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: XYM2X

Calculation Name: 4J26-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 4J26

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 -3087900.217212
FMO2-HF: Nuclear repulsion 2991504.345913
FMO2-HF: Total energy -96395.871299
FMO2-MP2: Total energy -96666.515428


3D Structure
Snapshot
 
Ligand structure

EST

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.
-87.301-74.52586.481-31.628-67.6260.106


Interactive mode: IFIE and PIEDA for fragment #235(B:600:EST)


Summations of interaction energy for fragment #235(B:600:EST)
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.
-87.301-74.52586.481-31.628-67.626-0.106
Interaction energy analysis for fragmet #235(B:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.106 / q_NPA : -0.113
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].
1B264SER10.7630.86226.496-0.104-0.1040.0000.0000.0000.000
2B265PRO00.0660.02325.841-0.001-0.0010.0000.0000.0000.000
3B266GLU-1-0.788-0.87225.2540.1100.1100.0000.0000.0000.000
4B267GLN00.035-0.00324.5260.0090.0090.0000.0000.0000.000
5B268LEU00.0030.04222.190-0.006-0.0060.0000.0000.0000.000
6B269VAL00.020-0.01919.4760.0010.0010.0000.0000.0000.000
7B270LEU0-0.073-0.01519.9790.0130.0130.0000.0000.0000.000
8B271THR00.0600.01820.354-0.010-0.0100.0000.0000.0000.000
9B272LEU0-0.014-0.01516.574-0.013-0.0130.0000.0000.0000.000
10B273LEU0-0.026-0.01615.7160.0100.0100.0000.0000.0000.000
11B274GLU-1-0.868-0.93816.5840.0060.0060.0000.0000.0000.000
12B275ALA00.0210.01215.471-0.032-0.0320.0000.0000.0000.000
13B276GLU-1-0.807-0.86411.2820.0650.0650.0000.0000.0000.000
14B277PRO0-0.0070.0008.9350.0100.0100.0000.0000.0000.000
15B278PRO0-0.027-0.00911.9050.0510.0510.0000.0000.0000.000
16B279HIS00.025-0.0049.935-0.199-0.1990.0000.0000.0000.000
17B280VAL0-0.0090.0007.2870.0030.0030.0000.0000.0000.000
18B281LEU0-0.033-0.0119.1810.1410.1410.0000.0000.0000.000
19B282ILE0-0.053-0.0406.632-0.086-0.0860.0000.0000.0000.000
20B283SER00.010-0.0219.944-0.002-0.0020.0000.0000.0000.000
21B284ARG10.7750.86610.203-0.311-0.3110.0000.0000.0000.000
22B285PRO0-0.0060.01510.951-0.043-0.0430.0000.0000.0000.000
23B286SER0-0.0080.00213.8570.0330.0330.0000.0000.0000.000
24B287ALA0-0.021-0.01915.7320.0000.0000.0000.0000.0000.000
25B288PRO00.0030.00915.7780.0120.0120.0000.0000.0000.000
26B289PHE00.019-0.0049.708-0.033-0.0330.0000.0000.0000.000
27B290THR00.003-0.00112.253-0.018-0.0180.0000.0000.0000.000
28B291GLU-1-0.706-0.8417.598-1.146-1.1460.0000.0000.0000.000
29B292ALA00.0730.0328.022-0.071-0.0710.0000.0000.0000.000
30B293SER0-0.067-0.0339.1040.0760.0760.0000.0000.0000.000
31B294MET00.0420.0235.6830.0040.0040.0000.0000.0000.000
32B295MET00.0370.0222.415-5.646-3.6553.386-1.512-3.8650.015
33B296MET00.0390.0304.8420.1130.281-0.001-0.004-0.1630.000
34B297SER0-0.075-0.0477.253-0.130-0.1300.0000.0000.0000.000
35B298LEU00.0220.0062.403-3.282-0.5851.686-0.723-3.6610.000
36B299THR0-0.006-0.0252.633-6.118-2.9340.932-1.382-2.735-0.019
37B300LYS10.8100.9244.2820.2540.3930.000-0.015-0.1240.000
38B301LEU0-0.0200.0032.459-0.9620.4511.435-0.645-2.2030.004
39B302ALA00.0150.0022.494-2.051-0.4390.625-0.631-1.6070.002
40B303ASP-1-0.833-0.9023.890-0.396-0.2030.012-0.043-0.1620.000
41B304LYS10.8770.9226.8010.9560.9560.0000.0000.0000.000
42B305GLU-1-0.748-0.8391.538-26.877-39.98127.858-10.214-4.539-0.086
43B306LEU00.0140.0225.6770.6570.6570.0000.0000.0000.000
44B307VAL00.0270.0088.1930.2320.2320.0000.0000.0000.000
45B308HIS0-0.022-0.0147.8050.2370.2370.0000.0000.0000.000
46B309MET0-0.0510.0007.0510.2430.2430.0000.0000.0000.000
47B310ILE00.0240.0129.9810.1420.1420.0000.0000.0000.000
48B311SER0-0.072-0.05112.8440.0760.0760.0000.0000.0000.000
49B312TRP0-0.0160.00511.4760.0450.0450.0000.0000.0000.000
50B313ALA00.0530.01513.4400.0490.0490.0000.0000.0000.000
51B314LYS10.8480.91215.2410.0680.0680.0000.0000.0000.000
52B315LYS10.8130.91915.2740.1210.1210.0000.0000.0000.000
53B316ILE0-0.028-0.00115.7850.0140.0140.0000.0000.0000.000
54B317PRO0-0.008-0.00920.1710.0010.0010.0000.0000.0000.000
55B318GLY0-0.006-0.01623.1610.0120.0120.0000.0000.0000.000
56B319PHE0-0.001-0.01516.8560.0100.0100.0000.0000.0000.000
57B320VAL0-0.011-0.00220.931-0.006-0.0060.0000.0000.0000.000
58B321GLU-1-0.826-0.91722.6490.0300.0300.0000.0000.0000.000
59B322LEU0-0.0590.00820.9770.0050.0050.0000.0000.0000.000
60B323SER0-0.001-0.01824.919-0.009-0.0090.0000.0000.0000.000
61B324LEU00.021-0.00921.3830.0050.0050.0000.0000.0000.000
62B325PHE00.0270.01321.8990.0020.0020.0000.0000.0000.000
63B326ASP-1-0.712-0.81420.9820.0950.0950.0000.0000.0000.000
64B327GLN0-0.026-0.01219.0720.0000.0000.0000.0000.0000.000
65B328VAL00.0200.00817.0640.0010.0010.0000.0000.0000.000
66B329ARG10.8580.91516.045-0.097-0.0970.0000.0000.0000.000
67B330LEU0-0.016-0.00815.7850.0320.0320.0000.0000.0000.000
68B331LEU0-0.0110.00511.8930.0470.0470.0000.0000.0000.000
69B332GLU-1-0.745-0.87611.7750.2660.2660.0000.0000.0000.000
70B333SER0-0.0440.00711.0540.0800.0800.0000.0000.0000.000
71B334CYS0-0.080-0.02911.1330.0650.0650.0000.0000.0000.000
72B335TRP00.0730.0204.9250.2610.2610.0000.0000.0000.000
73B336MET00.0170.0222.456-1.486-1.1784.514-0.822-4.000-0.002
74B337GLU-1-0.832-0.9304.2700.7200.9460.000-0.027-0.1980.000
75B338VAL0-0.010-0.0246.7150.1760.1760.0000.0000.0000.000
76B339LEU0-0.0060.0042.480-4.665-0.9923.156-1.568-5.2610.015
77B340MET0-0.0360.0102.157-1.0210.7415.760-1.553-5.969-0.005
78B341MET0-0.0040.0043.613-0.0650.0620.0060.048-0.1810.000
79B342GLY0-0.008-0.0015.097-0.390-0.331-0.001-0.007-0.0510.000
80B343LEU0-0.0170.0032.380-3.760-1.7503.415-1.229-4.1960.008
81B344MET0-0.027-0.0034.430-1.210-1.0250.000-0.037-0.1480.000
82B345TRP0-0.027-0.0167.354-0.282-0.2820.0000.0000.0000.000
83B346ARG10.7570.8502.2770.7861.8940.716-0.606-1.2180.004
84B347SER00.003-0.0087.303-0.125-0.1250.0000.0000.0000.000
85B348ILE00.0130.0239.976-0.139-0.1390.0000.0000.0000.000
86B349ASP-1-0.867-0.95212.5790.4310.4310.0000.0000.0000.000
87B350HIS0-0.074-0.03012.673-0.094-0.0940.0000.0000.0000.000
88B351PRO0-0.021-0.01712.9390.0840.0840.0000.0000.0000.000
89B352GLY0-0.0130.00112.975-0.033-0.0330.0000.0000.0000.000
90B353LYS10.8550.90710.986-0.422-0.4220.0000.0000.0000.000
91B354LEU00.0000.0124.565-0.1110.051-0.001-0.004-0.1570.000
92B355ILE0-0.002-0.0077.996-0.027-0.0270.0000.0000.0000.000
93B356PHE00.0240.0042.255-5.303-1.7494.211-1.423-6.3420.014
94B357ALA00.0640.0294.959-1.312-1.200-0.001-0.004-0.1070.000
95B358PRO00.005-0.0087.7650.2010.2010.0000.0000.0000.000
96B359ASP-1-0.752-0.87210.631-0.150-0.1500.0000.0000.0000.000
97B360LEU0-0.048-0.0355.676-0.098-0.0980.0000.0000.0000.000
98B361VAL0-0.0140.0088.6530.3290.3290.0000.0000.0000.000
99B362LEU0-0.0040.0116.159-0.276-0.2760.0000.0000.0000.000
100B363ASP-1-0.795-0.8959.7230.4970.4970.0000.0000.0000.000
101B364ARG10.7170.8179.850-0.129-0.1290.0000.0000.0000.000
102B365ASP-1-0.808-0.89810.633-0.134-0.1340.0000.0000.0000.000
103B366GLU-1-0.729-0.83410.8860.1520.1520.0000.0000.0000.000
104B367GLY00.0430.0148.319-0.100-0.1000.0000.0000.0000.000
105B368LYS10.8170.8868.989-0.132-0.1320.0000.0000.0000.000
106B369CYS0-0.121-0.02710.119-0.042-0.0420.0000.0000.0000.000
107B370VAL0-0.022-0.0254.992-0.079-0.0790.0000.0000.0000.000
108B371GLU-1-0.795-0.8767.744-1.144-1.1440.0000.0000.0000.000
109B372GLY00.0170.0096.496-0.721-0.7210.0000.0000.0000.000
110B373ILE0-0.006-0.0082.204-1.222-0.8173.769-0.575-3.5990.001
111B374LEU0-0.050-0.0124.6310.5370.633-0.001-0.005-0.0890.000
112B375GLU-1-0.753-0.8547.8830.1150.1150.0000.0000.0000.000
113B376ILE0-0.009-0.0052.705-1.1410.0750.477-0.236-1.4560.000
114B377PHE00.024-0.0083.443-0.5430.3740.017-0.118-0.8160.000
115B378ASP-1-0.778-0.8756.1650.4920.4920.0000.0000.0000.000
116B379MET0-0.0350.0197.5070.0580.0580.0000.0000.0000.000
117B380LEU00.0380.0262.757-0.978-0.0210.387-0.192-1.152-0.001
118B381LEU00.0250.0416.9470.0170.0170.0000.0000.0000.000
119B382ALA00.0000.0129.654-0.063-0.0630.0000.0000.0000.000
120B383THR0-0.044-0.0439.294-0.092-0.0920.0000.0000.0000.000
121B384THR00.009-0.0128.3000.0370.0370.0000.0000.0000.000
122B385SER0-0.020-0.01410.692-0.092-0.0920.0000.0000.0000.000
123B386ARG10.8750.94713.069-0.449-0.4490.0000.0000.0000.000
124B387PHE00.0490.00911.254-0.066-0.0660.0000.0000.0000.000
125B388ARG10.7990.88914.233-0.543-0.5430.0000.0000.0000.000
126B389GLU-1-0.834-0.90316.4330.3180.3180.0000.0000.0000.000
127B390LEU0-0.038-0.02017.815-0.047-0.0470.0000.0000.0000.000
128B391LYS10.8660.94118.892-0.280-0.2800.0000.0000.0000.000
129B392LEU00.0060.02713.274-0.035-0.0350.0000.0000.0000.000
130B393GLN00.003-0.01117.322-0.004-0.0040.0000.0000.0000.000
131B394HIS00.0750.04213.3580.0500.0500.0000.0000.0000.000
132B395LYS10.8570.91116.131-0.118-0.1180.0000.0000.0000.000
133B396GLU-1-0.728-0.83317.6760.2680.2680.0000.0000.0000.000
134B397TYR0-0.006-0.0169.1210.0450.0450.0000.0000.0000.000
135B398LEU0-0.0240.00513.2440.0270.0270.0000.0000.0000.000
136B399CYS0-0.038-0.01214.897-0.022-0.0220.0000.0000.0000.000
137B400VAL00.0270.00212.641-0.011-0.0110.0000.0000.0000.000
138B401LYS10.8260.9048.484-0.201-0.2010.0000.0000.0000.000
139B402ALA00.0230.00712.222-0.021-0.0210.0000.0000.0000.000
140B403MET0-0.041-0.02415.308-0.019-0.0190.0000.0000.0000.000
141B404ILE0-0.015-0.0039.869-0.020-0.0200.0000.0000.0000.000
142B405LEU00.0140.00013.363-0.004-0.0040.0000.0000.0000.000
143B406LEU0-0.027-0.01214.405-0.021-0.0210.0000.0000.0000.000
144B407ASN0-0.048-0.02516.996-0.028-0.0280.0000.0000.0000.000
145B408SER0-0.033-0.02014.286-0.006-0.0060.0000.0000.0000.000
146B409SER00.003-0.03516.021-0.039-0.0390.0000.0000.0000.000
147B410MET00.0230.01916.683-0.018-0.0180.0000.0000.0000.000
148B411TYR00.0710.03219.917-0.014-0.0140.0000.0000.0000.000
149B412PRO00.006-0.00222.606-0.010-0.0100.0000.0000.0000.000
150B413LEU00.0380.03619.861-0.011-0.0110.0000.0000.0000.000
151B414VAL00.0140.02522.662-0.010-0.0100.0000.0000.0000.000
152B415THR0-0.077-0.05125.091-0.010-0.0100.0000.0000.0000.000
153B416ALA0-0.0080.00726.418-0.006-0.0060.0000.0000.0000.000
154B417THR0-0.061-0.04724.511-0.003-0.0030.0000.0000.0000.000
155B418GLN0-0.048-0.03326.228-0.009-0.0090.0000.0000.0000.000
156B419ASP-1-0.849-0.90828.3270.0550.0550.0000.0000.0000.000
157B420ALA0-0.036-0.00530.946-0.002-0.0020.0000.0000.0000.000
158B421ASP-1-0.828-0.91730.5450.0500.0500.0000.0000.0000.000
159B422SER0-0.018-0.01925.4880.0000.0000.0000.0000.0000.000
160B423SER00.0600.01726.0730.0060.0060.0000.0000.0000.000
161B424ARG10.8620.91427.016-0.042-0.0420.0000.0000.0000.000
162B425LYS10.8110.90725.902-0.035-0.0350.0000.0000.0000.000
163B426LEU00.0320.03320.4460.0030.0030.0000.0000.0000.000
164B427ALA00.0180.00723.3730.0120.0120.0000.0000.0000.000
165B428HIS0-0.011-0.00425.6180.0080.0080.0000.0000.0000.000
166B429LEU00.0050.00320.3680.0050.0050.0000.0000.0000.000
167B430LEU00.0140.01519.5170.0100.0100.0000.0000.0000.000
168B431ASN0-0.0050.01022.2230.0120.0120.0000.0000.0000.000
169B432ALA0-0.015-0.01225.0760.0040.0040.0000.0000.0000.000
170B433VAL00.010-0.00918.721-0.001-0.0010.0000.0000.0000.000
171B434THR00.011-0.00121.8770.0190.0190.0000.0000.0000.000
172B435ASP-1-0.808-0.90023.0580.1130.1130.0000.0000.0000.000
173B436ALA0-0.024-0.00522.996-0.002-0.0020.0000.0000.0000.000
174B437LEU00.0520.02118.6960.0020.0020.0000.0000.0000.000
175B438VAL00.002-0.00122.1860.0030.0030.0000.0000.0000.000
176B439TRP0-0.023-0.00924.195-0.003-0.0030.0000.0000.0000.000
177B440VAL0-0.053-0.03021.257-0.006-0.0060.0000.0000.0000.000
178B441ILE00.0130.01721.5090.0000.0000.0000.0000.0000.000
179B442ALA0-0.0100.01524.757-0.005-0.0050.0000.0000.0000.000
180B443LYS10.8240.91525.760-0.129-0.1290.0000.0000.0000.000
181B444SER0-0.066-0.04824.931-0.001-0.0010.0000.0000.0000.000
182B445GLY00.0000.00026.981-0.001-0.0010.0000.0000.0000.000
183B446ILE0-0.032-0.00126.336-0.009-0.0090.0000.0000.0000.000
184B447SER00.0540.02030.471-0.001-0.0010.0000.0000.0000.000
185B448SER00.0800.02431.2050.0060.0060.0000.0000.0000.000
186B449GLN00.0200.02830.9540.0010.0010.0000.0000.0000.000
187B450GLN00.0290.00028.6300.0040.0040.0000.0000.0000.000
188B451GLN0-0.023-0.01826.8970.0140.0140.0000.0000.0000.000
189B452SER00.0050.00026.0150.0110.0110.0000.0000.0000.000
190B453MET0-0.024-0.01625.5290.0060.0060.0000.0000.0000.000
191B454ARG10.7330.83720.479-0.245-0.2450.0000.0000.0000.000
192B455LEU00.0350.01021.4330.0240.0240.0000.0000.0000.000
193B456ALA00.0120.00621.1810.0170.0170.0000.0000.0000.000
194B457ASN00.000-0.01420.2530.0080.0080.0000.0000.0000.000
195B458LEU0-0.022-0.01616.7790.0330.0330.0000.0000.0000.000
196B459LEU00.0210.01616.1030.0450.0450.0000.0000.0000.000
197B460MET0-0.009-0.00216.7530.0100.0100.0000.0000.0000.000
198B461LEU0-0.0300.00013.643-0.002-0.0020.0000.0000.0000.000
199B462LEU00.0400.01811.9790.0540.0540.0000.0000.0000.000
200B463SER0-0.042-0.02412.3620.0090.0090.0000.0000.0000.000
201B464HIS0-0.019-0.00811.341-0.022-0.0220.0000.0000.0000.000
202B465VAL00.0150.0167.1560.0280.0280.0000.0000.0000.000
203B466ARG10.8620.9347.817-0.446-0.4460.0000.0000.0000.000
204B467HIS0-0.036-0.0379.794-0.026-0.0260.0000.0000.0000.000
205B468ALA00.0150.0015.515-0.060-0.0600.0000.0000.0000.000
206B469SER00.009-0.0334.656-0.236-0.054-0.001-0.017-0.1640.000
207B470ASN00.0190.0205.7530.1040.1040.0000.0000.0000.000
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209B472GLY00.0210.0052.215-1.495-0.8312.376-1.351-1.6880.001
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