Manual

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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: 5P4NP

Calculation Name: 1ERE-D-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 1ERE

Chain ID: D

ChEMBL ID: CHEMBL206

UniProt ID: P03372

Base Structure: X-ray

Registration Date: 2017-02-24

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement BioStationViewer:StructureComplemation (agonist templeate: 1A52)
Water A bridging water among Glu353, Arg394 and ligand.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandCharge EST=0
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3151388.208186
FMO2-HF: Nuclear repulsion 3053174.845449
FMO2-HF: Total energy -98213.362736
FMO2-MP2: Total energy -98490.505804


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.
-127.936-141.441151.973-80.080-58.3920.192


Interactive mode: IFIE and PIEDA for fragment #237(D:600:EST)


Summations of interaction energy for fragment #237(D: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.
-127.936-141.441151.973-80.08-58.392-0.192
Interaction energy analysis for fragmet #237(D:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.191 / q_NPA : ******
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].
1D309SER10.87330.064-0.083-0.0830.0000.0000.0000.000
2D310LEU00.08525.565-0.003-0.0030.0000.0000.0000.000
3D311THR00.03829.4600.0040.0040.0000.0000.0000.000
4D312ALA00.03927.0320.0050.0050.0000.0000.0000.000
5D313ASP-1-0.77826.0220.1650.1650.0000.0000.0000.000
6D314GLN00.03526.0240.0040.0040.0000.0000.0000.000
7D315MET0-0.04021.431-0.005-0.0050.0000.0000.0000.000
8D316VAL00.06321.1890.0110.0110.0000.0000.0000.000
9D317SER00.01820.8070.0180.0180.0000.0000.0000.000
10D318ALA0-0.00321.0710.0030.0030.0000.0000.0000.000
11D319LEU0-0.04217.462-0.004-0.0040.0000.0000.0000.000
12D320LEU0-0.02116.7630.0240.0240.0000.0000.0000.000
13D321ASP-1-0.90317.1490.1650.1650.0000.0000.0000.000
14D322ALA0-0.16416.030-0.020-0.0200.0000.0000.0000.000
15D323GLU-1-0.88511.5430.6690.6690.0000.0000.0000.000
16D324PRO0-0.0198.797-0.075-0.0750.0000.0000.0000.000
17D325PRO0-0.01410.3710.0910.0910.0000.0000.0000.000
18D326ILE00.0078.001-0.032-0.0320.0000.0000.0000.000
19D327LEU0-0.0336.495-0.017-0.0170.0000.0000.0000.000
20D328TYR00.0188.1850.2670.2670.0000.0000.0000.000
21D329SER00.0157.728-0.305-0.3050.0000.0000.0000.000
22D330GLU-1-0.8948.867-0.526-0.5260.0000.0000.0000.000
23D331TYR0-0.06411.0540.0570.0570.0000.0000.0000.000
24D332ASP-1-0.78412.663-0.027-0.0270.0000.0000.0000.000
25D333PRO0-0.03516.043-0.002-0.0020.0000.0000.0000.000
26D334THR0-0.07717.2630.0140.0140.0000.0000.0000.000
27D335ARG10.93314.2220.2090.2090.0000.0000.0000.000
28D336PRO00.01315.4140.0110.0110.0000.0000.0000.000
29D337PHE00.03010.359-0.027-0.0270.0000.0000.0000.000
30D338SER00.01111.891-0.010-0.0100.0000.0000.0000.000
31D339GLU-1-0.7348.632-0.673-0.6730.0000.0000.0000.000
32D340ALA00.0328.6170.0270.0270.0000.0000.0000.000
33D341SER0-0.0969.6450.0040.0040.0000.0000.0000.000
34D342MET0-0.0036.2090.0340.0340.0000.0000.0000.000
35D343MET00.0322.873-4.018-1.5660.465-0.900-2.0160.009
36D344GLY00.0265.204-0.125-0.1250.0000.0000.0000.000
37D345LEU00.0016.933-0.280-0.2800.0000.0000.0000.000
38D346LEU0-0.0122.547-3.320-0.5800.833-0.568-3.0050.001
39D347THR00.0392.583-7.592-3.9371.175-1.684-3.146-0.022
40D348ASN0-0.0263.937-0.339-0.1730.002-0.009-0.1590.000
41D349LEU0-0.0472.837-0.7780.6110.185-0.344-1.2310.002
42D350ALA00.0222.500-2.899-0.7001.177-0.942-2.4350.000
43D351ASP-1-0.8733.5060.0380.1930.0510.061-0.2670.001
44D352ARG10.9236.4691.4801.4800.0000.0000.0000.000
45D353GLU-1-0.7331.217-47.354-88.07497.346-55.884-0.743-0.172
46D354LEU00.0245.8530.6860.6860.0000.0000.0000.000
47D355VAL00.0218.2050.2610.2610.0000.0000.0000.000
48D356HIS0-0.0528.4190.2340.2340.0000.0000.0000.000
49D357MET0-0.0226.9080.1210.1210.0000.0000.0000.000
50D358ILE00.0659.8540.1040.1040.0000.0000.0000.000
51D359ASN0-0.05213.2200.0740.0740.0000.0000.0000.000
52D360TRP0-0.02911.8000.0560.0560.0000.0000.0000.000
53D361ALA00.04513.6690.0270.0270.0000.0000.0000.000
54D362LYS10.85715.2260.0220.0220.0000.0000.0000.000
55D363ARG10.89316.748-0.084-0.0840.0000.0000.0000.000
56D364VAL00.00515.9350.0160.0160.0000.0000.0000.000
57D365PRO0-0.03418.852-0.022-0.0220.0000.0000.0000.000
58D366GLY00.01322.4440.0110.0110.0000.0000.0000.000
59D367PHE00.02217.752-0.011-0.0110.0000.0000.0000.000
60D368VAL0-0.01621.564-0.016-0.0160.0000.0000.0000.000
61D369ASP-1-0.92123.4480.0460.0460.0000.0000.0000.000
62D370LEU0-0.02622.125-0.002-0.0020.0000.0000.0000.000
63D371THR0-0.06925.599-0.010-0.0100.0000.0000.0000.000
64D372LEU0-0.00523.8300.0000.0000.0000.0000.0000.000
65D373HIS0-0.00622.572-0.006-0.0060.0000.0000.0000.000
66D374ASP-1-0.78421.282-0.008-0.0080.0000.0000.0000.000
67D375GLN0-0.10019.7120.0010.0010.0000.0000.0000.000
68D376VAL00.02417.1970.0070.0070.0000.0000.0000.000
69D377HIS00.03616.488-0.010-0.0100.0000.0000.0000.000
70D378LEU0-0.05116.0550.0040.0040.0000.0000.0000.000
71D379LEU0-0.04512.5350.0280.0280.0000.0000.0000.000
72D380GLU-1-0.88212.281-0.080-0.0800.0000.0000.0000.000
73D381CYS0-0.08811.534-0.008-0.0080.0000.0000.0000.000
74D382ALA00.00511.267-0.005-0.0050.0000.0000.0000.000
75D383TRP00.0393.932-0.4010.0550.002-0.037-0.4210.000
76D384LEU00.0432.372-2.017-0.0351.060-0.446-2.596-0.003
77D385GLU-1-0.8474.9650.3520.479-0.001-0.002-0.1240.000
78D386ILE0-0.0326.8100.2760.2760.0000.0000.0000.000
79D387LEU0-0.0112.514-3.526-0.0712.232-1.507-4.1800.005
80D388MET0-0.0602.170-2.7600.8102.151-1.345-4.376-0.009
81D389ILE0-0.0143.8270.1450.3230.0050.021-0.2040.000
82D390GLY00.0295.578-0.192-0.1920.0000.0000.0000.000
83D391LEU0-0.0072.150-1.997-1.2873.468-0.910-3.2690.000
84D392VAL0-0.0064.395-0.897-0.7620.000-0.026-0.1090.000
85D393TRP0-0.0207.373-0.294-0.2940.0000.0000.0000.000
86D394ARG10.8332.155-11.760-10.2452.332-1.566-2.2800.017
87D395SER0-0.0347.359-0.225-0.2250.0000.0000.0000.000
88D396MET00.0069.858-0.168-0.1680.0000.0000.0000.000
89D397GLU-1-0.94612.8740.6530.6530.0000.0000.0000.000
90D398HIS00.00412.621-0.041-0.0410.0000.0000.0000.000
91D399PRO00.01113.1440.0670.0670.0000.0000.0000.000
92D400GLY0-0.06513.779-0.040-0.0400.0000.0000.0000.000
93D401LYS10.87111.420-0.587-0.5870.0000.0000.0000.000
94D402LEU00.0395.0850.0190.0190.0000.0000.0000.000
95D403LEU0-0.0218.149-0.118-0.1180.0000.0000.0000.000
96D404PHE00.0172.550-5.448-1.2342.345-1.297-5.2620.015
97D405ALA00.0414.999-0.247-0.192-0.001-0.007-0.0480.000
98D406PRO00.0197.6000.0720.0720.0000.0000.0000.000
99D407ASN00.00710.8760.0070.0070.0000.0000.0000.000
100D408LEU0-0.0196.831-0.148-0.1480.0000.0000.0000.000
101D409LEU0-0.0249.3930.3080.3080.0000.0000.0000.000
102D410LEU0-0.0156.712-0.216-0.2160.0000.0000.0000.000
103D411ASP-1-0.80510.2380.4800.4800.0000.0000.0000.000
104D412ARG10.88010.400-0.213-0.2130.0000.0000.0000.000
105D413ASN0-0.08111.020-0.128-0.1280.0000.0000.0000.000
106D414GLN00.04310.640-0.023-0.0230.0000.0000.0000.000
107D415GLY00.0577.697-0.050-0.0500.0000.0000.0000.000
108D416LYS10.8578.265-0.212-0.2120.0000.0000.0000.000
109D417CYS0-0.08210.062-0.032-0.0320.0000.0000.0000.000
110D418VAL0-0.0045.0270.0000.0000.0000.0000.0000.000
111D419GLU-1-0.8387.820-0.796-0.7960.0000.0000.0000.000
112D420GLY00.0096.668-0.595-0.5950.0000.0000.0000.000
113D421MET0-0.0073.035-1.800-0.6071.178-0.464-1.908-0.001
114D422VAL0-0.0305.0640.4850.559-0.0010.000-0.0720.000
115D423GLU-1-0.8318.173-0.408-0.4080.0000.0000.0000.000
116D424ILE00.0212.089-0.912-0.3882.354-0.531-2.3470.002
117D425PHE00.0263.866-0.1000.4110.002-0.048-0.4640.000
118D426ASP-1-0.7976.9040.3340.3340.0000.0000.0000.000
119D427MET0-0.0586.8460.0500.0500.0000.0000.0000.000
120D428LEU00.0582.645-0.9600.0030.305-0.188-1.0800.000
121D429LEU0-0.0107.183-0.018-0.0180.0000.0000.0000.000
122D430ALA0-0.02010.001-0.043-0.0430.0000.0000.0000.000
123D431THR0-0.0129.253-0.095-0.0950.0000.0000.0000.000
124D432SER0-0.0159.049-0.079-0.0790.0000.0000.0000.000
125D433SER0-0.03410.938-0.079-0.0790.0000.0000.0000.000
126D434ARG10.93814.237-0.372-0.3720.0000.0000.0000.000
127D435PHE00.07710.490-0.072-0.0720.0000.0000.0000.000
128D436ARG10.92013.705-0.662-0.6620.0000.0000.0000.000
129D437MET0-0.08116.887-0.064-0.0640.0000.0000.0000.000
130D438MET0-0.10518.494-0.036-0.0360.0000.0000.0000.000
131D439ASN00.02919.2930.0110.0110.0000.0000.0000.000
132D440LEU0-0.04113.728-0.032-0.0320.0000.0000.0000.000
133D441GLN00.03817.3090.0200.0200.0000.0000.0000.000
134D442GLY00.06415.8730.0390.0390.0000.0000.0000.000
135D443GLU-1-0.88116.6240.3450.3450.0000.0000.0000.000
136D444GLU-1-0.74617.9970.3370.3370.0000.0000.0000.000
137D445PHE0-0.0169.1380.0120.0120.0000.0000.0000.000
138D446VAL00.03613.8200.0230.0230.0000.0000.0000.000
139D447CYS0-0.04215.272-0.045-0.0450.0000.0000.0000.000
140D448LEU00.01313.903-0.032-0.0320.0000.0000.0000.000
141D449LYS10.9019.387-0.805-0.8050.0000.0000.0000.000
142D450SER00.04812.641-0.042-0.0420.0000.0000.0000.000
143D451ILE0-0.06215.725-0.042-0.0420.0000.0000.0000.000
144D452ILE0-0.02710.564-0.037-0.0370.0000.0000.0000.000
145D453LEU0-0.01113.889-0.040-0.0400.0000.0000.0000.000
146D454LEU00.00314.758-0.047-0.0470.0000.0000.0000.000
147D455ASN0-0.00517.052-0.047-0.0470.0000.0000.0000.000
148D456SER0-0.09112.987-0.017-0.0170.0000.0000.0000.000
149D457GLY00.05116.078-0.028-0.0280.0000.0000.0000.000
150D458VAL00.05118.036-0.016-0.0160.0000.0000.0000.000
151D459TYR0-0.09720.566-0.013-0.0130.0000.0000.0000.000
152D460THR00.00818.700-0.005-0.0050.0000.0000.0000.000
153D461PHE00.03321.286-0.008-0.0080.0000.0000.0000.000
154D462LEU00.07024.4980.0020.0020.0000.0000.0000.000
155D463SER0-0.03227.1480.0010.0010.0000.0000.0000.000
156D464SER0-0.02630.0720.0010.0010.0000.0000.0000.000
157D465THR0-0.02330.7490.0020.0020.0000.0000.0000.000
158D466LEU00.06832.4300.0020.0020.0000.0000.0000.000
159D467LYS11.01630.5510.0110.0110.0000.0000.0000.000
160D468SER00.01428.2720.0040.0040.0000.0000.0000.000
161D469LEU0-0.03829.0090.0050.0050.0000.0000.0000.000
162D470GLU-1-0.88531.2480.0200.0200.0000.0000.0000.000
163D471GLU-1-0.80226.2220.0240.0240.0000.0000.0000.000
164D472LYS10.83725.447-0.006-0.0060.0000.0000.0000.000
165D473ASP-1-0.90627.1380.0480.0480.0000.0000.0000.000
166D474HIS0-0.08326.1120.0090.0090.0000.0000.0000.000
167D475ILE00.04821.9260.0110.0110.0000.0000.0000.000
168D476HIS00.01424.4300.0210.0210.0000.0000.0000.000
169D477ARG10.92626.322-0.050-0.0500.0000.0000.0000.000
170D478VAL0-0.02622.8360.0070.0070.0000.0000.0000.000
171D479LEU0-0.01219.9900.0200.0200.0000.0000.0000.000
172D480ASP-1-0.89023.5560.1150.1150.0000.0000.0000.000
173D481LYS10.88525.803-0.119-0.1190.0000.0000.0000.000
174D482ILE00.02519.6790.0080.0080.0000.0000.0000.000
175D483THR0-0.00723.1290.0220.0220.0000.0000.0000.000
176D484ASP-1-0.94324.4070.1270.1270.0000.0000.0000.000
177D485THR0-0.11923.289-0.003-0.0030.0000.0000.0000.000
178D486LEU00.03519.6300.0070.0070.0000.0000.0000.000
179D487ILE0-0.00223.5300.0040.0040.0000.0000.0000.000
180D488HIS0-0.05026.926-0.006-0.0060.0000.0000.0000.000
181D489LEU0-0.02521.810-0.006-0.0060.0000.0000.0000.000
182D490MET0-0.01522.656-0.008-0.0080.0000.0000.0000.000
183D491ALA0-0.00326.708-0.006-0.0060.0000.0000.0000.000
184D492LYS10.85626.754-0.185-0.1850.0000.0000.0000.000
185D493ALA0-0.01626.781-0.003-0.0030.0000.0000.0000.000
186D494GLY0-0.04428.891-0.003-0.0030.0000.0000.0000.000
187D495LEU0-0.00426.1130.0010.0010.0000.0000.0000.000
188D496THR0-0.03530.804-0.005-0.0050.0000.0000.0000.000
189D497LEU00.08831.8240.0070.0070.0000.0000.0000.000
190D498GLN00.00932.0230.0020.0020.0000.0000.0000.000
191D499GLN00.02229.2330.0060.0060.0000.0000.0000.000
192D500GLN0-0.01627.7020.0100.0100.0000.0000.0000.000
193D501HIS00.06226.8840.0050.0050.0000.0000.0000.000
194D502GLN0-0.08226.9250.0100.0100.0000.0000.0000.000
195D503ARG10.76720.222-0.310-0.3100.0000.0000.0000.000
196D504LEU00.04222.2370.0220.0220.0000.0000.0000.000
197D505ALA00.03521.8040.0150.0150.0000.0000.0000.000
198D506GLN0-0.08421.2400.0250.0250.0000.0000.0000.000
199D507LEU0-0.02117.2530.0210.0210.0000.0000.0000.000
200D508LEU00.06316.9710.0300.0300.0000.0000.0000.000
201D509LEU0-0.01217.485-0.003-0.0030.0000.0000.0000.000
202D510ILE0-0.04212.766-0.011-0.0110.0000.0000.0000.000
203D511LEU00.03412.9750.0270.0270.0000.0000.0000.000
204D512SER00.01413.091-0.028-0.0280.0000.0000.0000.000
205D513HIS0-0.02812.212-0.048-0.0480.0000.0000.0000.000
206D514ILE00.0187.912-0.020-0.0200.0000.0000.0000.000
207D515ARG10.9698.932-0.129-0.1290.0000.0000.0000.000
208D516HIS0-0.0559.998-0.134-0.1340.0000.0000.0000.000
209D517MET0-0.0256.202-0.049-0.0490.0000.0000.0000.000
210D518SER00.0475.451-0.199-0.1990.0000.0000.0000.000
211D519ASN00.0346.065-0.213-0.2130.0000.0000.0000.000
212D520LYS10.8746.4240.3460.3460.0000.0000.0000.000
213D521GLY00.0292.775-1.200-0.4870.430-0.412-0.7310.000
214D522MET00.0473.360-1.919-0.4830.068-0.512-0.993-0.006
215D523GLU-1-0.9575.073-0.502-0.420-0.001-0.003-0.0780.000
216D524HIS0-0.0171.738-17.446-26.95623.329-7.389-6.431-0.051
217D525LEU00.0212.392-3.580-0.3963.580-1.652-5.1120.005
218D526TYR00.0583.304-0.479-0.6900.1900.607-0.5860.003
219D527SER00.0076.231-0.071-0.0710.0000.0000.0000.000
220D528MET0-0.0113.6160.2770.5710.001-0.046-0.2500.000
221D529LYS10.9926.1300.2260.2260.0000.0000.0000.000
222D530CYS0-0.0928.506-0.032-0.0320.0000.0000.0000.000
223D531LYS10.7278.3100.7130.7130.0000.0000.0000.000
224D532ASN0-0.05611.1360.0270.0270.0000.0000.0000.000
225D533VAL0-0.0158.159-0.020-0.0200.0000.0000.0000.000
226D534VAL0-0.0465.5410.0280.0280.0000.0000.0000.000
227D535PRO0-0.0357.521-0.050-0.0500.0000.0000.0000.000
228D536LEU00.0259.5110.0300.0300.0000.0000.0000.000
229D537TYR0-0.0597.700-0.047-0.0470.0000.0000.0000.000
230D538ASP-1-0.82510.759-0.247-0.2470.0000.0000.0000.000
231D539LEU0-0.00711.1830.0390.0390.0000.0000.0000.000
232D540LEU0-0.0134.360-0.2430.0030.000-0.014-0.2320.000
233D541LEU0-0.0927.9990.1380.1380.0000.0000.0000.000
234D542GLU-1-0.9699.824-0.184-0.1840.0000.0000.0000.000
235D543MET0-0.0518.5410.0450.0450.0000.0000.0000.000
236D544LEU-1-0.9546.171-0.054-0.0540.0000.0000.0000.000
238D60HOH0-0.0172.013-3.009-4.4465.711-2.036-2.2370.012