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: QY54Y

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 OptAll
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 -2564624.63741
FMO2-HF: Nuclear repulsion 2478088.748596
FMO2-HF: Total energy -86535.888814
FMO2-MP2: Total energy -86785.712162


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.
-4.356-2.6135.775-2.983-4.5360.005
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 : 0.068 / q_NPA : 0.017
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].
3A39VAL00.0150.0073.365-2.565-0.5450.140-1.042-1.1180.006
4A40MET0-0.005-0.0032.280-3.163-3.8505.633-1.795-3.152-0.001
5A41SER00.0310.0143.7600.4830.8930.002-0.146-0.2660.000
6A42LEU0-0.011-0.0045.9700.3810.3810.0000.0000.0000.000
7A43ILE0-0.011-0.0106.0740.1940.1940.0000.0000.0000.000
8A44VAL00.0410.0177.2070.1210.1210.0000.0000.0000.000
9A45LEU00.0320.0199.9950.1440.1440.0000.0000.0000.000
10A46ALA0-0.033-0.00812.1510.0890.0890.0000.0000.0000.000
11A47ILE00.0000.01711.4540.0680.0680.0000.0000.0000.000
12A48VAL00.0300.03314.3000.0360.0360.0000.0000.0000.000
13A49PHE00.009-0.00716.4770.0480.0480.0000.0000.0000.000
14A50GLY00.008-0.00117.5920.0310.0310.0000.0000.0000.000
15A51ASN0-0.022-0.04417.6240.0530.0530.0000.0000.0000.000
16A52VAL00.0210.01420.5490.0220.0220.0000.0000.0000.000
17A53LEU0-0.035-0.01521.7010.0210.0210.0000.0000.0000.000
18A54VAL0-0.025-0.01523.3680.0170.0170.0000.0000.0000.000
19A55ILE00.0230.00324.1230.0130.0130.0000.0000.0000.000
20A56THR00.003-0.00126.5190.0110.0110.0000.0000.0000.000
21A57ALA0-0.0230.00028.2040.0090.0090.0000.0000.0000.000
22A58ILE0-0.046-0.03129.3220.0090.0090.0000.0000.0000.000
23A59ALA0-0.042-0.02630.7360.0060.0060.0000.0000.0000.000
24A60LYS10.7930.87132.4320.0680.0680.0000.0000.0000.000
25A61PHE00.0860.06631.6110.0030.0030.0000.0000.0000.000
26A62GLU-1-0.817-0.89535.781-0.057-0.0570.0000.0000.0000.000
27A63ARG10.9500.96637.6430.0450.0450.0000.0000.0000.000
28A64LEU00.0220.02231.4190.0010.0010.0000.0000.0000.000
29A65GLN0-0.0210.02834.468-0.006-0.0060.0000.0000.0000.000
30A66THR0-0.002-0.01535.6860.0020.0020.0000.0000.0000.000
31A67VAL00.0220.00835.470-0.004-0.0040.0000.0000.0000.000
32A68THR00.0290.01132.354-0.003-0.0030.0000.0000.0000.000
33A69ASN0-0.009-0.01631.115-0.008-0.0080.0000.0000.0000.000
34A70TYR00.0320.02730.778-0.006-0.0060.0000.0000.0000.000
35A71PHE00.0110.01030.831-0.006-0.0060.0000.0000.0000.000
36A72ILE00.002-0.00126.613-0.008-0.0080.0000.0000.0000.000
37A73THR00.018-0.00126.241-0.012-0.0120.0000.0000.0000.000
38A74SER00.0050.01226.316-0.008-0.0080.0000.0000.0000.000
39A75LEU00.008-0.00123.410-0.009-0.0090.0000.0000.0000.000
40A76ALA00.0080.01521.997-0.017-0.0170.0000.0000.0000.000
41A77CYS0-0.052-0.02621.445-0.018-0.0180.0000.0000.0000.000
42A78ALA0-0.040-0.00821.623-0.014-0.0140.0000.0000.0000.000
43A79ASP-1-0.765-0.84117.254-0.342-0.3420.0000.0000.0000.000
44A80LEU00.001-0.00216.813-0.039-0.0390.0000.0000.0000.000
45A81VAL00.004-0.00317.464-0.026-0.0260.0000.0000.0000.000
46A82MET00.0500.02414.744-0.012-0.0120.0000.0000.0000.000
47A83GLY00.011-0.00413.136-0.061-0.0610.0000.0000.0000.000
48A84LEU0-0.045-0.03313.258-0.052-0.0520.0000.0000.0000.000
49A85ALA0-0.029-0.00915.6430.0140.0140.0000.0000.0000.000
50A86VAL0-0.0050.00813.3490.0210.0210.0000.0000.0000.000
51A87VAL00.0400.0118.482-0.035-0.0350.0000.0000.0000.000
52A88PRO0-0.048-0.0089.186-0.117-0.1170.0000.0000.0000.000
53A89PHE0-0.044-0.02410.050-0.019-0.0190.0000.0000.0000.000
54A90GLY0-0.047-0.0027.644-0.090-0.0900.0000.0000.0000.000
55A108PHE00.0450.00721.118-0.001-0.0010.0000.0000.0000.000
56A109TRP00.006-0.00312.4600.0300.0300.0000.0000.0000.000
57A110THR00.0520.01017.654-0.006-0.0060.0000.0000.0000.000
58A111SER0-0.023-0.00819.0210.0070.0070.0000.0000.0000.000
59A112ILE0-0.010-0.00918.6140.0100.0100.0000.0000.0000.000
60A113ASP-1-0.849-0.90515.772-0.328-0.3280.0000.0000.0000.000
61A114VAL00.0290.00718.4200.0060.0060.0000.0000.0000.000
62A115LEU0-0.0320.00221.7200.0060.0060.0000.0000.0000.000
63A116CYS0-0.032-0.01619.2500.0070.0070.0000.0000.0000.000
64A117VAL00.0320.02418.4440.0120.0120.0000.0000.0000.000
65A118THR0-0.016-0.02921.2320.0130.0130.0000.0000.0000.000
66A119ALA00.0360.03124.7700.0120.0120.0000.0000.0000.000
67A120SER0-0.054-0.02022.0970.0090.0090.0000.0000.0000.000
68A121ILE0-0.009-0.00624.4980.0110.0110.0000.0000.0000.000
69A122GLU-1-0.830-0.91626.388-0.084-0.0840.0000.0000.0000.000
70A123THR0-0.033-0.03627.4210.0110.0110.0000.0000.0000.000
71A124LEU0-0.058-0.03524.7350.0090.0090.0000.0000.0000.000
72A125CYS0-0.043-0.00529.1590.0110.0110.0000.0000.0000.000
73A126VAL00.0280.01832.2170.0080.0080.0000.0000.0000.000
74A127ILE0-0.041-0.02329.8970.0060.0060.0000.0000.0000.000
75A128ALA00.0060.00833.1420.0060.0060.0000.0000.0000.000
76A129VAL00.0450.02334.7430.0060.0060.0000.0000.0000.000
77A130ASP-1-0.750-0.84736.238-0.061-0.0610.0000.0000.0000.000
78A131ARG10.7610.84135.1500.0660.0660.0000.0000.0000.000
79A132TYR00.0240.01238.1240.0030.0030.0000.0000.0000.000
80A133PHE00.001-0.00140.5780.0040.0040.0000.0000.0000.000
81A134ALA0-0.076-0.03440.5680.0020.0020.0000.0000.0000.000
82A135ILE0-0.064-0.04239.7860.0020.0020.0000.0000.0000.000
83A136THR0-0.014-0.00843.8220.0020.0020.0000.0000.0000.000
84A137SER0-0.0070.01645.9950.0020.0020.0000.0000.0000.000
85A138PRO00.0080.01647.8300.0010.0010.0000.0000.0000.000
86A139PHE00.022-0.01449.4570.0020.0020.0000.0000.0000.000
87A140LYS10.9020.95747.1480.0290.0290.0000.0000.0000.000
88A141TYR00.0210.01437.258-0.002-0.0020.0000.0000.0000.000
89A142GLN00.018-0.00439.677-0.004-0.0040.0000.0000.0000.000
90A143SER0-0.011-0.00740.0940.0030.0030.0000.0000.0000.000
91A144LEU00.0190.00742.1000.0000.0000.0000.0000.0000.000
92A145LEU0-0.0120.00239.1800.0010.0010.0000.0000.0000.000
93A146THR0-0.001-0.01640.948-0.002-0.0020.0000.0000.0000.000
94A147LYS10.9070.94238.4290.0580.0580.0000.0000.0000.000
95A148ASN00.0490.03839.276-0.004-0.0040.0000.0000.0000.000
96A149LYS11.0020.99640.1280.0460.0460.0000.0000.0000.000
97A150ALA00.0300.02036.793-0.002-0.0020.0000.0000.0000.000
98A151ARG10.9290.95735.5180.0720.0720.0000.0000.0000.000
99A152VAL00.0030.00635.840-0.004-0.0040.0000.0000.0000.000
100A153ILE00.0450.01335.813-0.001-0.0010.0000.0000.0000.000
101A154ILE00.002-0.00131.138-0.003-0.0030.0000.0000.0000.000
102A155LEU0-0.023-0.00532.262-0.006-0.0060.0000.0000.0000.000
103A156MET0-0.013-0.01533.468-0.002-0.0020.0000.0000.0000.000
104A157VAL00.0300.01829.543-0.001-0.0010.0000.0000.0000.000
105A158TRP0-0.032-0.01624.269-0.006-0.0060.0000.0000.0000.000
106A159ILE00.003-0.00429.586-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0060.00332.0840.0000.0000.0000.0000.0000.000
108A161SER00.0030.00126.479-0.002-0.0020.0000.0000.0000.000
109A162GLY0-0.0130.00227.350-0.010-0.0100.0000.0000.0000.000
110A163LEU0-0.072-0.02728.9960.0010.0010.0000.0000.0000.000
111A164THR0-0.0120.00426.7320.0060.0060.0000.0000.0000.000
112A203SER00.0890.03727.7380.0030.0030.0000.0000.0000.000
113A204SER00.0390.01726.106-0.002-0.0020.0000.0000.0000.000
114A205ILE00.0230.01028.0440.0010.0010.0000.0000.0000.000
115A206VAL00.0120.00831.4730.0030.0030.0000.0000.0000.000
116A207SER00.0290.00027.6890.0020.0020.0000.0000.0000.000
117A208PHE00.010-0.00724.016-0.009-0.0090.0000.0000.0000.000
118A209TYR00.0010.00427.8800.0040.0040.0000.0000.0000.000
119A210VAL00.0180.01630.7710.0040.0040.0000.0000.0000.000
120A211PRO00.0300.02129.5770.0040.0040.0000.0000.0000.000
121A212LEU0-0.006-0.00326.8530.0030.0030.0000.0000.0000.000
122A213VAL0-0.019-0.01230.5590.0050.0050.0000.0000.0000.000
123A214ILE0-0.003-0.00433.9240.0050.0050.0000.0000.0000.000
124A215MET0-0.0060.01127.7870.0060.0060.0000.0000.0000.000
125A216VAL00.0240.00230.5820.0030.0030.0000.0000.0000.000
126A217PHE00.000-0.00233.1250.0050.0050.0000.0000.0000.000
127A218VAL0-0.0100.00036.7240.0040.0040.0000.0000.0000.000
128A219TYR00.018-0.00832.7700.0030.0030.0000.0000.0000.000
129A220SER0-0.030-0.00635.6790.0040.0040.0000.0000.0000.000
130A221ARG10.8750.92037.1890.0410.0410.0000.0000.0000.000
131A222VAL00.0040.01337.3380.0030.0030.0000.0000.0000.000
132A223PHE0-0.035-0.01335.1690.0040.0040.0000.0000.0000.000
133A224GLN00.0420.00638.3860.0050.0050.0000.0000.0000.000
134A225GLU-1-0.836-0.90941.572-0.033-0.0330.0000.0000.0000.000
135A226ALA00.0060.00140.4490.0020.0020.0000.0000.0000.000
136A227LYS10.8200.90338.3680.0340.0340.0000.0000.0000.000
137A228ARG10.9530.98343.1730.0290.0290.0000.0000.0000.000
138A229GLN00.0400.01545.5640.0020.0020.0000.0000.0000.000
139A230LEU0-0.039-0.01641.5410.0010.0010.0000.0000.0000.000
140A231GLN0-0.038-0.01845.4660.0030.0030.0000.0000.0000.000
141A232LYS11.0081.01948.5200.0210.0210.0000.0000.0000.000
142A233ILE0-0.061-0.02046.8290.0000.0000.0000.0000.0000.000
143A234ASP-1-0.776-0.87051.186-0.016-0.0160.0000.0000.0000.000
144A235LYS10.8810.91750.2950.0160.0160.0000.0000.0000.000
145A236SER00.017-0.00653.2290.0010.0010.0000.0000.0000.000
146A237GLU-1-0.803-0.91050.973-0.021-0.0210.0000.0000.0000.000
147A238GLY0-0.075-0.04349.4420.0000.0000.0000.0000.0000.000
148A239ARG10.7930.90148.4390.0160.0160.0000.0000.0000.000
149A240PHE0-0.0020.01252.8020.0010.0010.0000.0000.0000.000
150A241HIS0-0.076-0.02752.1300.0010.0010.0000.0000.0000.000
151A242VAL0-0.0020.00655.8260.0010.0010.0000.0000.0000.000
152A264PHE00.0210.01040.0320.0000.0000.0000.0000.0000.000
153A265CYS00.0330.02243.1410.0010.0010.0000.0000.0000.000
154A266LEU00.0500.01340.097-0.003-0.0030.0000.0000.0000.000
155A267LYS10.9110.94436.7320.0450.0450.0000.0000.0000.000
156A268GLU-1-0.773-0.89637.684-0.051-0.0510.0000.0000.0000.000
157A269HIS00.0420.03237.607-0.002-0.0020.0000.0000.0000.000
158A270LYS10.9330.96434.2060.0310.0310.0000.0000.0000.000
159A271ALA00.0080.01633.136-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0390.01032.933-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9230.97528.6600.0510.0510.0000.0000.0000.000
162A274THR0-0.011-0.01528.033-0.002-0.0020.0000.0000.0000.000
163A275LEU00.0060.00127.996-0.007-0.0070.0000.0000.0000.000
164A276GLY00.0540.02729.066-0.004-0.0040.0000.0000.0000.000
165A277ILE0-0.053-0.03225.5470.0000.0000.0000.0000.0000.000
166A278ILE0-0.035-0.00123.754-0.006-0.0060.0000.0000.0000.000
167A279MET0-0.002-0.00624.290-0.010-0.0100.0000.0000.0000.000
168A280GLY0-0.0040.00025.756-0.003-0.0030.0000.0000.0000.000
169A281THR0-0.050-0.02919.7300.0020.0020.0000.0000.0000.000
170A282PHE00.0420.02020.666-0.007-0.0070.0000.0000.0000.000
171A283THR00.005-0.00321.931-0.007-0.0070.0000.0000.0000.000
172A284LEU00.022-0.00421.029-0.001-0.0010.0000.0000.0000.000
173A285CYS0-0.085-0.02817.165-0.005-0.0050.0000.0000.0000.000
174A286TRP00.0300.03416.336-0.023-0.0230.0000.0000.0000.000
175A287LEU0-0.0070.00320.1930.0050.0050.0000.0000.0000.000
176A288PRO0-0.026-0.01918.5070.0060.0060.0000.0000.0000.000
177A289PHE0-0.0310.00517.026-0.004-0.0040.0000.0000.0000.000
178A290PHE00.016-0.01019.7650.0100.0100.0000.0000.0000.000
179A291ILE0-0.088-0.02422.9630.0200.0200.0000.0000.0000.000
180A311LEU00.0360.00314.042-0.019-0.0190.0000.0000.0000.000
181A312ASN00.0140.00212.8950.0210.0210.0000.0000.0000.000
182A313TRP00.0200.0108.959-0.037-0.0370.0000.0000.0000.000
183A314ILE0-0.0020.00010.973-0.030-0.0300.0000.0000.0000.000
184A315GLY00.0570.02213.3830.0110.0110.0000.0000.0000.000
185A316TYR0-0.032-0.04310.163-0.006-0.0060.0000.0000.0000.000
186A317VAL0-0.018-0.00110.723-0.028-0.0280.0000.0000.0000.000
187A318ASN00.015-0.00912.8880.0530.0530.0000.0000.0000.000
188A319SER0-0.014-0.03213.8910.0230.0230.0000.0000.0000.000
189A320GLY0-0.0080.00414.3110.0160.0160.0000.0000.0000.000
190A321PHE0-0.036-0.02215.2150.0470.0470.0000.0000.0000.000
191A322ASN00.0490.01618.0020.0390.0390.0000.0000.0000.000
192A323PRO00.0540.01818.6110.0250.0250.0000.0000.0000.000
193A324LEU00.0210.02617.1420.0220.0220.0000.0000.0000.000
194A325ILE0-0.005-0.01020.5180.0220.0220.0000.0000.0000.000
195A326TYR00.020-0.01223.5550.0140.0140.0000.0000.0000.000
196A327CYS0-0.045-0.00523.1080.0080.0080.0000.0000.0000.000
197A328ARG10.9180.94325.3090.0370.0370.0000.0000.0000.000
198A329SER0-0.037-0.01927.5170.0040.0040.0000.0000.0000.000
199A330PRO0-0.0130.03028.3520.0050.0050.0000.0000.0000.000
200A331ASP-1-0.925-0.97430.883-0.055-0.0550.0000.0000.0000.000
201A332PHE00.0620.01727.5370.0030.0030.0000.0000.0000.000
202A333ARG10.8600.94027.6160.0440.0440.0000.0000.0000.000
203A334ILE00.0110.00729.0530.0020.0020.0000.0000.0000.000
204A335ALA00.0110.01630.803-0.002-0.0020.0000.0000.0000.000
205A336PHE00.036-0.00723.5900.0000.0000.0000.0000.0000.000
206A337GLN00.0050.02624.2420.0050.0050.0000.0000.0000.000
207A338GLU-1-0.844-0.95727.083-0.034-0.0340.0000.0000.0000.000
208A339LEU00.0290.03427.4750.0040.0040.0000.0000.0000.000
209A340LEU0-0.035-0.00223.8140.0000.0000.0000.0000.0000.000
210A341CYS0-0.033-0.02828.1910.0050.0050.0000.0000.0000.000
211A342LEU00.0350.03031.4210.0040.0040.0000.0000.0000.000
212A343ARG10.9890.99221.6530.0550.0550.0000.0000.0000.000
213A344ARG10.8820.93625.1600.0100.0100.0000.0000.0000.000
214A345SER00.0140.00730.4440.0040.0040.0000.0000.0000.000
215A346SER0-0.0050.01432.7970.0010.0010.0000.0000.0000.000
216A347LEU0-0.043-0.02435.2180.0010.0010.0000.0000.0000.000
217A348LYS10.8970.96730.7570.0240.0240.0000.0000.0000.000