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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: P84YP

Calculation Name: 2YLY-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: n-cyclopropyl-4-oxidanyl-n-[(2r)-2-oxidanyl-2-phenyl-propyl]benzenesulfonamide

ligand 3-letter code: SU4

PDB ID: 2YLY

Chain ID: B

ChEMBL ID: CHEMBL242

UniProt ID: Q92731

Base Structure: X-ray

Registration Date: 2017-06-23

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Homology modeling
Water No
Procedure Auto-FMO protocol ver. 1.2017021
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3052316.574812
FMO2-HF: Nuclear repulsion 2955324.040104
FMO2-HF: Total energy -96992.534708
FMO2-MP2: Total energy -97263.657754


3D Structure
Snapshot
 
Ligand structure

SU4

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.
-70.949-49.32480.312-25.108-76.8270.054


Interactive mode: IFIE and PIEDA for fragment #235(B:1499:SU4)


Summations of interaction energy for fragment #235(B:1499:SU4)
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.
-70.949-49.32480.312-25.108-76.827-0.054
Interaction energy analysis for fragmet #235(B:1499:SU4)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.045
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].
1B264SER10.8640.91229.812-0.030-0.0300.0000.0000.0000.000
2B265PRO00.1750.07326.435-0.023-0.0230.0000.0000.0000.000
3B266GLU-1-0.925-0.95325.275-0.012-0.0120.0000.0000.0000.000
4B267GLN00.002-0.01025.533-0.033-0.0330.0000.0000.0000.000
5B268LEU00.0100.03922.155-0.030-0.0300.0000.0000.0000.000
6B269VAL00.0320.02120.701-0.028-0.0280.0000.0000.0000.000
7B270LEU0-0.037-0.00120.666-0.026-0.0260.0000.0000.0000.000
8B271THR0-0.014-0.03821.539-0.034-0.0340.0000.0000.0000.000
9B272LEU0-0.001-0.01517.045-0.053-0.0530.0000.0000.0000.000
10B273LEU0-0.055-0.01716.718-0.063-0.0630.0000.0000.0000.000
11B274GLU-1-0.913-0.96717.309-0.406-0.4060.0000.0000.0000.000
12B275ALA0-0.057-0.03016.657-0.086-0.0860.0000.0000.0000.000
13B276GLU-1-0.962-0.98511.986-0.846-0.8460.0000.0000.0000.000
14B277PRO0-0.0300.0008.855-0.023-0.0230.0000.0000.0000.000
15B278PRO0-0.0250.00110.6140.0210.0210.0000.0000.0000.000
16B279HIS00.0410.0007.683-0.578-0.5780.0000.0000.0000.000
17B280VAL0-0.018-0.0074.7310.2740.330-0.001-0.001-0.0540.000
18B281LEU0-0.0060.0086.840-0.041-0.0410.0000.0000.0000.000
19B282ILE0-0.059-0.0456.594-0.341-0.3410.0000.0000.0000.000
20B283SER00.004-0.0119.2720.3590.3590.0000.0000.0000.000
21B284ARG10.8950.92212.2511.2941.2940.0000.0000.0000.000
22B285PRO00.0430.02614.4150.1400.1400.0000.0000.0000.000
23B286SER00.0270.02716.902-0.104-0.1040.0000.0000.0000.000
24B287ALA0-0.011-0.01615.721-0.017-0.0170.0000.0000.0000.000
25B288PRO00.0230.01816.924-0.013-0.0130.0000.0000.0000.000
26B289PHE00.0690.0449.822-0.207-0.2070.0000.0000.0000.000
27B290THR0-0.070-0.04811.8340.0390.0390.0000.0000.0000.000
28B291GLU-1-0.831-0.9369.110-0.715-0.7150.0000.0000.0000.000
29B292ALA00.0660.0347.987-0.230-0.2300.0000.0000.0000.000
30B293SER00.022-0.0019.020-0.270-0.2700.0000.0000.0000.000
31B294MET00.0090.0646.011-0.593-0.5930.0000.0000.0000.000
32B295MET00.0840.0262.395-3.636-2.2192.743-0.791-3.3690.003
33B296MET0-0.073-0.0175.216-0.335-0.3350.0000.0000.0000.000
34B297SER0-0.063-0.0606.658-0.164-0.1640.0000.0000.0000.000
35B298LEU00.0000.0111.884-2.187-4.00410.915-1.872-7.2270.006
36B299THR00.013-0.0062.507-5.694-3.8213.339-1.391-3.820-0.013
37B300LYS10.8640.9623.3723.4293.3040.0110.345-0.2310.000
38B301LEU0-0.042-0.0412.0440.215-0.0864.549-1.152-3.0960.008
39B302ALA0-0.0070.0022.267-2.596-1.1961.329-0.776-1.9530.000
40B303ASP-1-0.843-0.9234.258-2.098-1.7990.005-0.073-0.2310.000
41B304LYS10.8730.9276.8304.1864.1860.0000.0000.0000.000
42B305GLU-1-0.860-0.9322.008-29.990-25.9384.160-4.533-3.678-0.063
43B306LEU00.0260.0085.8231.3501.3500.0000.0000.0000.000
44B307VAL00.0110.0188.3420.6040.6040.0000.0000.0000.000
45B308HIS0-0.050-0.0318.3280.5980.5980.0000.0000.0000.000
46B309MET0-0.0250.0197.2680.5350.5350.0000.0000.0000.000
47B310ILE00.1080.05310.2930.3560.3560.0000.0000.0000.000
48B311SER0-0.058-0.02813.4770.2050.2050.0000.0000.0000.000
49B312TRP0-0.028-0.02011.9210.1720.1720.0000.0000.0000.000
50B313ALA00.012-0.01013.8860.1420.1420.0000.0000.0000.000
51B314LYS10.8790.93915.5340.5960.5960.0000.0000.0000.000
52B315LYS10.9050.95815.4070.8830.8830.0000.0000.0000.000
53B316ILE00.0020.02715.1520.0480.0480.0000.0000.0000.000
54B317PRO0-0.029-0.03119.4460.0130.0130.0000.0000.0000.000
55B318GLY00.0380.01423.1710.0440.0440.0000.0000.0000.000
56B319PHE0-0.005-0.00217.2530.0310.0310.0000.0000.0000.000
57B320VAL00.023-0.00121.6180.0170.0170.0000.0000.0000.000
58B321GLU-1-0.929-0.94623.747-0.081-0.0810.0000.0000.0000.000
59B322LEU0-0.067-0.02021.6550.0290.0290.0000.0000.0000.000
60B323SER00.0410.02424.952-0.046-0.0460.0000.0000.0000.000
61B324LEU00.0550.02522.3230.0290.0290.0000.0000.0000.000
62B325PHE0-0.0020.00021.3960.0150.0150.0000.0000.0000.000
63B326ASP-1-0.836-0.89820.4300.2900.2900.0000.0000.0000.000
64B327GLN0-0.053-0.03619.0460.0200.0200.0000.0000.0000.000
65B328VAL00.0640.03116.4550.0350.0350.0000.0000.0000.000
66B329ARG10.9800.98415.547-0.316-0.3160.0000.0000.0000.000
67B330LEU0-0.105-0.03715.3370.1740.1740.0000.0000.0000.000
68B331LEU00.0370.01712.4370.2140.2140.0000.0000.0000.000
69B332GLU-1-0.882-0.94711.0670.7470.7470.0000.0000.0000.000
70B333SER0-0.040-0.02110.7020.3770.3770.0000.0000.0000.000
71B334CYS0-0.054-0.0269.4360.2240.2240.0000.0000.0000.000
72B335TRP00.0900.0543.2830.4311.2090.016-0.102-0.6920.000
73B336MET00.0170.0212.0250.8081.4556.546-1.591-5.6030.012
74B337GLU-1-0.860-0.9574.0133.9434.4610.003-0.079-0.4420.000
75B338VAL00.007-0.0036.029-0.677-0.6770.0000.0000.0000.000
76B339LEU0-0.013-0.0092.575-4.004-2.2014.449-1.527-4.7250.008
77B340MET0-0.0100.0012.169-9.479-7.6337.493-2.623-6.716-0.021
78B341MET0-0.025-0.0053.1890.096-0.0570.0380.400-0.2850.000
79B342GLY0-0.006-0.0044.824-0.163-0.1630.0000.0000.0000.000
80B343LEU0-0.0040.0032.372-1.4660.2620.854-0.648-1.9330.003
81B344MET0-0.027-0.0174.0920.2430.4590.002-0.041-0.1760.000
82B345TRP00.0020.0097.381-0.029-0.0290.0000.0000.0000.000
83B346ARG10.8230.9272.294-3.432-3.9324.151-1.273-2.3770.016
84B347SER00.0360.0007.398-0.052-0.0520.0000.0000.0000.000
85B348ILE0-0.0320.0019.8640.0870.0870.0000.0000.0000.000
86B349ASP-1-0.928-0.95312.5690.3060.3060.0000.0000.0000.000
87B350HIS00.020-0.01513.091-0.065-0.0650.0000.0000.0000.000
88B351PRO0-0.054-0.03614.0550.1490.1490.0000.0000.0000.000
89B352GLY00.0010.00013.830-0.113-0.1130.0000.0000.0000.000
90B353LYS10.9650.99011.073-0.290-0.2900.0000.0000.0000.000
91B354LEU0-0.026-0.0085.3210.2780.2780.0000.0000.0000.000
92B355ILE0-0.0020.0107.808-0.439-0.4390.0000.0000.0000.000
93B356PHE00.0240.0072.490-5.791-1.4883.103-1.496-5.9110.003
94B357ALA00.0410.0203.766-1.180-0.8120.019-0.130-0.2570.000
95B358PRO0-0.020-0.0186.5600.5670.5670.0000.0000.0000.000
96B359ASP-1-0.818-0.9199.975-2.438-2.4380.0000.0000.0000.000
97B360LEU0-0.022-0.0065.753-0.190-0.1900.0000.0000.0000.000
98B361VAL0-0.021-0.0047.8780.0690.0690.0000.0000.0000.000
99B362LEU00.0310.0265.672-0.137-0.1370.0000.0000.0000.000
100B363ASP-1-0.860-0.9468.4700.8510.8510.0000.0000.0000.000
101B364ARG10.9560.9819.300-1.278-1.2780.0000.0000.0000.000
102B365ASP-1-0.909-0.93711.1190.5300.5300.0000.0000.0000.000
103B366GLU-1-0.932-0.9799.505-0.244-0.2440.0000.0000.0000.000
104B367GLY00.0570.0186.748-0.187-0.1870.0000.0000.0000.000
105B368LYS10.7920.8817.541-0.575-0.5750.0000.0000.0000.000
106B369CYS0-0.091-0.0259.060-0.023-0.0230.0000.0000.0000.000
107B370VAL00.0300.0235.224-0.214-0.2140.0000.0000.0000.000
108B371GLU-1-0.954-0.9848.0721.1611.1610.0000.0000.0000.000
109B372GLY00.0910.0477.2590.1200.1200.0000.0000.0000.000
110B373ILE0-0.049-0.0142.397-0.062-0.1395.402-0.744-4.5810.000
111B374LEU0-0.027-0.0264.3101.0041.1350.000-0.021-0.1090.000
112B375GLU-1-0.896-0.9426.9242.4962.4960.0000.0000.0000.000
113B376ILE00.0210.0092.922-2.770-0.2830.390-0.826-2.0510.008
114B377PHE00.004-0.0102.0310.096-0.5673.016-0.539-1.8140.000
115B378ASP-1-0.898-0.9415.9401.7891.7890.0000.0000.0000.000
116B379MET0-0.041-0.0097.884-0.152-0.1520.0000.0000.0000.000
117B380LEU00.0580.0413.447-1.779-0.9430.020-0.166-0.6900.001
118B381LEU00.0120.0438.064-0.966-0.9660.0000.0000.0000.000
119B382ALA0-0.0060.01810.978-0.488-0.4880.0000.0000.0000.000
120B383THR0-0.011-0.04310.379-0.443-0.4430.0000.0000.0000.000
121B384THR0-0.015-0.0389.933-0.338-0.3380.0000.0000.0000.000
122B385SER0-0.113-0.07511.811-0.396-0.3960.0000.0000.0000.000
123B386ARG10.8790.93815.294-1.236-1.2360.0000.0000.0000.000
124B387PHE00.0510.02011.297-0.186-0.1860.0000.0000.0000.000
125B388ARG10.9120.95713.937-1.063-1.0630.0000.0000.0000.000
126B389GLU-1-0.910-0.94516.8320.8210.8210.0000.0000.0000.000
127B390LEU0-0.034-0.01018.375-0.073-0.0730.0000.0000.0000.000
128B391LYS10.9330.97918.993-0.506-0.5060.0000.0000.0000.000
129B392LEU00.0030.02013.218-0.043-0.0430.0000.0000.0000.000
130B393GLN00.0220.00716.815-0.080-0.0800.0000.0000.0000.000
131B394HIS00.0620.02313.7940.1120.1120.0000.0000.0000.000
132B395LYS10.9790.97515.7760.0480.0480.0000.0000.0000.000
133B396GLU-1-0.726-0.83617.7300.4040.4040.0000.0000.0000.000
134B397TYR00.0450.0158.7090.0880.0880.0000.0000.0000.000
135B398LEU0-0.0170.00513.3520.0700.0700.0000.0000.0000.000
136B399CYS0-0.036-0.00414.6630.0040.0040.0000.0000.0000.000
137B400VAL00.0550.02112.4210.0550.0550.0000.0000.0000.000
138B401LYS10.9050.9646.8810.8530.8530.0000.0000.0000.000
139B402ALA00.0510.02111.8690.0960.0960.0000.0000.0000.000
140B403MET0-0.028-0.01714.7880.0460.0460.0000.0000.0000.000
141B404ILE0-0.039-0.0109.7500.0130.0130.0000.0000.0000.000
142B405LEU00.010-0.00912.7980.1470.1470.0000.0000.0000.000
143B406LEU0-0.027-0.00813.8370.0030.0030.0000.0000.0000.000
144B407ASN00.014-0.01516.502-0.143-0.1430.0000.0000.0000.000
145B408SER0-0.036-0.01213.750-0.010-0.0100.0000.0000.0000.000
146B409SER00.0230.00315.413-0.006-0.0060.0000.0000.0000.000
147B410MET00.0190.02718.135-0.086-0.0860.0000.0000.0000.000
148B411TYR00.0400.01619.763-0.028-0.0280.0000.0000.0000.000
149B412PRO00.0190.01217.798-0.059-0.0590.0000.0000.0000.000
150B413LEU00.0120.02221.013-0.051-0.0510.0000.0000.0000.000
151B414VAL0-0.009-0.01223.708-0.046-0.0460.0000.0000.0000.000
152B415THR0-0.057-0.03723.358-0.031-0.0310.0000.0000.0000.000
153B416ALA0-0.0010.00723.875-0.023-0.0230.0000.0000.0000.000
154B417THR0-0.080-0.03525.853-0.052-0.0520.0000.0000.0000.000
155B418GLN0-0.045-0.02326.639-0.055-0.0550.0000.0000.0000.000
156B419ASP-1-0.833-0.90028.5210.2380.2380.0000.0000.0000.000
157B420ALA00.0170.01029.177-0.026-0.0260.0000.0000.0000.000
158B421ASP-1-0.804-0.91230.6570.1120.1120.0000.0000.0000.000
159B422SER0-0.068-0.05124.6680.0010.0010.0000.0000.0000.000
160B423SER00.014-0.01425.6500.0200.0200.0000.0000.0000.000
161B424ARG10.8400.89926.723-0.206-0.2060.0000.0000.0000.000
162B425LYS10.8760.94027.342-0.048-0.0480.0000.0000.0000.000
163B426LEU00.0200.02120.344-0.014-0.0140.0000.0000.0000.000
164B427ALA00.0110.00223.7330.0240.0240.0000.0000.0000.000
165B428HIS0-0.046-0.01425.9110.0100.0100.0000.0000.0000.000
166B429LEU00.0300.00821.0240.0020.0020.0000.0000.0000.000
167B430LEU00.0160.01619.461-0.005-0.0050.0000.0000.0000.000
168B431ASN00.0080.00922.4880.0370.0370.0000.0000.0000.000
169B432ALA00.0190.03324.254-0.011-0.0110.0000.0000.0000.000
170B433VAL0-0.002-0.01118.229-0.024-0.0240.0000.0000.0000.000
171B434THR0-0.028-0.03321.3740.0400.0400.0000.0000.0000.000
172B435ASP-1-0.915-0.95823.0330.2150.2150.0000.0000.0000.000
173B436ALA0-0.093-0.04622.063-0.019-0.0190.0000.0000.0000.000
174B437LEU00.015-0.00218.548-0.021-0.0210.0000.0000.0000.000
175B438VAL00.011-0.01121.9780.0010.0010.0000.0000.0000.000
176B439TRP00.0070.00024.797-0.018-0.0180.0000.0000.0000.000
177B440VAL0-0.034-0.02620.715-0.019-0.0190.0000.0000.0000.000
178B441ILE0-0.0360.00721.4830.0030.0030.0000.0000.0000.000
179B442ALA0-0.0010.00424.995-0.004-0.0040.0000.0000.0000.000
180B443LYS10.8720.93126.689-0.085-0.0850.0000.0000.0000.000
181B444SER0-0.0090.00625.430-0.012-0.0120.0000.0000.0000.000
182B445GLY0-0.0360.00027.455-0.004-0.0040.0000.0000.0000.000
183B446ILE00.009-0.00527.0150.0070.0070.0000.0000.0000.000
184B447SER00.0230.00731.4540.0020.0020.0000.0000.0000.000
185B448SER00.037-0.00231.7910.0180.0180.0000.0000.0000.000
186B449GLN00.0270.02731.9590.0010.0010.0000.0000.0000.000
187B450GLN00.028-0.01129.4980.0500.0500.0000.0000.0000.000
188B451GLN00.0010.01827.6570.0270.0270.0000.0000.0000.000
189B452SER00.0280.00826.4820.0290.0290.0000.0000.0000.000
190B453MET0-0.039-0.02126.5110.0450.0450.0000.0000.0000.000
191B454ARG10.7510.84319.931-0.399-0.3990.0000.0000.0000.000
192B455LEU00.0050.00922.0570.0530.0530.0000.0000.0000.000
193B456ALA00.0620.01121.3820.0660.0660.0000.0000.0000.000
194B457ASN0-0.064-0.02421.1250.0310.0310.0000.0000.0000.000
195B458LEU00.0540.01616.9790.1120.1120.0000.0000.0000.000
196B459LEU0-0.017-0.00216.5110.1330.1330.0000.0000.0000.000
197B460MET0-0.033-0.01817.5270.1000.1000.0000.0000.0000.000
198B461LEU0-0.037-0.01814.3050.1280.1280.0000.0000.0000.000
199B462LEU00.0200.00712.0990.2810.2810.0000.0000.0000.000
200B463SER0-0.0140.01412.6780.2500.2500.0000.0000.0000.000
201B464HIS0-0.019-0.01413.2480.3570.3570.0000.0000.0000.000
202B465VAL00.0200.0227.6450.4940.4940.0000.0000.0000.000
203B466ARG10.8820.9388.743-1.822-1.8220.0000.0000.0000.000
204B467HIS0-0.028-0.0189.8120.3520.3520.0000.0000.0000.000
205B468ALA00.0530.0136.6210.1300.1300.0000.0000.0000.000
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