FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 89JLY

Calculation Name: 4L11-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L11

Chain ID: A

ChEMBL ID:

UniProt ID: Q7QJX3

Base Structure: X-ray

Registration Date: 2023-09-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2228025.418549
FMO2-HF: Nuclear repulsion 2147603.085017
FMO2-HF: Total energy -80422.333532
FMO2-MP2: Total energy -80654.227624


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:537:THR)


Summations of interaction energy for fragment #1(A:537:THR)
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.
-5.98-3.123-0.004-1.221-1.630.003
Interaction energy analysis for fragmet #1(A:537:THR)
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 : -0.006
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].
3A539ARG10.9410.9673.654-5.005-2.292-0.002-1.208-1.5030.003
4A540TYR00.0930.0405.842-0.518-0.480-0.001-0.005-0.0310.000
5A541HIS00.0630.0176.8060.0420.0420.0000.0000.0000.000
6A542THR0-0.007-0.0085.424-0.099-0.0990.0000.0000.0000.000
7A543GLN0-0.038-0.0256.819-0.204-0.2040.0000.0000.0000.000
8A544MET00.0110.01810.135-0.083-0.0830.0000.0000.0000.000
9A545LEU0-0.028-0.02812.201-0.074-0.0740.0000.0000.0000.000
10A546ARG10.8980.9506.323-0.875-0.8750.0000.0000.0000.000
11A547VAL00.0350.01913.474-0.049-0.0490.0000.0000.0000.000
12A548ARG10.8260.90615.239-0.211-0.2110.0000.0000.0000.000
13A549GLU-1-0.885-0.94114.6430.1480.1480.0000.0000.0000.000
14A550PHE00.0400.02416.928-0.023-0.0230.0000.0000.0000.000
15A551ILE00.025-0.00119.286-0.021-0.0210.0000.0000.0000.000
16A552ARG10.8680.96420.684-0.100-0.1000.0000.0000.0000.000
17A553PHE0-0.013-0.02118.244-0.017-0.0170.0000.0000.0000.000
18A554HIS10.8270.92621.340-0.121-0.1210.0000.0000.0000.000
19A555GLN00.0600.03024.9950.0030.0030.0000.0000.0000.000
20A556ILE00.0290.02923.004-0.003-0.0030.0000.0000.0000.000
21A557PRO00.0280.02127.0770.0020.0020.0000.0000.0000.000
22A558ASN00.0700.01727.8260.0130.0130.0000.0000.0000.000
23A559PRO0-0.007-0.00228.3160.0080.0080.0000.0000.0000.000
24A560LEU00.0380.03625.3400.0030.0030.0000.0000.0000.000
25A561ARG10.8270.89223.344-0.140-0.1400.0000.0000.0000.000
26A562GLN0-0.006-0.01623.5830.0020.0020.0000.0000.0000.000
27A563ARG10.7870.86124.375-0.131-0.1310.0000.0000.0000.000
28A564LEU0-0.0050.00120.6240.0100.0100.0000.0000.0000.000
29A565GLU-1-0.787-0.88019.5830.2050.2050.0000.0000.0000.000
30A566GLU-1-0.821-0.88319.8370.1840.1840.0000.0000.0000.000
31A567TYR0-0.020-0.01017.9280.0050.0050.0000.0000.0000.000
32A568PHE0-0.032-0.01811.4980.0230.0230.0000.0000.0000.000
33A569GLN0-0.044-0.01215.6670.0450.0450.0000.0000.0000.000
34A570HIS0-0.055-0.02616.7360.0470.0470.0000.0000.0000.000
35A571ALA00.0160.00316.427-0.018-0.0180.0000.0000.0000.000
36A572TRP00.0080.0128.506-0.009-0.0090.0000.0000.0000.000
37A573THR0-0.0020.0089.715-0.013-0.0130.0000.0000.0000.000
38A574TYR00.0150.0004.5110.0940.200-0.001-0.008-0.0960.000
39A575THR00.0310.0135.345-0.091-0.0910.0000.0000.0000.000
40A576ASN00.0070.0046.269-0.029-0.0290.0000.0000.0000.000
41A577GLY00.0750.0155.9430.0400.0400.0000.0000.0000.000
42A578ILE0-0.1700.0106.9550.0010.0010.0000.0000.0000.000
43A579ASP-1-0.777-0.8597.2731.0201.0200.0000.0000.0000.000
44A580MET00.0270.0119.601-0.035-0.0350.0000.0000.0000.000
45A581ASN00.0620.00413.2890.0100.0100.0000.0000.0000.000
46A582SER00.038-0.05612.527-0.002-0.0020.0000.0000.0000.000
47A583VAL00.0450.00011.157-0.038-0.0380.0000.0000.0000.000
48A584LEU0-0.060-0.00313.664-0.010-0.0100.0000.0000.0000.000
49A585LYS10.9790.98315.779-0.122-0.1220.0000.0000.0000.000
50A586GLY0-0.065-0.02416.141-0.013-0.0130.0000.0000.0000.000
51A587PHE0-0.0300.00116.2390.0110.0110.0000.0000.0000.000
52A588PRO00.0110.01519.696-0.014-0.0140.0000.0000.0000.000
53A589GLU-1-0.844-0.93823.2490.0950.0950.0000.0000.0000.000
54A590CYS0-0.060-0.04925.971-0.002-0.0020.0000.0000.0000.000
55A591LEU00.0160.00922.684-0.003-0.0030.0000.0000.0000.000
56A592GLN00.0360.01522.1850.0100.0100.0000.0000.0000.000
57A593ALA00.0370.02823.983-0.006-0.0060.0000.0000.0000.000
58A594ASP-1-0.859-0.94127.7060.0900.0900.0000.0000.0000.000
59A595ILE0-0.054-0.01421.569-0.003-0.0030.0000.0000.0000.000
60A596CYS0-0.0160.00425.534-0.005-0.0050.0000.0000.0000.000
61A597LEU00.0150.02027.274-0.006-0.0060.0000.0000.0000.000
62A598HIS0-0.084-0.05526.885-0.009-0.0090.0000.0000.0000.000
63A599LEU0-0.041-0.04123.578-0.003-0.0030.0000.0000.0000.000
64A600ASN00.002-0.01728.277-0.005-0.0050.0000.0000.0000.000
65A601ARG10.9520.98631.338-0.070-0.0700.0000.0000.0000.000
66A602ASN0-0.104-0.02529.285-0.001-0.0010.0000.0000.0000.000
67A603LEU00.0380.03732.474-0.003-0.0030.0000.0000.0000.000
68A604LEU0-0.029-0.01934.172-0.003-0.0030.0000.0000.0000.000
69A605ASN0-0.053-0.03836.275-0.002-0.0020.0000.0000.0000.000
70A606ASN0-0.101-0.05635.867-0.003-0.0030.0000.0000.0000.000
71A607CYS0-0.0020.02137.241-0.003-0.0030.0000.0000.0000.000
72A608SER00.0450.01539.1940.0010.0010.0000.0000.0000.000
73A609ALA00.0070.00541.016-0.001-0.0010.0000.0000.0000.000
74A610PHE0-0.029-0.03637.3850.0000.0000.0000.0000.0000.000
75A611GLU-1-0.857-0.90942.3060.0300.0300.0000.0000.0000.000
76A612ALA0-0.027-0.02644.954-0.001-0.0010.0000.0000.0000.000
77A613ALA0-0.0340.00643.2840.0000.0000.0000.0000.0000.000
78A614SER00.0380.02245.3210.0020.0020.0000.0000.0000.000
79A615PRO00.0190.00143.4500.0010.0010.0000.0000.0000.000
80A616GLY0-0.071-0.03342.6150.0020.0020.0000.0000.0000.000
81A617CYS00.0500.04042.6370.0020.0020.0000.0000.0000.000
82A618LEU00.0430.01339.9390.0020.0020.0000.0000.0000.000
83A619ARG10.9100.95038.418-0.041-0.0410.0000.0000.0000.000
84A620ALA00.0350.02237.6420.0030.0030.0000.0000.0000.000
85A621LEU00.0570.03737.4540.0020.0020.0000.0000.0000.000
86A622SER0-0.114-0.06534.3070.0030.0030.0000.0000.0000.000
87A623LEU0-0.038-0.02633.0160.0050.0050.0000.0000.0000.000
88A624LYS10.7470.87532.740-0.035-0.0350.0000.0000.0000.000
89A625PHE0-0.028-0.00131.623-0.001-0.0010.0000.0000.0000.000
90A626LYS10.8500.94927.020-0.042-0.0420.0000.0000.0000.000
91A627THR00.0380.00824.469-0.002-0.0020.0000.0000.0000.000
92A628THR0-0.109-0.06222.3140.0030.0030.0000.0000.0000.000
93A629HIS0-0.030-0.02419.0240.0050.0050.0000.0000.0000.000
94A630ALA00.0330.01919.8000.0080.0080.0000.0000.0000.000
95A631PRO0-0.0080.00417.2240.0040.0040.0000.0000.0000.000
96A632PRO0-0.0200.00718.318-0.007-0.0070.0000.0000.0000.000
97A633GLY0-0.051-0.03320.025-0.005-0.0050.0000.0000.0000.000
98A634ASP-1-0.883-0.97620.8460.0340.0340.0000.0000.0000.000
99A635ILE0-0.043-0.01123.094-0.001-0.0010.0000.0000.0000.000
100A636LEU0-0.0360.00125.3890.0020.0020.0000.0000.0000.000
101A637VAL0-0.032-0.01527.4540.0010.0010.0000.0000.0000.000
102A638HIS00.000-0.00827.478-0.006-0.0060.0000.0000.0000.000
103A639LYS10.8480.93132.5050.0070.0070.0000.0000.0000.000
104A640GLY0-0.021-0.01436.0350.0010.0010.0000.0000.0000.000
105A641ASP-1-0.797-0.90531.8880.0050.0050.0000.0000.0000.000
106A642VAL0-0.014-0.00435.4630.0000.0000.0000.0000.0000.000
107A643LEU0-0.0100.01335.6380.0020.0020.0000.0000.0000.000
108A644THR0-0.032-0.00732.5990.0020.0020.0000.0000.0000.000
109A645TYR0-0.015-0.03130.3840.0050.0050.0000.0000.0000.000
110A646LEU0-0.0150.02233.836-0.003-0.0030.0000.0000.0000.000
111A647TYR0-0.024-0.03328.2130.0060.0060.0000.0000.0000.000
112A648PHE00.0660.02531.917-0.003-0.0030.0000.0000.0000.000
113A649ILE0-0.024-0.00729.1040.0050.0050.0000.0000.0000.000
114A650ALA00.0310.01327.967-0.001-0.0010.0000.0000.0000.000
115A651ARG10.8550.91325.082-0.072-0.0720.0000.0000.0000.000
116A652GLY00.0390.01026.1970.0020.0020.0000.0000.0000.000
117A653SER00.002-0.00926.771-0.002-0.0020.0000.0000.0000.000
118A654ILE00.0150.00627.1550.0000.0000.0000.0000.0000.000
119A655GLU-1-0.780-0.87529.701-0.015-0.0150.0000.0000.0000.000
120A656ILE00.004-0.00231.4570.0010.0010.0000.0000.0000.000
121A657LEU0-0.049-0.01730.929-0.002-0.0020.0000.0000.0000.000
122A658LYS10.8070.87635.0600.0060.0060.0000.0000.0000.000
123A659ASP-1-0.932-0.95336.177-0.017-0.0170.0000.0000.0000.000
124A660ASP-1-0.953-0.98535.796-0.019-0.0190.0000.0000.0000.000
125A661VAL0-0.035-0.01434.4270.0020.0020.0000.0000.0000.000
126A662VAL00.0240.01336.3410.0000.0000.0000.0000.0000.000
127A663MET0-0.033-0.01036.8910.0010.0010.0000.0000.0000.000
128A664ALA0-0.019-0.00933.6740.0000.0000.0000.0000.0000.000
129A665ILE0-0.0090.00233.1280.0010.0010.0000.0000.0000.000
130A666LEU00.016-0.01831.4370.0000.0000.0000.0000.0000.000
131A667GLY00.0340.02630.8740.0010.0010.0000.0000.0000.000
132A668LYS10.7350.85231.765-0.020-0.0200.0000.0000.0000.000
133A669ASP-1-0.852-0.92233.8680.0350.0350.0000.0000.0000.000
134A670ASP-1-0.821-0.89834.3810.0150.0150.0000.0000.0000.000
135A671ILE00.0110.00134.4490.0030.0030.0000.0000.0000.000
136A672PHE00.0110.00430.273-0.003-0.0030.0000.0000.0000.000
137A673GLY00.0470.00935.3870.0030.0030.0000.0000.0000.000
138A674GLU-1-0.741-0.86337.4340.0100.0100.0000.0000.0000.000
139A675ASN00.0860.02540.1010.0030.0030.0000.0000.0000.000
140A676PRO0-0.019-0.02040.186-0.001-0.0010.0000.0000.0000.000
141A677CYS0-0.0200.00843.0920.0000.0000.0000.0000.0000.000
142A678ILE00.0080.01446.0320.0000.0000.0000.0000.0000.000
143A679HIS0-0.050-0.01544.383-0.002-0.0020.0000.0000.0000.000
144A680SER00.0270.01947.3300.0010.0010.0000.0000.0000.000
145A681THR0-0.022-0.00847.2730.0000.0000.0000.0000.0000.000
146A682LEU0-0.023-0.01339.3230.0010.0010.0000.0000.0000.000
147A683GLY00.0270.01642.398-0.002-0.0020.0000.0000.0000.000
148A684LYS10.8810.92239.4900.0000.0000.0000.0000.0000.000
149A685SER0-0.005-0.00835.4110.0000.0000.0000.0000.0000.000
150A686ASN00.0390.02638.059-0.001-0.0010.0000.0000.0000.000
151A687SER0-0.013-0.01336.467-0.001-0.0010.0000.0000.0000.000
152A688ASN00.0150.01130.5010.0010.0010.0000.0000.0000.000
153A689VAL00.0240.01729.3050.0000.0000.0000.0000.0000.000
154A690LYS10.8120.89625.3610.0150.0150.0000.0000.0000.000
155A691ALA00.0140.01623.4920.0010.0010.0000.0000.0000.000
156A692LEU0-0.015-0.00324.425-0.005-0.0050.0000.0000.0000.000
157A693THR0-0.003-0.02022.846-0.006-0.0060.0000.0000.0000.000
158A694TYR00.019-0.00114.6820.0020.0020.0000.0000.0000.000
159A695CYS0-0.077-0.02321.424-0.007-0.0070.0000.0000.0000.000
160A696ASP-1-0.825-0.87023.0270.0970.0970.0000.0000.0000.000
161A697LEU0-0.006-0.01025.044-0.007-0.0070.0000.0000.0000.000
162A698HIS00.0460.03526.9650.0080.0080.0000.0000.0000.000
163A699LYS10.9230.96025.373-0.057-0.0570.0000.0000.0000.000
164A700ILE00.0220.01430.8790.0040.0040.0000.0000.0000.000
165A701HIS0-0.0120.00033.095-0.002-0.0020.0000.0000.0000.000
166A702ARG10.9380.95234.763-0.018-0.0180.0000.0000.0000.000
167A703ASP-1-0.773-0.89437.9470.0210.0210.0000.0000.0000.000
168A704ASP-1-0.835-0.91034.3610.0410.0410.0000.0000.0000.000
169A705LEU0-0.009-0.00738.1120.0010.0010.0000.0000.0000.000
170A706LEU00.009-0.01939.904-0.001-0.0010.0000.0000.0000.000
171A707ASP-1-0.796-0.88040.2500.0300.0300.0000.0000.0000.000
172A708VAL0-0.076-0.05239.6520.0000.0000.0000.0000.0000.000
173A709LEU0-0.011-0.02042.6950.0000.0000.0000.0000.0000.000
174A710ASP-1-0.892-0.92645.6380.0210.0210.0000.0000.0000.000
175A711LEU0-0.140-0.06443.2360.0000.0000.0000.0000.0000.000
176A712PHE0-0.073-0.04243.8270.0010.0010.0000.0000.0000.000
177A713PRO00.0450.03347.9560.0000.0000.0000.0000.0000.000
178A714GLU-1-0.895-0.97149.4120.0250.0250.0000.0000.0000.000
179A715PHE0-0.027-0.02142.9670.0000.0000.0000.0000.0000.000
180A716TYR0-0.013-0.01947.9530.0000.0000.0000.0000.0000.000
181A717ASP-1-0.885-0.94249.1950.0160.0160.0000.0000.0000.000
182A718SER00.0220.00147.949-0.001-0.0010.0000.0000.0000.000
183A719PHE00.0050.01340.8660.0000.0000.0000.0000.0000.000
184A720VAL0-0.036-0.02745.7920.0000.0000.0000.0000.0000.000
185A721ASN0-0.103-0.03947.8030.0000.0000.0000.0000.0000.000
186A722SER00.0020.00245.956-0.001-0.0010.0000.0000.0000.000
187A723LEU0-0.078-0.02739.9980.0010.0010.0000.0000.0000.000
188A724GLU-1-0.937-0.96742.6070.0140.0140.0000.0000.0000.000
189A725ILE0-0.071-0.03739.4600.0010.0010.0000.0000.0000.000
190A726THR0-0.0080.00838.159-0.001-0.0010.0000.0000.0000.000
191A727TYR00.018-0.00537.508-0.002-0.0020.0000.0000.0000.000
192A728ASN00.039-0.00238.8940.0020.0020.0000.0000.0000.000
193A729MET0-0.048-0.01434.577-0.001-0.0010.0000.0000.0000.000
194A730ARG10.8020.91239.655-0.009-0.0090.0000.0000.0000.000
195A731ASP-1-0.812-0.89641.979-0.003-0.0030.0000.0000.0000.000
196A732GLU-1-0.939-0.97143.5810.0060.0060.0000.0000.0000.000
197A733GLU-1-0.933-0.96444.410-0.005-0.0050.0000.0000.0000.000