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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: PJ79X

Calculation Name: 2YLY-A-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: A

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 -3052461.382282
FMO2-HF: Nuclear repulsion 2955468.747027
FMO2-HF: Total energy -96992.635256
FMO2-MP2: Total energy -97263.674134


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.
-77.719-67.69689.991-26.138-73.8770.073


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


Summations of interaction energy for fragment #235(A: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.
-77.719-67.69689.991-26.138-73.877-0.073
Interaction energy analysis for fragmet #235(A:1499:SU4)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.074 / q_NPA : -0.051
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].
1A264SER10.8320.90129.739-0.002-0.0020.0000.0000.0000.000
2A265PRO00.1290.05226.313-0.026-0.0260.0000.0000.0000.000
3A266GLU-1-0.932-0.95925.050-0.036-0.0360.0000.0000.0000.000
4A267GLN00.0600.01825.365-0.005-0.0050.0000.0000.0000.000
5A268LEU00.0030.02022.061-0.041-0.0410.0000.0000.0000.000
6A269VAL00.0340.00419.947-0.027-0.0270.0000.0000.0000.000
7A270LEU0-0.017-0.00420.330-0.041-0.0410.0000.0000.0000.000
8A271THR00.0060.01321.014-0.043-0.0430.0000.0000.0000.000
9A272LEU00.023-0.00415.825-0.060-0.0600.0000.0000.0000.000
10A273LEU0-0.072-0.04016.349-0.069-0.0690.0000.0000.0000.000
11A274GLU-1-0.951-0.97316.632-0.462-0.4620.0000.0000.0000.000
12A275ALA0-0.053-0.02716.215-0.117-0.1170.0000.0000.0000.000
13A276GLU-1-0.934-0.97411.571-1.065-1.0650.0000.0000.0000.000
14A277PRO0-0.035-0.0058.3150.0050.0050.0000.0000.0000.000
15A278PRO0-0.0180.00110.0230.0100.0100.0000.0000.0000.000
16A279HIS00.012-0.0097.584-0.758-0.7580.0000.0000.0000.000
17A280VAL00.0020.0155.0810.6420.6420.0000.0000.0000.000
18A281LEU00.0090.0067.0290.1130.1130.0000.0000.0000.000
19A282ILE0-0.070-0.0527.370-0.295-0.2950.0000.0000.0000.000
20A283SER00.0260.02710.5470.3780.3780.0000.0000.0000.000
21A284ARG10.8710.92011.6660.9430.9430.0000.0000.0000.000
22A285PRO0-0.0020.03114.3980.1570.1570.0000.0000.0000.000
23A286SER0-0.054-0.05215.821-0.118-0.1180.0000.0000.0000.000
24A287ALA00.0390.03417.9170.0700.0700.0000.0000.0000.000
25A288PRO00.0300.00016.251-0.096-0.0960.0000.0000.0000.000
26A289PHE00.0620.03010.160-0.150-0.1500.0000.0000.0000.000
27A290THR0-0.009-0.00312.5890.0740.0740.0000.0000.0000.000
28A291GLU-1-0.826-0.9069.172-0.660-0.6600.0000.0000.0000.000
29A292ALA00.1030.0469.277-0.150-0.1500.0000.0000.0000.000
30A293SER0-0.095-0.0619.905-0.328-0.3280.0000.0000.0000.000
31A294MET00.0500.0266.516-0.366-0.3660.0000.0000.0000.000
32A295MET00.0470.0473.996-1.399-1.0950.000-0.023-0.2810.000
33A296MET00.0250.0065.720-0.924-0.9240.0000.0000.0000.000
34A297SER0-0.074-0.0427.784-0.133-0.1330.0000.0000.0000.000
35A298LEU00.0120.0112.097-3.233-1.9954.699-0.925-5.012-0.001
36A299THR00.010-0.0112.871-4.547-2.7070.207-0.694-1.353-0.005
37A300LYS10.9170.9664.3782.7902.9460.000-0.008-0.1470.000
38A301LEU0-0.055-0.0182.362-0.7930.7442.874-1.092-3.3190.008
39A302ALA00.0300.0132.183-3.421-2.6773.712-1.421-3.034-0.002
40A303ASP-1-0.880-0.9423.587-1.351-1.1090.0330.049-0.3240.000
41A304LYS10.9210.9546.5944.7234.7230.0000.0000.0000.000
42A305GLU-1-0.846-0.8931.605-42.466-47.33820.691-10.466-5.353-0.098
43A306LEU00.0320.0055.5551.7281.7280.0000.0000.0000.000
44A307VAL00.0370.0268.1640.7350.7350.0000.0000.0000.000
45A308HIS0-0.042-0.0307.9730.8130.8130.0000.0000.0000.000
46A309MET0-0.0170.0286.8790.5590.5590.0000.0000.0000.000
47A310ILE00.1040.06510.0780.4060.4060.0000.0000.0000.000
48A311SER0-0.115-0.06213.1880.2560.2560.0000.0000.0000.000
49A312TRP00.004-0.00711.6200.1640.1640.0000.0000.0000.000
50A313ALA00.016-0.00213.6030.1570.1570.0000.0000.0000.000
51A314LYS10.9050.94115.3570.7770.7770.0000.0000.0000.000
52A315LYS10.8990.95514.8181.0651.0650.0000.0000.0000.000
53A316ILE00.0110.03415.4570.0430.0430.0000.0000.0000.000
54A317PRO0-0.022-0.02819.2820.0190.0190.0000.0000.0000.000
55A318GLY00.0410.01723.1110.0520.0520.0000.0000.0000.000
56A319PHE0-0.009-0.00317.0320.0260.0260.0000.0000.0000.000
57A320VAL00.0280.00021.3840.0160.0160.0000.0000.0000.000
58A321GLU-1-0.931-0.95323.588-0.120-0.1200.0000.0000.0000.000
59A322LEU0-0.060-0.02021.4720.0320.0320.0000.0000.0000.000
60A323SER00.0310.03024.980-0.046-0.0460.0000.0000.0000.000
61A324LEU00.0610.02322.3670.0140.0140.0000.0000.0000.000
62A325PHE00.0040.00921.1640.0270.0270.0000.0000.0000.000
63A326ASP-1-0.854-0.93220.2750.2970.2970.0000.0000.0000.000
64A327GLN0-0.071-0.04919.0570.0160.0160.0000.0000.0000.000
65A328VAL00.0300.02415.8840.0200.0200.0000.0000.0000.000
66A329ARG10.9270.97015.351-0.445-0.4450.0000.0000.0000.000
67A330LEU0-0.081-0.02215.4120.1660.1660.0000.0000.0000.000
68A331LEU00.0190.00112.1410.2080.2080.0000.0000.0000.000
69A332GLU-1-0.815-0.93011.0150.6210.6210.0000.0000.0000.000
70A333SER0-0.056-0.03410.5790.4400.4400.0000.0000.0000.000
71A334CYS0-0.063-0.0269.4140.2370.2370.0000.0000.0000.000
72A335TRP00.0890.0482.6460.3531.2810.276-0.169-1.0350.000
73A336MET00.0100.0212.8890.3363.1071.517-0.852-3.4360.007
74A337GLU-1-0.872-0.9623.9315.8766.3490.008-0.079-0.4020.000
75A338VAL00.006-0.0086.408-0.479-0.4790.0000.0000.0000.000
76A339LEU0-0.016-0.0022.798-5.969-2.2082.675-1.350-5.0860.009
77A340MET0-0.029-0.0062.345-14.529-9.8046.359-2.950-8.1340.002
78A341MET0-0.036-0.0033.268-1.011-1.0460.0120.293-0.2700.000
79A342GLY00.0290.0154.684-0.422-0.322-0.001-0.009-0.0910.000
80A343LEU0-0.003-0.0031.950-1.488-0.8143.875-1.320-3.2290.007
81A344MET0-0.038-0.0123.6320.4170.6920.014-0.047-0.2430.000
82A345TRP0-0.010-0.0027.133-0.044-0.0440.0000.0000.0000.000
83A346ARG10.8120.9011.964-3.300-6.0018.241-2.273-3.2670.024
84A347SER0-0.011-0.0136.881-0.024-0.0240.0000.0000.0000.000
85A348ILE0-0.0190.0109.4280.1370.1370.0000.0000.0000.000
86A349ASP-1-0.924-0.95012.1570.3730.3730.0000.0000.0000.000
87A350HIS0-0.020-0.02411.914-0.113-0.1130.0000.0000.0000.000
88A351PRO0-0.024-0.02213.4480.1930.1930.0000.0000.0000.000
89A352GLY0-0.0080.00013.541-0.127-0.1270.0000.0000.0000.000
90A353LYS10.9530.98910.948-0.368-0.3680.0000.0000.0000.000
91A354LEU00.0080.0035.0560.2810.2810.0000.0000.0000.000
92A355ILE00.0010.0007.599-0.393-0.3930.0000.0000.0000.000
93A356PHE00.0590.0202.183-5.676-1.5833.684-1.785-5.992-0.001
94A357ALA00.0330.0163.505-1.002-0.4210.074-0.249-0.4060.000
95A358PRO0-0.024-0.0206.2890.5760.5760.0000.0000.0000.000
96A359ASP-1-0.896-0.9429.864-1.671-1.6710.0000.0000.0000.000
97A360LEU0-0.026-0.0268.3110.1980.1980.0000.0000.0000.000
98A361VAL0-0.028-0.0108.160-0.022-0.0220.0000.0000.0000.000
99A362LEU00.0050.0195.419-0.146-0.1460.0000.0000.0000.000
100A363ASP-1-0.786-0.9108.6711.1601.1600.0000.0000.0000.000
101A364ARG10.9020.9579.079-1.434-1.4340.0000.0000.0000.000
102A365ASP-1-1.015-1.02210.4450.8730.8730.0000.0000.0000.000
103A366GLU-1-0.892-0.9459.8600.0370.0370.0000.0000.0000.000
104A367GLY00.008-0.0037.228-0.213-0.2130.0000.0000.0000.000
105A368LYS10.9060.9407.811-0.733-0.7330.0000.0000.0000.000
106A369CYS0-0.098-0.0349.062-0.156-0.1560.0000.0000.0000.000
107A370VAL00.0290.0196.384-0.135-0.1350.0000.0000.0000.000
108A371GLU-1-0.944-0.9699.0150.9170.9170.0000.0000.0000.000
109A372GLY00.0160.0037.939-0.169-0.1690.0000.0000.0000.000
110A373ILE0-0.028-0.0132.718-1.180-0.3754.007-0.765-4.0480.007
111A374LEU0-0.023-0.0125.2740.8050.8050.0000.0000.0000.000
112A375GLU-1-0.888-0.9537.6402.7152.7150.0000.0000.0000.000
113A376ILE00.0190.0052.420-1.820-0.6952.966-0.763-3.3270.005
114A377PHE00.0240.0162.376-0.0550.3642.252-0.506-2.166-0.003
115A378ASP-1-0.833-0.9165.7491.9541.9540.0000.0000.0000.000
116A379MET0-0.057-0.0147.654-0.178-0.1780.0000.0000.0000.000
117A380LEU00.0490.0383.141-2.201-1.0290.100-0.320-0.9530.002
118A381LEU00.0230.0417.773-1.049-1.0490.0000.0000.0000.000
119A382ALA0-0.018-0.00310.631-0.535-0.5350.0000.0000.0000.000
120A383THR0-0.027-0.05010.213-0.507-0.5070.0000.0000.0000.000
121A384THR0-0.029-0.0399.666-0.352-0.3520.0000.0000.0000.000
122A385SER0-0.064-0.02811.629-0.405-0.4050.0000.0000.0000.000
123A386ARG11.0051.00315.161-1.326-1.3260.0000.0000.0000.000
124A387PHE00.018-0.00811.205-0.214-0.2140.0000.0000.0000.000
125A388ARG10.8880.95213.631-1.239-1.2390.0000.0000.0000.000
126A389GLU-1-0.938-0.97716.4420.7420.7420.0000.0000.0000.000
127A390LEU0-0.067-0.03517.855-0.106-0.1060.0000.0000.0000.000
128A391LYS10.9070.97818.828-0.594-0.5940.0000.0000.0000.000
129A392LEU0-0.0010.02513.072-0.054-0.0540.0000.0000.0000.000
130A393GLN00.0410.00816.444-0.037-0.0370.0000.0000.0000.000
131A394HIS00.0510.01713.2760.1360.1360.0000.0000.0000.000
132A395LYS10.9770.97415.5040.0520.0520.0000.0000.0000.000
133A396GLU-1-0.737-0.83817.4890.4400.4400.0000.0000.0000.000
134A397TYR00.0350.0098.4650.1050.1050.0000.0000.0000.000
135A398LEU0-0.027-0.00113.1770.0850.0850.0000.0000.0000.000
136A399CYS0-0.041-0.00714.5510.0070.0070.0000.0000.0000.000
137A400VAL00.0640.02512.4910.0570.0570.0000.0000.0000.000
138A401LYS10.9110.9607.9640.8690.8690.0000.0000.0000.000
139A402ALA00.0070.01412.0730.0860.0860.0000.0000.0000.000
140A403MET0-0.032-0.01715.1090.0420.0420.0000.0000.0000.000
141A404ILE0-0.042-0.01110.147-0.007-0.0070.0000.0000.0000.000
142A405LEU00.006-0.01012.9740.1300.1300.0000.0000.0000.000
143A406LEU0-0.039-0.01414.031-0.018-0.0180.0000.0000.0000.000
144A407ASN00.009-0.00916.813-0.163-0.1630.0000.0000.0000.000
145A408SER0-0.005-0.00513.651-0.015-0.0150.0000.0000.0000.000
146A409SER00.0180.00915.2670.0660.0660.0000.0000.0000.000
147A410MET0-0.067-0.00415.675-0.025-0.0250.0000.0000.0000.000
148A411TYR0-0.024-0.00411.808-0.130-0.1300.0000.0000.0000.000
149A412PRO0-0.018-0.01517.407-0.061-0.0610.0000.0000.0000.000
150A413LEU00.0580.04117.6730.0290.0290.0000.0000.0000.000
151A414VAL0-0.059-0.03619.856-0.005-0.0050.0000.0000.0000.000
152A415THR00.018-0.00822.337-0.016-0.0160.0000.0000.0000.000
153A416ALA0-0.0010.00424.7960.0100.0100.0000.0000.0000.000
154A417THR0-0.009-0.00928.2290.0020.0020.0000.0000.0000.000
155A418GLN0-0.086-0.06726.696-0.026-0.0260.0000.0000.0000.000
156A419ASP-1-0.785-0.85225.5230.0170.0170.0000.0000.0000.000
157A420ALA00.0160.00827.9460.0130.0130.0000.0000.0000.000
158A421ASP-1-0.800-0.92028.4220.1390.1390.0000.0000.0000.000
159A422SER0-0.0330.00227.830-0.003-0.0030.0000.0000.0000.000
160A423SER00.0530.01625.020-0.008-0.0080.0000.0000.0000.000
161A424ARG10.8000.87426.611-0.129-0.1290.0000.0000.0000.000
162A425LYS10.8880.94627.163-0.037-0.0370.0000.0000.0000.000
163A426LEU00.0440.03820.316-0.028-0.0280.0000.0000.0000.000
164A427ALA00.0160.00623.9720.0250.0250.0000.0000.0000.000
165A428HIS0-0.032-0.00926.1780.0210.0210.0000.0000.0000.000
166A429LEU00.017-0.00121.2820.0010.0010.0000.0000.0000.000
167A430LEU00.0300.02519.887-0.009-0.0090.0000.0000.0000.000
168A431ASN00.0070.00822.8400.0420.0420.0000.0000.0000.000
169A432ALA00.0110.03024.406-0.012-0.0120.0000.0000.0000.000
170A433VAL00.005-0.00918.336-0.028-0.0280.0000.0000.0000.000
171A434THR0-0.037-0.03621.4390.0450.0450.0000.0000.0000.000
172A435ASP-1-0.905-0.95523.2000.2210.2210.0000.0000.0000.000
173A436ALA0-0.087-0.04421.976-0.021-0.0210.0000.0000.0000.000
174A437LEU00.0180.00218.551-0.023-0.0230.0000.0000.0000.000
175A438VAL0-0.008-0.01421.9600.0020.0020.0000.0000.0000.000
176A439TRP00.0230.01124.354-0.025-0.0250.0000.0000.0000.000
177A440VAL0-0.029-0.02520.544-0.024-0.0240.0000.0000.0000.000
178A441ILE0-0.0150.00121.730-0.003-0.0030.0000.0000.0000.000
179A442ALA00.0000.00224.803-0.003-0.0030.0000.0000.0000.000
180A443LYS10.8720.93026.303-0.081-0.0810.0000.0000.0000.000
181A444SER0-0.0220.00225.026-0.013-0.0130.0000.0000.0000.000
182A445GLY0-0.0350.00127.055-0.003-0.0030.0000.0000.0000.000
183A446ILE00.008-0.00426.8210.0080.0080.0000.0000.0000.000
184A447SER00.0300.01231.2020.0010.0010.0000.0000.0000.000
185A448SER00.0680.01531.6800.0210.0210.0000.0000.0000.000
186A449GLN00.0210.02331.9910.0020.0020.0000.0000.0000.000
187A450GLN00.019-0.01629.4400.0530.0530.0000.0000.0000.000
188A451GLN0-0.0290.01127.5110.0330.0330.0000.0000.0000.000
189A452SER00.0280.01026.4610.0350.0350.0000.0000.0000.000
190A453MET0-0.039-0.02126.5140.0480.0480.0000.0000.0000.000
191A454ARG10.7750.85219.815-0.433-0.4330.0000.0000.0000.000
192A455LEU00.0060.00722.1080.0600.0600.0000.0000.0000.000
193A456ALA00.0600.01121.3890.0760.0760.0000.0000.0000.000
194A457ASN0-0.075-0.03220.9960.0380.0380.0000.0000.0000.000
195A458LEU00.0510.01717.0250.1200.1200.0000.0000.0000.000
196A459LEU0-0.0020.00416.5760.1450.1450.0000.0000.0000.000
197A460MET0-0.037-0.02117.7690.1010.1010.0000.0000.0000.000
198A461LEU0-0.049-0.02314.3110.1160.1160.0000.0000.0000.000
199A462LEU00.0340.01312.2890.3020.3020.0000.0000.0000.000
200A463SER0-0.0100.01613.0460.2570.2570.0000.0000.0000.000
201A464HIS0-0.030-0.01913.1390.3170.3170.0000.0000.0000.000
202A465VAL00.0110.0197.8150.4680.4680.0000.0000.0000.000
203A466ARG10.8700.9268.952-1.869-1.8690.0000.0000.0000.000
204A467HIS0-0.024-0.0199.7850.2670.2670.0000.0000.0000.000
205A468ALA00.0450.0106.4450.0040.0040.0000.0000.0000.000
206A469SER00.0540.0065.3711.0451.0450.0000.0000.0000.000
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