FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8JM7Y

Calculation Name: 3OLS-A-Xray165

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 3OLS

Chain ID: A

ChEMBL ID: CHEMBL242

UniProt ID: Q92731

Base Structure: X-ray

Registration Date: 2020-10-14

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Water(s) essential for molecular recognition.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2968996.139744
FMO2-HF: Nuclear repulsion 2873830.398229
FMO2-HF: Total energy -95165.741515
FMO2-MP2: Total energy -95432.711168


3D Structure
Snapshot
 
Ligand structure

EST

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy (frag 1-230,232 : frag 231)
"
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.
-111.9638-92.894987.8312-39.3506-67.54950.1468


Interactive mode: IFIE and PIEDA for fragment #231(A:600:EST )


Summations of interaction energy for fragment #231(A:600: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.
-111.966-92.89687.828-39.354-67.55-0.125
Interaction energy analysis for fragmet #231(A:600:EST )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.127 / 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].
1A266GLU 0-0.09626.560-0.024-0.0240.0000.0000.0000.000
2A267GLN 00.14525.5320.0170.0170.0000.0000.0000.000
3A268LEU 0-0.00421.9700.0000.0000.0000.0000.0000.000
4A269VAL 00.03120.7880.0090.0090.0000.0000.0000.000
5A270LEU 0-0.01820.5400.0290.0290.0000.0000.0000.000
6A271THR 00.05820.646-0.004-0.0040.0000.0000.0000.000
7A272LEU 0-0.03416.953-0.002-0.0020.0000.0000.0000.000
8A273LEU 0-0.03116.3040.0280.0280.0000.0000.0000.000
9A274GLU -1-0.96016.7780.1590.1590.0000.0000.0000.000
10A275ALA 0-0.05415.765-0.032-0.0320.0000.0000.0000.000
11A276GLU -1-0.83311.1520.7480.7480.0000.0000.0000.000
12A277PRO 0-0.0488.450-0.070-0.0700.0000.0000.0000.000
13A278PRO 0-0.00110.3180.0950.0950.0000.0000.0000.000
14A279HIS 00.0297.770-0.067-0.0670.0000.0000.0000.000
15A280VAL 0-0.0125.7370.0660.0660.0000.0000.0000.000
16A281LEU 0-0.0257.3790.0850.0850.0000.0000.0000.000
17A282ILE 0-0.0406.443-0.174-0.1740.0000.0000.0000.000
18A283SER 00.0429.5810.1440.1440.0000.0000.0000.000
19A284ARG 10.77711.683-0.298-0.2980.0000.0000.0000.000
20A285PRO 0-0.00911.723-0.017-0.0170.0000.0000.0000.000
21A286SER 0-0.00714.8320.0380.0380.0000.0000.0000.000
22A287ALA 0-0.02317.3460.0160.0160.0000.0000.0000.000
23A288PRO 00.02316.1730.0010.0010.0000.0000.0000.000
24A289PHE 0-0.0139.980-0.017-0.0170.0000.0000.0000.000
25A290THR 00.02312.259-0.007-0.0070.0000.0000.0000.000
26A291GLU -1-0.7758.271-1.004-1.0040.0000.0000.0000.000
27A292ALA 00.0678.469-0.028-0.0280.0000.0000.0000.000
28A293SER 0-0.0339.3140.0270.0270.0000.0000.0000.000
29A294MET 00.0326.176-0.032-0.0320.0000.0000.0000.000
30A295MET 00.0392.348-4.731-3.0792.493-1.254-2.8920.018
31A296MET 0-0.0045.147-0.0420.093-0.001-0.003-0.1310.000
32A297SER 0-0.0177.108-0.200-0.2000.0000.0000.0000.000
33A298LEU 00.0102.250-3.752-1.1853.285-1.059-4.7930.002
34A299THR 00.0142.439-8.254-4.9182.471-1.773-4.035-0.029
35A300LYS 10.8274.0010.7820.9870.001-0.012-0.1950.000
36A301LEU 00.0012.218-1.0550.5381.173-0.639-2.1280.003
37A302ALA 00.0642.361-3.048-0.9091.970-1.215-2.8950.003
38A303ASP -1-0.8143.538-0.0060.0990.0510.088-0.2440.001
39A304LYS 10.9056.4681.3311.3310.0000.0000.0000.000
40A305GLU -1-0.7571.428-33.766-53.19942.890-18.333-5.124-0.122
41A306LEU 00.0355.6990.7920.7920.0000.0000.0000.000
42A307VAL 0-0.0138.1330.2670.2670.0000.0000.0000.000
43A308HIS 0-0.0628.5780.2910.2910.0000.0000.0000.000
44A309MET 0-0.0047.0450.1570.1570.0000.0000.0000.000
45A310ILE 00.0359.8640.1320.1320.0000.0000.0000.000
46A311SER 0-0.03713.2950.0530.0530.0000.0000.0000.000
47A312TRP 0-0.02911.5480.0670.0670.0000.0000.0000.000
48A313ALA 00.05713.5560.0280.0280.0000.0000.0000.000
49A314LYS 10.90815.2270.0120.0120.0000.0000.0000.000
50A315LYS 10.94515.859-0.061-0.0610.0000.0000.0000.000
51A316ILE 0-0.01615.2650.0130.0130.0000.0000.0000.000
52A317PRO 00.01219.297-0.021-0.0210.0000.0000.0000.000
53A318GLY 0-0.01123.1990.0110.0110.0000.0000.0000.000
54A319PHE 00.06117.626-0.008-0.0080.0000.0000.0000.000
55A320VAL 0-0.01421.139-0.008-0.0080.0000.0000.0000.000
56A321GLU -1-0.93923.1470.0570.0570.0000.0000.0000.000
57A322LEU 0-0.07721.982-0.002-0.0020.0000.0000.0000.000
58A323SER 00.02925.500-0.010-0.0100.0000.0000.0000.000
59A324LEU 00.07122.9740.0080.0080.0000.0000.0000.000
60A325PHE 00.02122.4580.0040.0040.0000.0000.0000.000
61A326ASP -1-0.80521.7320.0890.0890.0000.0000.0000.000
62A327GLN 0-0.07119.6980.0130.0130.0000.0000.0000.000
63A328VAL 00.02817.7770.0230.0230.0000.0000.0000.000
64A329ARG 10.88816.660-0.059-0.0590.0000.0000.0000.000
65A330LEU 0-0.04916.6150.0170.0170.0000.0000.0000.000
66A331LEU 0-0.00612.7940.0550.0550.0000.0000.0000.000
67A332GLU -1-0.91112.3590.1270.1270.0000.0000.0000.000
68A333SER 0-0.09911.7040.0240.0240.0000.0000.0000.000
69A334CYS 0-0.04211.0980.0350.0350.0000.0000.0000.000
70A335TRP 00.0844.356-0.0840.2370.000-0.009-0.3120.000
71A336MET 00.0402.457-1.505-0.3992.684-0.544-3.246-0.001
72A337GLU -1-0.8614.5800.9801.121-0.001-0.009-0.1310.000
73A338VAL 0-0.0266.8880.3290.3290.0000.0000.0000.000
74A339LEU 0-0.0312.766-3.439-0.1562.013-1.312-3.9830.012
75A340MET 0-0.0462.418-0.9661.5672.282-1.265-3.550-0.009
76A341MET 00.0143.723-0.181-0.0350.0050.041-0.1920.000
77A342GLY 0-0.0015.622-0.415-0.4150.0000.0000.0000.000
78A343LEU 0-0.0112.344-3.116-1.2762.523-0.971-3.3920.004
79A344MET 0-0.0244.388-1.444-1.2960.000-0.030-0.1180.000
80A345TRP 00.0077.399-0.435-0.4350.0000.0000.0000.000
81A346ARG 10.7742.294-11.161-9.0841.277-1.356-1.9990.019
82A347SER 0-0.0037.406-0.272-0.2720.0000.0000.0000.000
83A348ILE 0-0.03110.069-0.242-0.2420.0000.0000.0000.000
84A349ASP -1-0.91712.6870.5080.5080.0000.0000.0000.000
85A350HIS 0-0.05213.016-0.138-0.1380.0000.0000.0000.000
86A351PRO 00.02213.2740.0800.0800.0000.0000.0000.000
87A352GLY 0-0.02913.598-0.036-0.0360.0000.0000.0000.000
88A353LYS 10.91111.228-0.572-0.5720.0000.0000.0000.000
89A354LEU 0-0.0014.795-0.0520.089-0.001-0.003-0.1380.000
90A355ILE 0-0.0148.161-0.165-0.1650.0000.0000.0000.000
91A356PHE 00.0392.514-4.772-1.1233.363-1.335-5.6770.015
92A357ALA 00.0654.893-0.699-0.596-0.001-0.008-0.0950.000
93A358PRO 0-0.0627.6670.0970.0970.0000.0000.0000.000
94A359ASP -1-0.86111.1890.1130.1130.0000.0000.0000.000
95A360LEU 0-0.0606.381-0.124-0.1240.0000.0000.0000.000
96A361VAL 0-0.0178.9720.4320.4320.0000.0000.0000.000
97A362LEU 0-0.0136.505-0.227-0.2270.0000.0000.0000.000
98A363ASP -1-0.8169.9840.5560.5560.0000.0000.0000.000
99A364ARG 10.84610.107-0.097-0.0970.0000.0000.0000.000
100A365ASP -1-0.88410.923-0.067-0.0670.0000.0000.0000.000
101A366GLU -1-0.76310.6240.1530.1530.0000.0000.0000.000
102A367GLY 00.0488.154-0.096-0.0960.0000.0000.0000.000
103A368LYS 10.8418.917-0.145-0.1450.0000.0000.0000.000
104A369CYS 0-0.0799.452-0.015-0.0150.0000.0000.0000.000
105A370VAL 00.0054.706-0.0880.019-0.001-0.003-0.1030.000
106A371GLU -1-0.9337.745-1.258-1.2580.0000.0000.0000.000
107A372GLY 00.0416.821-0.592-0.5920.0000.0000.0000.000
108A373ILE 0-0.0162.365-1.958-0.5341.623-0.396-2.6510.000
109A374LEU 0-0.0295.0460.4860.588-0.001-0.002-0.1000.000
110A375GLU -1-0.9008.069-0.403-0.4030.0000.0000.0000.000
111A376ILE 00.0392.558-1.1720.0940.877-0.304-1.8390.000
112A377PHE 0-0.0043.543-0.1300.5710.010-0.091-0.6190.000
113A378ASP -1-0.7896.3950.3270.3270.0000.0000.0000.000
114A379MET 0-0.0536.8160.1390.1390.0000.0000.0000.000
115A380LEU 00.0142.588-0.8670.0760.385-0.205-1.1230.000
116A381LEU 00.0307.0550.0740.0740.0000.0000.0000.000
117A382ALA 0-0.0359.811-0.024-0.0240.0000.0000.0000.000
118A383THR 0-0.0339.309-0.066-0.0660.0000.0000.0000.000
119A384THR 00.0158.4360.0680.0680.0000.0000.0000.000
120A385SER 0-0.02011.026-0.070-0.0700.0000.0000.0000.000
121A386ARG 10.96314.177-0.393-0.3930.0000.0000.0000.000
122A387PHE 00.02910.994-0.066-0.0660.0000.0000.0000.000
123A388ARG 10.87913.369-0.733-0.7330.0000.0000.0000.000
124A389GLU -1-1.00516.6250.2810.2810.0000.0000.0000.000
125A390LEU 0-0.06517.667-0.047-0.0470.0000.0000.0000.000
126A391LYS 10.96319.355-0.337-0.3370.0000.0000.0000.000
127A392LEU 0-0.02513.504-0.033-0.0330.0000.0000.0000.000
128A393GLN 0-0.01917.523-0.002-0.0020.0000.0000.0000.000
129A394HIS 00.04714.009-0.034-0.0340.0000.0000.0000.000
130A395LYS 10.99216.533-0.250-0.2500.0000.0000.0000.000
131A396GLU -1-0.74118.2160.3820.3820.0000.0000.0000.000
132A397TYR 0-0.0129.4120.1000.1000.0000.0000.0000.000
133A398LEU 0-0.02513.7740.0460.0460.0000.0000.0000.000
134A399CYS 0-0.05715.479-0.029-0.0290.0000.0000.0000.000
135A400VAL 00.04613.017-0.021-0.0210.0000.0000.0000.000
136A401LYS 10.8788.959-0.946-0.9460.0000.0000.0000.000
137A402ALA 00.02412.560-0.021-0.0210.0000.0000.0000.000
138A403MET 0-0.04615.519-0.051-0.0510.0000.0000.0000.000
139A404ILE 0-0.01310.342-0.034-0.0340.0000.0000.0000.000
140A405LEU 0-0.03413.854-0.040-0.0400.0000.0000.0000.000
141A406LEU 0-0.03214.679-0.058-0.0580.0000.0000.0000.000
142A407ASN 0-0.02617.022-0.068-0.0680.0000.0000.0000.000
143A408SER 00.04015.7110.0090.0090.0000.0000.0000.000
144A409SER 0-0.06417.696-0.021-0.0210.0000.0000.0000.000
145A410MET 00.04019.8660.0040.0040.0000.0000.0000.000
146A411TYR 00.00520.050-0.003-0.0030.0000.0000.0000.000
147A412PRO 00.02524.5820.0020.0020.0000.0000.0000.000
148A413LEU 00.05622.382-0.006-0.0060.0000.0000.0000.000
149A414VAL 00.01926.5590.0010.0010.0000.0000.0000.000
150A415THR 00.02226.562-0.004-0.0040.0000.0000.0000.000
151A416ALA 00.00929.366-0.005-0.0050.0000.0000.0000.000
152A417THR 0-0.07331.4830.0050.0050.0000.0000.0000.000
153A418GLN 0-0.03529.818-0.003-0.0030.0000.0000.0000.000
154A419ASP -1-0.94532.6610.0320.0320.0000.0000.0000.000
155A420ALA 00.08734.4160.0020.0020.0000.0000.0000.000
156A421ASP -1-0.97232.1740.0670.0670.0000.0000.0000.000
157A422SER 0-0.03526.6460.0060.0060.0000.0000.0000.000
158A423SER 00.05526.9390.0100.0100.0000.0000.0000.000
159A424ARG 10.95827.767-0.071-0.0710.0000.0000.0000.000
160A425LYS 10.90826.338-0.086-0.0860.0000.0000.0000.000
161A426LEU 00.02821.3160.0090.0090.0000.0000.0000.000
162A427ALA 0-0.00624.6720.0160.0160.0000.0000.0000.000
163A428HIS 0-0.02326.4930.0110.0110.0000.0000.0000.000
164A429LEU 00.02421.8850.0080.0080.0000.0000.0000.000
165A430LEU 00.04420.0950.0180.0180.0000.0000.0000.000
166A431ASN 0-0.04222.8400.0170.0170.0000.0000.0000.000
167A432ALA 00.06525.4080.0050.0050.0000.0000.0000.000
168A433VAL 0-0.04318.8350.0090.0090.0000.0000.0000.000
169A434THR 0-0.01722.2500.0240.0240.0000.0000.0000.000
170A435ASP -1-0.89623.3160.1710.1710.0000.0000.0000.000
171A436ALA 0-0.09222.686-0.001-0.0010.0000.0000.0000.000
172A437LEU 00.02919.4120.0080.0080.0000.0000.0000.000
173A438VAL 00.03722.5920.0020.0020.0000.0000.0000.000
174A439TRP 00.00625.4400.0000.0000.0000.0000.0000.000
175A440VAL 0-0.07521.694-0.006-0.0060.0000.0000.0000.000
176A441ILE 00.00822.234-0.005-0.0050.0000.0000.0000.000
177A442ALA 00.01925.434-0.008-0.0080.0000.0000.0000.000
178A443LYS 10.85026.475-0.224-0.2240.0000.0000.0000.000
179A444SER 0-0.05326.765-0.009-0.0090.0000.0000.0000.000
180A445GLY 0-0.00428.781-0.007-0.0070.0000.0000.0000.000
181A446ILE 0-0.01427.592-0.011-0.0110.0000.0000.0000.000
182A447SER 00.03631.774-0.003-0.0030.0000.0000.0000.000
183A448SER 00.06332.0530.0110.0110.0000.0000.0000.000
184A449GLN 00.05731.8660.0020.0020.0000.0000.0000.000
185A450GLN 00.02729.102-0.001-0.0010.0000.0000.0000.000
186A451GLN 0-0.02827.7450.0210.0210.0000.0000.0000.000
187A452SER 00.01326.9770.0130.0130.0000.0000.0000.000
188A453MET 0-0.01825.7900.0120.0120.0000.0000.0000.000
189A454ARG 10.73820.605-0.344-0.3440.0000.0000.0000.000
190A455LEU 00.03022.2560.0300.0300.0000.0000.0000.000
191A456ALA 00.02321.9100.0210.0210.0000.0000.0000.000
192A457ASN 0-0.02920.7180.0030.0030.0000.0000.0000.000
193A458LEU 0-0.01417.3390.0320.0320.0000.0000.0000.000
194A459LEU 00.02317.1000.0390.0390.0000.0000.0000.000
195A460MET 0-0.03417.943-0.006-0.0060.0000.0000.0000.000
196A461LEU 0-0.02213.961-0.019-0.0190.0000.0000.0000.000
197A462LEU 00.00813.3550.0640.0640.0000.0000.0000.000
198A463SER 00.02713.0910.0110.0110.0000.0000.0000.000
199A464HIS 00.00012.170-0.036-0.0360.0000.0000.0000.000
200A465VAL 00.0237.829-0.015-0.0150.0000.0000.0000.000
201A466ARG 10.9528.601-0.296-0.2960.0000.0000.0000.000
202A467HIS 0-0.04810.026-0.102-0.1020.0000.0000.0000.000
203A468ALA 00.0555.967-0.147-0.1470.0000.0000.0000.000
204A469SER 00.0505.399-0.247-0.2470.0000.0000.0000.000
205A470ASN 0-0.0246.190-0.124-0.1240.0000.0000.0000.000
206A471LYS 10.9676.1080.3890.3890.0000.0000.0000.000
207A472GLY 00.0292.243-1.226-0.9061.855-0.933-1.2420.000
208A473MET 00.0172.677-1.696-0.3830.693-0.091-1.915-0.019
209A474GLU -1-0.9455.045-0.659-0.572-0.001-0.007-0.0790.000
210A475HIS 0-0.0322.124-15.156-13.1075.943-3.163-4.828-0.042
211A476LEU 00.0402.098-4.139-2.2405.752-2.072-5.5790.008
212A477LEU 00.0223.336-0.790-0.5140.1260.106-0.5080.002
213A478ASN 0-0.0236.3530.3660.3660.0000.0000.0000.000
214A479MET 0-0.0463.6930.2430.4910.001-0.035-0.2140.000
215A480LYS 10.9756.2770.0980.0980.0000.0000.0000.000
216A481CYS 0-0.0048.559-0.030-0.0300.0000.0000.0000.000
217A482LYS 10.88510.0510.5910.5910.0000.0000.0000.000
218A483ASN 0-0.03911.5700.0150.0150.0000.0000.0000.000
219A484VAL 0-0.0448.1180.0180.0180.0000.0000.0000.000
220A485VAL 0-0.0336.016-0.005-0.0050.0000.0000.0000.000
221A486PRO 0-0.0409.2390.0730.0730.0000.0000.0000.000
222A487VAL 00.0356.348-0.007-0.0070.0000.0000.0000.000
223A488TYR 0-0.0249.2580.0090.0090.0000.0000.0000.000
224A489ASP -1-0.88911.082-0.326-0.3260.0000.0000.0000.000
225A490LEU 00.04211.0820.0520.0520.0000.0000.0000.000
226A491LEU 00.0144.8710.0560.0560.0000.0000.0000.000
227A492LEU 0-0.0728.9010.1530.1530.0000.0000.0000.000
228A493GLU -1-0.98710.783-0.029-0.0290.0000.0000.0000.000
229A494MET 0-0.0829.2660.0110.0110.0000.0000.0000.000
230A495LEU -1-0.9975.6980.2140.2140.0000.0000.0000.000
232A228HOH 0-0.0222.307-3.022-2.4742.089-1.157-1.4800.010