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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: P7QKP

Calculation Name: 4J24-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 4J24

Chain ID: A

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 -3085824.197254
FMO2-HF: Nuclear repulsion 2989428.238289
FMO2-HF: Total energy -96395.958965
FMO2-MP2: Total energy -96666.591255


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.
-80.442-62.92274.119-27.055-64.5920.071


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


Summations of interaction energy for fragment #235(K: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.
-80.442-62.92274.119-27.055-64.592-0.071
Interaction energy analysis for fragmet #235(K:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.073 / q_NPA : -0.079
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].
1K264SER10.8430.90429.490-0.041-0.0410.0000.0000.0000.000
2K265PRO00.1590.06226.233-0.003-0.0030.0000.0000.0000.000
3K266GLU-1-0.778-0.87024.7600.0770.0770.0000.0000.0000.000
4K267GLN00.0510.02024.4340.0030.0030.0000.0000.0000.000
5K268LEU00.0280.04422.533-0.005-0.0050.0000.0000.0000.000
6K269VAL00.033-0.00919.100-0.002-0.0020.0000.0000.0000.000
7K270LEU0-0.070-0.01219.7580.0100.0100.0000.0000.0000.000
8K271THR00.0260.00520.022-0.009-0.0090.0000.0000.0000.000
9K272LEU0-0.013-0.01916.902-0.010-0.0100.0000.0000.0000.000
10K273LEU0-0.034-0.00815.5990.0210.0210.0000.0000.0000.000
11K274GLU-1-0.844-0.94415.503-0.004-0.0040.0000.0000.0000.000
12K275ALA00.0110.00715.097-0.032-0.0320.0000.0000.0000.000
13K276GLU-1-0.783-0.84910.4330.1090.1090.0000.0000.0000.000
14K277PRO0-0.0160.0067.4210.0040.0040.0000.0000.0000.000
15K278PRO0-0.029-0.01310.1020.0900.0900.0000.0000.0000.000
16K279HIS0-0.015-0.0146.491-0.327-0.3270.0000.0000.0000.000
17K280VAL0-0.044-0.0185.3780.4450.4450.0000.0000.0000.000
18K281LEU00.0090.0106.6870.0870.0870.0000.0000.0000.000
19K282ILE0-0.082-0.0566.657-0.208-0.2080.0000.0000.0000.000
20K283SER0-0.012-0.0259.2240.1430.1430.0000.0000.0000.000
21K284ARG10.7520.84211.735-0.335-0.3350.0000.0000.0000.000
22K285PRO0-0.0090.00711.766-0.049-0.0490.0000.0000.0000.000
23K286SER0-0.0090.00314.9420.0070.0070.0000.0000.0000.000
24K287ALA0-0.027-0.02315.923-0.016-0.0160.0000.0000.0000.000
25K288PRO00.0020.00016.2630.0180.0180.0000.0000.0000.000
26K289PHE00.0170.01710.4660.0030.0030.0000.0000.0000.000
27K290THR00.005-0.00411.870-0.036-0.0360.0000.0000.0000.000
28K291GLU-1-0.753-0.8727.791-0.681-0.6810.0000.0000.0000.000
29K292ALA00.0540.0348.6190.1030.1030.0000.0000.0000.000
30K293SER00.001-0.01310.0650.1020.1020.0000.0000.0000.000
31K294MET00.0260.0146.1470.0130.0130.0000.0000.0000.000
32K295MET00.0670.0472.306-2.431-1.3572.626-0.858-2.8420.007
33K296MET00.0100.0395.9440.2110.2110.0000.0000.0000.000
34K297SER0-0.044-0.0247.777-0.158-0.1580.0000.0000.0000.000
35K298LEU00.019-0.0032.527-2.966-0.4650.919-0.530-2.8900.001
36K299THR00.031-0.0032.894-4.567-1.8840.469-1.200-1.951-0.015
37K300LYS10.8540.9314.524-0.537-0.394-0.001-0.008-0.1360.000
38K301LEU0-0.034-0.0062.218-1.469-0.0252.575-0.886-3.1340.006
39K302ALA00.0390.0092.289-3.442-1.3452.392-1.370-3.1200.003
40K303ASP-1-0.837-0.9213.529-0.182-0.1420.0710.244-0.3550.001
41K304LYS10.8720.9446.2360.8770.8770.0000.0000.0000.000
42K305GLU-1-0.764-0.8571.626-23.901-31.49016.865-5.762-3.515-0.054
43K306LEU00.0440.0295.3740.5310.638-0.001-0.001-0.1060.000
44K307VAL00.0090.0078.0050.1190.1190.0000.0000.0000.000
45K308HIS0-0.034-0.0377.8150.2230.2230.0000.0000.0000.000
46K309MET0-0.0170.0317.0050.1140.1140.0000.0000.0000.000
47K310ILE00.0330.0219.3190.1100.1100.0000.0000.0000.000
48K311SER0-0.051-0.02511.9920.0630.0630.0000.0000.0000.000
49K312TRP0-0.004-0.00510.7530.0650.0650.0000.0000.0000.000
50K313ALA00.0510.01212.6290.0410.0410.0000.0000.0000.000
51K314LYS10.7760.88014.6680.0220.0220.0000.0000.0000.000
52K315LYS10.8170.92614.0960.1400.1400.0000.0000.0000.000
53K316ILE0-0.0180.00814.4490.0110.0110.0000.0000.0000.000
54K317PRO0-0.010-0.01418.7620.0000.0000.0000.0000.0000.000
55K318GLY0-0.018-0.00722.2740.0110.0110.0000.0000.0000.000
56K319PHE00.026-0.01217.1130.0020.0020.0000.0000.0000.000
57K320VAL0-0.046-0.01119.588-0.004-0.0040.0000.0000.0000.000
58K321GLU-1-0.803-0.90821.8510.0210.0210.0000.0000.0000.000
59K322LEU0-0.0300.01921.2390.0010.0010.0000.0000.0000.000
60K323SER0-0.005-0.01824.926-0.005-0.0050.0000.0000.0000.000
61K324LEU00.0360.00321.2320.0040.0040.0000.0000.0000.000
62K325PHE00.0360.02021.8550.0060.0060.0000.0000.0000.000
63K326ASP-1-0.750-0.82021.0140.0600.0600.0000.0000.0000.000
64K327GLN0-0.037-0.01319.0350.0040.0040.0000.0000.0000.000
65K328VAL00.0200.00816.8980.0110.0110.0000.0000.0000.000
66K329ARG10.8740.92916.182-0.053-0.0530.0000.0000.0000.000
67K330LEU0-0.052-0.02816.3530.0130.0130.0000.0000.0000.000
68K331LEU00.0270.01312.1710.0280.0280.0000.0000.0000.000
69K332GLU-1-0.880-0.95211.8710.1820.1820.0000.0000.0000.000
70K333SER0-0.017-0.01311.6110.0200.0200.0000.0000.0000.000
71K334CYS0-0.084-0.03510.570-0.011-0.0110.0000.0000.0000.000
72K335TRP00.0740.0214.395-0.1670.1650.000-0.011-0.3210.000
73K336MET00.0210.0292.506-1.671-1.2323.604-0.616-3.427-0.002
74K337GLU-1-0.796-0.8834.1110.0180.3100.000-0.047-0.2450.000
75K338VAL0-0.016-0.0156.5640.1830.1830.0000.0000.0000.000
76K339LEU0-0.0070.0092.677-4.293-0.9673.087-1.460-4.9530.014
77K340MET0-0.028-0.0072.342-2.0580.1984.791-1.861-5.187-0.014
78K341MET0-0.030-0.0073.3810.4130.1770.0210.473-0.2580.000
79K342GLY00.0150.0114.430-0.608-0.485-0.001-0.018-0.1040.000
80K343LEU00.0160.0192.295-3.669-2.1484.373-1.405-4.4900.004
81K344MET0-0.015-0.0023.959-1.331-1.0210.005-0.069-0.2460.000
82K345TRP0-0.019-0.0126.831-0.295-0.2950.0000.0000.0000.000
83K346ARG10.7240.8192.3342.4323.6300.431-0.642-0.9870.002
84K347SER00.008-0.0097.290-0.125-0.1250.0000.0000.0000.000
85K348ILE00.0070.0199.861-0.132-0.1320.0000.0000.0000.000
86K349ASP-1-0.868-0.94412.5630.3290.3290.0000.0000.0000.000
87K350HIS0-0.058-0.03012.531-0.070-0.0700.0000.0000.0000.000
88K351PRO0-0.031-0.02013.4300.0380.0380.0000.0000.0000.000
89K352GLY0-0.0010.00113.256-0.005-0.0050.0000.0000.0000.000
90K353LYS10.8190.88911.224-0.370-0.3700.0000.0000.0000.000
91K354LEU00.0040.0074.804-0.004-0.0040.0000.0000.0000.000
92K355ILE0-0.007-0.0018.0950.0100.0100.0000.0000.0000.000
93K356PHE00.0300.0042.067-4.042-1.2443.510-1.291-5.0170.008
94K357ALA00.0450.0284.932-1.167-1.052-0.001-0.006-0.1090.000
95K358PRO0-0.013-0.0167.5840.1730.1730.0000.0000.0000.000
96K359ASP-1-0.767-0.87110.666-0.077-0.0770.0000.0000.0000.000
97K360LEU0-0.026-0.0136.775-0.033-0.0330.0000.0000.0000.000
98K361VAL00.0390.0378.9900.3610.3610.0000.0000.0000.000
99K362LEU0-0.022-0.0076.451-0.185-0.1850.0000.0000.0000.000
100K363ASP-1-0.788-0.88710.0680.3980.3980.0000.0000.0000.000
101K364ARG10.7860.84810.425-0.030-0.0300.0000.0000.0000.000
102K365ASP-1-0.825-0.91010.958-0.129-0.1290.0000.0000.0000.000
103K366GLU-1-0.737-0.84111.0940.2850.2850.0000.0000.0000.000
104K367GLY00.0270.0098.313-0.059-0.0590.0000.0000.0000.000
105K368LYS10.8300.9088.966-0.063-0.0630.0000.0000.0000.000
106K369CYS0-0.083-0.02110.401-0.046-0.0460.0000.0000.0000.000
107K370VAL00.038-0.0085.2700.0830.0830.0000.0000.0000.000
108K371GLU-1-0.829-0.8917.713-0.865-0.8650.0000.0000.0000.000
109K372GLY00.0360.0176.728-0.570-0.5700.0000.0000.0000.000
110K373ILE0-0.0170.0072.441-1.272-0.0850.993-0.328-1.8510.001
111K374LEU0-0.001-0.0035.1170.2760.357-0.001-0.001-0.0790.000
112K375GLU-1-0.823-0.8997.624-0.493-0.4930.0000.0000.0000.000
113K376ILE00.0250.0092.375-1.060-0.2681.946-0.377-2.361-0.001
114K377PHE0-0.010-0.0164.1790.0290.4580.000-0.023-0.4060.000
115K378ASP-1-0.741-0.8346.3930.1860.1860.0000.0000.0000.000
116K379MET0-0.039-0.0037.2090.0820.0820.0000.0000.0000.000
117K380LEU00.0430.0312.460-1.1630.0050.825-0.315-1.6770.000
118K381LEU00.0210.0296.8400.0880.0880.0000.0000.0000.000
119K382ALA0-0.0170.0119.935-0.013-0.0130.0000.0000.0000.000
120K383THR0-0.028-0.0418.569-0.042-0.0420.0000.0000.0000.000
121K384THR0-0.017-0.0218.0630.0710.0710.0000.0000.0000.000
122K385SER0-0.051-0.03610.379-0.053-0.0530.0000.0000.0000.000
123K386ARG10.8160.87913.501-0.210-0.2100.0000.0000.0000.000
124K387PHE00.017-0.0019.040-0.054-0.0540.0000.0000.0000.000
125K388ARG10.8880.95613.092-0.458-0.4580.0000.0000.0000.000
126K389GLU-1-0.859-0.90016.6000.1580.1580.0000.0000.0000.000
127K390LEU00.0210.01217.376-0.026-0.0260.0000.0000.0000.000
128K391LYS10.8220.91418.516-0.200-0.2000.0000.0000.0000.000
129K392LEU0-0.0090.02412.911-0.026-0.0260.0000.0000.0000.000
130K393GLN0-0.004-0.01816.8080.0050.0050.0000.0000.0000.000
131K394HIS00.0750.04112.8550.0430.0430.0000.0000.0000.000
132K395LYS10.8610.91315.683-0.073-0.0730.0000.0000.0000.000
133K396GLU-1-0.727-0.82817.3010.1780.1780.0000.0000.0000.000
134K397TYR0-0.016-0.0328.7500.0490.0490.0000.0000.0000.000
135K398LEU0-0.0370.00212.7380.0300.0300.0000.0000.0000.000
136K399CYS0-0.036-0.01214.485-0.013-0.0130.0000.0000.0000.000
137K400VAL00.0390.00712.557-0.010-0.0100.0000.0000.0000.000
138K401LYS10.8480.9228.198-0.320-0.3200.0000.0000.0000.000
139K402ALA00.0180.01111.946-0.012-0.0120.0000.0000.0000.000
140K403MET0-0.041-0.02815.180-0.017-0.0170.0000.0000.0000.000
141K404ILE0-0.024-0.0049.553-0.018-0.0180.0000.0000.0000.000
142K405LEU00.0140.00213.221-0.017-0.0170.0000.0000.0000.000
143K406LEU0-0.034-0.02114.582-0.026-0.0260.0000.0000.0000.000
144K407ASN0-0.059-0.04316.707-0.024-0.0240.0000.0000.0000.000
145K408SER00.0080.01814.351-0.016-0.0160.0000.0000.0000.000
146K409SER00.0200.00615.281-0.008-0.0080.0000.0000.0000.000
147K410MET00.0160.04214.388-0.016-0.0160.0000.0000.0000.000
148K411TYR0-0.038-0.03218.0600.0050.0050.0000.0000.0000.000
149K412PRO00.0420.02521.038-0.007-0.0070.0000.0000.0000.000
150K413LEU00.0290.01624.092-0.001-0.0010.0000.0000.0000.000
151K414VAL0-0.007-0.00527.065-0.001-0.0010.0000.0000.0000.000
152K415THR0-0.026-0.02324.1410.0000.0000.0000.0000.0000.000
153K416ALA00.0370.03726.5530.0010.0010.0000.0000.0000.000
154K417THR0-0.011-0.02127.597-0.003-0.0030.0000.0000.0000.000
155K418GLN0-0.012-0.01928.329-0.001-0.0010.0000.0000.0000.000
156K419ASP-1-0.846-0.91729.5080.0350.0350.0000.0000.0000.000
157K420ALA00.0000.00230.5810.0020.0020.0000.0000.0000.000
158K421ASP-1-0.865-0.93531.3140.0250.0250.0000.0000.0000.000
159K422SER0-0.026-0.02426.1450.0000.0000.0000.0000.0000.000
160K423SER00.0090.00226.0200.0060.0060.0000.0000.0000.000
161K424ARG10.9070.94627.062-0.035-0.0350.0000.0000.0000.000
162K425LYS10.7780.87426.469-0.027-0.0270.0000.0000.0000.000
163K426LEU00.0190.01520.6200.0030.0030.0000.0000.0000.000
164K427ALA00.0390.01823.8780.0070.0070.0000.0000.0000.000
165K428HIS00.0110.01326.0240.0000.0000.0000.0000.0000.000
166K429LEU0-0.026-0.01022.3800.0010.0010.0000.0000.0000.000
167K430LEU00.0230.02219.8460.0080.0080.0000.0000.0000.000
168K431ASN0-0.072-0.02222.5650.0040.0040.0000.0000.0000.000
169K432ALA00.0380.01824.8320.0050.0050.0000.0000.0000.000
170K433VAL0-0.024-0.01718.2850.0010.0010.0000.0000.0000.000
171K434THR00.004-0.00621.2680.0150.0150.0000.0000.0000.000
172K435ASP-1-0.867-0.93422.8460.0680.0680.0000.0000.0000.000
173K436ALA0-0.059-0.03022.067-0.001-0.0010.0000.0000.0000.000
174K437LEU00.0290.00918.4570.0030.0030.0000.0000.0000.000
175K438VAL00.0190.00821.6970.0010.0010.0000.0000.0000.000
176K439TRP0-0.022-0.00323.534-0.003-0.0030.0000.0000.0000.000
177K440VAL0-0.042-0.03320.638-0.004-0.0040.0000.0000.0000.000
178K441ILE00.0090.01821.5610.0000.0000.0000.0000.0000.000
179K442ALA0-0.0020.01824.471-0.004-0.0040.0000.0000.0000.000
180K443LYS10.7920.89225.505-0.085-0.0850.0000.0000.0000.000
181K444SER0-0.041-0.03024.7450.0000.0000.0000.0000.0000.000
182K445GLY0-0.009-0.00526.738-0.001-0.0010.0000.0000.0000.000
183K446ILE0-0.0240.00626.314-0.006-0.0060.0000.0000.0000.000
184K447SER00.0300.00630.415-0.002-0.0020.0000.0000.0000.000
185K448SER00.0780.03531.1660.0050.0050.0000.0000.0000.000
186K449GLN00.0650.02331.1560.0030.0030.0000.0000.0000.000
187K450GLN00.0170.01228.7650.0060.0060.0000.0000.0000.000
188K451GLN0-0.032-0.02126.9070.0080.0080.0000.0000.0000.000
189K452SER0-0.002-0.00826.1530.0060.0060.0000.0000.0000.000
190K453MET0-0.0060.00625.6090.0050.0050.0000.0000.0000.000
191K454ARG10.7660.84420.197-0.163-0.1630.0000.0000.0000.000
192K455LEU00.0350.01321.6860.0150.0150.0000.0000.0000.000
193K456ALA00.0140.00621.6090.0080.0080.0000.0000.0000.000
194K457ASN0-0.051-0.04620.0870.0040.0040.0000.0000.0000.000
195K458LEU00.010-0.00616.4760.0130.0130.0000.0000.0000.000
196K459LEU0-0.0080.00316.7300.0190.0190.0000.0000.0000.000
197K460MET0-0.0030.00017.502-0.005-0.0050.0000.0000.0000.000
198K461LEU0-0.0140.01113.429-0.009-0.0090.0000.0000.0000.000
199K462LEU00.0300.01212.8740.0150.0150.0000.0000.0000.000
200K463SER0-0.029-0.01613.258-0.023-0.0230.0000.0000.0000.000
201K464HIS0-0.026-0.01011.204-0.032-0.0320.0000.0000.0000.000
202K465VAL00.0100.0077.858-0.042-0.0420.0000.0000.0000.000
203K466ARG10.8290.8788.693-0.180-0.1800.0000.0000.0000.000
204K467HIS00.0120.01010.058-0.029-0.0290.0000.0000.0000.000
205K468ALA00.0310.0015.588-0.119-0.1190.0000.0000.0000.000
206K469SER0-0.009-0.0054.908-0.473-0.339-0.001-0.002-0.1310.000
207K470ASN0-0.029-0.0146.3890.0030.0030.0000.0000.0000.000
208K471LYS10.7930.8845.1120.7200.7200.0000.0000.0000.000
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210K473MET0-0.0010.0063.1831.3461.9140.0770.265-0.910-0.005
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