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: 2N47R

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1609452.482553
FMO2-HF: Nuclear repulsion 1538496.385163
FMO2-HF: Total energy -70956.09739
FMO2-MP2: Total energy -71167.792891


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.
1.9573.8450.011-0.911-0.9870.001
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 : -0.017 / q_NPA : -0.022
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].
3A115ARG10.9010.9513.891-1.450-0.148-0.014-0.761-0.5270.001
4A116GLY00.0240.0267.2390.2880.2880.0000.0000.0000.000
5A117HIS00.003-0.00610.903-0.117-0.1170.0000.0000.0000.000
6A118ASP-1-0.813-0.91114.121-0.098-0.0980.0000.0000.0000.000
7A119LEU0-0.011-0.00417.5250.0230.0230.0000.0000.0000.000
8A120GLU-1-0.808-0.87221.068-0.030-0.0300.0000.0000.0000.000
9A121ILE0-0.036-0.03324.5370.0110.0110.0000.0000.0000.000
10A122GLU-1-0.837-0.89627.3650.0050.0050.0000.0000.0000.000
11A123VAL0-0.061-0.04330.3630.0050.0050.0000.0000.0000.000
12A124ALA00.0500.03433.056-0.003-0.0030.0000.0000.0000.000
13A125VAL0-0.029-0.00636.5850.0010.0010.0000.0000.0000.000
14A126PHE00.0400.03139.1550.0000.0000.0000.0000.0000.000
15A127LEU00.0380.01542.955-0.001-0.0010.0000.0000.0000.000
16A128GLU-1-0.875-0.96844.7970.0000.0000.0000.0000.0000.000
17A129GLU-1-0.826-0.88840.8220.0050.0050.0000.0000.0000.000
18A130THR0-0.022-0.00841.079-0.001-0.0010.0000.0000.0000.000
19A131LEU0-0.059-0.03242.614-0.002-0.0020.0000.0000.0000.000
20A132ALA0-0.025-0.00843.825-0.001-0.0010.0000.0000.0000.000
21A133GLU-1-0.859-0.90037.826-0.010-0.0100.0000.0000.0000.000
22A134GLN00.002-0.00338.1450.0010.0010.0000.0000.0000.000
23A135THR0-0.038-0.02735.890-0.002-0.0020.0000.0000.0000.000
24A136ARG10.7880.87234.204-0.006-0.0060.0000.0000.0000.000
25A137THR00.021-0.01432.666-0.001-0.0010.0000.0000.0000.000
26A138ILE00.0080.02728.7870.0010.0010.0000.0000.0000.000
27A139SER00.0390.00929.5870.0010.0010.0000.0000.0000.000
28A140TYR0-0.031-0.02821.789-0.003-0.0030.0000.0000.0000.000
29A141ASN00.027-0.00624.694-0.001-0.0010.0000.0000.0000.000
30A142LEU0-0.044-0.02317.315-0.013-0.0130.0000.0000.0000.000
31A143PRO00.031-0.00218.2080.0160.0160.0000.0000.0000.000
32A144VAL00.0020.00116.5770.0190.0190.0000.0000.0000.000
33A145TYR0-0.008-0.00413.685-0.041-0.0410.0000.0000.0000.000
34A146ASN00.1330.06714.1730.0830.0830.0000.0000.0000.000
35A147VAL00.0070.0198.9010.0210.0210.0000.0000.0000.000
36A148PHE0-0.148-0.09711.4180.0180.0180.0000.0000.0000.000
37A149GLY00.0800.04811.5380.0570.0570.0000.0000.0000.000
38A150MET0-0.083-0.04213.563-0.071-0.0710.0000.0000.0000.000
39A151ILE0-0.018-0.02216.5170.0370.0370.0000.0000.0000.000
40A152GLU-1-0.950-0.97218.3990.2870.2870.0000.0000.0000.000
41A153SER00.0110.01720.750-0.022-0.0220.0000.0000.0000.000
42A154GLU-1-0.887-0.94822.1240.1020.1020.0000.0000.0000.000
43A155THR0-0.0190.01020.392-0.008-0.0080.0000.0000.0000.000
44A156PRO00.0150.02022.537-0.004-0.0040.0000.0000.0000.000
45A157LYS10.8530.93919.091-0.088-0.0880.0000.0000.0000.000
46A158THR00.014-0.00625.584-0.003-0.0030.0000.0000.0000.000
47A159LEU0-0.060-0.00325.6010.0000.0000.0000.0000.0000.000
48A160ASN0-0.036-0.02028.399-0.004-0.0040.0000.0000.0000.000
49A161VAL00.0180.01028.722-0.003-0.0030.0000.0000.0000.000
50A162LYS10.8580.90731.7200.0100.0100.0000.0000.0000.000
51A163ILE00.0010.00833.592-0.004-0.0040.0000.0000.0000.000
52A164PRO00.018-0.01034.2090.0010.0010.0000.0000.0000.000
53A165ALA00.0600.04237.4390.0010.0010.0000.0000.0000.000
54A166GLY00.0470.02740.668-0.003-0.0030.0000.0000.0000.000
55A167VAL0-0.115-0.03935.539-0.002-0.0020.0000.0000.0000.000
56A168VAL00.0300.00037.0220.0010.0010.0000.0000.0000.000
57A169ASP-1-0.822-0.91336.528-0.011-0.0110.0000.0000.0000.000
58A170GLY00.0580.03333.670-0.003-0.0030.0000.0000.0000.000
59A171GLN0-0.060-0.02932.133-0.002-0.0020.0000.0000.0000.000
60A172ARG10.8370.90025.6830.0320.0320.0000.0000.0000.000
61A173ILE0-0.049-0.01627.392-0.005-0.0050.0000.0000.0000.000
62A174ARG10.8110.90318.1470.1290.1290.0000.0000.0000.000
63A175LEU0-0.007-0.00822.5290.0010.0010.0000.0000.0000.000
64A176LYS10.9380.96516.5570.1590.1590.0000.0000.0000.000
65A177GLY0-0.024-0.00915.2260.0120.0120.0000.0000.0000.000
66A178GLN0-0.009-0.01315.9290.0410.0410.0000.0000.0000.000
67A179GLY00.0400.04016.3450.0030.0030.0000.0000.0000.000
68A180THR0-0.013-0.01212.1100.0030.0030.0000.0000.0000.000
69A181PRO00.024-0.00211.234-0.083-0.0830.0000.0000.0000.000
70A182GLY00.0700.0417.4050.0090.0090.0000.0000.0000.000
71A183GLU-1-0.980-0.9818.0830.7220.7220.0000.0000.0000.000
72A184ASN0-0.014-0.0296.7890.4850.4850.0000.0000.0000.000
73A185GLY0-0.013-0.0023.2912.5492.8310.023-0.085-0.2190.000
74A186GLY00.0070.0104.023-1.278-0.9740.002-0.065-0.2410.000
75A187PRO0-0.064-0.0235.5370.3360.3360.0000.0000.0000.000
76A188ASN00.0370.0119.1740.0040.0040.0000.0000.0000.000
77A189GLY0-0.039-0.01611.722-0.070-0.0700.0000.0000.0000.000
78A190ASP-1-0.801-0.88314.121-0.121-0.1210.0000.0000.0000.000
79A191LEU0-0.030-0.00517.7680.0140.0140.0000.0000.0000.000
80A192TRP0-0.029-0.04119.947-0.012-0.0120.0000.0000.0000.000
81A193LEU00.0160.01624.1320.0090.0090.0000.0000.0000.000
82A194VAL0-0.012-0.01427.563-0.008-0.0080.0000.0000.0000.000
83A195ILE0-0.010-0.01230.0270.0050.0050.0000.0000.0000.000
84A196HIS0-0.078-0.05333.636-0.003-0.0030.0000.0000.0000.000
85A197ILE0-0.047-0.00636.1460.0020.0020.0000.0000.0000.000
86A198ALA00.0420.02039.728-0.001-0.0010.0000.0000.0000.000
87A199PRO0-0.028-0.02841.4750.0000.0000.0000.0000.0000.000
88A200HIS00.0280.02644.9400.0010.0010.0000.0000.0000.000
89A201PRO0-0.001-0.00747.983-0.001-0.0010.0000.0000.0000.000
90A202LEU0-0.057-0.03051.2520.0000.0000.0000.0000.0000.000
91A203PHE0-0.035-0.01450.255-0.001-0.0010.0000.0000.0000.000
92A204ASP-1-0.852-0.90649.186-0.007-0.0070.0000.0000.0000.000
93A205ILE0-0.035-0.04044.6500.0000.0000.0000.0000.0000.000
94A206VAL00.0270.01747.716-0.001-0.0010.0000.0000.0000.000
95A207GLY0-0.008-0.00245.2940.0000.0000.0000.0000.0000.000
96A208HIS00.026-0.00743.6310.0010.0010.0000.0000.0000.000
97A209ASN0-0.022-0.00947.3040.0010.0010.0000.0000.0000.000
98A210LEU00.0490.03248.2820.0000.0000.0000.0000.0000.000
99A211GLU-1-0.826-0.88251.592-0.011-0.0110.0000.0000.0000.000
100A212ILE00.0630.03353.8780.0010.0010.0000.0000.0000.000
101A213VAL0-0.0070.01256.5040.0000.0000.0000.0000.0000.000
102A214LEU0-0.001-0.01459.1070.0010.0010.0000.0000.0000.000
103A215PRO0-0.043-0.02161.9310.0000.0000.0000.0000.0000.000
104A216LEU00.0350.01764.8420.0000.0000.0000.0000.0000.000
105A217ALA00.0230.01168.4110.0000.0000.0000.0000.0000.000
106A218PRO00.003-0.00971.7530.0000.0000.0000.0000.0000.000
107A219TRP00.046-0.00273.8310.0000.0000.0000.0000.0000.000
108A220GLU-1-0.886-0.93070.646-0.002-0.0020.0000.0000.0000.000
109A221ALA0-0.0290.00170.9470.0000.0000.0000.0000.0000.000
110A222ALA0-0.009-0.00272.5740.0000.0000.0000.0000.0000.000
111A223LEU0-0.009-0.01476.2660.0000.0000.0000.0000.0000.000
112A224GLY00.0010.01973.5800.0000.0000.0000.0000.0000.000
113A225ALA00.010-0.00971.6860.0000.0000.0000.0000.0000.000
114A226LYS10.9020.95469.9490.0030.0030.0000.0000.0000.000
115A227VAL00.0560.02865.5960.0000.0000.0000.0000.0000.000
116A228THR0-0.012-0.00463.1520.0000.0000.0000.0000.0000.000
117A229VAL0-0.015-0.00259.4740.0000.0000.0000.0000.0000.000
118A230PRO00.0490.03556.7250.0000.0000.0000.0000.0000.000
119A231THR0-0.019-0.03854.437-0.001-0.0010.0000.0000.0000.000
120A232LEU00.0590.03748.2130.0010.0010.0000.0000.0000.000
121A233LYS10.8520.92250.8330.0030.0030.0000.0000.0000.000
122A234GLU-1-0.801-0.87753.466-0.002-0.0020.0000.0000.0000.000
123A235SER00.005-0.01357.203-0.001-0.0010.0000.0000.0000.000
124A236ILE0-0.030-0.01659.3970.0000.0000.0000.0000.0000.000
125A237LEU0-0.0290.00862.2320.0000.0000.0000.0000.0000.000
126A238LEU00.0230.00462.8720.0000.0000.0000.0000.0000.000
127A239THR0-0.021-0.02565.8920.0000.0000.0000.0000.0000.000
128A240VAL0-0.016-0.00367.5080.0000.0000.0000.0000.0000.000
129A241PRO0-0.0100.00069.3270.0000.0000.0000.0000.0000.000
130A242PRO00.0600.01972.4390.0000.0000.0000.0000.0000.000
131A243GLY0-0.0010.01974.8550.0000.0000.0000.0000.0000.000
132A244SER0-0.065-0.03369.239-0.001-0.0010.0000.0000.0000.000
133A245GLN0-0.015-0.02468.6580.0000.0000.0000.0000.0000.000
134A246ALA0-0.002-0.00366.8910.0000.0000.0000.0000.0000.000
135A247GLY00.0160.00962.8640.0000.0000.0000.0000.0000.000
136A248GLN0-0.024-0.00362.637-0.001-0.0010.0000.0000.0000.000
137A249ARG10.8040.87155.1760.0110.0110.0000.0000.0000.000
138A250LEU0-0.0010.00961.9380.0000.0000.0000.0000.0000.000
139A251ARG10.8100.88556.7570.0110.0110.0000.0000.0000.000
140A252ILE00.000-0.00158.3220.0000.0000.0000.0000.0000.000
141A253LYS10.9530.95957.1530.0100.0100.0000.0000.0000.000
142A254GLY0-0.010-0.00753.9510.0010.0010.0000.0000.0000.000
143A255LYS10.8250.92053.3280.0050.0050.0000.0000.0000.000
144A256GLY00.0170.02351.4210.0000.0000.0000.0000.0000.000
145A257LEU00.0060.00144.3690.0010.0010.0000.0000.0000.000
146A258VAL0-0.0070.00245.533-0.001-0.0010.0000.0000.0000.000
147A259SER0-0.055-0.01542.971-0.001-0.0010.0000.0000.0000.000
148A260LYS10.8420.89337.8730.0230.0230.0000.0000.0000.000
149A261THR00.0140.00142.2480.0010.0010.0000.0000.0000.000
150A262HIS00.0050.01945.4050.0010.0010.0000.0000.0000.000
151A263THR0-0.004-0.00547.1410.0010.0010.0000.0000.0000.000
152A264GLY0-0.0010.00549.3170.0000.0000.0000.0000.0000.000
153A265ASP-1-0.808-0.88350.953-0.011-0.0110.0000.0000.0000.000
154A266LEU00.0110.01453.2730.0000.0000.0000.0000.0000.000
155A267PHE0-0.034-0.03054.7310.0000.0000.0000.0000.0000.000
156A268ALA00.0470.02757.3600.0000.0000.0000.0000.0000.000
157A269VAL0-0.007-0.01757.7800.0000.0000.0000.0000.0000.000
158A270ILE00.0070.01060.7220.0010.0010.0000.0000.0000.000
159A271LYS10.9860.99861.9000.0030.0030.0000.0000.0000.000
160A272ILE0-0.0070.00664.8770.0000.0000.0000.0000.0000.000
161A273VAL0-0.040-0.02565.6630.0000.0000.0000.0000.0000.000
162A274MET00.0110.00368.7910.0000.0000.0000.0000.0000.000
163A275PRO00.0080.01771.0620.0000.0000.0000.0000.0000.000
164A276THR00.0370.00472.3910.0000.0000.0000.0000.0000.000
165A277LYS10.8870.94574.492-0.001-0.0010.0000.0000.0000.000
166A278PRO00.0170.01377.8350.0000.0000.0000.0000.0000.000
167A279ASP-1-0.859-0.94680.5220.0000.0000.0000.0000.0000.000
168A280GLU-1-0.888-0.94784.1830.0000.0000.0000.0000.0000.000
169A281LYS10.9480.99286.0780.0000.0000.0000.0000.0000.000
170A282ALA00.0620.02381.6440.0000.0000.0000.0000.0000.000
171A283ARG10.9320.96083.7730.0000.0000.0000.0000.0000.000
172A284GLU-1-0.897-0.94684.666-0.001-0.0010.0000.0000.0000.000
173A285LEU0-0.023-0.01084.4550.0000.0000.0000.0000.0000.000
174A286TRP00.001-0.01476.9320.0000.0000.0000.0000.0000.000
175A287GLN0-0.050-0.02283.5470.0000.0000.0000.0000.0000.000
176A288GLN0-0.002-0.00186.4740.0000.0000.0000.0000.0000.000
177A289LEU0-0.014-0.01681.0190.0000.0000.0000.0000.0000.000
178A290ALA0-0.0090.00083.3460.0000.0000.0000.0000.0000.000
179A291ALA0-0.008-0.00684.3060.0000.0000.0000.0000.0000.000
180A292ALA0-0.038-0.01885.7260.0000.0000.0000.0000.0000.000
181A293GLU-1-0.921-0.96181.473-0.005-0.0050.0000.0000.0000.000
182A294ALA0-0.033-0.00182.8350.0000.0000.0000.0000.0000.000
183A295SER0-0.077-0.03483.8860.0000.0000.0000.0000.0000.000
184A296PHE00.0110.00374.4750.0000.0000.0000.0000.0000.000
185A297ASP-1-0.823-0.91778.010-0.006-0.0060.0000.0000.0000.000
186A298PRO0-0.003-0.00373.8660.0000.0000.0000.0000.0000.000
187A299ARG10.9170.96673.2170.0050.0050.0000.0000.0000.000
188A300LYS10.9560.98174.4070.0060.0060.0000.0000.0000.000
189A301THR0-0.046-0.03569.6960.0000.0000.0000.0000.0000.000
190A302TRP0-0.068-0.01769.4680.0000.0000.0000.0000.0000.000