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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: Q86MY

Calculation Name: 1X76-A-Xray165

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-carbonitrile

ligand 3-letter code: 697

PDB ID: 1X76

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 -2962957.244183
FMO2-HF: Nuclear repulsion 2867783.663997
FMO2-HF: Total energy -95173.580186
FMO2-MP2: Total energy -95440.24005


3D Structure
Snapshot
 
Ligand structure

697

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.
-122.6452-105.673580.3273-39.3425-57.95650.1117


Interactive mode: IFIE and PIEDA for fragment #231(A:201:697 )


Summations of interaction energy for fragment #231(A:201:697 )
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.
-122.647-105.67680.323-39.341-57.958-0.095
Interaction energy analysis for fragmet #231(A:201:697 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.095 / 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 0-0.10125.855-0.011-0.0110.0000.0000.0000.000
2A267GLN 00.12625.244-0.003-0.0030.0000.0000.0000.000
3A268LEU 00.01022.304-0.021-0.0210.0000.0000.0000.000
4A269VAL 00.02319.918-0.011-0.0110.0000.0000.0000.000
5A270LEU 00.00920.261-0.006-0.0060.0000.0000.0000.000
6A271THR 00.02420.840-0.037-0.0370.0000.0000.0000.000
7A272LEU 0-0.01516.725-0.036-0.0360.0000.0000.0000.000
8A273LEU 0-0.01716.089-0.023-0.0230.0000.0000.0000.000
9A274GLU -1-0.95016.544-0.229-0.2290.0000.0000.0000.000
10A275ALA 0-0.06715.666-0.073-0.0730.0000.0000.0000.000
11A276GLU -1-0.85011.018-0.205-0.2050.0000.0000.0000.000
12A277PRO 0-0.0438.231-0.052-0.0520.0000.0000.0000.000
13A278PRO 0-0.00610.7550.1350.1350.0000.0000.0000.000
14A279HIS 00.0178.784-0.452-0.4520.0000.0000.0000.000
15A280VAL 0-0.0106.1370.1590.1590.0000.0000.0000.000
16A281LEU 0-0.0017.710-0.002-0.0020.0000.0000.0000.000
17A282ILE 0-0.0036.922-0.321-0.3210.0000.0000.0000.000
18A283SER 0-0.0779.5660.1240.1240.0000.0000.0000.000
19A284ARG 10.89611.6460.2280.2280.0000.0000.0000.000
20A285PRO 0-0.01514.0360.0990.0990.0000.0000.0000.000
21A286SER 0-0.00716.3210.0380.0380.0000.0000.0000.000
22A287ALA 00.05916.616-0.029-0.0290.0000.0000.0000.000
23A288PRO 00.00715.9840.0420.0420.0000.0000.0000.000
24A289PHE 00.02110.667-0.126-0.1260.0000.0000.0000.000
25A290THR 00.01013.2790.0170.0170.0000.0000.0000.000
26A291GLU -1-0.8448.466-0.690-0.6900.0000.0000.0000.000
27A292ALA 00.0128.895-0.133-0.1330.0000.0000.0000.000
28A293SER 0-0.01710.250-0.093-0.0930.0000.0000.0000.000
29A294MET 00.0127.1730.0130.0130.0000.0000.0000.000
30A295MET 00.0612.231-1.951-2.2654.145-1.107-2.7250.015
31A296MET 00.0025.604-0.888-0.8880.0000.0000.0000.000
32A297SER 0-0.0237.450-0.554-0.5540.0000.0000.0000.000
33A298LEU 0-0.0072.992-5.383-1.4541.062-1.074-3.9180.012
34A299THR 0-0.0072.643-8.886-5.9610.605-1.395-2.135-0.019
35A300LYS 10.9414.5801.6181.747-0.001-0.010-0.1180.000
36A301LEU 0-0.0682.161-0.2391.2841.308-0.698-2.1340.002
37A302ALA 00.0212.386-2.970-1.1211.035-0.904-1.9800.000
38A303ASP -1-0.8593.683-1.228-1.0660.0370.020-0.2190.000
39A304LYS 10.9066.7063.2713.2710.0000.0000.0000.000
40A305GLU -1-0.7831.485-41.737-55.69835.289-15.813-5.516-0.125
41A306LEU 00.0455.8401.2491.2490.0000.0000.0000.000
42A307VAL 00.0228.2450.6650.6650.0000.0000.0000.000
43A308HIS 0-0.0468.1860.6170.6170.0000.0000.0000.000
44A309MET 0-0.0356.9890.4790.4790.0000.0000.0000.000
45A310ILE 00.0489.7620.3700.3700.0000.0000.0000.000
46A311SER 0-0.07213.0700.2370.2370.0000.0000.0000.000
47A312TRP 0-0.01611.5370.1460.1460.0000.0000.0000.000
48A313ALA 00.07113.5720.1340.1340.0000.0000.0000.000
49A314LYS 10.91915.3060.6740.6740.0000.0000.0000.000
50A315LYS 10.89716.4000.6090.6090.0000.0000.0000.000
51A316ILE 0-0.00715.2210.0660.0660.0000.0000.0000.000
52A317PRO 0-0.03119.299-0.009-0.0090.0000.0000.0000.000
53A318GLY 00.05723.1190.0280.0280.0000.0000.0000.000
54A319PHE 00.04217.5760.0060.0060.0000.0000.0000.000
55A320VAL 0-0.01121.350-0.015-0.0150.0000.0000.0000.000
56A321GLU -1-0.96623.230-0.175-0.1750.0000.0000.0000.000
57A322LEU 0-0.09321.7360.0250.0250.0000.0000.0000.000
58A323SER 00.02625.463-0.034-0.0340.0000.0000.0000.000
59A324LEU 00.03522.664-0.002-0.0020.0000.0000.0000.000
60A325PHE 00.01522.914-0.029-0.0290.0000.0000.0000.000
61A326ASP -1-0.77422.891-0.122-0.1220.0000.0000.0000.000
62A327GLN 0-0.08719.822-0.035-0.0350.0000.0000.0000.000
63A328VAL 00.04718.304-0.022-0.0220.0000.0000.0000.000
64A329ARG 10.94117.7460.0480.0480.0000.0000.0000.000
65A330LEU 0-0.05717.1740.0270.0270.0000.0000.0000.000
66A331LEU 00.01512.6920.0580.0580.0000.0000.0000.000
67A332GLU -1-0.90113.088-0.555-0.5550.0000.0000.0000.000
68A333SER 0-0.07613.1530.0510.0510.0000.0000.0000.000
69A334CYS 0-0.06011.6790.1100.1100.0000.0000.0000.000
70A335TRP 00.0564.8300.2260.2260.0000.0000.0000.000
71A336MET 00.0483.251-1.4520.4680.334-0.457-1.7970.004
72A337GLU -1-0.8865.3161.6721.6720.0000.0000.0000.000
73A338VAL 0-0.0326.7180.3200.3200.0000.0000.0000.000
74A339LEU 0-0.0172.705-3.240-0.3342.897-1.474-4.3290.012
75A340MET 0-0.0322.659-0.5322.0211.441-1.229-2.765-0.011
76A341MET 0-0.0143.4940.4930.5440.0040.126-0.1810.000
77A342GLY 00.0075.365-0.249-0.2490.0000.0000.0000.000
78A343LEU 00.0092.583-2.555-0.6590.600-0.693-1.8040.005
79A344MET 0-0.0334.478-0.779-0.6170.000-0.020-0.1420.000
80A345TRP 0-0.0137.506-0.324-0.3240.0000.0000.0000.000
81A346ARG 10.7852.294-7.085-5.5131.446-1.189-1.8290.016
82A347SER 0-0.0027.517-0.120-0.1200.0000.0000.0000.000
83A348ILE 0-0.02410.208-0.050-0.0500.0000.0000.0000.000
84A349ASP -1-0.92912.9190.7620.7620.0000.0000.0000.000
85A350HIS 0-0.07413.151-0.128-0.1280.0000.0000.0000.000
86A351PRO 0-0.00714.0820.2720.2720.0000.0000.0000.000
87A352GLY 0-0.02213.762-0.131-0.1310.0000.0000.0000.000
88A353LYS 10.95311.861-1.074-1.0740.0000.0000.0000.000
89A354LEU 00.0135.382-0.0310.084-0.001-0.002-0.1110.000
90A355ILE 0-0.0198.438-0.248-0.2480.0000.0000.0000.000
91A356PHE 00.0252.977-5.553-1.2671.118-1.344-4.0590.017
92A357ALA 00.0394.405-2.381-2.244-0.001-0.017-0.1190.000
93A358PRO 0-0.0197.0880.5290.5290.0000.0000.0000.000
94A359ASP -1-0.80210.202-1.023-1.0230.0000.0000.0000.000
95A360LEU 0-0.0545.289-0.174-0.1740.0000.0000.0000.000
96A361VAL 0-0.0188.4050.5160.5160.0000.0000.0000.000
97A362LEU 00.0036.863-0.183-0.1830.0000.0000.0000.000
98A363ASP -1-0.81310.3871.9941.9940.0000.0000.0000.000
99A364ARG 10.9149.519-1.763-1.7630.0000.0000.0000.000
100A365ASP -1-0.95510.3711.4231.4230.0000.0000.0000.000
101A366GLU -1-0.93110.7910.9120.9120.0000.0000.0000.000
102A367GLY 00.0097.861-0.080-0.0800.0000.0000.0000.000
103A368LYS 10.8948.524-1.363-1.3630.0000.0000.0000.000
104A369CYS 0-0.10510.912-0.260-0.2600.0000.0000.0000.000
105A370VAL 00.0405.002-0.342-0.3420.0000.0000.0000.000
106A371GLU -1-0.8987.738-0.322-0.3220.0000.0000.0000.000
107A372GLY 00.0386.594-1.040-1.0400.0000.0000.0000.000
108A373ILE 0-0.0162.399-2.331-0.5732.087-0.773-3.0720.006
109A374LEU 0-0.0374.9753.1893.261-0.001-0.003-0.0690.000
110A375GLU -1-0.8887.6481.7901.7900.0000.0000.0000.000
111A376ILE 00.0512.672-1.158-0.5212.757-0.712-2.6810.009
112A377PHE 00.0182.973-1.958-0.1920.528-0.552-1.7420.008
113A378ASP -1-0.8065.2361.7301.771-0.001-0.003-0.0370.000
114A379MET 0-0.1056.761-0.661-0.6610.0000.0000.0000.000
115A380LEU 00.0232.990-2.262-1.4720.462-0.280-0.9720.004
116A381LEU 00.0207.252-1.206-1.2060.0000.0000.0000.000
117A382ALA 0-0.0209.852-0.688-0.6880.0000.0000.0000.000
118A383THR 0-0.00810.428-0.592-0.5920.0000.0000.0000.000
119A384THR 0-0.0149.411-0.397-0.3970.0000.0000.0000.000
120A385SER 0-0.03811.622-0.391-0.3910.0000.0000.0000.000
121A386ARG 10.95614.952-1.335-1.3350.0000.0000.0000.000
122A387PHE 00.04411.170-0.248-0.2480.0000.0000.0000.000
123A388ARG 10.90813.682-1.866-1.8660.0000.0000.0000.000
124A389GLU -1-0.97916.6430.9870.9870.0000.0000.0000.000
125A390LEU 0-0.07217.582-0.124-0.1240.0000.0000.0000.000
126A391LYS 10.95719.057-0.749-0.7490.0000.0000.0000.000
127A392LEU 0-0.01113.159-0.090-0.0900.0000.0000.0000.000
128A393GLN 0-0.03317.214-0.068-0.0680.0000.0000.0000.000
129A394HIS 00.05813.673-0.025-0.0250.0000.0000.0000.000
130A395LYS 11.00316.003-0.206-0.2060.0000.0000.0000.000
131A396GLU -1-0.72917.5140.5640.5640.0000.0000.0000.000
132A397TYR 0-0.0119.0120.0820.0820.0000.0000.0000.000
133A398LEU 0-0.01813.3990.0200.0200.0000.0000.0000.000
134A399CYS 0-0.04115.027-0.055-0.0550.0000.0000.0000.000
135A400VAL 00.03812.545-0.031-0.0310.0000.0000.0000.000
136A401LYS 10.8678.8490.0430.0430.0000.0000.0000.000
137A402ALA 00.01512.239-0.064-0.0640.0000.0000.0000.000
138A403MET 0-0.04015.256-0.033-0.0330.0000.0000.0000.000
139A404ILE 0-0.02210.124-0.023-0.0230.0000.0000.0000.000
140A405LEU 00.01913.517-0.031-0.0310.0000.0000.0000.000
141A406LEU 0-0.02614.534-0.045-0.0450.0000.0000.0000.000
142A407ASN 0-0.02617.127-0.078-0.0780.0000.0000.0000.000
143A408SER 0-0.04714.7240.0160.0160.0000.0000.0000.000
144A409SER 0-0.00516.807-0.064-0.0640.0000.0000.0000.000
145A410MET 0-0.01419.1870.0550.0550.0000.0000.0000.000
146A411TYR 00.02221.966-0.035-0.0350.0000.0000.0000.000
147A412PRO 00.00323.9130.0310.0310.0000.0000.0000.000
148A413LEU 00.03525.555-0.015-0.0150.0000.0000.0000.000
149A414VAL 0-0.06527.844-0.001-0.0010.0000.0000.0000.000
150A415THR 0-0.02227.973-0.023-0.0230.0000.0000.0000.000
151A416ALA 00.00530.2630.0150.0150.0000.0000.0000.000
152A417THR 0-0.02028.808-0.011-0.0110.0000.0000.0000.000
153A418GLN 0-0.00632.2320.0160.0160.0000.0000.0000.000
154A419ASP -1-0.81229.046-0.044-0.0440.0000.0000.0000.000
155A420ALA 0-0.04231.5470.0130.0130.0000.0000.0000.000
156A421ASP -1-0.96931.836-0.097-0.0970.0000.0000.0000.000
157A422SER 00.04726.5740.0000.0000.0000.0000.0000.000
158A423SER 00.02727.3250.0120.0120.0000.0000.0000.000
159A424ARG 10.95627.6250.0360.0360.0000.0000.0000.000
160A425LYS 10.92027.5970.1070.1070.0000.0000.0000.000
161A426LEU 00.05321.1860.0050.0050.0000.0000.0000.000
162A427ALA 00.00124.2480.0240.0240.0000.0000.0000.000
163A428HIS 0-0.01726.1860.0290.0290.0000.0000.0000.000
164A429LEU 00.01521.5830.0180.0180.0000.0000.0000.000
165A430LEU 00.01119.8900.0210.0210.0000.0000.0000.000
166A431ASN 0-0.04122.6090.0310.0310.0000.0000.0000.000
167A432ALA 00.05924.7030.0170.0170.0000.0000.0000.000
168A433VAL 0-0.01118.5410.0110.0110.0000.0000.0000.000
169A434THR 0-0.04021.7540.0530.0530.0000.0000.0000.000
170A435ASP -1-0.95522.9570.1790.1790.0000.0000.0000.000
171A436ALA 00.00022.2780.0030.0030.0000.0000.0000.000
172A437LEU 00.01919.0580.0130.0130.0000.0000.0000.000
173A438VAL 00.01522.0890.0220.0220.0000.0000.0000.000
174A439TRP 00.02724.4850.0010.0010.0000.0000.0000.000
175A440VAL 0-0.03721.221-0.007-0.0070.0000.0000.0000.000
176A441ILE 0-0.01422.1200.0070.0070.0000.0000.0000.000
177A442ALA 00.03525.1540.0000.0000.0000.0000.0000.000
178A443LYS 10.81726.962-0.214-0.2140.0000.0000.0000.000
179A444SER 0-0.07425.812-0.006-0.0060.0000.0000.0000.000
180A445GLY 00.01227.8280.0020.0020.0000.0000.0000.000
181A446ILE 0-0.01826.914-0.005-0.0050.0000.0000.0000.000
182A447SER 00.05530.980-0.015-0.0150.0000.0000.0000.000
183A448SER 00.08731.3440.0200.0200.0000.0000.0000.000
184A449GLN 00.01731.4940.0320.0320.0000.0000.0000.000
185A450GLN 00.02029.1040.0440.0440.0000.0000.0000.000
186A451GLN 0-0.01827.3600.0300.0300.0000.0000.0000.000
187A452SER 00.01026.4980.0160.0160.0000.0000.0000.000
188A453MET 0-0.01426.3850.0380.0380.0000.0000.0000.000
189A454ARG 10.75120.376-0.561-0.5610.0000.0000.0000.000
190A455LEU 00.02122.0030.0550.0550.0000.0000.0000.000
191A456ALA 00.02821.7010.0370.0370.0000.0000.0000.000
192A457ASN 0-0.01220.9250.0780.0780.0000.0000.0000.000
193A458LEU 0-0.01716.8770.1010.1010.0000.0000.0000.000
194A459LEU 00.02116.7690.0930.0930.0000.0000.0000.000
195A460MET 0-0.03917.8370.0330.0330.0000.0000.0000.000
196A461LEU 0-0.01314.2400.0640.0640.0000.0000.0000.000
197A462LEU 00.02412.5530.2250.2250.0000.0000.0000.000
198A463SER 0-0.01013.4180.0290.0290.0000.0000.0000.000
199A464HIS 00.00312.539-0.002-0.0020.0000.0000.0000.000
200A465VAL 00.0008.0120.4600.4600.0000.0000.0000.000
201A466ARG 10.9949.093-0.355-0.3550.0000.0000.0000.000
202A467HIS 0-0.06010.467-0.389-0.3890.0000.0000.0000.000
203A468ALA 00.0446.031-0.144-0.1440.0000.0000.0000.000
204A469SER 0-0.0036.0680.7270.7270.0000.0000.0000.000
205A470ASN 00.0387.825-0.338-0.3380.0000.0000.0000.000
206A471LYS 10.9456.921-1.298-1.2980.0000.0000.0000.000
207A472GLY 00.0333.717-1.556-0.9870.034-0.188-0.4150.001
208A473MET 00.0204.008-2.806-1.8900.053-0.187-0.7830.000
209A474GLU -1-0.9496.350-0.877-0.8770.0000.0000.0000.000
210A475HIS 0-0.0101.772-24.433-29.59517.999-7.029-5.808-0.068
211A476LEU 00.0452.190-3.0310.0422.257-1.218-4.1120.005
212A477LEU 00.0213.461-0.275-0.2850.1110.305-0.4060.003
213A478ASN 00.0126.2570.4910.4910.0000.0000.0000.000
214A479MET 0-0.0253.386-0.2140.4290.025-0.225-0.4430.001
215A480LYS 10.9796.3011.2831.2830.0000.0000.0000.000
216A481CYS 0-0.0578.6360.1450.1450.0000.0000.0000.000
217A482LYS 10.8808.9421.2471.2470.0000.0000.0000.000
218A483ASN 0-0.07311.0120.0800.0800.0000.0000.0000.000
219A484VAL 0-0.0018.1930.0550.0550.0000.0000.0000.000
220A485VAL 0-0.0525.2710.0770.0770.0000.0000.0000.000
221A486PRO 0-0.0328.5720.0510.0510.0000.0000.0000.000
222A487VAL 00.0279.616-0.193-0.1930.0000.0000.0000.000
223A488TYR 0-0.0128.410-0.025-0.0250.0000.0000.0000.000
224A489ASP -1-0.87510.903-1.328-1.3280.0000.0000.0000.000
225A490LEU 00.05610.7220.0610.0610.0000.0000.0000.000
226A491LEU 0-0.0104.897-0.092-0.0920.0000.0000.0000.000
227A492LEU 0-0.1028.7110.1720.1720.0000.0000.0000.000
228A493GLU -1-0.96510.702-0.800-0.8000.0000.0000.0000.000
229A494MET 0-0.0669.4150.1630.1630.0000.0000.0000.000
230A495LEU -1-0.9876.673-0.741-0.7410.0000.0000.0000.000
232A7HOH 0-0.0152.256-1.579-1.5412.694-1.196-1.5370.008