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: 49GKN

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2561054.560334
FMO2-HF: Nuclear repulsion 2474521.016394
FMO2-HF: Total energy -86533.54394
FMO2-MP2: Total energy -86783.805568


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.
-4.863-2.0164.696-2.613-4.9310.008
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 : 0.070 / q_NPA : 0.020
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].
3A39VAL00.0220.0082.747-2.719-0.8451.477-1.263-2.0890.010
4A40MET0-0.003-0.0052.283-3.262-2.5403.218-1.290-2.650-0.002
5A41SER00.0530.0393.9080.4460.6970.001-0.060-0.1920.000
6A42LEU0-0.033-0.0146.3260.3200.3200.0000.0000.0000.000
7A43ILE0-0.048-0.0365.9750.2040.2040.0000.0000.0000.000
8A44VAL00.0540.0298.1040.0820.0820.0000.0000.0000.000
9A45LEU00.0370.00910.7800.1240.1240.0000.0000.0000.000
10A46ALA0-0.021-0.01212.2960.0880.0880.0000.0000.0000.000
11A47ILE0-0.0390.00812.0670.0520.0520.0000.0000.0000.000
12A48VAL00.0080.00314.5860.0270.0270.0000.0000.0000.000
13A49PHE00.0130.01916.9350.0440.0440.0000.0000.0000.000
14A50GLY00.0140.00817.9410.0270.0270.0000.0000.0000.000
15A51ASN0-0.014-0.02217.6240.0470.0470.0000.0000.0000.000
16A52VAL00.0150.00020.9390.0140.0140.0000.0000.0000.000
17A53LEU0-0.031-0.02722.0770.0180.0180.0000.0000.0000.000
18A54VAL00.0030.00023.9020.0160.0160.0000.0000.0000.000
19A55ILE00.0400.02624.4000.0120.0120.0000.0000.0000.000
20A56THR00.0000.00127.0480.0110.0110.0000.0000.0000.000
21A57ALA00.0100.01728.2540.0080.0080.0000.0000.0000.000
22A58ILE0-0.046-0.01929.3820.0070.0070.0000.0000.0000.000
23A59ALA0-0.050-0.03131.1190.0060.0060.0000.0000.0000.000
24A60LYS10.8540.90830.8420.0940.0940.0000.0000.0000.000
25A61PHE00.0520.04731.8340.0040.0040.0000.0000.0000.000
26A62GLU-1-0.855-0.90935.833-0.054-0.0540.0000.0000.0000.000
27A63ARG10.9680.97538.0990.0410.0410.0000.0000.0000.000
28A64LEU0-0.023-0.00431.5270.0000.0000.0000.0000.0000.000
29A65GLN0-0.065-0.03134.441-0.009-0.0090.0000.0000.0000.000
30A66THR0-0.038-0.03735.7350.0030.0030.0000.0000.0000.000
31A67VAL00.0640.02335.530-0.004-0.0040.0000.0000.0000.000
32A68THR00.0500.03432.609-0.004-0.0040.0000.0000.0000.000
33A69ASN0-0.040-0.02831.290-0.008-0.0080.0000.0000.0000.000
34A70TYR00.0260.01331.563-0.003-0.0030.0000.0000.0000.000
35A71PHE00.009-0.00230.932-0.004-0.0040.0000.0000.0000.000
36A72ILE0-0.0050.00626.625-0.007-0.0070.0000.0000.0000.000
37A73THR0-0.006-0.00626.366-0.009-0.0090.0000.0000.0000.000
38A74SER0-0.0100.00827.184-0.008-0.0080.0000.0000.0000.000
39A75LEU0-0.001-0.01123.441-0.007-0.0070.0000.0000.0000.000
40A76ALA00.0040.01622.284-0.015-0.0150.0000.0000.0000.000
41A77CYS00.005-0.00821.643-0.018-0.0180.0000.0000.0000.000
42A78ALA0-0.018-0.00721.715-0.009-0.0090.0000.0000.0000.000
43A79ASP-1-0.776-0.84317.360-0.319-0.3190.0000.0000.0000.000
44A80LEU0-0.0080.00416.906-0.033-0.0330.0000.0000.0000.000
45A81VAL00.0510.01017.686-0.027-0.0270.0000.0000.0000.000
46A82MET0-0.003-0.00715.0710.0000.0000.0000.0000.0000.000
47A83GLY00.038-0.00913.454-0.052-0.0520.0000.0000.0000.000
48A84LEU0-0.073-0.04113.388-0.061-0.0610.0000.0000.0000.000
49A85ALA0-0.022-0.01815.7720.0300.0300.0000.0000.0000.000
50A86VAL00.0000.02113.8190.0110.0110.0000.0000.0000.000
51A87VAL00.0530.0288.813-0.029-0.0290.0000.0000.0000.000
52A88PRO0-0.0330.0089.560-0.114-0.1140.0000.0000.0000.000
53A89PHE0-0.062-0.02510.271-0.057-0.0570.0000.0000.0000.000
54A90GLY0-0.031-0.0018.226-0.105-0.1050.0000.0000.0000.000
55A108PHE00.0480.00521.778-0.002-0.0020.0000.0000.0000.000
56A109TRP00.000-0.01712.6250.0240.0240.0000.0000.0000.000
57A110THR00.0400.01817.812-0.015-0.0150.0000.0000.0000.000
58A111SER0-0.033-0.00719.6720.0110.0110.0000.0000.0000.000
59A112ILE0-0.019-0.01818.7200.0090.0090.0000.0000.0000.000
60A113ASP-1-0.879-0.93416.265-0.328-0.3280.0000.0000.0000.000
61A114VAL00.0240.01319.0890.0010.0010.0000.0000.0000.000
62A115LEU0-0.0110.01322.3220.0050.0050.0000.0000.0000.000
63A116CYS0-0.028-0.01620.0480.0080.0080.0000.0000.0000.000
64A117VAL00.0340.00418.7180.0090.0090.0000.0000.0000.000
65A118THR0-0.030-0.02721.8180.0110.0110.0000.0000.0000.000
66A119ALA00.0270.02824.8810.0130.0130.0000.0000.0000.000
67A120SER0-0.018-0.00322.7860.0080.0080.0000.0000.0000.000
68A121ILE0-0.052-0.01625.1590.0100.0100.0000.0000.0000.000
69A122GLU-1-0.817-0.90226.781-0.087-0.0870.0000.0000.0000.000
70A123THR0-0.008-0.02928.0200.0110.0110.0000.0000.0000.000
71A124LEU0-0.097-0.05224.9520.0090.0090.0000.0000.0000.000
72A125CYS0-0.0070.00529.3310.0100.0100.0000.0000.0000.000
73A126VAL00.0350.02432.3540.0070.0070.0000.0000.0000.000
74A127ILE0-0.0080.00430.4460.0070.0070.0000.0000.0000.000
75A128ALA00.0220.01532.9870.0060.0060.0000.0000.0000.000
76A129VAL00.0400.02434.6970.0060.0060.0000.0000.0000.000
77A130ASP-1-0.782-0.86336.579-0.059-0.0590.0000.0000.0000.000
78A131ARG10.7740.84035.1390.0640.0640.0000.0000.0000.000
79A132TYR00.0320.01838.2090.0040.0040.0000.0000.0000.000
80A133PHE0-0.011-0.02340.5250.0030.0030.0000.0000.0000.000
81A134ALA0-0.064-0.02440.9640.0020.0020.0000.0000.0000.000
82A135ILE0-0.054-0.03240.4080.0020.0020.0000.0000.0000.000
83A136THR0-0.050-0.01643.8450.0020.0020.0000.0000.0000.000
84A137SER0-0.0070.01845.8690.0020.0020.0000.0000.0000.000
85A138PRO00.0140.01247.7730.0010.0010.0000.0000.0000.000
86A139PHE00.004-0.01949.7200.0020.0020.0000.0000.0000.000
87A140LYS10.8940.94347.0860.0280.0280.0000.0000.0000.000
88A141TYR00.0650.04137.807-0.002-0.0020.0000.0000.0000.000
89A142GLN00.022-0.01439.420-0.004-0.0040.0000.0000.0000.000
90A143SER0-0.023-0.02240.3270.0030.0030.0000.0000.0000.000
91A144LEU00.0370.02642.1970.0000.0000.0000.0000.0000.000
92A145LEU0-0.038-0.01139.5380.0010.0010.0000.0000.0000.000
93A146THR00.005-0.01041.428-0.002-0.0020.0000.0000.0000.000
94A147LYS10.9890.98939.0930.0560.0560.0000.0000.0000.000
95A148ASN00.0610.03339.760-0.004-0.0040.0000.0000.0000.000
96A149LYS10.9750.99240.5570.0450.0450.0000.0000.0000.000
97A150ALA00.0430.03737.337-0.001-0.0010.0000.0000.0000.000
98A151ARG10.9620.96136.0930.0700.0700.0000.0000.0000.000
99A152VAL0-0.011-0.00436.483-0.004-0.0040.0000.0000.0000.000
100A153ILE00.0290.01836.606-0.001-0.0010.0000.0000.0000.000
101A154ILE0-0.0010.00631.721-0.003-0.0030.0000.0000.0000.000
102A155LEU0-0.050-0.03532.890-0.006-0.0060.0000.0000.0000.000
103A156MET0-0.040-0.03633.820-0.003-0.0030.0000.0000.0000.000
104A157VAL00.0290.02329.9280.0010.0010.0000.0000.0000.000
105A158TRP0-0.023-0.00124.982-0.007-0.0070.0000.0000.0000.000
106A159ILE00.0530.01929.927-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0180.01732.4210.0010.0010.0000.0000.0000.000
108A161SER00.0060.01026.5090.0000.0000.0000.0000.0000.000
109A162GLY0-0.033-0.01527.764-0.009-0.0090.0000.0000.0000.000
110A163LEU0-0.107-0.04629.2550.0000.0000.0000.0000.0000.000
111A164THR0-0.029-0.00427.3550.0070.0070.0000.0000.0000.000
112A203SER00.1020.03828.0160.0030.0030.0000.0000.0000.000
113A204SER00.0640.03626.544-0.003-0.0030.0000.0000.0000.000
114A205ILE00.0260.00728.4260.0010.0010.0000.0000.0000.000
115A206VAL0-0.018-0.00931.2740.0040.0040.0000.0000.0000.000
116A207SER00.0460.00627.5190.0010.0010.0000.0000.0000.000
117A208PHE00.000-0.01524.345-0.007-0.0070.0000.0000.0000.000
118A209TYR00.0150.00428.2890.0040.0040.0000.0000.0000.000
119A210VAL00.0370.03231.1230.0020.0020.0000.0000.0000.000
120A211PRO00.0070.00929.6310.0050.0050.0000.0000.0000.000
121A212LEU00.005-0.00727.0860.0010.0010.0000.0000.0000.000
122A213VAL0-0.080-0.03630.7610.0050.0050.0000.0000.0000.000
123A214ILE00.0150.00334.0070.0050.0050.0000.0000.0000.000
124A215MET00.0130.03228.1100.0060.0060.0000.0000.0000.000
125A216VAL00.0320.00630.7410.0010.0010.0000.0000.0000.000
126A217PHE0-0.028-0.02733.3820.0050.0050.0000.0000.0000.000
127A218VAL0-0.021-0.00136.8810.0040.0040.0000.0000.0000.000
128A219TYR00.0430.01632.2680.0030.0030.0000.0000.0000.000
129A220SER0-0.0140.00736.0860.0040.0040.0000.0000.0000.000
130A221ARG10.8900.92437.2660.0400.0400.0000.0000.0000.000
131A222VAL00.0120.01537.8890.0030.0030.0000.0000.0000.000
132A223PHE0-0.079-0.03934.8960.0030.0030.0000.0000.0000.000
133A224GLN00.0380.02438.1030.0050.0050.0000.0000.0000.000
134A225GLU-1-0.910-0.93941.262-0.031-0.0310.0000.0000.0000.000
135A226ALA00.0320.01840.5130.0010.0010.0000.0000.0000.000
136A227LYS10.8100.88538.9060.0300.0300.0000.0000.0000.000
137A228ARG10.9760.98043.5940.0270.0270.0000.0000.0000.000
138A229GLN00.0580.02545.9050.0020.0020.0000.0000.0000.000
139A230LEU0-0.0120.00641.8100.0010.0010.0000.0000.0000.000
140A231GLN00.005-0.00545.4700.0030.0030.0000.0000.0000.000
141A232LYS10.9160.99948.4620.0200.0200.0000.0000.0000.000
142A233ILE0-0.039-0.02747.0910.0000.0000.0000.0000.0000.000
143A234ASP-1-0.795-0.87951.297-0.014-0.0140.0000.0000.0000.000
144A235LYS10.9010.93149.7420.0140.0140.0000.0000.0000.000
145A236SER00.018-0.01152.4460.0000.0000.0000.0000.0000.000
146A237GLU-1-0.860-0.93051.409-0.019-0.0190.0000.0000.0000.000
147A238GLY0-0.004-0.00449.8180.0000.0000.0000.0000.0000.000
148A239ARG10.7680.87748.3090.0140.0140.0000.0000.0000.000
149A240PHE00.0200.00752.8380.0010.0010.0000.0000.0000.000
150A241HIS0-0.109-0.04351.8850.0010.0010.0000.0000.0000.000
151A242VAL00.0230.03555.5810.0010.0010.0000.0000.0000.000
152A264PHE0-0.012-0.00440.2320.0000.0000.0000.0000.0000.000
153A265CYS00.0760.04343.4750.0010.0010.0000.0000.0000.000
154A266LEU00.037-0.00340.072-0.002-0.0020.0000.0000.0000.000
155A267LYS10.8930.93237.1150.0430.0430.0000.0000.0000.000
156A268GLU-1-0.793-0.88737.966-0.046-0.0460.0000.0000.0000.000
157A269HIS00.0500.03438.564-0.001-0.0010.0000.0000.0000.000
158A270LYS10.9380.95734.3180.0280.0280.0000.0000.0000.000
159A271ALA00.0170.02433.293-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0420.01433.163-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9130.96228.5500.0480.0480.0000.0000.0000.000
162A274THR0-0.006-0.02128.111-0.002-0.0020.0000.0000.0000.000
163A275LEU0-0.012-0.01327.992-0.007-0.0070.0000.0000.0000.000
164A276GLY00.0680.02629.763-0.003-0.0030.0000.0000.0000.000
165A277ILE0-0.062-0.02625.4180.0020.0020.0000.0000.0000.000
166A278ILE0-0.035-0.00223.767-0.005-0.0050.0000.0000.0000.000
167A279MET0-0.006-0.00524.424-0.010-0.0100.0000.0000.0000.000
168A280GLY00.0050.00126.1130.0000.0000.0000.0000.0000.000
169A281THR0-0.051-0.01119.8830.0080.0080.0000.0000.0000.000
170A282PHE00.0430.01520.389-0.010-0.0100.0000.0000.0000.000
171A283THR0-0.0050.00522.051-0.004-0.0040.0000.0000.0000.000
172A284LEU00.015-0.01221.143-0.001-0.0010.0000.0000.0000.000
173A285CYS0-0.057-0.01117.319-0.006-0.0060.0000.0000.0000.000
174A286TRP00.0300.01716.493-0.022-0.0220.0000.0000.0000.000
175A287LEU00.0340.02420.1340.0080.0080.0000.0000.0000.000
176A288PRO0-0.046-0.03418.9710.0040.0040.0000.0000.0000.000
177A289PHE0-0.0170.00117.063-0.001-0.0010.0000.0000.0000.000
178A290PHE00.0170.00419.9220.0040.0040.0000.0000.0000.000
179A291ILE0-0.077-0.01423.0350.0200.0200.0000.0000.0000.000
180A311LEU00.0360.00113.843-0.023-0.0230.0000.0000.0000.000
181A312ASN00.0190.00212.8650.0350.0350.0000.0000.0000.000
182A313TRP00.0250.0158.784-0.047-0.0470.0000.0000.0000.000
183A314ILE0-0.008-0.00910.851-0.030-0.0300.0000.0000.0000.000
184A315GLY00.0450.02713.1380.0190.0190.0000.0000.0000.000
185A316TYR00.006-0.01110.002-0.003-0.0030.0000.0000.0000.000
186A317VAL00.0430.03210.9890.0010.0010.0000.0000.0000.000
187A318ASN0-0.116-0.06513.1400.0500.0500.0000.0000.0000.000
188A319SER00.044-0.02113.9550.0180.0180.0000.0000.0000.000
189A320GLY0-0.027-0.00414.7900.0110.0110.0000.0000.0000.000
190A321PHE0-0.008-0.01415.7160.0390.0390.0000.0000.0000.000
191A322ASN00.0830.02818.1830.0370.0370.0000.0000.0000.000
192A323PRO0-0.0020.00719.0360.0230.0230.0000.0000.0000.000
193A324LEU0-0.0010.00417.2910.0150.0150.0000.0000.0000.000
194A325ILE0-0.032-0.01820.8140.0210.0210.0000.0000.0000.000
195A326TYR00.013-0.03223.6920.0110.0110.0000.0000.0000.000
196A327CYS0-0.0220.01123.4740.0090.0090.0000.0000.0000.000
197A328ARG10.9460.96025.4560.0230.0230.0000.0000.0000.000
198A329SER0-0.021-0.02627.7020.0030.0030.0000.0000.0000.000
199A330PRO0-0.0390.03728.1240.0050.0050.0000.0000.0000.000
200A331ASP-1-0.907-0.96230.756-0.050-0.0500.0000.0000.0000.000
201A332PHE00.0550.00927.2800.0010.0010.0000.0000.0000.000
202A333ARG10.9260.99726.5790.0370.0370.0000.0000.0000.000
203A334ILE00.012-0.00328.889-0.002-0.0020.0000.0000.0000.000
204A335ALA00.0220.02130.678-0.002-0.0020.0000.0000.0000.000
205A336PHE00.016-0.01023.706-0.002-0.0020.0000.0000.0000.000
206A337GLN0-0.047-0.02524.3020.0030.0030.0000.0000.0000.000
207A338GLU-1-0.956-0.99527.431-0.029-0.0290.0000.0000.0000.000
208A339LEU00.0060.02627.8030.0030.0030.0000.0000.0000.000
209A340LEU0-0.055-0.01523.937-0.001-0.0010.0000.0000.0000.000
210A341CYS0-0.039-0.02828.4150.0050.0050.0000.0000.0000.000
211A342LEU00.0360.02231.5650.0040.0040.0000.0000.0000.000
212A343ARG11.0191.02421.8240.0390.0390.0000.0000.0000.000
213A344ARG10.9410.95524.595-0.001-0.0010.0000.0000.0000.000
214A345SER0-0.007-0.00830.2050.0030.0030.0000.0000.0000.000
215A346SER00.0500.05032.871-0.001-0.0010.0000.0000.0000.000
216A347LEU0-0.003-0.01834.8120.0010.0010.0000.0000.0000.000
217A348LYS10.8990.96930.3730.0120.0120.0000.0000.0000.000