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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: 3XNQP

Calculation Name: 1SJ0-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2s,3r)-2-(4-(2-(piperidin-1-yl)ethoxy)phenyl)-2,3-dihydro-3-(4-hydroxyphenyl)benzo[b][1,4]oxathiin-6-ol

ligand 3-letter code: E4D

PDB ID: 1SJ0

Chain ID: A

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 (antagonist templeate: 1YIM)
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 E4D=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3179318.633399
FMO2-HF: Nuclear repulsion 3080158.544936
FMO2-HF: Total energy -99160.088463
FMO2-MP2: Total energy -99439.023603


3D Structure
Snapshot
 
Ligand structure

E4D

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.
-330.261-284.754106.942-51.570-100.8760.238


Interactive mode: IFIE and PIEDA for fragment #237(A:600:E4D)


Summations of interaction energy for fragment #237(A:600:E4D)
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.
-330.261-284.754106.942-51.57-100.876-0.238
Interaction energy analysis for fragmet #237(A:600:E4D)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / 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].
1A309SER10.84730.1439.4759.4750.0000.0000.0000.000
2A310LEU00.13025.1510.2750.2750.0000.0000.0000.000
3A311THR0-0.02029.143-0.117-0.1170.0000.0000.0000.000
4A312ALA00.08626.825-0.263-0.2630.0000.0000.0000.000
5A313ASP-1-0.79825.684-9.171-9.1710.0000.0000.0000.000
6A314GLN0-0.02425.992-0.202-0.2020.0000.0000.0000.000
7A315MET0-0.00121.918-0.425-0.4250.0000.0000.0000.000
8A316VAL00.04921.178-0.480-0.4800.0000.0000.0000.000
9A317SER00.03720.776-0.217-0.2170.0000.0000.0000.000
10A318ALA0-0.01121.341-0.263-0.2630.0000.0000.0000.000
11A319LEU0-0.04617.033-0.512-0.5120.0000.0000.0000.000
12A320LEU0-0.03116.584-0.564-0.5640.0000.0000.0000.000
13A321ASP-1-0.94616.963-11.910-11.9100.0000.0000.0000.000
14A322ALA0-0.08115.822-0.287-0.2870.0000.0000.0000.000
15A323GLU-1-0.78811.263-17.767-17.7670.0000.0000.0000.000
16A324PRO0-0.0908.496-0.005-0.0050.0000.0000.0000.000
17A325PRO0-0.00510.0890.7770.7770.0000.0000.0000.000
18A326ILE00.0157.968-1.551-1.5510.0000.0000.0000.000
19A327LEU0-0.0276.5560.8160.8160.0000.0000.0000.000
20A328TYR00.0397.6830.4450.4450.0000.0000.0000.000
21A329SER00.0097.278-2.426-2.4260.0000.0000.0000.000
22A330GLU-1-0.9138.355-21.517-21.5170.0000.0000.0000.000
23A331TYR0-0.08510.749-0.509-0.5090.0000.0000.0000.000
24A332ASP-1-0.79013.165-13.216-13.2160.0000.0000.0000.000
25A333PRO0-0.02715.8510.0650.0650.0000.0000.0000.000
26A334THR0-0.10217.1250.6060.6060.0000.0000.0000.000
27A335ARG10.87817.04815.42115.4210.0000.0000.0000.000
28A336PRO0-0.01418.414-0.213-0.2130.0000.0000.0000.000
29A337PHE00.04110.876-0.532-0.5320.0000.0000.0000.000
30A338SER0-0.03515.157-0.592-0.5920.0000.0000.0000.000
31A339GLU-1-0.86716.742-13.911-13.9110.0000.0000.0000.000
32A340ALA0-0.01212.256-0.600-0.6000.0000.0000.0000.000
33A341SER00.0129.429-0.907-0.9070.0000.0000.0000.000
34A342MET00.0616.283-1.233-1.2330.0000.0000.0000.000
35A343MET00.0752.265-1.944-1.0333.521-0.970-3.4610.009
36A344GLY0-0.0514.339-5.306-5.0860.000-0.022-0.1980.000
37A345LEU00.0457.001-2.325-2.3250.0000.0000.0000.000
38A346LEU0-0.0192.342-7.299-3.7024.301-1.919-5.9790.012
39A347THR0-0.0531.853-11.651-7.5935.827-3.433-6.452-0.012
40A348ASN0-0.0233.413-6.521-6.2940.0380.456-0.721-0.001
41A349LEU0-0.0392.601-0.0541.2850.278-0.309-1.3070.000
42A350ALA00.0292.826-5.080-1.5272.850-1.588-4.8150.006
43A351ASP-1-0.8362.039-116.523-108.0227.462-7.873-8.089-0.102
44A352ARG10.8743.42733.89634.0610.0060.152-0.3230.000
45A353GLU-1-0.8002.036-60.868-56.4087.866-6.405-5.921-0.093
46A354LEU00.0041.9612.7221.8004.024-0.652-2.451-0.006
47A355VAL00.0505.2903.6413.691-0.001-0.001-0.0480.000
48A356HIS0-0.0378.3064.4944.4940.0000.0000.0000.000
49A357MET0-0.0575.8102.1962.1960.0000.0000.0000.000
50A358ILE00.0627.5402.2212.2210.0000.0000.0000.000
51A359ASN0-0.00110.2821.5971.5970.0000.0000.0000.000
52A360TRP0-0.00811.5670.9230.9230.0000.0000.0000.000
53A361ALA00.04012.4071.2471.2470.0000.0000.0000.000
54A362LYS10.87813.90918.82218.8220.0000.0000.0000.000
55A363ARG10.86516.51415.22015.2200.0000.0000.0000.000
56A364VAL00.01115.7440.7790.7790.0000.0000.0000.000
57A365PRO0-0.03918.6200.1540.1540.0000.0000.0000.000
58A366GLY00.01022.125-0.038-0.0380.0000.0000.0000.000
59A367PHE00.02713.115-0.030-0.0300.0000.0000.0000.000
60A368VAL0-0.00718.162-0.360-0.3600.0000.0000.0000.000
61A369ASP-1-0.95419.656-11.547-11.5470.0000.0000.0000.000
62A370LEU0-0.04917.7560.3130.3130.0000.0000.0000.000
63A371THR0-0.07219.643-0.276-0.2760.0000.0000.0000.000
64A372LEU00.05616.100-0.401-0.4010.0000.0000.0000.000
65A373HIS00.00814.968-1.307-1.3070.0000.0000.0000.000
66A374ASP-1-0.81514.975-15.366-15.3660.0000.0000.0000.000
67A375GLN0-0.05313.918-1.447-1.4470.0000.0000.0000.000
68A376VAL00.0269.631-1.329-1.3290.0000.0000.0000.000
69A377HIS0-0.00710.280-2.409-2.4090.0000.0000.0000.000
70A378LEU0-0.05911.781-0.821-0.8210.0000.0000.0000.000
71A379LEU00.0217.986-0.852-0.8520.0000.0000.0000.000
72A380GLU-1-0.9486.824-30.839-30.8390.0000.0000.0000.000
73A381CYS0-0.0967.548-1.241-1.2410.0000.0000.0000.000
74A382ALA00.0249.687-0.088-0.0880.0000.0000.0000.000
75A383TRP00.0442.185-11.228-6.9454.433-2.022-6.695-0.021
76A384LEU0-0.0062.417-2.895-0.4710.950-0.491-2.883-0.004
77A385GLU-1-0.8315.483-16.920-16.9200.0000.0000.0000.000
78A386ILE00.0017.1282.1792.1790.0000.0000.0000.000
79A387LEU0-0.0222.443-2.9111.1542.181-1.518-4.7290.012
80A388MET0-0.0372.6242.2565.5160.896-1.087-3.069-0.002
81A389ILE0-0.0223.9281.7411.8780.001-0.007-0.1310.000
82A390GLY00.0445.4251.0481.0480.0000.0000.0000.000
83A391LEU0-0.0172.995-2.2770.3130.669-0.729-2.5300.005
84A392VAL0-0.0274.9580.1870.282-0.001-0.010-0.0850.000
85A393TRP00.0307.8160.7240.7240.0000.0000.0000.000
86A394ARG10.7902.27217.57619.4041.620-1.364-2.0830.018
87A395SER0-0.0347.8320.2090.2090.0000.0000.0000.000
88A396MET00.00610.5540.3610.3610.0000.0000.0000.000
89A397GLU-1-0.97713.327-11.059-11.0590.0000.0000.0000.000
90A398HIS0-0.04113.0370.2880.2880.0000.0000.0000.000
91A399PRO00.01814.089-0.298-0.2980.0000.0000.0000.000
92A400GLY0-0.05614.6070.0820.0820.0000.0000.0000.000
93A401LYS10.89411.61612.48812.4880.0000.0000.0000.000
94A402LEU00.0375.6640.0990.0990.0000.0000.0000.000
95A403LEU00.0078.832-0.330-0.3300.0000.0000.0000.000
96A404PHE00.0242.452-5.457-1.3012.107-1.137-5.1250.009
97A405ALA00.0674.780-3.116-2.873-0.001-0.010-0.2310.000
98A406PRO00.0257.3791.0381.0380.0000.0000.0000.000
99A407ASN0-0.00810.2550.2030.2030.0000.0000.0000.000
100A408LEU0-0.0465.751-0.322-0.3220.0000.0000.0000.000
101A409LEU00.0418.444-0.246-0.2460.0000.0000.0000.000
102A410LEU0-0.0516.7860.1470.1470.0000.0000.0000.000
103A411ASP-1-0.8299.907-12.978-12.9780.0000.0000.0000.000
104A412ARG10.87610.33512.58212.5820.0000.0000.0000.000
105A413ASN0-0.00810.857-0.352-0.3520.0000.0000.0000.000
106A414GLN00.1249.861-0.152-0.1520.0000.0000.0000.000
107A415GLY00.0827.029-0.983-0.9830.0000.0000.0000.000
108A416LYS10.7957.44711.79411.7940.0000.0000.0000.000
109A417CYS0-0.1039.4310.3330.3330.0000.0000.0000.000
110A418VAL0-0.0095.212-0.213-0.2130.0000.0000.0000.000
111A419GLU-1-0.9086.893-19.238-19.2380.0000.0000.0000.000
112A420GLY00.1206.411-2.200-2.2000.0000.0000.0000.000
113A421MET0-0.0502.850-4.684-3.5001.359-0.494-2.049-0.001
114A422VAL0-0.0434.6321.3281.427-0.001-0.001-0.0970.000
115A423GLU-1-0.8747.198-15.508-15.5080.0000.0000.0000.000
116A424ILE00.0242.916-2.1310.9930.832-1.078-2.8770.012
117A425PHE0-0.0113.7430.7011.2040.001-0.041-0.4630.000
118A426ASP-1-0.7577.111-13.132-13.1320.0000.0000.0000.000
119A427MET0-0.0487.2560.7200.7200.0000.0000.0000.000
120A428LEU00.0654.073-0.2650.4580.047-0.122-0.6490.000
121A429LEU0-0.0128.5220.4520.4520.0000.0000.0000.000
122A430ALA0-0.03011.0290.5290.5290.0000.0000.0000.000
123A431THR0-0.01310.1380.3850.3850.0000.0000.0000.000
124A432SER0-0.01910.4680.4080.4080.0000.0000.0000.000
125A433SER0-0.01112.0520.4010.4010.0000.0000.0000.000
126A434ARG10.94315.27710.94210.9420.0000.0000.0000.000
127A435PHE00.06010.7500.3570.3570.0000.0000.0000.000
128A436ARG10.90014.46311.63911.6390.0000.0000.0000.000
129A437MET0-0.02017.4560.2370.2370.0000.0000.0000.000
130A438MET0-0.08018.7160.2220.2220.0000.0000.0000.000
131A439ASN00.01519.8760.0290.0290.0000.0000.0000.000
132A440LEU0-0.07714.1710.1180.1180.0000.0000.0000.000
133A441GLN00.03117.896-0.067-0.0670.0000.0000.0000.000
134A442GLY00.05515.737-0.378-0.3780.0000.0000.0000.000
135A443GLU-1-0.87516.359-11.179-11.1790.0000.0000.0000.000
136A444GLU-1-0.76618.414-10.585-10.5850.0000.0000.0000.000
137A445PHE00.0028.910-0.402-0.4020.0000.0000.0000.000
138A446VAL00.01713.721-0.668-0.6680.0000.0000.0000.000
139A447CYS0-0.04114.970-0.278-0.2780.0000.0000.0000.000
140A448LEU0-0.02214.128-0.310-0.3100.0000.0000.0000.000
141A449LYS10.8568.94618.18418.1840.0000.0000.0000.000
142A450SER00.02812.587-1.020-1.0200.0000.0000.0000.000
143A451ILE0-0.00515.466-0.068-0.0680.0000.0000.0000.000
144A452ILE0-0.02210.509-0.014-0.0140.0000.0000.0000.000
145A453LEU00.00212.173-0.552-0.5520.0000.0000.0000.000
146A454LEU0-0.01614.163-0.069-0.0690.0000.0000.0000.000
147A455ASN00.00417.4450.7080.7080.0000.0000.0000.000
148A456SER0-0.07613.5190.7370.7370.0000.0000.0000.000
149A457GLY00.05414.721-0.065-0.0650.0000.0000.0000.000
150A458VAL00.02315.4600.4110.4110.0000.0000.0000.000
151A459TYR0-0.08319.0120.6470.6470.0000.0000.0000.000
152A460THR0-0.00215.5900.5890.5890.0000.0000.0000.000
153A461PHE00.00017.508-0.183-0.1830.0000.0000.0000.000
154A462LEU00.02616.3380.6610.6610.0000.0000.0000.000
155A463SER0-0.01920.6370.5870.5870.0000.0000.0000.000
156A464SER0-0.02424.107-0.131-0.1310.0000.0000.0000.000
157A465THR00.00426.1900.3530.3530.0000.0000.0000.000
158A466LEU00.08428.081-0.114-0.1140.0000.0000.0000.000
159A467LYS11.00123.18411.92111.9210.0000.0000.0000.000
160A468SER0-0.01223.382-0.144-0.1440.0000.0000.0000.000
161A469LEU0-0.00624.890-0.192-0.1920.0000.0000.0000.000
162A470GLU-1-0.91027.461-9.694-9.6940.0000.0000.0000.000
163A471GLU-1-0.79321.189-12.914-12.9140.0000.0000.0000.000
164A472LYS10.90722.76911.98311.9830.0000.0000.0000.000
165A473ASP-1-0.88224.190-9.773-9.7730.0000.0000.0000.000
166A474HIS0-0.03522.8270.5390.5390.0000.0000.0000.000
167A475ILE00.01119.325-0.010-0.0100.0000.0000.0000.000
168A476HIS00.01523.065-0.070-0.0700.0000.0000.0000.000
169A477ARG10.91725.45210.12610.1260.0000.0000.0000.000
170A478VAL0-0.05822.3070.2250.2250.0000.0000.0000.000
171A479LEU0-0.01420.122-0.046-0.0460.0000.0000.0000.000
172A480ASP-1-0.85623.654-9.937-9.9370.0000.0000.0000.000
173A481LYS10.88725.3499.9489.9480.0000.0000.0000.000
174A482ILE0-0.00319.1600.2120.2120.0000.0000.0000.000
175A483THR0-0.03223.1110.0340.0340.0000.0000.0000.000
176A484ASP-1-0.90624.839-9.072-9.0720.0000.0000.0000.000
177A485THR0-0.07923.1250.3080.3080.0000.0000.0000.000
178A486LEU00.03019.9320.1480.1480.0000.0000.0000.000
179A487ILE0-0.00523.8410.2470.2470.0000.0000.0000.000
180A488HIS0-0.01127.0520.2130.2130.0000.0000.0000.000
181A489LEU00.00721.7380.2210.2210.0000.0000.0000.000
182A490MET0-0.04222.8180.2560.2560.0000.0000.0000.000
183A491ALA0-0.00727.0540.2160.2160.0000.0000.0000.000
184A492LYS10.82328.7008.8788.8780.0000.0000.0000.000
185A493ALA0-0.03927.0340.1450.1450.0000.0000.0000.000
186A494GLY0-0.01829.1730.0920.0920.0000.0000.0000.000
187A495LEU0-0.02826.7440.1370.1370.0000.0000.0000.000
188A496THR00.05031.2740.0680.0680.0000.0000.0000.000
189A497LEU00.06732.164-0.166-0.1660.0000.0000.0000.000
190A498GLN0-0.01432.216-0.146-0.1460.0000.0000.0000.000
191A499GLN00.05929.382-0.148-0.1480.0000.0000.0000.000
192A500GLN0-0.02227.972-0.324-0.3240.0000.0000.0000.000
193A501HIS00.03227.015-0.148-0.1480.0000.0000.0000.000
194A502GLN0-0.05726.949-0.301-0.3010.0000.0000.0000.000
195A503ARG10.77420.9989.7099.7090.0000.0000.0000.000
196A504LEU00.02522.543-0.354-0.3540.0000.0000.0000.000
197A505ALA00.02022.022-0.419-0.4190.0000.0000.0000.000
198A506GLN0-0.03621.315-0.412-0.4120.0000.0000.0000.000
199A507LEU00.00317.662-0.359-0.3590.0000.0000.0000.000
200A508LEU00.03417.265-0.557-0.5570.0000.0000.0000.000
201A509LEU0-0.04218.368-0.367-0.3670.0000.0000.0000.000
202A510ILE0-0.01613.517-0.271-0.2710.0000.0000.0000.000
203A511LEU00.01113.275-0.616-0.6160.0000.0000.0000.000
204A512SER0-0.02114.163-0.711-0.7110.0000.0000.0000.000
205A513HIS00.00313.331-0.475-0.4750.0000.0000.0000.000
206A514ILE00.0158.499-0.485-0.4850.0000.0000.0000.000
207A515ARG10.9709.17416.30816.3080.0000.0000.0000.000
208A516HIS0-0.0579.503-1.042-1.0420.0000.0000.0000.000
209A517MET00.0106.707-0.485-0.4850.0000.0000.0000.000
210A518SER00.0555.066-1.954-1.9540.0000.0000.0000.000
211A519ASN0-0.0055.270-2.621-2.6210.0000.0000.0000.000
212A520LYS10.9156.43316.36716.3670.0000.0000.0000.000
213A521GLY00.0302.442-1.602-0.8482.146-1.353-1.5480.008
214A522MET0-0.0132.892-3.141-3.2210.6780.967-1.565-0.009
215A523GLU-1-0.9465.102-20.100-19.985-0.001-0.008-0.1060.000
216A524HIS00.0081.577-29.832-48.18639.552-13.744-7.455-0.076
217A525LEU00.0182.147-8.876-4.1064.400-1.774-7.3960.010
218A526TYR0-0.0554.655-2.770-2.5170.000-0.017-0.2350.000
219A527SER0-0.0365.6282.9712.9710.0000.0000.0000.000
220A528MET0-0.0545.255-0.014-0.0140.0000.0000.0000.000
221A529LYS10.9615.62633.16233.1620.0000.0000.0000.000
222A530CYS0-0.1072.828-2.036-1.0540.187-0.224-0.9450.000
223A531LYS10.9031.97243.55143.3396.303-1.345-4.747-0.011
224A532ASN00.0063.649-3.117-2.6270.009-0.172-0.327-0.001
225A533VAL0-0.0066.1233.4743.4740.0000.0000.0000.000
226A534VAL00.0466.864-2.724-2.7240.0000.0000.0000.000
227A535PRO00.0376.188-5.019-5.0190.0000.0000.0000.000
228A536LEU00.0052.412-3.111-2.1840.904-0.222-1.608-0.004
229A537TYR00.0315.1060.5000.555-0.001-0.001-0.0530.000
230A538ASP-1-0.8298.686-22.700-22.7000.0000.0000.0000.000
231A539LEU0-0.0403.782-0.553-0.2460.006-0.050-0.2620.000
232A540LEU0-0.0375.020-0.056-0.0560.0000.0000.0000.000
233A541LEU0-0.0427.5601.7821.7820.0000.0000.0000.000
234A542GLU-1-0.96910.503-19.485-19.4850.0000.0000.0000.000
235A543MET0-0.1034.803-0.127-0.1270.0000.0000.0000.000
236A544LEU-1-0.94910.447-16.897-16.8970.0000.0000.0000.000
238A1005HOH0-0.0182.339-0.1240.5031.494-0.952-1.1680.004