FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: XNZ1Q

Calculation Name: 3NY9-A-Xray44

Preferred Name: Beta-2 adrenergic receptor

Target Type: SINGLE PROTEIN

Ligand Name: cholesterol

ligand 3-letter code: CLR

PDB ID: 3NY9

Chain ID: A

ChEMBL ID: CHEMBL210

UniProt ID: P07550

Base Structure: X-ray

Registration Date: 2019-02-27

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHL
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20190208
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 438
LigandResidueName JSZ
LigandFragmentNumber 438
LigandCharge JSZ=1
Software ABINIT-MP 7.2
Total energy (hartree)
FMO2-HF: Electronic energy -7664216.24702
FMO2-HF: Nuclear repulsion 7486515.8947
FMO2-HF: Total energy -177700.35232
FMO2-MP2: Total energy -178213.465256


3D Structure
Snapshot
 
Ligand structure

JSZ

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.
-207.567-177.81999.860-47.191-82.4240.244


Interactive mode: IFIE and PIEDA for fragment #438(A:1203:JSZ)


Summations of interaction energy for fragment #438(A:1203:JSZ)
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.
-207.567-177.81999.86-47.191-82.424-0.244
Interaction energy analysis for fragmet #438(A:1203:JSZ)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.755 / q_NPA : 0.858
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].
1A32TRP00.0540.01517.476-0.155-0.1550.0000.0000.0000.000
2A33VAL00.0350.00116.904-0.479-0.4790.0000.0000.0000.000
3A34VAL00.0500.02518.027-0.722-0.7220.0000.0000.0000.000
4A35GLY00.0010.00219.663-0.270-0.2700.0000.0000.0000.000
5A36MET00.0150.00514.321-0.552-0.5520.0000.0000.0000.000
6A37GLY00.0910.05615.659-0.879-0.8790.0000.0000.0000.000
7A38ILE0-0.0050.01516.722-0.398-0.3980.0000.0000.0000.000
8A39VAL0-0.006-0.00515.037-0.219-0.2190.0000.0000.0000.000
9A40MET0-0.019-0.0179.939-0.316-0.3160.0000.0000.0000.000
10A41SER0-0.013-0.01613.799-0.907-0.9070.0000.0000.0000.000
11A42LEU0-0.040-0.03216.2580.1520.1520.0000.0000.0000.000
12A43ILE0-0.0140.00511.7240.1920.1920.0000.0000.0000.000
13A44VAL00.0260.01811.908-0.052-0.0520.0000.0000.0000.000
14A45LEU00.0090.00513.9790.3010.3010.0000.0000.0000.000
15A46ALA00.0010.01116.2100.5590.5590.0000.0000.0000.000
16A47ILE0-0.0150.00110.0780.5260.5260.0000.0000.0000.000
17A48VAL00.0180.00614.1710.3770.3770.0000.0000.0000.000
18A49PHE0-0.033-0.01216.1340.7110.7110.0000.0000.0000.000
19A50GLY00.0330.00618.0990.6110.6110.0000.0000.0000.000
20A51ASN0-0.014-0.03713.4121.2901.2900.0000.0000.0000.000
21A52VAL00.0380.02217.1730.4180.4180.0000.0000.0000.000
22A53LEU0-0.0050.04719.7280.7960.7960.0000.0000.0000.000
23A54VAL0-0.033-0.02119.1120.6060.6060.0000.0000.0000.000
24A55ILE00.000-0.00416.9450.5350.5350.0000.0000.0000.000
25A56THR0-0.016-0.04321.1740.5000.5000.0000.0000.0000.000
26A57ALA0-0.029-0.01424.4200.5780.5780.0000.0000.0000.000
27A58ILE0-0.062-0.03822.1930.5250.5250.0000.0000.0000.000
28A59ALA0-0.029-0.01325.0070.3710.3710.0000.0000.0000.000
29A60LYS10.9260.98826.7579.7749.7740.0000.0000.0000.000
30A61PHE00.0290.01529.3070.4310.4310.0000.0000.0000.000
31A62GLU-1-0.838-0.92930.220-9.210-9.2100.0000.0000.0000.000
32A63ARG10.8540.94431.6178.6528.6520.0000.0000.0000.000
33A64LEU0-0.021-0.01027.134-0.049-0.0490.0000.0000.0000.000
34A65GLN00.0590.04526.903-0.523-0.5230.0000.0000.0000.000
35A66THR0-0.060-0.04126.5820.2010.2010.0000.0000.0000.000
36A67VAL00.0380.00923.001-0.335-0.3350.0000.0000.0000.000
37A68THR00.0090.00121.444-0.377-0.3770.0000.0000.0000.000
38A69ASN00.0380.00920.992-0.852-0.8520.0000.0000.0000.000
39A70TYR0-0.0190.01521.464-0.211-0.2110.0000.0000.0000.000
40A71PHE00.0180.00317.236-0.459-0.4590.0000.0000.0000.000
41A72ILE00.0010.00316.626-0.793-0.7930.0000.0000.0000.000
42A73THR00.009-0.00317.270-0.572-0.5720.0000.0000.0000.000
43A74SER0-0.0220.00513.686-0.741-0.7410.0000.0000.0000.000
44A75LEU0-0.001-0.00511.541-0.907-0.9070.0000.0000.0000.000
45A76ALA00.0480.02013.019-1.214-1.2140.0000.0000.0000.000
46A77CYS0-0.039-0.01914.036-0.486-0.4860.0000.0000.0000.000
47A78ALA00.0040.0069.473-0.712-0.7120.0000.0000.0000.000
48A79ASP-1-0.812-0.8789.353-28.298-28.2980.0000.0000.0000.000
49A80LEU0-0.039-0.02010.692-0.547-0.5470.0000.0000.0000.000
50A81VAL0-0.011-0.0089.762-0.040-0.0400.0000.0000.0000.000
51A82MET00.0240.0283.078-2.795-2.3280.024-0.152-0.3390.001
52A83GLY00.008-0.0038.119-1.524-1.5240.0000.0000.0000.000
53A84LEU0-0.033-0.03010.8680.5980.5980.0000.0000.0000.000
54A85ALA0-0.006-0.01310.3070.5350.5350.0000.0000.0000.000
55A86VAL00.0040.0154.326-1.079-0.933-0.001-0.012-0.1330.000
56A87VAL00.0160.0126.488-1.758-1.7580.0000.0000.0000.000
57A88PRO00.0070.0157.9490.2520.2520.0000.0000.0000.000
58A89PHE00.012-0.0087.5701.5481.5480.0000.0000.0000.000
59A90GLY00.0540.0335.463-1.823-1.8230.0000.0000.0000.000
60A91ALA0-0.023-0.0336.1111.4291.4290.0000.0000.0000.000
61A92ALA0-0.008-0.0019.6561.6681.6680.0000.0000.0000.000
62A93HIS0-0.0070.0095.0414.1664.1660.0000.0000.0000.000
63A94ILE0-0.033-0.0166.8511.8101.8100.0000.0000.0000.000
64A95LEU0-0.072-0.04910.0781.9511.9510.0000.0000.0000.000
65A96MET0-0.031-0.00812.7671.3861.3860.0000.0000.0000.000
66A97LYS10.8750.94811.98819.12119.1210.0000.0000.0000.000
67A98MET00.0410.03111.7050.9270.9270.0000.0000.0000.000
68A99TRP0-0.040-0.0056.834-1.902-1.9020.0000.0000.0000.000
69A100THR00.004-0.01410.9391.8601.8600.0000.0000.0000.000
70A101PHE0-0.061-0.03710.5661.2991.2990.0000.0000.0000.000
71A102GLY00.1050.07513.5380.2250.2250.0000.0000.0000.000
72A103ASN00.1020.03211.724-3.100-3.1000.0000.0000.0000.000
73A104PHE0-0.0240.00111.174-1.628-1.6280.0000.0000.0000.000
74A105TRP00.0270.0009.902-1.133-1.1330.0000.0000.0000.000
75A191CYS00.0440.0426.466-4.239-4.2390.0000.0000.0000.000
76A107GLU-1-0.765-0.8896.401-31.920-31.9200.0000.0000.0000.000
77A108PHE0-0.064-0.0377.480-2.925-2.9250.0000.0000.0000.000
78A109TRP0-0.038-0.0212.422-7.772-6.9022.443-0.836-2.478-0.010
79A110THR00.016-0.0062.257-9.462-9.4611.964-0.402-1.563-0.002
80A111SER0-0.035-0.0323.946-3.946-3.7720.0000.021-0.1960.000
81A112ILE0-0.024-0.0116.9001.5131.5130.0000.0000.0000.000
82A113ASP-1-0.752-0.8201.623-148.613-154.52432.861-15.666-11.284-0.167
83A114VAL00.029-0.0052.160-4.603-1.2055.484-2.053-6.8280.004
84A115LEU0-0.0010.0193.2062.9054.2210.077-0.324-1.069-0.005
85A116CYS0-0.033-0.0095.8065.1625.1620.0000.0000.0000.000
86A117VAL00.0130.0162.1652.9174.1543.915-1.244-3.9080.001
87A118THR00.029-0.0012.4834.1475.6180.782-0.667-1.585-0.007
88A119ALA00.0210.0074.3003.3953.4620.001-0.025-0.0430.000
89A120SER0-0.0090.0377.2823.5953.5950.0000.0000.0000.000
90A121ILE0-0.0090.0065.1692.5532.5530.0000.0000.0000.000
91A122TRP00.0300.0167.0382.9972.9970.0000.0000.0000.000
92A123THR0-0.030-0.0629.9701.9991.9990.0000.0000.0000.000
93A124LEU0-0.051-0.01810.0391.5041.5040.0000.0000.0000.000
94A125CYS00.004-0.00411.6501.3131.3130.0000.0000.0000.000
95A126VAL0-0.0060.00613.4231.0641.0640.0000.0000.0000.000
96A127ILE0-0.032-0.01215.6100.9570.9570.0000.0000.0000.000
97A128ALA0-0.027-0.02816.3840.7480.7480.0000.0000.0000.000
98A129VAL00.0180.00817.3520.7130.7130.0000.0000.0000.000
99A130ASP-1-0.790-0.90419.553-10.389-10.3890.0000.0000.0000.000
100A131ARG10.7990.88921.31211.23611.2360.0000.0000.0000.000
101A132TYR00.0490.02122.4400.3980.3980.0000.0000.0000.000
102A133PHE00.0130.00022.2850.3900.3900.0000.0000.0000.000
103A134ALA0-0.0110.00925.8290.3100.3100.0000.0000.0000.000
104A135ILE0-0.061-0.02326.8370.3100.3100.0000.0000.0000.000
105A136THR0-0.022-0.00627.9120.2680.2680.0000.0000.0000.000
106A137SER0-0.0580.00230.3010.2990.2990.0000.0000.0000.000
107A138PRO00.040-0.00832.153-0.025-0.0250.0000.0000.0000.000
108A139PHE0-0.0190.01133.1910.1070.1070.0000.0000.0000.000
109A140LYS10.9040.96031.9177.6467.6460.0000.0000.0000.000
110A141TYR0-0.020-0.02429.095-0.099-0.0990.0000.0000.0000.000
111A142GLN0-0.0180.00028.966-0.266-0.2660.0000.0000.0000.000
112A143SER0-0.038-0.02924.8420.1120.1120.0000.0000.0000.000
113A144LEU00.0590.02526.9290.2130.2130.0000.0000.0000.000
114A145LEU0-0.051-0.00722.2230.1650.1650.0000.0000.0000.000
115A146THR00.0450.01626.522-0.010-0.0100.0000.0000.0000.000
116A147LYS10.9440.94925.9539.3289.3280.0000.0000.0000.000
117A148ASN00.0430.00724.970-0.606-0.6060.0000.0000.0000.000
118A149LYS10.9770.99324.5279.0249.0240.0000.0000.0000.000
119A150ALA00.0270.01421.568-0.316-0.3160.0000.0000.0000.000
120A151ARG10.9570.97820.18510.25110.2510.0000.0000.0000.000
121A152VAL00.0240.02520.040-0.455-0.4550.0000.0000.0000.000
122A153ILE00.0020.00316.690-0.416-0.4160.0000.0000.0000.000
123A154ILE00.0060.00915.449-0.557-0.5570.0000.0000.0000.000
124A155LEU00.0450.01814.834-0.913-0.9130.0000.0000.0000.000
125A156MET0-0.0060.00415.693-0.398-0.3980.0000.0000.0000.000
126A157VAL00.0000.01110.592-0.487-0.4870.0000.0000.0000.000
127A158TRP0-0.0080.00710.851-1.485-1.4850.0000.0000.0000.000
128A159ILE00.0180.01711.420-0.953-0.9530.0000.0000.0000.000
129A160VAL00.002-0.00610.617-0.448-0.4480.0000.0000.0000.000
130A161SER0-0.034-0.0576.976-0.558-0.5580.0000.0000.0000.000
131A162GLY00.0240.0097.534-1.992-1.9920.0000.0000.0000.000
132A163LEU0-0.044-0.02210.093-0.339-0.3390.0000.0000.0000.000
133A164THR0-0.028-0.0326.509-1.159-1.1590.0000.0000.0000.000
134A165SER0-0.0100.0105.059-1.911-1.827-0.001-0.002-0.0800.000
135A166PHE00.0390.0026.754-1.445-1.4450.0000.0000.0000.000
136A167LEU0-0.0130.00710.2640.2420.2420.0000.0000.0000.000
137A168PRO0-0.039-0.0287.5020.5310.5310.0000.0000.0000.000
138A169ILE0-0.0050.0055.576-0.307-0.3070.0000.0000.0000.000
139A170GLN0-0.001-0.0079.2751.7571.7570.0000.0000.0000.000
140A171MET0-0.049-0.01412.5531.2941.2940.0000.0000.0000.000
141A172HIS0-0.017-0.00811.4341.4541.4540.0000.0000.0000.000
142A173TRP00.0070.00310.233-0.216-0.2160.0000.0000.0000.000
143A174TYR0-0.0130.0025.9490.9480.9480.0000.0000.0000.000
144A175ARG10.9100.9776.44220.27120.2710.0000.0000.0000.000
145A176ALA0-0.0150.0247.3651.5241.5240.0000.0000.0000.000
146A177THR00.017-0.0119.2410.1770.1770.0000.0000.0000.000
147A178HIS00.0470.0317.9791.6461.6460.0000.0000.0000.000
148A179GLN00.007-0.02013.102-0.388-0.3880.0000.0000.0000.000
149A180GLU-1-0.949-0.98411.922-20.135-20.1350.0000.0000.0000.000
150A181ALA0-0.0140.0089.542-0.867-0.8670.0000.0000.0000.000
151A182ILE00.001-0.01211.268-0.552-0.5520.0000.0000.0000.000
152A183ASN0-0.0010.00014.1730.6430.6430.0000.0000.0000.000
153A190CYS0-0.109-0.02010.448-1.680-1.6800.0000.0000.0000.000
154A185TYR0-0.008-0.0037.8700.2060.2060.0000.0000.0000.000
155A186ALA0-0.027-0.01513.2860.1920.1920.0000.0000.0000.000
156A187GLU-1-0.867-0.89614.737-15.910-15.9100.0000.0000.0000.000
157A188GLU-1-0.876-0.95613.628-18.351-18.3510.0000.0000.0000.000
158A189THR0-0.106-0.07013.249-1.331-1.3310.0000.0000.0000.000
159A192ASP-1-0.883-0.9555.410-35.653-35.6530.0000.0000.0000.000
160A193PHE0-0.018-0.0262.097-4.165-2.0306.034-1.812-6.358-0.009
161A194PHE00.0270.0153.490-2.029-1.4270.020-0.214-0.408-0.001
162A195THR0-0.004-0.0192.338-4.599-2.6231.893-1.235-2.633-0.015
163A196ASN0-0.045-0.0344.7731.9882.072-0.001-0.007-0.0760.000
164A197GLN00.0720.0054.883-1.435-1.350-0.001-0.003-0.0810.000
165A198ALA00.0060.0186.5250.8670.8670.0000.0000.0000.000
166A199TYR00.0530.0252.754-1.5260.3450.213-0.481-1.603-0.002
167A200ALA00.0260.0292.511-0.0131.4561.996-1.312-2.1530.010
168A201ILE0-0.0030.0083.2076.8766.9250.2510.610-0.910-0.001
169A202ALA0-0.012-0.0135.9700.5760.5760.0000.0000.0000.000
170A203SER00.0220.0032.102-10.414-7.6843.626-2.523-3.8330.017
171A204SER00.0390.0292.507-7.782-5.1251.163-1.334-2.4870.000
172A205ILE0-0.022-0.0094.472-3.377-3.0820.001-0.043-0.2540.000
173A206VAL0-0.006-0.0026.297-0.414-0.4140.0000.0000.0000.000
174A207SER0-0.030-0.0322.245-3.653-2.4613.242-1.741-2.694-0.009
175A208PHE00.005-0.0063.380-1.913-1.2070.009-0.123-0.5910.000
176A209TYR0-0.001-0.0194.9720.6190.731-0.001-0.004-0.1070.000
177A210VAL00.0040.0078.4980.6230.6230.0000.0000.0000.000
178A211PRO0-0.0050.0067.3400.9510.9510.0000.0000.0000.000
179A212LEU00.0290.0188.7450.6470.6470.0000.0000.0000.000
180A213VAL0-0.009-0.01510.4380.7740.7740.0000.0000.0000.000
181A214ILE0-0.0030.00313.1500.8120.8120.0000.0000.0000.000
182A215MET00.0260.02112.5480.6040.6040.0000.0000.0000.000
183A216VAL0-0.016-0.00914.1030.5960.5960.0000.0000.0000.000
184A217PHE0-0.006-0.00116.5410.6920.6920.0000.0000.0000.000
185A218VAL0-0.016-0.01918.0940.5730.5730.0000.0000.0000.000
186A219TYR00.005-0.00518.2850.4930.4930.0000.0000.0000.000
187A220SER0-0.044-0.01320.2180.5230.5230.0000.0000.0000.000
188A221ARG10.9911.00322.37310.43610.4360.0000.0000.0000.000
189A222VAL0-0.0040.00522.2680.4100.4100.0000.0000.0000.000
190A223PHE0-0.018-0.02121.9090.3440.3440.0000.0000.0000.000
191A224GLN0-0.047-0.02426.0880.1870.1870.0000.0000.0000.000
192A225GLU-1-0.820-0.90027.837-8.169-8.1690.0000.0000.0000.000
193A226ALA00.009-0.00428.6740.2820.2820.0000.0000.0000.000
194A227LYS10.8600.92730.4628.4928.4920.0000.0000.0000.000
195A228ARG10.8880.93932.3118.1358.1350.0000.0000.0000.000
196A229GLN0-0.022-0.03031.4030.3350.3350.0000.0000.0000.000
197A230LEU0-0.0520.00234.4250.1090.1090.0000.0000.0000.000
198A1002ASN00.014-0.00136.8030.2550.2550.0000.0000.0000.000
199A1003ILE00.0580.01240.439-0.087-0.0870.0000.0000.0000.000
200A1004PHE00.0530.03841.7310.0000.0000.0000.0000.0000.000
201A1005GLU-1-0.809-0.92135.990-7.926-7.9260.0000.0000.0000.000
202A1006MET0-0.069-0.00139.750-0.033-0.0330.0000.0000.0000.000
203A1007LEU00.0340.01441.488-0.038-0.0380.0000.0000.0000.000
204A1008ARG10.8990.98938.8507.3897.3890.0000.0000.0000.000
205A1009ILE0-0.078-0.04936.966-0.110-0.1100.0000.0000.0000.000
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