Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: P59ZP

Calculation Name: 1YIN-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2r,3r,4s)-5-fluoro-3-(4-hydroxyphenyl)-4-methyl-2-[4-(2-piperidin-1-ylethoxy)phenyl]chroman-6-ol

ligand 3-letter code: CM3

PDB ID: 1YIN

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 CM3=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3177192.293319
FMO2-HF: Nuclear repulsion 3078252.77425
FMO2-HF: Total energy -98939.519069
FMO2-MP2: Total energy -99218.732331


3D Structure
Snapshot
 
Ligand structure

CM3

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.
-329.299-303.045130.005-52.243-104.0120.235


Interactive mode: IFIE and PIEDA for fragment #237(A:600:CM3)


Summations of interaction energy for fragment #237(A:600:CM3)
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.
-329.299-303.045130.005-52.243-104.012-0.235
Interaction energy analysis for fragmet #237(A:600:CM3)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.764 / 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].
1A309SER10.84731.3139.2519.2510.0000.0000.0000.000
2A310LEU00.10425.8600.2010.2010.0000.0000.0000.000
3A311THR0-0.01529.277-0.087-0.0870.0000.0000.0000.000
4A312ALA00.10626.890-0.318-0.3180.0000.0000.0000.000
5A313ASP-1-0.80325.630-9.317-9.3170.0000.0000.0000.000
6A314GLN0-0.00526.196-0.139-0.1390.0000.0000.0000.000
7A315MET0-0.01522.081-0.372-0.3720.0000.0000.0000.000
8A316VAL00.01621.327-0.399-0.3990.0000.0000.0000.000
9A317SER00.01020.800-0.240-0.2400.0000.0000.0000.000
10A318ALA0-0.00121.410-0.224-0.2240.0000.0000.0000.000
11A319LEU0-0.01717.125-0.480-0.4800.0000.0000.0000.000
12A320LEU0-0.03216.470-0.617-0.6170.0000.0000.0000.000
13A321ASP-1-0.92617.165-11.882-11.8820.0000.0000.0000.000
14A322ALA0-0.12116.193-0.364-0.3640.0000.0000.0000.000
15A323GLU-1-0.82511.300-17.884-17.8840.0000.0000.0000.000
16A324PRO0-0.0388.6730.0260.0260.0000.0000.0000.000
17A325PRO0-0.00910.1740.8520.8520.0000.0000.0000.000
18A326ILE00.0247.685-1.535-1.5350.0000.0000.0000.000
19A327LEU0-0.0366.6760.7450.7450.0000.0000.0000.000
20A328TYR00.0427.4480.1320.1320.0000.0000.0000.000
21A329SER0-0.0017.211-2.555-2.5550.0000.0000.0000.000
22A330GLU-1-0.9128.360-22.344-22.3440.0000.0000.0000.000
23A331TYR0-0.05010.642-0.365-0.3650.0000.0000.0000.000
24A332ASP-1-0.83513.108-13.198-13.1980.0000.0000.0000.000
25A333PRO0-0.02916.2120.0890.0890.0000.0000.0000.000
26A334THR0-0.04917.3710.6390.6390.0000.0000.0000.000
27A335ARG10.88017.16215.34515.3450.0000.0000.0000.000
28A336PRO0-0.00618.420-0.229-0.2290.0000.0000.0000.000
29A337PHE00.05411.028-0.518-0.5180.0000.0000.0000.000
30A338SER0-0.02815.175-0.712-0.7120.0000.0000.0000.000
31A339GLU-1-0.88016.344-14.196-14.1960.0000.0000.0000.000
32A340ALA0-0.03512.063-0.688-0.6880.0000.0000.0000.000
33A341SER00.0079.229-0.546-0.5460.0000.0000.0000.000
34A342MET00.0746.103-0.971-0.9710.0000.0000.0000.000
35A343MET00.0572.934-5.020-3.1841.386-0.734-2.4870.001
36A344GLY00.0164.224-5.261-5.0030.000-0.038-0.2190.000
37A345LEU00.0016.623-2.402-2.4020.0000.0000.0000.000
38A346LEU0-0.0442.097-6.221-5.0467.280-2.274-6.1820.012
39A347THR0-0.0102.077-12.292-7.4655.646-3.369-7.104-0.018
40A348ASN0-0.0133.492-10.260-10.1360.0340.502-0.660-0.001
41A349LEU0-0.0752.427-1.2850.6070.946-0.620-2.2170.001
42A350ALA00.0602.922-4.776-1.2073.095-1.665-4.9980.008
43A351ASP-1-0.7801.765-116.635-121.23722.977-9.358-9.017-0.112
44A352ARG10.8603.62232.98133.3140.003-0.001-0.3350.000
45A353GLU-1-0.7591.787-66.128-66.34515.077-8.214-6.646-0.112
46A354LEU00.0071.9723.5711.2695.959-0.790-2.867-0.004
47A355VAL00.0315.1133.4963.570-0.001-0.002-0.0710.000
48A356HIS00.0107.7973.3143.3140.0000.0000.0000.000
49A357MET0-0.0636.0802.3192.3190.0000.0000.0000.000
50A358ILE00.0287.4832.2162.2160.0000.0000.0000.000
51A359ASN0-0.02410.1331.1361.1360.0000.0000.0000.000
52A360TRP00.01211.8450.8760.8760.0000.0000.0000.000
53A361ALA00.06011.9231.3741.3740.0000.0000.0000.000
54A362LYS10.92913.69618.25718.2570.0000.0000.0000.000
55A363ARG10.88316.31414.98314.9830.0000.0000.0000.000
56A364VAL0-0.01915.7750.8490.8490.0000.0000.0000.000
57A365PRO0-0.02118.6650.0960.0960.0000.0000.0000.000
58A366GLY00.00821.520-0.056-0.0560.0000.0000.0000.000
59A367PHE00.04013.0790.0180.0180.0000.0000.0000.000
60A368VAL0-0.01917.518-0.270-0.2700.0000.0000.0000.000
61A369ASP-1-0.97319.517-11.510-11.5100.0000.0000.0000.000
62A370LEU0-0.04817.8250.3880.3880.0000.0000.0000.000
63A371THR0-0.10319.763-0.302-0.3020.0000.0000.0000.000
64A372LEU00.06114.998-0.262-0.2620.0000.0000.0000.000
65A373HIS0-0.02814.941-1.369-1.3690.0000.0000.0000.000
66A374ASP-1-0.79014.937-15.661-15.6610.0000.0000.0000.000
67A375GLN0-0.04713.708-1.343-1.3430.0000.0000.0000.000
68A376VAL00.0249.615-1.412-1.4120.0000.0000.0000.000
69A377HIS0-0.01510.372-2.363-2.3630.0000.0000.0000.000
70A378LEU0-0.07511.879-0.773-0.7730.0000.0000.0000.000
71A379LEU00.0078.118-0.817-0.8170.0000.0000.0000.000
72A380GLU-1-0.9626.812-31.365-31.3650.0000.0000.0000.000
73A381CYS0-0.0628.067-1.001-1.0010.0000.0000.0000.000
74A382ALA00.0229.7570.0530.0530.0000.0000.0000.000
75A383TRP00.0422.121-12.026-8.7356.525-2.133-7.683-0.019
76A384LEU00.0042.350-2.640-0.3830.937-0.455-2.739-0.004
77A385GLU-1-0.8285.350-16.155-16.039-0.001-0.002-0.1140.000
78A386ILE0-0.0097.1502.3002.3000.0000.0000.0000.000
79A387LEU0-0.0242.748-2.5761.1460.637-1.352-3.0060.009
80A388MET0-0.0092.5652.4076.0360.907-1.091-3.4440.004
81A389ILE0-0.0133.8890.8711.1070.004-0.031-0.2090.000
82A390GLY00.0345.6550.8280.8280.0000.0000.0000.000
83A391LEU0-0.0242.786-3.900-0.5771.189-1.087-3.4260.010
84A392VAL0-0.0064.697-0.527-0.3470.000-0.019-0.1610.000
85A393TRP0-0.0017.8630.6510.6510.0000.0000.0000.000
86A394ARG10.7682.26022.99024.6270.810-0.896-1.5520.010
87A395SER0-0.0267.8920.0770.0770.0000.0000.0000.000
88A396MET00.02410.4960.6040.6040.0000.0000.0000.000
89A397GLU-1-0.97713.510-10.982-10.9820.0000.0000.0000.000
90A398HIS0-0.01212.6840.2490.2490.0000.0000.0000.000
91A399PRO00.01013.132-0.315-0.3150.0000.0000.0000.000
92A400GLY0-0.04113.1460.0940.0940.0000.0000.0000.000
93A401LYS10.90010.86012.19412.1940.0000.0000.0000.000
94A402LEU00.0204.287-0.0400.117-0.001-0.008-0.1490.000
95A403LEU0-0.0087.801-0.321-0.3210.0000.0000.0000.000
96A404PHE00.0382.283-5.111-1.3463.074-1.312-5.5270.013
97A405ALA00.0394.480-3.648-3.424-0.001-0.018-0.2050.000
98A406PRO00.0397.1211.1851.1850.0000.0000.0000.000
99A407ASN0-0.00310.1860.1940.1940.0000.0000.0000.000
100A408LEU0-0.0465.636-0.063-0.0630.0000.0000.0000.000
101A409LEU00.0348.583-0.295-0.2950.0000.0000.0000.000
102A410LEU0-0.0526.9090.2650.2650.0000.0000.0000.000
103A411ASP-1-0.7849.463-13.140-13.1400.0000.0000.0000.000
104A412ARG10.8759.86012.39012.3900.0000.0000.0000.000
105A413ASN0-0.03910.737-0.472-0.4720.0000.0000.0000.000
106A414GLN00.03410.375-0.004-0.0040.0000.0000.0000.000
107A415GLY00.0447.035-0.921-0.9210.0000.0000.0000.000
108A416LYS10.8527.40011.82011.8200.0000.0000.0000.000
109A417CYS0-0.0529.5870.3150.3150.0000.0000.0000.000
110A418VAL0-0.0335.080-0.429-0.4290.0000.0000.0000.000
111A419GLU-1-0.9027.035-18.441-18.4410.0000.0000.0000.000
112A420GLY00.0846.227-2.510-2.5100.0000.0000.0000.000
113A421MET0-0.0402.882-4.225-3.2201.985-0.612-2.378-0.001
114A422VAL0-0.0544.4191.2851.397-0.001-0.003-0.1080.000
115A423GLU-1-0.8207.117-15.649-15.6490.0000.0000.0000.000
116A424ILE00.0062.491-1.8180.2312.878-1.114-3.8130.015
117A425PHE00.0423.8790.5091.0140.001-0.034-0.4720.000
118A426ASP-1-0.7796.448-13.004-13.0040.0000.0000.0000.000
119A427MET0-0.0487.0790.7060.7060.0000.0000.0000.000
120A428LEU00.0572.452-0.1900.1981.283-0.228-1.4440.000
121A429LEU0-0.0316.9960.5350.5350.0000.0000.0000.000
122A430ALA0-0.0329.5610.5350.5350.0000.0000.0000.000
123A431THR0-0.0079.1380.3720.3720.0000.0000.0000.000
124A432SER0-0.0169.6960.4500.4500.0000.0000.0000.000
125A433SER0-0.03111.4080.4650.4650.0000.0000.0000.000
126A434ARG10.98714.10910.86310.8630.0000.0000.0000.000
127A435PHE00.03911.0100.3850.3850.0000.0000.0000.000
128A436ARG10.93813.49511.69511.6950.0000.0000.0000.000
129A437MET0-0.09617.3560.2800.2800.0000.0000.0000.000
130A438MET0-0.08118.5470.1990.1990.0000.0000.0000.000
131A439ASN00.01719.3690.0380.0380.0000.0000.0000.000
132A440LEU0-0.07014.3900.1000.1000.0000.0000.0000.000
133A441GLN00.01617.822-0.047-0.0470.0000.0000.0000.000
134A442GLY00.06215.857-0.360-0.3600.0000.0000.0000.000
135A443GLU-1-0.89216.785-11.121-11.1210.0000.0000.0000.000
136A444GLU-1-0.76018.474-10.607-10.6070.0000.0000.0000.000
137A445PHE00.0079.268-0.351-0.3510.0000.0000.0000.000
138A446VAL00.02713.862-0.673-0.6730.0000.0000.0000.000
139A447CYS0-0.03115.137-0.285-0.2850.0000.0000.0000.000
140A448LEU0-0.02214.152-0.261-0.2610.0000.0000.0000.000
141A449LYS10.8569.18218.03218.0320.0000.0000.0000.000
142A450SER00.01213.045-0.881-0.8810.0000.0000.0000.000
143A451ILE0-0.00816.001-0.143-0.1430.0000.0000.0000.000
144A452ILE0-0.01610.5560.0200.0200.0000.0000.0000.000
145A453LEU0-0.00511.798-0.607-0.6070.0000.0000.0000.000
146A454LEU0-0.02013.921-0.019-0.0190.0000.0000.0000.000
147A455ASN0-0.00117.2080.6690.6690.0000.0000.0000.000
148A456SER0-0.07313.5290.7430.7430.0000.0000.0000.000
149A457GLY00.06315.074-0.171-0.1710.0000.0000.0000.000
150A458VAL00.04615.7400.4940.4940.0000.0000.0000.000
151A459TYR0-0.07519.2190.6770.6770.0000.0000.0000.000
152A460THR0-0.04315.7200.4700.4700.0000.0000.0000.000
153A461PHE00.01116.779-0.265-0.2650.0000.0000.0000.000
154A462LEU0-0.02018.2030.8270.8270.0000.0000.0000.000
155A463SER00.00921.9130.6430.6430.0000.0000.0000.000
156A464SER0-0.01624.391-0.128-0.1280.0000.0000.0000.000
157A465THR00.01525.9330.3630.3630.0000.0000.0000.000
158A466LEU00.04728.279-0.063-0.0630.0000.0000.0000.000
159A467LYS11.01823.60911.79311.7930.0000.0000.0000.000
160A468SER0-0.01123.589-0.127-0.1270.0000.0000.0000.000
161A469LEU0-0.00924.845-0.181-0.1810.0000.0000.0000.000
162A470GLU-1-0.89927.558-9.838-9.8380.0000.0000.0000.000
163A471GLU-1-0.77021.239-13.099-13.0990.0000.0000.0000.000
164A472LYS10.90722.80911.70111.7010.0000.0000.0000.000
165A473ASP-1-0.88924.655-9.671-9.6710.0000.0000.0000.000
166A474HIS0-0.04023.0450.5500.5500.0000.0000.0000.000
167A475ILE00.04719.8120.0400.0400.0000.0000.0000.000
168A476HIS0-0.00123.146-0.348-0.3480.0000.0000.0000.000
169A477ARG10.92425.38710.24310.2430.0000.0000.0000.000
170A478VAL0-0.05422.1120.2250.2250.0000.0000.0000.000
171A479LEU0-0.00420.070-0.030-0.0300.0000.0000.0000.000
172A480ASP-1-0.85623.685-9.880-9.8800.0000.0000.0000.000
173A481LYS10.89225.7989.8289.8280.0000.0000.0000.000
174A482ILE0-0.01819.7910.1390.1390.0000.0000.0000.000
175A483THR0-0.03023.5400.0170.0170.0000.0000.0000.000
176A484ASP-1-0.93124.929-9.012-9.0120.0000.0000.0000.000
177A485THR0-0.07923.4910.2800.2800.0000.0000.0000.000
178A486LEU00.00919.8110.1310.1310.0000.0000.0000.000
179A487ILE00.00323.9930.2030.2030.0000.0000.0000.000
180A488HIS0-0.04627.4090.3380.3380.0000.0000.0000.000
181A489LEU0-0.01922.1260.2290.2290.0000.0000.0000.000
182A490MET0-0.02523.0360.2480.2480.0000.0000.0000.000
183A491ALA0-0.00427.3080.2100.2100.0000.0000.0000.000
184A492LYS10.92725.6239.4859.4850.0000.0000.0000.000
185A493ALA0-0.06527.1550.1690.1690.0000.0000.0000.000
186A494GLY0-0.00129.3020.1210.1210.0000.0000.0000.000
187A495LEU0-0.04726.8360.1240.1240.0000.0000.0000.000
188A496THR00.03631.3620.0700.0700.0000.0000.0000.000
189A497LEU00.05732.222-0.182-0.1820.0000.0000.0000.000
190A498GLN00.02532.311-0.149-0.1490.0000.0000.0000.000
191A499GLN00.05729.753-0.186-0.1860.0000.0000.0000.000
192A500GLN00.00828.255-0.341-0.3410.0000.0000.0000.000
193A501HIS00.03627.244-0.113-0.1130.0000.0000.0000.000
194A502GLN0-0.07027.044-0.298-0.2980.0000.0000.0000.000
195A503ARG10.78721.1369.6819.6810.0000.0000.0000.000
196A504LEU00.01622.815-0.344-0.3440.0000.0000.0000.000
197A505ALA00.01222.275-0.386-0.3860.0000.0000.0000.000
198A506GLN0-0.05320.876-0.438-0.4380.0000.0000.0000.000
199A507LEU00.01317.822-0.323-0.3230.0000.0000.0000.000
200A508LEU00.04217.255-0.527-0.5270.0000.0000.0000.000
201A509LEU0-0.00317.839-0.401-0.4010.0000.0000.0000.000
202A510ILE0-0.05613.093-0.276-0.2760.0000.0000.0000.000
203A511LEU00.04913.421-0.555-0.5550.0000.0000.0000.000
204A512SER0-0.01713.816-0.645-0.6450.0000.0000.0000.000
205A513HIS0-0.04212.471-0.647-0.6470.0000.0000.0000.000
206A514ILE00.0078.308-0.376-0.3760.0000.0000.0000.000
207A515ARG10.9659.26215.95915.9590.0000.0000.0000.000
208A516HIS0-0.0509.594-1.027-1.0270.0000.0000.0000.000
209A517MET00.0116.079-0.442-0.4420.0000.0000.0000.000
210A518SER00.0595.252-1.735-1.7350.0000.0000.0000.000
211A519ASN00.0035.474-2.464-2.4640.0000.0000.0000.000
212A520LYS10.8406.13816.15916.1590.0000.0000.0000.000
213A521GLY00.0292.540-1.505-0.6622.287-1.455-1.6750.010
214A522MET0-0.0142.985-2.016-2.1260.2351.021-1.146-0.004
215A523GLU-1-0.8495.273-18.604-18.493-0.001-0.005-0.1060.000
216A524HIS0-0.0331.658-22.677-38.49634.847-11.235-7.793-0.053
217A525LEU00.0272.726-7.348-2.7323.832-1.594-6.8540.013
218A526TYR00.0054.838-3.731-3.7310.0000.0000.0000.000
219A527SER0-0.0705.9002.8712.8710.0000.0000.0000.000
220A528MET0-0.1434.180-0.886-0.6130.000-0.020-0.2520.000
221A529LYS10.9229.20421.59121.5910.0000.0000.0000.000
222A530CYS00.0553.562-5.877-5.1390.134-0.166-0.7050.000
223A531LYS10.8142.55362.88364.5990.397-0.332-1.7800.000
224A532ASN00.0203.322-11.165-10.1940.046-0.412-0.604-0.003
225A533VAL0-0.0455.8713.5093.5090.0000.0000.0000.000
226A534VAL00.0236.7543.6633.6630.0000.0000.0000.000
227A535PRO0-0.0386.038-4.782-4.7820.0000.0000.0000.000
228A536LEU00.0412.125-2.000-4.2125.243-0.519-2.512-0.008
229A537TYR00.0355.4630.3110.3110.0000.0000.0000.000
230A538ASP-1-0.8038.672-23.307-23.3070.0000.0000.0000.000
231A539LEU0-0.0082.871-0.907-0.1800.227-0.159-0.793-0.002
232A540LEU0-0.0294.8890.8290.8290.0000.0000.0000.000
233A541LEU0-0.0457.1061.9791.9790.0000.0000.0000.000
234A542GLU-1-0.9929.730-19.421-19.4210.0000.0000.0000.000
235A543MET0-0.1294.5020.2050.268-0.001-0.004-0.0580.000
236A544LEU-1-0.97610.186-17.266-17.2660.0000.0000.0000.000
238A1042HOH0-0.0302.8940.8021.5760.131-0.405-0.5010.000