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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: PGZ1X

Calculation Name: 1ZAF-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 3-bromo-6-hydroxy-2-(4-hydroxyphenyl)-1h-inden-1-one

ligand 3-letter code: 789

PDB ID: 1ZAF

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 -3072409.102596
FMO2-HF: Nuclear repulsion 2973488.823816
FMO2-HF: Total energy -98920.278779
FMO2-MP2: Total energy -99190.83214


3D Structure
Snapshot
 
Ligand structure

789

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.
-90.854-69.35364.149-25.567-60.0820.064


Interactive mode: IFIE and PIEDA for fragment #235(D:202:789)


Summations of interaction energy for fragment #235(D:202:789)
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.
-90.854-69.35364.149-25.567-60.082-0.064
Interaction energy analysis for fragmet #235(D:202:789)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.083
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].
1D264SER10.8340.91730.691-0.118-0.1180.0000.0000.0000.000
2D265PRO00.1590.06325.7060.0000.0000.0000.0000.0000.000
3D266GLU-1-0.760-0.86025.3410.1500.1500.0000.0000.0000.000
4D267GLN00.012-0.00125.2190.0030.0030.0000.0000.0000.000
5D268LEU00.0160.04020.502-0.002-0.0020.0000.0000.0000.000
6D269VAL00.0390.01621.1200.0100.0100.0000.0000.0000.000
7D270LEU0-0.034-0.01220.6240.0150.0150.0000.0000.0000.000
8D271THR00.045-0.00620.3040.0060.0060.0000.0000.0000.000
9D272LEU00.0290.01216.327-0.006-0.0060.0000.0000.0000.000
10D273LEU0-0.015-0.00515.5310.0150.0150.0000.0000.0000.000
11D274GLU-1-0.877-0.92415.6010.1120.1120.0000.0000.0000.000
12D275ALA00.0170.02314.849-0.018-0.0180.0000.0000.0000.000
13D276GLU-1-0.792-0.85410.7720.3420.3420.0000.0000.0000.000
14D277PRO00.0430.0317.038-0.013-0.0130.0000.0000.0000.000
15D278PRO0-0.0010.0118.801-0.063-0.0630.0000.0000.0000.000
16D279HIS0-0.052-0.0477.4260.0000.0000.0000.0000.0000.000
17D280VAL00.0420.0246.0730.2840.2840.0000.0000.0000.000
18D281LEU00.0010.0048.0860.1110.1110.0000.0000.0000.000
19D282ILE0-0.035-0.0286.357-0.005-0.0050.0000.0000.0000.000
20D283SER0-0.005-0.0199.675-0.016-0.0160.0000.0000.0000.000
21D284ARG10.7720.87311.855-0.267-0.2670.0000.0000.0000.000
22D285PRO0-0.0020.02413.326-0.057-0.0570.0000.0000.0000.000
23D286SER0-0.026-0.03116.2740.0080.0080.0000.0000.0000.000
24D287ALA0-0.015-0.00218.349-0.032-0.0320.0000.0000.0000.000
25D288PRO00.0350.01717.0890.0560.0560.0000.0000.0000.000
26D289PHE0-0.003-0.00210.8040.0230.0230.0000.0000.0000.000
27D290THR00.002-0.00612.886-0.107-0.1070.0000.0000.0000.000
28D291GLU-1-0.780-0.8887.269-2.051-2.0510.0000.0000.0000.000
29D292ALA00.0470.0268.3480.1090.1090.0000.0000.0000.000
30D293SER0-0.033-0.0229.9010.2820.2820.0000.0000.0000.000
31D294MET00.0360.0307.1300.1880.1880.0000.0000.0000.000
32D295MET00.0210.0133.512-2.290-0.2270.612-0.752-1.9230.008
33D296MET00.0020.0185.6900.9530.9530.0000.0000.0000.000
34D297SER0-0.039-0.0317.9430.1540.1540.0000.0000.0000.000
35D298LEU00.0080.0023.074-2.644-0.3190.188-0.549-1.9640.004
36D299THR00.022-0.0043.142-1.0481.1450.118-0.820-1.491-0.006
37D300LYS10.8050.8864.802-1.452-1.321-0.001-0.004-0.1260.000
38D301LEU0-0.0270.0012.210-1.760-0.5411.433-0.576-2.0760.002
39D302ALA00.0420.0082.298-4.196-2.3792.073-1.151-2.7390.006
40D303ASP-1-0.849-0.9303.7650.0400.3230.022-0.022-0.2830.000
41D304LYS10.8820.9427.009-0.535-0.5350.0000.0000.0000.000
42D305GLU-1-0.795-0.8671.608-27.519-35.40518.340-6.663-3.790-0.067
43D306LEU00.0270.0185.8220.3120.3120.0000.0000.0000.000
44D307VAL00.0090.0118.327-0.081-0.0810.0000.0000.0000.000
45D308HIS0-0.038-0.0227.4020.1230.1230.0000.0000.0000.000
46D309MET0-0.0450.0046.9740.0640.0640.0000.0000.0000.000
47D310ILE00.0350.0129.9800.0190.0190.0000.0000.0000.000
48D311SER0-0.038-0.02413.079-0.022-0.0220.0000.0000.0000.000
49D312TRP0-0.052-0.03111.4320.0200.0200.0000.0000.0000.000
50D313ALA00.0350.01113.379-0.002-0.0020.0000.0000.0000.000
51D314LYS10.7860.88915.157-0.248-0.2480.0000.0000.0000.000
52D315LYS10.8310.89516.975-0.147-0.1470.0000.0000.0000.000
53D316ILE0-0.039-0.00614.813-0.014-0.0140.0000.0000.0000.000
54D317PRO0-0.003-0.01119.2610.0020.0020.0000.0000.0000.000
55D318GLY00.0410.02322.3250.0140.0140.0000.0000.0000.000
56D319PHE00.025-0.00917.319-0.008-0.0080.0000.0000.0000.000
57D320VAL0-0.034-0.01320.4320.0020.0020.0000.0000.0000.000
58D321GLU-1-0.853-0.91522.1720.1480.1480.0000.0000.0000.000
59D322LEU0-0.0100.01521.499-0.015-0.0150.0000.0000.0000.000
60D323SER00.006-0.01325.0770.0000.0000.0000.0000.0000.000
61D324LEU00.0220.00423.3740.0180.0180.0000.0000.0000.000
62D325PHE00.0450.01323.3890.0220.0220.0000.0000.0000.000
63D326ASP-1-0.805-0.86622.3250.2170.2170.0000.0000.0000.000
64D327GLN0-0.045-0.03719.8150.0430.0430.0000.0000.0000.000
65D328VAL00.0080.02517.0520.0320.0320.0000.0000.0000.000
66D329ARG10.8960.93616.994-0.184-0.1840.0000.0000.0000.000
67D330LEU0-0.053-0.03017.3180.0270.0270.0000.0000.0000.000
68D331LEU00.0340.01212.1920.0530.0530.0000.0000.0000.000
69D332GLU-1-0.852-0.95212.7110.6450.6450.0000.0000.0000.000
70D333SER0-0.078-0.04713.0050.0650.0650.0000.0000.0000.000
71D334CYS0-0.071-0.03911.367-0.062-0.0620.0000.0000.0000.000
72D335TRP00.0620.0154.5680.2150.555-0.001-0.012-0.3280.000
73D336MET00.0260.0193.050-2.9820.3251.699-0.765-4.2410.005
74D337GLU-1-0.799-0.8974.6500.6960.887-0.001-0.008-0.1820.000
75D338VAL0-0.028-0.0136.311-0.004-0.0040.0000.0000.0000.000
76D339LEU00.0040.0072.651-3.502-1.0753.583-1.462-4.5480.010
77D340MET0-0.032-0.0052.322-2.6850.3182.992-1.553-4.442-0.004
78D341MET0-0.0110.0033.1150.5940.1310.0210.655-0.2130.000
79D342GLY00.0020.0045.213-0.320-0.3200.0000.0000.0000.000
80D343LEU0-0.0080.0102.294-3.919-1.6913.284-1.254-4.2580.009
81D344MET0-0.0100.0094.288-1.140-0.9300.001-0.050-0.1610.000
82D345TRP0-0.034-0.0187.129-0.290-0.2900.0000.0000.0000.000
83D346ARG10.7630.8502.3692.6163.5980.444-0.487-0.9390.001
84D347SER0-0.003-0.0107.522-0.063-0.0630.0000.0000.0000.000
85D348ILE0-0.0050.00510.165-0.139-0.1390.0000.0000.0000.000
86D349ASP-1-0.852-0.90812.8770.4390.4390.0000.0000.0000.000
87D350HIS00.006-0.01413.030-0.065-0.0650.0000.0000.0000.000
88D351PRO0-0.0160.00415.0920.0090.0090.0000.0000.0000.000
89D352GLY0-0.004-0.00513.285-0.051-0.0510.0000.0000.0000.000
90D353LYS10.8080.89311.279-0.405-0.4050.0000.0000.0000.000
91D354LEU0-0.0040.0025.112-0.161-0.0300.000-0.008-0.1220.000
92D355ILE00.0060.0018.1100.0420.0420.0000.0000.0000.000
93D356PHE00.0440.0082.823-4.706-1.4703.589-1.149-5.6770.011
94D357ALA00.0230.0064.508-1.899-1.763-0.001-0.012-0.1230.000
95D358PRO0-0.022-0.0197.2300.2500.2500.0000.0000.0000.000
96D359ASP-1-0.852-0.89010.8320.2920.2920.0000.0000.0000.000
97D360LEU0-0.033-0.0186.4220.0180.0180.0000.0000.0000.000
98D361VAL00.0260.0188.5610.3390.3390.0000.0000.0000.000
99D362LEU0-0.016-0.0096.911-0.175-0.111-0.0010.000-0.0630.000
100D363ASP-1-0.781-0.87510.3460.3930.3930.0000.0000.0000.000
101D364ARG10.8140.84810.5760.3110.3110.0000.0000.0000.000
102D365ASP-1-0.890-0.95011.645-0.142-0.1420.0000.0000.0000.000
103D366GLU-1-0.744-0.85611.6050.2100.2100.0000.0000.0000.000
104D367GLY00.0130.0128.370-0.101-0.1010.0000.0000.0000.000
105D368LYS10.7560.8548.9770.8620.8620.0000.0000.0000.000
106D369CYS0-0.079-0.01910.852-0.081-0.0810.0000.0000.0000.000
107D370VAL00.0140.0045.059-0.034-0.0340.0000.0000.0000.000
108D371GLU-1-0.825-0.8908.118-1.411-1.4110.0000.0000.0000.000
109D372GLY00.005-0.0046.683-1.333-1.3330.0000.0000.0000.000
110D373ILE0-0.019-0.0172.593-1.693-0.6903.275-0.696-3.5820.007
111D374LEU00.0200.0114.8230.8240.961-0.001-0.004-0.1330.000
112D375GLU-1-0.834-0.9047.427-1.490-1.4900.0000.0000.0000.000
113D376ILE00.016-0.0022.684-1.0970.2700.860-0.357-1.870-0.001
114D377PHE00.0210.0014.1950.1660.8440.035-0.106-0.6070.000
115D378ASP-1-0.758-0.8386.456-0.115-0.091-0.001-0.001-0.0230.000
116D379MET0-0.0390.0107.6460.2900.2900.0000.0000.0000.000
117D380LEU00.0450.0233.346-0.665-0.0450.602-0.183-1.038-0.002
118D381LEU00.0190.0277.6790.1240.1240.0000.0000.0000.000
119D382ALA0-0.0090.01410.320-0.005-0.0050.0000.0000.0000.000
120D383THR0-0.022-0.03210.337-0.019-0.0190.0000.0000.0000.000
121D384THR0-0.020-0.0279.4760.0850.0850.0000.0000.0000.000
122D385SER0-0.055-0.03711.623-0.049-0.0490.0000.0000.0000.000
123D386ARG10.8260.89015.005-0.187-0.1870.0000.0000.0000.000
124D387PHE00.044-0.0049.660-0.051-0.0510.0000.0000.0000.000
125D388ARG10.8040.90113.543-0.521-0.5210.0000.0000.0000.000
126D389GLU-1-0.861-0.90616.8590.1260.1260.0000.0000.0000.000
127D390LEU0-0.052-0.01917.552-0.026-0.0260.0000.0000.0000.000
128D391LYS10.9030.95819.084-0.194-0.1940.0000.0000.0000.000
129D392LEU0-0.0090.01913.353-0.017-0.0170.0000.0000.0000.000
130D393GLN0-0.019-0.02317.1930.0010.0010.0000.0000.0000.000
131D394HIS00.0820.04013.2810.0400.0400.0000.0000.0000.000
132D395LYS10.8250.89215.826-0.208-0.2080.0000.0000.0000.000
133D396GLU-1-0.750-0.85617.2200.2580.2580.0000.0000.0000.000
134D397TYR0-0.013-0.0178.7490.0490.0490.0000.0000.0000.000
135D398LEU0-0.051-0.01412.7960.0350.0350.0000.0000.0000.000
136D399CYS0-0.020-0.00514.6890.0020.0020.0000.0000.0000.000
137D400VAL00.0350.01212.172-0.006-0.0060.0000.0000.0000.000
138D401LYS10.7920.8888.173-0.525-0.5250.0000.0000.0000.000
139D402ALA00.0190.00611.7510.0210.0210.0000.0000.0000.000
140D403MET0-0.030-0.01614.976-0.015-0.0150.0000.0000.0000.000
141D404ILE0-0.013-0.0089.385-0.022-0.0220.0000.0000.0000.000
142D405LEU0-0.010-0.00212.9320.0100.0100.0000.0000.0000.000
143D406LEU0-0.0140.00714.076-0.034-0.0340.0000.0000.0000.000
144D407ASN0-0.044-0.01513.317-0.105-0.1050.0000.0000.0000.000
145D408SER0-0.0010.01115.055-0.051-0.0510.0000.0000.0000.000
146D409SER0-0.022-0.01616.471-0.031-0.0310.0000.0000.0000.000
147D410MET00.0180.01118.666-0.019-0.0190.0000.0000.0000.000
148D411TYR00.019-0.00121.4830.0080.0080.0000.0000.0000.000
149D412PRO00.0380.01523.857-0.016-0.0160.0000.0000.0000.000
150D413LEU00.0090.01125.572-0.014-0.0140.0000.0000.0000.000
151D414VAL0-0.037-0.01426.813-0.007-0.0070.0000.0000.0000.000
152D415THR0-0.021-0.02229.7580.0070.0070.0000.0000.0000.000
153D416ALA0-0.0010.02731.5160.0020.0020.0000.0000.0000.000
154D417THR0-0.030-0.01630.5690.0040.0040.0000.0000.0000.000
155D418GLN00.0430.02529.580-0.011-0.0110.0000.0000.0000.000
156D419ASP-1-0.845-0.91934.6170.0920.0920.0000.0000.0000.000
157D420ALA0-0.007-0.00933.3790.0020.0020.0000.0000.0000.000
158D421ASP-1-0.802-0.87930.5290.1330.1330.0000.0000.0000.000
159D422SER0-0.018-0.01726.5320.0100.0100.0000.0000.0000.000
160D423SER00.0470.01726.7530.0080.0080.0000.0000.0000.000
161D424ARG10.7740.87827.869-0.109-0.1090.0000.0000.0000.000
162D425LYS10.8060.88926.573-0.150-0.1500.0000.0000.0000.000
163D426LEU00.0230.01320.8340.0050.0050.0000.0000.0000.000
164D427ALA00.0270.01623.3960.0120.0120.0000.0000.0000.000
165D428HIS0-0.014-0.00425.589-0.002-0.0020.0000.0000.0000.000
166D429LEU0-0.013-0.00322.020-0.002-0.0020.0000.0000.0000.000
167D430LEU00.0180.01919.6830.0100.0100.0000.0000.0000.000
168D431ASN0-0.0080.01522.1630.0060.0060.0000.0000.0000.000
169D432ALA00.0480.02624.3340.0060.0060.0000.0000.0000.000
170D433VAL0-0.023-0.01918.061-0.001-0.0010.0000.0000.0000.000
171D434THR00.004-0.01320.6790.0170.0170.0000.0000.0000.000
172D435ASP-1-0.918-0.96622.0710.1410.1410.0000.0000.0000.000
173D436ALA0-0.066-0.03721.607-0.007-0.0070.0000.0000.0000.000
174D437LEU00.0130.00817.967-0.002-0.0020.0000.0000.0000.000
175D438VAL00.0320.01021.215-0.006-0.0060.0000.0000.0000.000
176D439TRP0-0.003-0.01724.675-0.010-0.0100.0000.0000.0000.000
177D440VAL0-0.029-0.02020.380-0.009-0.0090.0000.0000.0000.000
178D441ILE0-0.0130.00721.015-0.006-0.0060.0000.0000.0000.000
179D442ALA0-0.037-0.00124.359-0.009-0.0090.0000.0000.0000.000
180D443LYS10.8130.88825.775-0.148-0.1480.0000.0000.0000.000
181D444SER0-0.076-0.03824.533-0.002-0.0020.0000.0000.0000.000
182D445GLY00.0010.00226.565-0.004-0.0040.0000.0000.0000.000
183D446ILE0-0.0260.00026.297-0.011-0.0110.0000.0000.0000.000
184D447SER00.0490.01830.3930.0020.0020.0000.0000.0000.000
185D448SER00.0570.02631.1570.0020.0020.0000.0000.0000.000
186D449GLN00.0270.01330.6990.0020.0020.0000.0000.0000.000
187D450GLN00.0600.02028.9630.0070.0070.0000.0000.0000.000
188D451GLN0-0.046-0.02026.7490.0100.0100.0000.0000.0000.000
189D452SER00.002-0.00925.7870.0110.0110.0000.0000.0000.000
190D453MET0-0.0030.01125.8990.0050.0050.0000.0000.0000.000
191D454ARG10.8280.89620.431-0.208-0.2080.0000.0000.0000.000
192D455LEU00.0330.01121.4180.0190.0190.0000.0000.0000.000
193D456ALA00.0180.00921.1030.0160.0160.0000.0000.0000.000
194D457ASN0-0.058-0.05220.636-0.001-0.0010.0000.0000.0000.000
195D458LEU00.0260.01915.9780.0220.0220.0000.0000.0000.000
196D459LEU00.012-0.00416.5570.0250.0250.0000.0000.0000.000
197D460MET0-0.017-0.00717.910-0.006-0.0060.0000.0000.0000.000
198D461LEU0-0.0140.00913.867-0.027-0.0270.0000.0000.0000.000
199D462LEU00.0200.01613.2320.0510.0510.0000.0000.0000.000
200D463SER0-0.016-0.01813.1970.0270.0270.0000.0000.0000.000
201D464HIS00.0100.01211.852-0.070-0.0700.0000.0000.0000.000
202D465VAL00.0060.0107.548-0.031-0.0310.0000.0000.0000.000
203D466ARG10.8490.8988.656-0.324-0.3240.0000.0000.0000.000
204D467HIS0-0.005-0.00410.9600.0220.0220.0000.0000.0000.000
205D468ALA00.0860.0075.982-0.316-0.266-0.001-0.003-0.0460.000
206D469SER0-0.038-0.0055.777-0.078-0.0780.0000.0000.0000.000
207D470ASN00.008-0.0037.6940.0480.0480.0000.0000.0000.000
208D471LYS10.7800.8667.0572.0302.0300.0000.0000.0000.000
209D472GLY00.0420.0203.220-2.508-1.8130.254-0.421-0.5280.002
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