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: 52GQZ

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 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 -2566271.698382
FMO2-HF: Nuclear repulsion 2479735.684959
FMO2-HF: Total energy -86536.013423
FMO2-MP2: Total energy -86785.858098


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.
-4.228-2.7766.225-3.057-4.6210.005
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 : 0.070 / q_NPA : 0.018
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].
3A39VAL00.0150.0063.338-2.583-0.5630.155-1.043-1.1330.006
4A40MET0-0.004-0.0022.252-3.040-4.0186.068-1.868-3.222-0.001
5A41SER00.0310.0143.7660.4910.9010.002-0.146-0.2660.000
6A42LEU0-0.011-0.0045.9740.3810.3810.0000.0000.0000.000
7A43ILE0-0.009-0.0096.0890.1930.1930.0000.0000.0000.000
8A44VAL00.0420.0187.2170.1210.1210.0000.0000.0000.000
9A45LEU00.0300.01810.0050.1450.1450.0000.0000.0000.000
10A46ALA0-0.034-0.00912.1460.0900.0900.0000.0000.0000.000
11A47ILE00.0010.01711.5040.0680.0680.0000.0000.0000.000
12A48VAL00.0300.03414.2830.0360.0360.0000.0000.0000.000
13A49PHE00.008-0.00916.4560.0490.0490.0000.0000.0000.000
14A50GLY00.0100.00017.6060.0310.0310.0000.0000.0000.000
15A51ASN0-0.017-0.04217.6470.0530.0530.0000.0000.0000.000
16A52VAL00.0190.01320.5380.0230.0230.0000.0000.0000.000
17A53LEU0-0.040-0.02021.7410.0210.0210.0000.0000.0000.000
18A54VAL0-0.014-0.00823.4270.0170.0170.0000.0000.0000.000
19A55ILE00.0300.00824.1120.0140.0140.0000.0000.0000.000
20A56THR0-0.040-0.01026.4660.0130.0130.0000.0000.0000.000
21A57ALA00.0290.01828.1990.0090.0090.0000.0000.0000.000
22A58ILE0-0.026-0.02029.3140.0080.0080.0000.0000.0000.000
23A59ALA0-0.042-0.02430.9170.0060.0060.0000.0000.0000.000
24A60LYS10.8870.94230.0530.0990.0990.0000.0000.0000.000
25A61PHE00.0210.02431.7860.0050.0050.0000.0000.0000.000
26A62GLU-1-0.786-0.88436.016-0.060-0.0600.0000.0000.0000.000
27A63ARG10.9310.96337.7940.0450.0450.0000.0000.0000.000
28A64LEU00.0020.00731.5070.0000.0000.0000.0000.0000.000
29A65GLN0-0.0130.00934.590-0.008-0.0080.0000.0000.0000.000
30A66THR0-0.011-0.01635.7240.0030.0030.0000.0000.0000.000
31A67VAL00.0320.01335.477-0.004-0.0040.0000.0000.0000.000
32A68THR00.0220.01032.326-0.004-0.0040.0000.0000.0000.000
33A69ASN00.000-0.01231.097-0.009-0.0090.0000.0000.0000.000
34A70TYR0-0.0020.00030.798-0.006-0.0060.0000.0000.0000.000
35A71PHE00.0150.01130.882-0.006-0.0060.0000.0000.0000.000
36A72ILE0-0.001-0.00226.698-0.008-0.0080.0000.0000.0000.000
37A73THR00.007-0.00726.280-0.012-0.0120.0000.0000.0000.000
38A74SER00.0070.01426.394-0.007-0.0070.0000.0000.0000.000
39A75LEU00.0140.00123.471-0.009-0.0090.0000.0000.0000.000
40A76ALA00.0010.01022.060-0.017-0.0170.0000.0000.0000.000
41A77CYS0-0.051-0.02621.479-0.018-0.0180.0000.0000.0000.000
42A78ALA0-0.028-0.00321.639-0.014-0.0140.0000.0000.0000.000
43A79ASP-1-0.771-0.84217.355-0.338-0.3380.0000.0000.0000.000
44A80LEU0-0.002-0.00416.834-0.038-0.0380.0000.0000.0000.000
45A81VAL00.003-0.00317.448-0.027-0.0270.0000.0000.0000.000
46A82MET00.0510.02614.770-0.012-0.0120.0000.0000.0000.000
47A83GLY00.011-0.00413.141-0.062-0.0620.0000.0000.0000.000
48A84LEU0-0.047-0.03513.234-0.052-0.0520.0000.0000.0000.000
49A85ALA0-0.029-0.01015.6100.0130.0130.0000.0000.0000.000
50A86VAL0-0.0050.00813.3890.0210.0210.0000.0000.0000.000
51A87VAL00.0390.0108.520-0.036-0.0360.0000.0000.0000.000
52A88PRO0-0.045-0.0079.146-0.117-0.1170.0000.0000.0000.000
53A89PHE0-0.043-0.0269.831-0.030-0.0300.0000.0000.0000.000
54A90GLY0-0.0490.0007.611-0.096-0.0960.0000.0000.0000.000
55A108PHE00.0460.00721.095-0.001-0.0010.0000.0000.0000.000
56A109TRP00.002-0.00412.4700.0300.0300.0000.0000.0000.000
57A110THR00.0570.01317.688-0.006-0.0060.0000.0000.0000.000
58A111SER0-0.022-0.00719.0420.0070.0070.0000.0000.0000.000
59A112ILE0-0.012-0.00918.6040.0100.0100.0000.0000.0000.000
60A113ASP-1-0.848-0.90415.789-0.329-0.3290.0000.0000.0000.000
61A114VAL00.0300.00718.4340.0060.0060.0000.0000.0000.000
62A115LEU0-0.0310.00321.7240.0060.0060.0000.0000.0000.000
63A116CYS0-0.034-0.01919.2970.0070.0070.0000.0000.0000.000
64A117VAL00.0330.02518.5070.0120.0120.0000.0000.0000.000
65A118THR0-0.016-0.03021.2730.0130.0130.0000.0000.0000.000
66A119ALA00.0360.03124.8090.0120.0120.0000.0000.0000.000
67A120SER0-0.055-0.02022.1390.0090.0090.0000.0000.0000.000
68A121ILE0-0.013-0.00724.5410.0110.0110.0000.0000.0000.000
69A122GLU-1-0.832-0.91726.427-0.084-0.0840.0000.0000.0000.000
70A123THR0-0.030-0.03527.4680.0100.0100.0000.0000.0000.000
71A124LEU0-0.059-0.03524.7770.0090.0090.0000.0000.0000.000
72A125CYS0-0.041-0.00629.2040.0110.0110.0000.0000.0000.000
73A126VAL00.0330.02032.2570.0080.0080.0000.0000.0000.000
74A127ILE0-0.041-0.02229.9490.0060.0060.0000.0000.0000.000
75A128ALA00.0040.00633.1770.0060.0060.0000.0000.0000.000
76A129VAL00.0440.02234.7800.0060.0060.0000.0000.0000.000
77A130ASP-1-0.755-0.85036.293-0.061-0.0610.0000.0000.0000.000
78A131ARG10.7650.84535.1440.0660.0660.0000.0000.0000.000
79A132TYR0-0.010-0.01138.1790.0030.0030.0000.0000.0000.000
80A133PHE00.006-0.00140.6970.0040.0040.0000.0000.0000.000
81A134ALA0-0.076-0.03440.6300.0020.0020.0000.0000.0000.000
82A135ILE0-0.067-0.04740.0820.0020.0020.0000.0000.0000.000
83A136THR0-0.0060.00143.9810.0020.0020.0000.0000.0000.000
84A137SER0-0.0030.01846.0620.0020.0020.0000.0000.0000.000
85A138PRO00.0090.01547.9390.0010.0010.0000.0000.0000.000
86A139PHE00.019-0.01449.5200.0020.0020.0000.0000.0000.000
87A140LYS10.9040.95747.2160.0290.0290.0000.0000.0000.000
88A141TYR00.0310.01737.331-0.002-0.0020.0000.0000.0000.000
89A142GLN00.007-0.01039.717-0.004-0.0040.0000.0000.0000.000
90A143SER0-0.015-0.01140.1080.0030.0030.0000.0000.0000.000
91A144LEU00.0240.01042.1470.0000.0000.0000.0000.0000.000
92A145LEU0-0.014-0.00139.1140.0010.0010.0000.0000.0000.000
93A146THR0-0.006-0.01940.917-0.002-0.0020.0000.0000.0000.000
94A147LYS10.8960.95138.6450.0580.0580.0000.0000.0000.000
95A148ASN00.0550.04039.299-0.004-0.0040.0000.0000.0000.000
96A149LYS10.9950.98940.0410.0460.0460.0000.0000.0000.000
97A150ALA00.0240.02036.762-0.002-0.0020.0000.0000.0000.000
98A151ARG10.9390.95635.4830.0720.0720.0000.0000.0000.000
99A152VAL0-0.0070.00535.874-0.004-0.0040.0000.0000.0000.000
100A153ILE00.0410.01235.953-0.002-0.0020.0000.0000.0000.000
101A154ILE0-0.0030.00230.925-0.003-0.0030.0000.0000.0000.000
102A155LEU0-0.021-0.00632.266-0.006-0.0060.0000.0000.0000.000
103A156MET0-0.012-0.01633.462-0.002-0.0020.0000.0000.0000.000
104A157VAL00.0330.02129.545-0.001-0.0010.0000.0000.0000.000
105A158TRP0-0.032-0.01724.490-0.006-0.0060.0000.0000.0000.000
106A159ILE00.003-0.00429.607-0.004-0.0040.0000.0000.0000.000
107A160VAL00.0080.00432.1290.0000.0000.0000.0000.0000.000
108A161SER00.0020.00026.514-0.002-0.0020.0000.0000.0000.000
109A162GLY0-0.0140.00227.385-0.010-0.0100.0000.0000.0000.000
110A163LEU0-0.072-0.02729.0280.0010.0010.0000.0000.0000.000
111A164THR0-0.0130.00426.7840.0050.0050.0000.0000.0000.000
112A203SER00.0880.03827.7480.0030.0030.0000.0000.0000.000
113A204SER00.0390.01726.127-0.002-0.0020.0000.0000.0000.000
114A205ILE00.0230.01028.0700.0000.0000.0000.0000.0000.000
115A206VAL00.0120.00831.5270.0030.0030.0000.0000.0000.000
116A207SER00.0310.00127.7060.0020.0020.0000.0000.0000.000
117A208PHE00.011-0.00724.055-0.009-0.0090.0000.0000.0000.000
118A209TYR0-0.0010.00427.9100.0040.0040.0000.0000.0000.000
119A210VAL00.0190.01730.7840.0040.0040.0000.0000.0000.000
120A211PRO00.0320.02229.6180.0040.0040.0000.0000.0000.000
121A212LEU0-0.007-0.00326.8860.0030.0030.0000.0000.0000.000
122A213VAL0-0.019-0.01330.5960.0050.0050.0000.0000.0000.000
123A214ILE0-0.004-0.00333.9580.0050.0050.0000.0000.0000.000
124A215MET0-0.0070.01127.9330.0060.0060.0000.0000.0000.000
125A216VAL00.0250.00330.6280.0030.0030.0000.0000.0000.000
126A217PHE0-0.001-0.00233.1790.0050.0050.0000.0000.0000.000
127A218VAL0-0.0070.00236.7720.0040.0040.0000.0000.0000.000
128A219TYR00.018-0.00732.8190.0030.0030.0000.0000.0000.000
129A220SER0-0.031-0.00735.7320.0040.0040.0000.0000.0000.000
130A221ARG10.8710.91837.2220.0410.0410.0000.0000.0000.000
131A222VAL00.0050.01137.4720.0030.0030.0000.0000.0000.000
132A223PHE0-0.038-0.01435.2360.0040.0040.0000.0000.0000.000
133A224GLN00.0410.00538.4520.0050.0050.0000.0000.0000.000
134A225GLU-1-0.808-0.88841.653-0.033-0.0330.0000.0000.0000.000
135A226ALA00.0080.00240.5390.0020.0020.0000.0000.0000.000
136A227LYS10.8210.90438.5160.0340.0340.0000.0000.0000.000
137A228ARG10.9500.98243.2650.0290.0290.0000.0000.0000.000
138A229GLN00.0430.01745.6180.0020.0020.0000.0000.0000.000
139A230LEU0-0.038-0.01741.6390.0010.0010.0000.0000.0000.000
140A231GLN0-0.039-0.02045.5240.0030.0030.0000.0000.0000.000
141A232LYS11.0081.01948.5920.0210.0210.0000.0000.0000.000
142A233ILE0-0.059-0.01946.9170.0000.0000.0000.0000.0000.000
143A234ASP-1-0.773-0.86751.282-0.016-0.0160.0000.0000.0000.000
144A235LYS10.8850.92050.1680.0160.0160.0000.0000.0000.000
145A236SER00.011-0.00653.2190.0010.0010.0000.0000.0000.000
146A237GLU-1-0.801-0.90751.182-0.021-0.0210.0000.0000.0000.000
147A238GLY0-0.072-0.04149.5140.0000.0000.0000.0000.0000.000
148A239ARG10.7800.89148.3890.0160.0160.0000.0000.0000.000
149A240PHE00.0080.00152.8780.0010.0010.0000.0000.0000.000
150A241HIS0-0.087-0.02452.3860.0010.0010.0000.0000.0000.000
151A242VAL00.0090.01455.7130.0010.0010.0000.0000.0000.000
152A264PHE00.0240.01040.1450.0000.0000.0000.0000.0000.000
153A265CYS00.0390.02643.2410.0010.0010.0000.0000.0000.000
154A266LEU00.0550.01740.152-0.003-0.0030.0000.0000.0000.000
155A267LYS10.8830.92137.1530.0450.0450.0000.0000.0000.000
156A268GLU-1-0.769-0.88737.707-0.049-0.0490.0000.0000.0000.000
157A269HIS00.0410.03637.746-0.002-0.0020.0000.0000.0000.000
158A270LYS10.9330.96634.4020.0310.0310.0000.0000.0000.000
159A271ALA00.0050.01333.298-0.004-0.0040.0000.0000.0000.000
160A272LEU00.0360.01033.040-0.005-0.0050.0000.0000.0000.000
161A273LYS10.9250.97628.7640.0510.0510.0000.0000.0000.000
162A274THR0-0.011-0.01627.996-0.002-0.0020.0000.0000.0000.000
163A275LEU00.0070.00128.079-0.007-0.0070.0000.0000.0000.000
164A276GLY00.0550.02829.155-0.004-0.0040.0000.0000.0000.000
165A277ILE0-0.052-0.03125.6550.0000.0000.0000.0000.0000.000
166A278ILE0-0.034-0.00123.752-0.006-0.0060.0000.0000.0000.000
167A279MET00.000-0.00424.322-0.010-0.0100.0000.0000.0000.000
168A280GLY0-0.0040.00025.792-0.003-0.0030.0000.0000.0000.000
169A281THR0-0.051-0.03019.7710.0020.0020.0000.0000.0000.000
170A282PHE00.0420.02120.737-0.007-0.0070.0000.0000.0000.000
171A283THR00.005-0.00321.968-0.007-0.0070.0000.0000.0000.000
172A284LEU00.022-0.00321.110-0.001-0.0010.0000.0000.0000.000
173A285CYS0-0.085-0.02817.206-0.005-0.0050.0000.0000.0000.000
174A286TRP00.0270.03316.381-0.023-0.0230.0000.0000.0000.000
175A287LEU0-0.0090.00220.2360.0050.0050.0000.0000.0000.000
176A288PRO0-0.023-0.01718.6100.0050.0050.0000.0000.0000.000
177A289PHE0-0.0290.00617.048-0.003-0.0030.0000.0000.0000.000
178A290PHE00.016-0.00919.7600.0090.0090.0000.0000.0000.000
179A291ILE0-0.089-0.02522.9500.0200.0200.0000.0000.0000.000
180A311LEU00.0380.00414.128-0.019-0.0190.0000.0000.0000.000
181A312ASN00.0140.00212.9210.0200.0200.0000.0000.0000.000
182A313TRP00.0190.0109.016-0.036-0.0360.0000.0000.0000.000
183A314ILE0-0.0020.00011.031-0.029-0.0290.0000.0000.0000.000
184A315GLY00.0570.02113.4400.0120.0120.0000.0000.0000.000
185A316TYR0-0.029-0.04310.223-0.007-0.0070.0000.0000.0000.000
186A317VAL0-0.0170.00010.741-0.024-0.0240.0000.0000.0000.000
187A318ASN00.016-0.00712.9100.0520.0520.0000.0000.0000.000
188A319SER0-0.014-0.03213.9580.0230.0230.0000.0000.0000.000
189A320GLY0-0.0130.00114.3060.0160.0160.0000.0000.0000.000
190A321PHE0-0.037-0.02215.2150.0470.0470.0000.0000.0000.000
191A322ASN00.0480.01618.0100.0410.0410.0000.0000.0000.000
192A323PRO00.0490.01818.6930.0250.0250.0000.0000.0000.000
193A324LEU00.0220.02617.2700.0220.0220.0000.0000.0000.000
194A325ILE0-0.001-0.01120.6090.0210.0210.0000.0000.0000.000
195A326TYR00.003-0.01323.6400.0130.0130.0000.0000.0000.000
196A327CYS0-0.052-0.01023.1180.0090.0090.0000.0000.0000.000
197A328ARG10.9180.94525.5690.0370.0370.0000.0000.0000.000
198A329SER0-0.039-0.02327.5070.0040.0040.0000.0000.0000.000
199A330PRO0-0.0110.02928.4400.0050.0050.0000.0000.0000.000
200A331ASP-1-0.913-0.96630.974-0.055-0.0550.0000.0000.0000.000
201A332PHE00.0690.01927.4700.0020.0020.0000.0000.0000.000
202A333ARG10.8530.93427.6490.0430.0430.0000.0000.0000.000
203A334ILE00.0110.00529.1150.0020.0020.0000.0000.0000.000
204A335ALA00.0140.01830.810-0.002-0.0020.0000.0000.0000.000
205A336PHE00.030-0.01023.5750.0000.0000.0000.0000.0000.000
206A337GLN00.0080.02624.3780.0050.0050.0000.0000.0000.000
207A338GLU-1-0.839-0.95427.121-0.033-0.0330.0000.0000.0000.000
208A339LEU00.0200.02927.5480.0040.0040.0000.0000.0000.000
209A340LEU0-0.040-0.00623.8220.0000.0000.0000.0000.0000.000
210A341CYS0-0.031-0.02828.2010.0050.0050.0000.0000.0000.000
211A342LEU00.0380.03131.4300.0040.0040.0000.0000.0000.000
212A343ARG10.9870.99221.6940.0540.0540.0000.0000.0000.000
213A344ARG10.8820.93725.1920.0100.0100.0000.0000.0000.000
214A345SER00.0140.00630.4400.0040.0040.0000.0000.0000.000
215A346SER0-0.0040.01532.8330.0010.0010.0000.0000.0000.000
216A347LEU0-0.041-0.02335.2710.0010.0010.0000.0000.0000.000
217A348LYS10.8970.96730.7660.0240.0240.0000.0000.0000.000