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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: PKM3P

Calculation Name: 1U3Q-B-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: B

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 -3040322.328487
FMO2-HF: Nuclear repulsion 2943923.073847
FMO2-HF: Total energy -96399.25464
FMO2-MP2: Total energy -96669.692081


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.
-112.648-83.61051.351-29.078-51.3120.075


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


Summations of interaction energy for fragment #235(B: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.
-112.648-83.6151.351-29.078-51.312-0.075
Interaction energy analysis for fragmet #235(B:501:272)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.076 / q_NPA : -0.090
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].
1B264SER10.8580.91529.279-0.035-0.0350.0000.0000.0000.000
2B265PRO00.1600.06826.635-0.017-0.0170.0000.0000.0000.000
3B266GLU-1-0.912-0.94325.5810.0490.0490.0000.0000.0000.000
4B267GLN00.027-0.00525.837-0.004-0.0040.0000.0000.0000.000
5B268LEU00.0040.02922.244-0.030-0.0300.0000.0000.0000.000
6B269VAL00.0330.00220.695-0.019-0.0190.0000.0000.0000.000
7B270LEU0-0.043-0.03420.742-0.019-0.0190.0000.0000.0000.000
8B271THR00.0170.01420.976-0.042-0.0420.0000.0000.0000.000
9B272LEU0-0.006-0.00717.072-0.053-0.0530.0000.0000.0000.000
10B273LEU0-0.048-0.02916.570-0.038-0.0380.0000.0000.0000.000
11B274GLU-1-1.007-1.00217.206-0.488-0.4880.0000.0000.0000.000
12B275ALA00.015-0.00716.208-0.075-0.0750.0000.0000.0000.000
13B276GLU-1-0.826-0.89111.391-0.574-0.5740.0000.0000.0000.000
14B277PRO0-0.063-0.0128.603-0.096-0.0960.0000.0000.0000.000
15B278PRO00.0010.00410.8810.1210.1210.0000.0000.0000.000
16B279HIS00.018-0.0059.123-0.648-0.6480.0000.0000.0000.000
17B280VAL00.0070.0095.6470.3580.3580.0000.0000.0000.000
18B281LEU0-0.024-0.0258.4270.1800.1800.0000.0000.0000.000
19B282ILE0-0.074-0.0236.9140.1060.1060.0000.0000.0000.000
20B283SER00.0260.01210.2450.0650.0650.0000.0000.0000.000
21B284ARG10.8950.95712.011-0.398-0.3980.0000.0000.0000.000
22B285PRO0-0.039-0.01912.3380.0060.0060.0000.0000.0000.000
23B286SER0-0.0200.00115.5580.0920.0920.0000.0000.0000.000
24B287ALA00.0160.01218.4250.0520.0520.0000.0000.0000.000
25B288PRO00.014-0.00816.502-0.012-0.0120.0000.0000.0000.000
26B289PHE00.0230.02110.602-0.076-0.0760.0000.0000.0000.000
27B290THR0-0.0020.00312.7570.0250.0250.0000.0000.0000.000
28B291GLU-1-0.755-0.8888.718-0.596-0.5960.0000.0000.0000.000
29B292ALA00.024-0.0068.718-0.023-0.0230.0000.0000.0000.000
30B293SER0-0.030-0.0139.438-0.104-0.1040.0000.0000.0000.000
31B294MET00.0400.0206.381-0.202-0.2020.0000.0000.0000.000
32B295MET00.0270.0283.613-2.110-0.4690.326-0.580-1.3880.006
33B296MET00.0120.0354.876-1.016-0.858-0.001-0.005-0.1520.000
34B297SER00.010-0.0147.477-0.522-0.5220.0000.0000.0000.000
35B298LEU0-0.026-0.0172.270-4.511-1.5031.908-1.260-3.6560.010
36B299THR0-0.002-0.0072.961-7.254-4.8410.181-1.047-1.548-0.010
37B300LYS10.9610.9884.9851.7421.878-0.001-0.011-0.1240.000
38B301LEU0-0.082-0.0422.4460.0821.7960.544-0.601-1.6570.000
39B302ALA00.0750.0242.658-3.815-1.8620.644-0.906-1.691-0.001
40B303ASP-1-0.801-0.9033.396-0.725-0.7590.0450.069-0.0800.000
41B304LYS10.9370.9646.5383.9053.9050.0000.0000.0000.000
42B305GLU-1-0.840-0.8981.531-48.332-57.48825.933-11.629-5.147-0.107
43B306LEU0-0.0040.0155.8641.3971.3970.0000.0000.0000.000
44B307VAL00.0190.0258.1600.7140.7140.0000.0000.0000.000
45B308HIS0-0.020-0.0248.2730.6440.6440.0000.0000.0000.000
46B309MET0-0.033-0.0096.9400.5690.5690.0000.0000.0000.000
47B310ILE00.0600.0339.9890.4330.4330.0000.0000.0000.000
48B311SER0-0.054-0.04113.2300.2450.2450.0000.0000.0000.000
49B312TRP0-0.032-0.01111.8760.1410.1410.0000.0000.0000.000
50B313ALA00.0600.02913.8400.1510.1510.0000.0000.0000.000
51B314LYS10.9060.94615.5320.6510.6510.0000.0000.0000.000
52B315LYS10.8980.97616.0150.7570.7570.0000.0000.0000.000
53B316ILE0-0.0180.00515.4560.0670.0670.0000.0000.0000.000
54B317PRO0-0.011-0.02819.6200.0020.0020.0000.0000.0000.000
55B318GLY00.0660.03323.3070.0310.0310.0000.0000.0000.000
56B319PHE00.0150.01417.5990.0070.0070.0000.0000.0000.000
57B320VAL0-0.002-0.01321.638-0.003-0.0030.0000.0000.0000.000
58B321GLU-1-0.983-0.98523.473-0.094-0.0940.0000.0000.0000.000
59B322LEU0-0.076-0.01621.8690.0240.0240.0000.0000.0000.000
60B323SER0-0.040-0.03325.481-0.038-0.0380.0000.0000.0000.000
61B324LEU00.0380.00423.3980.0000.0000.0000.0000.0000.000
62B325PHE00.0400.00722.402-0.018-0.0180.0000.0000.0000.000
63B326ASP-1-0.783-0.84022.3050.0260.0260.0000.0000.0000.000
64B327GLN0-0.090-0.04419.556-0.023-0.0230.0000.0000.0000.000
65B328VAL00.0410.01217.816-0.010-0.0100.0000.0000.0000.000
66B329ARG10.9781.01017.651-0.119-0.1190.0000.0000.0000.000
67B330LEU0-0.037-0.01817.1770.0710.0710.0000.0000.0000.000
68B331LEU00.014-0.00212.5860.1090.1090.0000.0000.0000.000
69B332GLU-1-0.884-0.95113.093-0.050-0.0500.0000.0000.0000.000
70B333SER0-0.046-0.01313.8390.1480.1480.0000.0000.0000.000
71B334CYS0-0.081-0.02411.8710.1510.1510.0000.0000.0000.000
72B335TRP00.0700.0165.4740.5610.5610.0000.0000.0000.000
73B336MET00.0220.0183.710-1.4741.1640.358-0.550-2.4460.003
74B337GLU-1-0.884-0.9565.5983.3283.431-0.001-0.008-0.0950.000
75B338VAL0-0.020-0.0117.0300.2450.2450.0000.0000.0000.000
76B339LEU0-0.0160.0032.539-3.124-0.4352.956-1.438-4.2070.013
77B340MET0-0.0140.0052.362-6.328-3.9465.776-2.129-6.0290.008
78B341MET00.0260.0253.637-0.886-0.7750.0060.045-0.1620.000
79B342GLY00.0080.0065.323-0.416-0.4160.0000.0000.0000.000
80B343LEU0-0.029-0.0142.362-2.987-0.8231.403-0.804-2.7630.007
81B344MET0-0.051-0.0224.349-0.801-0.6380.000-0.028-0.1350.000
82B345TRP0-0.013-0.0087.371-0.434-0.4340.0000.0000.0000.000
83B346ARG10.8740.9392.901-1.715-0.4080.098-0.535-0.8710.006
84B347SER00.0210.0147.433-0.154-0.1540.0000.0000.0000.000
85B348ILE0-0.0390.00410.097-0.012-0.0120.0000.0000.0000.000
86B349ASP-1-0.921-0.95212.6610.6420.6420.0000.0000.0000.000
87B350HIS0-0.061-0.04012.913-0.146-0.1460.0000.0000.0000.000
88B351PRO00.001-0.00213.7030.2460.2460.0000.0000.0000.000
89B352GLY00.0060.00514.512-0.137-0.1370.0000.0000.0000.000
90B353LYS10.9340.96912.461-0.806-0.8060.0000.0000.0000.000
91B354LEU00.0060.0176.1660.2450.2450.0000.0000.0000.000
92B355ILE0-0.017-0.0208.120-0.385-0.3850.0000.0000.0000.000
93B356PHE00.0430.0123.126-5.133-1.0441.019-1.107-4.0020.014
94B357ALA00.011-0.0034.353-2.799-2.6240.000-0.020-0.1540.000
95B358PRO0-0.020-0.0206.9100.6940.6940.0000.0000.0000.000
96B359ASP-1-0.895-0.94110.633-0.266-0.2660.0000.0000.0000.000
97B360LEU0-0.005-0.0066.507-0.089-0.0890.0000.0000.0000.000
98B361VAL0-0.039-0.0108.7910.3150.3150.0000.0000.0000.000
99B362LEU0-0.005-0.0117.803-0.202-0.2020.0000.0000.0000.000
100B363ASP-1-0.865-0.93511.3171.3631.3630.0000.0000.0000.000
101B364ARG10.8640.92111.589-1.379-1.3790.0000.0000.0000.000
102B365ASP-1-0.906-0.96311.9741.0481.0480.0000.0000.0000.000
103B366GLU-1-0.853-0.94011.7710.5670.5670.0000.0000.0000.000
104B367GLY0-0.007-0.0069.201-0.079-0.0790.0000.0000.0000.000
105B368LYS10.8810.9359.778-0.981-0.9810.0000.0000.0000.000
106B369CYS0-0.088-0.03810.581-0.144-0.1440.0000.0000.0000.000
107B370VAL0-0.024-0.0205.197-0.176-0.1760.0000.0000.0000.000
108B371GLU-1-0.880-0.9378.238-0.523-0.5230.0000.0000.0000.000
109B372GLY00.0360.0176.973-0.613-0.6130.0000.0000.0000.000
110B373ILE0-0.016-0.0033.235-1.782-0.1400.382-0.554-1.4700.005
111B374LEU0-0.017-0.0125.7661.5381.5380.0000.0000.0000.000
112B375GLU-1-0.905-0.9468.2951.0421.0420.0000.0000.0000.000
113B376ILE00.0090.0002.620-1.495-0.1050.945-0.562-1.7730.006
114B377PHE00.015-0.0084.8020.8531.2110.000-0.024-0.3320.000
115B378ASP-1-0.798-0.8887.0961.9311.9310.0000.0000.0000.000
116B379MET0-0.046-0.0137.583-0.034-0.0340.0000.0000.0000.000
117B380LEU00.0190.0192.997-2.032-0.5810.164-0.402-1.2120.003
118B381LEU00.0200.0177.612-0.752-0.7520.0000.0000.0000.000
119B382ALA0-0.015-0.00510.516-0.490-0.4900.0000.0000.0000.000
120B383THR0-0.013-0.0209.735-0.493-0.4930.0000.0000.0000.000
121B384THR0-0.005-0.0129.073-0.339-0.3390.0000.0000.0000.000
122B385SER0-0.050-0.03011.403-0.436-0.4360.0000.0000.0000.000
123B386ARG10.9280.97514.440-1.488-1.4880.0000.0000.0000.000
124B387PHE00.0300.00010.750-0.241-0.2410.0000.0000.0000.000
125B388ARG10.9200.95814.040-1.582-1.5820.0000.0000.0000.000
126B389GLU-1-0.960-0.96316.4840.6340.6340.0000.0000.0000.000
127B390LEU0-0.039-0.01317.500-0.114-0.1140.0000.0000.0000.000
128B391LYS10.9400.96818.975-0.663-0.6630.0000.0000.0000.000
129B392LEU0-0.0200.00412.947-0.080-0.0800.0000.0000.0000.000
130B393GLN00.0100.00616.905-0.082-0.0820.0000.0000.0000.000
131B394HIS00.0620.02313.499-0.017-0.0170.0000.0000.0000.000
132B395LYS10.9610.97615.765-0.090-0.0900.0000.0000.0000.000
133B396GLU-1-0.737-0.82417.6550.5470.5470.0000.0000.0000.000
134B397TYR00.0080.0019.0730.0910.0910.0000.0000.0000.000
135B398LEU00.0020.00613.5790.0470.0470.0000.0000.0000.000
136B399CYS0-0.066-0.00815.072-0.050-0.0500.0000.0000.0000.000
137B400VAL00.0520.01312.854-0.005-0.0050.0000.0000.0000.000
138B401LYS10.8600.9148.8770.3430.3430.0000.0000.0000.000
139B402ALA00.0060.01412.527-0.015-0.0150.0000.0000.0000.000
140B403MET0-0.059-0.02915.563-0.008-0.0080.0000.0000.0000.000
141B404ILE0-0.0110.00110.5810.0010.0010.0000.0000.0000.000
142B405LEU00.0230.00613.6180.0060.0060.0000.0000.0000.000
143B406LEU0-0.039-0.00914.916-0.029-0.0290.0000.0000.0000.000
144B407ASN0-0.006-0.00917.493-0.108-0.1080.0000.0000.0000.000
145B408SER0-0.035-0.01815.5520.0020.0020.0000.0000.0000.000
146B409SER0-0.044-0.03317.614-0.049-0.0490.0000.0000.0000.000
147B410MET00.0260.02820.198-0.028-0.0280.0000.0000.0000.000
148B411TYR00.0570.01224.101-0.038-0.0380.0000.0000.0000.000
149B412PRO00.0090.01324.297-0.027-0.0270.0000.0000.0000.000
150B413LEU00.0070.01126.207-0.020-0.0200.0000.0000.0000.000
151B414VAL00.0070.00928.094-0.020-0.0200.0000.0000.0000.000
152B415THR0-0.076-0.04630.321-0.010-0.0100.0000.0000.0000.000
153B416ALA0-0.0120.00330.909-0.008-0.0080.0000.0000.0000.000
154B417THR0-0.045-0.01532.751-0.018-0.0180.0000.0000.0000.000
155B418GLN0-0.009-0.00630.423-0.025-0.0250.0000.0000.0000.000
156B419ASP-1-0.850-0.92731.2470.1000.1000.0000.0000.0000.000
157B420ALA00.033-0.00131.760-0.009-0.0090.0000.0000.0000.000
158B421ASP-1-0.934-1.00831.4590.0170.0170.0000.0000.0000.000
159B422SER0-0.010-0.04926.5840.0070.0070.0000.0000.0000.000
160B423SER00.0910.04326.8580.0120.0120.0000.0000.0000.000
161B424ARG10.8430.94127.554-0.020-0.0200.0000.0000.0000.000
162B425LYS10.8850.96127.7610.0390.0390.0000.0000.0000.000
163B426LEU00.0670.05021.391-0.003-0.0030.0000.0000.0000.000
164B427ALA00.0180.02024.5920.0220.0220.0000.0000.0000.000
165B428HIS0-0.0060.00126.4830.0260.0260.0000.0000.0000.000
166B429LEU0-0.009-0.01921.7960.0080.0080.0000.0000.0000.000
167B430LEU0-0.011-0.01119.9360.0060.0060.0000.0000.0000.000
168B431ASN00.012-0.00522.7470.0490.0490.0000.0000.0000.000
169B432ALA00.0310.02724.9130.0080.0080.0000.0000.0000.000
170B433VAL0-0.004-0.00718.580-0.003-0.0030.0000.0000.0000.000
171B434THR0-0.022-0.01721.7970.0480.0480.0000.0000.0000.000
172B435ASP-1-0.896-0.95522.9850.2070.2070.0000.0000.0000.000
173B436ALA0-0.070-0.02722.217-0.006-0.0060.0000.0000.0000.000
174B437LEU00.0330.00218.9290.0010.0010.0000.0000.0000.000
175B438VAL00.0180.00921.9570.0150.0150.0000.0000.0000.000
176B439TRP00.0170.00924.796-0.006-0.0060.0000.0000.0000.000
177B440VAL0-0.034-0.02821.058-0.012-0.0120.0000.0000.0000.000
178B441ILE0-0.009-0.00121.8210.0050.0050.0000.0000.0000.000
179B442ALA00.0470.02424.789-0.004-0.0040.0000.0000.0000.000
180B443LYS10.7640.88526.690-0.193-0.1930.0000.0000.0000.000
181B444SER0-0.037-0.01825.684-0.009-0.0090.0000.0000.0000.000
182B445GLY0-0.0010.00127.480-0.001-0.0010.0000.0000.0000.000
183B446ILE0-0.033-0.01326.930-0.008-0.0080.0000.0000.0000.000
184B447SER00.0760.04831.137-0.013-0.0130.0000.0000.0000.000
185B448SER00.0620.03231.3260.0240.0240.0000.0000.0000.000
186B449GLN00.0340.00731.5230.0330.0330.0000.0000.0000.000
187B450GLN00.028-0.01129.1290.0030.0030.0000.0000.0000.000
188B451GLN0-0.010-0.00127.2120.0350.0350.0000.0000.0000.000
189B452SER00.0180.01926.4960.0220.0220.0000.0000.0000.000
190B453MET0-0.029-0.01526.4900.0420.0420.0000.0000.0000.000
191B454ARG10.7340.82720.024-0.548-0.5480.0000.0000.0000.000
192B455LEU00.0290.02521.9350.0620.0620.0000.0000.0000.000
193B456ALA00.006-0.00321.7340.0580.0580.0000.0000.0000.000
194B457ASN0-0.041-0.03721.0270.0800.0800.0000.0000.0000.000
195B458LEU0-0.0180.00416.8030.1160.1160.0000.0000.0000.000
196B459LEU00.0410.01416.8580.1400.1400.0000.0000.0000.000
197B460MET0-0.014-0.01117.8420.0820.0820.0000.0000.0000.000
198B461LEU0-0.0070.00014.3710.0640.0640.0000.0000.0000.000
199B462LEU00.0070.00113.4230.2980.2980.0000.0000.0000.000
200B463SER00.0050.00813.3890.1720.1720.0000.0000.0000.000
201B464HIS0-0.013-0.01512.7350.1060.1060.0000.0000.0000.000
202B465VAL00.0330.0318.2900.4700.4700.0000.0000.0000.000
203B466ARG10.9350.9758.952-0.692-0.6920.0000.0000.0000.000
204B467HIS0-0.086-0.04610.204-0.020-0.0200.0000.0000.0000.000
205B468ALA00.0460.0116.173-0.136-0.1360.0000.0000.0000.000
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