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: 22QLR

Calculation Name: 1YQ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YQ8

Chain ID: A

ChEMBL ID:

UniProt ID: P22536

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1575127.264422
FMO2-HF: Nuclear repulsion 1506977.308954
FMO2-HF: Total energy -68149.955468
FMO2-MP2: Total energy -68348.505147


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:142:VAL)


Summations of interaction energy for fragment #1(A:142:VAL)
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.
-4.887-0.78-0.033-2.357-1.7160.001
Interaction energy analysis for fragmet #1(A:142:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.002
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].
3A144VAL0-0.001-0.0023.836-2.9091.198-0.033-2.357-1.7160.001
4A145GLU-1-0.855-0.9116.026-1.298-1.2980.0000.0000.0000.000
5A146ASP-1-0.895-0.8528.726-0.447-0.4470.0000.0000.0000.000
6A147SER00.0140.00312.1540.0190.0190.0000.0000.0000.000
7A148GLY0-0.018-0.00115.2800.0390.0390.0000.0000.0000.000
8A149ALA0-0.0220.00018.6210.0360.0360.0000.0000.0000.000
9A150SER0-0.032-0.02817.617-0.052-0.0520.0000.0000.0000.000
10A151PHE00.0870.00518.9040.0310.0310.0000.0000.0000.000
11A152GLY0-0.0070.00517.172-0.045-0.0450.0000.0000.0000.000
12A153GLH0-0.091-0.13010.8120.0010.0010.0000.0000.0000.000
13A154SER0-0.0100.01813.103-0.059-0.0590.0000.0000.0000.000
14A155LEU00.1710.0797.9490.1250.1250.0000.0000.0000.000
15A156LEU0-0.141-0.09110.955-0.011-0.0110.0000.0000.0000.000
16A157ASP-1-0.892-0.93212.839-0.085-0.0850.0000.0000.0000.000
17A158THR0-0.0160.0018.2000.0390.0390.0000.0000.0000.000
18A159THR0-0.086-0.05011.0940.1240.1240.0000.0000.0000.000
19A160SER00.011-0.01914.093-0.016-0.0160.0000.0000.0000.000
20A161GLU-1-0.864-0.94615.1980.0970.0970.0000.0000.0000.000
21A162PRO00.0590.02012.5410.0310.0310.0000.0000.0000.000
22A163GLY0-0.060-0.0109.5900.0060.0060.0000.0000.0000.000
23A164LYS10.8590.9249.739-0.158-0.1580.0000.0000.0000.000
24A165ILE00.0030.0085.826-0.052-0.0520.0000.0000.0000.000
25A166LEU0-0.0110.0109.176-0.019-0.0190.0000.0000.0000.000
26A167VAL00.0820.00010.458-0.070-0.0700.0000.0000.0000.000
27A168LYS10.7820.94612.9980.3310.3310.0000.0000.0000.000
28A169ARG10.9680.98416.6920.1120.1120.0000.0000.0000.000
29A170ILE00.0270.01419.477-0.005-0.0050.0000.0000.0000.000
30A171SER0-0.014-0.00522.0180.0110.0110.0000.0000.0000.000
31A172GLY00.0560.02425.680-0.011-0.0110.0000.0000.0000.000
32A173GLY0-0.020-0.00428.7440.0120.0120.0000.0000.0000.000
33A174SER0-0.031-0.04131.1030.0080.0080.0000.0000.0000.000
34A175GLY00.0110.01134.536-0.002-0.0020.0000.0000.0000.000
35A176ILE0-0.034-0.01329.000-0.005-0.0050.0000.0000.0000.000
36A177THR0-0.041-0.01231.2530.0120.0120.0000.0000.0000.000
37A178VAL0-0.0130.00525.712-0.008-0.0080.0000.0000.0000.000
38A179THR0-0.006-0.00527.8660.0140.0140.0000.0000.0000.000
39A180ASP-1-0.943-0.99023.941-0.186-0.1860.0000.0000.0000.000
40A181TYR0-0.0500.00825.5450.0230.0230.0000.0000.0000.000
41A182GLY00.027-0.00523.425-0.015-0.0150.0000.0000.0000.000
42A183ASP-1-0.985-0.99421.230-0.268-0.2680.0000.0000.0000.000
43A184GLN0-0.053-0.02120.288-0.043-0.0430.0000.0000.0000.000
44A185VAL0-0.0030.00720.9650.0250.0250.0000.0000.0000.000
45A186GLU-1-0.889-0.95223.349-0.186-0.1860.0000.0000.0000.000
46A187ILE0-0.057-0.02423.5980.0130.0130.0000.0000.0000.000
47A188GLU-1-0.892-0.93727.637-0.137-0.1370.0000.0000.0000.000
48A189ALA0-0.013-0.02831.4180.0010.0010.0000.0000.0000.000
49A190SER0-0.037-0.01533.8520.0080.0080.0000.0000.0000.000
50A199VAL00.0020.00337.304-0.002-0.0020.0000.0000.0000.000
51A200THR0-0.033-0.04437.7970.0000.0000.0000.0000.0000.000
52A201ASP-1-0.754-0.86640.017-0.072-0.0720.0000.0000.0000.000
53A202ALA00.0030.00143.679-0.001-0.0010.0000.0000.0000.000
54A203LEU0-0.0100.01246.6910.0010.0010.0000.0000.0000.000
55A204SER0-0.029-0.02050.0620.0010.0010.0000.0000.0000.000
56A205LEU00.003-0.01752.6940.0010.0010.0000.0000.0000.000
57A206MET00.0120.02456.2070.0000.0000.0000.0000.0000.000
58A207TYR0-0.043-0.06959.3520.0010.0010.0000.0000.0000.000
59A208SER00.1090.03862.3590.0000.0000.0000.0000.0000.000
60A209THR00.0050.00865.7950.0000.0000.0000.0000.0000.000
61A210SER0-0.053-0.03166.6740.0010.0010.0000.0000.0000.000
62A211THR0-0.049-0.03161.7130.0000.0000.0000.0000.0000.000
63A212GLY00.0640.02063.231-0.001-0.0010.0000.0000.0000.000
64A213GLY00.0140.04564.6440.0000.0000.0000.0000.0000.000
65A214PRO0-0.027-0.00166.8710.0010.0010.0000.0000.0000.000
66A215ALA00.0540.00670.3710.0000.0000.0000.0000.0000.000
67A216SER0-0.014-0.02973.1120.0000.0000.0000.0000.0000.000
68A217ILE0-0.0280.00368.7420.0000.0000.0000.0000.0000.000
69A218ALA00.016-0.00972.5960.0000.0000.0000.0000.0000.000
70A219ALA0-0.006-0.00174.626-0.001-0.0010.0000.0000.0000.000
71A220ASN0-0.122-0.05575.2920.0000.0000.0000.0000.0000.000
72A221ALA00.0780.02473.8340.0010.0010.0000.0000.0000.000
73A222LEU0-0.043-0.01567.996-0.001-0.0010.0000.0000.0000.000
74A223THR0-0.001-0.00469.2310.0010.0010.0000.0000.0000.000
75A224ASP-1-0.882-0.96563.864-0.035-0.0350.0000.0000.0000.000
76A225PHE0-0.004-0.02062.9020.0010.0010.0000.0000.0000.000
77A226ASP-1-0.789-0.84462.681-0.033-0.0330.0000.0000.0000.000
78A227LEU0-0.056-0.01658.3950.0000.0000.0000.0000.0000.000
79A228SER0-0.048-0.04858.690-0.001-0.0010.0000.0000.0000.000
80A229GLY00.013-0.01059.1370.0000.0000.0000.0000.0000.000
81A230ALA0-0.044-0.00258.5390.0000.0000.0000.0000.0000.000
82A231LEU00.0040.01156.5260.0000.0000.0000.0000.0000.000
83A232THR0-0.013-0.02751.3090.0000.0000.0000.0000.0000.000
84A233VAL0-0.031-0.00252.7910.0000.0000.0000.0000.0000.000
85A234ASN0-0.009-0.01446.332-0.003-0.0030.0000.0000.0000.000
86A235SER00.014-0.00746.8420.0030.0030.0000.0000.0000.000
87A236VAL0-0.0010.01741.654-0.001-0.0010.0000.0000.0000.000
88A237GLY00.0610.05441.9210.0000.0000.0000.0000.0000.000
89A238THR0-0.035-0.03042.7460.0020.0020.0000.0000.0000.000
90A239GLY0-0.006-0.00244.0640.0030.0030.0000.0000.0000.000
91A240LEU0-0.041-0.01645.3750.0030.0030.0000.0000.0000.000
92A241THR00.0140.00948.6240.0010.0010.0000.0000.0000.000
93A242LYS10.8870.97251.2840.0420.0420.0000.0000.0000.000
94A243SER0-0.022-0.05854.9940.0010.0010.0000.0000.0000.000
95A244ALA00.0430.00257.5420.0000.0000.0000.0000.0000.000
96A245ALA0-0.045-0.00859.4950.0010.0010.0000.0000.0000.000
97A246GLY00.040-0.00258.3830.0000.0000.0000.0000.0000.000
98A247ILE0-0.0050.01052.0170.0000.0000.0000.0000.0000.000
99A248GLN0-0.0330.00852.5840.0020.0020.0000.0000.0000.000
100A249LEU00.004-0.00248.474-0.002-0.0020.0000.0000.0000.000
101A250ALA00.0110.00945.5320.0020.0020.0000.0000.0000.000
102A251ALA00.0730.01245.095-0.001-0.0010.0000.0000.0000.000
103A252GLY0-0.010-0.00542.302-0.002-0.0020.0000.0000.0000.000
104A253LYS10.8650.92240.5210.0710.0710.0000.0000.0000.000
105A254SER00.0220.05044.1170.0000.0000.0000.0000.0000.000
106A255GLY0-0.036-0.01343.203-0.005-0.0050.0000.0000.0000.000
107A256LEU00.010-0.00343.6160.0040.0040.0000.0000.0000.000
108A257TYR0-0.024-0.05645.508-0.003-0.0030.0000.0000.0000.000
109A258GLN00.0220.01347.9210.0010.0010.0000.0000.0000.000
110A259ILE0-0.029-0.03149.5300.0000.0000.0000.0000.0000.000
111A260THR00.0240.01452.9520.0000.0000.0000.0000.0000.000
112A261MET0-0.0350.01055.5660.0000.0000.0000.0000.0000.000
113A262THR0-0.049-0.03558.8920.0000.0000.0000.0000.0000.000
114A263VAL00.0250.01561.1990.0010.0010.0000.0000.0000.000
115A264LYS10.9000.94964.6880.0370.0370.0000.0000.0000.000
116A265ASN00.0590.02066.9990.0000.0000.0000.0000.0000.000
117A266ASN00.0620.01170.2210.0000.0000.0000.0000.0000.000
118A267THR0-0.0010.00672.4340.0000.0000.0000.0000.0000.000
119A268VAL00.0000.02574.3600.0010.0010.0000.0000.0000.000
120A269THR0-0.029-0.00474.042-0.001-0.0010.0000.0000.0000.000
121A270THR00.0190.01775.6620.0000.0000.0000.0000.0000.000
122A271GLY00.0760.05476.2140.0000.0000.0000.0000.0000.000
123A272ASN0-0.003-0.01672.013-0.001-0.0010.0000.0000.0000.000
124A273TYR0-0.020-0.02668.5560.0010.0010.0000.0000.0000.000
125A274LEU0-0.024-0.01168.937-0.001-0.0010.0000.0000.0000.000
126A275LEU0-0.014-0.00963.0190.0000.0000.0000.0000.0000.000
127A276ARG10.8990.94663.3930.0340.0340.0000.0000.0000.000
128A277VAL00.0270.03556.9000.0000.0000.0000.0000.0000.000
129A278LYS10.8630.93159.6730.0350.0350.0000.0000.0000.000
130A279TYR00.009-0.01751.439-0.001-0.0010.0000.0000.0000.000
131A280GLY00.0390.03757.038-0.001-0.0010.0000.0000.0000.000
132A281SER0-0.038-0.03357.9190.0010.0010.0000.0000.0000.000
133A282SER0-0.0170.01157.1730.0000.0000.0000.0000.0000.000
134A283ASP-1-0.957-0.98659.318-0.037-0.0370.0000.0000.0000.000
135A284PHE00.0350.01256.1210.0000.0000.0000.0000.0000.000
136A285VAL00.008-0.01161.1680.0010.0010.0000.0000.0000.000
137A286VAL00.017-0.00162.797-0.001-0.0010.0000.0000.0000.000
138A287ALA00.0080.01465.3320.0010.0010.0000.0000.0000.000
139A288CYS0-0.043-0.02465.938-0.001-0.0010.0000.0000.0000.000
140A289PRO00.0370.02768.6520.0010.0010.0000.0000.0000.000
141A290ALA0-0.0270.00871.094-0.001-0.0010.0000.0000.0000.000
142A291SER00.0490.00272.2700.0000.0000.0000.0000.0000.000
143A292SER0-0.008-0.03773.2260.0000.0000.0000.0000.0000.000
144A293LEU0-0.023-0.00470.9750.0000.0000.0000.0000.0000.000
145A294THR0-0.0100.01667.945-0.001-0.0010.0000.0000.0000.000
146A295ALA00.0060.01869.7520.0000.0000.0000.0000.0000.000
147A296GLY0-0.016-0.03267.3030.0000.0000.0000.0000.0000.000
148A297GLY00.0370.02665.6500.0010.0010.0000.0000.0000.000
149A298THR0-0.035-0.04059.323-0.001-0.0010.0000.0000.0000.000
150A299ILE00.0120.02259.4120.0010.0010.0000.0000.0000.000
151A300SER0-0.030-0.02154.377-0.001-0.0010.0000.0000.0000.000
152A301LEU00.000-0.01654.3760.0010.0010.0000.0000.0000.000
153A302LEU00.0250.04547.214-0.002-0.0020.0000.0000.0000.000
154A303ILE0-0.012-0.00650.7950.0010.0010.0000.0000.0000.000
155A304TYR00.0180.00544.807-0.004-0.0040.0000.0000.0000.000
156A305CYS0-0.042-0.00448.4510.0030.0030.0000.0000.0000.000
157A306ASN00.018-0.00447.988-0.005-0.0050.0000.0000.0000.000
158A307VAL0-0.052-0.02747.0650.0020.0020.0000.0000.0000.000
159A308LEU0-0.061-0.02647.946-0.001-0.0010.0000.0000.0000.000
160A309GLY0-0.001-0.00749.1670.0000.0000.0000.0000.0000.000
161A310VAL0-0.056-0.01649.7550.0020.0020.0000.0000.0000.000
162A311VAL00.0770.01852.0650.0000.0000.0000.0000.0000.000
163A312SER0-0.030-0.00553.994-0.001-0.0010.0000.0000.0000.000
164A313LEU0-0.023-0.02155.4930.0010.0010.0000.0000.0000.000
165A314ASP-1-0.744-0.84651.199-0.046-0.0460.0000.0000.0000.000
166A315VAL0-0.022-0.02452.969-0.001-0.0010.0000.0000.0000.000
167A316LEU0-0.0190.00052.2180.0000.0000.0000.0000.0000.000
168A317LYS10.9220.98056.1290.0350.0350.0000.0000.0000.000
169A318PHE00.051-0.00755.626-0.001-0.0010.0000.0000.0000.000
170A319SER0-0.0170.00261.5150.0020.0020.0000.0000.0000.000
171A320LEU00.0610.02864.117-0.001-0.0010.0000.0000.0000.000
172A321CYS0-0.0090.02267.2040.0010.0010.0000.0000.0000.000
173A322ASN00.0120.02170.6870.0000.0000.0000.0000.0000.000
174A323ASP-1-0.805-0.92973.390-0.029-0.0290.0000.0000.0000.000
175A324GLY00.0270.01575.7730.0010.0010.0000.0000.0000.000
176A325ALA0-0.017-0.01277.3160.0010.0010.0000.0000.0000.000
177A326ALA0-0.0040.00576.059-0.001-0.0010.0000.0000.0000.000
178A327LEU0-0.034-0.01270.2270.0000.0000.0000.0000.0000.000
179A328SER00.0230.01272.9520.0000.0000.0000.0000.0000.000
180A329ASN0-0.080-0.04772.2870.0000.0000.0000.0000.0000.000
181A330TYR0-0.040-0.01466.558-0.001-0.0010.0000.0000.0000.000
182A331ILE00.0010.00863.0930.0000.0000.0000.0000.0000.000
183A332ILE0-0.026-0.00761.537-0.001-0.0010.0000.0000.0000.000
184A333ASN0-0.0070.00057.5960.0010.0010.0000.0000.0000.000
185A334ILE00.0110.01655.8790.0000.0000.0000.0000.0000.000
186A335THR0-0.0030.01550.751-0.001-0.0010.0000.0000.0000.000
187A336ALA0-0.0030.00950.9220.0000.0000.0000.0000.0000.000
188A337ALA00.0420.01045.950-0.001-0.0010.0000.0000.0000.000
189A338LYS10.9150.99140.2850.0850.0850.0000.0000.0000.000
190A339ILE00.005-0.00742.122-0.003-0.0030.0000.0000.0000.000
191A340ASN0-0.0180.01437.987-0.003-0.0030.0000.0000.0000.000