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: P3LLX

Calculation Name: 1U9E-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 2-(4-hydroxy-phenyl)benzofuran-5-ol

ligand 3-letter code: 397

PDB ID: 1U9E

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 -3079766.775886
FMO2-HF: Nuclear repulsion 2983455.907238
FMO2-HF: Total energy -96310.868649
FMO2-MP2: Total energy -96581.13114


3D Structure
Snapshot
 
Ligand structure

397

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.
-88.490-68.00065.580-26.934-59.1370.034


Interactive mode: IFIE and PIEDA for fragment #235(C:201:397)


Summations of interaction energy for fragment #235(C:201:397)
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.
-88.49-6865.58-26.934-59.137-0.034
Interaction energy analysis for fragmet #235(C:201:397)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.076
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].
1C264SER10.7850.88729.620-0.038-0.0380.0000.0000.0000.000
2C265PRO00.1580.07427.251-0.006-0.0060.0000.0000.0000.000
3C266GLU-1-0.804-0.88823.9300.0710.0710.0000.0000.0000.000
4C267GLN00.0160.00524.0670.0000.0000.0000.0000.0000.000
5C268LEU00.0220.02121.639-0.012-0.0120.0000.0000.0000.000
6C269VAL00.0090.00519.202-0.005-0.0050.0000.0000.0000.000
7C270LEU0-0.009-0.00919.558-0.009-0.0090.0000.0000.0000.000
8C271THR00.0150.00420.543-0.016-0.0160.0000.0000.0000.000
9C272LEU0-0.012-0.00316.251-0.019-0.0190.0000.0000.0000.000
10C273LEU0-0.012-0.00515.775-0.020-0.0200.0000.0000.0000.000
11C274GLU-1-0.912-0.95116.213-0.139-0.1390.0000.0000.0000.000
12C275ALA00.0150.01215.797-0.040-0.0400.0000.0000.0000.000
13C276GLU-1-0.756-0.81910.465-0.250-0.2500.0000.0000.0000.000
14C277PRO0-0.0180.0048.0440.0220.0220.0000.0000.0000.000
15C278PRO0-0.023-0.01110.5010.0940.0940.0000.0000.0000.000
16C279HIS0-0.019-0.0137.050-0.396-0.3960.0000.0000.0000.000
17C280VAL0-0.0120.0035.5670.3940.3940.0000.0000.0000.000
18C281LEU00.0200.0217.0580.1480.1480.0000.0000.0000.000
19C282ILE00.0290.0136.393-0.151-0.1510.0000.0000.0000.000
20C283SER0-0.076-0.0378.9890.0370.0370.0000.0000.0000.000
21C284ARG10.8300.91211.414-0.378-0.3780.0000.0000.0000.000
22C285PRO00.009-0.00213.720-0.001-0.0010.0000.0000.0000.000
23C286SER0-0.042-0.02013.7120.0670.0670.0000.0000.0000.000
24C287ALA0-0.0120.00214.669-0.022-0.0220.0000.0000.0000.000
25C288PRO00.0430.02314.3010.0790.0790.0000.0000.0000.000
26C289PHE0-0.037-0.01210.1620.0280.0280.0000.0000.0000.000
27C290THR00.0200.01211.756-0.064-0.0640.0000.0000.0000.000
28C291GLU-1-0.772-0.8707.267-0.429-0.4290.0000.0000.0000.000
29C292ALA00.0530.0248.2010.2650.2650.0000.0000.0000.000
30C293SER0-0.005-0.0079.7000.0720.0720.0000.0000.0000.000
31C294MET0-0.0010.0126.3960.1110.1110.0000.0000.0000.000
32C295MET00.0220.0232.253-2.034-0.5962.190-0.894-2.7340.012
33C296MET00.0190.0435.557-0.403-0.4030.0000.0000.0000.000
34C297SER0-0.039-0.0387.745-0.365-0.3650.0000.0000.0000.000
35C298LEU00.008-0.0102.241-4.581-1.4282.684-1.342-4.4950.015
36C299THR0-0.012-0.0253.092-5.610-3.3240.141-1.108-1.319-0.011
37C300LYS10.8880.9555.291-0.087-0.002-0.001-0.004-0.0800.000
38C301LEU0-0.065-0.0332.148-1.246-0.1713.953-1.295-3.7330.007
39C302ALA00.0290.0122.353-2.057-0.8830.662-0.565-1.2710.001
40C303ASP-1-0.832-0.9073.896-0.1680.0190.010-0.046-0.1500.000
41C304LYS10.8480.9127.0121.2111.2110.0000.0000.0000.000
42C305GLU-1-0.789-0.8831.603-28.770-36.93818.832-6.918-3.747-0.071
43C306LEU00.0390.0285.9560.6840.6840.0000.0000.0000.000
44C307VAL00.0120.0168.2240.2990.2990.0000.0000.0000.000
45C308HIS0-0.017-0.0148.6560.3330.3330.0000.0000.0000.000
46C309MET0-0.0270.0176.5920.2960.2960.0000.0000.0000.000
47C310ILE00.0440.0099.8910.2040.2040.0000.0000.0000.000
48C311SER0-0.052-0.03513.0730.1130.1130.0000.0000.0000.000
49C312TRP0-0.027-0.01311.3380.0730.0730.0000.0000.0000.000
50C313ALA00.0550.02313.2490.0780.0780.0000.0000.0000.000
51C314LYS10.7900.89115.2140.1460.1460.0000.0000.0000.000
52C315LYS10.8110.90815.0430.3160.3160.0000.0000.0000.000
53C316ILE0-0.0160.00415.0310.0270.0270.0000.0000.0000.000
54C317PRO0-0.002-0.00619.3310.0100.0100.0000.0000.0000.000
55C318GLY00.0110.00622.7250.0130.0130.0000.0000.0000.000
56C319PHE00.038-0.00117.3170.0120.0120.0000.0000.0000.000
57C320VAL0-0.030-0.01320.730-0.002-0.0020.0000.0000.0000.000
58C321GLU-1-0.772-0.87622.469-0.019-0.0190.0000.0000.0000.000
59C322LEU0-0.0360.00921.2680.0110.0110.0000.0000.0000.000
60C323SER0-0.001-0.02425.108-0.010-0.0100.0000.0000.0000.000
61C324LEU00.0220.00122.8610.0030.0030.0000.0000.0000.000
62C325PHE00.0650.02122.7550.0020.0020.0000.0000.0000.000
63C326ASP-1-0.739-0.81421.9260.0570.0570.0000.0000.0000.000
64C327GLN0-0.043-0.03219.588-0.005-0.0050.0000.0000.0000.000
65C328VAL0-0.0020.02217.836-0.025-0.0250.0000.0000.0000.000
66C329ARG10.9160.95017.162-0.064-0.0640.0000.0000.0000.000
67C330LEU0-0.051-0.00217.0920.0400.0400.0000.0000.0000.000
68C331LEU00.0300.01512.0590.0640.0640.0000.0000.0000.000
69C332GLU-1-0.871-0.95212.8960.2160.2160.0000.0000.0000.000
70C333SER0-0.074-0.04313.4770.0990.0990.0000.0000.0000.000
71C334CYS0-0.066-0.02111.8830.0320.0320.0000.0000.0000.000
72C335TRP00.0800.0295.3640.4830.4830.0000.0000.0000.000
73C336MET00.0150.0193.119-2.7160.3471.030-0.726-3.3670.007
74C337GLU-1-0.826-0.9085.1191.1751.307-0.001-0.002-0.1290.000
75C338VAL0-0.018-0.0156.4580.0970.0970.0000.0000.0000.000
76C339LEU0-0.0070.0122.558-4.105-1.9395.518-1.750-5.9350.014
77C340MET0-0.021-0.0052.283-0.8411.4912.686-1.331-3.687-0.004
78C341MET0-0.027-0.0063.1220.421-0.1240.0080.783-0.2460.000
79C342GLY00.0040.0044.807-0.481-0.397-0.001-0.008-0.0750.000
80C343LEU00.0220.0172.350-3.285-1.8153.242-1.195-3.5170.007
81C344MET0-0.0130.0014.181-1.222-0.9440.002-0.072-0.2090.000
82C345TRP0-0.011-0.0026.908-0.284-0.2840.0000.0000.0000.000
83C346ARG10.7470.8392.3252.7953.7980.639-0.574-1.0680.002
84C347SER0-0.005-0.0167.295-0.054-0.0540.0000.0000.0000.000
85C348ILE00.0190.0239.908-0.091-0.0910.0000.0000.0000.000
86C349ASP-1-0.855-0.92912.4620.4070.4070.0000.0000.0000.000
87C350HIS0-0.034-0.01012.684-0.074-0.0740.0000.0000.0000.000
88C351PRO00.0040.02013.8510.0710.0710.0000.0000.0000.000
89C352GLY00.0260.02014.860-0.012-0.0120.0000.0000.0000.000
90C353LYS10.8870.91712.619-0.464-0.4640.0000.0000.0000.000
91C354LEU0-0.0050.0067.0940.0260.0260.0000.0000.0000.000
92C355ILE0-0.028-0.0198.1430.0640.0640.0000.0000.0000.000
93C356PHE00.0490.0222.637-5.050-1.0792.957-1.381-5.5460.015
94C357ALA00.0600.0244.366-1.507-1.3240.000-0.029-0.1540.000
95C358PRO00.0130.0006.9790.2550.2550.0000.0000.0000.000
96C359ASP-1-0.753-0.8709.739-0.366-0.3660.0000.0000.0000.000
97C360LEU0-0.032-0.0215.079-0.115-0.1150.0000.0000.0000.000
98C361VAL0-0.0180.0058.4310.4990.4990.0000.0000.0000.000
99C362LEU00.0170.0177.329-0.046-0.0460.0000.0000.0000.000
100C363ASP-1-0.852-0.93711.0490.5820.5820.0000.0000.0000.000
101C364ARG10.8120.86611.404-0.222-0.2220.0000.0000.0000.000
102C365ASP-1-0.826-0.89112.0010.1430.1430.0000.0000.0000.000
103C366GLU-1-0.752-0.90012.3690.7040.7040.0000.0000.0000.000
104C367GLY00.0310.0139.1480.0010.0010.0000.0000.0000.000
105C368LYS10.8240.8999.669-0.465-0.4650.0000.0000.0000.000
106C369CYS0-0.101-0.02911.756-0.092-0.0920.0000.0000.0000.000
107C370VAL00.001-0.0295.5550.1470.1470.0000.0000.0000.000
108C371GLU-1-0.812-0.8857.427-1.036-1.0360.0000.0000.0000.000
109C372GLY00.0250.0156.535-0.853-0.8530.0000.0000.0000.000
110C373ILE0-0.0110.0173.105-1.867-0.2290.639-0.563-1.7130.007
111C374LEU00.0130.0045.8830.6960.6960.0000.0000.0000.000
112C375GLU-1-0.841-0.9017.589-0.974-0.9740.0000.0000.0000.000
113C376ILE00.007-0.0042.482-1.1060.0120.835-0.287-1.6660.000
114C377PHE0-0.002-0.0105.3420.3240.530-0.001-0.006-0.1990.000
115C378ASP-1-0.781-0.8807.8900.3540.3540.0000.0000.0000.000
116C379MET0-0.030-0.0067.1110.1050.1050.0000.0000.0000.000
117C380LEU00.0310.0274.082-0.1810.0620.000-0.017-0.2260.000
118C381LEU0-0.0030.0208.368-0.064-0.0640.0000.0000.0000.000
119C382ALA0-0.0180.00311.579-0.073-0.0730.0000.0000.0000.000
120C383THR0-0.008-0.02610.004-0.093-0.0930.0000.0000.0000.000
121C384THR0-0.036-0.0379.2520.0160.0160.0000.0000.0000.000
122C385SER0-0.075-0.05111.343-0.088-0.0880.0000.0000.0000.000
123C386ARG10.8240.90514.428-0.348-0.3480.0000.0000.0000.000
124C387PHE00.0560.0079.938-0.080-0.0800.0000.0000.0000.000
125C388ARG10.8730.93613.648-0.648-0.6480.0000.0000.0000.000
126C389GLU-1-0.818-0.87816.7180.2660.2660.0000.0000.0000.000
127C390LEU0-0.0070.00617.422-0.041-0.0410.0000.0000.0000.000
128C391LYS10.8170.90818.391-0.282-0.2820.0000.0000.0000.000
129C392LEU0-0.0040.01913.019-0.035-0.0350.0000.0000.0000.000
130C393GLN0-0.032-0.02716.805-0.013-0.0130.0000.0000.0000.000
131C394HIS00.0270.01213.133-0.019-0.0190.0000.0000.0000.000
132C395LYS10.8800.90916.206-0.089-0.0890.0000.0000.0000.000
133C396GLU-1-0.724-0.82317.3640.2190.2190.0000.0000.0000.000
134C397TYR0-0.040-0.0468.8950.0280.0280.0000.0000.0000.000
135C398LEU0-0.0180.00513.1860.0240.0240.0000.0000.0000.000
136C399CYS0-0.031-0.00814.965-0.021-0.0210.0000.0000.0000.000
137C400VAL00.012-0.00111.955-0.003-0.0030.0000.0000.0000.000
138C401LYS10.8530.9128.1290.1890.1890.0000.0000.0000.000
139C402ALA00.0220.01312.054-0.016-0.0160.0000.0000.0000.000
140C403MET0-0.040-0.02915.443-0.005-0.0050.0000.0000.0000.000
141C404ILE0-0.015-0.0109.421-0.013-0.0130.0000.0000.0000.000
142C405LEU00.0150.01413.413-0.002-0.0020.0000.0000.0000.000
143C406LEU0-0.019-0.01214.696-0.015-0.0150.0000.0000.0000.000
144C407ASN0-0.031-0.02117.252-0.028-0.0280.0000.0000.0000.000
145C408SER0-0.0260.01415.008-0.010-0.0100.0000.0000.0000.000
146C409SER00.028-0.01017.081-0.052-0.0520.0000.0000.0000.000
147C410MET00.0360.02417.9790.0030.0030.0000.0000.0000.000
148C411TYR00.0550.03121.203-0.006-0.0060.0000.0000.0000.000
149C412PRO00.0370.01223.427-0.004-0.0040.0000.0000.0000.000
150C413LEU00.0330.01819.901-0.006-0.0060.0000.0000.0000.000
151C414VAL0-0.009-0.00724.065-0.004-0.0040.0000.0000.0000.000
152C415THR0-0.027-0.02626.122-0.007-0.0070.0000.0000.0000.000
153C416ALA00.0360.01626.894-0.004-0.0040.0000.0000.0000.000
154C417THR0-0.027-0.03225.542-0.006-0.0060.0000.0000.0000.000
155C418GLN0-0.031-0.01627.782-0.006-0.0060.0000.0000.0000.000
156C419ASP-1-0.955-0.96431.1140.0100.0100.0000.0000.0000.000
157C420ALA00.0080.00428.831-0.004-0.0040.0000.0000.0000.000
158C421ASP-1-0.840-0.87530.6850.0130.0130.0000.0000.0000.000
159C422SER0-0.041-0.06325.9450.0010.0010.0000.0000.0000.000
160C423SER0-0.0120.01827.0440.0040.0040.0000.0000.0000.000
161C424ARG10.8210.86227.369-0.018-0.0180.0000.0000.0000.000
162C425LYS10.7740.88825.337-0.002-0.0020.0000.0000.0000.000
163C426LEU00.0250.01020.900-0.002-0.0020.0000.0000.0000.000
164C427ALA00.0040.00024.0300.0090.0090.0000.0000.0000.000
165C428HIS0-0.0020.00425.9420.0080.0080.0000.0000.0000.000
166C429LEU00.0070.01120.7040.0030.0030.0000.0000.0000.000
167C430LEU00.0150.01619.6430.0060.0060.0000.0000.0000.000
168C431ASN0-0.0120.00022.4280.0100.0100.0000.0000.0000.000
169C432ALA00.0110.00924.9440.0020.0020.0000.0000.0000.000
170C433VAL00.002-0.00818.504-0.001-0.0010.0000.0000.0000.000
171C434THR0-0.028-0.02121.7970.0180.0180.0000.0000.0000.000
172C435ASP-1-0.919-0.96423.1270.0690.0690.0000.0000.0000.000
173C436ALA0-0.021-0.02122.7040.0000.0000.0000.0000.0000.000
174C437LEU00.0150.00118.8590.0030.0030.0000.0000.0000.000
175C438VAL00.0160.01222.2440.0040.0040.0000.0000.0000.000
176C439TRP00.0290.00425.669-0.005-0.0050.0000.0000.0000.000
177C440VAL0-0.012-0.01321.174-0.004-0.0040.0000.0000.0000.000
178C441ILE0-0.0110.00821.8020.0010.0010.0000.0000.0000.000
179C442ALA00.0060.02124.982-0.003-0.0030.0000.0000.0000.000
180C443LYS10.8370.91426.998-0.083-0.0830.0000.0000.0000.000
181C444SER0-0.036-0.02426.045-0.004-0.0040.0000.0000.0000.000
182C445GLY0-0.008-0.00128.036-0.002-0.0020.0000.0000.0000.000
183C446ILE0-0.0240.00527.034-0.005-0.0050.0000.0000.0000.000
184C447SER00.0490.01631.202-0.003-0.0030.0000.0000.0000.000
185C448SER00.0800.03431.5490.0090.0090.0000.0000.0000.000
186C449GLN00.0420.02431.0640.0090.0090.0000.0000.0000.000
187C450GLN00.0270.00028.9700.0120.0120.0000.0000.0000.000
188C451GLN0-0.041-0.02227.1280.0120.0120.0000.0000.0000.000
189C452SER00.0190.00526.1700.0100.0100.0000.0000.0000.000
190C453MET0-0.0030.00825.7410.0120.0120.0000.0000.0000.000
191C454ARG10.7600.83820.133-0.199-0.1990.0000.0000.0000.000
192C455LEU00.0430.01621.5830.0220.0220.0000.0000.0000.000
193C456ALA00.0220.00821.5970.0150.0150.0000.0000.0000.000
194C457ASN0-0.039-0.03120.0210.0260.0260.0000.0000.0000.000
195C458LEU00.0470.01516.2360.0290.0290.0000.0000.0000.000
196C459LEU00.0010.01416.9560.0320.0320.0000.0000.0000.000
197C460MET00.0040.00418.1120.0090.0090.0000.0000.0000.000
198C461LEU0-0.051-0.00814.1030.0180.0180.0000.0000.0000.000
199C462LEU00.0160.00813.1970.0830.0830.0000.0000.0000.000
200C463SER0-0.018-0.01213.3980.0440.0440.0000.0000.0000.000
201C464HIS0-0.058-0.03612.430-0.042-0.0420.0000.0000.0000.000
202C465VAL0-0.007-0.0027.6390.0400.0400.0000.0000.0000.000
203C466ARG10.8160.8829.156-0.386-0.3860.0000.0000.0000.000
204C467HIS0-0.052-0.02310.292-0.059-0.0590.0000.0000.0000.000
205C468ALA00.0470.0006.807-0.141-0.1410.0000.0000.0000.000
206C469SER0-0.0030.0055.547-0.028-0.0280.0000.0000.0000.000
207C470ASN00.0330.0096.4000.1360.1360.0000.0000.0000.000
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