780.0020.0020.0000.0000.0000.000
23A135THR0-0.032-0.01535.594-0.001-0.0010.0000.0000.0000.000
24A136ARG10.7900.88834.078-0.012-0.0120.0000.0000.0000.000
25A137THR00.016-0.00732.074-0.001-0.0010.0000.0000.0000.000
26A138ILE00.0080.02128.262-0.001-0.0010.0000.0000.0000.000
27A139SER00.022-0.00129.0320.0020.0020.0000.0000.0000.000
28A140TYR0-0.049-0.03720.662-0.005-0.0050.0000.0000.0000.000
29A141ASN0-0.011-0.01624.0820.0020.0020.0000.0000.0000.000
30A142LEU0-0.020-0.01016.653-0.015-0.0150.0000.0000.0000.000
31A143PRO00.0120.00218.1860.0190.0190.0000.0000.0000.000
32A144VAL0-0.0240.00016.6890.0270.0270.0000.0000.0000.000
33A145TYR00.003-0.01513.414-0.038-0.0380.0000.0000.0000.000
34A146ASN00.0840.04414.0530.0950.0950.0000.0000.0000.000
35A147VAL00.025-0.0039.0830.0120.0120.0000.0000.0000.000
36A148PHE0-0.097-0.04611.3540.0070.0070.0000.0000.0000.000
37A149GLY0-0.007-0.00212.590-0.037-0.0370.0000.0000.0000.000
38A150MET0-0.065-0.01413.400-0.067-0.0670.0000.0000.0000.000
39A151ILE00.006-0.00116.4390.0450.0450.0000.0000.0000.000
40A152GLU-1-0.919-0.97717.9480.3000.3000.0000.0000.0000.000
41A153SER00.0050.01720.571-0.027-0.0270.0000.0000.0000.000
42A154GLU-1-0.841-0.92121.0270.1220.1220.0000.0000.0000.000
43A155THR0-0.0270.00520.167-0.001-0.0010.0000.0000.0000.000
44A156PRO00.018-0.00522.398-0.006-0.0060.0000.0000.0000.000
45A157LYS10.8900.95518.449-0.112-0.1120.0000.0000.0000.000
46A158THR0-0.018-0.01425.091-0.006-0.0060.0000.0000.0000.000
47A159LEU0-0.0230.00525.0120.0020.0020.0000.0000.0000.000
48A160ASN0-0.050-0.03927.779-0.004-0.0040.0000.0000.0000.000
49A161VAL00.0300.01528.434-0.002-0.0020.0000.0000.0000.000
50A162LYS10.8440.90631.3840.0010.0010.0000.0000.0000.000
51A163ILE00.0210.01833.073-0.004-0.0040.0000.0000.0000.000
52A164PRO0-0.005-0.01833.8320.0010.0010.0000.0000.0000.000
53A165ALA00.0520.04737.0490.0000.0000.0000.0000.0000.000
54A166GLY00.0610.03839.727-0.003-0.0030.0000.0000.0000.000
55A167VAL0-0.086-0.03735.067-0.003-0.0030.0000.0000.0000.000
56A168VAL0-0.007-0.01336.4680.0010.0010.0000.0000.0000.000
57A169ASP-1-0.769-0.89335.959-0.008-0.0080.0000.0000.0000.000
58A170GLY00.0260.02233.134-0.003-0.0030.0000.0000.0000.000
59A171GLN0-0.043-0.01531.684-0.003-0.0030.0000.0000.0000.000
60A172ARG10.8040.86625.5310.0300.0300.0000.0000.0000.000
61A173ILE0-0.035-0.01626.636-0.005-0.0050.0000.0000.0000.000
62A174ARG10.8050.90917.4620.1260.1260.0000.0000.0000.000
63A175LEU0-0.004-0.00921.9540.0000.0000.0000.0000.0000.000
64A176LYS10.9500.96415.7140.1400.1400.0000.0000.0000.000
65A177GLY00.000-0.01314.7350.0130.0130.0000.0000.0000.000
66A178GLN00.0040.01515.7140.0500.0500.0000.0000.0000.000
67A179GLY00.0210.02416.1570.0060.0060.0000.0000.0000.000
68A180THR0-0.024-0.02211.8790.0000.0000.0000.0000.0000.000
69A181PRO00.015-0.01411.213-0.076-0.0760.0000.0000.0000.000
70A182GLY00.0810.0487.363-0.035-0.0350.0000.0000.0000.000
71A183GLU-1-0.989-0.9787.6670.8860.8860.0000.0000.0000.000
72A184ASN0-0.028-0.0426.2780.4180.4180.0000.0000.0000.000
73A185GLY00.0090.0052.3083.8324.3031.842-1.306-1.0080.000
74A186GLY0-0.0030.0063.138-2.411-2.1060.1780.184-0.667-0.005
75A187PRO0-0.063-0.0234.6200.3230.401-0.001-0.008-0.0700.000
76A188ASN00.0380.0068.2660.0440.0440.0000.0000.0000.000
77A189GLY00.0140.01910.981-0.117-0.1170.0000.0000.0000.000
78A190ASP-1-0.837-0.88613.524-0.080-0.0800.0000.0000.0000.000
79A191LEU0-0.0130.00517.1330.0130.0130.0000.0000.0000.000
80A192TRP0-0.037-0.04019.184-0.013-0.0130.0000.0000.0000.000
81A193LEU00.0380.02623.5480.0070.0070.0000.0000.0000.000
82A194VAL0-0.021-0.02226.991-0.009-0.0090.0000.0000.0000.000
83A195ILE0-0.008-0.00329.5400.0050.0050.0000.0000.0000.000
84A196HIS0-0.072-0.04233.202-0.004-0.0040.0000.0000.0000.000
85A197ILE0-0.059-0.03535.8470.0020.0020.0000.0000.0000.000
86A198ALA00.0250.01739.516-0.001-0.0010.0000.0000.0000.000
87A199PRO0-0.018-0.01741.4270.0000.0000.0000.0000.0000.000
88A200HIS00.010-0.00244.7560.0010.0010.0000.0000.0000.000
89A201PRO0-0.016-0.02147.534-0.001-0.0010.0000.0000.0000.000
90A202LEU0-0.066-0.02350.8370.0000.0000.0000.0000.0000.000
91A203PHE0-0.044-0.02749.6480.0000.0000.0000.0000.0000.000
92A204ASP-1-0.839-0.89548.774-0.007-0.0070.0000.0000.0000.000
93A205ILE0-0.017-0.03044.3890.0000.0000.0000.0000.0000.000
94A206VAL0-0.013-0.00247.135-0.001-0.0010.0000.0000.0000.000
95A207GLY00.003-0.00344.7690.0000.0000.0000.0000.0000.000
96A208HIS00.034-0.00143.3830.0020.0020.0000.0000.0000.000
97A209ASN0-0.0200.00246.7410.0020.0020.0000.0000.0000.000
98A210LEU00.0470.03047.5470.0000.0000.0000.0000.0000.000
99A211GLU-1-0.842-0.88750.867-0.010-0.0100.0000.0000.0000.000
100A212ILE00.0530.02853.1510.0010.0010.0000.0000.0000.000
101A213VAL0-0.0050.00355.8950.0000.0000.0000.0000.0000.000
102A214LEU00.0090.00358.6650.0010.0010.0000.0000.0000.000
103A215PRO0-0.043-0.01961.5290.0000.0000.0000.0000.0000.000
104A216LEU00.0350.01664.4390.0000.0000.0000.0000.0000.000
105A217ALA00.0190.00868.0680.0000.0000.0000.0000.0000.000
106A218PRO0-0.019-0.02571.4390.0000.0000.0000.0000.0000.000
107A219TRP00.0620.01673.5890.0000.0000.0000.0000.0000.000
108A220GLU-1-0.883-0.92870.513-0.001-0.0010.0000.0000.0000.000
109A221ALA0-0.027-0.00870.4360.0000.0000.0000.0000.0000.000
110A222ALA00.0000.00372.0510.0000.0000.0000.0000.0000.000
111A223LEU0-0.001-0.00975.7030.0000.0000.0000.0000.0000.000
112A224GLY00.0060.02673.2260.0000.0000.0000.0000.0000.000
113A225ALA0-0.003-0.01271.0440.0000.0000.0000.0000.0000.000
114A226LYS10.8940.93969.3430.0020.0020.0000.0000.0000.000
115A227VAL00.0580.02964.9250.0000.0000.0000.0000.0000.000
116A228THR0-0.023-0.01962.4300.0000.0000.0000.0000.0000.000
117A229VAL00.0000.01658.8650.0000.0000.0000.0000.0000.000
118A230PRO00.0400.02056.2800.0000.0000.0000.0000.0000.000
119A231THR0-0.014-0.03953.812-0.001-0.0010.0000.0000.0000.000
120A232LEU00.0090.01847.6660.0010.0010.0000.0000.0000.000
121A233LYS10.8750.92150.081-0.001-0.0010.0000.0000.0000.000
122A234GLU-1-0.809-0.88552.7290.0010.0010.0000.0000.0000.000
123A235SER00.0110.00756.560-0.001-0.0010.0000.0000.0000.000
124A236ILE0-0.019-0.00658.9820.0000.0000.0000.0000.0000.000
125A237LEU0-0.0140.00361.7510.0000.0000.0000.0000.0000.000
126A238LEU00.0220.02262.3290.0000.0000.0000.0000.0000.000
127A239THR0-0.032-0.02965.0720.0000.0000.0000.0000.0000.000
128A240VAL0-0.0040.00467.1770.0000.0000.0000.0000.0000.000
129A241PRO00.0040.00768.8940.0000.0000.0000.0000.0000.000
130A242PRO00.0430.01971.9150.0000.0000.0000.0000.0000.000
131A243GLY0-0.0060.01074.2330.0000.0000.0000.0000.0000.000
132A244SER0-0.026-0.01469.103-0.001-0.0010.0000.0000.0000.000
133A245GLN0-0.036-0.03368.5210.0000.0000.0000.0000.0000.000
134A246ALA0-0.005-0.01566.0270.0000.0000.0000.0000.0000.000
135A247GLY00.0010.00362.1910.0000.0000.0000.0000.0000.000
136A248GLN0-0.011-0.00362.132-0.001-0.0010.0000.0000.0000.000
137A249ARG10.8080.86854.8740.0110.0110.0000.0000.0000.000
138A250LEU00.0020.00661.3230.0000.0000.0000.0000.0000.000
139A251ARG10.8140.89356.1390.0100.0100.0000.0000.0000.000
140A252ILE0-0.0050.00257.7180.0000.0000.0000.0000.0000.000
141A253LYS10.9410.95756.6290.0080.0080.0000.0000.0000.000
142A254GLY0-0.005-0.00953.3060.0010.0010.0000.0000.0000.000
143A255LYS10.8420.92352.9580.0030.0030.0000.0000.0000.000
144A256GLY00.0040.01850.4620.0000.0000.0000.0000.0000.000
145A257LEU00.013-0.00343.4700.0010.0010.0000.0000.0000.000
146A258VAL0-0.017-0.00244.675-0.001-0.0010.0000.0000.0000.000
147A259SER0-0.035-0.03242.608-0.001-0.0010.0000.0000.0000.000
148A260LYS10.8100.86836.8880.0180.0180.0000.0000.0000.000
149A261THR0-0.007-0.00241.6130.0000.0000.0000.0000.0000.000
150A262HIS00.0110.02144.8700.0000.0000.0000.0000.0000.000
151A263THR00.0000.01346.6670.0000.0000.0000.0000.0000.000
152A264GLY00.0050.01848.7620.0000.0000.0000.0000.0000.000
153A265ASP-1-0.811-0.88450.455-0.008-0.0080.0000.0000.0000.000
154A266LEU00.0390.03152.5550.0000.0000.0000.0000.0000.000
155A267PHE0-0.049-0.04554.1210.0000.0000.0000.0000.0000.000
156A268ALA00.0510.02556.9940.0000.0000.0000.0000.0000.000
157A269VAL0-0.016-0.00457.3160.0000.0000.0000.0000.0000.000
158A270ILE00.0040.00960.2660.0010.0010.0000.0000.0000.000
159A271LYS10.9120.95562.0230.0030.0030.0000.0000.0000.000
160A272ILE00.0350.02564.4040.0000.0000.0000.0000.0000.000
161A273VAL0-0.043-0.02465.4420.0000.0000.0000.0000.0000.000
162A274MET00.0250.00568.3780.0000.0000.0000.0000.0000.000
163A275PRO00.0020.01470.8230.0000.0000.0000.0000.0000.000
164A276THR00.0410.01172.3260.0000.0000.0000.0000.0000.000
165A277LYS10.8850.92974.256-0.001-0.0010.0000.0000.0000.000
166A278PRO00.0440.04377.6110.0000.0000.0000.0000.0000.000
167A279ASP-1-0.830-0.92480.2980.0010.0010.0000.0000.0000.000
168A280GLU-1-0.787-0.88283.7240.0000.0000.0000.0000.0000.000
169A281LYS10.9140.96886.0220.0000.0000.0000.0000.0000.000
170A282ALA00.0350.00581.2410.0000.0000.0000.0000.0000.000
171A283ARG10.8240.89883.2220.0000.0000.0000.0000.0000.000
172A284GLU-1-0.857-0.92284.310-0.001-0.0010.0000.0000.0000.000
173A285LEU0-0.053-0.02483.7190.0000.0000.0000.0000.0000.000
174A286TRP00.015-0.00376.6670.0000.0000.0000.0000.0000.000
175A287GLN0-0.050-0.02783.0220.0000.0000.0000.0000.0000.000
176A288GLN00.010-0.00886.2050.0000.0000.0000.0000.0000.000
177A289LEU0-0.020-0.01180.7090.0000.0000.0000.0000.0000.000
178A290ALA0-0.022-0.01083.1070.0000.0000.0000.0000.0000.000
179A291ALA0-0.020-0.01084.0230.0000.0000.0000.0000.0000.000
180A292ALA0-0.046-0.02585.4190.0000.0000.0000.0000.0000.000
181A293GLU-1-0.896-0.95281.164-0.004-0.0040.0000.0000.0000.000
182A294ALA0-0.032-0.00382.4870.0000.0000.0000.0000.0000.000
183A295SER0-0.064-0.02183.0190.0000.0000.0000.0000.0000.000
184A296PHE00.0120.00773.9950.0000.0000.0000.0000.0000.000
185A297ASP-1-0.780-0.88677.905-0.006-0.0060.0000.0000.0000.000
186A298PRO0-0.036-0.02173.0760.0000.0000.0000.0000.0000.000
187A299ARG10.8980.95172.4250.0050.0050.0000.0000.0000.000
188A300LYS10.9050.94773.9030.0060.0060.0000.0000.0000.000
189A301THR00.000-0.00368.8310.0000.0000.0000.0000.0000.000
190A302TRP0-0.072-0.02669.0590.0000.0000.0000.0000.0000.000