Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K9QZ3

Calculation Name: 2R4R-A-Xray372

Preferred Name: Beta-2 adrenergic receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2R4R

Chain ID: A

ChEMBL ID: CHEMBL210

UniProt ID: P07550

Base Structure: X-ray

Registration Date: 2023-06-26

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2563179.661367
FMO2-HF: Nuclear repulsion 2476648.178726
FMO2-HF: Total energy -86531.482641
FMO2-MP2: Total energy -86782.13769


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:37:GLY)


Summations of interaction energy for fragment #1(A:37:GLY)
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.
-4.964-2.384.648-2.51-4.7240.006
Interaction energy analysis for fragmet #1(A:37:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.011
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].
3A39VAL00.0200.0082.772-2.303-0.5941.579-1.202-2.0860.010
4A40MET0-0.005-0.0072.600-3.446-2.7673.069-1.264-2.485-0.004
5A41SER00.0710.0473.930-0.0240.1720.000-0.044-0.1530.000
6A42LEU0-0.033-0.0166.3200.3270.3270.0000.0000.0000.000
7A43ILE0-0.044-0.0316.1190.1990.1990.0000.0000.0000.000
8A44VAL00.0620.0258.1200.0770.0770.0000.0000.0000.000
9A45LEU00.0330.00810.7740.1190.1190.0000.0000.0000.000
10A46ALA0-0.019-0.01212.3380.0850.0850.0000.0000.0000.000
11A47ILE0-0.0300.00111.5090.0550.0550.0000.0000.0000.000
12A48VAL0-0.0120.00314.5750.0260.0260.0000.0000.0000.000
13A49PHE00.0110.01316.9430.0420.0420.0000.0000.0000.000
14A50GLY00.0130.00817.9560.0260.0260.0000.0000.0000.000
15A51ASN0-0.028-0.02917.5620.0430.0430.0000.0000.0000.000
16A52VAL00.016-0.01820.7060.0140.0140.0000.0000.0000.000
17A53LEU0-0.008-0.02522.3310.0180.0180.0000.0000.0000.000
18A54VAL00.0070.00623.4280.0150.0150.0000.0000.0000.000
19A55ILE00.0590.04324.1650.0120.0120.0000.0000.0000.000
20A56THR0-0.0220.00227.0580.0100.0100.0000.0000.0000.000
21A57ALA00.0100.01428.2680.0080.0080.0000.0000.0000.000
22A58ILE0-0.037-0.00129.3110.0070.0070.0000.0000.0000.000
23A59ALA0-0.079-0.05231.1260.0060.0060.0000.0000.0000.000
24A60LYS10.8990.93730.5380.0910.0910.0000.0000.0000.000
25A61PHE00.0220.03631.7500.0040.0040.0000.0000.0000.000
26A62GLU-1-0.868-0.92435.846-0.050-0.0500.0000.0000.0000.000
27A63ARG10.9430.96238.0430.0390.0390.0000.0000.0000.000
28A64LEU0-0.031-0.01031.6640.0000.0000.0000.0000.0000.000
29A65GLN0-0.018-0.00134.449-0.006-0.0060.0000.0000.0000.000
30A66THR0-0.059-0.05035.7350.0030.0030.0000.0000.0000.000
31A67VAL00.0760.03535.533-0.004-0.0040.0000.0000.0000.000
32A68THR00.0470.02732.569-0.003-0.0030.0000.0000.0000.000
33A69ASN0-0.025-0.03731.379-0.008-0.0080.0000.0000.0000.000
34A70TYR00.0120.01231.567-0.004-0.0040.0000.0000.0000.000
35A71PHE00.0300.00830.939-0.004-0.0040.0000.0000.0000.000
36A72ILE0-0.0210.02626.465-0.006-0.0060.0000.0000.0000.000
37A73THR0-0.028-0.01926.368-0.012-0.0120.0000.0000.0000.000
38A74SER0-0.0070.01227.178-0.009-0.0090.0000.0000.0000.000
39A75LEU0-0.004-0.01923.348-0.007-0.0070.0000.0000.0000.000
40A76ALA00.0150.02522.283-0.014-0.0140.0000.0000.0000.000
41A77CYS0-0.006-0.01821.637-0.017-0.0170.0000.0000.0000.000
42A78ALA0-0.013-0.00221.725-0.009-0.0090.0000.0000.0000.000
43A79ASP-1-0.760-0.82717.469-0.306-0.3060.0000.0000.0000.000
44A80LEU0-0.008-0.00216.900-0.032-0.0320.0000.0000.0000.000
45A81VAL00.0340.00717.681-0.027-0.0270.0000.0000.0000.000
46A82MET0-0.002-0.01114.8000.0030.0030.0000.0000.0000.000
47A83GLY00.039-0.01513.502-0.051-0.0510.0000.0000.0000.000
48A84LEU0-0.073-0.03713.384-0.058-0.0580.0000.0000.0000.000
49A85ALA0-0.010-0.01315.8020.0280.0280.0000.0000.0000.000
50A86VAL00.0070.02413.7440.0110.0110.0000.0000.0000.000
51A87VAL00.0290.0339.034-0.033-0.0330.0000.0000.0000.000
52A88PRO0-0.0410.0059.557-0.118-0.1180.0000.0000.0000.000
53A89PHE0-0.061-0.03110.270-0.043-0.0430.0000.0000.0000.000
54A90GLY0-0.0060.0107.1680.0360.0360.0000.0000.0000.000
55A108PHE00.0410.00121.867-0.002-0.0020.0000.0000.0000.000
56A109TRP0-0.002-0.01612.4840.0220.0220.0000.0000.0000.000
57A110THR00.0440.02017.811-0.015-0.0150.0000.0000.0000.000
58A111SER0-0.031-0.00719.6720.0100.0100.0000.0000.0000.000
59A112ILE0-0.014-0.01518.6610.0090.0090.0000.0000.0000.000
60A113ASP-1-0.904-0.94216.324-0.308-0.3080.0000.0000.0000.000
61A114VAL00.0730.04119.0870.0020.0020.0000.0000.0000.000
62A115LEU0-0.0460.02922.3200.0060.0060.0000.0000.0000.000
63A116CYS0-0.047-0.02120.0700.0040.0040.0000.0000.0000.000
64A117VAL00.0420.00518.7900.0090.0090.0000.0000.0000.000
65A118THR0-0.061-0.06421.8140.0150.0150.0000.0000.0000.000
66A119ALA00.0750.04824.9120.0120.0120.0000.0000.0000.000
67A120SER0-0.0270.00222.7510.0070.0070.0000.0000.0000.000
68A121ILE0-0.043-0.01225.1550.0090.0090.0000.0000.0000.000
69A122GLU-1-0.818-0.89426.767-0.083-0.0830.0000.0000.0000.000
70A123THR0-0.001-0.04228.0170.0110.0110.0000.0000.0000.000
71A124LEU0-0.082-0.04425.6560.0090.0090.0000.0000.0000.000
72A125CYS0-0.013-0.00229.3210.0100.0100.0000.0000.0000.000
73A126VAL00.0300.02732.3560.0070.0070.0000.0000.0000.000
74A127ILE0-0.0080.00330.7480.0070.0070.0000.0000.0000.000
75A128ALA00.0160.01933.0210.0060.0060.0000.0000.0000.000
76A129VAL00.0490.02034.6880.0060.0060.0000.0000.0000.000
77A130ASP-1-0.809-0.91136.587-0.056-0.0560.0000.0000.0000.000
78A131ARG10.8280.86935.0720.0600.0600.0000.0000.0000.000
79A132TYR00.0200.01438.2040.0040.0040.0000.0000.0000.000
80A133PHE0-0.011-0.04040.5180.0030.0030.0000.0000.0000.000
81A134ALA0-0.063-0.02640.9200.0020.0020.0000.0000.0000.000
82A135ILE0-0.040-0.01940.7480.0020.0020.0000.0000.0000.000
83A136THR0-0.077-0.00943.8410.0020.0020.0000.0000.0000.000
84A137SER0-0.0130.00545.8700.0020.0020.0000.0000.0000.000
85A138PRO00.0290.02447.7690.0010.0010.0000.0000.0000.000
86A139PHE00.029-0.01549.7060.0020.0020.0000.0000.0000.000
87A140LYS10.8690.93547.1030.0270.0270.0000.0000.0000.000
88A141TYR00.0630.04038.184-0.002-0.0020.0000.0000.0000.000
89A142GLN00.002-0.01439.392-0.003-0.0030.0000.0000.0000.000
90A143SER0-0.0120.00540.3010.0030.0030.0000.0000.0000.000
91A144LEU00.0300.02142.1940.0000.0000.0000.0000.0000.000
92A145LEU0-0.048-0.01439.2770.0010.0010.0000.0000.0000.000
93A146THR0-0.010-0.02541.427-0.002-0.0020.0000.0000.0000.000
94A147LYS11.0020.99239.2310.0520.0520.0000.0000.0000.000
95A148ASN00.1090.06939.754-0.004-0.0040.0000.0000.0000.000
96A149LYS10.9660.98040.5520.0430.0430.0000.0000.0000.000
97A150ALA00.0360.03337.376-0.001-0.0010.0000.0000.0000.000
98A151ARG10.9600.94836.0980.0680.0680.0000.0000.0000.000
99A152VAL0-0.008-0.00336.479-0.003-0.0030.0000.0000.0000.000
100A153ILE00.0210.01236.574-0.001-0.0010.0000.0000.0000.000
101A154ILE00.0030.00632.050-0.003-0.0030.0000.0000.0000.000
102A155LEU0-0.045-0.02732.886-0.005-0.0050.0000.0000.0000.000
103A156MET0-0.046-0.04133.816-0.002-0.0020.0000.0000.0000.000
104A157VAL00.0280.03030.0730.0010.0010.0000.0000.0000.000
105A158TRP0-0.0150.00425.203-0.007-0.0070.0000.0000.0000.000
106A159ILE00.0590.02229.924-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0130.01632.4180.0010.0010.0000.0000.0000.000
108A161SER00.001-0.00827.094-0.003-0.0030.0000.0000.0000.000
109A162GLY0-0.045-0.03027.761-0.009-0.0090.0000.0000.0000.000
110A163LEU0-0.107-0.04929.2530.0000.0000.0000.0000.0000.000
111A164THR0-0.0160.01327.3030.0070.0070.0000.0000.0000.000
112A203SER00.1010.03727.9600.0010.0010.0000.0000.0000.000
113A204SER00.0780.03926.444-0.003-0.0030.0000.0000.0000.000
114A205ILE00.0310.01428.4250.0010.0010.0000.0000.0000.000
115A206VAL0-0.023-0.01531.2430.0040.0040.0000.0000.0000.000
116A207SER00.032-0.01027.303-0.002-0.0020.0000.0000.0000.000
117A208PHE00.0120.00524.476-0.006-0.0060.0000.0000.0000.000
118A209TYR00.016-0.00228.2810.0040.0040.0000.0000.0000.000
119A210VAL00.0260.02831.1010.0020.0020.0000.0000.0000.000
120A211PRO0-0.0160.01329.5060.0050.0050.0000.0000.0000.000
121A212LEU00.029-0.01227.1750.0010.0010.0000.0000.0000.000
122A213VAL0-0.094-0.03730.7430.0050.0050.0000.0000.0000.000
123A214ILE00.0120.00233.9870.0050.0050.0000.0000.0000.000
124A215MET00.0160.03628.0830.0060.0060.0000.0000.0000.000
125A216VAL00.0270.00930.7360.0010.0010.0000.0000.0000.000
126A217PHE0-0.027-0.03333.3680.0050.0050.0000.0000.0000.000
127A218VAL0-0.0010.01736.7300.0040.0040.0000.0000.0000.000
128A219TYR00.0240.02331.5860.0030.0030.0000.0000.0000.000
129A220SER0-0.0120.00936.0750.0040.0040.0000.0000.0000.000
130A221ARG10.9680.97337.2540.0390.0390.0000.0000.0000.000
131A222VAL00.0060.00837.8160.0030.0030.0000.0000.0000.000
132A223PHE0-0.077-0.03635.1090.0030.0030.0000.0000.0000.000
133A224GLN00.0310.02838.0960.0040.0040.0000.0000.0000.000
134A225GLU-1-0.997-0.98841.254-0.028-0.0280.0000.0000.0000.000
135A226ALA00.0350.01640.5290.0010.0010.0000.0000.0000.000
136A227LYS10.8580.91339.8080.0270.0270.0000.0000.0000.000
137A228ARG10.9750.98343.5900.0250.0250.0000.0000.0000.000
138A229GLN00.0870.03745.8060.0020.0020.0000.0000.0000.000
139A230LEU0-0.032-0.00941.8770.0010.0010.0000.0000.0000.000
140A231GLN0-0.019-0.03245.4690.0030.0030.0000.0000.0000.000
141A232LYS10.9140.99848.4610.0190.0190.0000.0000.0000.000
142A233ILE0-0.024-0.02146.9570.0000.0000.0000.0000.0000.000
143A234ASP-1-0.817-0.90651.297-0.013-0.0130.0000.0000.0000.000
144A235LYS10.9390.96449.5890.0130.0130.0000.0000.0000.000
145A236SER00.0580.03252.4500.0000.0000.0000.0000.0000.000
146A237GLU-1-0.913-0.96051.345-0.017-0.0170.0000.0000.0000.000
147A238GLY0-0.007-0.00549.8270.0000.0000.0000.0000.0000.000
148A239ARG10.7200.85549.0330.0130.0130.0000.0000.0000.000
149A240PHE00.0120.00152.8460.0010.0010.0000.0000.0000.000
150A241HIS0-0.059-0.02451.1720.0010.0010.0000.0000.0000.000
151A242VAL00.0440.05355.5900.0000.0000.0000.0000.0000.000
152A264PHE0-0.008-0.00540.2180.0000.0000.0000.0000.0000.000
153A265CYS00.0650.05043.4690.0010.0010.0000.0000.0000.000
154A266LEU00.029-0.00739.873-0.002-0.0020.0000.0000.0000.000
155A267LYS10.9830.99235.6910.0410.0410.0000.0000.0000.000
156A268GLU-1-0.872-0.94437.970-0.043-0.0430.0000.0000.0000.000
157A269HIS00.015-0.00338.564-0.001-0.0010.0000.0000.0000.000
158A270LYS10.9290.95034.3770.0270.0270.0000.0000.0000.000
159A271ALA00.0050.01133.295-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0580.02133.163-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9420.98829.1070.0430.0430.0000.0000.0000.000
162A274THR0-0.061-0.03528.780-0.004-0.0040.0000.0000.0000.000
163A275LEU00.020-0.01827.991-0.006-0.0060.0000.0000.0000.000
164A276GLY00.1030.02929.758-0.003-0.0030.0000.0000.0000.000
165A277ILE0-0.083-0.03324.8630.0010.0010.0000.0000.0000.000
166A278ILE0-0.0250.01524.003-0.004-0.0040.0000.0000.0000.000
167A279MET0-0.009-0.02524.417-0.010-0.0100.0000.0000.0000.000
168A280GLY0-0.019-0.00326.1040.0000.0000.0000.0000.0000.000
169A281THR0-0.043-0.01219.8530.0070.0070.0000.0000.0000.000
170A282PHE00.0260.00620.175-0.008-0.0080.0000.0000.0000.000
171A283THR0-0.0190.01522.039-0.005-0.0050.0000.0000.0000.000
172A284LEU00.010-0.02421.163-0.001-0.0010.0000.0000.0000.000
173A285CYS0-0.067-0.01517.350-0.005-0.0050.0000.0000.0000.000
174A286TRP00.0440.02216.835-0.019-0.0190.0000.0000.0000.000
175A287LEU00.0130.01320.1140.0070.0070.0000.0000.0000.000
176A288PRO0-0.038-0.03218.9680.0040.0040.0000.0000.0000.000
177A289PHE0-0.0170.00917.132-0.001-0.0010.0000.0000.0000.000
178A290PHE00.009-0.00119.8950.0030.0030.0000.0000.0000.000
179A291ILE0-0.057-0.00723.1680.0140.0140.0000.0000.0000.000
180A311LEU00.0400.00713.039-0.012-0.0120.0000.0000.0000.000
181A312ASN00.0240.00012.8780.0360.0360.0000.0000.0000.000
182A313TRP00.0190.0158.757-0.040-0.0400.0000.0000.0000.000
183A314ILE0-0.003-0.00910.827-0.030-0.0300.0000.0000.0000.000
184A315GLY00.0460.02513.1180.0180.0180.0000.0000.0000.000
185A316TYR00.025-0.0089.714-0.001-0.0010.0000.0000.0000.000
186A317VAL00.0390.03711.1250.0010.0010.0000.0000.0000.000
187A318ASN0-0.093-0.05713.1320.0480.0480.0000.0000.0000.000
188A319SER00.051-0.01713.8290.0140.0140.0000.0000.0000.000
189A320GLY0-0.030-0.00914.7970.0110.0110.0000.0000.0000.000
190A321PHE0-0.006-0.01215.7220.0380.0380.0000.0000.0000.000
191A322ASN00.0950.03418.1850.0390.0390.0000.0000.0000.000
192A323PRO0-0.0050.00319.0790.0230.0230.0000.0000.0000.000
193A324LEU0-0.0060.00717.1990.0140.0140.0000.0000.0000.000
194A325ILE0-0.028-0.01720.8230.0200.0200.0000.0000.0000.000
195A326TYR00.043-0.03523.6980.0120.0120.0000.0000.0000.000
196A327CYS0-0.0050.01623.3680.0090.0090.0000.0000.0000.000
197A328ARG10.9210.94625.8020.0200.0200.0000.0000.0000.000
198A329SER0-0.037-0.02827.7130.0030.0030.0000.0000.0000.000
199A330PRO0-0.0920.01628.0870.0050.0050.0000.0000.0000.000
200A331ASP-1-0.896-0.96030.767-0.048-0.0480.0000.0000.0000.000
201A332PHE00.0550.01227.2290.0010.0010.0000.0000.0000.000
202A333ARG10.9090.98626.7050.0360.0360.0000.0000.0000.000
203A334ILE00.0250.01028.906-0.002-0.0020.0000.0000.0000.000
204A335ALA00.0360.02430.469-0.002-0.0020.0000.0000.0000.000
205A336PHE00.012-0.02224.063-0.002-0.0020.0000.0000.0000.000
206A337GLN0-0.057-0.02425.833-0.002-0.0020.0000.0000.0000.000
207A338GLU-1-0.966-1.00827.451-0.028-0.0280.0000.0000.0000.000
208A339LEU00.0180.04727.2320.0030.0030.0000.0000.0000.000
209A340LEU0-0.066-0.02023.849-0.001-0.0010.0000.0000.0000.000
210A341CYS0-0.032-0.02628.4390.0050.0050.0000.0000.0000.000
211A342LEU00.0440.02231.5910.0040.0040.0000.0000.0000.000
212A343ARG11.0001.01122.3530.0340.0340.0000.0000.0000.000
213A344ARG10.9040.93724.3600.0000.0000.0000.0000.0000.000
214A345SER0-0.016-0.02130.2300.0030.0030.0000.0000.0000.000
215A346SER00.0390.05632.894-0.002-0.0020.0000.0000.0000.000
216A347LEU00.017-0.00834.8360.0010.0010.0000.0000.0000.000
217A348LYS10.9460.99630.0550.0050.0050.0000.0000.0000.000