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: 76Y3K

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1609086.327833
FMO2-HF: Nuclear repulsion 1538131.505646
FMO2-HF: Total energy -70954.822188
FMO2-MP2: Total energy -71166.639604


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.
1.9683.8720.01-0.917-0.9950.001
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 : -0.013 / q_NPA : -0.017
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].
3A115ARG10.8940.9403.891-1.510-0.210-0.015-0.757-0.5280.001
4A116GLY00.0230.0277.2390.2970.2970.0000.0000.0000.000
5A117HIS00.004-0.00210.906-0.110-0.1100.0000.0000.0000.000
6A118ASP-1-0.784-0.88414.121-0.093-0.0930.0000.0000.0000.000
7A119LEU0-0.021-0.01317.5250.0250.0250.0000.0000.0000.000
8A120GLU-1-0.886-0.93221.068-0.023-0.0230.0000.0000.0000.000
9A121ILE0-0.033-0.03024.5370.0110.0110.0000.0000.0000.000
10A122GLU-1-0.885-0.93327.3710.0050.0050.0000.0000.0000.000
11A123VAL0-0.077-0.04930.4110.0050.0050.0000.0000.0000.000
12A124ALA00.0390.02333.059-0.004-0.0040.0000.0000.0000.000
13A125VAL0-0.044-0.01036.6740.0010.0010.0000.0000.0000.000
14A126PHE00.0360.02839.1560.0000.0000.0000.0000.0000.000
15A127LEU00.0290.00742.956-0.001-0.0010.0000.0000.0000.000
16A128GLU-1-0.896-0.97744.7950.0000.0000.0000.0000.0000.000
17A129GLU-1-0.876-0.94341.1240.0040.0040.0000.0000.0000.000
18A130THR00.0070.00941.570-0.001-0.0010.0000.0000.0000.000
19A131LEU0-0.067-0.04142.609-0.002-0.0020.0000.0000.0000.000
20A132ALA0-0.032-0.01143.807-0.001-0.0010.0000.0000.0000.000
21A133GLU-1-0.895-0.94137.816-0.011-0.0110.0000.0000.0000.000
22A134GLN00.0070.01238.3890.0000.0000.0000.0000.0000.000
23A135THR0-0.033-0.02535.811-0.002-0.0020.0000.0000.0000.000
24A136ARG10.8430.91934.115-0.007-0.0070.0000.0000.0000.000
25A137THR00.016-0.00932.687-0.001-0.0010.0000.0000.0000.000
26A138ILE00.0140.02628.8860.0020.0020.0000.0000.0000.000
27A139SER00.011-0.00229.5730.0040.0040.0000.0000.0000.000
28A140TYR0-0.028-0.02322.171-0.007-0.0070.0000.0000.0000.000
29A141ASN00.0800.02524.7520.0040.0040.0000.0000.0000.000
30A142LEU0-0.027-0.02117.484-0.012-0.0120.0000.0000.0000.000
31A143PRO00.0290.00118.1830.0160.0160.0000.0000.0000.000
32A144VAL00.0100.00916.6060.0200.0200.0000.0000.0000.000
33A145TYR0-0.0200.00213.674-0.035-0.0350.0000.0000.0000.000
34A146ASN00.1570.06114.1730.0810.0810.0000.0000.0000.000
35A147VAL00.0280.0339.0150.0180.0180.0000.0000.0000.000
36A148PHE0-0.124-0.08911.4390.0030.0030.0000.0000.0000.000
37A149GLY00.0600.03511.5640.0600.0600.0000.0000.0000.000
38A150MET0-0.106-0.05113.592-0.061-0.0610.0000.0000.0000.000
39A151ILE0-0.020-0.02317.479-0.023-0.0230.0000.0000.0000.000
40A152GLU-1-0.980-0.98418.9360.2740.2740.0000.0000.0000.000
41A153SER00.0040.01920.612-0.022-0.0220.0000.0000.0000.000
42A154GLU-1-0.947-0.99122.1240.1050.1050.0000.0000.0000.000
43A155THR0-0.035-0.00120.522-0.009-0.0090.0000.0000.0000.000
44A156PRO00.0280.03822.555-0.004-0.0040.0000.0000.0000.000
45A157LYS10.8560.94219.627-0.090-0.0900.0000.0000.0000.000
46A158THR00.0230.00225.597-0.004-0.0040.0000.0000.0000.000
47A159LEU0-0.0280.00825.903-0.001-0.0010.0000.0000.0000.000
48A160ASN0-0.036-0.01928.402-0.005-0.0050.0000.0000.0000.000
49A161VAL00.0360.02028.987-0.003-0.0030.0000.0000.0000.000
50A162LYS10.8920.94831.7170.0100.0100.0000.0000.0000.000
51A163ILE00.0000.00533.458-0.004-0.0040.0000.0000.0000.000
52A164PRO00.0270.00034.2250.0010.0010.0000.0000.0000.000
53A165ALA00.0610.04037.4300.0010.0010.0000.0000.0000.000
54A166GLY00.0430.02240.657-0.003-0.0030.0000.0000.0000.000
55A167VAL0-0.109-0.03735.577-0.002-0.0020.0000.0000.0000.000
56A168VAL00.0320.00637.0360.0020.0020.0000.0000.0000.000
57A169ASP-1-0.879-0.94336.528-0.012-0.0120.0000.0000.0000.000
58A170GLY00.0850.04833.673-0.003-0.0030.0000.0000.0000.000
59A171GLN0-0.068-0.02832.133-0.002-0.0020.0000.0000.0000.000
60A172ARG10.9080.95925.5280.0350.0350.0000.0000.0000.000
61A173ILE0-0.051-0.02027.394-0.006-0.0060.0000.0000.0000.000
62A174ARG10.8780.94918.3690.1250.1250.0000.0000.0000.000
63A175LEU0-0.028-0.00822.4420.0000.0000.0000.0000.0000.000
64A176LYS10.9250.95616.7490.1600.1600.0000.0000.0000.000
65A177GLY0-0.031-0.01015.2210.0110.0110.0000.0000.0000.000
66A178GLN0-0.024-0.03115.9280.0380.0380.0000.0000.0000.000
67A179GLY00.0510.04816.3500.0030.0030.0000.0000.0000.000
68A180THR0-0.010-0.01311.7550.0040.0040.0000.0000.0000.000
69A181PRO00.019-0.01011.057-0.093-0.0930.0000.0000.0000.000
70A182GLY00.0660.0417.3950.0020.0020.0000.0000.0000.000
71A183GLU-1-0.990-0.9828.0150.7620.7620.0000.0000.0000.000
72A184ASN0-0.003-0.0276.7440.4770.4770.0000.0000.0000.000
73A185GLY0-0.012-0.0033.3142.6832.9820.023-0.094-0.2270.000
74A186GLY00.0010.0064.021-1.294-0.9890.002-0.066-0.2400.000
75A187PRO0-0.065-0.0225.5280.3500.3500.0000.0000.0000.000
76A188ASN00.0320.0059.162-0.041-0.0410.0000.0000.0000.000
77A189GLY0-0.041-0.01811.720-0.069-0.0690.0000.0000.0000.000
78A190ASP-1-0.850-0.92314.120-0.116-0.1160.0000.0000.0000.000
79A191LEU0-0.017-0.01117.7640.0150.0150.0000.0000.0000.000
80A192TRP0-0.020-0.03120.396-0.012-0.0120.0000.0000.0000.000
81A193LEU00.0210.01624.1300.0090.0090.0000.0000.0000.000
82A194VAL00.002-0.00827.658-0.008-0.0080.0000.0000.0000.000
83A195ILE0-0.003-0.01030.0270.0050.0050.0000.0000.0000.000
84A196HIS00.0020.00233.636-0.003-0.0030.0000.0000.0000.000
85A197ILE0-0.040-0.01236.1460.0020.0020.0000.0000.0000.000
86A198ALA00.0490.01739.728-0.001-0.0010.0000.0000.0000.000
87A199PRO0-0.039-0.02641.4750.0000.0000.0000.0000.0000.000
88A200HIS00.0550.03844.9400.0010.0010.0000.0000.0000.000
89A201PRO0-0.004-0.00847.983-0.001-0.0010.0000.0000.0000.000
90A202LEU0-0.063-0.03351.2520.0000.0000.0000.0000.0000.000
91A203PHE0-0.042-0.01450.187-0.001-0.0010.0000.0000.0000.000
92A204ASP-1-0.850-0.90749.172-0.006-0.0060.0000.0000.0000.000
93A205ILE0-0.022-0.03044.6840.0000.0000.0000.0000.0000.000
94A206VAL00.0210.01347.716-0.001-0.0010.0000.0000.0000.000
95A207GLY0-0.010-0.00245.2230.0000.0000.0000.0000.0000.000
96A208HIS00.024-0.00943.5800.0020.0020.0000.0000.0000.000
97A209ASN0-0.0200.00047.2350.0020.0020.0000.0000.0000.000
98A210LEU00.0410.02748.1910.0000.0000.0000.0000.0000.000
99A211GLU-1-0.866-0.92451.592-0.011-0.0110.0000.0000.0000.000
100A212ILE00.0570.03553.8780.0010.0010.0000.0000.0000.000
101A213VAL00.0020.01656.5040.0000.0000.0000.0000.0000.000
102A214LEU0-0.007-0.01559.1070.0010.0010.0000.0000.0000.000
103A215PRO0-0.035-0.03361.9120.0000.0000.0000.0000.0000.000
104A216LEU00.0270.02264.8420.0000.0000.0000.0000.0000.000
105A217ALA00.0220.01268.4110.0000.0000.0000.0000.0000.000
106A218PRO0-0.005-0.01371.7530.0000.0000.0000.0000.0000.000
107A219TRP00.047-0.00273.8310.0000.0000.0000.0000.0000.000
108A220GLU-1-0.887-0.92970.621-0.002-0.0020.0000.0000.0000.000
109A221ALA0-0.0240.00470.9910.0000.0000.0000.0000.0000.000
110A222ALA0-0.014-0.00272.5740.0000.0000.0000.0000.0000.000
111A223LEU0-0.011-0.01676.2660.0000.0000.0000.0000.0000.000
112A224GLY00.0020.01973.5800.0000.0000.0000.0000.0000.000
113A225ALA00.005-0.01071.6110.0000.0000.0000.0000.0000.000
114A226LYS10.9150.95769.9500.0030.0030.0000.0000.0000.000
115A227VAL00.0570.03165.3160.0000.0000.0000.0000.0000.000
116A228THR0-0.0020.00163.1550.0000.0000.0000.0000.0000.000
117A229VAL0-0.039-0.01559.4270.0000.0000.0000.0000.0000.000
118A230PRO00.0620.03356.6930.0000.0000.0000.0000.0000.000
119A231THR0-0.020-0.02054.191-0.001-0.0010.0000.0000.0000.000
120A232LEU00.0540.02347.9260.0010.0010.0000.0000.0000.000
121A233LYS10.8920.95250.3560.0040.0040.0000.0000.0000.000
122A234GLU-1-0.829-0.89853.463-0.002-0.0020.0000.0000.0000.000
123A235SER00.002-0.01557.201-0.001-0.0010.0000.0000.0000.000
124A236ILE0-0.020-0.00259.5680.0000.0000.0000.0000.0000.000
125A237LEU0-0.0300.00262.2280.0000.0000.0000.0000.0000.000
126A238LEU00.0220.00463.0750.0000.0000.0000.0000.0000.000
127A239THR0-0.027-0.02965.8870.0010.0010.0000.0000.0000.000
128A240VAL0-0.0160.00267.6030.0000.0000.0000.0000.0000.000
129A241PRO0-0.017-0.00469.2840.0000.0000.0000.0000.0000.000
130A242PRO00.0640.02372.4390.0000.0000.0000.0000.0000.000
131A243GLY0-0.0080.01474.8540.0000.0000.0000.0000.0000.000
132A244SER0-0.093-0.06169.208-0.001-0.0010.0000.0000.0000.000
133A245GLN00.0260.00868.5410.0000.0000.0000.0000.0000.000
134A246ALA00.000-0.00166.8350.0000.0000.0000.0000.0000.000
135A247GLY00.0180.00862.8640.0000.0000.0000.0000.0000.000
136A248GLN0-0.0100.00062.637-0.001-0.0010.0000.0000.0000.000
137A249ARG10.8540.92055.3490.0120.0120.0000.0000.0000.000
138A250LEU00.0050.00761.9160.0000.0000.0000.0000.0000.000
139A251ARG10.8700.93956.9920.0120.0120.0000.0000.0000.000
140A252ILE00.0150.01158.2180.0000.0000.0000.0000.0000.000
141A253LYS10.9300.95257.0530.0110.0110.0000.0000.0000.000
142A254GLY0-0.005-0.00253.9300.0010.0010.0000.0000.0000.000
143A255LYS10.7890.89953.3190.0050.0050.0000.0000.0000.000
144A256GLY00.0270.02651.4130.0010.0010.0000.0000.0000.000
145A257LEU0-0.002-0.00444.7070.0010.0010.0000.0000.0000.000
146A258VAL00.0010.01245.070-0.001-0.0010.0000.0000.0000.000
147A259SER0-0.044-0.01042.840-0.001-0.0010.0000.0000.0000.000
148A260LYS10.8200.88437.9650.0240.0240.0000.0000.0000.000
149A261THR00.008-0.00242.1850.0010.0010.0000.0000.0000.000
150A262HIS00.0140.02145.3430.0010.0010.0000.0000.0000.000
151A263THR0-0.006-0.01147.0760.0010.0010.0000.0000.0000.000
152A264GLY0-0.0230.00049.2550.0000.0000.0000.0000.0000.000
153A265ASP-1-0.836-0.94650.885-0.011-0.0110.0000.0000.0000.000
154A266LEU00.0060.01453.2450.0000.0000.0000.0000.0000.000
155A267PHE0-0.041-0.03254.8390.0000.0000.0000.0000.0000.000
156A268ALA00.0450.02657.3600.0000.0000.0000.0000.0000.000
157A269VAL0-0.002-0.02057.9860.0000.0000.0000.0000.0000.000
158A270ILE0-0.0090.00660.7220.0010.0010.0000.0000.0000.000
159A271LYS10.9860.99761.8600.0030.0030.0000.0000.0000.000
160A272ILE0-0.0050.00664.8770.0000.0000.0000.0000.0000.000
161A273VAL0-0.039-0.02365.6480.0000.0000.0000.0000.0000.000
162A274MET00.016-0.00168.7910.0000.0000.0000.0000.0000.000
163A275PRO00.0130.01971.0620.0000.0000.0000.0000.0000.000
164A276THR00.0450.01472.5010.0000.0000.0000.0000.0000.000
165A277LYS10.8920.95474.492-0.001-0.0010.0000.0000.0000.000
166A278PRO00.0170.01077.8350.0000.0000.0000.0000.0000.000
167A279ASP-1-0.874-0.96580.5220.0010.0010.0000.0000.0000.000
168A280GLU-1-0.894-0.94384.1830.0000.0000.0000.0000.0000.000
169A281LYS10.9561.00086.0150.0000.0000.0000.0000.0000.000
170A282ALA00.0550.01781.6840.0000.0000.0000.0000.0000.000
171A283ARG10.9250.94883.7730.0000.0000.0000.0000.0000.000
172A284GLU-1-0.907-0.94284.666-0.001-0.0010.0000.0000.0000.000
173A285LEU0-0.023-0.01984.6520.0000.0000.0000.0000.0000.000
174A286TRP00.001-0.00977.0210.0000.0000.0000.0000.0000.000
175A287GLN0-0.037-0.01083.5470.0000.0000.0000.0000.0000.000
176A288GLN0-0.002-0.00486.4740.0000.0000.0000.0000.0000.000
177A289LEU0-0.003-0.01280.8310.0000.0000.0000.0000.0000.000
178A290ALA0-0.014-0.00283.3460.0000.0000.0000.0000.0000.000
179A291ALA0-0.009-0.00584.3060.0000.0000.0000.0000.0000.000
180A292ALA0-0.045-0.02285.6680.0000.0000.0000.0000.0000.000
181A293GLU-1-0.926-0.96281.375-0.005-0.0050.0000.0000.0000.000
182A294ALA0-0.029-0.00382.8350.0000.0000.0000.0000.0000.000
183A295SER0-0.070-0.03283.8640.0000.0000.0000.0000.0000.000
184A296PHE0-0.005-0.00374.6130.0000.0000.0000.0000.0000.000
185A297ASP-1-0.849-0.94177.592-0.006-0.0060.0000.0000.0000.000
186A298PRO0-0.035-0.01473.8790.0000.0000.0000.0000.0000.000
187A299ARG10.8990.94573.0320.0050.0050.0000.0000.0000.000
188A300LYS11.0361.03774.2300.0070.0070.0000.0000.0000.000
189A301THR0-0.061-0.04169.6650.0000.0000.0000.0000.0000.000
190A302TRP0-0.041-0.00369.3030.0000.0000.0000.0000.0000.000