Manual

About

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: XQGYX

Calculation Name: 4J24-C-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 4J24

Chain ID: C

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 -3051632.178228
FMO2-HF: Nuclear repulsion 2955236.348194
FMO2-HF: Total energy -96395.830034
FMO2-MP2: Total energy -96666.287196


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.
-83.289-63.76776.441-27.702-68.2620.091


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


Summations of interaction energy for fragment #235(J: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.
-83.289-63.76776.441-27.702-68.262-0.091
Interaction energy analysis for fragmet #235(J:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.089 / q_NPA : -0.082
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].
1J264SER10.8430.90430.207-0.009-0.0090.0000.0000.0000.000
2J265PRO00.1610.06327.023-0.003-0.0030.0000.0000.0000.000
3J266GLU-1-0.778-0.87025.5050.0500.0500.0000.0000.0000.000
4J267GLN00.0490.02125.1850.0020.0020.0000.0000.0000.000
5J268LEU00.0270.04323.282-0.004-0.0040.0000.0000.0000.000
6J269VAL00.031-0.01019.813-0.004-0.0040.0000.0000.0000.000
7J270LEU0-0.067-0.00920.5250.0120.0120.0000.0000.0000.000
8J271THR00.0260.00220.689-0.006-0.0060.0000.0000.0000.000
9J272LEU0-0.015-0.02017.612-0.013-0.0130.0000.0000.0000.000
10J273LEU0-0.028-0.00516.1860.0130.0130.0000.0000.0000.000
11J274GLU-1-0.844-0.94316.144-0.017-0.0170.0000.0000.0000.000
12J275ALA00.0070.00615.736-0.030-0.0300.0000.0000.0000.000
13J276GLU-1-0.781-0.84911.0520.0480.0480.0000.0000.0000.000
14J277PRO0-0.0130.0068.050-0.002-0.0020.0000.0000.0000.000
15J278PRO0-0.031-0.01410.6500.1010.1010.0000.0000.0000.000
16J279HIS0-0.009-0.0147.201-0.229-0.2290.0000.0000.0000.000
17J280VAL0-0.025-0.0055.4670.2710.2710.0000.0000.0000.000
18J281LEU00.0090.0127.2290.1920.1920.0000.0000.0000.000
19J282ILE0-0.077-0.0566.586-0.258-0.2580.0000.0000.0000.000
20J283SER0-0.017-0.0259.3690.1480.1480.0000.0000.0000.000
21J284ARG10.7530.84411.658-0.560-0.5600.0000.0000.0000.000
22J285PRO0-0.0070.00511.578-0.076-0.0760.0000.0000.0000.000
23J286SER0-0.023-0.00614.7490.0110.0110.0000.0000.0000.000
24J287ALA0-0.009-0.00916.652-0.032-0.0320.0000.0000.0000.000
25J288PRO0-0.008-0.00915.7340.0410.0410.0000.0000.0000.000
26J289PHE00.0060.01010.1760.0160.0160.0000.0000.0000.000
27J290THR00.0170.00812.531-0.050-0.0500.0000.0000.0000.000
28J291GLU-1-0.701-0.8467.9900.0670.0670.0000.0000.0000.000
29J292ALA00.0790.0308.2480.2640.2640.0000.0000.0000.000
30J293SER0-0.064-0.0339.4820.1040.1040.0000.0000.0000.000
31J294MET00.0560.0335.563-0.001-0.0010.0000.0000.0000.000
32J295MET00.0520.0352.390-3.298-1.8252.349-0.813-3.0090.007
33J296MET00.0260.0415.556-0.064-0.0640.0000.0000.0000.000
34J297SER0-0.046-0.0267.532-0.340-0.3400.0000.0000.0000.000
35J298LEU00.015-0.0052.227-3.642-1.0512.814-0.870-4.5340.002
36J299THR00.000-0.0232.731-5.381-2.6510.644-1.184-2.190-0.017
37J300LYS10.8930.9414.410-0.907-0.7580.000-0.008-0.1410.000
38J301LEU0-0.0240.0012.184-1.3280.0602.868-0.998-3.2580.006
39J302ALA00.0470.0112.297-3.118-1.0711.573-1.105-2.5140.004
40J303ASP-1-0.837-0.9193.489-0.282-0.1410.0430.083-0.2670.001
41J304LYS10.8630.9396.7070.9170.9170.0000.0000.0000.000
42J305GLU-1-0.780-0.8671.566-25.496-36.45423.250-8.303-3.989-0.071
43J306LEU00.0370.0295.6520.6030.6030.0000.0000.0000.000
44J307VAL00.0140.0068.1480.2130.2130.0000.0000.0000.000
45J308HIS0-0.034-0.0408.3660.2400.2400.0000.0000.0000.000
46J309MET00.0020.0378.1010.1750.1750.0000.0000.0000.000
47J310ILE00.0160.0129.8430.1350.1350.0000.0000.0000.000
48J311SER0-0.057-0.02812.4590.0840.0840.0000.0000.0000.000
49J312TRP00.008-0.00211.2470.0570.0570.0000.0000.0000.000
50J313ALA00.0520.01613.1670.0520.0520.0000.0000.0000.000
51J314LYS10.8590.92115.0660.1370.1370.0000.0000.0000.000
52J315LYS10.8170.93014.7060.1880.1880.0000.0000.0000.000
53J316ILE0-0.0240.00415.1590.0190.0190.0000.0000.0000.000
54J317PRO0-0.011-0.02219.320-0.001-0.0010.0000.0000.0000.000
55J318GLY00.0250.01123.1550.0050.0050.0000.0000.0000.000
56J319PHE00.0540.02017.5170.0000.0000.0000.0000.0000.000
57J320VAL0-0.025-0.01621.200-0.004-0.0040.0000.0000.0000.000
58J321GLU-1-0.904-0.94222.908-0.034-0.0340.0000.0000.0000.000
59J322LEU0-0.0010.02221.3990.0040.0040.0000.0000.0000.000
60J323SER0-0.026-0.03924.961-0.004-0.0040.0000.0000.0000.000
61J324LEU00.015-0.00622.758-0.003-0.0030.0000.0000.0000.000
62J325PHE00.0440.02022.607-0.004-0.0040.0000.0000.0000.000
63J326ASP-1-0.755-0.80621.321-0.054-0.0540.0000.0000.0000.000
64J327GLN0-0.096-0.05119.210-0.012-0.0120.0000.0000.0000.000
65J328VAL00.0290.02417.250-0.015-0.0150.0000.0000.0000.000
66J329ARG10.8890.93116.6560.0610.0610.0000.0000.0000.000
67J330LEU0-0.037-0.01916.6640.0000.0000.0000.0000.0000.000
68J331LEU00.001-0.00513.1800.0100.0100.0000.0000.0000.000
69J332GLU-1-0.869-0.95312.401-0.042-0.0420.0000.0000.0000.000
70J333SER0-0.037-0.00711.7950.0010.0010.0000.0000.0000.000
71J334CYS0-0.066-0.01911.008-0.012-0.0120.0000.0000.0000.000
72J335TRP00.0560.0094.571-0.1830.103-0.001-0.005-0.2810.000
73J336MET00.0040.0272.509-1.634-0.7542.899-0.567-3.213-0.001
74J337GLU-1-0.791-0.8904.5500.0110.190-0.001-0.009-0.1700.000
75J338VAL0-0.039-0.0216.7310.2240.2240.0000.0000.0000.000
76J339LEU00.0020.0122.652-3.979-0.6732.560-1.429-4.4370.012
77J340MET0-0.0330.0032.267-1.7410.7334.570-1.444-5.601-0.007
78J341MET0-0.010-0.0063.6080.0010.1180.0060.069-0.1910.000
79J342GLY0-0.0030.0035.227-0.279-0.2790.0000.0000.0000.000
80J343LEU00.0100.0162.324-3.425-1.8963.725-1.185-4.0690.005
81J344MET0-0.022-0.0034.366-1.056-0.8550.000-0.035-0.1670.000
82J345TRP0-0.027-0.0147.197-0.220-0.2200.0000.0000.0000.000
83J346ARG10.7460.8382.7590.3171.1250.145-0.295-0.6580.001
84J347SER00.009-0.0107.421-0.069-0.0690.0000.0000.0000.000
85J348ILE00.0080.01910.056-0.131-0.1310.0000.0000.0000.000
86J349ASP-1-0.876-0.94212.8140.3500.3500.0000.0000.0000.000
87J350HIS0-0.056-0.02812.496-0.059-0.0590.0000.0000.0000.000
88J351PRO0-0.023-0.01213.3850.0310.0310.0000.0000.0000.000
89J352GLY0-0.007-0.00313.3170.0090.0090.0000.0000.0000.000
90J353LYS10.8250.89111.134-0.471-0.4710.0000.0000.0000.000
91J354LEU0-0.0010.0064.731-0.177-0.033-0.001-0.004-0.1400.000
92J355ILE0-0.0130.0007.9630.0720.0720.0000.0000.0000.000
93J356PHE00.0240.0012.096-4.766-1.7194.454-1.487-6.0140.011
94J357ALA00.0430.0295.041-1.026-0.916-0.001-0.005-0.1040.000
95J358PRO0-0.014-0.0167.7560.1540.1540.0000.0000.0000.000
96J359ASP-1-0.766-0.87110.8880.0740.0740.0000.0000.0000.000
97J360LEU0-0.025-0.0106.534-0.019-0.0190.0000.0000.0000.000
98J361VAL00.0320.0338.9000.3770.3770.0000.0000.0000.000
99J362LEU0-0.023-0.0076.415-0.173-0.1730.0000.0000.0000.000
100J363ASP-1-0.784-0.8839.9680.4910.4910.0000.0000.0000.000
101J364ARG10.7900.8469.938-0.017-0.0170.0000.0000.0000.000
102J365ASP-1-0.807-0.90410.4880.0070.0070.0000.0000.0000.000
103J366GLU-1-0.738-0.83910.6970.5810.5810.0000.0000.0000.000
104J367GLY00.0210.0118.0170.0190.0190.0000.0000.0000.000
105J368LYS10.8100.8898.453-0.260-0.2600.0000.0000.0000.000
106J369CYS0-0.082-0.0299.311-0.022-0.0220.0000.0000.0000.000
107J370VAL00.002-0.0064.641-0.0210.108-0.001-0.003-0.1250.000
108J371GLU-1-0.813-0.8947.665-0.794-0.7940.0000.0000.0000.000
109J372GLY00.0350.0176.628-0.514-0.5140.0000.0000.0000.000
110J373ILE0-0.0160.0112.165-1.436-0.7342.692-0.516-2.8770.001
111J374LEU0-0.015-0.0104.6570.0810.195-0.001-0.004-0.1100.000
112J375GLU-1-0.862-0.9326.937-0.982-0.9820.0000.0000.0000.000
113J376ILE00.028-0.0032.520-1.356-0.2992.084-0.437-2.7040.000
114J377PHE00.007-0.0063.9480.0010.5960.001-0.045-0.5520.000
115J378ASP-1-0.743-0.8356.1340.1880.1880.0000.0000.0000.000
116J379MET0-0.064-0.0086.8680.1190.1190.0000.0000.0000.000
117J380LEU00.0460.0242.362-0.937-0.1241.212-0.285-1.740-0.002
118J381LEU00.0270.0356.6790.0840.0840.0000.0000.0000.000
119J382ALA00.0000.0179.645-0.012-0.0120.0000.0000.0000.000
120J383THR0-0.039-0.0359.007-0.037-0.0370.0000.0000.0000.000
121J384THR00.003-0.0138.1940.0690.0690.0000.0000.0000.000
122J385SER0-0.059-0.03010.560-0.036-0.0360.0000.0000.0000.000
123J386ARG10.9330.96812.545-0.059-0.0590.0000.0000.0000.000
124J387PHE00.0310.0029.978-0.048-0.0480.0000.0000.0000.000
125J388ARG10.8530.93413.439-0.434-0.4340.0000.0000.0000.000
126J389GLU-1-0.945-0.98416.7180.1300.1300.0000.0000.0000.000
127J390LEU0-0.015-0.01117.572-0.024-0.0240.0000.0000.0000.000
128J391LYS10.8680.94218.985-0.150-0.1500.0000.0000.0000.000
129J392LEU0-0.0070.02013.526-0.022-0.0220.0000.0000.0000.000
130J393GLN0-0.004-0.01617.3660.0170.0170.0000.0000.0000.000
131J394HIS00.0780.04113.7330.0300.0300.0000.0000.0000.000
132J395LYS10.8560.90916.285-0.053-0.0530.0000.0000.0000.000
133J396GLU-1-0.728-0.82917.8440.1220.1220.0000.0000.0000.000
134J397TYR0-0.011-0.0289.3340.0270.0270.0000.0000.0000.000
135J398LEU0-0.0440.00113.3910.0110.0110.0000.0000.0000.000
136J399CYS0-0.032-0.01015.063-0.023-0.0230.0000.0000.0000.000
137J400VAL00.0320.00812.929-0.017-0.0170.0000.0000.0000.000
138J401LYS10.8450.9148.622-0.163-0.1630.0000.0000.0000.000
139J402ALA00.0130.00912.439-0.031-0.0310.0000.0000.0000.000
140J403MET0-0.030-0.02315.654-0.016-0.0160.0000.0000.0000.000
141J404ILE0-0.029-0.00910.026-0.015-0.0150.0000.0000.0000.000
142J405LEU00.0120.00013.836-0.026-0.0260.0000.0000.0000.000
143J406LEU0-0.043-0.01514.987-0.021-0.0210.0000.0000.0000.000
144J407ASN0-0.040-0.02317.127-0.006-0.0060.0000.0000.0000.000
145J408SER00.0010.01414.766-0.016-0.0160.0000.0000.0000.000
146J409SER00.025-0.00315.717-0.023-0.0230.0000.0000.0000.000
147J410MET0-0.0250.00018.5140.0070.0070.0000.0000.0000.000
148J411TYR00.0270.00619.497-0.006-0.0060.0000.0000.0000.000
149J412PRO0-0.0120.00823.3370.0070.0070.0000.0000.0000.000
150J413LEU0-0.009-0.00826.369-0.002-0.0020.0000.0000.0000.000
151J414VAL00.0180.01029.6630.0020.0020.0000.0000.0000.000
152J415THR0-0.021-0.01033.1950.0010.0010.0000.0000.0000.000
153J416ALA0-0.005-0.01033.842-0.002-0.0020.0000.0000.0000.000
154J417THR0-0.007-0.01032.2690.0010.0010.0000.0000.0000.000
155J418GLN00.0200.01735.3270.0010.0010.0000.0000.0000.000
156J419ASP-1-0.779-0.86832.119-0.032-0.0320.0000.0000.0000.000
157J420ALA00.0230.02031.3730.0020.0020.0000.0000.0000.000
158J421ASP-1-0.776-0.89731.248-0.032-0.0320.0000.0000.0000.000
159J422SER0-0.031-0.04125.782-0.002-0.0020.0000.0000.0000.000
160J423SER0-0.063-0.04027.3870.0010.0010.0000.0000.0000.000
161J424ARG10.8370.89427.9150.0310.0310.0000.0000.0000.000
162J425LYS10.7980.90427.3050.0370.0370.0000.0000.0000.000
163J426LEU00.0390.01621.1840.0030.0030.0000.0000.0000.000
164J427ALA00.0130.00624.3420.0040.0040.0000.0000.0000.000
165J428HIS0-0.018-0.00726.5800.0040.0040.0000.0000.0000.000
166J429LEU0-0.001-0.01221.5500.0040.0040.0000.0000.0000.000
167J430LEU00.0050.01120.4250.0080.0080.0000.0000.0000.000
168J431ASN0-0.0160.01223.0190.0070.0070.0000.0000.0000.000
169J432ALA00.0620.03525.3850.0060.0060.0000.0000.0000.000
170J433VAL0-0.036-0.02418.8090.0060.0060.0000.0000.0000.000
171J434THR0-0.007-0.01321.7250.0140.0140.0000.0000.0000.000
172J435ASP-1-0.911-0.96423.2400.0150.0150.0000.0000.0000.000
173J436ALA0-0.068-0.03622.6940.0040.0040.0000.0000.0000.000
174J437LEU00.0230.00718.9060.0080.0080.0000.0000.0000.000
175J438VAL00.0210.00922.2450.0060.0060.0000.0000.0000.000
176J439TRP0-0.021-0.00224.2530.0020.0020.0000.0000.0000.000
177J440VAL0-0.044-0.03521.2430.0010.0010.0000.0000.0000.000
178J441ILE00.0080.01821.9810.0050.0050.0000.0000.0000.000
179J442ALA0-0.0050.01724.9880.0000.0000.0000.0000.0000.000
180J443LYS10.7950.89026.130-0.056-0.0560.0000.0000.0000.000
181J444SER0-0.041-0.02925.1250.0030.0030.0000.0000.0000.000
182J445GLY0-0.007-0.00427.1280.0010.0010.0000.0000.0000.000
183J446ILE0-0.0180.00826.528-0.005-0.0050.0000.0000.0000.000
184J447SER00.0510.01830.658-0.003-0.0030.0000.0000.0000.000
185J448SER00.0650.02431.5700.0020.0020.0000.0000.0000.000
186J449GLN00.0560.03031.4650.0040.0040.0000.0000.0000.000
187J450GLN00.011-0.00128.6990.0050.0050.0000.0000.0000.000
188J451GLN0-0.033-0.02027.2940.0040.0040.0000.0000.0000.000
189J452SER00.005-0.00326.5060.0020.0020.0000.0000.0000.000
190J453MET0-0.0110.00125.861-0.001-0.0010.0000.0000.0000.000
191J454ARG10.7660.84820.715-0.122-0.1220.0000.0000.0000.000
192J455LEU00.0320.01221.9760.0090.0090.0000.0000.0000.000
193J456ALA00.0180.00721.9450.0010.0010.0000.0000.0000.000
194J457ASN0-0.051-0.04520.419-0.006-0.0060.0000.0000.0000.000
195J458LEU00.0220.00716.6530.0050.0050.0000.0000.0000.000
196J459LEU00.002-0.00317.1470.0050.0050.0000.0000.0000.000
197J460MET0-0.0110.00018.081-0.016-0.0160.0000.0000.0000.000
198J461LEU0-0.0180.00114.015-0.023-0.0230.0000.0000.0000.000
199J462LEU00.0320.02813.2990.0070.0070.0000.0000.0000.000
200J463SER0-0.047-0.02913.092-0.029-0.0290.0000.0000.0000.000
201J464HIS00.003-0.00212.196-0.067-0.0670.0000.0000.0000.000
202J465VAL00.0070.0057.620-0.043-0.0430.0000.0000.0000.000
203J466ARG10.8120.8818.4250.0250.0250.0000.0000.0000.000
204J467HIS0-0.026-0.00710.075-0.071-0.0710.0000.0000.0000.000
205J468ALA00.032-0.0015.943-0.188-0.1880.0000.0000.0000.000
206J469SER00.011-0.0055.181-0.594-0.473-0.001-0.004-0.1160.000
207J470ASN00.0140.0036.159-0.198-0.1980.0000.0000.0000.000
208J471LYS10.8260.9135.9131.0981.0980.0000.0000.0000.000
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