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: XY42P

Calculation Name: 1X76-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-carbonitrile

ligand 3-letter code: 697

PDB ID: 1X76

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 -3084418.035344
FMO2-HF: Nuclear repulsion 2988015.316061
FMO2-HF: Total energy -96402.719282
FMO2-MP2: Total energy -96673.258308


3D Structure
Snapshot
 
Ligand structure

697

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.
-101.829-79.48570.034-28.678-63.7030.035


Interactive mode: IFIE and PIEDA for fragment #235(C:201:697)


Summations of interaction energy for fragment #235(C:201:697)
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.
-101.829-79.48570.034-28.678-63.703-0.035
Interaction energy analysis for fragmet #235(C:201:697)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / 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].
1C264SER10.7930.86129.194-0.065-0.0650.0000.0000.0000.000
2C265PRO00.1360.07027.022-0.015-0.0150.0000.0000.0000.000
3C266GLU-1-0.794-0.85924.0690.1090.1090.0000.0000.0000.000
4C267GLN0-0.004-0.01023.7120.0000.0000.0000.0000.0000.000
5C268LEU00.0380.03321.483-0.026-0.0260.0000.0000.0000.000
6C269VAL00.008-0.00118.847-0.023-0.0230.0000.0000.0000.000
7C270LEU0-0.019-0.01219.257-0.012-0.0120.0000.0000.0000.000
8C271THR00.0170.00720.103-0.032-0.0320.0000.0000.0000.000
9C272LEU0-0.024-0.00316.254-0.040-0.0400.0000.0000.0000.000
10C273LEU0-0.009-0.00815.387-0.041-0.0410.0000.0000.0000.000
11C274GLU-1-0.910-0.95015.780-0.295-0.2950.0000.0000.0000.000
12C275ALA00.0130.00915.385-0.076-0.0760.0000.0000.0000.000
13C276GLU-1-0.821-0.86210.498-0.531-0.5310.0000.0000.0000.000
14C277PRO00.0020.0077.4550.0180.0180.0000.0000.0000.000
15C278PRO0-0.0020.00410.1600.1870.1870.0000.0000.0000.000
16C279HIS00.012-0.0088.647-0.502-0.5020.0000.0000.0000.000
17C280VAL0-0.041-0.0156.0760.2850.2850.0000.0000.0000.000
18C281LEU00.0270.0267.048-0.095-0.0950.0000.0000.0000.000
19C282ILE00.0250.0166.083-0.282-0.2820.0000.0000.0000.000
20C283SER0-0.079-0.0398.651-0.029-0.0290.0000.0000.0000.000
21C284ARG10.8270.91611.138-0.188-0.1880.0000.0000.0000.000
22C285PRO00.011-0.00313.4460.0520.0520.0000.0000.0000.000
23C286SER0-0.036-0.02213.6320.0700.0700.0000.0000.0000.000
24C287ALA0-0.0050.00714.4940.0170.0170.0000.0000.0000.000
25C288PRO00.0460.02514.1870.0510.0510.0000.0000.0000.000
26C289PHE0-0.029-0.0079.859-0.186-0.1860.0000.0000.0000.000
27C290THR00.0090.00111.9280.0280.0280.0000.0000.0000.000
28C291GLU-1-0.805-0.8967.399-1.594-1.5940.0000.0000.0000.000
29C292ALA00.0560.0258.168-0.146-0.1460.0000.0000.0000.000
30C293SER0-0.013-0.01110.270-0.029-0.0290.0000.0000.0000.000
31C294MET00.0090.0156.8890.1470.1470.0000.0000.0000.000
32C295MET00.0190.0252.435-3.117-2.1322.803-0.957-2.8310.011
33C296MET0-0.0080.0125.874-0.443-0.4430.0000.0000.0000.000
34C297SER0-0.001-0.0237.659-0.190-0.1900.0000.0000.0000.000
35C298LEU00.009-0.0122.870-5.868-1.2892.247-1.276-5.5490.011
36C299THR00.002-0.0232.651-7.730-5.0700.616-1.260-2.016-0.017
37C300LYS10.8780.9544.8850.9601.082-0.001-0.008-0.1140.000
38C301LEU0-0.059-0.0282.238-1.1400.2193.900-1.338-3.9210.008
39C302ALA00.0130.0052.337-2.472-0.6671.010-0.895-1.9190.000
40C303ASP-1-0.829-0.9093.661-1.307-1.1380.029-0.009-0.1890.000
41C304LYS10.8470.9096.6612.4122.4120.0000.0000.0000.000
42C305GLU-1-0.787-0.8831.626-28.030-35.55216.804-5.887-3.395-0.064
43C306LEU00.0410.0255.8640.9500.9500.0000.0000.0000.000
44C307VAL0-0.0020.0088.1940.5520.5520.0000.0000.0000.000
45C308HIS0-0.030-0.0268.5260.4870.4870.0000.0000.0000.000
46C309MET0-0.0240.0206.6600.4260.4260.0000.0000.0000.000
47C310ILE00.022-0.0029.8590.3380.3380.0000.0000.0000.000
48C311SER0-0.062-0.04312.8080.2280.2280.0000.0000.0000.000
49C312TRP00.0180.01411.0810.0580.0580.0000.0000.0000.000
50C313ALA00.0490.01713.0080.1450.1450.0000.0000.0000.000
51C314LYS10.8680.92715.0700.6070.6070.0000.0000.0000.000
52C315LYS10.8000.91114.4960.6850.6850.0000.0000.0000.000
53C316ILE0-0.025-0.00115.5120.0600.0600.0000.0000.0000.000
54C317PRO0-0.004-0.00819.7470.0030.0030.0000.0000.0000.000
55C318GLY0-0.012-0.00223.1070.0270.0270.0000.0000.0000.000
56C319PHE00.013-0.01417.0960.0090.0090.0000.0000.0000.000
57C320VAL00.0050.00021.245-0.019-0.0190.0000.0000.0000.000
58C321GLU-1-0.839-0.91122.928-0.175-0.1750.0000.0000.0000.000
59C322LEU0-0.0250.01920.9940.0320.0320.0000.0000.0000.000
60C323SER0-0.010-0.01724.797-0.032-0.0320.0000.0000.0000.000
61C324LEU0-0.011-0.01223.790-0.019-0.0190.0000.0000.0000.000
62C325PHE00.0370.01621.033-0.026-0.0260.0000.0000.0000.000
63C326ASP-1-0.735-0.85021.157-0.223-0.2230.0000.0000.0000.000
64C327GLN0-0.107-0.06019.334-0.064-0.0640.0000.0000.0000.000
65C328VAL0-0.0170.00016.754-0.075-0.0750.0000.0000.0000.000
66C329ARG10.9270.96616.4890.1430.1430.0000.0000.0000.000
67C330LEU0-0.070-0.00617.0060.0510.0510.0000.0000.0000.000
68C331LEU00.0270.00811.6440.0610.0610.0000.0000.0000.000
69C332GLU-1-0.861-0.95512.921-0.502-0.5020.0000.0000.0000.000
70C333SER0-0.025-0.01113.4870.0520.0520.0000.0000.0000.000
71C334CYS0-0.063-0.03511.7770.1020.1020.0000.0000.0000.000
72C335TRP00.0660.0284.8310.2020.2020.0000.0000.0000.000
73C336MET00.0130.0223.257-1.7890.4320.385-0.452-2.1550.004
74C337GLU-1-0.791-0.8715.3281.5741.5740.0000.0000.0000.000
75C338VAL0-0.041-0.0226.5620.2760.2760.0000.0000.0000.000
76C339LEU0-0.0090.0092.588-3.916-1.4624.390-1.613-5.2310.012
77C340MET0-0.0280.0022.416-0.4872.1171.847-1.237-3.214-0.006
78C341MET0-0.020-0.0033.2580.5870.3660.0060.442-0.2270.000
79C342GLY00.0070.0064.876-0.261-0.188-0.001-0.008-0.0640.000
80C343LEU00.0050.0082.312-2.883-1.4213.305-1.288-3.4800.008
81C344MET0-0.023-0.0014.049-0.703-0.3950.003-0.079-0.2320.000
82C345TRP0-0.036-0.0146.876-0.233-0.2330.0000.0000.0000.000
83C346ARG10.7650.8582.3792.6873.7240.554-0.557-1.0340.003
84C347SER00.0170.0017.0690.0900.0900.0000.0000.0000.000
85C348ILE00.0280.0239.6950.0320.0320.0000.0000.0000.000
86C349ASP-1-0.881-0.94712.4891.0811.0810.0000.0000.0000.000
87C350HIS0-0.051-0.01712.201-0.023-0.0230.0000.0000.0000.000
88C351PRO00.0210.03113.6520.2690.2690.0000.0000.0000.000
89C352GLY00.0250.01912.323-0.143-0.1430.0000.0000.0000.000
90C353LYS10.8580.91310.596-1.227-1.2270.0000.0000.0000.000
91C354LEU00.0050.0105.064-0.0280.112-0.001-0.003-0.1350.000
92C355ILE0-0.013-0.0147.907-0.224-0.2240.0000.0000.0000.000
93C356PHE00.0240.0112.583-6.781-2.3873.347-1.637-6.1050.018
94C357ALA00.0910.0324.523-1.771-1.601-0.001-0.020-0.1500.000
95C358PRO00.0150.0027.0050.4090.4090.0000.0000.0000.000
96C359ASP-1-0.744-0.8689.525-0.756-0.7560.0000.0000.0000.000
97C360LEU0-0.040-0.0234.331-0.542-0.2870.000-0.028-0.2280.000
98C361VAL0-0.029-0.0028.4210.8420.8420.0000.0000.0000.000
99C362LEU00.0300.0266.532-0.243-0.2430.0000.0000.0000.000
100C363ASP-1-0.874-0.9539.8762.4132.4130.0000.0000.0000.000
101C364ARG10.8100.8758.517-1.843-1.8430.0000.0000.0000.000
102C365ASP-1-0.814-0.8969.4811.3981.3980.0000.0000.0000.000
103C366GLU-1-0.770-0.90410.1161.1951.1950.0000.0000.0000.000
104C367GLY00.0290.0087.778-0.221-0.2210.0000.0000.0000.000
105C368LYS10.8310.9018.414-1.461-1.4610.0000.0000.0000.000
106C369CYS0-0.112-0.03611.320-0.248-0.2480.0000.0000.0000.000
107C370VAL00.010-0.0185.622-0.237-0.2370.0000.0000.0000.000
108C371GLU-1-0.802-0.8677.692-1.430-1.4300.0000.0000.0000.000
109C372GLY00.0270.0136.694-1.107-1.1070.0000.0000.0000.000
110C373ILE0-0.0250.0082.520-1.638-0.2132.450-0.786-3.0880.006
111C374LEU00.0120.0094.8423.4243.524-0.001-0.003-0.0960.000
112C375GLU-1-0.843-0.9097.4431.7651.7650.0000.0000.0000.000
113C376ILE00.0110.0002.909-1.859-0.4811.534-0.601-2.3110.007
114C377PHE00.012-0.0042.925-1.811-0.0370.721-0.552-1.9430.009
115C378ASP-1-0.785-0.8825.1861.4701.509-0.001-0.004-0.0350.000
116C379MET0-0.027-0.0067.000-0.611-0.6110.0000.0000.0000.000
117C380LEU00.0300.0252.913-2.086-1.3720.871-0.330-1.2560.005
118C381LEU00.0120.0187.037-1.270-1.2700.0000.0000.0000.000
119C382ALA0-0.0110.0019.870-0.636-0.6360.0000.0000.0000.000
120C383THR0-0.026-0.0329.854-0.612-0.6120.0000.0000.0000.000
121C384THR0-0.035-0.0399.113-0.392-0.3920.0000.0000.0000.000
122C385SER0-0.078-0.05911.151-0.386-0.3860.0000.0000.0000.000
123C386ARG10.8340.91514.412-1.351-1.3510.0000.0000.0000.000
124C387PHE00.0500.0109.696-0.266-0.2660.0000.0000.0000.000
125C388ARG10.8860.95013.536-1.944-1.9440.0000.0000.0000.000
126C389GLU-1-0.837-0.88716.5611.0841.0840.0000.0000.0000.000
127C390LEU0-0.017-0.00517.230-0.127-0.1270.0000.0000.0000.000
128C391LYS10.8160.91418.864-0.858-0.8580.0000.0000.0000.000
129C392LEU00.0000.02213.272-0.090-0.0900.0000.0000.0000.000
130C393GLN0-0.014-0.02117.103-0.045-0.0450.0000.0000.0000.000
131C394HIS00.0600.02413.7000.0190.0190.0000.0000.0000.000
132C395LYS10.8900.92416.229-0.182-0.1820.0000.0000.0000.000
133C396GLU-1-0.718-0.82717.4510.4990.4990.0000.0000.0000.000
134C397TYR0-0.018-0.0218.9780.0280.0280.0000.0000.0000.000
135C398LEU0-0.0290.00413.1490.0020.0020.0000.0000.0000.000
136C399CYS0-0.025-0.00814.864-0.059-0.0590.0000.0000.0000.000
137C400VAL00.0360.00712.267-0.026-0.0260.0000.0000.0000.000
138C401LYS10.8360.9048.3310.4560.4560.0000.0000.0000.000
139C402ALA00.0170.00612.228-0.086-0.0860.0000.0000.0000.000
140C403MET0-0.034-0.01415.661-0.011-0.0110.0000.0000.0000.000
141C404ILE0-0.005-0.0069.788-0.027-0.0270.0000.0000.0000.000
142C405LEU0-0.015-0.00313.563-0.041-0.0410.0000.0000.0000.000
143C406LEU00.0040.02314.714-0.064-0.0640.0000.0000.0000.000
144C407ASN0-0.049-0.03216.007-0.005-0.0050.0000.0000.0000.000
145C408SER00.0280.00415.1400.0760.0760.0000.0000.0000.000
146C409SER0-0.010-0.00316.199-0.041-0.0410.0000.0000.0000.000
147C410MET0-0.059-0.03017.1360.0390.0390.0000.0000.0000.000
148C411TYR00.0200.00920.1570.0090.0090.0000.0000.0000.000
149C412PRO00.0080.01122.728-0.020-0.0200.0000.0000.0000.000
150C413LEU0-0.020-0.00220.535-0.008-0.0080.0000.0000.0000.000
151C414VAL00.008-0.00424.300-0.033-0.0330.0000.0000.0000.000
152C415THR00.0250.00427.1760.0200.0200.0000.0000.0000.000
153C416ALA00.0460.00330.5420.0000.0000.0000.0000.0000.000
154C417THR0-0.049-0.03031.109-0.003-0.0030.0000.0000.0000.000
155C418GLN00.0210.02326.1260.0090.0090.0000.0000.0000.000
156C419ASP-1-0.779-0.86427.832-0.080-0.0800.0000.0000.0000.000
157C420ALA00.0270.00729.9790.0100.0100.0000.0000.0000.000
158C421ASP-1-0.839-0.91230.303-0.122-0.1220.0000.0000.0000.000
159C422SER00.018-0.03125.4120.0140.0140.0000.0000.0000.000
160C423SER0-0.041-0.00726.6840.0170.0170.0000.0000.0000.000
161C424ARG10.7860.87227.8970.0890.0890.0000.0000.0000.000
162C425LYS10.7880.90826.4100.1500.1500.0000.0000.0000.000
163C426LEU00.0440.02221.1640.0090.0090.0000.0000.0000.000
164C427ALA00.0140.00823.6250.0240.0240.0000.0000.0000.000
165C428HIS00.000-0.00125.8710.0320.0320.0000.0000.0000.000
166C429LEU00.0070.00820.2710.0210.0210.0000.0000.0000.000
167C430LEU00.0430.02519.5930.0230.0230.0000.0000.0000.000
168C431ASN0-0.021-0.00122.3920.0390.0390.0000.0000.0000.000
169C432ALA00.0080.00624.6870.0200.0200.0000.0000.0000.000
170C433VAL00.000-0.00918.4490.0120.0120.0000.0000.0000.000
171C434THR0-0.036-0.02621.8050.0520.0520.0000.0000.0000.000
172C435ASP-1-0.929-0.96523.2850.1390.1390.0000.0000.0000.000
173C436ALA0-0.002-0.01322.7210.0130.0130.0000.0000.0000.000
174C437LEU00.000-0.00218.7750.0160.0160.0000.0000.0000.000
175C438VAL00.0240.01022.2750.0260.0260.0000.0000.0000.000
176C439TRP00.0170.00225.6470.0020.0020.0000.0000.0000.000
177C440VAL0-0.022-0.02321.344-0.002-0.0020.0000.0000.0000.000
178C441ILE0-0.0100.00921.7730.0140.0140.0000.0000.0000.000
179C442ALA00.0070.02225.0210.0040.0040.0000.0000.0000.000
180C443LYS10.8230.91127.006-0.202-0.2020.0000.0000.0000.000
181C444SER0-0.025-0.02225.906-0.003-0.0030.0000.0000.0000.000
182C445GLY0-0.007-0.00127.9300.0020.0020.0000.0000.0000.000
183C446ILE0-0.0240.00526.943-0.008-0.0080.0000.0000.0000.000
184C447SER00.0480.01631.118-0.015-0.0150.0000.0000.0000.000
185C448SER00.0800.03431.5090.0250.0250.0000.0000.0000.000
186C449GLN00.0400.02331.0590.0220.0220.0000.0000.0000.000
187C450GLN00.0280.00028.9130.0400.0400.0000.0000.0000.000
188C451GLN0-0.041-0.02127.1350.0250.0250.0000.0000.0000.000
189C452SER00.0200.00626.1720.0170.0170.0000.0000.0000.000
190C453MET0-0.0030.00725.6410.0380.0380.0000.0000.0000.000
191C454ARG10.7680.84820.388-0.493-0.4930.0000.0000.0000.000
192C455LEU00.0400.01321.5750.0510.0510.0000.0000.0000.000
193C456ALA00.0250.00921.5030.0330.0330.0000.0000.0000.000
194C457ASN0-0.043-0.03819.9740.1100.1100.0000.0000.0000.000
195C458LEU00.0230.00916.2920.0970.0970.0000.0000.0000.000
196C459LEU0-0.011-0.00216.8570.0410.0410.0000.0000.0000.000
197C460MET0-0.010-0.00918.1070.0320.0320.0000.0000.0000.000
198C461LEU0-0.0130.00813.0540.1150.1150.0000.0000.0000.000
199C462LEU00.0170.01813.2730.1760.1760.0000.0000.0000.000
200C463SER00.0110.00113.7180.0530.0530.0000.0000.0000.000
201C464HIS0-0.059-0.03312.4760.0650.0650.0000.0000.0000.000
202C465VAL00.0050.0027.7160.3450.3450.0000.0000.0000.000
203C466ARG10.8390.9079.100-0.213-0.2130.0000.0000.0000.000
204C467HIS0-0.046-0.01210.610-0.294-0.2940.0000.0000.0000.000
205C468ALA00.0390.0026.473-0.111-0.1110.0000.0000.0000.000
206C469SER0-0.020-0.0376.3620.6550.6550.0000.0000.0000.000
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