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

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FMODB ID: 662GZ

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1574405.244223
FMO2-HF: Nuclear repulsion 1506254.181861
FMO2-HF: Total energy -68151.062362
FMO2-MP2: Total energy -68349.436351


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.
-4.692-0.574-0.032-2.358-1.7280.002
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 : 0.009 / q_NPA : 0.001
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].
3A144VAL0-0.010-0.0053.836-2.8341.284-0.032-2.358-1.7280.002
4A145GLU-1-0.932-0.9545.831-1.208-1.2080.0000.0000.0000.000
5A146ASP-1-0.886-0.9088.545-0.357-0.3570.0000.0000.0000.000
6A147SER00.0020.00011.9320.0120.0120.0000.0000.0000.000
7A148GLY0-0.0160.00515.1010.0360.0360.0000.0000.0000.000
8A149ALA0-0.030-0.00818.4110.0310.0310.0000.0000.0000.000
9A150SER0-0.030-0.02417.438-0.046-0.0460.0000.0000.0000.000
10A151PHE00.074-0.00418.9160.0300.0300.0000.0000.0000.000
11A152GLY00.0280.02517.262-0.044-0.0440.0000.0000.0000.000
12A153GLH0-0.052-0.04910.888-0.024-0.0240.0000.0000.0000.000
13A154SER00.0070.02413.188-0.063-0.0630.0000.0000.0000.000
14A155LEU00.1270.0697.9340.1120.1120.0000.0000.0000.000
15A156LEU0-0.081-0.07010.962-0.010-0.0100.0000.0000.0000.000
16A157ASP-1-0.855-0.90812.853-0.119-0.1190.0000.0000.0000.000
17A158THR00.0040.0118.1760.0330.0330.0000.0000.0000.000
18A159THR0-0.055-0.03811.0290.1180.1180.0000.0000.0000.000
19A160SER00.000-0.02214.015-0.021-0.0210.0000.0000.0000.000
20A161GLU-1-0.816-0.91615.2170.0880.0880.0000.0000.0000.000
21A162PRO00.0580.02412.6660.0190.0190.0000.0000.0000.000
22A163GLY0-0.059-0.0099.652-0.001-0.0010.0000.0000.0000.000
23A164LYS10.8020.8849.748-0.051-0.0510.0000.0000.0000.000
24A165ILE0-0.0060.0055.699-0.038-0.0380.0000.0000.0000.000
25A166LEU0-0.026-0.0059.188-0.028-0.0280.0000.0000.0000.000
26A167VAL00.0410.01310.426-0.052-0.0520.0000.0000.0000.000
27A168LYS10.7840.91013.0030.2930.2930.0000.0000.0000.000
28A169ARG10.9690.98216.7010.1380.1380.0000.0000.0000.000
29A170ILE00.0340.01419.479-0.002-0.0020.0000.0000.0000.000
30A171SER0-0.0030.00822.0200.0150.0150.0000.0000.0000.000
31A172GLY00.0380.01225.683-0.010-0.0100.0000.0000.0000.000
32A173GLY0-0.023-0.00528.7480.0120.0120.0000.0000.0000.000
33A174SER0-0.018-0.03631.1120.0070.0070.0000.0000.0000.000
34A175GLY00.0060.00934.600-0.002-0.0020.0000.0000.0000.000
35A176ILE0-0.037-0.01528.955-0.006-0.0060.0000.0000.0000.000
36A177THR0-0.046-0.01831.2280.0120.0120.0000.0000.0000.000
37A178VAL00.0020.01025.600-0.007-0.0070.0000.0000.0000.000
38A179THR0-0.003-0.00227.8610.0120.0120.0000.0000.0000.000
39A180ASP-1-0.945-0.98223.696-0.213-0.2130.0000.0000.0000.000
40A181TYR0-0.081-0.02725.6460.0230.0230.0000.0000.0000.000
41A182GLY00.005-0.01523.449-0.015-0.0150.0000.0000.0000.000
42A183ASP-1-0.986-0.99121.538-0.290-0.2900.0000.0000.0000.000
43A184GLN0-0.040-0.01920.353-0.044-0.0440.0000.0000.0000.000
44A185VAL0-0.0090.00320.7810.0260.0260.0000.0000.0000.000
45A186GLU-1-0.853-0.92023.415-0.190-0.1900.0000.0000.0000.000
46A187ILE0-0.050-0.02323.3890.0130.0130.0000.0000.0000.000
47A188GLU-1-0.907-0.94927.720-0.135-0.1350.0000.0000.0000.000
48A189ALA0-0.021-0.01931.5010.0010.0010.0000.0000.0000.000
49A190SER0-0.011-0.00633.8440.0070.0070.0000.0000.0000.000
50A199VAL0-0.0060.00137.269-0.002-0.0020.0000.0000.0000.000
51A200THR0-0.018-0.03937.6650.0000.0000.0000.0000.0000.000
52A201ASP-1-0.778-0.86340.022-0.074-0.0740.0000.0000.0000.000
53A202ALA00.018-0.00343.6840.0000.0000.0000.0000.0000.000
54A203LEU0-0.0240.00646.6940.0010.0010.0000.0000.0000.000
55A204SER0-0.030-0.02350.0640.0010.0010.0000.0000.0000.000
56A205LEU00.003-0.01552.6940.0010.0010.0000.0000.0000.000
57A206MET00.0100.01556.2070.0000.0000.0000.0000.0000.000
58A207TYR0-0.030-0.05059.3500.0010.0010.0000.0000.0000.000
59A208SER00.0970.04162.3590.0010.0010.0000.0000.0000.000
60A209THR00.0070.00665.7930.0000.0000.0000.0000.0000.000
61A210SER0-0.048-0.02866.5420.0010.0010.0000.0000.0000.000
62A211THR0-0.049-0.03561.713-0.001-0.0010.0000.0000.0000.000
63A212GLY00.0610.02463.229-0.001-0.0010.0000.0000.0000.000
64A213GLY00.0240.04964.6430.0000.0000.0000.0000.0000.000
65A214PRO0-0.028-0.00466.8710.0010.0010.0000.0000.0000.000
66A215ALA00.0480.01370.3720.0000.0000.0000.0000.0000.000
67A216SER0-0.020-0.03173.1120.0000.0000.0000.0000.0000.000
68A217ILE0-0.0230.00868.5190.0000.0000.0000.0000.0000.000
69A218ALA00.011-0.01172.5990.0000.0000.0000.0000.0000.000
70A219ALA0-0.009-0.00374.611-0.001-0.0010.0000.0000.0000.000
71A220ASN0-0.099-0.04375.2340.0000.0000.0000.0000.0000.000
72A221ALA00.0760.02773.7970.0010.0010.0000.0000.0000.000
73A222LEU0-0.038-0.00767.687-0.001-0.0010.0000.0000.0000.000
74A223THR00.0180.01069.1300.0010.0010.0000.0000.0000.000
75A224ASP-1-0.855-0.93063.824-0.034-0.0340.0000.0000.0000.000
76A225PHE00.009-0.01262.9140.0010.0010.0000.0000.0000.000
77A226ASP-1-0.783-0.83662.687-0.034-0.0340.0000.0000.0000.000
78A227LEU0-0.042-0.02958.2860.0000.0000.0000.0000.0000.000
79A228SER0-0.037-0.04958.693-0.001-0.0010.0000.0000.0000.000
80A229GLY00.004-0.01559.137-0.001-0.0010.0000.0000.0000.000
81A230ALA0-0.050-0.00358.5780.0000.0000.0000.0000.0000.000
82A231LEU00.0090.01156.6930.0000.0000.0000.0000.0000.000
83A232THR00.000-0.02651.3720.0000.0000.0000.0000.0000.000
84A233VAL0-0.0260.00353.0170.0000.0000.0000.0000.0000.000
85A234ASN0-0.014-0.01346.507-0.003-0.0030.0000.0000.0000.000
86A235SER00.0320.00347.1540.0030.0030.0000.0000.0000.000
87A236VAL0-0.0150.00841.606-0.001-0.0010.0000.0000.0000.000
88A237GLY00.0640.05641.9220.0000.0000.0000.0000.0000.000
89A238THR0-0.027-0.02942.7470.0020.0020.0000.0000.0000.000
90A239GLY0-0.017-0.00444.1010.0030.0030.0000.0000.0000.000
91A240LEU0-0.031-0.00845.3820.0030.0030.0000.0000.0000.000
92A241THR00.0190.01148.6290.0010.0010.0000.0000.0000.000
93A242LYS10.8670.95651.2880.0420.0420.0000.0000.0000.000
94A243SER0-0.021-0.04954.9980.0010.0010.0000.0000.0000.000
95A244ALA00.0380.00557.5460.0000.0000.0000.0000.0000.000
96A245ALA0-0.046-0.01359.5400.0010.0010.0000.0000.0000.000
97A246GLY00.0310.00658.4060.0000.0000.0000.0000.0000.000
98A247ILE0-0.0150.00352.0160.0000.0000.0000.0000.0000.000
99A248GLN0-0.0260.02252.4180.0020.0020.0000.0000.0000.000
100A249LEU00.013-0.00248.594-0.002-0.0020.0000.0000.0000.000
101A250ALA0-0.0020.00345.5570.0020.0020.0000.0000.0000.000
102A251ALA00.0640.00745.187-0.001-0.0010.0000.0000.0000.000
103A252GLY00.001-0.00242.334-0.003-0.0030.0000.0000.0000.000
104A253LYS10.8570.91840.6560.0710.0710.0000.0000.0000.000
105A254SER00.0230.03444.1650.0000.0000.0000.0000.0000.000
106A255GLY0-0.028-0.01243.265-0.005-0.0050.0000.0000.0000.000
107A256LEU00.016-0.00143.4210.0040.0040.0000.0000.0000.000
108A257TYR0-0.017-0.04845.499-0.003-0.0030.0000.0000.0000.000
109A258GLN00.0130.01147.8880.0010.0010.0000.0000.0000.000
110A259ILE0-0.016-0.02549.4600.0000.0000.0000.0000.0000.000
111A260THR0-0.027-0.00952.8880.0000.0000.0000.0000.0000.000
112A261MET0-0.0130.02855.5180.0000.0000.0000.0000.0000.000
113A262THR0-0.002-0.01358.4970.0000.0000.0000.0000.0000.000
114A263VAL00.0030.00361.1700.0010.0010.0000.0000.0000.000
115A264LYS10.9030.95464.6660.0370.0370.0000.0000.0000.000
116A265ASN00.0660.01766.9920.0000.0000.0000.0000.0000.000
117A266ASN00.0640.01870.0370.0000.0000.0000.0000.0000.000
118A267THR00.0030.01072.4400.0000.0000.0000.0000.0000.000
119A268VAL00.0080.02774.3950.0010.0010.0000.0000.0000.000
120A269THR0-0.0210.00774.024-0.001-0.0010.0000.0000.0000.000
121A270THR00.0460.03075.6460.0000.0000.0000.0000.0000.000
122A271GLY00.0350.03676.1770.0000.0000.0000.0000.0000.000
123A272ASN0-0.039-0.05072.004-0.001-0.0010.0000.0000.0000.000
124A273TYR0-0.022-0.03968.5530.0010.0010.0000.0000.0000.000
125A274LEU0-0.022-0.00768.867-0.001-0.0010.0000.0000.0000.000
126A275LEU0-0.005-0.01063.1200.0000.0000.0000.0000.0000.000
127A276ARG10.8640.92663.3570.0340.0340.0000.0000.0000.000
128A277VAL00.0160.02256.9010.0000.0000.0000.0000.0000.000
129A278LYS10.8370.90559.7560.0350.0350.0000.0000.0000.000
130A279TYR00.015-0.01451.640-0.001-0.0010.0000.0000.0000.000
131A280GLY00.0400.03657.1040.0000.0000.0000.0000.0000.000
132A281SER0-0.030-0.03057.9760.0010.0010.0000.0000.0000.000
133A282SER0-0.0360.00557.2110.0000.0000.0000.0000.0000.000
134A283ASP-1-0.932-0.98359.390-0.037-0.0370.0000.0000.0000.000
135A284PHE00.0230.01156.2300.0000.0000.0000.0000.0000.000
136A285VAL00.013-0.01061.1260.0000.0000.0000.0000.0000.000
137A286VAL00.019-0.00162.659-0.001-0.0010.0000.0000.0000.000
138A287ALA0-0.0040.01265.2510.0010.0010.0000.0000.0000.000
139A288CYS0-0.032-0.01765.868-0.001-0.0010.0000.0000.0000.000
140A289PRO00.0330.02768.5990.0010.0010.0000.0000.0000.000
141A290ALA0-0.0190.00971.057-0.001-0.0010.0000.0000.0000.000
142A291SER00.0480.01172.3910.0000.0000.0000.0000.0000.000
143A292SER0-0.008-0.03773.2160.0000.0000.0000.0000.0000.000
144A293LEU0-0.026-0.00270.998-0.001-0.0010.0000.0000.0000.000
145A294THR0-0.0120.01067.830-0.001-0.0010.0000.0000.0000.000
146A295ALA00.0060.01669.7420.0000.0000.0000.0000.0000.000
147A296GLY0-0.014-0.03167.2850.0000.0000.0000.0000.0000.000
148A297GLY00.0410.02865.6140.0010.0010.0000.0000.0000.000
149A298THR0-0.041-0.04359.275-0.001-0.0010.0000.0000.0000.000
150A299ILE00.0110.02359.2970.0010.0010.0000.0000.0000.000
151A300SER0-0.033-0.02754.388-0.001-0.0010.0000.0000.0000.000
152A301LEU0-0.005-0.01454.3080.0010.0010.0000.0000.0000.000
153A302LEU00.0310.04247.038-0.002-0.0020.0000.0000.0000.000
154A303ILE0-0.012-0.00550.7100.0010.0010.0000.0000.0000.000
155A304TYR00.0100.00445.116-0.004-0.0040.0000.0000.0000.000
156A305CYS0-0.041-0.00348.5250.0030.0030.0000.0000.0000.000
157A306ASN00.0340.00848.052-0.005-0.0050.0000.0000.0000.000
158A307VAL0-0.047-0.02047.1020.0020.0020.0000.0000.0000.000
159A308LEU0-0.057-0.02547.985-0.001-0.0010.0000.0000.0000.000
160A309GLY0-0.002-0.00649.1920.0000.0000.0000.0000.0000.000
161A310VAL0-0.072-0.02449.7810.0020.0020.0000.0000.0000.000
162A311VAL00.0840.02151.9350.0000.0000.0000.0000.0000.000
163A312SER0-0.025-0.00554.006-0.001-0.0010.0000.0000.0000.000
164A313LEU0-0.034-0.02755.5070.0010.0010.0000.0000.0000.000
165A314ASP-1-0.736-0.84551.216-0.046-0.0460.0000.0000.0000.000
166A315VAL0-0.038-0.03453.010-0.001-0.0010.0000.0000.0000.000
167A316LEU0-0.0100.01052.1150.0010.0010.0000.0000.0000.000
168A317LYS10.9460.98756.1910.0350.0350.0000.0000.0000.000
169A318PHE00.055-0.00755.533-0.001-0.0010.0000.0000.0000.000
170A319SER0-0.020-0.00761.5710.0020.0020.0000.0000.0000.000
171A320LEU00.0390.01263.852-0.001-0.0010.0000.0000.0000.000
172A321CYS0-0.0060.02267.1450.0010.0010.0000.0000.0000.000
173A322ASN00.0060.00970.6340.0000.0000.0000.0000.0000.000
174A323ASP-1-0.778-0.89973.340-0.029-0.0290.0000.0000.0000.000
175A324GLY00.0240.01275.7100.0010.0010.0000.0000.0000.000
176A325ALA0-0.021-0.00977.2720.0010.0010.0000.0000.0000.000
177A326ALA0-0.0090.00176.012-0.001-0.0010.0000.0000.0000.000
178A327LEU0-0.039-0.01470.2900.0000.0000.0000.0000.0000.000
179A328SER00.0270.01772.9540.0000.0000.0000.0000.0000.000
180A329ASN0-0.079-0.05072.3360.0000.0000.0000.0000.0000.000
181A330TYR0-0.055-0.02866.579-0.001-0.0010.0000.0000.0000.000
182A331ILE0-0.0050.00163.1810.0000.0000.0000.0000.0000.000
183A332ILE0-0.034-0.01761.736-0.001-0.0010.0000.0000.0000.000
184A333ASN0-0.0220.00157.8030.0000.0000.0000.0000.0000.000
185A334ILE00.0230.02255.8250.0000.0000.0000.0000.0000.000
186A335THR0-0.0030.02150.804-0.001-0.0010.0000.0000.0000.000
187A336ALA00.0010.00851.0640.0000.0000.0000.0000.0000.000
188A337ALA00.0380.00945.967-0.001-0.0010.0000.0000.0000.000
189A338LYS10.9000.98040.0010.0860.0860.0000.0000.0000.000
190A339ILE00.007-0.00742.068-0.003-0.0030.0000.0000.0000.000
191A340ASN0-0.0310.01038.006-0.002-0.0020.0000.0000.0000.000