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FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: P9K2P

Calculation Name: 4J24-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 4J24

Chain ID: B

ChEMBL ID: CHEMBL242

UniProt ID: Q92731

Base Structure: X-ray

Registration Date: 2017-06-23

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.2017021
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3069363.378398
FMO2-HF: Nuclear repulsion 2972967.424404
FMO2-HF: Total energy -96395.953994
FMO2-MP2: Total energy -96666.519266


3D Structure
Snapshot
 
Ligand structure

EST

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.
-83.932-62.94572.710-27.093-66.6010.083


Interactive mode: IFIE and PIEDA for fragment #235(I:600:EST)


Summations of interaction energy for fragment #235(I:600:EST)
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.
-83.932-62.94572.71-27.093-66.601-0.083
Interaction energy analysis for fragmet #235(I:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.083 / q_NPA : -0.078
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].
1I264SER10.8760.92629.147-0.083-0.0830.0000.0000.0000.000
2I265PRO00.1550.06326.173-0.002-0.0020.0000.0000.0000.000
3I266GLU-1-0.740-0.85224.5770.1290.1290.0000.0000.0000.000
4I267GLN0-0.004-0.00923.6810.0080.0080.0000.0000.0000.000
5I268LEU0-0.0230.02622.215-0.003-0.0030.0000.0000.0000.000
6I269VAL00.042-0.00118.8080.0040.0040.0000.0000.0000.000
7I270LEU0-0.063-0.01819.1790.0140.0140.0000.0000.0000.000
8I271THR00.0520.01219.593-0.009-0.0090.0000.0000.0000.000
9I272LEU0-0.017-0.01316.168-0.009-0.0090.0000.0000.0000.000
10I273LEU0-0.019-0.00715.1040.0190.0190.0000.0000.0000.000
11I274GLU-1-0.856-0.93215.5650.0300.0300.0000.0000.0000.000
12I275ALA00.0060.00115.158-0.034-0.0340.0000.0000.0000.000
13I276GLU-1-0.785-0.84310.5060.2370.2370.0000.0000.0000.000
14I277PRO00.0040.0007.545-0.018-0.0180.0000.0000.0000.000
15I278PRO0-0.035-0.0089.9010.0830.0830.0000.0000.0000.000
16I279HIS0-0.026-0.0166.371-0.317-0.3170.0000.0000.0000.000
17I280VAL0-0.022-0.0045.6180.4330.4330.0000.0000.0000.000
18I281LEU0-0.019-0.0117.2200.1470.1470.0000.0000.0000.000
19I282ILE0-0.027-0.0226.619-0.060-0.0600.0000.0000.0000.000
20I283SER00.020-0.0139.7550.0840.0840.0000.0000.0000.000
21I284ARG10.7550.84411.288-0.194-0.1940.0000.0000.0000.000
22I285PRO0-0.0090.00211.495-0.027-0.0270.0000.0000.0000.000
23I286SER0-0.0060.00014.5360.0120.0120.0000.0000.0000.000
24I287ALA0-0.026-0.02116.222-0.002-0.0020.0000.0000.0000.000
25I288PRO00.0150.01115.6110.0090.0090.0000.0000.0000.000
26I289PHE00.0020.01610.0520.0030.0030.0000.0000.0000.000
27I290THR0-0.023-0.02511.387-0.026-0.0260.0000.0000.0000.000
28I291GLU-1-0.705-0.8587.944-0.996-0.9960.0000.0000.0000.000
29I292ALA00.0690.0378.2420.0550.0550.0000.0000.0000.000
30I293SER0-0.027-0.0199.5810.0740.0740.0000.0000.0000.000
31I294MET00.0200.0165.804-0.007-0.0070.0000.0000.0000.000
32I295MET00.0620.0422.450-3.000-2.1153.315-0.897-3.3030.008
33I296MET0-0.0080.0395.6380.2510.2510.0000.0000.0000.000
34I297SER0-0.033-0.0327.515-0.108-0.1080.0000.0000.0000.000
35I298LEU00.010-0.0012.310-3.355-0.7872.289-0.771-4.0850.001
36I299THR0-0.015-0.0312.647-6.338-2.8831.238-1.673-3.020-0.025
37I300LYS10.8780.9444.285-0.1190.0170.000-0.009-0.1270.000
38I301LEU0-0.0140.0112.175-1.349-0.0561.876-0.660-2.5090.004
39I302ALA00.0190.0052.231-2.684-0.9332.668-1.428-2.9910.005
40I303ASP-1-0.747-0.8683.527-0.0410.0050.0580.216-0.3200.001
41I304LYS10.7890.8876.5160.4870.4870.0000.0000.0000.000
42I305GLU-1-0.745-0.8451.687-24.032-28.85212.895-4.741-3.335-0.052
43I306LEU00.0190.0145.5690.6540.6540.0000.0000.0000.000
44I307VAL00.0060.0037.9600.1220.1220.0000.0000.0000.000
45I308HIS0-0.012-0.0128.0560.2590.2590.0000.0000.0000.000
46I309MET0-0.0250.0186.7780.1090.1090.0000.0000.0000.000
47I310ILE00.0140.0039.6560.1020.1020.0000.0000.0000.000
48I311SER0-0.062-0.03812.5900.0410.0410.0000.0000.0000.000
49I312TRP00.0000.01111.1300.0390.0390.0000.0000.0000.000
50I313ALA00.0530.01213.0220.0210.0210.0000.0000.0000.000
51I314LYS10.7970.89315.136-0.055-0.0550.0000.0000.0000.000
52I315LYS10.8150.92414.3420.0640.0640.0000.0000.0000.000
53I316ILE0-0.0130.00615.0680.0040.0040.0000.0000.0000.000
54I317PRO0-0.002-0.00619.4570.0020.0020.0000.0000.0000.000
55I318GLY00.0550.03122.5590.0140.0140.0000.0000.0000.000
56I319PHE00.017-0.00917.3170.0000.0000.0000.0000.0000.000
57I320VAL0-0.050-0.02720.542-0.004-0.0040.0000.0000.0000.000
58I321GLU-1-0.843-0.92322.2960.0640.0640.0000.0000.0000.000
59I322LEU0-0.0110.02021.220-0.002-0.0020.0000.0000.0000.000
60I323SER0-0.014-0.03624.950-0.008-0.0080.0000.0000.0000.000
61I324LEU00.009-0.00923.5980.0080.0080.0000.0000.0000.000
62I325PHE00.0400.02422.7250.0030.0030.0000.0000.0000.000
63I326ASP-1-0.758-0.81721.1020.1330.1330.0000.0000.0000.000
64I327GLN0-0.041-0.02819.6930.0160.0160.0000.0000.0000.000
65I328VAL0-0.0140.00916.7670.0090.0090.0000.0000.0000.000
66I329ARG10.9100.93216.339-0.118-0.1180.0000.0000.0000.000
67I330LEU0-0.0230.00116.6860.0200.0200.0000.0000.0000.000
68I331LEU00.0160.00012.2260.0560.0560.0000.0000.0000.000
69I332GLU-1-0.879-0.96311.9040.3050.3050.0000.0000.0000.000
70I333SER0-0.056-0.01011.4890.0390.0390.0000.0000.0000.000
71I334CYS0-0.024-0.00710.6750.0420.0420.0000.0000.0000.000
72I335TRP00.0510.0124.325-0.0490.2920.000-0.014-0.3270.000
73I336MET00.0170.0232.619-1.531-0.5832.507-0.500-2.9550.000
74I337GLU-1-0.776-0.8794.2380.6180.8510.000-0.030-0.2020.000
75I338VAL0-0.029-0.0286.4380.2460.2460.0000.0000.0000.000
76I339LEU0-0.0060.0102.680-4.537-1.1253.022-1.603-4.8310.015
77I340MET0-0.036-0.0022.259-0.9640.5414.862-1.594-4.773-0.005
78I341MET0-0.022-0.0113.3030.099-0.0610.0140.385-0.2380.000
79I342GLY0-0.0040.0024.805-0.634-0.550-0.001-0.008-0.0750.000
80I343LEU00.0130.0172.323-4.158-2.3344.207-1.366-4.6650.006
81I344MET0-0.0110.0004.195-1.421-1.1720.002-0.057-0.1940.000
82I345TRP0-0.025-0.0107.039-0.346-0.3460.0000.0000.0000.000
83I346ARG10.7300.8152.3762.7983.9530.297-0.567-0.8850.002
84I347SER00.005-0.0107.403-0.156-0.1560.0000.0000.0000.000
85I348ILE00.0100.01810.029-0.131-0.1310.0000.0000.0000.000
86I349ASP-1-0.866-0.93712.6450.3450.3450.0000.0000.0000.000
87I350HIS0-0.054-0.02412.720-0.081-0.0810.0000.0000.0000.000
88I351PRO0-0.029-0.02113.6340.0450.0450.0000.0000.0000.000
89I352GLY00.0000.00213.298-0.011-0.0110.0000.0000.0000.000
90I353LYS10.8250.89511.163-0.319-0.3190.0000.0000.0000.000
91I354LEU00.0020.0054.9440.0230.0230.0000.0000.0000.000
92I355ILE0-0.0150.0008.194-0.045-0.0450.0000.0000.0000.000
93I356PHE00.0370.0052.150-4.661-1.2753.300-1.311-5.3750.010
94I357ALA00.0470.0274.988-1.493-1.382-0.001-0.004-0.1060.000
95I358PRO0-0.021-0.0267.7580.1870.1870.0000.0000.0000.000
96I359ASP-1-0.850-0.89211.255-0.011-0.0110.0000.0000.0000.000
97I360LEU0-0.036-0.0086.442-0.019-0.0190.0000.0000.0000.000
98I361VAL00.0150.0148.9290.3260.3260.0000.0000.0000.000
99I362LEU0-0.0080.0036.392-0.184-0.1840.0000.0000.0000.000
100I363ASP-1-0.798-0.89010.0900.3610.3610.0000.0000.0000.000
101I364ARG10.8020.85010.0070.0350.0350.0000.0000.0000.000
102I365ASP-1-0.807-0.90610.548-0.245-0.2450.0000.0000.0000.000
103I366GLU-1-0.750-0.84210.8840.1240.1240.0000.0000.0000.000
104I367GLY00.0300.0138.095-0.084-0.0840.0000.0000.0000.000
105I368LYS10.8100.8938.528-0.033-0.0330.0000.0000.0000.000
106I369CYS0-0.091-0.0289.794-0.059-0.0590.0000.0000.0000.000
107I370VAL00.024-0.0015.0530.0840.0840.0000.0000.0000.000
108I371GLU-1-0.816-0.8907.640-1.125-1.1250.0000.0000.0000.000
109I372GLY00.0320.0176.672-0.648-0.6480.0000.0000.0000.000
110I373ILE0-0.0110.0132.258-1.313-0.4292.364-0.482-2.7650.001
111I374LEU0-0.025-0.0154.7870.3530.449-0.001-0.002-0.0930.000
112I375GLU-1-0.821-0.8957.078-0.572-0.5720.0000.0000.0000.000
113I376ILE00.0410.0082.390-1.049-0.3092.474-0.469-2.7450.000
114I377PHE0-0.011-0.0133.8840.0660.5950.001-0.043-0.4870.000
115I378ASP-1-0.750-0.8396.3270.1750.1750.0000.0000.0000.000
116I379MET0-0.049-0.0107.2580.1050.1050.0000.0000.0000.000
117I380LEU00.0350.0282.488-0.9700.0200.695-0.259-1.427-0.001
118I381LEU00.0200.0287.0030.0580.0580.0000.0000.0000.000
119I382ALA0-0.0170.01510.060-0.024-0.0240.0000.0000.0000.000
120I383THR0-0.013-0.0288.906-0.037-0.0370.0000.0000.0000.000
121I384THR0-0.016-0.0318.4000.0700.0700.0000.0000.0000.000
122I385SER0-0.062-0.04810.795-0.069-0.0690.0000.0000.0000.000
123I386ARG10.8460.91613.832-0.276-0.2760.0000.0000.0000.000
124I387PHE00.0410.0019.801-0.065-0.0650.0000.0000.0000.000
125I388ARG10.8630.94413.119-0.509-0.5090.0000.0000.0000.000
126I389GLU-1-0.886-0.93216.8520.1940.1940.0000.0000.0000.000
127I390LEU0-0.009-0.00217.069-0.027-0.0270.0000.0000.0000.000
128I391LYS10.8250.91318.443-0.247-0.2470.0000.0000.0000.000
129I392LEU00.0020.02413.079-0.030-0.0300.0000.0000.0000.000
130I393GLN00.011-0.00516.924-0.005-0.0050.0000.0000.0000.000
131I394HIS00.0860.04612.8630.0560.0560.0000.0000.0000.000
132I395LYS10.8250.89015.780-0.122-0.1220.0000.0000.0000.000
133I396GLU-1-0.738-0.83717.2350.2530.2530.0000.0000.0000.000
134I397TYR0-0.020-0.0398.7760.0620.0620.0000.0000.0000.000
135I398LEU0-0.0080.00912.7430.0450.0450.0000.0000.0000.000
136I399CYS0-0.042-0.01714.519-0.011-0.0110.0000.0000.0000.000
137I400VAL00.0420.01012.531-0.008-0.0080.0000.0000.0000.000
138I401LYS10.8350.9168.271-0.517-0.5170.0000.0000.0000.000
139I402ALA00.0270.01012.045-0.002-0.0020.0000.0000.0000.000
140I403MET0-0.038-0.02515.228-0.022-0.0220.0000.0000.0000.000
141I404ILE00.0070.00610.196-0.023-0.0230.0000.0000.0000.000
142I405LEU00.006-0.00313.497-0.028-0.0280.0000.0000.0000.000
143I406LEU0-0.028-0.01214.458-0.034-0.0340.0000.0000.0000.000
144I407ASN0-0.041-0.02817.086-0.035-0.0350.0000.0000.0000.000
145I408SER0-0.038-0.00813.909-0.030-0.0300.0000.0000.0000.000
146I409SER00.0230.00515.507-0.025-0.0250.0000.0000.0000.000
147I410MET00.0490.01417.282-0.016-0.0160.0000.0000.0000.000
148I411TYR0-0.025-0.00918.688-0.013-0.0130.0000.0000.0000.000
149I412PRO00.0190.01421.8270.0020.0020.0000.0000.0000.000
150I413LEU0-0.0020.01424.793-0.007-0.0070.0000.0000.0000.000
151I414VAL00.0500.02727.6490.0040.0040.0000.0000.0000.000
152I415THR0-0.077-0.06829.829-0.007-0.0070.0000.0000.0000.000
153I416ALA00.0090.00227.375-0.002-0.0020.0000.0000.0000.000
154I417THR00.0040.01426.0910.0000.0000.0000.0000.0000.000
155I418GLN00.0020.00729.1930.0030.0030.0000.0000.0000.000
156I419ASP-1-0.823-0.87732.9700.0530.0530.0000.0000.0000.000
157I420ALA00.0110.00030.7920.0000.0000.0000.0000.0000.000
158I421ASP-1-0.823-0.92530.6930.0760.0760.0000.0000.0000.000
159I422SER0-0.018-0.02926.0700.0070.0070.0000.0000.0000.000
160I423SER00.0350.01726.5490.0110.0110.0000.0000.0000.000
161I424ARG10.7840.86527.328-0.057-0.0570.0000.0000.0000.000
162I425LYS10.7960.90526.011-0.072-0.0720.0000.0000.0000.000
163I426LEU00.0140.01620.5270.0050.0050.0000.0000.0000.000
164I427ALA00.0290.01723.4440.0130.0130.0000.0000.0000.000
165I428HIS0-0.042-0.02425.605-0.001-0.0010.0000.0000.0000.000
166I429LEU0-0.0050.00220.8290.0010.0010.0000.0000.0000.000
167I430LEU00.0150.01519.4430.0110.0110.0000.0000.0000.000
168I431ASN0-0.065-0.02322.1290.0080.0080.0000.0000.0000.000
169I432ALA00.0250.01724.8940.0050.0050.0000.0000.0000.000
170I433VAL0-0.013-0.01518.488-0.001-0.0010.0000.0000.0000.000
171I434THR00.021-0.00321.5020.0200.0200.0000.0000.0000.000
172I435ASP-1-0.872-0.93422.6700.1210.1210.0000.0000.0000.000
173I436ALA0-0.071-0.04122.768-0.006-0.0060.0000.0000.0000.000
174I437LEU00.0270.01718.6130.0010.0010.0000.0000.0000.000
175I438VAL00.0110.00521.996-0.002-0.0020.0000.0000.0000.000
176I439TRP0-0.011-0.00825.382-0.005-0.0050.0000.0000.0000.000
177I440VAL0-0.028-0.02820.982-0.009-0.0090.0000.0000.0000.000
178I441ILE00.0070.01421.439-0.002-0.0020.0000.0000.0000.000
179I442ALA0-0.0080.01724.649-0.007-0.0070.0000.0000.0000.000
180I443LYS10.7950.89225.098-0.136-0.1360.0000.0000.0000.000
181I444SER0-0.059-0.03724.5110.0000.0000.0000.0000.0000.000
182I445GLY0-0.007-0.00326.521-0.002-0.0020.0000.0000.0000.000
183I446ILE0-0.0210.00425.884-0.009-0.0090.0000.0000.0000.000
184I447SER00.0310.00730.025-0.001-0.0010.0000.0000.0000.000
185I448SER00.0780.03630.8040.0080.0080.0000.0000.0000.000
186I449GLN00.0680.02430.8730.0040.0040.0000.0000.0000.000
187I450GLN00.0210.01428.1840.0110.0110.0000.0000.0000.000
188I451GLN0-0.032-0.01926.6150.0140.0140.0000.0000.0000.000
189I452SER0-0.008-0.01125.8940.0110.0110.0000.0000.0000.000
190I453MET00.0010.00724.9310.0100.0100.0000.0000.0000.000
191I454ARG10.7740.85720.179-0.222-0.2220.0000.0000.0000.000
192I455LEU00.0390.01321.3250.0230.0230.0000.0000.0000.000
193I456ALA00.0180.00821.5000.0140.0140.0000.0000.0000.000
194I457ASN0-0.030-0.02319.4410.0130.0130.0000.0000.0000.000
195I458LEU00.0170.00716.0380.0220.0220.0000.0000.0000.000
196I459LEU00.0030.00016.8000.0280.0280.0000.0000.0000.000
197I460MET0-0.007-0.00418.027-0.003-0.0030.0000.0000.0000.000
198I461LEU0-0.0200.01013.541-0.006-0.0060.0000.0000.0000.000
199I462LEU00.0190.01913.1080.0510.0510.0000.0000.0000.000
200I463SER0-0.036-0.02713.0560.0050.0050.0000.0000.0000.000
201I464HIS0-0.028-0.01911.615-0.045-0.0450.0000.0000.0000.000
202I465VAL00.0260.0117.415-0.011-0.0110.0000.0000.0000.000
203I466ARG10.8260.8978.465-0.353-0.3530.0000.0000.0000.000
204I467HIS0-0.0030.00510.003-0.019-0.0190.0000.0000.0000.000
205I468ALA00.0410.0085.854-0.118-0.1180.0000.0000.0000.000
206I469SER0-0.069-0.0405.120-0.365-0.244-0.001-0.006-0.1140.000
207I470ASN00.0180.0036.2290.0070.0070.0000.0000.0000.000
208I471LYS10.7790.8675.7200.8920.8920.0000.0000.0000.000
209I472GLY00.0330.0032.306-1.753-0.9541.276-0.817-1.2580.000
210I473MET00.0050.0032.9470.1051.4820.307-0.325-1.359-0.011
211I474GLU-1-0.853-0.9095.398-0.900-0.823-0.001-0.004-0.0730.000
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219I482LYS10.7540.8508.2880.9690.9690.0000.0000.0000.000
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223I486PRO0-0.0310.0019.7410.0850.0850.0000.0000.0000.000
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