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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: PGJ1X

Calculation Name: 1U3Q-D-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 4-(6-hydroxy-benzo[d]isoxazol-3-yl)benzene-1,3-diol

ligand 3-letter code: 272

PDB ID: 1U3Q

Chain ID: D

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 -3035643.492589
FMO2-HF: Nuclear repulsion 2939243.997373
FMO2-HF: Total energy -96399.495216
FMO2-MP2: Total energy -96669.805558


3D Structure
Snapshot
 
Ligand structure

272

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.
-115.823-101.51975.080-38.527-50.8590.078


Interactive mode: IFIE and PIEDA for fragment #235(D:501:272)


Summations of interaction energy for fragment #235(D:501:272)
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.
-115.823-101.51975.08-38.527-50.859-0.078
Interaction energy analysis for fragmet #235(D:501:272)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.112
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].
1D264SER10.8410.90729.6210.0170.0170.0000.0000.0000.000
2D265PRO00.1830.07626.675-0.023-0.0230.0000.0000.0000.000
3D266GLU-1-0.899-0.93825.5820.0030.0030.0000.0000.0000.000
4D267GLN00.020-0.00725.721-0.010-0.0100.0000.0000.0000.000
5D268LEU0-0.0030.01822.462-0.032-0.0320.0000.0000.0000.000
6D269VAL00.0230.00120.810-0.026-0.0260.0000.0000.0000.000
7D270LEU0-0.021-0.01220.730-0.029-0.0290.0000.0000.0000.000
8D271THR00.0360.02620.859-0.042-0.0420.0000.0000.0000.000
9D272LEU0-0.033-0.02717.105-0.059-0.0590.0000.0000.0000.000
10D273LEU0-0.021-0.02016.552-0.060-0.0600.0000.0000.0000.000
11D274GLU-1-0.990-0.99116.990-0.371-0.3710.0000.0000.0000.000
12D275ALA0-0.066-0.03216.262-0.081-0.0810.0000.0000.0000.000
13D276GLU-1-0.797-0.88411.490-0.857-0.8570.0000.0000.0000.000
14D277PRO0-0.060-0.0098.981-0.006-0.0060.0000.0000.0000.000
15D278PRO0-0.011-0.00210.9010.0950.0950.0000.0000.0000.000
16D279HIS00.0410.0038.091-0.618-0.6180.0000.0000.0000.000
17D280VAL00.0040.0185.5110.5440.5440.0000.0000.0000.000
18D281LEU0-0.066-0.0397.3970.0790.0790.0000.0000.0000.000
19D282ILE0-0.0280.0186.5970.0170.0170.0000.0000.0000.000
20D283SER0-0.022-0.0219.6420.1980.1980.0000.0000.0000.000
21D284ARG10.8640.92112.367-0.522-0.5220.0000.0000.0000.000
22D285PRO0-0.0310.00113.227-0.032-0.0320.0000.0000.0000.000
23D286SER00.0200.01816.1940.1000.1000.0000.0000.0000.000
24D287ALA0-0.051-0.05218.311-0.006-0.0060.0000.0000.0000.000
25D288PRO0-0.0060.00017.3100.0310.0310.0000.0000.0000.000
26D289PHE00.0220.01111.190-0.039-0.0390.0000.0000.0000.000
27D290THR0-0.0020.00212.9040.0010.0010.0000.0000.0000.000
28D291GLU-1-0.820-0.9228.590-0.576-0.5760.0000.0000.0000.000
29D292ALA00.0310.0108.893-0.015-0.0150.0000.0000.0000.000
30D293SER00.0200.0059.354-0.045-0.0450.0000.0000.0000.000
31D294MET00.0150.0256.930-0.244-0.2440.0000.0000.0000.000
32D295MET00.0480.0293.202-1.752-0.1420.169-0.503-1.2760.005
33D296MET0-0.022-0.0025.025-0.784-0.621-0.001-0.004-0.1590.000
34D297SER0-0.037-0.0447.711-0.508-0.5080.0000.0000.0000.000
35D298LEU0-0.001-0.0072.386-4.499-1.3221.537-1.222-3.4920.012
36D299THR00.0170.0093.409-5.236-3.9430.035-0.501-0.826-0.003
37D300LYS10.9740.9905.1360.9891.103-0.001-0.010-0.1030.000
38D301LEU0-0.042-0.0142.312-0.7491.2091.213-0.807-2.3640.003
39D302ALA00.0660.0192.577-3.909-2.0530.539-0.876-1.519-0.002
40D303ASP-1-0.860-0.9283.371-0.970-0.9920.0400.081-0.0980.000
41D304LYS10.9460.9676.8563.2073.2070.0000.0000.0000.000
42D305GLU-1-0.835-0.8821.356-51.525-77.27651.551-21.558-4.243-0.120
43D306LEU0-0.0020.0165.8491.2791.2790.0000.0000.0000.000
44D307VAL00.0140.0068.0220.7090.7090.0000.0000.0000.000
45D308HIS0-0.033-0.0228.1670.7120.7120.0000.0000.0000.000
46D309MET0-0.037-0.0027.0190.6250.6250.0000.0000.0000.000
47D310ILE00.0660.0379.8810.4460.4460.0000.0000.0000.000
48D311SER0-0.028-0.02113.2120.2710.2710.0000.0000.0000.000
49D312TRP0-0.039-0.01811.3400.1410.1410.0000.0000.0000.000
50D313ALA00.0520.01913.5710.1620.1620.0000.0000.0000.000
51D314LYS10.9120.95615.3460.6880.6880.0000.0000.0000.000
52D315LYS10.9010.96115.9260.8860.8860.0000.0000.0000.000
53D316ILE0-0.0240.01015.3080.0720.0720.0000.0000.0000.000
54D317PRO0-0.018-0.02819.3620.0120.0120.0000.0000.0000.000
55D318GLY00.0490.02423.1840.0330.0330.0000.0000.0000.000
56D319PHE00.0110.00917.6400.0170.0170.0000.0000.0000.000
57D320VAL0-0.008-0.01521.637-0.012-0.0120.0000.0000.0000.000
58D321GLU-1-0.959-0.98023.332-0.197-0.1970.0000.0000.0000.000
59D322LEU0-0.064-0.00921.7270.0350.0350.0000.0000.0000.000
60D323SER0-0.009-0.00425.384-0.038-0.0380.0000.0000.0000.000
61D324LEU00.0580.00423.4110.0000.0000.0000.0000.0000.000
62D325PHE00.0550.01622.386-0.022-0.0220.0000.0000.0000.000
63D326ASP-1-0.778-0.84522.504-0.027-0.0270.0000.0000.0000.000
64D327GLN0-0.076-0.04719.648-0.037-0.0370.0000.0000.0000.000
65D328VAL00.0230.01117.870-0.038-0.0380.0000.0000.0000.000
66D329ARG10.9170.96217.536-0.040-0.0400.0000.0000.0000.000
67D330LEU0-0.047-0.02117.4040.0660.0660.0000.0000.0000.000
68D331LEU0-0.022-0.01912.6300.0630.0630.0000.0000.0000.000
69D332GLU-1-0.870-0.96113.100-0.223-0.2230.0000.0000.0000.000
70D333SER0-0.0350.00313.8000.1280.1280.0000.0000.0000.000
71D334CYS0-0.061-0.01612.0440.1780.1780.0000.0000.0000.000
72D335TRP00.0870.0275.3990.3450.3450.0000.0000.0000.000
73D336MET00.0410.0283.167-2.6440.3860.910-0.710-3.2300.007
74D337GLU-1-0.813-0.9035.6922.9022.9020.0000.0000.0000.000
75D338VAL0-0.007-0.0046.9580.2720.2720.0000.0000.0000.000
76D339LEU0-0.034-0.0082.642-3.279-0.7683.477-1.436-4.5520.010
77D340MET0-0.037-0.0022.392-6.806-2.7543.785-2.048-5.7890.006
78D341MET00.0110.0153.714-0.719-0.6110.0030.033-0.1440.000
79D342GLY0-0.003-0.0075.290-0.294-0.2940.0000.0000.0000.000
80D343LEU0-0.037-0.0222.122-2.673-0.9541.941-0.920-2.7410.007
81D344MET0-0.023-0.0103.984-1.012-0.7750.003-0.059-0.1810.000
82D345TRP00.0080.0087.273-0.350-0.3500.0000.0000.0000.000
83D346ARG10.8820.9452.578-1.736-0.1000.400-0.757-1.2800.010
84D347SER00.0120.0117.197-0.028-0.0280.0000.0000.0000.000
85D348ILE0-0.0380.0089.786-0.028-0.0280.0000.0000.0000.000
86D349ASP-1-0.912-0.95212.4870.5380.5380.0000.0000.0000.000
87D350HIS0-0.071-0.03812.720-0.103-0.1030.0000.0000.0000.000
88D351PRO0-0.012-0.02113.6070.2310.2310.0000.0000.0000.000
89D352GLY00.0010.00014.320-0.125-0.1250.0000.0000.0000.000
90D353LYS10.9020.96712.181-0.828-0.8280.0000.0000.0000.000
91D354LEU0-0.0120.0056.0480.1080.1080.0000.0000.0000.000
92D355ILE0-0.016-0.0247.962-0.286-0.2860.0000.0000.0000.000
93D356PHE00.0180.0022.747-5.928-1.8982.529-1.373-5.1860.012
94D357ALA00.0410.0034.947-2.268-2.164-0.001-0.008-0.0950.000
95D358PRO0-0.022-0.0047.6500.5020.5020.0000.0000.0000.000
96D359ASP-1-0.895-0.95511.304-0.063-0.0630.0000.0000.0000.000
97D360LEU0-0.016-0.0096.777-0.073-0.0730.0000.0000.0000.000
98D361VAL0-0.013-0.0029.1880.4460.4460.0000.0000.0000.000
99D362LEU0-0.007-0.0217.520-0.202-0.2020.0000.0000.0000.000
100D363ASP-1-0.788-0.92110.8221.4961.4960.0000.0000.0000.000
101D364ARG10.9160.96311.589-1.299-1.2990.0000.0000.0000.000
102D365ASP-1-0.892-0.94412.6180.8860.8860.0000.0000.0000.000
103D366GLU-1-0.879-0.89111.4600.6900.6900.0000.0000.0000.000
104D367GLY00.005-0.0059.263-0.057-0.0570.0000.0000.0000.000
105D368LYS10.9140.9559.850-0.800-0.8000.0000.0000.0000.000
106D369CYS0-0.107-0.05411.293-0.147-0.1470.0000.0000.0000.000
107D370VAL00.0310.0085.114-0.116-0.1160.0000.0000.0000.000
108D371GLU-1-0.865-0.9238.223-0.400-0.4000.0000.0000.0000.000
109D372GLY00.0110.0146.783-0.742-0.7420.0000.0000.0000.000
110D373ILE0-0.0160.0073.281-1.440-0.0390.255-0.462-1.1940.005
111D374LEU0-0.022-0.0085.7001.5301.5300.0000.0000.0000.000
112D375GLU-1-0.904-0.9528.2171.3121.3120.0000.0000.0000.000
113D376ILE00.0380.0142.596-1.3670.1180.789-0.515-1.7580.004
114D377PHE00.009-0.0044.7690.7531.107-0.001-0.014-0.3400.000
115D378ASP-1-0.854-0.9357.0141.9161.9160.0000.0000.0000.000
116D379MET0-0.037-0.0067.589-0.015-0.0150.0000.0000.0000.000
117D380LEU00.0180.0182.856-1.940-0.5440.185-0.349-1.2320.002
118D381LEU00.0350.0287.488-0.747-0.7470.0000.0000.0000.000
119D382ALA0-0.0010.01310.411-0.469-0.4690.0000.0000.0000.000
120D383THR00.001-0.0309.631-0.458-0.4580.0000.0000.0000.000
121D384THR00.006-0.0178.823-0.317-0.3170.0000.0000.0000.000
122D385SER0-0.063-0.05111.221-0.408-0.4080.0000.0000.0000.000
123D386ARG10.9010.96714.252-1.307-1.3070.0000.0000.0000.000
124D387PHE00.0340.00310.921-0.248-0.2480.0000.0000.0000.000
125D388ARG10.9010.97213.251-1.564-1.5640.0000.0000.0000.000
126D389GLU-1-0.954-0.96916.0580.7900.7900.0000.0000.0000.000
127D390LEU0-0.041-0.01517.272-0.112-0.1120.0000.0000.0000.000
128D391LYS10.9720.99718.508-0.618-0.6180.0000.0000.0000.000
129D392LEU0-0.0270.00612.681-0.088-0.0880.0000.0000.0000.000
130D393GLN0-0.012-0.01716.722-0.089-0.0890.0000.0000.0000.000
131D394HIS00.0480.01913.943-0.010-0.0100.0000.0000.0000.000
132D395LYS11.0030.98715.898-0.059-0.0590.0000.0000.0000.000
133D396GLU-1-0.747-0.83417.3210.4530.4530.0000.0000.0000.000
134D397TYR0-0.004-0.0048.8350.0540.0540.0000.0000.0000.000
135D398LEU00.0070.02013.3380.0150.0150.0000.0000.0000.000
136D399CYS0-0.053-0.01315.212-0.052-0.0520.0000.0000.0000.000
137D400VAL00.0350.00112.623-0.003-0.0030.0000.0000.0000.000
138D401LYS10.8180.9039.0750.8710.8710.0000.0000.0000.000
139D402ALA00.0130.00512.383-0.026-0.0260.0000.0000.0000.000
140D403MET0-0.043-0.02115.4110.0060.0060.0000.0000.0000.000
141D404ILE0-0.028-0.00510.3580.0210.0210.0000.0000.0000.000
142D405LEU00.005-0.00213.7760.0040.0040.0000.0000.0000.000
143D406LEU0-0.027-0.02814.880-0.011-0.0110.0000.0000.0000.000
144D407ASN0-0.016-0.00817.532-0.083-0.0830.0000.0000.0000.000
145D408SER0-0.038-0.00415.5190.0240.0240.0000.0000.0000.000
146D409SER0-0.024-0.00317.624-0.015-0.0150.0000.0000.0000.000
147D410MET0-0.025-0.01421.199-0.003-0.0030.0000.0000.0000.000
148D411TYR0-0.003-0.00624.225-0.006-0.0060.0000.0000.0000.000
149D412PRO00.0190.01926.297-0.010-0.0100.0000.0000.0000.000
150D413LEU0-0.028-0.02325.7060.0110.0110.0000.0000.0000.000
151D414VAL0-0.0070.01927.449-0.018-0.0180.0000.0000.0000.000
152D415THR0-0.035-0.01927.8090.0010.0010.0000.0000.0000.000
153D416ALA00.0140.01028.1910.0030.0030.0000.0000.0000.000
154D417THR0-0.022-0.00829.4580.0130.0130.0000.0000.0000.000
155D418GLN0-0.032-0.00931.3630.0100.0100.0000.0000.0000.000
156D419ASP-1-0.789-0.90829.545-0.003-0.0030.0000.0000.0000.000
157D420ALA00.036-0.00632.6920.0150.0150.0000.0000.0000.000
158D421ASP-1-0.893-0.95032.233-0.025-0.0250.0000.0000.0000.000
159D422SER0-0.003-0.02726.886-0.008-0.0080.0000.0000.0000.000
160D423SER00.0510.01427.7040.0100.0100.0000.0000.0000.000
161D424ARG10.8090.90628.2350.0200.0200.0000.0000.0000.000
162D425LYS10.9360.97627.7540.0930.0930.0000.0000.0000.000
163D426LEU00.0870.05721.562-0.009-0.0090.0000.0000.0000.000
164D427ALA00.0270.02224.4520.0170.0170.0000.0000.0000.000
165D428HIS0-0.023-0.01926.4150.0250.0250.0000.0000.0000.000
166D429LEU00.0030.00122.1410.0030.0030.0000.0000.0000.000
167D430LEU0-0.024-0.01220.0450.0010.0010.0000.0000.0000.000
168D431ASN0-0.044-0.02322.6820.0280.0280.0000.0000.0000.000
169D432ALA00.0500.03324.9190.0100.0100.0000.0000.0000.000
170D433VAL0-0.020-0.01318.664-0.003-0.0030.0000.0000.0000.000
171D434THR0-0.017-0.01921.9280.0440.0440.0000.0000.0000.000
172D435ASP-1-0.933-0.97122.9310.1420.1420.0000.0000.0000.000
173D436ALA0-0.019-0.00522.360-0.004-0.0040.0000.0000.0000.000
174D437LEU00.014-0.00318.9530.0030.0030.0000.0000.0000.000
175D438VAL00.0300.01722.0440.0230.0230.0000.0000.0000.000
176D439TRP00.0130.00825.0620.0000.0000.0000.0000.0000.000
177D440VAL0-0.025-0.02121.218-0.006-0.0060.0000.0000.0000.000
178D441ILE0-0.0100.01021.8080.0080.0080.0000.0000.0000.000
179D442ALA00.0230.02624.7660.0010.0010.0000.0000.0000.000
180D443LYS10.8150.91626.664-0.122-0.1220.0000.0000.0000.000
181D444SER0-0.023-0.01725.346-0.006-0.0060.0000.0000.0000.000
182D445GLY0-0.029-0.01727.2930.0030.0030.0000.0000.0000.000
183D446ILE0-0.044-0.01026.114-0.001-0.0010.0000.0000.0000.000
184D447SER00.0850.04230.265-0.015-0.0150.0000.0000.0000.000
185D448SER00.0470.02530.7910.0140.0140.0000.0000.0000.000
186D449GLN00.014-0.01331.2870.0310.0310.0000.0000.0000.000
187D450GLN00.019-0.00728.3260.0030.0030.0000.0000.0000.000
188D451GLN0-0.005-0.00726.7610.0300.0300.0000.0000.0000.000
189D452SER00.0220.01425.9180.0230.0230.0000.0000.0000.000
190D453MET0-0.0080.00525.8750.0430.0430.0000.0000.0000.000
191D454ARG10.7340.81819.809-0.466-0.4660.0000.0000.0000.000
192D455LEU00.0480.02521.4800.0630.0630.0000.0000.0000.000
193D456ALA00.0220.01121.3400.0500.0500.0000.0000.0000.000
194D457ASN0-0.032-0.02920.4290.0930.0930.0000.0000.0000.000
195D458LEU0-0.024-0.00916.4620.1140.1140.0000.0000.0000.000
196D459LEU00.016-0.00416.5930.1220.1220.0000.0000.0000.000
197D460MET0-0.025-0.01017.9240.0580.0580.0000.0000.0000.000
198D461LEU0-0.015-0.00614.2320.0900.0900.0000.0000.0000.000
199D462LEU00.0160.01012.7840.2930.2930.0000.0000.0000.000
200D463SER00.0050.01313.4500.0940.0940.0000.0000.0000.000
201D464HIS0-0.026-0.01512.4610.1540.1540.0000.0000.0000.000
202D465VAL00.0020.0048.1390.4220.4220.0000.0000.0000.000
203D466ARG10.9270.9588.924-0.563-0.5630.0000.0000.0000.000
204D467HIS0-0.083-0.04510.0910.0270.0270.0000.0000.0000.000
205D468ALA00.0560.0075.943-0.133-0.1330.0000.0000.0000.000
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207D470ASN0-0.009-0.0086.795-0.176-0.1760.0000.0000.0000.000
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