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: 4PK3P

Calculation Name: 1GWR-B-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 1GWR

Chain ID: B

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 -3130168.90254
FMO2-HF: Nuclear repulsion 3031957.349991
FMO2-HF: Total energy -98211.552549
FMO2-MP2: Total energy -98488.77015


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.
-116.091-93.36579.992-41.749-60.9710.136


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


Summations of interaction energy for fragment #237(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.
-116.091-93.36579.992-41.749-60.971-0.136
Interaction energy analysis for fragmet #237(B:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.135 / 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].
1B309SER10.87030.623-0.073-0.0730.0000.0000.0000.000
2B310LEU00.07625.816-0.005-0.0050.0000.0000.0000.000
3B311THR0-0.00129.6660.0080.0080.0000.0000.0000.000
4B312ALA00.06527.3300.0040.0040.0000.0000.0000.000
5B313ASP-1-0.76526.2430.1580.1580.0000.0000.0000.000
6B314GLN00.02826.1740.0060.0060.0000.0000.0000.000
7B315MET00.00821.819-0.013-0.0130.0000.0000.0000.000
8B316VAL00.03521.3740.0130.0130.0000.0000.0000.000
9B317SER0-0.02421.1240.0090.0090.0000.0000.0000.000
10B318ALA0-0.01721.680-0.006-0.0060.0000.0000.0000.000
11B319LEU0-0.03217.272-0.011-0.0110.0000.0000.0000.000
12B320LEU0-0.00816.8990.0150.0150.0000.0000.0000.000
13B321ASP-1-0.93016.9010.0750.0750.0000.0000.0000.000
14B322ALA0-0.09416.027-0.043-0.0430.0000.0000.0000.000
15B323GLU-1-0.83811.4410.5420.5420.0000.0000.0000.000
16B324PRO0-0.0498.646-0.080-0.0800.0000.0000.0000.000
17B325PRO00.0099.3690.1460.1460.0000.0000.0000.000
18B326ILE00.0057.318-0.210-0.2100.0000.0000.0000.000
19B327LEU0-0.0436.0240.1600.1600.0000.0000.0000.000
20B328TYR00.0267.6950.2880.2880.0000.0000.0000.000
21B329SER00.0387.242-0.514-0.5140.0000.0000.0000.000
22B330GLU-1-0.8738.791-0.236-0.2360.0000.0000.0000.000
23B331TYR0-0.10312.0520.0880.0880.0000.0000.0000.000
24B332ASP-1-0.64815.291-0.079-0.0790.0000.0000.0000.000
25B333PRO0-0.12315.9250.1070.1070.0000.0000.0000.000
26B334THR0-0.07417.2910.0320.0320.0000.0000.0000.000
27B335ARG11.08015.9820.1770.1770.0000.0000.0000.000
28B336PRO0-0.12216.4930.0270.0270.0000.0000.0000.000
29B337PHE0-0.07811.224-0.021-0.0210.0000.0000.0000.000
30B338SER0-0.00912.5540.0010.0010.0000.0000.0000.000
31B339GLU-1-0.8008.807-0.528-0.5280.0000.0000.0000.000
32B340ALA00.0319.0410.0010.0010.0000.0000.0000.000
33B341SER0-0.0239.8970.0020.0020.0000.0000.0000.000
34B342MET00.0026.154-0.005-0.0050.0000.0000.0000.000
35B343MET00.0282.630-3.766-1.4050.769-1.084-2.0470.014
36B344GLY00.0265.487-0.098-0.0980.0000.0000.0000.000
37B345LEU0-0.0397.312-0.312-0.3120.0000.0000.0000.000
38B346LEU0-0.0172.443-3.432-0.8741.178-0.606-3.1300.001
39B347THR00.0552.617-7.513-4.1100.996-1.590-2.809-0.022
40B348ASN00.0204.208-0.463-0.3170.000-0.014-0.1320.000
41B349LEU0-0.0482.355-0.7850.9390.880-0.636-1.9680.002
42B350ALA0-0.0022.448-3.097-0.9711.830-1.122-2.8340.002
43B351ASP-1-0.8563.493-0.297-0.1450.0700.103-0.3250.001
44B352ARG10.8396.3112.4272.4270.0000.0000.0000.000
45B353GLU-1-0.7881.413-41.222-60.73247.649-22.447-5.692-0.135
46B354LEU00.0515.9090.8910.8910.0000.0000.0000.000
47B355VAL00.0378.3960.3330.3330.0000.0000.0000.000
48B356HIS0-0.0358.2310.3440.3440.0000.0000.0000.000
49B357MET0-0.0377.0860.2300.2300.0000.0000.0000.000
50B358ILE00.0509.9170.1530.1530.0000.0000.0000.000
51B359ASN0-0.07513.3440.1160.1160.0000.0000.0000.000
52B360TRP0-0.01211.7350.0800.0800.0000.0000.0000.000
53B361ALA00.06313.7350.0540.0540.0000.0000.0000.000
54B362LYS10.94415.3690.1560.1560.0000.0000.0000.000
55B363ARG10.84917.1780.0310.0310.0000.0000.0000.000
56B364VAL0-0.00516.4780.0200.0200.0000.0000.0000.000
57B365PRO0-0.02619.118-0.019-0.0190.0000.0000.0000.000
58B366GLY00.01722.7610.0170.0170.0000.0000.0000.000
59B367PHE00.00618.168-0.006-0.0060.0000.0000.0000.000
60B368VAL00.01221.859-0.013-0.0130.0000.0000.0000.000
61B369ASP-1-0.95323.6040.0290.0290.0000.0000.0000.000
62B370LEU0-0.02622.0210.0020.0020.0000.0000.0000.000
63B371THR0-0.05525.735-0.016-0.0160.0000.0000.0000.000
64B372LEU00.04222.6000.0040.0040.0000.0000.0000.000
65B373HIS0-0.02322.445-0.010-0.0100.0000.0000.0000.000
66B374ASP-1-0.79221.6570.0150.0150.0000.0000.0000.000
67B375GLN0-0.13220.175-0.002-0.0020.0000.0000.0000.000
68B376VAL00.02917.4860.0110.0110.0000.0000.0000.000
69B377HIS00.01416.531-0.004-0.0040.0000.0000.0000.000
70B378LEU0-0.06516.1170.0190.0190.0000.0000.0000.000
71B379LEU0-0.03012.8880.0350.0350.0000.0000.0000.000
72B380GLU-1-0.88712.227-0.042-0.0420.0000.0000.0000.000
73B381CYS0-0.06911.5040.0080.0080.0000.0000.0000.000
74B382ALA00.00210.6600.0380.0380.0000.0000.0000.000
75B383TRP00.0523.849-0.3450.1520.002-0.038-0.4620.000
76B384LEU00.0292.108-2.058-0.5122.569-0.589-3.525-0.005
77B385GLU-1-0.8234.4000.5820.760-0.001-0.016-0.1610.000
78B386ILE0-0.0376.9330.3490.3490.0000.0000.0000.000
79B387LEU0-0.0102.575-3.548-0.0751.947-1.344-4.0760.011
80B388MET0-0.0452.585-2.3691.3591.322-1.296-3.754-0.010
81B389ILE0-0.0083.7930.0320.1420.0060.033-0.1490.000
82B390GLY00.0505.725-0.283-0.2830.0000.0000.0000.000
83B391LEU00.0042.324-3.049-0.7461.542-0.898-2.9470.004
84B392VAL0-0.0294.389-1.207-1.0750.000-0.024-0.1080.000
85B393TRP00.0017.607-0.419-0.4190.0000.0000.0000.000
86B394ARG10.8712.342-11.801-9.5361.049-1.375-1.9390.019
87B395SER0-0.0347.388-0.268-0.2680.0000.0000.0000.000
88B396MET00.03410.065-0.255-0.2550.0000.0000.0000.000
89B397GLU-1-0.94412.8650.7080.7080.0000.0000.0000.000
90B398HIS0-0.00812.952-0.126-0.1260.0000.0000.0000.000
91B399PRO0-0.01114.0240.0910.0910.0000.0000.0000.000
92B400GLY0-0.03413.978-0.059-0.0590.0000.0000.0000.000
93B401LYS10.91311.561-0.629-0.6290.0000.0000.0000.000
94B402LEU00.0175.2670.0050.0050.0000.0000.0000.000
95B403LEU0-0.0118.402-0.148-0.1480.0000.0000.0000.000
96B404PHE0-0.0022.169-4.901-1.6164.776-1.522-6.5390.016
97B405ALA00.0334.597-1.357-1.220-0.001-0.011-0.1240.000
98B406PRO00.0097.3380.2890.2890.0000.0000.0000.000
99B407ASN0-0.05210.4380.0060.0060.0000.0000.0000.000
100B408LEU0-0.0316.474-0.122-0.1220.0000.0000.0000.000
101B409LEU0-0.0099.0610.3970.3970.0000.0000.0000.000
102B410LEU0-0.0107.004-0.224-0.2240.0000.0000.0000.000
103B411ASP-1-0.83810.3580.6420.6420.0000.0000.0000.000
104B412ARG10.82711.200-0.348-0.3480.0000.0000.0000.000
105B413ASN0-0.07511.905-0.045-0.0450.0000.0000.0000.000
106B414GLN00.08811.3640.0030.0030.0000.0000.0000.000
107B415GLY00.0728.214-0.053-0.0530.0000.0000.0000.000
108B416LYS10.8938.691-0.288-0.2880.0000.0000.0000.000
109B417CYS0-0.07110.696-0.034-0.0340.0000.0000.0000.000
110B418VAL0-0.0265.373-0.009-0.0090.0000.0000.0000.000
111B419GLU-1-0.8698.354-0.611-0.6110.0000.0000.0000.000
112B420GLY00.0136.956-0.478-0.4780.0000.0000.0000.000
113B421MET0-0.0173.256-2.063-0.5850.445-0.332-1.5910.001
114B422VAL0-0.0155.4500.5190.5190.0000.0000.0000.000
115B423GLU-1-0.9077.743-0.282-0.2820.0000.0000.0000.000
116B424ILE00.0452.243-1.044-0.0991.461-0.373-2.0330.001
117B425PHE00.0344.8260.4970.4970.0000.0000.0000.000
118B426ASP-1-0.7836.9300.5640.5640.0000.0000.0000.000
119B427MET0-0.0537.7270.0140.0140.0000.0000.0000.000
120B428LEU00.0743.013-0.7390.0330.077-0.137-0.7120.000
121B429LEU0-0.0077.458-0.021-0.0210.0000.0000.0000.000
122B430ALA0-0.01910.501-0.088-0.0880.0000.0000.0000.000
123B431THR00.0019.361-0.134-0.1340.0000.0000.0000.000
124B432SER0-0.0079.856-0.106-0.1060.0000.0000.0000.000
125B433SER0-0.00411.432-0.150-0.1500.0000.0000.0000.000
126B434ARG10.87114.377-0.524-0.5240.0000.0000.0000.000
127B435PHE00.05210.847-0.093-0.0930.0000.0000.0000.000
128B436ARG10.86113.511-0.873-0.8730.0000.0000.0000.000
129B437MET0-0.08517.264-0.083-0.0830.0000.0000.0000.000
130B438MET0-0.07618.469-0.042-0.0420.0000.0000.0000.000
131B439ASN0-0.01619.691-0.010-0.0100.0000.0000.0000.000
132B440LEU0-0.04013.740-0.030-0.0300.0000.0000.0000.000
133B441GLN00.01817.725-0.017-0.0170.0000.0000.0000.000
134B442GLY00.03016.0510.0320.0320.0000.0000.0000.000
135B443GLU-1-0.87916.7550.3250.3250.0000.0000.0000.000
136B444GLU-1-0.77318.1080.3810.3810.0000.0000.0000.000
137B445PHE00.0009.4520.0260.0260.0000.0000.0000.000
138B446VAL00.04013.9630.0350.0350.0000.0000.0000.000
139B447CYS0-0.03715.323-0.052-0.0520.0000.0000.0000.000
140B448LEU0-0.01314.081-0.025-0.0250.0000.0000.0000.000
141B449LYS10.8789.299-0.705-0.7050.0000.0000.0000.000
142B450SER00.02412.577-0.059-0.0590.0000.0000.0000.000
143B451ILE0-0.02815.732-0.041-0.0410.0000.0000.0000.000
144B452ILE0-0.01910.244-0.029-0.0290.0000.0000.0000.000
145B453LEU0-0.04713.715-0.044-0.0440.0000.0000.0000.000
146B454LEU00.01814.518-0.051-0.0510.0000.0000.0000.000
147B455ASN00.00516.586-0.058-0.0580.0000.0000.0000.000
148B456SER0-0.10712.487-0.029-0.0290.0000.0000.0000.000
149B457GLY00.05115.678-0.020-0.0200.0000.0000.0000.000
150B458VAL00.08017.971-0.024-0.0240.0000.0000.0000.000
151B459TYR0-0.07320.481-0.024-0.0240.0000.0000.0000.000
152B460THR0-0.02018.050-0.004-0.0040.0000.0000.0000.000
153B461PHE00.02720.349-0.013-0.0130.0000.0000.0000.000
154B462LEU00.04423.3440.0020.0020.0000.0000.0000.000
155B463SER0-0.04426.1680.0000.0000.0000.0000.0000.000
156B464SER0-0.01928.7960.0020.0020.0000.0000.0000.000
157B465THR00.03031.047-0.001-0.0010.0000.0000.0000.000
158B466LEU00.02032.3560.0040.0040.0000.0000.0000.000
159B467LYS10.91130.443-0.009-0.0090.0000.0000.0000.000
160B468SER00.02328.1530.0030.0030.0000.0000.0000.000
161B469LEU0-0.06928.6450.0080.0080.0000.0000.0000.000
162B470GLU-1-0.82131.2920.0210.0210.0000.0000.0000.000
163B471GLU-1-0.81226.2920.0290.0290.0000.0000.0000.000
164B472LYS10.86325.414-0.045-0.0450.0000.0000.0000.000
165B473ASP-1-0.89126.7500.0720.0720.0000.0000.0000.000
166B474HIS0-0.06026.4520.0110.0110.0000.0000.0000.000
167B475ILE00.04621.6870.0090.0090.0000.0000.0000.000
168B476HIS0-0.00224.1530.0230.0230.0000.0000.0000.000
169B477ARG10.94226.189-0.063-0.0630.0000.0000.0000.000
170B478VAL0-0.01822.5850.0070.0070.0000.0000.0000.000
171B479LEU0-0.01719.8210.0220.0220.0000.0000.0000.000
172B480ASP-1-0.87623.5640.1480.1480.0000.0000.0000.000
173B481LYS10.89525.791-0.116-0.1160.0000.0000.0000.000
174B482ILE0-0.01519.5300.0090.0090.0000.0000.0000.000
175B483THR00.00522.9470.0240.0240.0000.0000.0000.000
176B484ASP-1-0.92324.3210.1460.1460.0000.0000.0000.000
177B485THR0-0.07023.371-0.003-0.0030.0000.0000.0000.000
178B486LEU00.02719.5570.0080.0080.0000.0000.0000.000
179B487ILE0-0.01823.3770.0050.0050.0000.0000.0000.000
180B488HIS0-0.05126.764-0.009-0.0090.0000.0000.0000.000
181B489LEU0-0.02721.829-0.008-0.0080.0000.0000.0000.000
182B490MET0-0.00722.811-0.012-0.0120.0000.0000.0000.000
183B491ALA0-0.01926.940-0.009-0.0090.0000.0000.0000.000
184B492LYS10.83327.506-0.176-0.1760.0000.0000.0000.000
185B493ALA0-0.03926.984-0.005-0.0050.0000.0000.0000.000
186B494GLY00.00029.1120.0000.0000.0000.0000.0000.000
187B495LEU0-0.08626.575-0.004-0.0040.0000.0000.0000.000
188B496THR00.02131.116-0.013-0.0130.0000.0000.0000.000
189B497LEU00.09332.0680.0100.0100.0000.0000.0000.000
190B498GLN0-0.00631.9680.0130.0130.0000.0000.0000.000
191B499GLN00.03029.9400.0020.0020.0000.0000.0000.000
192B500GLN0-0.00327.8720.0160.0160.0000.0000.0000.000
193B501HIS00.05926.8870.0250.0250.0000.0000.0000.000
194B502GLN0-0.02326.661-0.001-0.0010.0000.0000.0000.000
195B503ARG10.74420.794-0.354-0.3540.0000.0000.0000.000
196B504LEU00.05122.2680.0300.0300.0000.0000.0000.000
197B505ALA00.02621.9350.0210.0210.0000.0000.0000.000
198B506GLN0-0.03120.9370.0250.0250.0000.0000.0000.000
199B507LEU00.01017.3060.0390.0390.0000.0000.0000.000
200B508LEU00.03416.7910.0480.0480.0000.0000.0000.000
201B509LEU0-0.02417.8440.0040.0040.0000.0000.0000.000
202B510ILE0-0.03012.7860.0000.0000.0000.0000.0000.000
203B511LEU00.04412.9110.0680.0680.0000.0000.0000.000
204B512SER0-0.03713.0900.0100.0100.0000.0000.0000.000
205B513HIS00.01712.370-0.027-0.0270.0000.0000.0000.000
206B514ILE00.0378.0910.0470.0470.0000.0000.0000.000
207B515ARG10.9169.179-0.245-0.2450.0000.0000.0000.000
208B516HIS0-0.0749.807-0.082-0.0820.0000.0000.0000.000
209B517MET00.0046.035-0.028-0.0280.0000.0000.0000.000
210B518SER00.0435.283-0.112-0.1120.0000.0000.0000.000
211B519ASN00.0476.046-0.226-0.2260.0000.0000.0000.000
212B520LYS10.9486.6230.0790.0790.0000.0000.0000.000
213B521GLY0-0.0132.501-0.958-0.4090.893-0.591-0.8520.002
214B522MET00.0612.719-3.666-1.4010.558-0.904-1.919-0.020
215B523GLU-1-0.9895.011-0.383-0.291-0.001-0.003-0.0880.000
216B524HIS0-0.0272.181-12.561-10.4454.466-2.491-4.090-0.033
217B525LEU00.0292.128-3.577-0.9713.782-1.532-4.8560.007
218B526TYR00.0743.445-0.623-0.3140.0720.019-0.4010.002
219B527SER0-0.0296.2150.2200.2200.0000.0000.0000.000
220B528MET00.0053.8730.0930.3080.000-0.026-0.1900.000
221B529LYS10.9866.4590.2120.2120.0000.0000.0000.000
222B530CYS0-0.0838.662-0.032-0.0320.0000.0000.0000.000
223B531LYS10.8318.5410.7260.7260.0000.0000.0000.000
224B532ASN0-0.07111.5520.0080.0080.0000.0000.0000.000
225B533VAL00.0048.312-0.009-0.0090.0000.0000.0000.000
226B534VAL0-0.0455.9400.0370.0370.0000.0000.0000.000
227B535PRO0-0.0207.978-0.029-0.0290.0000.0000.0000.000
228B536LEU0-0.0209.7330.0180.0180.0000.0000.0000.000
229B537TYR0-0.0058.124-0.079-0.0790.0000.0000.0000.000
230B538ASP-1-0.87611.054-0.344-0.3440.0000.0000.0000.000
231B539LEU00.02911.2360.0450.0450.0000.0000.0000.000
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