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: Z69GN

Calculation Name: 2R4S-A-Xray372

Preferred Name: Beta-2 adrenergic receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2R4S

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 -2562015.346153
FMO2-HF: Nuclear repulsion 2475483.73204
FMO2-HF: Total energy -86531.614113
FMO2-MP2: Total energy -86782.227119


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.
-5.044-2.0763.86-2.391-4.4360.006
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 : 0.055 / 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].
3A39VAL00.0230.0092.824-2.405-0.4461.245-1.200-2.0040.010
4A40MET0-0.014-0.0112.624-3.291-2.4612.615-1.156-2.288-0.004
5A41SER00.0710.0443.984-0.1190.0600.000-0.035-0.1440.000
6A42LEU0-0.034-0.0166.3740.3310.3310.0000.0000.0000.000
7A43ILE0-0.040-0.0276.1010.2040.2040.0000.0000.0000.000
8A44VAL00.0620.0218.1310.0740.0740.0000.0000.0000.000
9A45LEU00.0360.01110.8080.1180.1180.0000.0000.0000.000
10A46ALA0-0.018-0.01212.3810.0840.0840.0000.0000.0000.000
11A47ILE0-0.0240.00511.4400.0530.0530.0000.0000.0000.000
12A48VAL0-0.0130.00014.6400.0240.0240.0000.0000.0000.000
13A49PHE00.0100.01416.9800.0410.0410.0000.0000.0000.000
14A50GLY00.0130.00617.9550.0260.0260.0000.0000.0000.000
15A51ASN0-0.029-0.02817.5480.0420.0420.0000.0000.0000.000
16A52VAL00.019-0.02020.7480.0130.0130.0000.0000.0000.000
17A53LEU0-0.008-0.02222.3290.0170.0170.0000.0000.0000.000
18A54VAL0-0.006-0.00123.4340.0150.0150.0000.0000.0000.000
19A55ILE00.0520.03724.1420.0110.0110.0000.0000.0000.000
20A56THR0-0.0090.01227.0460.0110.0110.0000.0000.0000.000
21A57ALA00.0330.02128.2820.0080.0080.0000.0000.0000.000
22A58ILE0-0.061-0.01129.2800.0070.0070.0000.0000.0000.000
23A59ALA0-0.064-0.03831.0740.0060.0060.0000.0000.0000.000
24A60LYS10.7700.84332.6270.0600.0600.0000.0000.0000.000
25A61PHE00.0230.04731.7190.0030.0030.0000.0000.0000.000
26A62GLU-1-0.858-0.92535.817-0.050-0.0500.0000.0000.0000.000
27A63ARG10.9510.96937.9120.0390.0390.0000.0000.0000.000
28A64LEU0-0.0180.00431.6270.0010.0010.0000.0000.0000.000
29A65GLN00.0780.05534.358-0.005-0.0050.0000.0000.0000.000
30A66THR0-0.051-0.04535.7250.0030.0030.0000.0000.0000.000
31A67VAL00.0760.03635.525-0.004-0.0040.0000.0000.0000.000
32A68THR00.0450.02432.606-0.003-0.0030.0000.0000.0000.000
33A69ASN0-0.026-0.04531.409-0.008-0.0080.0000.0000.0000.000
34A70TYR00.0120.01331.646-0.003-0.0030.0000.0000.0000.000
35A71PHE00.0400.01230.871-0.004-0.0040.0000.0000.0000.000
36A72ILE0-0.0250.03226.467-0.007-0.0070.0000.0000.0000.000
37A73THR0-0.023-0.01926.329-0.012-0.0120.0000.0000.0000.000
38A74SER0-0.0100.01127.163-0.008-0.0080.0000.0000.0000.000
39A75LEU0-0.005-0.02023.324-0.007-0.0070.0000.0000.0000.000
40A76ALA00.0180.02922.236-0.014-0.0140.0000.0000.0000.000
41A77CYS0-0.007-0.01621.683-0.017-0.0170.0000.0000.0000.000
42A78ALA0-0.022-0.00921.760-0.010-0.0100.0000.0000.0000.000
43A79ASP-1-0.761-0.83117.488-0.304-0.3040.0000.0000.0000.000
44A80LEU0-0.009-0.00216.929-0.033-0.0330.0000.0000.0000.000
45A81VAL00.0380.01017.733-0.027-0.0270.0000.0000.0000.000
46A82MET0-0.006-0.01314.7770.0030.0030.0000.0000.0000.000
47A83GLY00.039-0.01313.554-0.050-0.0500.0000.0000.0000.000
48A84LEU0-0.070-0.03613.430-0.059-0.0590.0000.0000.0000.000
49A85ALA0-0.010-0.01215.8720.0270.0270.0000.0000.0000.000
50A86VAL00.0090.02313.7480.0120.0120.0000.0000.0000.000
51A87VAL00.0300.0359.042-0.032-0.0320.0000.0000.0000.000
52A88PRO0-0.0450.0039.573-0.121-0.1210.0000.0000.0000.000
53A89PHE0-0.062-0.03310.306-0.043-0.0430.0000.0000.0000.000
54A90GLY0-0.0060.0107.1780.0390.0390.0000.0000.0000.000
55A108PHE00.0420.00221.884-0.002-0.0020.0000.0000.0000.000
56A109TRP0-0.005-0.02012.4870.0210.0210.0000.0000.0000.000
57A110THR00.0470.02317.711-0.017-0.0170.0000.0000.0000.000
58A111SER0-0.035-0.01219.6360.0110.0110.0000.0000.0000.000
59A112ILE0-0.019-0.01318.5750.0110.0110.0000.0000.0000.000
60A113ASP-1-0.901-0.94316.334-0.307-0.3070.0000.0000.0000.000
61A114VAL00.0740.04019.1130.0030.0030.0000.0000.0000.000
62A115LEU0-0.0470.02822.3550.0070.0070.0000.0000.0000.000
63A116CYS0-0.050-0.02220.0110.0030.0030.0000.0000.0000.000
64A117VAL00.0280.00018.7860.0090.0090.0000.0000.0000.000
65A118THR0-0.053-0.05921.8140.0150.0150.0000.0000.0000.000
66A119ALA00.0830.05124.9300.0120.0120.0000.0000.0000.000
67A120SER0-0.0230.01722.7520.0070.0070.0000.0000.0000.000
68A121ILE0-0.027-0.00825.1310.0090.0090.0000.0000.0000.000
69A122GLU-1-0.822-0.89326.712-0.083-0.0830.0000.0000.0000.000
70A123THR0-0.001-0.05427.9500.0110.0110.0000.0000.0000.000
71A124LEU0-0.096-0.05325.7840.0090.0090.0000.0000.0000.000
72A125CYS0-0.0160.00129.2680.0100.0100.0000.0000.0000.000
73A126VAL00.0250.02432.2970.0070.0070.0000.0000.0000.000
74A127ILE0-0.011-0.00230.7470.0070.0070.0000.0000.0000.000
75A128ALA00.0180.01733.0350.0060.0060.0000.0000.0000.000
76A129VAL00.0580.02434.6930.0060.0060.0000.0000.0000.000
77A130ASP-1-0.804-0.90636.563-0.056-0.0560.0000.0000.0000.000
78A131ARG10.8180.86835.0230.0600.0600.0000.0000.0000.000
79A132TYR00.0220.01138.1750.0040.0040.0000.0000.0000.000
80A133PHE0-0.011-0.03840.4680.0030.0030.0000.0000.0000.000
81A134ALA0-0.068-0.02840.9040.0020.0020.0000.0000.0000.000
82A135ILE0-0.033-0.01640.2920.0020.0020.0000.0000.0000.000
83A136THR0-0.078-0.01343.7900.0020.0020.0000.0000.0000.000
84A137SER0-0.0150.00545.8110.0020.0020.0000.0000.0000.000
85A138PRO00.0240.02547.6800.0010.0010.0000.0000.0000.000
86A139PHE00.042-0.01049.7020.0020.0020.0000.0000.0000.000
87A140LYS10.8620.93147.1250.0270.0270.0000.0000.0000.000
88A141TYR00.0610.03938.053-0.002-0.0020.0000.0000.0000.000
89A142GLN00.005-0.01739.432-0.003-0.0030.0000.0000.0000.000
90A143SER0-0.0090.00840.2950.0030.0030.0000.0000.0000.000
91A144LEU00.0310.02342.1650.0000.0000.0000.0000.0000.000
92A145LEU0-0.043-0.01339.3340.0010.0010.0000.0000.0000.000
93A146THR0-0.015-0.02641.372-0.002-0.0020.0000.0000.0000.000
94A147LYS10.9890.98539.1840.0530.0530.0000.0000.0000.000
95A148ASN00.1150.07439.788-0.004-0.0040.0000.0000.0000.000
96A149LYS10.9780.98040.6070.0430.0430.0000.0000.0000.000
97A150ALA00.0410.03737.342-0.002-0.0020.0000.0000.0000.000
98A151ARG10.9440.95036.1040.0680.0680.0000.0000.0000.000
99A152VAL0-0.025-0.01136.560-0.003-0.0030.0000.0000.0000.000
100A153ILE00.0240.01436.574-0.001-0.0010.0000.0000.0000.000
101A154ILE00.003-0.00731.812-0.002-0.0020.0000.0000.0000.000
102A155LEU0-0.029-0.01632.823-0.006-0.0060.0000.0000.0000.000
103A156MET0-0.050-0.03733.919-0.002-0.0020.0000.0000.0000.000
104A157VAL00.0210.02630.0210.0010.0010.0000.0000.0000.000
105A158TRP0-0.0090.00425.103-0.007-0.0070.0000.0000.0000.000
106A159ILE00.0620.02129.938-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0090.01332.4400.0010.0010.0000.0000.0000.000
108A161SER0-0.004-0.00627.138-0.003-0.0030.0000.0000.0000.000
109A162GLY0-0.035-0.02627.753-0.009-0.0090.0000.0000.0000.000
110A163LEU0-0.104-0.04629.2320.0000.0000.0000.0000.0000.000
111A164THR0-0.0160.01127.2820.0070.0070.0000.0000.0000.000
112A203SER00.1000.03727.9490.0010.0010.0000.0000.0000.000
113A204SER00.0730.04026.457-0.003-0.0030.0000.0000.0000.000
114A205ILE00.0270.01128.4170.0010.0010.0000.0000.0000.000
115A206VAL0-0.023-0.01731.2130.0040.0040.0000.0000.0000.000
116A207SER00.035-0.00627.326-0.001-0.0010.0000.0000.0000.000
117A208PHE00.0100.00124.466-0.006-0.0060.0000.0000.0000.000
118A209TYR00.0230.00028.2390.0040.0040.0000.0000.0000.000
119A210VAL00.0260.03031.0950.0020.0020.0000.0000.0000.000
120A211PRO0-0.0190.00929.4890.0050.0050.0000.0000.0000.000
121A212LEU00.033-0.01127.1300.0010.0010.0000.0000.0000.000
122A213VAL0-0.088-0.03230.7440.0050.0050.0000.0000.0000.000
123A214ILE00.0140.00233.9610.0050.0050.0000.0000.0000.000
124A215MET00.0140.03528.0010.0060.0060.0000.0000.0000.000
125A216VAL00.0250.00830.6740.0010.0010.0000.0000.0000.000
126A217PHE0-0.032-0.03833.3200.0050.0050.0000.0000.0000.000
127A218VAL0-0.0030.01436.6910.0040.0040.0000.0000.0000.000
128A219TYR00.0220.02031.5610.0020.0020.0000.0000.0000.000
129A220SER0-0.0150.01136.0250.0040.0040.0000.0000.0000.000
130A221ARG10.9810.98337.2380.0380.0380.0000.0000.0000.000
131A222VAL00.0090.01337.7900.0030.0030.0000.0000.0000.000
132A223PHE0-0.070-0.03435.0990.0030.0030.0000.0000.0000.000
133A224GLN00.0250.02138.1020.0050.0050.0000.0000.0000.000
134A225GLU-1-0.978-0.97841.232-0.028-0.0280.0000.0000.0000.000
135A226ALA00.0120.00940.4560.0010.0010.0000.0000.0000.000
136A227LYS10.8580.91239.7690.0260.0260.0000.0000.0000.000
137A228ARG10.9740.98243.5270.0250.0250.0000.0000.0000.000
138A229GLN00.0890.03745.7590.0020.0020.0000.0000.0000.000
139A230LEU0-0.027-0.00641.8110.0010.0010.0000.0000.0000.000
140A231GLN0-0.022-0.03245.4590.0030.0030.0000.0000.0000.000
141A232LYS10.9090.99448.4420.0180.0180.0000.0000.0000.000
142A233ILE0-0.025-0.02146.9800.0000.0000.0000.0000.0000.000
143A234ASP-1-0.821-0.90551.303-0.013-0.0130.0000.0000.0000.000
144A235LYS10.9490.97149.8090.0130.0130.0000.0000.0000.000
145A236SER00.0620.02852.4830.0000.0000.0000.0000.0000.000
146A237GLU-1-0.920-0.96351.104-0.017-0.0170.0000.0000.0000.000
147A238GLY0-0.013-0.00749.8330.0000.0000.0000.0000.0000.000
148A239ARG10.7270.86048.9750.0130.0130.0000.0000.0000.000
149A240PHE00.008-0.00452.9910.0010.0010.0000.0000.0000.000
150A241HIS0-0.063-0.02251.2840.0010.0010.0000.0000.0000.000
151A242VAL00.0480.05355.4970.0000.0000.0000.0000.0000.000
152A264PHE0-0.017-0.00940.1880.0000.0000.0000.0000.0000.000
153A265CYS00.0680.04843.5120.0010.0010.0000.0000.0000.000
154A266LEU00.031-0.00639.975-0.002-0.0020.0000.0000.0000.000
155A267LYS10.9810.99335.7820.0410.0410.0000.0000.0000.000
156A268GLU-1-0.874-0.94437.911-0.044-0.0440.0000.0000.0000.000
157A269HIS00.015-0.00438.518-0.001-0.0010.0000.0000.0000.000
158A270LYS10.9300.95134.3660.0270.0270.0000.0000.0000.000
159A271ALA00.0140.00733.233-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0480.02233.191-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9240.97729.1190.0430.0430.0000.0000.0000.000
162A274THR0-0.062-0.03128.756-0.004-0.0040.0000.0000.0000.000
163A275LEU00.030-0.02227.933-0.006-0.0060.0000.0000.0000.000
164A276GLY00.1020.03029.710-0.003-0.0030.0000.0000.0000.000
165A277ILE0-0.081-0.03024.7890.0020.0020.0000.0000.0000.000
166A278ILE0-0.0290.01824.012-0.004-0.0040.0000.0000.0000.000
167A279MET0-0.012-0.02424.505-0.010-0.0100.0000.0000.0000.000
168A280GLY0-0.017-0.00326.1160.0010.0010.0000.0000.0000.000
169A281THR0-0.042-0.01019.8320.0080.0080.0000.0000.0000.000
170A282PHE00.016-0.00220.132-0.007-0.0070.0000.0000.0000.000
171A283THR0-0.0090.01722.019-0.005-0.0050.0000.0000.0000.000
172A284LEU00.008-0.02421.0940.0000.0000.0000.0000.0000.000
173A285CYS0-0.069-0.01517.249-0.004-0.0040.0000.0000.0000.000
174A286TRP00.0460.02316.898-0.019-0.0190.0000.0000.0000.000
175A287LEU00.0190.01720.0890.0080.0080.0000.0000.0000.000
176A288PRO0-0.041-0.03718.8520.0040.0040.0000.0000.0000.000
177A289PHE0-0.0190.00317.065-0.002-0.0020.0000.0000.0000.000
178A290PHE00.0030.00019.8680.0030.0030.0000.0000.0000.000
179A291ILE0-0.051-0.00223.0940.0140.0140.0000.0000.0000.000
180A311LEU00.0350.00213.776-0.021-0.0210.0000.0000.0000.000
181A312ASN00.0260.00412.9250.0410.0410.0000.0000.0000.000
182A313TRP00.0170.0168.704-0.046-0.0460.0000.0000.0000.000
183A314ILE00.004-0.00810.774-0.030-0.0300.0000.0000.0000.000
184A315GLY00.0480.03013.0650.0180.0180.0000.0000.0000.000
185A316TYR00.023-0.0119.6910.0010.0010.0000.0000.0000.000
186A317VAL00.0330.03411.135-0.003-0.0030.0000.0000.0000.000
187A318ASN0-0.092-0.05413.1270.0480.0480.0000.0000.0000.000
188A319SER00.051-0.01413.8400.0130.0130.0000.0000.0000.000
189A320GLY0-0.026-0.00614.8140.0110.0110.0000.0000.0000.000
190A321PHE0-0.005-0.01215.7360.0380.0380.0000.0000.0000.000
191A322ASN00.0960.03518.2160.0390.0390.0000.0000.0000.000
192A323PRO0-0.0040.00519.0570.0230.0230.0000.0000.0000.000
193A324LEU0-0.0110.00617.1340.0130.0130.0000.0000.0000.000
194A325ILE0-0.032-0.01720.7920.0210.0210.0000.0000.0000.000
195A326TYR00.039-0.03623.6720.0120.0120.0000.0000.0000.000
196A327CYS0-0.0050.01423.3030.0090.0090.0000.0000.0000.000
197A328ARG10.9270.94825.8150.0190.0190.0000.0000.0000.000
198A329SER0-0.034-0.02927.7460.0030.0030.0000.0000.0000.000
199A330PRO0-0.0830.01728.1000.0050.0050.0000.0000.0000.000
200A331ASP-1-0.899-0.96130.753-0.048-0.0480.0000.0000.0000.000
201A332PHE00.0620.01627.1590.0010.0010.0000.0000.0000.000
202A333ARG10.9070.98626.6310.0370.0370.0000.0000.0000.000
203A334ILE00.0200.00628.923-0.002-0.0020.0000.0000.0000.000
204A335ALA00.0340.02330.514-0.002-0.0020.0000.0000.0000.000
205A336PHE00.015-0.02224.048-0.002-0.0020.0000.0000.0000.000
206A337GLN0-0.057-0.02425.835-0.002-0.0020.0000.0000.0000.000
207A338GLU-1-0.969-1.00927.480-0.029-0.0290.0000.0000.0000.000
208A339LEU00.0240.05227.2660.0030.0030.0000.0000.0000.000
209A340LEU0-0.060-0.01723.845-0.001-0.0010.0000.0000.0000.000
210A341CYS0-0.035-0.02928.4710.0050.0050.0000.0000.0000.000
211A342LEU00.0440.02531.6420.0040.0040.0000.0000.0000.000
212A343ARG11.0011.01222.3500.0350.0350.0000.0000.0000.000
213A344ARG10.9010.93424.3400.0000.0000.0000.0000.0000.000
214A345SER0-0.014-0.02030.2540.0030.0030.0000.0000.0000.000
215A346SER00.0390.05232.895-0.001-0.0010.0000.0000.0000.000
216A347LEU00.017-0.00634.8130.0010.0010.0000.0000.0000.000
217A348LYS10.9440.99730.0810.0060.0060.0000.0000.0000.000