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: PKL3X

Calculation Name: 1X7B-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 2-(3-fluoro-4-hydroxyphenyl)-7-vinyl-1,3-benzoxazol-5-ol

ligand 3-letter code: 041

PDB ID: 1X7B

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 -3089052.231587
FMO2-HF: Nuclear repulsion 2992549.595066
FMO2-HF: Total energy -96502.636522
FMO2-MP2: Total energy -96773.371777


3D Structure
Snapshot
 
Ligand structure

041

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.
-105.601-79.33873.585-31.825-68.0320.030


Interactive mode: IFIE and PIEDA for fragment #235(C:201:041)


Summations of interaction energy for fragment #235(C:201:041)
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.
-105.601-79.33873.585-31.825-68.032-0.03
Interaction energy analysis for fragmet #235(C:201:041)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.088
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].
1C264SER10.7880.89329.978-0.127-0.1270.0000.0000.0000.000
2C265PRO00.1650.07725.754-0.010-0.0100.0000.0000.0000.000
3C266GLU-1-0.777-0.85625.0910.1670.1670.0000.0000.0000.000
4C267GLN00.019-0.00324.873-0.001-0.0010.0000.0000.0000.000
5C268LEU00.0080.02321.452-0.012-0.0120.0000.0000.0000.000
6C269VAL00.018-0.01220.4040.0070.0070.0000.0000.0000.000
7C270LEU0-0.013-0.01320.0710.0040.0040.0000.0000.0000.000
8C271THR00.0020.00720.755-0.021-0.0210.0000.0000.0000.000
9C272LEU0-0.002-0.00316.430-0.011-0.0110.0000.0000.0000.000
10C273LEU0-0.013-0.00516.0680.0080.0080.0000.0000.0000.000
11C274GLU-1-0.918-0.96016.521-0.055-0.0550.0000.0000.0000.000
12C275ALA00.0010.00915.171-0.053-0.0530.0000.0000.0000.000
13C276GLU-1-0.733-0.81311.0760.1350.1350.0000.0000.0000.000
14C277PRO0-0.0110.0118.008-0.017-0.0170.0000.0000.0000.000
15C278PRO0-0.019-0.00910.8500.1110.1110.0000.0000.0000.000
16C279HIS0-0.016-0.0217.522-0.559-0.5590.0000.0000.0000.000
17C280VAL0-0.0080.0075.5800.3030.3030.0000.0000.0000.000
18C281LEU00.0220.0206.915-0.143-0.1430.0000.0000.0000.000
19C282ILE00.0190.0106.190-0.127-0.1270.0000.0000.0000.000
20C283SER0-0.079-0.0428.7200.1950.1950.0000.0000.0000.000
21C284ARG10.8090.89811.5180.1460.1460.0000.0000.0000.000
22C285PRO00.0480.01713.658-0.024-0.0240.0000.0000.0000.000
23C286SER0-0.001-0.01513.865-0.005-0.0050.0000.0000.0000.000
24C287ALA0-0.050-0.01214.9340.0470.0470.0000.0000.0000.000
25C288PRO00.0520.02814.0280.0200.0200.0000.0000.0000.000
26C289PHE0-0.036-0.00910.2880.0170.0170.0000.0000.0000.000
27C290THR00.0350.01112.434-0.046-0.0460.0000.0000.0000.000
28C291GLU-1-0.781-0.8867.127-1.407-1.4070.0000.0000.0000.000
29C292ALA00.0190.0048.9080.1900.1900.0000.0000.0000.000
30C293SER0-0.019-0.02011.4730.0820.0820.0000.0000.0000.000
31C294MET0-0.0050.0087.0300.0830.0830.0000.0000.0000.000
32C295MET00.0160.0132.546-1.068-0.5572.647-0.778-2.3800.011
33C296MET0-0.0010.0196.1050.2960.2960.0000.0000.0000.000
34C297SER0-0.003-0.0227.652-0.372-0.3720.0000.0000.0000.000
35C298LEU00.005-0.0112.820-6.891-1.8732.059-1.485-5.5920.015
36C299THR00.0280.0032.783-5.081-2.7620.307-0.996-1.631-0.013
37C300LYS10.8760.9505.288-0.520-0.391-0.001-0.005-0.1230.000
38C301LEU0-0.070-0.0272.248-1.538-0.1693.513-1.229-3.6540.004
39C302ALA00.0320.0102.341-2.828-1.3350.979-0.817-1.6550.001
40C303ASP-1-0.844-0.9093.6790.0460.2880.025-0.030-0.2370.000
41C304LYS10.8560.9106.8491.5001.5000.0000.0000.0000.000
42C305GLU-1-0.789-0.8791.607-32.142-39.86318.583-7.158-3.705-0.071
43C306LEU00.0380.0245.9260.8730.8730.0000.0000.0000.000
44C307VAL00.0080.0188.3110.3250.3250.0000.0000.0000.000
45C308HIS0-0.028-0.0248.4910.3800.3800.0000.0000.0000.000
46C309MET0-0.0100.0316.5910.3000.3000.0000.0000.0000.000
47C310ILE00.0420.0199.7960.2390.2390.0000.0000.0000.000
48C311SER0-0.088-0.05512.7230.1190.1190.0000.0000.0000.000
49C312TRP0-0.010-0.00610.7970.0680.0680.0000.0000.0000.000
50C313ALA00.0490.00412.9130.0610.0610.0000.0000.0000.000
51C314LYS10.8630.91715.093-0.030-0.0300.0000.0000.0000.000
52C315LYS10.7890.91014.6880.1750.1750.0000.0000.0000.000
53C316ILE0-0.0080.00915.6580.0100.0100.0000.0000.0000.000
54C317PRO0-0.016-0.00819.8790.0090.0090.0000.0000.0000.000
55C318GLY00.0120.00523.2200.0180.0180.0000.0000.0000.000
56C319PHE00.036-0.00917.2900.0180.0180.0000.0000.0000.000
57C320VAL00.0070.00220.932-0.002-0.0020.0000.0000.0000.000
58C321GLU-1-0.800-0.88222.7610.1150.1150.0000.0000.0000.000
59C322LEU0-0.0410.01221.2260.0110.0110.0000.0000.0000.000
60C323SER0-0.022-0.04724.965-0.018-0.0180.0000.0000.0000.000
61C324LEU00.011-0.00522.8390.0110.0110.0000.0000.0000.000
62C325PHE00.0800.03622.6210.0070.0070.0000.0000.0000.000
63C326ASP-1-0.754-0.81821.7530.2420.2420.0000.0000.0000.000
64C327GLN0-0.097-0.05919.3380.0160.0160.0000.0000.0000.000
65C328VAL0-0.0080.01017.566-0.025-0.0250.0000.0000.0000.000
66C329ARG10.9190.96017.110-0.255-0.2550.0000.0000.0000.000
67C330LEU0-0.071-0.02417.3010.0580.0580.0000.0000.0000.000
68C331LEU00.0490.02311.8790.1020.1020.0000.0000.0000.000
69C332GLU-1-0.868-0.94812.8230.5790.5790.0000.0000.0000.000
70C333SER0-0.023-0.01013.1890.1370.1370.0000.0000.0000.000
71C334CYS0-0.097-0.03311.3680.0430.0430.0000.0000.0000.000
72C335TRP00.1020.0425.2770.3320.561-0.001-0.003-0.2250.000
73C336MET00.0170.0173.020-3.473-0.5631.136-0.756-3.2890.007
74C337GLU-1-0.765-0.8625.0501.9462.061-0.001-0.004-0.1110.000
75C338VAL00.007-0.0196.5390.3720.3720.0000.0000.0000.000
76C339LEU0-0.036-0.0062.582-3.907-1.3465.413-2.010-5.9640.011
77C340MET0-0.0290.0122.435-2.6012.2773.247-2.468-5.6570.016
78C341MET0-0.0110.0003.286-1.051-1.2430.0500.481-0.3400.002
79C342GLY00.0030.0035.113-0.931-0.881-0.001-0.008-0.0420.000
80C343LEU00.0020.0152.470-4.408-2.0232.165-1.584-2.9670.013
81C344MET0-0.015-0.0074.282-2.300-2.0410.001-0.036-0.2230.000
82C345TRP0-0.0060.0087.145-0.625-0.6250.0000.0000.0000.000
83C346ARG10.7540.8402.4554.1975.1160.296-0.426-0.7890.001
84C347SER0-0.002-0.0127.184-0.348-0.3480.0000.0000.0000.000
85C348ILE00.0070.0239.804-0.141-0.1410.0000.0000.0000.000
86C349ASP-1-0.859-0.93612.4920.4010.4010.0000.0000.0000.000
87C350HIS0-0.037-0.01012.559-0.128-0.1280.0000.0000.0000.000
88C351PRO00.0050.01713.5900.0900.0900.0000.0000.0000.000
89C352GLY00.0250.02012.227-0.024-0.0240.0000.0000.0000.000
90C353LYS10.8680.91610.463-0.307-0.3070.0000.0000.0000.000
91C354LEU00.0180.0224.658-0.0680.052-0.001-0.005-0.1150.000
92C355ILE0-0.031-0.0258.201-0.214-0.2140.0000.0000.0000.000
93C356PHE00.0360.0172.427-4.413-0.3582.957-1.412-5.6000.012
94C357ALA00.0560.0214.389-2.203-2.095-0.001-0.025-0.0830.000
95C358PRO00.012-0.0036.9520.4810.4810.0000.0000.0000.000
96C359ASP-1-0.745-0.8599.737-0.944-0.9440.0000.0000.0000.000
97C360LEU0-0.026-0.0144.896-0.022-0.0220.0000.0000.0000.000
98C361VAL0-0.020-0.0018.2450.2960.2960.0000.0000.0000.000
99C362LEU00.0150.0085.787-0.029-0.0290.0000.0000.0000.000
100C363ASP-1-0.856-0.9378.8440.4280.4280.0000.0000.0000.000
101C364ARG10.8070.8738.530-0.019-0.0190.0000.0000.0000.000
102C365ASP-1-0.815-0.8949.481-0.195-0.1950.0000.0000.0000.000
103C366GLU-1-0.780-0.90110.1530.1730.1730.0000.0000.0000.000
104C367GLY00.0510.0297.814-0.067-0.0670.0000.0000.0000.000
105C368LYS10.8270.9008.485-0.180-0.1800.0000.0000.0000.000
106C369CYS0-0.158-0.05911.103-0.044-0.0440.0000.0000.0000.000
107C370VAL00.029-0.0155.4080.0540.0540.0000.0000.0000.000
108C371GLU-1-0.805-0.8737.234-1.870-1.8700.0000.0000.0000.000
109C372GLY00.0280.0136.723-1.083-1.0830.0000.0000.0000.000
110C373ILE0-0.0190.0082.723-2.045-0.4142.412-0.837-3.2060.009
111C374LEU00.0140.0084.9240.5100.603-0.001-0.002-0.0900.000
112C375GLU-1-0.863-0.9197.303-1.024-1.0240.0000.0000.0000.000
113C376ILE00.0270.0042.374-1.635-0.3691.767-0.585-2.448-0.002
114C377PHE0-0.002-0.0112.797-0.8810.4030.560-0.404-1.4410.004
115C378ASP-1-0.777-0.8815.0020.3110.333-0.001-0.003-0.0180.000
116C379MET0-0.041-0.0096.8510.2710.2710.0000.0000.0000.000
117C380LEU00.0370.0242.706-0.5050.0770.493-0.227-0.8480.000
118C381LEU00.0120.0206.7320.1520.1520.0000.0000.0000.000
119C382ALA0-0.014-0.0029.531-0.027-0.0270.0000.0000.0000.000
120C383THR0-0.035-0.0369.671-0.075-0.0750.0000.0000.0000.000
121C384THR0-0.040-0.0399.2100.0910.0910.0000.0000.0000.000
122C385SER0-0.047-0.04111.280-0.126-0.1260.0000.0000.0000.000
123C386ARG10.8490.91814.675-0.480-0.4800.0000.0000.0000.000
124C387PHE00.0650.01410.129-0.105-0.1050.0000.0000.0000.000
125C388ARG10.8740.93313.670-0.748-0.7480.0000.0000.0000.000
126C389GLU-1-0.858-0.89516.4460.3430.3430.0000.0000.0000.000
127C390LEU0-0.033-0.01017.243-0.066-0.0660.0000.0000.0000.000
128C391LYS10.8670.93918.783-0.350-0.3500.0000.0000.0000.000
129C392LEU00.0000.02013.103-0.047-0.0470.0000.0000.0000.000
130C393GLN0-0.019-0.02216.963-0.030-0.0300.0000.0000.0000.000
131C394HIS00.0190.01113.5190.0000.0000.0000.0000.0000.000
132C395LYS10.8660.90116.335-0.155-0.1550.0000.0000.0000.000
133C396GLU-1-0.744-0.82917.4310.4070.4070.0000.0000.0000.000
134C397TYR0-0.032-0.0459.1150.0870.0870.0000.0000.0000.000
135C398LEU0-0.0180.00913.0980.0900.0900.0000.0000.0000.000
136C399CYS0-0.031-0.01115.059-0.012-0.0120.0000.0000.0000.000
137C400VAL00.0260.00412.257-0.001-0.0010.0000.0000.0000.000
138C401LYS10.8530.9268.307-0.495-0.4950.0000.0000.0000.000
139C402ALA00.0030.00611.949-0.005-0.0050.0000.0000.0000.000
140C403MET0-0.049-0.03515.260-0.028-0.0280.0000.0000.0000.000
141C404ILE0-0.026-0.0129.278-0.022-0.0220.0000.0000.0000.000
142C405LEU0-0.004-0.00912.778-0.011-0.0110.0000.0000.0000.000
143C406LEU00.0140.00913.697-0.069-0.0690.0000.0000.0000.000
144C407ASN0-0.032-0.01113.604-0.163-0.1630.0000.0000.0000.000
145C408SER0-0.018-0.00315.422-0.076-0.0760.0000.0000.0000.000
146C409SER0-0.021-0.02817.081-0.070-0.0700.0000.0000.0000.000
147C410MET00.008-0.00120.358-0.048-0.0480.0000.0000.0000.000
148C411TYR0-0.030-0.03622.246-0.023-0.0230.0000.0000.0000.000
149C412PRO00.0040.00423.530-0.019-0.0190.0000.0000.0000.000
150C413LEU0-0.0080.01524.018-0.020-0.0200.0000.0000.0000.000
151C414VAL0-0.033-0.00724.810-0.014-0.0140.0000.0000.0000.000
152C415THR0-0.062-0.04527.810-0.017-0.0170.0000.0000.0000.000
153C416ALA00.002-0.00530.936-0.001-0.0010.0000.0000.0000.000
154C417THR0-0.057-0.03932.677-0.010-0.0100.0000.0000.0000.000
155C418GLN0-0.0170.01528.3860.0180.0180.0000.0000.0000.000
156C419ASP-1-0.713-0.82028.1130.1850.1850.0000.0000.0000.000
157C420ALA00.0200.01129.380-0.007-0.0070.0000.0000.0000.000
158C421ASP-1-0.885-0.94830.1640.1300.1300.0000.0000.0000.000
159C422SER0-0.006-0.03426.0160.0040.0040.0000.0000.0000.000
160C423SER0-0.007-0.02425.8240.0190.0190.0000.0000.0000.000
161C424ARG10.9060.94326.540-0.121-0.1210.0000.0000.0000.000
162C425LYS10.7440.86625.232-0.146-0.1460.0000.0000.0000.000
163C426LEU00.0180.01120.5140.0060.0060.0000.0000.0000.000
164C427ALA00.0200.01023.3510.0220.0220.0000.0000.0000.000
165C428HIS0-0.020-0.01225.3380.0080.0080.0000.0000.0000.000
166C429LEU0-0.0200.00420.4410.0000.0000.0000.0000.0000.000
167C430LEU00.0400.02119.0050.0090.0090.0000.0000.0000.000
168C431ASN0-0.0340.00121.9360.0020.0020.0000.0000.0000.000
169C432ALA00.0540.02124.7460.0020.0020.0000.0000.0000.000
170C433VAL0-0.002-0.01018.146-0.006-0.0060.0000.0000.0000.000
171C434THR0-0.032-0.02321.2160.0290.0290.0000.0000.0000.000
172C435ASP-1-0.912-0.96422.6530.1910.1910.0000.0000.0000.000
173C436ALA0-0.032-0.02421.858-0.011-0.0110.0000.0000.0000.000
174C437LEU00.0070.00218.401-0.005-0.0050.0000.0000.0000.000
175C438VAL00.0230.01121.630-0.007-0.0070.0000.0000.0000.000
176C439TRP00.0340.00825.142-0.020-0.0200.0000.0000.0000.000
177C440VAL0-0.016-0.01521.001-0.019-0.0190.0000.0000.0000.000
178C441ILE00.0000.01221.325-0.011-0.0110.0000.0000.0000.000
179C442ALA00.0030.02224.708-0.015-0.0150.0000.0000.0000.000
180C443LYS10.8200.90126.688-0.173-0.1730.0000.0000.0000.000
181C444SER0-0.029-0.02225.115-0.012-0.0120.0000.0000.0000.000
182C445GLY0-0.009-0.00127.110-0.007-0.0070.0000.0000.0000.000
183C446ILE0-0.0170.00926.039-0.011-0.0110.0000.0000.0000.000
184C447SER00.0470.01630.2210.0010.0010.0000.0000.0000.000
185C448SER00.0660.02330.9040.0150.0150.0000.0000.0000.000
186C449GLN00.0540.03130.7140.0200.0200.0000.0000.0000.000
187C450GLN00.0310.01028.0160.0250.0250.0000.0000.0000.000
188C451GLN0-0.036-0.02126.5430.0260.0260.0000.0000.0000.000
189C452SER00.0110.00325.8280.0220.0220.0000.0000.0000.000
190C453MET00.003-0.00325.8270.0190.0190.0000.0000.0000.000
191C454ARG10.7460.84820.357-0.342-0.3420.0000.0000.0000.000
192C455LEU00.0360.01221.2220.0430.0430.0000.0000.0000.000
193C456ALA00.0220.00921.3130.0350.0350.0000.0000.0000.000
194C457ASN0-0.044-0.04119.5630.0380.0380.0000.0000.0000.000
195C458LEU00.0100.00316.0220.0580.0580.0000.0000.0000.000
196C459LEU00.0020.00216.5180.0660.0660.0000.0000.0000.000
197C460MET0-0.032-0.01317.8720.0190.0190.0000.0000.0000.000
198C461LEU00.0050.00513.5210.0120.0120.0000.0000.0000.000
199C462LEU00.0130.01513.0220.1680.1680.0000.0000.0000.000
200C463SER0-0.011-0.01613.2040.0870.0870.0000.0000.0000.000
201C464HIS0-0.0090.00411.7420.0130.0130.0000.0000.0000.000
202C465VAL00.0230.0117.1620.1110.1110.0000.0000.0000.000
203C466ARG10.7860.8948.773-0.800-0.8000.0000.0000.0000.000
204C467HIS0-0.047-0.0239.678-0.051-0.0510.0000.0000.0000.000
205C468ALA00.0210.0065.840-0.177-0.1770.0000.0000.0000.000
206C469SER00.015-0.0275.3640.0810.0810.0000.0000.0000.000
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