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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: R12M8

Calculation Name: 1X78-A-Xray165

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: [5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]acetonitrile

ligand 3-letter code: 244

PDB ID: 1X78

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 -2978547.261354
FMO2-HF: Nuclear repulsion 2883334.635477
FMO2-HF: Total energy -95212.625878
FMO2-MP2: Total energy -95479.545676


3D Structure
Snapshot
 
Ligand structure

244

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.
-122.7890-108.510991.1702-41.5918-63.85650.1227


Interactive mode: IFIE and PIEDA for fragment #231(A:201:244 )


Summations of interaction energy for fragment #231(A:201:244 )
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.
-122.79-108.51191.171-41.594-63.857-0.112
Interaction energy analysis for fragmet #231(A:201:244 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.110 / 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 0-0.08725.7970.0070.0070.0000.0000.0000.000
2A267GLN 00.12725.1740.0100.0100.0000.0000.0000.000
3A268LEU 00.01821.846-0.011-0.0110.0000.0000.0000.000
4A269VAL 00.02220.170-0.006-0.0060.0000.0000.0000.000
5A270LEU 00.00220.2130.0060.0060.0000.0000.0000.000
6A271THR 00.00720.845-0.018-0.0180.0000.0000.0000.000
7A272LEU 0-0.00916.760-0.028-0.0280.0000.0000.0000.000
8A273LEU 0-0.01916.142-0.009-0.0090.0000.0000.0000.000
9A274GLU -1-0.94116.464-0.081-0.0810.0000.0000.0000.000
10A275ALA 0-0.07115.678-0.057-0.0570.0000.0000.0000.000
11A276GLU -1-0.86811.1210.0400.0400.0000.0000.0000.000
12A277PRO 0-0.0518.332-0.052-0.0520.0000.0000.0000.000
13A278PRO 0-0.01310.6470.1300.1300.0000.0000.0000.000
14A279HIS 00.0158.785-0.350-0.3500.0000.0000.0000.000
15A280VAL 0-0.0036.1370.1120.1120.0000.0000.0000.000
16A281LEU 00.0077.5930.0310.0310.0000.0000.0000.000
17A282ILE 0-0.0076.826-0.314-0.3140.0000.0000.0000.000
18A283SER 0-0.0769.4640.0840.0840.0000.0000.0000.000
19A284ARG 10.88711.591-0.627-0.6270.0000.0000.0000.000
20A285PRO 0-0.01513.7780.0880.0880.0000.0000.0000.000
21A286SER 0-0.01516.2030.0900.0900.0000.0000.0000.000
22A287ALA 00.05716.517-0.071-0.0710.0000.0000.0000.000
23A288PRO 00.01816.1320.1370.1370.0000.0000.0000.000
24A289PHE 00.01110.561-0.065-0.0650.0000.0000.0000.000
25A290THR 00.02513.508-0.008-0.0080.0000.0000.0000.000
26A291GLU -1-0.8419.1110.0600.0600.0000.0000.0000.000
27A292ALA 00.0109.1210.1270.1270.0000.0000.0000.000
28A293SER 0-0.0319.7920.0580.0580.0000.0000.0000.000
29A294MET 00.0266.087-0.107-0.1070.0000.0000.0000.000
30A295MET 00.0602.073-0.271-3.5817.699-1.297-3.0920.014
31A296MET 0-0.0055.148-0.841-0.691-0.001-0.003-0.1460.000
32A297SER 0-0.0227.317-0.659-0.6590.0000.0000.0000.000
33A298LEU 00.0162.603-5.424-2.1382.032-1.213-4.1050.010
34A299THR 00.0022.578-10.681-7.0881.084-1.778-2.899-0.026
35A300LYS 10.9474.1560.7410.8880.000-0.016-0.1310.000
36A301LEU 0-0.0921.970-0.2760.8062.474-1.014-2.5430.002
37A302ALA 00.0382.198-2.873-1.1742.136-1.262-2.5740.000
38A303ASP -1-0.8603.607-0.475-0.3410.0630.091-0.2880.001
39A304LYS 10.8786.6322.3762.3760.0000.0000.0000.000
40A305GLU -1-0.7871.455-40.089-57.84441.202-17.939-5.508-0.129
41A306LEU 00.0395.8831.0371.0370.0000.0000.0000.000
42A307VAL 00.0308.2390.4950.4950.0000.0000.0000.000
43A308HIS 0-0.0428.3000.4970.4970.0000.0000.0000.000
44A309MET 0-0.0156.9910.3570.3570.0000.0000.0000.000
45A310ILE 00.0539.8920.2730.2730.0000.0000.0000.000
46A311SER 0-0.06813.3260.1670.1670.0000.0000.0000.000
47A312TRP 0-0.02911.6090.1130.1130.0000.0000.0000.000
48A313ALA 00.08813.5860.0970.0970.0000.0000.0000.000
49A314LYS 10.91115.3680.4680.4680.0000.0000.0000.000
50A315LYS 10.90216.1560.4010.4010.0000.0000.0000.000
51A316ILE 0-0.02815.3560.0500.0500.0000.0000.0000.000
52A317PRO 0-0.00919.333-0.013-0.0130.0000.0000.0000.000
53A318GLY 00.05223.1440.0150.0150.0000.0000.0000.000
54A319PHE 00.03917.689-0.003-0.0030.0000.0000.0000.000
55A320VAL 0-0.00221.361-0.017-0.0170.0000.0000.0000.000
56A321GLU -1-0.97523.201-0.134-0.1340.0000.0000.0000.000
57A322LEU 0-0.10321.7520.0130.0130.0000.0000.0000.000
58A323SER 00.01925.521-0.020-0.0200.0000.0000.0000.000
59A324LEU 00.04622.574-0.003-0.0030.0000.0000.0000.000
60A325PHE 00.02422.917-0.020-0.0200.0000.0000.0000.000
61A326ASP -1-0.74322.912-0.183-0.1830.0000.0000.0000.000
62A327GLN 0-0.06919.770-0.030-0.0300.0000.0000.0000.000
63A328VAL 00.03718.247-0.015-0.0150.0000.0000.0000.000
64A329ARG 10.87717.9490.1650.1650.0000.0000.0000.000
65A330LEU 0-0.05617.2490.0000.0000.0000.0000.0000.000
66A331LEU 00.00112.8580.0270.0270.0000.0000.0000.000
67A332GLU -1-0.88313.102-0.445-0.4450.0000.0000.0000.000
68A333SER 0-0.08113.4690.0000.0000.0000.0000.0000.000
69A334CYS 0-0.07911.7370.0150.0150.0000.0000.0000.000
70A335TRP 00.0675.2730.2770.2770.0000.0000.0000.000
71A336MET 00.0463.745-1.4620.4720.144-0.431-1.6460.002
72A337GLU -1-0.8315.3000.6910.6910.0000.0000.0000.000
73A338VAL 0-0.0226.6580.4130.4130.0000.0000.0000.000
74A339LEU 0-0.0152.685-3.203-0.2912.868-1.446-4.3340.013
75A340MET 0-0.0182.731-1.0931.9731.055-1.125-2.995-0.009
76A341MET 0-0.0223.6240.4090.5140.0030.064-0.1720.000
77A342GLY 0-0.0025.296-0.212-0.2120.0000.0000.0000.000
78A343LEU 0-0.0022.548-2.482-0.6250.534-0.645-1.7460.004
79A344MET 0-0.0334.493-0.969-0.8040.000-0.021-0.1440.000
80A345TRP 0-0.0067.585-0.353-0.3530.0000.0000.0000.000
81A346ARG 10.7942.352-7.010-5.5991.260-1.010-1.6600.012
82A347SER 0-0.0087.530-0.009-0.0090.0000.0000.0000.000
83A348ILE 00.00310.233-0.130-0.1300.0000.0000.0000.000
84A349ASP -1-0.95512.9660.8320.8320.0000.0000.0000.000
85A350HIS 0-0.05812.942-0.118-0.1180.0000.0000.0000.000
86A351PRO 0-0.03014.1050.2860.2860.0000.0000.0000.000
87A352GLY 0-0.01013.087-0.132-0.1320.0000.0000.0000.000
88A353LYS 10.95710.866-1.466-1.4660.0000.0000.0000.000
89A354LEU 00.0144.437-0.290-0.1060.000-0.016-0.1670.000
90A355ILE 0-0.0228.264-0.070-0.0700.0000.0000.0000.000
91A356PHE 00.0272.985-6.908-2.1841.366-1.521-4.5690.020
92A357ALA 00.0394.299-2.579-2.4360.000-0.025-0.1170.000
93A358PRO 0-0.0146.9550.5510.5510.0000.0000.0000.000
94A359ASP -1-0.7879.806-0.304-0.3040.0000.0000.0000.000
95A360LEU 0-0.0575.207-0.229-0.2290.0000.0000.0000.000
96A361VAL 0-0.0308.3950.7400.7400.0000.0000.0000.000
97A362LEU 00.0006.045-0.185-0.1850.0000.0000.0000.000
98A363ASP -1-0.8149.4492.3262.3260.0000.0000.0000.000
99A364ARG 10.8919.082-1.119-1.1190.0000.0000.0000.000
100A365ASP -1-0.95510.1441.2031.2030.0000.0000.0000.000
101A366GLU -1-0.86510.4031.9411.9410.0000.0000.0000.000
102A367GLY 00.0137.7660.1160.1160.0000.0000.0000.000
103A368LYS 10.8628.377-1.447-1.4470.0000.0000.0000.000
104A369CYS 0-0.10711.074-0.347-0.3470.0000.0000.0000.000
105A370VAL 00.0505.217-0.152-0.1520.0000.0000.0000.000
106A371GLU -1-0.9148.292-0.970-0.9700.0000.0000.0000.000
107A372GLY 00.0346.761-0.953-0.9530.0000.0000.0000.000
108A373ILE 0-0.0202.411-3.223-1.8602.700-0.948-3.1160.007
109A374LEU 0-0.0085.3412.0832.163-0.001-0.001-0.0780.000
110A375GLU -1-0.9587.167-0.934-0.9340.0000.0000.0000.000
111A376ILE 00.0502.441-1.924-1.0493.097-0.741-3.231-0.003
112A377PHE 00.0262.468-0.5430.0912.481-0.674-2.4420.010
113A378ASP -1-0.8105.1851.3531.386-0.001-0.005-0.0270.000
114A379MET 0-0.0726.656-0.180-0.1800.0000.0000.0000.000
115A380LEU 00.0343.018-1.339-0.5170.621-0.343-1.1000.005
116A381LEU 00.0217.263-0.682-0.6820.0000.0000.0000.000
117A382ALA 0-0.0109.604-0.481-0.4810.0000.0000.0000.000
118A383THR 0-0.01510.533-0.417-0.4170.0000.0000.0000.000
119A384THR 0-0.0159.514-0.176-0.1760.0000.0000.0000.000
120A385SER 0-0.04811.702-0.291-0.2910.0000.0000.0000.000
121A386ARG 10.93614.884-0.872-0.8720.0000.0000.0000.000
122A387PHE 00.04811.094-0.193-0.1930.0000.0000.0000.000
123A388ARG 10.92414.064-1.689-1.6890.0000.0000.0000.000
124A389GLU -1-0.99016.8330.7060.7060.0000.0000.0000.000
125A390LEU 0-0.07117.648-0.106-0.1060.0000.0000.0000.000
126A391LYS 10.94319.222-0.657-0.6570.0000.0000.0000.000
127A392LEU 0-0.01713.364-0.073-0.0730.0000.0000.0000.000
128A393GLN 0-0.02817.204-0.018-0.0180.0000.0000.0000.000
129A394HIS 00.05813.616-0.043-0.0430.0000.0000.0000.000
130A395LYS 11.00116.001-0.222-0.2220.0000.0000.0000.000
131A396GLU -1-0.73217.6170.4560.4560.0000.0000.0000.000
132A397TYR 00.0038.9540.0510.0510.0000.0000.0000.000
133A398LEU 0-0.02113.4530.0040.0040.0000.0000.0000.000
134A399CYS 0-0.03915.113-0.059-0.0590.0000.0000.0000.000
135A400VAL 00.05112.780-0.045-0.0450.0000.0000.0000.000
136A401LYS 10.8998.901-0.213-0.2130.0000.0000.0000.000
137A402ALA 00.00912.316-0.075-0.0750.0000.0000.0000.000
138A403MET 0-0.04415.313-0.041-0.0410.0000.0000.0000.000
139A404ILE 0-0.02510.384-0.038-0.0380.0000.0000.0000.000
140A405LEU 00.01513.439-0.057-0.0570.0000.0000.0000.000
141A406LEU 0-0.02814.501-0.051-0.0510.0000.0000.0000.000
142A407ASN 0-0.01917.059-0.047-0.0470.0000.0000.0000.000
143A408SER 0-0.01914.902-0.015-0.0150.0000.0000.0000.000
144A409SER 00.04317.018-0.053-0.0530.0000.0000.0000.000
145A410MET 0-0.00617.8870.0230.0230.0000.0000.0000.000
146A411TYR 00.03317.8770.0140.0140.0000.0000.0000.000
147A412PRO 00.05322.9140.0070.0070.0000.0000.0000.000
148A413LEU 0-0.00223.7260.0130.0130.0000.0000.0000.000
149A414VAL 0-0.01523.9580.0100.0100.0000.0000.0000.000
150A415THR 0-0.07726.870-0.003-0.0030.0000.0000.0000.000
151A416ALA 0-0.00529.5740.0050.0050.0000.0000.0000.000
152A417THR 00.03829.9680.0050.0050.0000.0000.0000.000
153A418GLN 0-0.07432.1170.0020.0020.0000.0000.0000.000
154A419ASP -1-0.90733.602-0.075-0.0750.0000.0000.0000.000
155A420ALA 00.04431.2090.0020.0020.0000.0000.0000.000
156A421ASP -1-0.86331.879-0.113-0.1130.0000.0000.0000.000
157A422SER 0-0.01726.6470.0050.0050.0000.0000.0000.000
158A423SER 00.02127.3610.0040.0040.0000.0000.0000.000
159A424ARG 10.89827.8000.0810.0810.0000.0000.0000.000
160A425LYS 10.88727.6570.1170.1170.0000.0000.0000.000
161A426LEU 00.05121.3160.0090.0090.0000.0000.0000.000
162A427ALA 00.01824.3620.0170.0170.0000.0000.0000.000
163A428HIS 0-0.01926.4380.0200.0200.0000.0000.0000.000
164A429LEU 00.00221.5750.0170.0170.0000.0000.0000.000
165A430LEU 00.00720.1260.0220.0220.0000.0000.0000.000
166A431ASN 0-0.02722.6530.0280.0280.0000.0000.0000.000
167A432ALA 00.06324.7070.0180.0180.0000.0000.0000.000
168A433VAL 0-0.01818.5790.0180.0180.0000.0000.0000.000
169A434THR 0-0.04021.7430.0410.0410.0000.0000.0000.000
170A435ASP -1-0.92723.0480.1110.1110.0000.0000.0000.000
171A436ALA 0-0.04922.2640.0120.0120.0000.0000.0000.000
172A437LEU 00.03019.0210.0200.0200.0000.0000.0000.000
173A438VAL 00.01922.1410.0230.0230.0000.0000.0000.000
174A439TRP 00.02224.1940.0090.0090.0000.0000.0000.000
175A440VAL 0-0.04221.2800.0020.0020.0000.0000.0000.000
176A441ILE 0-0.01222.1170.0100.0100.0000.0000.0000.000
177A442ALA 00.03425.2340.0030.0030.0000.0000.0000.000
178A443LYS 10.82327.121-0.177-0.1770.0000.0000.0000.000
179A444SER 0-0.08025.846-0.001-0.0010.0000.0000.0000.000
180A445GLY 00.01727.8980.0040.0040.0000.0000.0000.000
181A446ILE 0-0.00326.976-0.004-0.0040.0000.0000.0000.000
182A447SER 00.03931.101-0.012-0.0120.0000.0000.0000.000
183A448SER 00.08731.4790.0130.0130.0000.0000.0000.000
184A449GLN 00.01431.4260.0150.0150.0000.0000.0000.000
185A450GLN 00.03229.1160.0250.0250.0000.0000.0000.000
186A451GLN 0-0.02727.4560.0190.0190.0000.0000.0000.000
187A452SER 00.01726.4960.0080.0080.0000.0000.0000.000
188A453MET 00.00626.3970.0110.0110.0000.0000.0000.000
189A454ARG 10.73920.420-0.454-0.4540.0000.0000.0000.000
190A455LEU 00.03122.0340.0390.0390.0000.0000.0000.000
191A456ALA 00.02621.7360.0160.0160.0000.0000.0000.000
192A457ASN 0-0.02821.0350.0240.0240.0000.0000.0000.000
193A458LEU 0-0.00817.0270.0640.0640.0000.0000.0000.000
194A459LEU 00.01516.8820.0450.0450.0000.0000.0000.000
195A460MET 0-0.04917.938-0.018-0.0180.0000.0000.0000.000
196A461LEU 0-0.00914.2080.0010.0010.0000.0000.0000.000
197A462LEU 00.02012.8870.0920.0920.0000.0000.0000.000
198A463SER 0-0.00613.569-0.050-0.0500.0000.0000.0000.000
199A464HIS 00.01812.404-0.165-0.1650.0000.0000.0000.000
200A465VAL 00.0158.1030.0510.0510.0000.0000.0000.000
201A466ARG 10.9048.833-0.056-0.0560.0000.0000.0000.000
202A467HIS 0-0.0719.753-0.421-0.4210.0000.0000.0000.000
203A468ALA 00.0676.048-0.389-0.3890.0000.0000.0000.000
204A469SER 00.0054.825-1.151-1.054-0.001-0.005-0.0910.000
205A470ASN 00.0196.163-0.499-0.4990.0000.0000.0000.000
206A471LYS 10.9505.8350.9180.9180.0000.0000.0000.000
207A472GLY 00.0182.767-2.644-2.1590.672-0.566-0.5920.000
208A473MET 00.0003.3520.0250.5850.0680.270-0.898-0.001
209A474GLU -1-0.9636.448-1.925-1.9250.0000.0000.0000.000
210A475HIS 00.0231.897-23.632-24.22611.889-5.493-5.802-0.065
211A476LEU 00.0552.137-3.178-0.3933.942-1.671-5.0560.010
212A477LEU 00.0383.4220.7430.5340.1060.536-0.4330.002
213A478ASN 0-0.0345.9290.4840.4840.0000.0000.0000.000
214A479MET 00.0092.9170.0380.9860.124-0.343-0.7290.003
215A480LYS 10.9835.8841.0901.0900.0000.0000.0000.000
216A481CYS 0-0.0778.2020.0850.0850.0000.0000.0000.000
217A482LYS 10.8948.6141.2371.2370.0000.0000.0000.000
218A483ASN 0-0.06610.7140.0980.0980.0000.0000.0000.000
219A484VAL 00.0027.5220.0490.0490.0000.0000.0000.000
220A485VAL 0-0.0624.7870.0850.192-0.001-0.003-0.1040.000
221A486PRO 0-0.0258.097-0.068-0.0680.0000.0000.0000.000
222A487VAL 00.0249.365-0.064-0.0640.0000.0000.0000.000
223A488TYR 0-0.0237.669-0.082-0.0820.0000.0000.0000.000
224A489ASP -1-0.85510.798-0.734-0.7340.0000.0000.0000.000
225A490LEU 00.03210.5800.0360.0360.0000.0000.0000.000
226A491LEU 0-0.0054.976-0.031-0.0310.0000.0000.0000.000
227A492LEU 0-0.0968.9290.1590.1590.0000.0000.0000.000
228A493GLU -1-0.98310.803-0.567-0.5670.0000.0000.0000.000
229A494MET 0-0.0479.7520.0630.0630.0000.0000.0000.000
230A495LEU -1-0.9796.849-0.641-0.6410.0000.0000.0000.000
232A3HOH 0-0.0142.410-1.341-0.5751.556-1.000-1.3220.006