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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: P48NP

Calculation Name: 1U3R-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 2-(5-hydroxy-naphthalen-1-yl)-1,3-benzooxazol-6-ol

ligand 3-letter code: 338

PDB ID: 1U3R

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 -3089352.610845
FMO2-HF: Nuclear repulsion 2992873.094043
FMO2-HF: Total energy -96479.516803
FMO2-MP2: Total energy -96750.28943


3D Structure
Snapshot
 
Ligand structure

338

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.
-94.715-74.35282.680-30.082-72.9620.047


Interactive mode: IFIE and PIEDA for fragment #235(D:201:338)


Summations of interaction energy for fragment #235(D:201:338)
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.
-94.715-74.35282.68-30.082-72.962-0.047
Interaction energy analysis for fragmet #235(D:201:338)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.087
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].
1D264SER10.7920.86128.618-0.112-0.1120.0000.0000.0000.000
2D265PRO00.1340.06826.356-0.006-0.0060.0000.0000.0000.000
3D266GLU-1-0.792-0.86023.5940.1510.1510.0000.0000.0000.000
4D267GLN00.000-0.00923.4670.0030.0030.0000.0000.0000.000
5D268LEU00.0460.04421.568-0.011-0.0110.0000.0000.0000.000
6D269VAL00.0080.01318.505-0.004-0.0040.0000.0000.0000.000
7D270LEU0-0.019-0.00819.0430.0010.0010.0000.0000.0000.000
8D271THR0-0.017-0.02719.819-0.016-0.0160.0000.0000.0000.000
9D272LEU0-0.0150.00315.847-0.014-0.0140.0000.0000.0000.000
10D273LEU0-0.011-0.01015.162-0.016-0.0160.0000.0000.0000.000
11D274GLU-1-0.943-0.97415.686-0.019-0.0190.0000.0000.0000.000
12D275ALA0-0.033-0.01015.154-0.040-0.0400.0000.0000.0000.000
13D276GLU-1-0.795-0.87310.6670.0950.0950.0000.0000.0000.000
14D277PRO0-0.0270.0076.951-0.040-0.0400.0000.0000.0000.000
15D278PRO00.0080.0068.7790.1500.1500.0000.0000.0000.000
16D279HIS00.019-0.0047.124-0.379-0.3790.0000.0000.0000.000
17D280VAL0-0.016-0.0095.6110.2570.2570.0000.0000.0000.000
18D281LEU00.0060.0136.6660.0350.0350.0000.0000.0000.000
19D282ILE00.0230.0146.661-0.285-0.2850.0000.0000.0000.000
20D283SER0-0.103-0.0609.172-0.064-0.0640.0000.0000.0000.000
21D284ARG10.7900.87812.212-0.517-0.5170.0000.0000.0000.000
22D285PRO00.0320.00914.1900.0180.0180.0000.0000.0000.000
23D286SER0-0.018-0.01213.1410.0870.0870.0000.0000.0000.000
24D287ALA0-0.017-0.00714.711-0.057-0.0570.0000.0000.0000.000
25D288PRO00.0500.03714.8400.0750.0750.0000.0000.0000.000
26D289PHE0-0.051-0.01610.720-0.037-0.0370.0000.0000.0000.000
27D290THR00.0260.02712.274-0.037-0.0370.0000.0000.0000.000
28D291GLU-1-0.830-0.9379.534-0.002-0.0020.0000.0000.0000.000
29D292ALA00.0320.0168.3660.0690.0690.0000.0000.0000.000
30D293SER0-0.014-0.0148.5800.0700.0700.0000.0000.0000.000
31D294MET00.0350.0226.0160.1230.1230.0000.0000.0000.000
32D295MET0-0.0140.0072.897-2.840-0.3390.738-0.905-2.3340.011
33D296MET0-0.0120.0084.073-0.600-0.3340.002-0.036-0.2310.000
34D297SER00.014-0.0076.576-0.346-0.3460.0000.0000.0000.000
35D298LEU00.002-0.0032.563-4.919-1.6364.136-1.503-5.9170.013
36D299THR00.002-0.0152.330-5.443-3.4263.024-1.374-3.668-0.014
37D300LYS10.8770.9583.3310.5680.6190.0380.174-0.2630.000
38D301LEU0-0.066-0.0182.510-1.7480.3492.255-1.099-3.2530.009
39D302ALA00.0270.0082.501-3.153-1.2750.705-0.722-1.8600.003
40D303ASP-1-0.835-0.9093.876-0.672-0.3810.006-0.055-0.2430.000
41D304LYS10.8630.9227.1611.0421.0420.0000.0000.0000.000
42D305GLU-1-0.792-0.8871.598-25.942-34.64619.170-6.632-3.834-0.068
43D306LEU00.0460.0355.8860.6630.6630.0000.0000.0000.000
44D307VAL00.0070.0168.5100.2890.2890.0000.0000.0000.000
45D308HIS0-0.026-0.0198.1120.2730.2730.0000.0000.0000.000
46D309MET0-0.0200.0246.6710.3350.3350.0000.0000.0000.000
47D310ILE00.0290.0159.7590.2100.2100.0000.0000.0000.000
48D311SER0-0.046-0.03812.4380.1180.1180.0000.0000.0000.000
49D312TRP0-0.0060.01311.2720.0760.0760.0000.0000.0000.000
50D313ALA00.0730.02913.1740.0650.0650.0000.0000.0000.000
51D314LYS10.8440.91314.9930.1170.1170.0000.0000.0000.000
52D315LYS10.8210.90214.3800.2070.2070.0000.0000.0000.000
53D316ILE0-0.0240.00615.1760.0240.0240.0000.0000.0000.000
54D317PRO0-0.026-0.02119.280-0.003-0.0030.0000.0000.0000.000
55D318GLY00.008-0.00922.8320.0190.0190.0000.0000.0000.000
56D319PHE00.010-0.00417.0430.0090.0090.0000.0000.0000.000
57D320VAL0-0.010-0.00620.863-0.009-0.0090.0000.0000.0000.000
58D321GLU-1-0.863-0.92822.7840.0280.0280.0000.0000.0000.000
59D322LEU0-0.0380.00221.1470.0070.0070.0000.0000.0000.000
60D323SER0-0.036-0.04424.990-0.018-0.0180.0000.0000.0000.000
61D324LEU00.028-0.00121.4640.0080.0080.0000.0000.0000.000
62D325PHE00.0650.03021.9050.0000.0000.0000.0000.0000.000
63D326ASP-1-0.716-0.80621.8130.0790.0790.0000.0000.0000.000
64D327GLN0-0.019-0.01219.2790.0020.0020.0000.0000.0000.000
65D328VAL00.0000.00517.1040.0060.0060.0000.0000.0000.000
66D329ARG10.9190.96316.798-0.086-0.0860.0000.0000.0000.000
67D330LEU0-0.044-0.01317.0430.0560.0560.0000.0000.0000.000
68D331LEU00.014-0.00311.9650.0940.0940.0000.0000.0000.000
69D332GLU-1-0.812-0.90112.5970.2450.2450.0000.0000.0000.000
70D333SER0-0.035-0.01512.7960.0820.0820.0000.0000.0000.000
71D334CYS0-0.055-0.00411.5960.1400.1400.0000.0000.0000.000
72D335TRP00.0470.0134.4070.1710.5990.000-0.031-0.3970.000
73D336MET00.0090.0183.216-1.5341.7981.723-0.816-4.2400.009
74D337GLU-1-0.791-0.8865.0901.7502.014-0.001-0.007-0.2560.000
75D338VAL0-0.020-0.0246.4970.0580.0580.0000.0000.0000.000
76D339LEU0-0.0120.0102.491-4.453-2.0946.437-2.062-6.7330.013
77D340MET0-0.023-0.0032.190-4.647-1.9345.298-2.067-5.944-0.014
78D341MET0-0.026-0.0063.403-0.066-0.4150.0230.522-0.1960.000
79D342GLY00.0020.0074.746-0.382-0.324-0.001-0.015-0.0410.000
80D343LEU00.0100.0132.111-1.818-1.7695.365-1.695-3.7190.008
81D344MET0-0.0180.0043.620-0.661-0.4510.012-0.048-0.1740.000
82D345TRP00.0000.0016.661-0.239-0.2390.0000.0000.0000.000
83D346ARG10.7620.8622.500-0.3570.6850.708-0.587-1.1630.005
84D347SER00.003-0.0116.8400.0000.0000.0000.0000.0000.000
85D348ILE00.0240.0269.427-0.107-0.1070.0000.0000.0000.000
86D349ASP-1-0.860-0.92911.9810.6360.6360.0000.0000.0000.000
87D350HIS0-0.034-0.01212.239-0.097-0.0970.0000.0000.0000.000
88D351PRO00.0050.01813.4960.0930.0930.0000.0000.0000.000
89D352GLY00.0230.02314.107-0.016-0.0160.0000.0000.0000.000
90D353LYS10.8780.91412.090-0.715-0.7150.0000.0000.0000.000
91D354LEU0-0.0020.0096.243-0.017-0.0170.0000.0000.0000.000
92D355ILE0-0.032-0.0227.6220.0700.0700.0000.0000.0000.000
93D356PHE00.0350.0172.937-5.466-1.1732.717-1.382-5.6270.015
94D357ALA00.0530.0224.065-1.040-0.6870.003-0.059-0.2980.000
95D358PRO0-0.009-0.0116.6450.2090.2090.0000.0000.0000.000
96D359ASP-1-0.725-0.8629.8260.0670.0670.0000.0000.0000.000
97D360LEU0-0.014-0.0055.078-0.145-0.1450.0000.0000.0000.000
98D361VAL0-0.0170.0007.9970.7010.7010.0000.0000.0000.000
99D362LEU00.0040.0077.419-0.114-0.1140.0000.0000.0000.000
100D363ASP-1-0.841-0.93510.9660.8980.8980.0000.0000.0000.000
101D364ARG10.7950.86910.503-0.317-0.3170.0000.0000.0000.000
102D365ASP-1-0.813-0.89610.7180.2000.2000.0000.0000.0000.000
103D366GLU-1-0.774-0.89411.4450.8990.8990.0000.0000.0000.000
104D367GLY00.0510.0277.884-0.075-0.0750.0000.0000.0000.000
105D368LYS10.7870.8708.307-0.679-0.6790.0000.0000.0000.000
106D369CYS0-0.085-0.0229.275-0.265-0.2650.0000.0000.0000.000
107D370VAL00.0400.0095.200-0.064-0.0640.0000.0000.0000.000
108D371GLU-1-0.808-0.8856.157-2.795-2.7950.0000.0000.0000.000
109D372GLY00.0440.0216.923-0.636-0.6360.0000.0000.0000.000
110D373ILE00.0080.0232.624-1.159-0.5454.000-0.854-3.7590.009
111D374LEU0-0.010-0.0054.9680.9011.025-0.001-0.002-0.1220.000
112D375GLU-1-0.837-0.9097.493-0.338-0.3380.0000.0000.0000.000
113D376ILE00.0060.0002.336-0.994-0.0401.307-0.351-1.909-0.001
114D377PHE00.0130.0014.2320.2220.6950.001-0.073-0.4010.000
115D378ASP-1-0.791-0.8887.1390.5730.5730.0000.0000.0000.000
116D379MET0-0.0260.0017.2230.1060.1060.0000.0000.0000.000
117D380LEU00.0360.0233.926-0.3710.0100.001-0.051-0.3310.000
118D381LEU00.0220.0307.752-0.158-0.1580.0000.0000.0000.000
119D382ALA0-0.0220.01110.779-0.136-0.1360.0000.0000.0000.000
120D383THR0-0.019-0.0289.347-0.133-0.1330.0000.0000.0000.000
121D384THR0-0.037-0.0429.022-0.032-0.0320.0000.0000.0000.000
122D385SER0-0.057-0.04511.284-0.139-0.1390.0000.0000.0000.000
123D386ARG10.7700.85514.235-0.538-0.5380.0000.0000.0000.000
124D387PHE00.0660.0119.406-0.099-0.0990.0000.0000.0000.000
125D388ARG10.8510.93113.156-0.907-0.9070.0000.0000.0000.000
126D389GLU-1-0.866-0.89316.7920.3520.3520.0000.0000.0000.000
127D390LEU00.0150.00817.545-0.044-0.0440.0000.0000.0000.000
128D391LYS10.8230.91617.919-0.427-0.4270.0000.0000.0000.000
129D392LEU00.0130.03312.497-0.048-0.0480.0000.0000.0000.000
130D393GLN0-0.013-0.02016.343-0.010-0.0100.0000.0000.0000.000
131D394HIS00.0200.01313.423-0.026-0.0260.0000.0000.0000.000
132D395LYS10.9230.93415.623-0.182-0.1820.0000.0000.0000.000
133D396GLU-1-0.721-0.82516.8990.3630.3630.0000.0000.0000.000
134D397TYR0-0.023-0.0288.3460.0550.0550.0000.0000.0000.000
135D398LEU0-0.0120.00812.6480.0330.0330.0000.0000.0000.000
136D399CYS0-0.018-0.00814.477-0.020-0.0200.0000.0000.0000.000
137D400VAL00.0260.00212.312-0.007-0.0070.0000.0000.0000.000
138D401LYS10.8280.9098.261-0.184-0.1840.0000.0000.0000.000
139D402ALA00.0290.01311.822-0.007-0.0070.0000.0000.0000.000
140D403MET0-0.046-0.03515.135-0.013-0.0130.0000.0000.0000.000
141D404ILE0-0.004-0.0019.901-0.021-0.0210.0000.0000.0000.000
142D405LEU00.0160.00813.508-0.012-0.0120.0000.0000.0000.000
143D406LEU0-0.028-0.00814.489-0.032-0.0320.0000.0000.0000.000
144D407ASN0-0.041-0.03017.352-0.049-0.0490.0000.0000.0000.000
145D408SER0-0.058-0.01814.692-0.020-0.0200.0000.0000.0000.000
146D409SER00.0230.00016.2890.0140.0140.0000.0000.0000.000
147D410MET0-0.040-0.01718.871-0.044-0.0440.0000.0000.0000.000
148D411TYR0-0.045-0.02619.0340.0110.0110.0000.0000.0000.000
149D412PRO00.0350.00821.001-0.004-0.0040.0000.0000.0000.000
150D413LEU00.0410.01923.797-0.014-0.0140.0000.0000.0000.000
151D414VAL0-0.024-0.01227.270-0.002-0.0020.0000.0000.0000.000
152D415THR0-0.054-0.03625.126-0.009-0.0090.0000.0000.0000.000
153D416ALA00.0190.02226.2870.0100.0100.0000.0000.0000.000
154D417THR0-0.018-0.03126.898-0.017-0.0170.0000.0000.0000.000
155D418GLN0-0.046-0.00626.6630.0080.0080.0000.0000.0000.000
156D419ASP-1-0.858-0.92227.6920.0700.0700.0000.0000.0000.000
157D420ALA00.037-0.01430.1670.0020.0020.0000.0000.0000.000
158D421ASP-1-0.789-0.88731.4540.0540.0540.0000.0000.0000.000
159D422SER0-0.037-0.01326.0720.0050.0050.0000.0000.0000.000
160D423SER00.0470.00826.3920.0130.0130.0000.0000.0000.000
161D424ARG10.8300.90927.259-0.046-0.0460.0000.0000.0000.000
162D425LYS10.8270.90526.910-0.039-0.0390.0000.0000.0000.000
163D426LEU00.0400.03820.6220.0030.0030.0000.0000.0000.000
164D427ALA00.0290.01423.4680.0190.0190.0000.0000.0000.000
165D428HIS0-0.017-0.00925.6560.0110.0110.0000.0000.0000.000
166D429LEU0-0.0060.00120.5500.0080.0080.0000.0000.0000.000
167D430LEU00.0210.02019.3930.0110.0110.0000.0000.0000.000
168D431ASN0-0.0090.01022.0930.0180.0180.0000.0000.0000.000
169D432ALA00.006-0.00124.7140.0040.0040.0000.0000.0000.000
170D433VAL0-0.005-0.00818.1580.0000.0000.0000.0000.0000.000
171D434THR0-0.023-0.02021.3380.0270.0270.0000.0000.0000.000
172D435ASP-1-0.934-0.96922.8920.1490.1490.0000.0000.0000.000
173D436ALA0-0.008-0.01622.2060.0010.0010.0000.0000.0000.000
174D437LEU00.0060.00218.4810.0050.0050.0000.0000.0000.000
175D438VAL00.0180.00721.7700.0040.0040.0000.0000.0000.000
176D439TRP00.0160.00125.201-0.006-0.0060.0000.0000.0000.000
177D440VAL0-0.030-0.02620.560-0.007-0.0070.0000.0000.0000.000
178D441ILE0-0.0020.01321.4580.0010.0010.0000.0000.0000.000
179D442ALA00.0070.02224.441-0.006-0.0060.0000.0000.0000.000
180D443LYS10.8160.90826.234-0.174-0.1740.0000.0000.0000.000
181D444SER0-0.026-0.02325.229-0.005-0.0050.0000.0000.0000.000
182D445GLY0-0.009-0.00327.233-0.003-0.0030.0000.0000.0000.000
183D446ILE0-0.0370.00126.282-0.009-0.0090.0000.0000.0000.000
184D447SER00.0600.02330.471-0.006-0.0060.0000.0000.0000.000
185D448SER00.0620.02731.0590.0140.0140.0000.0000.0000.000
186D449GLN00.0450.02130.8250.0170.0170.0000.0000.0000.000
187D450GLN00.0300.00928.5770.0020.0020.0000.0000.0000.000
188D451GLN0-0.020-0.01926.6940.0190.0190.0000.0000.0000.000
189D452SER00.0140.00425.8720.0150.0150.0000.0000.0000.000
190D453MET00.0020.00525.6380.0200.0200.0000.0000.0000.000
191D454ARG10.7570.84219.784-0.333-0.3330.0000.0000.0000.000
192D455LEU00.0430.01521.4170.0330.0330.0000.0000.0000.000
193D456ALA00.0260.00921.3820.0260.0260.0000.0000.0000.000
194D457ASN0-0.028-0.02920.0690.0350.0350.0000.0000.0000.000
195D458LEU00.0230.00916.1040.0490.0490.0000.0000.0000.000
196D459LEU0-0.009-0.00116.7830.0440.0440.0000.0000.0000.000
197D460MET0-0.019-0.01217.8630.0210.0210.0000.0000.0000.000
198D461LEU0-0.0210.00212.9960.0370.0370.0000.0000.0000.000
199D462LEU00.0220.02312.9500.1250.1250.0000.0000.0000.000
200D463SER00.0180.00213.0900.0990.0990.0000.0000.0000.000
201D464HIS0-0.064-0.03011.775-0.020-0.0200.0000.0000.0000.000
202D465VAL00.0000.0007.2550.1310.1310.0000.0000.0000.000
203D466ARG10.8160.8958.625-0.427-0.4270.0000.0000.0000.000
204D467HIS0-0.040-0.02210.314-0.013-0.0130.0000.0000.0000.000
205D468ALA00.0240.0056.569-0.110-0.1100.0000.0000.0000.000
206D469SER00.0230.0025.6860.5310.5310.0000.0000.0000.000
207D470ASN00.022-0.0036.8300.2240.2240.0000.0000.0000.000
208D471LYS10.7860.8835.9740.8200.8200.0000.0000.0000.000
209D472GLY00.0180.0032.602-2.276-1.5591.199-0.893-1.0220.003
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