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: NP7KP

Calculation Name: 2YJA-B-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 2YJA

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 -3143360.729793
FMO2-HF: Nuclear repulsion 3045145.647252
FMO2-HF: Total energy -98215.082541
FMO2-MP2: Total energy -98491.995374


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.
-134.833-145.228156.636-80.615-65.6280.192


Interactive mode: IFIE and PIEDA for fragment #237(B:1550:EST)


Summations of interaction energy for fragment #237(B:1550: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.
-134.833-145.228156.636-80.615-65.628-0.192
Interaction energy analysis for fragmet #237(B:1550:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.194 / 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].
1B309SER10.83630.303-0.105-0.1050.0000.0000.0000.000
2B310LEU00.10625.240-0.005-0.0050.0000.0000.0000.000
3B311THR00.03029.1770.0050.0050.0000.0000.0000.000
4B312ALA00.07726.7890.0060.0060.0000.0000.0000.000
5B313ASP-1-0.88225.5610.1970.1970.0000.0000.0000.000
6B314GLN0-0.00625.5900.0090.0090.0000.0000.0000.000
7B315MET00.00022.1060.0030.0030.0000.0000.0000.000
8B316VAL00.05520.7840.0150.0150.0000.0000.0000.000
9B317SER0-0.02120.5650.0190.0190.0000.0000.0000.000
10B318ALA0-0.01821.1590.0030.0030.0000.0000.0000.000
11B319LEU0-0.02717.089-0.001-0.0010.0000.0000.0000.000
12B320LEU0-0.01716.3210.0330.0330.0000.0000.0000.000
13B321ASP-1-0.89916.6380.1620.1620.0000.0000.0000.000
14B322ALA0-0.04615.780-0.027-0.0270.0000.0000.0000.000
15B323GLU-1-0.85311.2950.7720.7720.0000.0000.0000.000
16B324PRO0-0.0248.502-0.087-0.0870.0000.0000.0000.000
17B325PRO0-0.00610.5250.0740.0740.0000.0000.0000.000
18B326ILE00.0028.661-0.039-0.0390.0000.0000.0000.000
19B327LEU0-0.0376.031-0.073-0.0730.0000.0000.0000.000
20B328TYR00.0247.8970.2400.2400.0000.0000.0000.000
21B329SER00.0297.536-0.347-0.3470.0000.0000.0000.000
22B330GLU-1-0.9788.499-0.240-0.2400.0000.0000.0000.000
23B331TYR0-0.02011.3390.0660.0660.0000.0000.0000.000
24B332ASP-1-0.93614.604-0.070-0.0700.0000.0000.0000.000
25B333PRO00.05712.627-0.013-0.0130.0000.0000.0000.000
26B334THR0-0.03815.3030.0520.0520.0000.0000.0000.000
27B335ARG10.94616.160-0.019-0.0190.0000.0000.0000.000
28B336PRO0-0.05216.7390.0030.0030.0000.0000.0000.000
29B337PHE00.03910.8080.0080.0080.0000.0000.0000.000
30B338SER00.01412.701-0.020-0.0200.0000.0000.0000.000
31B339GLU-1-0.7838.461-0.924-0.9240.0000.0000.0000.000
32B340ALA00.0578.562-0.046-0.0460.0000.0000.0000.000
33B341SER0-0.0179.433-0.008-0.0080.0000.0000.0000.000
34B342MET0-0.0186.069-0.026-0.0260.0000.0000.0000.000
35B343MET00.0562.614-4.765-2.2311.015-1.101-2.4480.013
36B344GLY00.0325.186-0.210-0.099-0.001-0.001-0.1090.000
37B345LEU0-0.0337.224-0.223-0.2230.0000.0000.0000.000
38B346LEU0-0.0172.354-3.491-0.7361.581-0.717-3.6180.001
39B347THR00.0182.374-8.244-5.0022.343-1.893-3.691-0.029
40B348ASN00.0124.041-0.173-0.0240.001-0.011-0.1390.000
41B349LEU0-0.0632.479-0.8810.8160.545-0.532-1.7100.003
42B350ALA00.0412.440-2.874-0.6961.726-1.090-2.8140.002
43B351ASP-1-0.8383.640-0.1210.0570.0500.030-0.2580.001
44B352ARG10.9006.6701.5841.5840.0000.0000.0000.000
45B353GLU-1-0.7311.231-50.705-91.43498.973-56.614-1.631-0.176
46B354LEU00.0165.6530.7220.7220.0000.0000.0000.000
47B355VAL00.0028.1360.2470.2470.0000.0000.0000.000
48B356HIS0-0.0468.6070.2490.2490.0000.0000.0000.000
49B357MET0-0.0256.9170.1390.1390.0000.0000.0000.000
50B358ILE00.0609.8930.1020.1020.0000.0000.0000.000
51B359ASN0-0.05013.3160.0560.0560.0000.0000.0000.000
52B360TRP00.01811.5020.0610.0610.0000.0000.0000.000
53B361ALA00.03813.4350.0240.0240.0000.0000.0000.000
54B362LYS10.90515.1040.0300.0300.0000.0000.0000.000
55B363ARG10.83817.012-0.133-0.1330.0000.0000.0000.000
56B364VAL0-0.00715.5020.0230.0230.0000.0000.0000.000
57B365PRO0-0.03918.478-0.027-0.0270.0000.0000.0000.000
58B366GLY00.01622.0250.0130.0130.0000.0000.0000.000
59B367PHE00.04317.422-0.011-0.0110.0000.0000.0000.000
60B368VAL0-0.02321.132-0.016-0.0160.0000.0000.0000.000
61B369ASP-1-0.92423.2020.0680.0680.0000.0000.0000.000
62B370LEU0-0.06221.725-0.005-0.0050.0000.0000.0000.000
63B371THR0-0.06625.401-0.012-0.0120.0000.0000.0000.000
64B372LEU00.01722.8600.0040.0040.0000.0000.0000.000
65B373HIS0-0.03022.153-0.010-0.0100.0000.0000.0000.000
66B374ASP-1-0.82421.4270.0170.0170.0000.0000.0000.000
67B375GLN0-0.08019.5520.0040.0040.0000.0000.0000.000
68B376VAL00.00617.3220.0120.0120.0000.0000.0000.000
69B377HIS00.01516.475-0.009-0.0090.0000.0000.0000.000
70B378LEU0-0.06916.2340.0070.0070.0000.0000.0000.000
71B379LEU0-0.03312.5650.0400.0400.0000.0000.0000.000
72B380GLU-1-0.87612.136-0.057-0.0570.0000.0000.0000.000
73B381CYS0-0.09811.528-0.010-0.0100.0000.0000.0000.000
74B382ALA00.01510.976-0.001-0.0010.0000.0000.0000.000
75B383TRP00.0423.911-0.3950.0890.002-0.039-0.4470.000
76B384LEU00.0142.261-2.235-0.1431.538-0.500-3.130-0.004
77B385GLU-1-0.8444.4170.3640.544-0.001-0.017-0.1620.000
78B386ILE0-0.0336.7080.3090.3090.0000.0000.0000.000
79B387LEU0-0.0152.517-3.184-0.1132.610-1.423-4.2580.007
80B388MET0-0.0382.377-2.7990.3284.087-1.683-5.531-0.018
81B389ILE0-0.0123.7720.2330.3970.0090.039-0.2120.000
82B390GLY00.0305.510-0.277-0.2770.0000.0000.0000.000
83B391LEU00.0092.210-2.751-1.1142.705-0.984-3.3590.004
84B392VAL0-0.0204.457-1.035-0.9100.000-0.023-0.1020.000
85B393TRP00.0077.493-0.348-0.3480.0000.0000.0000.000
86B394ARG10.7952.094-13.950-12.6983.033-1.725-2.5600.024
87B395SER0-0.0247.526-0.257-0.2570.0000.0000.0000.000
88B396MET0-0.02510.175-0.227-0.2270.0000.0000.0000.000
89B397GLU-1-0.99113.1660.5920.5920.0000.0000.0000.000
90B398HIS0-0.01912.494-0.155-0.1550.0000.0000.0000.000
91B399PRO0-0.01413.2670.0660.0660.0000.0000.0000.000
92B400GLY0-0.03614.068-0.052-0.0520.0000.0000.0000.000
93B401LYS10.89811.589-0.612-0.6120.0000.0000.0000.000
94B402LEU00.0285.1410.0130.0130.0000.0000.0000.000
95B403LEU0-0.0128.323-0.179-0.1790.0000.0000.0000.000
96B404PHE00.0272.593-5.563-1.2522.868-1.563-5.6170.021
97B405ALA00.0484.627-0.235-0.145-0.001-0.014-0.0750.000
98B406PRO00.0037.2660.0660.0660.0000.0000.0000.000
99B407ASN0-0.02210.3280.0080.0080.0000.0000.0000.000
100B408LEU0-0.0146.240-0.119-0.1190.0000.0000.0000.000
101B409LEU00.0078.8900.4350.4350.0000.0000.0000.000
102B410LEU0-0.0316.680-0.272-0.2720.0000.0000.0000.000
103B411ASP-1-0.82910.4970.4660.4660.0000.0000.0000.000
104B412ARG10.85910.653-0.160-0.1600.0000.0000.0000.000
105B413ASN0-0.08911.596-0.166-0.1660.0000.0000.0000.000
106B414GLN00.03911.168-0.002-0.0020.0000.0000.0000.000
107B415GLY00.0748.132-0.073-0.0730.0000.0000.0000.000
108B416LYS10.8898.325-0.215-0.2150.0000.0000.0000.000
109B417CYS0-0.0739.967-0.018-0.0180.0000.0000.0000.000
110B418VAL0-0.0104.799-0.126-0.022-0.001-0.003-0.1000.000
111B419GLU-1-0.9247.937-0.878-0.8780.0000.0000.0000.000
112B420GLY00.0296.617-0.671-0.6710.0000.0000.0000.000
113B421MET0-0.0272.131-1.419-1.3154.230-0.606-3.7280.004
114B422VAL0-0.0375.1740.5890.664-0.0010.000-0.0740.000
115B423GLU-1-0.8637.775-0.385-0.3850.0000.0000.0000.000
116B424ILE00.0162.165-0.676-0.4452.801-0.442-2.5900.001
117B425PHE00.0194.1010.1060.5320.000-0.027-0.3990.000
118B426ASP-1-0.7506.6530.3890.3890.0000.0000.0000.000
119B427MET0-0.0277.5500.0560.0560.0000.0000.0000.000
120B428LEU00.0832.991-0.989-0.0150.167-0.188-0.9540.000
121B429LEU00.0087.212-0.020-0.0200.0000.0000.0000.000
122B430ALA0-0.02610.058-0.059-0.0590.0000.0000.0000.000
123B431THR0-0.0169.039-0.114-0.1140.0000.0000.0000.000
124B432SER00.0069.378-0.092-0.0920.0000.0000.0000.000
125B433SER0-0.04911.145-0.119-0.1190.0000.0000.0000.000
126B434ARG10.91914.122-0.448-0.4480.0000.0000.0000.000
127B435PHE00.05710.447-0.084-0.0840.0000.0000.0000.000
128B436ARG10.96014.804-0.689-0.6890.0000.0000.0000.000
129B437MET0-0.07017.070-0.051-0.0510.0000.0000.0000.000
130B438MET0-0.05518.144-0.036-0.0360.0000.0000.0000.000
131B439ASN00.00919.470-0.001-0.0010.0000.0000.0000.000
132B440LEU0-0.03213.611-0.030-0.0300.0000.0000.0000.000
133B441GLN00.01317.2880.0190.0190.0000.0000.0000.000
134B442GLY00.06415.6820.0420.0420.0000.0000.0000.000
135B443GLU-1-0.88716.2460.4170.4170.0000.0000.0000.000
136B444GLU-1-0.76517.8770.3930.3930.0000.0000.0000.000
137B445PHE00.0208.8810.0170.0170.0000.0000.0000.000
138B446VAL00.02613.4940.0420.0420.0000.0000.0000.000
139B447CYS0-0.04714.967-0.045-0.0450.0000.0000.0000.000
140B448LEU0-0.00413.750-0.028-0.0280.0000.0000.0000.000
141B449LYS10.8559.052-0.989-0.9890.0000.0000.0000.000
142B450SER0-0.01612.313-0.062-0.0620.0000.0000.0000.000
143B451ILE00.00415.448-0.050-0.0500.0000.0000.0000.000
144B452ILE0-0.0249.924-0.038-0.0380.0000.0000.0000.000
145B453LEU0-0.00713.672-0.052-0.0520.0000.0000.0000.000
146B454LEU0-0.00214.565-0.054-0.0540.0000.0000.0000.000
147B455ASN00.00816.777-0.050-0.0500.0000.0000.0000.000
148B456SER0-0.09012.474-0.019-0.0190.0000.0000.0000.000
149B457GLY00.08515.423-0.031-0.0310.0000.0000.0000.000
150B458VAL00.00117.652-0.023-0.0230.0000.0000.0000.000
151B459TYR0-0.08720.106-0.015-0.0150.0000.0000.0000.000
152B460THR0-0.04017.611-0.006-0.0060.0000.0000.0000.000
153B461PHE00.06620.848-0.008-0.0080.0000.0000.0000.000
154B462LEU00.02723.031-0.004-0.0040.0000.0000.0000.000
155B463SER00.00525.7900.0090.0090.0000.0000.0000.000
156B464SER00.02727.974-0.003-0.0030.0000.0000.0000.000
157B465THR0-0.03029.8940.0030.0030.0000.0000.0000.000
158B466LEU00.02132.4340.0030.0030.0000.0000.0000.000
159B467LYS11.00130.450-0.022-0.0220.0000.0000.0000.000
160B468SER00.04327.4370.0060.0060.0000.0000.0000.000
161B469LEU0-0.07228.7800.0060.0060.0000.0000.0000.000
162B470GLU-1-0.94030.6510.0350.0350.0000.0000.0000.000
163B471GLU-1-0.74425.5320.0430.0430.0000.0000.0000.000
164B472LYS10.94025.339-0.024-0.0240.0000.0000.0000.000
165B473ASP-1-0.88226.5720.0810.0810.0000.0000.0000.000
166B474HIS0-0.03725.4300.0070.0070.0000.0000.0000.000
167B475ILE00.03121.5730.0130.0130.0000.0000.0000.000
168B476HIS00.01223.8720.0270.0270.0000.0000.0000.000
169B477ARG10.86025.764-0.070-0.0700.0000.0000.0000.000
170B478VAL0-0.04322.3630.0080.0080.0000.0000.0000.000
171B479LEU00.00419.3700.0220.0220.0000.0000.0000.000
172B480ASP-1-0.89323.0760.1480.1480.0000.0000.0000.000
173B481LYS10.88725.627-0.130-0.1300.0000.0000.0000.000
174B482ILE00.00519.1860.0070.0070.0000.0000.0000.000
175B483THR0-0.01522.7870.0230.0230.0000.0000.0000.000
176B484ASP-1-0.93324.2270.1570.1570.0000.0000.0000.000
177B485THR0-0.08422.946-0.004-0.0040.0000.0000.0000.000
178B486LEU00.00619.1140.0070.0070.0000.0000.0000.000
179B487ILE00.00123.2640.0020.0020.0000.0000.0000.000
180B488HIS00.00626.774-0.009-0.0090.0000.0000.0000.000
181B489LEU0-0.01421.604-0.008-0.0080.0000.0000.0000.000
182B490MET0-0.02822.397-0.009-0.0090.0000.0000.0000.000
183B491ALA00.00326.613-0.008-0.0080.0000.0000.0000.000
184B492LYS10.90328.091-0.214-0.2140.0000.0000.0000.000
185B493ALA0-0.04126.591-0.004-0.0040.0000.0000.0000.000
186B494GLY0-0.01328.725-0.001-0.0010.0000.0000.0000.000
187B495LEU0-0.03626.426-0.005-0.0050.0000.0000.0000.000
188B496THR00.03630.710-0.006-0.0060.0000.0000.0000.000
189B497LEU00.05331.6190.0080.0080.0000.0000.0000.000
190B498GLN00.00931.5490.0060.0060.0000.0000.0000.000
191B499GLN00.02229.1430.0060.0060.0000.0000.0000.000
192B500GLN0-0.00227.5030.0150.0150.0000.0000.0000.000
193B501HIS00.04826.5600.0140.0140.0000.0000.0000.000
194B502GLN0-0.05226.6150.0140.0140.0000.0000.0000.000
195B503ARG10.74320.335-0.365-0.3650.0000.0000.0000.000
196B504LEU00.04221.9830.0280.0280.0000.0000.0000.000
197B505ALA00.02221.6510.0170.0170.0000.0000.0000.000
198B506GLN0-0.05220.6600.0270.0270.0000.0000.0000.000
199B507LEU00.00317.1280.0270.0270.0000.0000.0000.000
200B508LEU00.03616.7170.0360.0360.0000.0000.0000.000
201B509LEU0-0.03017.366-0.003-0.0030.0000.0000.0000.000
202B510ILE0-0.04712.807-0.009-0.0090.0000.0000.0000.000
203B511LEU00.04612.7400.0440.0440.0000.0000.0000.000
204B512SER0-0.02012.980-0.030-0.0300.0000.0000.0000.000
205B513HIS0-0.03710.478-0.125-0.1250.0000.0000.0000.000
206B514ILE00.0237.439-0.006-0.0060.0000.0000.0000.000
207B515ARG10.9608.544-0.178-0.1780.0000.0000.0000.000
208B516HIS0-0.0409.865-0.103-0.1030.0000.0000.0000.000
209B517MET0-0.0025.808-0.051-0.0510.0000.0000.0000.000
210B518SER00.0585.375-0.213-0.2130.0000.0000.0000.000
211B519ASN00.0076.133-0.238-0.2380.0000.0000.0000.000
212B520LYS10.8536.5430.3950.3950.0000.0000.0000.000
213B521GLY00.0232.383-0.966-0.4741.329-0.752-1.0690.002
214B522MET00.0492.687-2.550-0.6720.693-0.547-2.024-0.021
215B523GLU-1-0.9065.180-0.501-0.415-0.001-0.003-0.0820.000
216B524HIS0-0.0671.807-16.081-22.79118.087-5.525-5.851-0.042
217B525LEU00.0642.177-3.448-0.3142.675-1.407-4.4020.004
218B526TYR00.0493.511-1.080-0.7920.0850.086-0.4590.002
219B527SER0-0.0256.2350.1800.1800.0000.0000.0000.000
220B528MET00.0153.988-0.0020.2140.000-0.021-0.1950.000
221B529LYS10.9376.2550.2890.2890.0000.0000.0000.000
222B530CYS0-0.0978.522-0.029-0.0290.0000.0000.0000.000
223B531LYS10.9049.5360.7880.7880.0000.0000.0000.000
224B532ASN0-0.05011.3320.0280.0280.0000.0000.0000.000
225B533VAL0-0.0238.8190.0180.0180.0000.0000.0000.000
226B534VAL0-0.0125.953-0.014-0.0140.0000.0000.0000.000
227B535PRO0-0.0349.1490.0450.0450.0000.0000.0000.000
228B536LEU0-0.0065.969-0.045-0.0450.0000.0000.0000.000
229B537TYR0-0.0189.6250.0310.0310.0000.0000.0000.000
230B538ASP-1-0.87911.107-0.222-0.2220.0000.0000.0000.000
231B539LEU00.01811.0560.0310.0310.0000.0000.0000.000
232B540LEU0-0.0114.8360.0160.0160.0000.0000.0000.000
233B541LEU0-0.1148.3790.1000.1000.0000.0000.0000.000
234B542GLU-1-0.94710.304-0.151-0.1510.0000.0000.0000.000
235B543MET0-0.0778.7080.0450.0450.0000.0000.0000.000
236B544LEU-1-0.9715.520-0.093-0.0930.0000.0000.0000.000
238B2025HOH0-0.0112.188-2.651-2.9923.489-1.319-1.8300.009