Manual

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: XV91P

Calculation Name: 1X78-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: [5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]acetonitrile

ligand 3-letter code: 244

PDB ID: 1X78

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 -3084637.182094
FMO2-HF: Nuclear repulsion 2988195.368311
FMO2-HF: Total energy -96441.813783
FMO2-MP2: Total energy -96712.467559


3D Structure
Snapshot
 
Ligand structure

244

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.
-104.635-79.31069.907-29.768-65.4700.043


Interactive mode: IFIE and PIEDA for fragment #235(C:201:244)


Summations of interaction energy for fragment #235(C:201:244)
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.
-104.635-79.3169.907-29.768-65.47-0.043
Interaction energy analysis for fragmet #235(C:201:244)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / 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].
1C264SER10.8140.87029.366-0.043-0.0430.0000.0000.0000.000
2C265PRO00.1250.05728.169-0.002-0.0020.0000.0000.0000.000
3C266GLU-1-0.755-0.83825.0820.0850.0850.0000.0000.0000.000
4C267GLN0-0.0110.00324.1100.0060.0060.0000.0000.0000.000
5C268LEU00.0300.02622.145-0.012-0.0120.0000.0000.0000.000
6C269VAL00.004-0.00618.808-0.018-0.0180.0000.0000.0000.000
7C270LEU0-0.007-0.00819.4850.0000.0000.0000.0000.0000.000
8C271THR00.0050.00120.396-0.020-0.0200.0000.0000.0000.000
9C272LEU0-0.0170.00116.508-0.031-0.0310.0000.0000.0000.000
10C273LEU0-0.002-0.00215.752-0.030-0.0300.0000.0000.0000.000
11C274GLU-1-0.901-0.94816.031-0.196-0.1960.0000.0000.0000.000
12C275ALA00.0030.00415.605-0.055-0.0550.0000.0000.0000.000
13C276GLU-1-0.805-0.85510.734-0.395-0.3950.0000.0000.0000.000
14C277PRO0-0.0080.0057.7620.0180.0180.0000.0000.0000.000
15C278PRO0-0.0010.00210.5200.1700.1700.0000.0000.0000.000
16C279HIS00.009-0.0108.997-0.312-0.3120.0000.0000.0000.000
17C280VAL0-0.033-0.0136.0060.2420.2420.0000.0000.0000.000
18C281LEU00.0200.0266.797-0.192-0.1920.0000.0000.0000.000
19C282ILE00.0180.0166.299-0.348-0.3480.0000.0000.0000.000
20C283SER0-0.084-0.0488.764-0.064-0.0640.0000.0000.0000.000
21C284ARG10.8110.90711.516-0.879-0.8790.0000.0000.0000.000
22C285PRO00.0250.00913.7060.0340.0340.0000.0000.0000.000
23C286SER00.0090.01215.0490.1340.1340.0000.0000.0000.000
24C287ALA00.0200.00015.578-0.093-0.0930.0000.0000.0000.000
25C288PRO00.0490.03714.6030.1120.1120.0000.0000.0000.000
26C289PHE0-0.016-0.00310.495-0.143-0.1430.0000.0000.0000.000
27C290THR00.0300.00512.659-0.005-0.0050.0000.0000.0000.000
28C291GLU-1-0.778-0.8728.020-0.540-0.5400.0000.0000.0000.000
29C292ALA00.0250.0129.0260.0910.0910.0000.0000.0000.000
30C293SER0-0.040-0.02810.309-0.010-0.0100.0000.0000.0000.000
31C294MET0-0.0320.0186.639-0.353-0.3530.0000.0000.0000.000
32C295MET00.0730.0432.568-2.656-0.8771.234-0.816-2.1980.012
33C296MET00.0020.0465.593-0.656-0.6560.0000.0000.0000.000
34C297SER0-0.043-0.0447.774-0.463-0.4630.0000.0000.0000.000
35C298LEU00.0190.0022.493-4.721-1.2501.947-1.114-4.3040.010
36C299THR0-0.024-0.0342.976-7.366-4.5990.276-1.319-1.725-0.015
37C300LYS10.8800.9485.0040.0950.196-0.001-0.007-0.0940.000
38C301LEU0-0.061-0.0242.212-1.2520.0413.649-1.264-3.6780.007
39C302ALA00.0260.0112.279-2.073-0.7500.920-0.716-1.5260.001
40C303ASP-1-0.837-0.9103.824-0.794-0.6050.016-0.042-0.1640.000
41C304LYS10.8450.9086.9071.6331.6330.0000.0000.0000.000
42C305GLU-1-0.779-0.8771.600-29.639-37.78718.926-7.027-3.750-0.075
43C306LEU00.0350.0286.0010.7780.7780.0000.0000.0000.000
44C307VAL00.0090.0128.2490.4190.4190.0000.0000.0000.000
45C308HIS0-0.030-0.0288.5560.3920.3920.0000.0000.0000.000
46C309MET0-0.0300.0176.6860.3610.3610.0000.0000.0000.000
47C310ILE00.0210.00110.0300.2730.2730.0000.0000.0000.000
48C311SER0-0.071-0.04512.9100.1830.1830.0000.0000.0000.000
49C312TRP00.0140.00811.1820.0310.0310.0000.0000.0000.000
50C313ALA00.0460.01813.2000.1210.1210.0000.0000.0000.000
51C314LYS10.8820.92815.0180.5080.5080.0000.0000.0000.000
52C315LYS10.7920.91114.8110.5280.5280.0000.0000.0000.000
53C316ILE0-0.0160.00315.4050.0520.0520.0000.0000.0000.000
54C317PRO0-0.008-0.00619.6610.0000.0000.0000.0000.0000.000
55C318GLY00.005-0.00122.9380.0170.0170.0000.0000.0000.000
56C319PHE00.023-0.01217.2510.0000.0000.0000.0000.0000.000
57C320VAL00.0080.00321.375-0.014-0.0140.0000.0000.0000.000
58C321GLU-1-0.811-0.88923.131-0.176-0.1760.0000.0000.0000.000
59C322LEU0-0.0470.00221.4970.0220.0220.0000.0000.0000.000
60C323SER0-0.007-0.03625.236-0.018-0.0180.0000.0000.0000.000
61C324LEU0-0.011-0.01224.281-0.016-0.0160.0000.0000.0000.000
62C325PHE00.0560.02821.778-0.016-0.0160.0000.0000.0000.000
63C326ASP-1-0.729-0.80821.835-0.270-0.2700.0000.0000.0000.000
64C327GLN0-0.086-0.05219.743-0.043-0.0430.0000.0000.0000.000
65C328VAL0-0.021-0.00217.562-0.049-0.0490.0000.0000.0000.000
66C329ARG10.8620.93017.2780.2140.2140.0000.0000.0000.000
67C330LEU0-0.0350.01416.988-0.001-0.0010.0000.0000.0000.000
68C331LEU00.0430.01612.1350.0100.0100.0000.0000.0000.000
69C332GLU-1-0.849-0.94712.978-0.485-0.4850.0000.0000.0000.000
70C333SER0-0.030-0.02413.810-0.007-0.0070.0000.0000.0000.000
71C334CYS0-0.085-0.03212.0320.0080.0080.0000.0000.0000.000
72C335TRP00.0800.0275.3670.1790.1790.0000.0000.0000.000
73C336MET00.0250.0243.857-1.7510.2770.152-0.450-1.7290.001
74C337GLU-1-0.834-0.9135.4890.5850.5850.0000.0000.0000.000
75C338VAL0-0.027-0.0166.7390.3750.3750.0000.0000.0000.000
76C339LEU0-0.0130.0112.578-4.014-1.6615.450-1.777-6.0260.014
77C340MET0-0.0310.0062.372-1.1191.6252.955-1.288-4.411-0.005
78C341MET0-0.016-0.0043.4980.2970.3390.0030.151-0.1970.000
79C342GLY00.0080.0054.886-0.208-0.142-0.001-0.008-0.0580.000
80C343LEU00.0090.0122.320-2.984-1.2562.432-1.140-3.0200.007
81C344MET0-0.0100.0074.137-0.943-0.6490.002-0.078-0.2180.000
82C345TRP0-0.019-0.0087.009-0.294-0.2940.0000.0000.0000.000
83C346ARG10.7650.8572.2762.2093.2470.947-0.709-1.2760.004
84C347SER00.0150.0017.2020.1700.1700.0000.0000.0000.000
85C348ILE00.0040.0179.832-0.050-0.0500.0000.0000.0000.000
86C349ASP-1-0.904-0.95012.4991.1781.1780.0000.0000.0000.000
87C350HIS00.0470.02912.2960.0340.0340.0000.0000.0000.000
88C351PRO0-0.0030.01614.3390.1310.1310.0000.0000.0000.000
89C352GLY00.0210.01512.760-0.043-0.0430.0000.0000.0000.000
90C353LYS10.8430.90710.782-1.396-1.3960.0000.0000.0000.000
91C354LEU00.0170.0214.469-0.366-0.1770.000-0.014-0.1750.000
92C355ILE0-0.022-0.0197.855-0.055-0.0550.0000.0000.0000.000
93C356PHE00.0350.0152.612-7.823-2.9953.817-1.871-6.7740.021
94C357ALA00.0460.0124.087-2.157-1.8710.003-0.069-0.2200.000
95C358PRO0-0.009-0.0156.6330.4570.4570.0000.0000.0000.000
96C359ASP-1-0.744-0.8679.742-0.123-0.1230.0000.0000.0000.000
97C360LEU0-0.054-0.0245.030-0.166-0.1660.0000.0000.0000.000
98C361VAL0-0.0060.0048.0340.8430.8430.0000.0000.0000.000
99C362LEU00.0220.0136.443-0.185-0.1850.0000.0000.0000.000
100C363ASP-1-0.857-0.9509.0622.6592.6590.0000.0000.0000.000
101C364ARG10.8180.8848.844-1.451-1.4510.0000.0000.0000.000
102C365ASP-1-0.861-0.9179.6201.2981.2980.0000.0000.0000.000
103C366GLU-1-0.753-0.8999.9011.9231.9230.0000.0000.0000.000
104C367GLY00.0470.0306.9620.2230.2230.0000.0000.0000.000
105C368LYS10.7650.8647.907-1.798-1.7980.0000.0000.0000.000
106C369CYS0-0.097-0.03310.137-0.432-0.4320.0000.0000.0000.000
107C370VAL00.028-0.0104.408-0.223-0.078-0.001-0.005-0.1400.000
108C371GLU-1-0.786-0.8667.037-1.755-1.7550.0000.0000.0000.000
109C372GLY00.0130.0106.527-1.164-1.1640.0000.0000.0000.000
110C373ILE0-0.0170.0112.799-2.539-0.5542.536-0.907-3.6140.010
111C374LEU0-0.004-0.0084.9762.2132.321-0.001-0.002-0.1050.000
112C375GLU-1-0.863-0.9157.417-0.513-0.5130.0000.0000.0000.000
113C376ILE00.0320.0042.513-2.260-0.7071.605-0.650-2.508-0.002
114C377PHE00.0190.0042.822-0.5150.9741.000-0.499-1.9900.007
115C378ASP-1-0.788-0.8915.1051.3081.354-0.001-0.004-0.0410.000
116C379MET0-0.036-0.0116.928-0.338-0.3380.0000.0000.0000.000
117C380LEU00.0360.0232.982-1.633-0.7870.750-0.344-1.2530.004
118C381LEU00.0120.0197.071-0.823-0.8230.0000.0000.0000.000
119C382ALA0-0.0150.0019.648-0.500-0.5000.0000.0000.0000.000
120C383THR0-0.022-0.0329.963-0.457-0.4570.0000.0000.0000.000
121C384THR0-0.026-0.0319.289-0.210-0.2100.0000.0000.0000.000
122C385SER0-0.076-0.05111.389-0.284-0.2840.0000.0000.0000.000
123C386ARG10.8320.90414.375-0.885-0.8850.0000.0000.0000.000
124C387PHE00.0500.0059.716-0.221-0.2210.0000.0000.0000.000
125C388ARG10.8520.92313.828-1.645-1.6450.0000.0000.0000.000
126C389GLU-1-0.831-0.88116.7930.7360.7360.0000.0000.0000.000
127C390LEU0-0.011-0.00217.442-0.092-0.0920.0000.0000.0000.000
128C391LYS10.8160.91119.068-0.681-0.6810.0000.0000.0000.000
129C392LEU00.0050.02113.386-0.074-0.0740.0000.0000.0000.000
130C393GLN0-0.015-0.02117.084-0.002-0.0020.0000.0000.0000.000
131C394HIS00.0190.01013.256-0.051-0.0510.0000.0000.0000.000
132C395LYS10.8640.90216.255-0.127-0.1270.0000.0000.0000.000
133C396GLU-1-0.728-0.82717.5770.3490.3490.0000.0000.0000.000
134C397TYR0-0.020-0.0259.0100.0100.0100.0000.0000.0000.000
135C398LEU0-0.0120.00713.372-0.020-0.0200.0000.0000.0000.000
136C399CYS0-0.036-0.01315.076-0.061-0.0610.0000.0000.0000.000
137C400VAL00.0160.00512.147-0.039-0.0390.0000.0000.0000.000
138C401LYS10.8500.9058.4520.3240.3240.0000.0000.0000.000
139C402ALA00.0130.01212.405-0.091-0.0910.0000.0000.0000.000
140C403MET0-0.032-0.02615.775-0.017-0.0170.0000.0000.0000.000
141C404ILE0-0.011-0.0109.865-0.027-0.0270.0000.0000.0000.000
142C405LEU0-0.035-0.00913.561-0.054-0.0540.0000.0000.0000.000
143C406LEU00.0100.00115.051-0.035-0.0350.0000.0000.0000.000
144C407ASN0-0.041-0.02617.4540.0200.0200.0000.0000.0000.000
145C408SER0-0.014-0.00414.7850.0040.0040.0000.0000.0000.000
146C409SER00.0240.00916.813-0.035-0.0350.0000.0000.0000.000
147C410MET00.0640.02819.5090.0010.0010.0000.0000.0000.000
148C411TYR00.0680.04720.2470.0060.0060.0000.0000.0000.000
149C412PRO0-0.011-0.01121.4930.0190.0190.0000.0000.0000.000
150C413LEU0-0.0160.00523.8250.0130.0130.0000.0000.0000.000
151C414VAL0-0.014-0.00424.3090.0170.0170.0000.0000.0000.000
152C415THR0-0.036-0.01325.4740.0030.0030.0000.0000.0000.000
153C416ALA0-0.013-0.01228.0370.0050.0050.0000.0000.0000.000
154C417THR0-0.035-0.02930.3880.0090.0090.0000.0000.0000.000
155C418GLN0-0.0180.01528.488-0.008-0.0080.0000.0000.0000.000
156C419ASP-1-0.815-0.90728.779-0.171-0.1710.0000.0000.0000.000
157C420ALA00.020-0.00730.1110.0020.0020.0000.0000.0000.000
158C421ASP-1-0.855-0.90432.081-0.107-0.1070.0000.0000.0000.000
159C422SER0-0.002-0.02326.2980.0060.0060.0000.0000.0000.000
160C423SER00.011-0.00726.211-0.004-0.0040.0000.0000.0000.000
161C424ARG10.8170.89626.8860.1190.1190.0000.0000.0000.000
162C425LYS10.7820.88125.5140.1790.1790.0000.0000.0000.000
163C426LEU00.0110.01021.0520.0080.0080.0000.0000.0000.000
164C427ALA00.0120.00823.9830.0130.0130.0000.0000.0000.000
165C428HIS0-0.023-0.01425.7800.0220.0220.0000.0000.0000.000
166C429LEU0-0.0030.00720.9480.0180.0180.0000.0000.0000.000
167C430LEU00.0190.01519.7570.0190.0190.0000.0000.0000.000
168C431ASN0-0.0140.01022.5860.0340.0340.0000.0000.0000.000
169C432ALA00.006-0.00225.1800.0200.0200.0000.0000.0000.000
170C433VAL0-0.001-0.00418.8380.0170.0170.0000.0000.0000.000
171C434THR0-0.016-0.01822.0260.0370.0370.0000.0000.0000.000
172C435ASP-1-0.846-0.93323.2500.0560.0560.0000.0000.0000.000
173C436ALA0-0.043-0.01923.1350.0180.0180.0000.0000.0000.000
174C437LEU00.0410.00919.0430.0200.0200.0000.0000.0000.000
175C438VAL00.0220.01822.5470.0270.0270.0000.0000.0000.000
176C439TRP0-0.056-0.04325.9510.0130.0130.0000.0000.0000.000
177C440VAL0-0.027-0.02121.1580.0070.0070.0000.0000.0000.000
178C441ILE0-0.0030.01322.0140.0190.0190.0000.0000.0000.000
179C442ALA00.0100.02625.0880.0100.0100.0000.0000.0000.000
180C443LYS10.8250.90726.690-0.147-0.1470.0000.0000.0000.000
181C444SER0-0.034-0.02625.1590.0080.0080.0000.0000.0000.000
182C445GLY0-0.009-0.00327.1670.0090.0090.0000.0000.0000.000
183C446ILE0-0.0160.01026.281-0.006-0.0060.0000.0000.0000.000
184C447SER00.0500.01830.439-0.012-0.0120.0000.0000.0000.000
185C448SER00.0640.02231.3020.0120.0120.0000.0000.0000.000
186C449GLN00.0410.02331.2000.0070.0070.0000.0000.0000.000
187C450GLN00.0400.01228.3740.0210.0210.0000.0000.0000.000
188C451GLN0-0.039-0.02226.9900.0120.0120.0000.0000.0000.000
189C452SER00.0120.00326.3080.0030.0030.0000.0000.0000.000
190C453MET00.0010.00425.5960.0110.0110.0000.0000.0000.000
191C454ARG10.7700.85520.588-0.364-0.3640.0000.0000.0000.000
192C455LEU00.0460.01721.6900.0300.0300.0000.0000.0000.000
193C456ALA00.0170.00721.8110.0050.0050.0000.0000.0000.000
194C457ASN0-0.030-0.03120.0780.0570.0570.0000.0000.0000.000
195C458LEU00.0410.01416.4450.0450.0450.0000.0000.0000.000
196C459LEU00.0040.01617.1160.0090.0090.0000.0000.0000.000
197C460MET0-0.0010.00318.198-0.017-0.0170.0000.0000.0000.000
198C461LEU0-0.045-0.00614.0680.0260.0260.0000.0000.0000.000
199C462LEU00.0160.00913.1860.0870.0870.0000.0000.0000.000
200C463SER0-0.017-0.01213.561-0.048-0.0480.0000.0000.0000.000
201C464HIS0-0.055-0.03511.991-0.041-0.0410.0000.0000.0000.000
202C465VAL00.0060.0047.7540.0440.0440.0000.0000.0000.000
203C466ARG10.8130.8878.6980.1690.1690.0000.0000.0000.000
204C467HIS0-0.050-0.0199.649-0.362-0.3620.0000.0000.0000.000
205C468ALA00.0300.0075.896-0.344-0.3440.0000.0000.0000.000
206C469SER00.0440.0034.833-1.265-1.153-0.001-0.006-0.1060.000
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