Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 3Q3GL

Calculation Name: 4LUB-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LUB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DUV6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 191
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2125845.360883
FMO2-HF: Nuclear repulsion 2052284.572554
FMO2-HF: Total energy -73560.78833
FMO2-MP2: Total energy -73780.98389


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:4:ACE )


Summations of interaction energy for fragment #1(A:4:ACE )
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.
-0.1881.2020.023-0.722-0.692-0.002
Interaction energy analysis for fragmet #1(A:4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.008
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].
3A6MET 00.0030.0273.8060.8192.024-0.006-0.545-0.654-0.001
4A7LYS 10.9961.0095.7000.5410.5410.0000.0000.0000.000
5A8ILE 00.0000.0018.4710.1490.1490.0000.0000.0000.000
6A9ALA 00.0180.02511.232-0.025-0.0250.0000.0000.0000.000
7A10TYR 0-0.009-0.00614.5150.0300.0300.0000.0000.0000.000
8A11LEU 00.0250.01717.058-0.006-0.0060.0000.0000.0000.000
9A12GLY 00.0020.02720.668-0.003-0.0030.0000.0000.0000.000
10A13PRO 00.005-0.01321.4830.0130.0130.0000.0000.0000.000
11A14SER 00.012-0.02618.980-0.004-0.0040.0000.0000.0000.000
12A15GLY 0-0.0150.00019.5040.0140.0140.0000.0000.0000.000
13A16SER 0-0.035-0.00421.0240.0140.0140.0000.0000.0000.000
14A17PHE 00.019-0.01220.915-0.005-0.0050.0000.0000.0000.000
15A18THR 00.0610.01718.2980.0080.0080.0000.0000.0000.000
16A19HIS 00.0480.05114.4590.0230.0230.0000.0000.0000.000
17A20ASN 00.019-0.00815.984-0.020-0.0200.0000.0000.0000.000
18A21VAL 0-0.0090.01517.0330.0090.0090.0000.0000.0000.000
19A22ALA 00.004-0.00213.1320.0180.0180.0000.0000.0000.000
20A23LEU 0-0.059-0.03412.210-0.011-0.0110.0000.0000.0000.000
21A24HIS 0-0.017-0.00212.3860.0060.0060.0000.0000.0000.000
22A25ALA 0-0.0100.01013.0330.0380.0380.0000.0000.0000.000
23A26PHE 0-0.004-0.0288.3020.0720.0720.0000.0000.0000.000
24A27PRO 00.0460.0368.423-0.129-0.1290.0000.0000.0000.000
25A28ALA 0-0.072-0.0413.336-0.169-0.0450.021-0.051-0.0940.000
26A29ALA 0-0.047-0.0163.786-1.207-1.1460.008-0.1260.056-0.001
27A30ASP -1-0.919-0.9635.934-0.778-0.7780.0000.0000.0000.000
28A31LEU 00.0020.0048.4200.1670.1670.0000.0000.0000.000
29A32LEU 0-0.015-0.02111.6260.0290.0290.0000.0000.0000.000
30A33PRO 0-0.0200.00514.6400.0390.0390.0000.0000.0000.000
31A34PHE 00.017-0.00516.487-0.001-0.0010.0000.0000.0000.000
32A35GLU -1-0.935-0.96620.963-0.085-0.0850.0000.0000.0000.000
33A36ASN 00.0490.01724.3160.0080.0080.0000.0000.0000.000
34A37ILE 00.0530.02023.534-0.009-0.0090.0000.0000.0000.000
35A38THR 0-0.058-0.07923.555-0.001-0.0010.0000.0000.0000.000
36A39GLU -1-0.949-0.98823.289-0.098-0.0980.0000.0000.0000.000
37A40VAL 0-0.061-0.01518.301-0.013-0.0130.0000.0000.0000.000
38A41ILE 0-0.004-0.00619.301-0.007-0.0070.0000.0000.0000.000
39A42LYS 10.9710.99120.8260.0660.0660.0000.0000.0000.000
40A43ALA 00.0190.04417.722-0.004-0.0040.0000.0000.0000.000
41A44TYR 0-0.024-0.00315.398-0.013-0.0130.0000.0000.0000.000
42A45GLU -1-0.860-0.90717.811-0.047-0.0470.0000.0000.0000.000
43A46SER 0-0.108-0.06920.523-0.001-0.0010.0000.0000.0000.000
44A47LYS 10.9070.94716.7950.0490.0490.0000.0000.0000.000
45A48GLN 0-0.041-0.01715.872-0.042-0.0420.0000.0000.0000.000
46A49VAL 0-0.052-0.02312.481-0.072-0.0720.0000.0000.0000.000
47A50CYS 0-0.073-0.0419.9300.0400.0400.0000.0000.0000.000
48A51PHE 00.0410.0049.4730.0560.0560.0000.0000.0000.000
49A52ALA 00.0230.01713.299-0.054-0.0540.0000.0000.0000.000
50A53ILE 0-0.044-0.00313.6390.0290.0290.0000.0000.0000.000
51A54VAL 00.0190.00017.255-0.016-0.0160.0000.0000.0000.000
52A55PRO 0-0.039-0.00120.9970.0120.0120.0000.0000.0000.000
53A56VAL 00.0260.01323.806-0.001-0.0010.0000.0000.0000.000
54A57GLU -1-0.863-0.91726.2320.0040.0040.0000.0000.0000.000
55A58ASN 00.0000.01927.9420.0010.0010.0000.0000.0000.000
56A59SER 0-0.032-0.01030.3810.0020.0020.0000.0000.0000.000
57A60ILE 0-0.038-0.02332.5900.0020.0020.0000.0000.0000.000
58A61GLU -1-0.900-0.96433.205-0.023-0.0230.0000.0000.0000.000
59A62GLY 00.0180.03533.6950.0010.0010.0000.0000.0000.000
60A63SER 00.006-0.00231.038-0.001-0.0010.0000.0000.0000.000
61A64VAL 0-0.020-0.00727.542-0.002-0.0020.0000.0000.0000.000
62A65HIS 00.005-0.01530.140-0.001-0.0010.0000.0000.0000.000
63A66GLU -1-0.776-0.84328.442-0.057-0.0570.0000.0000.0000.000
64A67THR 00.007-0.00724.874-0.003-0.0030.0000.0000.0000.000
65A68PHE 00.0170.00127.4220.0020.0020.0000.0000.0000.000
66A69ASP -1-0.777-0.87629.722-0.020-0.0200.0000.0000.0000.000
67A70TYR 0-0.040-0.04325.4280.0010.0010.0000.0000.0000.000
68A71LEU 00.0400.01223.5830.0010.0010.0000.0000.0000.000
69A72PHE 0-0.028-0.01127.6510.0050.0050.0000.0000.0000.000
70A73HIS 0-0.073-0.04931.1660.0000.0000.0000.0000.0000.000
71A74GLN 0-0.069-0.02629.399-0.001-0.0010.0000.0000.0000.000
72A75ALA 00.0430.04824.9840.0000.0000.0000.0000.0000.000
73A76LYS 10.8720.93025.8830.0130.0130.0000.0000.0000.000
74A77ILE 00.0140.01220.7080.0020.0020.0000.0000.0000.000
75A78GLU -1-0.878-0.93821.7800.0370.0370.0000.0000.0000.000
76A79ALA 0-0.009-0.01220.210-0.002-0.0020.0000.0000.0000.000
77A80VAL 0-0.0090.00615.6610.0070.0070.0000.0000.0000.000
78A81ALA 0-0.013-0.02316.5080.0220.0220.0000.0000.0000.000
79A82GLU -1-0.802-0.87418.4960.0050.0050.0000.0000.0000.000
80A83ILE 00.0090.01315.8390.0100.0100.0000.0000.0000.000
81A84ILE 0-0.025-0.01620.309-0.012-0.0120.0000.0000.0000.000
82A85LEU 0-0.024-0.02019.9750.0030.0030.0000.0000.0000.000
83A86NME 0-0.0120.00123.678-0.005-0.0050.0000.0000.0000.000
84A172ACE 0-0.005-0.00530.1100.0010.0010.0000.0000.0000.000
85A173GLU -1-0.908-0.96326.985-0.054-0.0540.0000.0000.0000.000
86A174ASN 0-0.016-0.03925.2720.0060.0060.0000.0000.0000.000
87A175TYR 0-0.026-0.03726.322-0.003-0.0030.0000.0000.0000.000
88A176THR 00.0200.02526.1820.0000.0000.0000.0000.0000.000
89A177ARG 10.7680.87024.469-0.006-0.0060.0000.0000.0000.000
90A178PHE 00.0250.00220.012-0.010-0.0100.0000.0000.0000.000
91A179TRP 0-0.019-0.01120.4560.0100.0100.0000.0000.0000.000
92A180VAL 00.013-0.00313.943-0.020-0.0200.0000.0000.0000.000
93A181LEU 0-0.026-0.01717.1420.0180.0180.0000.0000.0000.000
94A182GLY 00.035-0.01215.388-0.020-0.0200.0000.0000.0000.000
95A183ASP -1-0.977-0.97515.4860.0700.0700.0000.0000.0000.000
96A184GLU -1-0.912-0.95714.6630.1930.1930.0000.0000.0000.000
97A185THR 0-0.020-0.02714.320-0.010-0.0100.0000.0000.0000.000
98A186PRO 0-0.0300.01010.1290.0530.0530.0000.0000.0000.000
99A187THR 0-0.039-0.0338.5210.0410.0410.0000.0000.0000.000
100A188ILE 00.0020.0059.779-0.019-0.0190.0000.0000.0000.000
101A189HIS 0-0.073-0.0247.891-0.044-0.0440.0000.0000.0000.000
102A190LEU 0-0.001-0.00512.935-0.037-0.0370.0000.0000.0000.000
103A191LYS 10.9050.96416.585-0.054-0.0540.0000.0000.0000.000
104A192GLU -1-0.915-0.96418.9480.1390.1390.0000.0000.0000.000
105A193GLU -1-0.913-0.96320.5450.0570.0570.0000.0000.0000.000
106A194ASP -1-0.838-0.92723.5460.0490.0490.0000.0000.0000.000
107A195GLN 0-0.0080.01521.5970.0010.0010.0000.0000.0000.000
108A196LYS 10.9310.97525.073-0.039-0.0390.0000.0000.0000.000
109A197ILE 00.0040.00225.8140.0050.0050.0000.0000.0000.000
110A198SER 0-0.046-0.00627.419-0.005-0.0050.0000.0000.0000.000
111A199LEU 0-0.001-0.01828.9850.0000.0000.0000.0000.0000.000
112A200ALA 0-0.0050.00931.732-0.003-0.0030.0000.0000.0000.000
113A201LEU 0-0.017-0.02033.5200.0010.0010.0000.0000.0000.000
114A202THR 00.006-0.00337.121-0.003-0.0030.0000.0000.0000.000
115A203LEU 0-0.010-0.00839.9580.0020.0020.0000.0000.0000.000
116A204PRO 00.0340.00943.500-0.001-0.0010.0000.0000.0000.000
117A205ASP -1-0.927-0.96346.6410.0010.0010.0000.0000.0000.000
118A206ASN 0-0.041-0.01543.1720.0000.0000.0000.0000.0000.000
119A207LEU 00.0500.02345.504-0.001-0.0010.0000.0000.0000.000
120A208PRO 00.011-0.01045.1120.0010.0010.0000.0000.0000.000
121A209GLY 0-0.0240.00246.1260.0010.0010.0000.0000.0000.000
122A210ALA 00.005-0.00246.5890.0010.0010.0000.0000.0000.000
123A211LEU 00.0430.02140.8240.0010.0010.0000.0000.0000.000
124A212TYR 00.0300.00443.8960.0010.0010.0000.0000.0000.000
125A213LYS 10.9440.99345.924-0.007-0.0070.0000.0000.0000.000
126A214ALA 00.0560.03640.4610.0010.0010.0000.0000.0000.000
127A215LEU 00.021-0.00240.2440.0020.0020.0000.0000.0000.000
128A216SER 0-0.029-0.03042.2150.0010.0010.0000.0000.0000.000
129A217THR 0-0.050-0.01740.5730.0010.0010.0000.0000.0000.000
130A218PHE 00.000-0.00735.4710.0010.0010.0000.0000.0000.000
131A219ALA 00.0200.01740.2260.0020.0020.0000.0000.0000.000
132A220TRP 0-0.108-0.06342.7330.0020.0020.0000.0000.0000.000
133A221ARG 10.7900.88739.984-0.025-0.0250.0000.0000.0000.000
134A222GLY 0-0.011-0.00440.6150.0020.0020.0000.0000.0000.000
135A223ILE 0-0.058-0.01635.0990.0020.0020.0000.0000.0000.000
136A224ASP -1-0.859-0.91835.8750.0260.0260.0000.0000.0000.000
137A225LEU 0-0.046-0.04234.9950.0010.0010.0000.0000.0000.000
138A226THR 0-0.050-0.02731.838-0.001-0.0010.0000.0000.0000.000
139A227LYS 10.9000.94630.278-0.004-0.0040.0000.0000.0000.000
140A228ILE 0-0.023-0.01134.6130.0010.0010.0000.0000.0000.000
141A229GLU -1-0.870-0.92234.559-0.007-0.0070.0000.0000.0000.000
142A230SER 0-0.087-0.03036.6830.0010.0010.0000.0000.0000.000
143A231ARG 10.8390.89934.2720.0160.0160.0000.0000.0000.000
144A232PRO 00.000-0.00937.7560.0010.0010.0000.0000.0000.000
145A233LEU 00.0060.00638.580-0.001-0.0010.0000.0000.0000.000
146A234LYS 10.8410.92836.2130.0210.0210.0000.0000.0000.000
147A235THR 0-0.009-0.03641.153-0.001-0.0010.0000.0000.0000.000
148A236ILE 0-0.021-0.01344.222-0.001-0.0010.0000.0000.0000.000
149A237LEU 0-0.012-0.02146.0300.0000.0000.0000.0000.0000.000
150A238GLY 00.0020.00246.5050.0010.0010.0000.0000.0000.000
151A239GLU -1-0.832-0.85644.405-0.005-0.0050.0000.0000.0000.000
152A240TYR 0-0.042-0.03540.734-0.001-0.0010.0000.0000.0000.000
153A241PHE 0-0.0050.01333.3820.0010.0010.0000.0000.0000.000
154A242PHE 00.021-0.02137.576-0.001-0.0010.0000.0000.0000.000
155A243ILE 0-0.0300.00131.1140.0010.0010.0000.0000.0000.000
156A244ILE 0-0.014-0.00533.7060.0000.0000.0000.0000.0000.000
157A245ASP -1-0.794-0.88529.6880.0160.0160.0000.0000.0000.000
158A246PHE 0-0.027-0.03331.005-0.001-0.0010.0000.0000.0000.000
159A247GLU -1-0.855-0.92530.3200.0420.0420.0000.0000.0000.000
160A248ASN 0-0.070-0.04526.506-0.007-0.0070.0000.0000.0000.000
161A249HIS 0-0.0060.00828.9550.0050.0050.0000.0000.0000.000
162A250ASN 0-0.012-0.01531.0370.0050.0050.0000.0000.0000.000
163A251GLU -1-0.815-0.92026.7350.0710.0710.0000.0000.0000.000
164A252LYS 10.9090.96531.604-0.048-0.0480.0000.0000.0000.000
165A253LEU 0-0.026-0.01634.778-0.003-0.0030.0000.0000.0000.000
166A254VAL 00.0520.02931.759-0.004-0.0040.0000.0000.0000.000
167A255SER 0-0.009-0.00533.984-0.003-0.0030.0000.0000.0000.000
168A256PHE 0-0.032-0.02135.358-0.002-0.0020.0000.0000.0000.000
169A257ALA 00.0430.03537.064-0.003-0.0030.0000.0000.0000.000
170A258LEU 0-0.0040.00032.761-0.003-0.0030.0000.0000.0000.000
171A259GLU -1-0.930-0.96037.4670.0270.0270.0000.0000.0000.000
172A260GLU -1-0.789-0.87440.2220.0190.0190.0000.0000.0000.000
173A261LEU 0-0.025-0.01137.415-0.002-0.0020.0000.0000.0000.000
174A262THR 00.0140.00039.483-0.002-0.0020.0000.0000.0000.000
175A263SER 0-0.123-0.05441.880-0.002-0.0020.0000.0000.0000.000
176A264ILE 0-0.060-0.02544.363-0.001-0.0010.0000.0000.0000.000
177A265GLY 0-0.031-0.01344.782-0.001-0.0010.0000.0000.0000.000
178A266ILE 0-0.088-0.04039.844-0.002-0.0020.0000.0000.0000.000
179A267HIS 00.0200.01638.6410.0030.0030.0000.0000.0000.000
180A268TYR 00.004-0.01132.858-0.001-0.0010.0000.0000.0000.000
181A269LYS 10.8280.91228.9360.0080.0080.0000.0000.0000.000
182A270ILE 00.010-0.00626.7180.0000.0000.0000.0000.0000.000
183A271LEU 0-0.021-0.00726.966-0.002-0.0020.0000.0000.0000.000
184A272GLY 00.0590.02423.980-0.003-0.0030.0000.0000.0000.000
185A273LYS 10.9070.96723.315-0.056-0.0560.0000.0000.0000.000
186A274TYR 0-0.0040.01720.8620.0050.0050.0000.0000.0000.000
187A275ALA 00.0740.04819.292-0.004-0.0040.0000.0000.0000.000
188A276VAL 0-0.037-0.03120.552-0.008-0.0080.0000.0000.0000.000
189A277TYR 00.016-0.00416.7680.0070.0070.0000.0000.0000.000
190A278ARG 10.8100.89420.164-0.056-0.0560.0000.0000.0000.000
191A279LEU -1-0.902-0.95318.6070.0460.0460.0000.0000.0000.000