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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: PJN9P

Calculation Name: 1ZAF-A-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: 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 -3092467.793869
FMO2-HF: Nuclear repulsion 2993547.545859
FMO2-HF: Total energy -98920.24801
FMO2-MP2: Total energy -99190.808583


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.
-95.281-79.66271.378-28.250-58.7470.074


Interactive mode: IFIE and PIEDA for fragment #235(C:201:789)


Summations of interaction energy for fragment #235(C:201:789)
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.
-95.281-79.66271.378-28.25-58.747-0.074
Interaction energy analysis for fragmet #235(C:201:789)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.074 / q_NPA : -0.094
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].
1C264SER10.7850.88630.365-0.144-0.1440.0000.0000.0000.000
2C265PRO00.1540.07027.0680.0020.0020.0000.0000.0000.000
3C266GLU-1-0.819-0.89624.3810.2130.2130.0000.0000.0000.000
4C267GLN00.0140.00324.3580.0050.0050.0000.0000.0000.000
5C268LEU00.0250.02321.7370.0000.0000.0000.0000.0000.000
6C269VAL00.0120.00019.4400.0120.0120.0000.0000.0000.000
7C270LEU0-0.017-0.01219.8750.0120.0120.0000.0000.0000.000
8C271THR00.0100.00120.813-0.003-0.0030.0000.0000.0000.000
9C272LEU0-0.0040.00516.4050.0040.0040.0000.0000.0000.000
10C273LEU0-0.021-0.01015.9790.0190.0190.0000.0000.0000.000
11C274GLU-1-0.913-0.95216.5230.1820.1820.0000.0000.0000.000
12C275ALA00.0010.00515.244-0.014-0.0140.0000.0000.0000.000
13C276GLU-1-0.782-0.84710.9990.4390.4390.0000.0000.0000.000
14C277PRO0-0.0080.0048.078-0.010-0.0100.0000.0000.0000.000
15C278PRO00.0060.00711.0950.0410.0410.0000.0000.0000.000
16C279HIS00.007-0.0179.947-0.139-0.1390.0000.0000.0000.000
17C280VAL0-0.0120.0006.2120.1170.1170.0000.0000.0000.000
18C281LEU00.0070.0177.262-0.133-0.1330.0000.0000.0000.000
19C282ILE00.0390.0246.596-0.127-0.1270.0000.0000.0000.000
20C283SER0-0.071-0.0328.6520.0560.0560.0000.0000.0000.000
21C284ARG10.8650.91412.293-0.460-0.4600.0000.0000.0000.000
22C285PRO00.0530.06110.296-0.016-0.0160.0000.0000.0000.000
23C286SER0-0.041-0.04212.281-0.090-0.0900.0000.0000.0000.000
24C287ALA00.0400.02214.8950.0080.0080.0000.0000.0000.000
25C288PRO00.0250.01015.6650.0650.0650.0000.0000.0000.000
26C289PHE00.0050.02010.9840.0220.0220.0000.0000.0000.000
27C290THR00.0090.00613.093-0.113-0.1130.0000.0000.0000.000
28C291GLU-1-0.791-0.8947.887-2.008-2.0080.0000.0000.0000.000
29C292ALA00.0490.0158.8170.1050.1050.0000.0000.0000.000
30C293SER0-0.008-0.01110.5160.2000.2000.0000.0000.0000.000
31C294MET00.0010.0196.9820.2370.2370.0000.0000.0000.000
32C295MET00.0570.0382.536-2.010-0.7451.689-0.668-2.2860.008
33C296MET0-0.0220.0086.1220.8530.8530.0000.0000.0000.000
34C297SER0-0.018-0.0427.8860.0600.0600.0000.0000.0000.000
35C298LEU0-0.012-0.0093.117-4.204-0.3450.677-0.936-3.6000.010
36C299THR00.007-0.0213.246-1.2360.4940.058-0.653-1.134-0.005
37C300LYS10.8460.9315.230-1.179-1.098-0.001-0.002-0.0790.000
38C301LEU0-0.072-0.0272.356-1.504-0.0391.401-0.699-2.1670.004
39C302ALA00.0430.0152.364-3.429-1.6950.992-0.743-1.9830.003
40C303ASP-1-0.822-0.9063.8910.3730.6260.009-0.040-0.2220.000
41C304LYS10.8520.9156.989-0.481-0.4810.0000.0000.0000.000
42C305GLU-1-0.789-0.8741.564-27.453-38.09922.935-8.281-4.008-0.077
43C306LEU00.0360.0305.9030.2990.2990.0000.0000.0000.000
44C307VAL00.0130.0128.528-0.078-0.0780.0000.0000.0000.000
45C308HIS0-0.033-0.0318.4680.0660.0660.0000.0000.0000.000
46C309MET0-0.0120.0206.9060.0340.0340.0000.0000.0000.000
47C310ILE00.0040.00110.0470.0280.0280.0000.0000.0000.000
48C311SER0-0.070-0.04912.912-0.019-0.0190.0000.0000.0000.000
49C312TRP0-0.020-0.00111.0900.0080.0080.0000.0000.0000.000
50C313ALA00.0500.00813.157-0.003-0.0030.0000.0000.0000.000
51C314LYS10.8710.92615.084-0.287-0.2870.0000.0000.0000.000
52C315LYS10.8080.91914.854-0.215-0.2150.0000.0000.0000.000
53C316ILE0-0.033-0.00115.197-0.013-0.0130.0000.0000.0000.000
54C317PRO0-0.001-0.00519.628-0.003-0.0030.0000.0000.0000.000
55C318GLY0-0.029-0.02622.6570.0110.0110.0000.0000.0000.000
56C319PHE00.013-0.01117.3830.0010.0010.0000.0000.0000.000
57C320VAL0-0.0040.00520.9110.0010.0010.0000.0000.0000.000
58C321GLU-1-0.848-0.91722.8050.1760.1760.0000.0000.0000.000
59C322LEU0-0.048-0.00121.597-0.016-0.0160.0000.0000.0000.000
60C323SER0-0.012-0.03125.2680.0030.0030.0000.0000.0000.000
61C324LEU00.0140.00222.8550.0150.0150.0000.0000.0000.000
62C325PHE00.0690.02822.7540.0260.0260.0000.0000.0000.000
63C326ASP-1-0.707-0.78622.1990.1920.1920.0000.0000.0000.000
64C327GLN0-0.046-0.02819.6740.0410.0410.0000.0000.0000.000
65C328VAL00.0180.01918.0720.0470.0470.0000.0000.0000.000
66C329ARG10.9100.95817.441-0.192-0.1920.0000.0000.0000.000
67C330LEU0-0.092-0.01217.263-0.005-0.0050.0000.0000.0000.000
68C331LEU00.029-0.01212.8410.0690.0690.0000.0000.0000.000
69C332GLU-1-0.855-0.95513.0670.5380.5380.0000.0000.0000.000
70C333SER0-0.055-0.03813.0030.0470.0470.0000.0000.0000.000
71C334CYS0-0.095-0.01911.8330.0150.0150.0000.0000.0000.000
72C335TRP00.0580.0204.7950.2300.514-0.001-0.006-0.2770.000
73C336MET00.0290.0254.224-0.4380.7160.034-0.180-1.0070.001
74C337GLU-1-0.796-0.8855.2500.8070.8070.0000.0000.0000.000
75C338VAL0-0.006-0.0176.6670.0750.0750.0000.0000.0000.000
76C339LEU0-0.0060.0112.690-3.955-1.0463.040-1.399-4.5490.011
77C340MET0-0.036-0.0062.607-1.0541.3450.878-0.906-2.371-0.005
78C341MET0-0.024-0.0053.4080.1900.1480.0050.193-0.1550.000
79C342GLY00.0020.0035.058-0.423-0.359-0.001-0.006-0.0570.000
80C343LEU00.0050.0112.326-4.265-2.1483.779-1.373-4.5240.013
81C344MET0-0.0130.0024.320-1.274-1.0640.001-0.056-0.1550.000
82C345TRP00.0000.0007.105-0.342-0.3420.0000.0000.0000.000
83C346ARG10.7510.8532.2761.9022.8630.611-0.545-1.0260.002
84C347SER00.007-0.0067.413-0.107-0.1070.0000.0000.0000.000
85C348ILE00.0330.03010.057-0.165-0.1650.0000.0000.0000.000
86C349ASP-1-0.865-0.93612.6130.5360.5360.0000.0000.0000.000
87C350HIS0-0.043-0.02112.648-0.136-0.1360.0000.0000.0000.000
88C351PRO00.0110.02513.6480.0520.0520.0000.0000.0000.000
89C352GLY00.0230.00513.1460.0120.0120.0000.0000.0000.000
90C353LYS10.8480.91411.056-0.539-0.5390.0000.0000.0000.000
91C354LEU00.0110.0185.016-0.220-0.0780.000-0.011-0.1310.000
92C355ILE0-0.012-0.0198.3790.0500.0500.0000.0000.0000.000
93C356PHE00.0330.0052.856-5.044-1.7983.399-1.191-5.4550.013
94C357ALA00.0380.0144.608-1.462-1.349-0.001-0.010-0.1020.000
95C358PRO0-0.007-0.0127.2610.1870.1870.0000.0000.0000.000
96C359ASP-1-0.783-0.8809.8700.3620.3620.0000.0000.0000.000
97C360LEU0-0.014-0.0125.826-0.097-0.0970.0000.0000.0000.000
98C361VAL0-0.0160.0048.5680.2740.2740.0000.0000.0000.000
99C362LEU00.0330.0246.726-0.195-0.126-0.001-0.001-0.0680.000
100C363ASP-1-0.861-0.9429.6890.6260.6260.0000.0000.0000.000
101C364ARG10.8180.8779.3550.1460.1460.0000.0000.0000.000
102C365ASP-1-0.828-0.89610.227-0.506-0.5060.0000.0000.0000.000
103C366GLU-1-0.788-0.90410.7650.4170.4170.0000.0000.0000.000
104C367GLY00.0230.0167.509-0.094-0.0940.0000.0000.0000.000
105C368LYS10.7800.8638.209-0.279-0.2790.0000.0000.0000.000
106C369CYS0-0.109-0.04210.438-0.128-0.1280.0000.0000.0000.000
107C370VAL00.0130.0054.565-0.0550.091-0.001-0.004-0.1410.000
108C371GLU-1-0.806-0.8806.737-3.351-3.3510.0000.0000.0000.000
109C372GLY00.0220.0256.398-1.308-1.3080.0000.0000.0000.000
110C373ILE00.0150.0142.547-2.162-0.3501.652-0.669-2.7950.005
111C374LEU0-0.039-0.0175.0150.7870.921-0.001-0.005-0.1280.000
112C375GLU-1-0.838-0.9067.404-1.657-1.6570.0000.0000.0000.000
113C376ILE00.0280.0022.410-1.0380.2571.836-0.536-2.595-0.001
114C377PHE00.009-0.0043.350-0.1890.8210.507-0.192-1.3260.000
115C378ASP-1-0.788-0.8856.3230.0330.063-0.001-0.001-0.0280.000
116C379MET0-0.0250.0147.3310.3210.3210.0000.0000.0000.000
117C380LEU00.0410.0322.999-0.521-0.3101.591-0.312-1.490-0.003
118C381LEU00.0250.0297.4600.0450.064-0.0010.000-0.0180.000
119C382ALA0-0.0130.02010.319-0.034-0.0340.0000.0000.0000.000
120C383THR0-0.020-0.0329.936-0.040-0.0400.0000.0000.0000.000
121C384THR0-0.036-0.0419.2660.0840.0840.0000.0000.0000.000
122C385SER0-0.043-0.04211.460-0.066-0.0660.0000.0000.0000.000
123C386ARG10.8260.89114.736-0.248-0.2480.0000.0000.0000.000
124C387PHE00.0530.00410.158-0.065-0.0650.0000.0000.0000.000
125C388ARG10.8430.92813.644-0.643-0.6430.0000.0000.0000.000
126C389GLU-1-0.859-0.90417.0860.1550.1550.0000.0000.0000.000
127C390LEU0-0.0010.00617.426-0.032-0.0320.0000.0000.0000.000
128C391LYS10.8210.91118.696-0.289-0.2890.0000.0000.0000.000
129C392LEU00.0000.02013.300-0.031-0.0310.0000.0000.0000.000
130C393GLN0-0.016-0.02117.0730.0130.0130.0000.0000.0000.000
131C394HIS00.0230.01213.556-0.019-0.0190.0000.0000.0000.000
132C395LYS10.8890.92116.398-0.212-0.2120.0000.0000.0000.000
133C396GLU-1-0.725-0.82617.5730.3080.3080.0000.0000.0000.000
134C397TYR0-0.029-0.0309.1150.0410.0410.0000.0000.0000.000
135C398LEU0-0.0160.00413.3740.0370.0370.0000.0000.0000.000
136C399CYS0-0.038-0.00915.283-0.011-0.0110.0000.0000.0000.000
137C400VAL00.035-0.00112.423-0.005-0.0050.0000.0000.0000.000
138C401LYS10.8360.9118.617-0.561-0.5610.0000.0000.0000.000
139C402ALA00.0190.00912.2350.0060.0060.0000.0000.0000.000
140C403MET0-0.053-0.02515.582-0.027-0.0270.0000.0000.0000.000
141C404ILE00.002-0.0039.459-0.036-0.0360.0000.0000.0000.000
142C405LEU0-0.003-0.00213.1320.0010.0010.0000.0000.0000.000
143C406LEU00.0050.01514.320-0.028-0.0280.0000.0000.0000.000
144C407ASN0-0.004-0.00213.562-0.097-0.0970.0000.0000.0000.000
145C408SER0-0.023-0.00214.196-0.067-0.0670.0000.0000.0000.000
146C409SER0-0.018-0.00715.426-0.037-0.0370.0000.0000.0000.000
147C410MET00.0130.01016.533-0.042-0.0420.0000.0000.0000.000
148C411TYR00.015-0.00519.4740.0130.0130.0000.0000.0000.000
149C412PRO00.0560.02519.520-0.003-0.0030.0000.0000.0000.000
150C413LEU00.0260.01822.2420.0040.0040.0000.0000.0000.000
151C414VAL0-0.032-0.02023.828-0.004-0.0040.0000.0000.0000.000
152C415THR0-0.055-0.02025.264-0.022-0.0220.0000.0000.0000.000
153C416ALA00.012-0.00525.965-0.007-0.0070.0000.0000.0000.000
154C417THR0-0.032-0.00724.4810.0130.0130.0000.0000.0000.000
155C418GLN0-0.073-0.04726.866-0.007-0.0070.0000.0000.0000.000
156C419ASP-1-0.876-0.95430.2020.0850.0850.0000.0000.0000.000
157C420ALA00.0010.00532.285-0.002-0.0020.0000.0000.0000.000
158C421ASP-1-0.829-0.92231.2420.1250.1250.0000.0000.0000.000
159C422SER0-0.017-0.00926.4110.0130.0130.0000.0000.0000.000
160C423SER00.0530.03426.7030.0130.0130.0000.0000.0000.000
161C424ARG10.8460.90827.376-0.096-0.0960.0000.0000.0000.000
162C425LYS10.8290.89526.937-0.146-0.1460.0000.0000.0000.000
163C426LEU00.0330.02920.7710.0100.0100.0000.0000.0000.000
164C427ALA00.0200.01023.4360.0130.0130.0000.0000.0000.000
165C428HIS0-0.012-0.00725.5450.0010.0010.0000.0000.0000.000
166C429LEU00.0000.01120.6230.0020.0020.0000.0000.0000.000
167C430LEU00.0450.02719.0490.0110.0110.0000.0000.0000.000
168C431ASN0-0.0110.01122.005-0.002-0.0020.0000.0000.0000.000
169C432ALA00.0170.00124.786-0.001-0.0010.0000.0000.0000.000
170C433VAL0-0.003-0.00918.267-0.001-0.0010.0000.0000.0000.000
171C434THR0-0.031-0.02121.5950.0120.0120.0000.0000.0000.000
172C435ASP-1-0.910-0.96223.0000.1510.1510.0000.0000.0000.000
173C436ALA0-0.026-0.02022.484-0.003-0.0030.0000.0000.0000.000
174C437LEU00.0090.00018.7720.0030.0030.0000.0000.0000.000
175C438VAL00.0250.01322.208-0.004-0.0040.0000.0000.0000.000
176C439TRP00.0380.00825.697-0.008-0.0080.0000.0000.0000.000
177C440VAL0-0.007-0.00921.214-0.007-0.0070.0000.0000.0000.000
178C441ILE0-0.0090.00721.865-0.004-0.0040.0000.0000.0000.000
179C442ALA00.0040.02425.169-0.009-0.0090.0000.0000.0000.000
180C443LYS10.8320.90926.849-0.175-0.1750.0000.0000.0000.000
181C444SER0-0.043-0.03025.527-0.002-0.0020.0000.0000.0000.000
182C445GLY0-0.005-0.00127.532-0.004-0.0040.0000.0000.0000.000
183C446ILE0-0.0270.00326.633-0.012-0.0120.0000.0000.0000.000
184C447SER00.0480.01630.796-0.003-0.0030.0000.0000.0000.000
185C448SER00.0690.02831.4430.0080.0080.0000.0000.0000.000
186C449GLN00.0350.03031.2000.0090.0090.0000.0000.0000.000
187C450GLN00.028-0.00328.825-0.004-0.0040.0000.0000.0000.000
188C451GLN0-0.021-0.01527.1040.0150.0150.0000.0000.0000.000
189C452SER00.0170.00326.2680.0120.0120.0000.0000.0000.000
190C453MET00.0020.00425.9270.0070.0070.0000.0000.0000.000
191C454ARG10.7490.84220.473-0.269-0.2690.0000.0000.0000.000
192C455LEU00.0420.01521.7320.0220.0220.0000.0000.0000.000
193C456ALA00.0240.00921.6800.0130.0130.0000.0000.0000.000
194C457ASN0-0.048-0.03520.343-0.001-0.0010.0000.0000.0000.000
195C458LEU00.0130.00516.3990.0190.0190.0000.0000.0000.000
196C459LEU0-0.0120.00117.0400.0270.0270.0000.0000.0000.000
197C460MET0-0.016-0.01018.407-0.008-0.0080.0000.0000.0000.000
198C461LEU00.0080.01413.256-0.027-0.0270.0000.0000.0000.000
199C462LEU0-0.0070.00613.7270.0490.0490.0000.0000.0000.000
200C463SER0-0.026-0.01714.190-0.010-0.0100.0000.0000.0000.000
201C464HIS0-0.013-0.00712.717-0.042-0.0420.0000.0000.0000.000
202C465VAL00.0040.0088.769-0.030-0.0300.0000.0000.0000.000
203C466ARG10.8290.8799.672-0.271-0.2710.0000.0000.0000.000
204C467HIS0-0.041-0.03111.025-0.087-0.0870.0000.0000.0000.000
205C468ALA00.0500.0047.008-0.245-0.2450.0000.0000.0000.000
206C469SER0-0.0150.0006.864-0.095-0.0950.0000.0000.0000.000
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