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: R1378

Calculation Name: 1YQ8-A-Xray316

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: 2021-09-06

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 -1574810.195475
FMO2-HF: Nuclear repulsion 1506660.863901
FMO2-HF: Total energy -68149.331575
FMO2-MP2: Total energy -68347.862844


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.
-3.888-0.713-0.019-1.815-1.341-0.004
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 : -0.022
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].
3A144VAL 00.0070.0023.836-2.0491.126-0.019-1.815-1.341-0.004
4A145GLU -1-0.855-0.9136.010-1.390-1.3900.0000.0000.0000.000
5A146ASP -1-0.903-0.8538.710-0.562-0.5620.0000.0000.0000.000
6A147SER 00.0200.00512.1360.0180.0180.0000.0000.0000.000
7A148GLY 0-0.010-0.00215.2640.0370.0370.0000.0000.0000.000
8A149ALA 0-0.0230.00118.6030.0410.0410.0000.0000.0000.000
9A150SER 0-0.038-0.02917.603-0.047-0.0470.0000.0000.0000.000
10A151PHE 00.0930.00818.9040.0240.0240.0000.0000.0000.000
11A152GLY 0-0.0070.00517.172-0.039-0.0390.0000.0000.0000.000
12A153GLH 0-0.093-0.13010.8060.0260.0260.0000.0000.0000.000
13A154SER 0-0.0090.01813.103-0.041-0.0410.0000.0000.0000.000
14A155LEU 00.1720.0807.9520.1420.1420.0000.0000.0000.000
15A156LEU 0-0.141-0.09110.955-0.016-0.0160.0000.0000.0000.000
16A157ASP -1-0.893-0.93212.8390.0250.0250.0000.0000.0000.000
17A158THR 0-0.0130.0038.1980.0650.0650.0000.0000.0000.000
18A159THR 0-0.091-0.05111.0940.1070.1070.0000.0000.0000.000
19A160SER 00.014-0.01914.093-0.010-0.0100.0000.0000.0000.000
20A161GLU -1-0.866-0.94815.1990.2200.2200.0000.0000.0000.000
21A162PRO 00.0600.02112.5440.0520.0520.0000.0000.0000.000
22A163GLY 0-0.060-0.0099.5910.0250.0250.0000.0000.0000.000
23A164LYS 10.8580.9249.740-0.277-0.2770.0000.0000.0000.000
24A165ILE 00.0010.0075.828-0.113-0.1130.0000.0000.0000.000
25A166LEU 0-0.0080.0119.1780.0380.0380.0000.0000.0000.000
26A167VAL 00.080-0.00210.462-0.060-0.0600.0000.0000.0000.000
27A168LYS 10.7810.94513.0010.2410.2410.0000.0000.0000.000
28A169ARG 10.9670.98416.695-0.022-0.0220.0000.0000.0000.000
29A170ILE 00.0260.01319.481-0.016-0.0160.0000.0000.0000.000
30A171SER 0-0.014-0.00622.0210.0120.0120.0000.0000.0000.000
31A172GLY 00.0530.02325.683-0.014-0.0140.0000.0000.0000.000
32A173GLY 0-0.024-0.00628.7480.0100.0100.0000.0000.0000.000
33A174SER 0-0.021-0.03631.1060.0070.0070.0000.0000.0000.000
34A175GLY 00.0210.01834.536-0.004-0.0040.0000.0000.0000.000
35A176ILE 0-0.038-0.01429.003-0.006-0.0060.0000.0000.0000.000
36A177THR 0-0.040-0.01331.2560.0110.0110.0000.0000.0000.000
37A178VAL 0-0.0190.00225.716-0.008-0.0080.0000.0000.0000.000
38A179THR 0-0.004-0.00427.8690.0140.0140.0000.0000.0000.000
39A180ASP -1-0.944-0.99124.241-0.045-0.0450.0000.0000.0000.000
40A181TYR 0-0.0520.00725.7470.0190.0190.0000.0000.0000.000
41A182GLY 00.026-0.00523.737-0.007-0.0070.0000.0000.0000.000
42A183ASP -1-0.989-0.99521.373-0.098-0.0980.0000.0000.0000.000
43A184GLN 0-0.053-0.02120.443-0.029-0.0290.0000.0000.0000.000
44A185VAL 0-0.0020.00721.0730.0150.0150.0000.0000.0000.000
45A186GLU -1-0.891-0.95423.485-0.113-0.1130.0000.0000.0000.000
46A187ILE 0-0.055-0.02323.5950.0090.0090.0000.0000.0000.000
47A188GLU -1-0.897-0.94027.651-0.084-0.0840.0000.0000.0000.000
48A189ALA 0-0.011-0.02631.4270.0000.0000.0000.0000.0000.000
49A190SER 0-0.042-0.01833.8480.0070.0070.0000.0000.0000.000
50A199VAL 00.0100.00837.299-0.003-0.0030.0000.0000.0000.000
51A200THR 0-0.024-0.03837.8000.0010.0010.0000.0000.0000.000
52A201ASP -1-0.763-0.87040.020-0.041-0.0410.0000.0000.0000.000
53A202ALA 00.0040.00343.683-0.002-0.0020.0000.0000.0000.000
54A203LEU 0-0.0090.01146.6950.0030.0030.0000.0000.0000.000
55A204SER 0-0.032-0.02050.0660.0000.0000.0000.0000.0000.000
56A205LEU 00.002-0.01852.6980.0020.0020.0000.0000.0000.000
57A206MET 00.0070.02256.211-0.001-0.0010.0000.0000.0000.000
58A207TYR 0-0.042-0.06859.3560.0010.0010.0000.0000.0000.000
59A208SER 00.1160.03862.3630.0000.0000.0000.0000.0000.000
60A209THR 0-0.0010.00865.7980.0000.0000.0000.0000.0000.000
61A210SER 0-0.057-0.03366.6780.0010.0010.0000.0000.0000.000
62A211THR 0-0.049-0.03161.7170.0000.0000.0000.0000.0000.000
63A212GLY 00.0650.02063.234-0.001-0.0010.0000.0000.0000.000
64A213GLY 00.0100.04564.6470.0000.0000.0000.0000.0000.000
65A214PRO 0-0.022-0.00166.8740.0010.0010.0000.0000.0000.000
66A215ALA 00.0520.00570.3740.0000.0000.0000.0000.0000.000
67A216SER 0-0.014-0.03073.1160.0000.0000.0000.0000.0000.000
68A217ILE 0-0.0290.00368.7450.0000.0000.0000.0000.0000.000
69A218ALA 00.018-0.00872.5990.0000.0000.0000.0000.0000.000
70A219ALA 0-0.008-0.00274.626-0.001-0.0010.0000.0000.0000.000
71A220ASN 0-0.121-0.05575.2840.0000.0000.0000.0000.0000.000
72A221ALA 00.0760.02473.8330.0000.0000.0000.0000.0000.000
73A222LEU 0-0.043-0.01467.9960.0000.0000.0000.0000.0000.000
74A223THR 0-0.004-0.00769.2350.0000.0000.0000.0000.0000.000
75A224ASP -1-0.875-0.96263.866-0.022-0.0220.0000.0000.0000.000
76A225PHE 0-0.008-0.02262.9050.0010.0010.0000.0000.0000.000
77A226ASP -1-0.791-0.84462.684-0.017-0.0170.0000.0000.0000.000
78A227LEU 0-0.054-0.01558.3990.0000.0000.0000.0000.0000.000
79A228SER 0-0.044-0.04658.6940.0000.0000.0000.0000.0000.000
80A229GLY 00.009-0.01259.1400.0000.0000.0000.0000.0000.000
81A230ALA 0-0.048-0.00458.5420.0000.0000.0000.0000.0000.000
82A231LEU 00.0070.01256.5620.0010.0010.0000.0000.0000.000
83A232THR 0-0.017-0.02751.312-0.001-0.0010.0000.0000.0000.000
84A233VAL 0-0.032-0.00252.8660.0010.0010.0000.0000.0000.000
85A234ASN 0-0.010-0.01446.422-0.002-0.0020.0000.0000.0000.000
86A235SER 00.017-0.00646.8220.0010.0010.0000.0000.0000.000
87A236VAL 0-0.0070.01541.6580.0000.0000.0000.0000.0000.000
88A237GLY 00.0680.05841.925-0.001-0.0010.0000.0000.0000.000
89A238THR 0-0.045-0.03542.7500.0010.0010.0000.0000.0000.000
90A239GLY 0-0.0010.00044.0670.0020.0020.0000.0000.0000.000
91A240LEU 0-0.042-0.01345.3790.0010.0010.0000.0000.0000.000
92A241THR 00.0140.00848.6270.0010.0010.0000.0000.0000.000
93A242LYS 10.8870.97251.2870.0190.0190.0000.0000.0000.000
94A243SER 0-0.024-0.06054.9980.0010.0010.0000.0000.0000.000
95A244ALA 00.038-0.00157.5450.0000.0000.0000.0000.0000.000
96A245ALA 0-0.044-0.00859.4980.0000.0000.0000.0000.0000.000
97A246GLY 00.040-0.00258.386-0.001-0.0010.0000.0000.0000.000
98A247ILE 0-0.0080.00952.0210.0010.0010.0000.0000.0000.000
99A248GLN 0-0.0280.01052.5870.0000.0000.0000.0000.0000.000
100A249LEU 00.0080.00148.474-0.001-0.0010.0000.0000.0000.000
101A250ALA 00.0070.00645.5350.0020.0020.0000.0000.0000.000
102A251ALA 00.0650.00845.098-0.002-0.0020.0000.0000.0000.000
103A252GLY 0-0.014-0.00742.302-0.001-0.0010.0000.0000.0000.000
104A253LYS 10.8630.92140.5290.0430.0430.0000.0000.0000.000
105A254SER 00.0050.03744.1160.0000.0000.0000.0000.0000.000
106A255GLY 00.0500.03243.203-0.003-0.0030.0000.0000.0000.000
107A256LEU 0-0.044-0.02043.6160.0030.0030.0000.0000.0000.000
108A257TYR 0-0.033-0.06145.5080.0000.0000.0000.0000.0000.000
109A258GLN 00.0150.00847.913-0.001-0.0010.0000.0000.0000.000
110A259ILE 0-0.029-0.03149.5220.0020.0020.0000.0000.0000.000
111A260THR 00.0200.01152.944-0.001-0.0010.0000.0000.0000.000
112A261MET 0-0.0380.00855.5600.0010.0010.0000.0000.0000.000
113A262THR 0-0.048-0.03458.8850.0000.0000.0000.0000.0000.000
114A263VAL 00.0240.01461.1940.0010.0010.0000.0000.0000.000
115A264LYS 10.8990.94864.6830.0240.0240.0000.0000.0000.000
116A265ASN 00.0590.01966.9950.0010.0010.0000.0000.0000.000
117A266ASN 00.0580.01070.2180.0000.0000.0000.0000.0000.000
118A267THR 0-0.0010.00672.4310.0000.0000.0000.0000.0000.000
119A268VAL 0-0.0040.02374.3550.0010.0010.0000.0000.0000.000
120A269THR 0-0.029-0.00474.037-0.001-0.0010.0000.0000.0000.000
121A270THR 00.0170.01575.6580.0000.0000.0000.0000.0000.000
122A271GLY 00.0760.05476.2080.0000.0000.0000.0000.0000.000
123A272ASN 0-0.001-0.01572.006-0.001-0.0010.0000.0000.0000.000
124A273TYR 0-0.018-0.02568.5500.0010.0010.0000.0000.0000.000
125A274LEU 0-0.025-0.01068.929-0.001-0.0010.0000.0000.0000.000
126A275LEU 0-0.015-0.00963.0120.0010.0010.0000.0000.0000.000
127A276ARG 10.9000.94663.3920.0230.0230.0000.0000.0000.000
128A277VAL 00.0300.03656.9000.0010.0010.0000.0000.0000.000
129A278LYS 10.8600.92959.6730.0230.0230.0000.0000.0000.000
130A279TYR 00.013-0.01451.4160.0000.0000.0000.0000.0000.000
131A280GLY 00.0420.03857.038-0.001-0.0010.0000.0000.0000.000
132A281SER 0-0.043-0.03657.9190.0010.0010.0000.0000.0000.000
133A282SER 0-0.0160.01257.1730.0000.0000.0000.0000.0000.000
134A283ASP -1-0.959-0.98659.318-0.027-0.0270.0000.0000.0000.000
135A284PHE 00.0410.01456.121-0.001-0.0010.0000.0000.0000.000
136A285VAL 00.004-0.01261.1680.0010.0010.0000.0000.0000.000
137A286VAL 00.020-0.00162.788-0.001-0.0010.0000.0000.0000.000
138A287ALA 00.0050.01265.3230.0010.0010.0000.0000.0000.000
139A288CYS 0-0.042-0.02465.931-0.001-0.0010.0000.0000.0000.000
140A289PRO 00.0350.02568.6450.0010.0010.0000.0000.0000.000
141A290ALA 0-0.0310.00871.088-0.001-0.0010.0000.0000.0000.000
142A291SER 00.0540.00272.2660.0000.0000.0000.0000.0000.000
143A292SER 0-0.013-0.03973.2220.0000.0000.0000.0000.0000.000
144A293LEU 0-0.025-0.00470.9720.0000.0000.0000.0000.0000.000
145A294THR 0-0.0070.01667.940-0.001-0.0010.0000.0000.0000.000
146A295ALA 00.0060.01869.7480.0000.0000.0000.0000.0000.000
147A296GLY 0-0.016-0.03067.2980.0000.0000.0000.0000.0000.000
148A297GLY 00.0330.02465.6440.0000.0000.0000.0000.0000.000
149A298THR 0-0.031-0.03959.3180.0000.0000.0000.0000.0000.000
150A299ILE 00.0090.02059.4030.0000.0000.0000.0000.0000.000
151A300SER 0-0.031-0.02154.369-0.001-0.0010.0000.0000.0000.000
152A301LEU 0-0.010-0.02154.3680.0000.0000.0000.0000.0000.000
153A302LEU 00.0330.05047.204-0.001-0.0010.0000.0000.0000.000
154A303ILE 0-0.026-0.01450.7910.0000.0000.0000.0000.0000.000
155A304TYR 00.0270.01244.808-0.002-0.0020.0000.0000.0000.000
156A305CYS 0-0.052-0.01048.4460.0030.0030.0000.0000.0000.000
157A306ASN 00.020-0.00247.988-0.003-0.0030.0000.0000.0000.000
158A307VAL 0-0.055-0.02847.0640.0020.0020.0000.0000.0000.000
159A308LEU 0-0.062-0.02747.9460.0000.0000.0000.0000.0000.000
160A309GLY 00.002-0.00649.1670.0010.0010.0000.0000.0000.000
161A310VAL 0-0.062-0.01949.7550.0030.0030.0000.0000.0000.000
162A311VAL 00.0800.01852.069-0.001-0.0010.0000.0000.0000.000
163A312SER 0-0.031-0.00453.997-0.001-0.0010.0000.0000.0000.000
164A313LEU 0-0.029-0.02555.4930.0000.0000.0000.0000.0000.000
165A314ASP -1-0.745-0.84351.199-0.030-0.0300.0000.0000.0000.000
166A315VAL 0-0.022-0.02352.9690.0000.0000.0000.0000.0000.000
167A316LEU 0-0.0100.00352.2170.0000.0000.0000.0000.0000.000
168A317LYS 10.9270.98256.1290.0230.0230.0000.0000.0000.000
169A318PHE 00.045-0.00755.626-0.001-0.0010.0000.0000.0000.000
170A319SER 0-0.0170.00261.5140.0010.0010.0000.0000.0000.000
171A320LEU 00.0570.02664.111-0.001-0.0010.0000.0000.0000.000
172A321CYS 0-0.0090.02167.1970.0010.0010.0000.0000.0000.000
173A322ASN 00.0130.02270.6800.0000.0000.0000.0000.0000.000
174A323ASP -1-0.810-0.92973.383-0.020-0.0200.0000.0000.0000.000
175A324GLY 00.0300.01675.7660.0010.0010.0000.0000.0000.000
176A325ALA 0-0.019-0.01577.3090.0010.0010.0000.0000.0000.000
177A326ALA 0-0.0040.00576.0530.0000.0000.0000.0000.0000.000
178A327LEU 0-0.036-0.01370.2210.0000.0000.0000.0000.0000.000
179A328SER 00.0270.01472.9560.0000.0000.0000.0000.0000.000
180A329ASN 0-0.085-0.04872.3340.0010.0010.0000.0000.0000.000
181A330TYR 0-0.038-0.01466.561-0.001-0.0010.0000.0000.0000.000
182A331ILE 0-0.0030.00663.1280.0010.0010.0000.0000.0000.000
183A332ILE 0-0.027-0.00861.541-0.001-0.0010.0000.0000.0000.000
184A333ASN 0-0.0040.00157.6100.0010.0010.0000.0000.0000.000
185A334ILE 00.0050.01455.882-0.001-0.0010.0000.0000.0000.000
186A335THR 00.0040.01650.7460.0010.0010.0000.0000.0000.000
187A336ALA 0-0.0090.00750.921-0.001-0.0010.0000.0000.0000.000
188A337ALA 00.0380.00545.9450.0000.0000.0000.0000.0000.000
189A338LYS 10.8770.97540.3580.0590.0590.0000.0000.0000.000
190A339ILE 0-0.028-0.02842.112-0.002-0.0020.0000.0000.0000.000
191A340ASN -1-0.852-0.91137.974-0.067-0.0670.0000.0000.0000.000