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

tag_button

FMODB ID: R94K8

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 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 -2559845.930365
FMO2-HF: Nuclear repulsion 2473312.354841
FMO2-HF: Total energy -86533.575525
FMO2-MP2: Total energy -86783.806025


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.
-4.899-1.5313.643-2.424-4.5860.008
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 : 0.069 / 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].
3A39VAL00.0250.0092.786-2.776-0.6991.223-1.265-2.0340.010
4A40MET0-0.013-0.0092.357-3.150-2.0932.420-1.107-2.371-0.002
5A41SER00.0530.0353.9600.3650.5990.000-0.052-0.1810.000
6A42LEU0-0.033-0.0146.3800.3280.3280.0000.0000.0000.000
7A43ILE0-0.044-0.0326.0260.2100.2100.0000.0000.0000.000
8A44VAL00.0560.0298.1230.0790.0790.0000.0000.0000.000
9A45LEU00.0400.01210.8140.1230.1230.0000.0000.0000.000
10A46ALA0-0.021-0.01312.3360.0870.0870.0000.0000.0000.000
11A47ILE0-0.0380.00812.0620.0510.0510.0000.0000.0000.000
12A48VAL00.0050.00014.6700.0260.0260.0000.0000.0000.000
13A49PHE00.0150.02016.9720.0430.0430.0000.0000.0000.000
14A50GLY00.0110.00517.9400.0270.0270.0000.0000.0000.000
15A51ASN0-0.015-0.02317.6140.0460.0460.0000.0000.0000.000
16A52VAL00.0180.00020.9860.0130.0130.0000.0000.0000.000
17A53LEU0-0.023-0.02122.0400.0180.0180.0000.0000.0000.000
18A54VAL0-0.010-0.00823.8540.0160.0160.0000.0000.0000.000
19A55ILE00.0340.01824.3590.0110.0110.0000.0000.0000.000
20A56THR00.0220.01327.0330.0090.0090.0000.0000.0000.000
21A57ALA0-0.0010.01328.2670.0080.0080.0000.0000.0000.000
22A58ILE0-0.069-0.02729.3480.0080.0080.0000.0000.0000.000
23A59ALA0-0.045-0.02731.0670.0070.0070.0000.0000.0000.000
24A60LYS10.7740.83032.5330.0660.0660.0000.0000.0000.000
25A61PHE00.0470.06631.7720.0030.0030.0000.0000.0000.000
26A62GLU-1-0.821-0.91235.803-0.055-0.0550.0000.0000.0000.000
27A63ARG10.9560.96937.9740.0420.0420.0000.0000.0000.000
28A64LEU0-0.0090.00831.4540.0010.0010.0000.0000.0000.000
29A65GLN0-0.0040.03434.350-0.007-0.0070.0000.0000.0000.000
30A66THR0-0.034-0.03735.7230.0030.0030.0000.0000.0000.000
31A67VAL00.0670.02635.523-0.004-0.0040.0000.0000.0000.000
32A68THR00.0470.03032.711-0.004-0.0040.0000.0000.0000.000
33A69ASN0-0.034-0.02731.307-0.008-0.0080.0000.0000.0000.000
34A70TYR00.0210.01331.642-0.003-0.0030.0000.0000.0000.000
35A71PHE00.013-0.00330.860-0.004-0.0040.0000.0000.0000.000
36A72ILE00.0000.01326.622-0.007-0.0070.0000.0000.0000.000
37A73THR0-0.002-0.00426.328-0.009-0.0090.0000.0000.0000.000
38A74SER0-0.0050.01027.161-0.008-0.0080.0000.0000.0000.000
39A75LEU0-0.006-0.01423.420-0.007-0.0070.0000.0000.0000.000
40A76ALA00.0040.01922.238-0.015-0.0150.0000.0000.0000.000
41A77CYS00.006-0.00621.688-0.018-0.0180.0000.0000.0000.000
42A78ALA0-0.025-0.01221.748-0.010-0.0100.0000.0000.0000.000
43A79ASP-1-0.774-0.84017.304-0.322-0.3220.0000.0000.0000.000
44A80LEU0-0.0090.00516.933-0.034-0.0340.0000.0000.0000.000
45A81VAL00.0540.01217.737-0.027-0.0270.0000.0000.0000.000
46A82MET0-0.006-0.00815.0790.0000.0000.0000.0000.0000.000
47A83GLY00.038-0.00713.510-0.051-0.0510.0000.0000.0000.000
48A84LEU0-0.071-0.04013.434-0.062-0.0620.0000.0000.0000.000
49A85ALA0-0.021-0.01815.8410.0300.0300.0000.0000.0000.000
50A86VAL00.0010.02013.8120.0120.0120.0000.0000.0000.000
51A87VAL00.0540.0308.843-0.029-0.0290.0000.0000.0000.000
52A88PRO0-0.0360.0079.575-0.115-0.1150.0000.0000.0000.000
53A89PHE0-0.062-0.02810.307-0.055-0.0550.0000.0000.0000.000
54A90GLY0-0.0300.0038.201-0.103-0.1030.0000.0000.0000.000
55A108PHE00.0460.00321.801-0.001-0.0010.0000.0000.0000.000
56A109TRP0-0.005-0.02012.5800.0240.0240.0000.0000.0000.000
57A110THR00.0420.02017.712-0.016-0.0160.0000.0000.0000.000
58A111SER0-0.030-0.00619.6370.0110.0110.0000.0000.0000.000
59A112ILE0-0.021-0.01618.6830.0110.0110.0000.0000.0000.000
60A113ASP-1-0.878-0.93416.308-0.328-0.3280.0000.0000.0000.000
61A114VAL00.0200.01019.1140.0010.0010.0000.0000.0000.000
62A115LEU0-0.0220.00522.3570.0060.0060.0000.0000.0000.000
63A116CYS0-0.029-0.01820.0110.0070.0070.0000.0000.0000.000
64A117VAL00.023-0.00118.6860.0100.0100.0000.0000.0000.000
65A118THR0-0.018-0.01721.8170.0120.0120.0000.0000.0000.000
66A119ALA00.0310.02924.9050.0130.0130.0000.0000.0000.000
67A120SER0-0.019-0.00322.8210.0080.0080.0000.0000.0000.000
68A121ILE0-0.033-0.00925.1440.0100.0100.0000.0000.0000.000
69A122GLU-1-0.823-0.90326.728-0.087-0.0870.0000.0000.0000.000
70A123THR0-0.006-0.03027.9600.0120.0120.0000.0000.0000.000
71A124LEU0-0.103-0.05724.9380.0090.0090.0000.0000.0000.000
72A125CYS0-0.0100.00629.2800.0100.0100.0000.0000.0000.000
73A126VAL00.0290.02232.2970.0070.0070.0000.0000.0000.000
74A127ILE0-0.0050.00030.4290.0070.0070.0000.0000.0000.000
75A128ALA00.0190.01233.0020.0060.0060.0000.0000.0000.000
76A129VAL00.0460.02634.7030.0060.0060.0000.0000.0000.000
77A130ASP-1-0.785-0.86236.553-0.059-0.0590.0000.0000.0000.000
78A131ARG10.7820.84535.1150.0640.0640.0000.0000.0000.000
79A132TYR00.0320.01338.1810.0040.0040.0000.0000.0000.000
80A133PHE0-0.004-0.02040.4760.0030.0030.0000.0000.0000.000
81A134ALA0-0.074-0.02840.9290.0020.0020.0000.0000.0000.000
82A135ILE0-0.053-0.02839.8740.0020.0020.0000.0000.0000.000
83A136THR0-0.056-0.01943.7960.0020.0020.0000.0000.0000.000
84A137SER00.0020.01845.8110.0020.0020.0000.0000.0000.000
85A138PRO00.0050.01047.6860.0010.0010.0000.0000.0000.000
86A139PHE00.004-0.01849.7280.0020.0020.0000.0000.0000.000
87A140LYS10.8950.94247.0660.0280.0280.0000.0000.0000.000
88A141TYR00.0630.04137.793-0.002-0.0020.0000.0000.0000.000
89A142GLN00.024-0.01339.355-0.004-0.0040.0000.0000.0000.000
90A143SER0-0.023-0.02140.3000.0030.0030.0000.0000.0000.000
91A144LEU00.0350.02642.1690.0000.0000.0000.0000.0000.000
92A145LEU0-0.038-0.01139.5260.0010.0010.0000.0000.0000.000
93A146THR00.012-0.00841.375-0.002-0.0020.0000.0000.0000.000
94A147LYS10.9820.98139.0200.0560.0560.0000.0000.0000.000
95A148ASN00.0590.03539.792-0.004-0.0040.0000.0000.0000.000
96A149LYS10.9870.99640.6120.0450.0450.0000.0000.0000.000
97A150ALA00.0420.03937.304-0.002-0.0020.0000.0000.0000.000
98A151ARG10.9450.96036.1060.0700.0700.0000.0000.0000.000
99A152VAL0-0.018-0.01236.564-0.003-0.0030.0000.0000.0000.000
100A153ILE00.0290.01436.654-0.001-0.0010.0000.0000.0000.000
101A154ILE00.0050.00331.505-0.002-0.0020.0000.0000.0000.000
102A155LEU0-0.035-0.02232.827-0.006-0.0060.0000.0000.0000.000
103A156MET0-0.048-0.03433.922-0.002-0.0020.0000.0000.0000.000
104A157VAL00.0220.01829.9490.0010.0010.0000.0000.0000.000
105A158TRP0-0.021-0.00124.880-0.008-0.0080.0000.0000.0000.000
106A159ILE00.0550.01729.941-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0120.01432.4430.0010.0010.0000.0000.0000.000
108A161SER00.0110.01426.5800.0000.0000.0000.0000.0000.000
109A162GLY0-0.027-0.01227.755-0.009-0.0090.0000.0000.0000.000
110A163LEU0-0.105-0.04529.2340.0000.0000.0000.0000.0000.000
111A164THR0-0.027-0.00127.3340.0070.0070.0000.0000.0000.000
112A203SER00.1020.03828.0170.0030.0030.0000.0000.0000.000
113A204SER00.0600.03726.535-0.003-0.0030.0000.0000.0000.000
114A205ILE00.0230.00428.4190.0010.0010.0000.0000.0000.000
115A206VAL0-0.021-0.01131.2390.0050.0050.0000.0000.0000.000
116A207SER00.0470.00427.5570.0020.0020.0000.0000.0000.000
117A208PHE0-0.003-0.01524.308-0.007-0.0070.0000.0000.0000.000
118A209TYR00.0190.00528.2640.0040.0040.0000.0000.0000.000
119A210VAL00.0380.03331.1210.0020.0020.0000.0000.0000.000
120A211PRO00.0030.00629.5750.0050.0050.0000.0000.0000.000
121A212LEU00.009-0.00727.0450.0010.0010.0000.0000.0000.000
122A213VAL0-0.073-0.03130.7650.0050.0050.0000.0000.0000.000
123A214ILE00.0150.00233.9840.0050.0050.0000.0000.0000.000
124A215MET00.0090.03028.0280.0050.0050.0000.0000.0000.000
125A216VAL00.0310.00630.6830.0010.0010.0000.0000.0000.000
126A217PHE0-0.033-0.03133.3370.0050.0050.0000.0000.0000.000
127A218VAL0-0.027-0.00636.8060.0040.0040.0000.0000.0000.000
128A219TYR00.0430.01632.2490.0030.0030.0000.0000.0000.000
129A220SER0-0.0130.00936.0380.0040.0040.0000.0000.0000.000
130A221ARG10.9050.93437.2520.0390.0390.0000.0000.0000.000
131A222VAL00.0140.02037.4530.0030.0030.0000.0000.0000.000
132A223PHE0-0.069-0.03434.8730.0030.0030.0000.0000.0000.000
133A224GLN00.0330.02038.1100.0050.0050.0000.0000.0000.000
134A225GLU-1-0.901-0.93541.242-0.031-0.0310.0000.0000.0000.000
135A226ALA00.0120.01240.4420.0010.0010.0000.0000.0000.000
136A227LYS10.8110.88238.8650.0300.0300.0000.0000.0000.000
137A228ARG10.9750.98043.5320.0270.0270.0000.0000.0000.000
138A229GLN00.0590.02545.9540.0020.0020.0000.0000.0000.000
139A230LEU0-0.0030.01041.7710.0010.0010.0000.0000.0000.000
140A231GLN00.007-0.00145.4610.0030.0030.0000.0000.0000.000
141A232LYS10.9080.99248.4430.0200.0200.0000.0000.0000.000
142A233ILE0-0.040-0.02647.0600.0000.0000.0000.0000.0000.000
143A234ASP-1-0.799-0.88351.303-0.014-0.0140.0000.0000.0000.000
144A235LYS10.9110.93549.9010.0140.0140.0000.0000.0000.000
145A236SER00.017-0.00752.4790.0000.0000.0000.0000.0000.000
146A237GLU-1-0.872-0.93751.238-0.019-0.0190.0000.0000.0000.000
147A238GLY0-0.007-0.00649.8240.0000.0000.0000.0000.0000.000
148A239ARG10.7830.88448.4380.0140.0140.0000.0000.0000.000
149A240PHE00.0120.00152.9820.0010.0010.0000.0000.0000.000
150A241HIS0-0.114-0.04351.7730.0010.0010.0000.0000.0000.000
151A242VAL00.0270.03655.4880.0010.0010.0000.0000.0000.000
152A264PHE0-0.017-0.00540.1800.0000.0000.0000.0000.0000.000
153A265CYS00.0740.04243.5190.0010.0010.0000.0000.0000.000
154A266LEU00.039-0.00240.118-0.002-0.0020.0000.0000.0000.000
155A267LYS10.9130.94336.5930.0430.0430.0000.0000.0000.000
156A268GLU-1-0.811-0.89637.907-0.047-0.0470.0000.0000.0000.000
157A269HIS00.0540.03238.518-0.001-0.0010.0000.0000.0000.000
158A270LYS10.9380.95834.3080.0280.0280.0000.0000.0000.000
159A271ALA00.0170.01933.231-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0440.02033.191-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9030.95428.5380.0480.0480.0000.0000.0000.000
162A274THR0-0.006-0.02028.128-0.002-0.0020.0000.0000.0000.000
163A275LEU0-0.008-0.01227.934-0.007-0.0070.0000.0000.0000.000
164A276GLY00.0640.02529.716-0.003-0.0030.0000.0000.0000.000
165A277ILE0-0.057-0.02325.3800.0020.0020.0000.0000.0000.000
166A278ILE0-0.038-0.00423.779-0.005-0.0050.0000.0000.0000.000
167A279MET0-0.010-0.00524.514-0.010-0.0100.0000.0000.0000.000
168A280GLY00.0060.00126.1280.0010.0010.0000.0000.0000.000
169A281THR0-0.048-0.00619.8800.0080.0080.0000.0000.0000.000
170A282PHE00.0370.01020.334-0.009-0.0090.0000.0000.0000.000
171A283THR0-0.0010.00522.033-0.004-0.0040.0000.0000.0000.000
172A284LEU00.015-0.01121.0850.0000.0000.0000.0000.0000.000
173A285CYS0-0.059-0.01217.247-0.005-0.0050.0000.0000.0000.000
174A286TRP00.0330.01916.501-0.022-0.0220.0000.0000.0000.000
175A287LEU00.0380.02820.1130.0090.0090.0000.0000.0000.000
176A288PRO0-0.053-0.04018.8620.0050.0050.0000.0000.0000.000
177A289PHE0-0.0140.00217.091-0.002-0.0020.0000.0000.0000.000
178A290PHE00.0110.00119.8990.0050.0050.0000.0000.0000.000
179A291ILE0-0.072-0.01023.0520.0200.0200.0000.0000.0000.000
180A311LEU00.033-0.00113.817-0.022-0.0220.0000.0000.0000.000
181A312ASN00.0190.00312.8980.0370.0370.0000.0000.0000.000
182A313TRP00.0250.0148.741-0.049-0.0490.0000.0000.0000.000
183A314ILE0-0.006-0.00910.801-0.030-0.0300.0000.0000.0000.000
184A315GLY00.0470.03113.0880.0200.0200.0000.0000.0000.000
185A316TYR00.004-0.0149.979-0.002-0.0020.0000.0000.0000.000
186A317VAL00.0370.03010.974-0.003-0.0030.0000.0000.0000.000
187A318ASN0-0.114-0.06513.1370.0510.0510.0000.0000.0000.000
188A319SER00.046-0.02013.9360.0170.0170.0000.0000.0000.000
189A320GLY0-0.0200.00014.8070.0110.0110.0000.0000.0000.000
190A321PHE0-0.011-0.01515.7310.0390.0390.0000.0000.0000.000
191A322ASN00.0890.03018.2140.0370.0370.0000.0000.0000.000
192A323PRO0-0.0010.00819.0140.0240.0240.0000.0000.0000.000
193A324LEU0-0.0060.00317.2580.0140.0140.0000.0000.0000.000
194A325ILE0-0.038-0.01920.7820.0210.0210.0000.0000.0000.000
195A326TYR00.021-0.02823.6650.0110.0110.0000.0000.0000.000
196A327CYS0-0.0210.01123.4820.0090.0090.0000.0000.0000.000
197A328ARG10.9460.96025.5170.0230.0230.0000.0000.0000.000
198A329SER0-0.020-0.02527.7340.0030.0030.0000.0000.0000.000
199A330PRO0-0.0390.03628.1260.0050.0050.0000.0000.0000.000
200A331ASP-1-0.916-0.96730.741-0.051-0.0510.0000.0000.0000.000
201A332PHE00.0590.01227.2860.0020.0020.0000.0000.0000.000
202A333ARG10.9260.99926.5820.0380.0380.0000.0000.0000.000
203A334ILE00.011-0.00428.904-0.002-0.0020.0000.0000.0000.000
204A335ALA00.0150.01830.684-0.002-0.0020.0000.0000.0000.000
205A336PHE00.022-0.01023.699-0.002-0.0020.0000.0000.0000.000
206A337GLN0-0.050-0.02524.2990.0030.0030.0000.0000.0000.000
207A338GLU-1-0.959-0.99727.458-0.030-0.0300.0000.0000.0000.000
208A339LEU00.0130.03027.7700.0030.0030.0000.0000.0000.000
209A340LEU0-0.048-0.01123.952-0.001-0.0010.0000.0000.0000.000
210A341CYS0-0.040-0.02928.4450.0050.0050.0000.0000.0000.000
211A342LEU00.0340.02031.6130.0040.0040.0000.0000.0000.000
212A343ARG11.0191.02421.8380.0410.0410.0000.0000.0000.000
213A344ARG10.9400.95424.6040.0000.0000.0000.0000.0000.000
214A345SER0-0.009-0.00930.2250.0030.0030.0000.0000.0000.000
215A346SER00.0530.05132.869-0.001-0.0010.0000.0000.0000.000
216A347LEU0-0.005-0.01934.7870.0010.0010.0000.0000.0000.000
217A348LYS10.9000.97030.3830.0130.0130.0000.0000.0000.000