Manual

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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: PLY9X

Calculation Name: 1X76-B-Xray11

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: 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 -3100246.833838
FMO2-HF: Nuclear repulsion 3003844.139131
FMO2-HF: Total energy -96402.694706
FMO2-MP2: Total energy -96673.218476


3D Structure
Snapshot
 
Ligand structure

697

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.
-95.186-65.12053.595-24.653-59.0110.023


Interactive mode: IFIE and PIEDA for fragment #235(D:202:697)


Summations of interaction energy for fragment #235(D:202:697)
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.
-95.186-65.1253.595-24.653-59.011-0.023
Interaction energy analysis for fragmet #235(D:202:697)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.062
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].
1D264SER10.8180.87828.571-0.030-0.0300.0000.0000.0000.000
2D265PRO00.1140.05226.582-0.016-0.0160.0000.0000.0000.000
3D266GLU-1-0.775-0.85323.9040.0640.0640.0000.0000.0000.000
4D267GLN00.0370.01623.2540.0030.0030.0000.0000.0000.000
5D268LEU00.0420.04521.146-0.032-0.0320.0000.0000.0000.000
6D269VAL00.004-0.00118.744-0.024-0.0240.0000.0000.0000.000
7D270LEU0-0.021-0.02918.652-0.016-0.0160.0000.0000.0000.000
8D271THR0-0.019-0.00919.532-0.038-0.0380.0000.0000.0000.000
9D272LEU00.016-0.00115.387-0.050-0.0500.0000.0000.0000.000
10D273LEU0-0.038-0.01114.660-0.042-0.0420.0000.0000.0000.000
11D274GLU-1-0.885-0.92915.359-0.503-0.5030.0000.0000.0000.000
12D275ALA0-0.004-0.01014.716-0.076-0.0760.0000.0000.0000.000
13D276GLU-1-0.773-0.83210.499-0.592-0.5920.0000.0000.0000.000
14D277PRO00.0400.0396.804-0.029-0.0290.0000.0000.0000.000
15D278PRO0-0.031-0.0169.4530.1630.1630.0000.0000.0000.000
16D279HIS0-0.076-0.0636.568-0.095-0.0950.0000.0000.0000.000
17D280VAL00.0060.0245.8220.3900.3900.0000.0000.0000.000
18D281LEU00.0300.0137.183-0.058-0.0580.0000.0000.0000.000
19D282ILE0-0.052-0.0176.336-0.348-0.3480.0000.0000.0000.000
20D283SER0-0.015-0.0139.2730.1880.1880.0000.0000.0000.000
21D284ARG10.8050.87211.249-1.119-1.1190.0000.0000.0000.000
22D285PRO0-0.0210.00211.881-0.056-0.0560.0000.0000.0000.000
23D286SER0-0.002-0.00514.8650.1100.1100.0000.0000.0000.000
24D287ALA0-0.038-0.02617.164-0.028-0.0280.0000.0000.0000.000
25D288PRO00.0090.00416.9130.0790.0790.0000.0000.0000.000
26D289PHE00.0020.01410.508-0.063-0.0630.0000.0000.0000.000
27D290THR00.002-0.02311.643-0.065-0.0650.0000.0000.0000.000
28D291GLU-1-0.743-0.8696.500-1.870-1.8700.0000.0000.0000.000
29D292ALA00.0430.0357.775-0.203-0.2030.0000.0000.0000.000
30D293SER0-0.015-0.0169.888-0.072-0.0720.0000.0000.0000.000
31D294MET00.0180.0137.1170.2860.2860.0000.0000.0000.000
32D295MET00.0360.0292.418-1.1670.9962.364-1.077-3.4490.011
33D296MET0-0.0140.0096.249-0.595-0.5950.0000.0000.0000.000
34D297SER0-0.019-0.0167.689-0.244-0.2440.0000.0000.0000.000
35D298LEU00.013-0.0033.042-5.089-1.1221.064-0.980-4.0510.010
36D299THR0-0.019-0.0302.824-6.190-4.0330.302-1.002-1.456-0.012
37D300LYS10.8540.9165.0631.5141.631-0.001-0.006-0.1110.000
38D301LEU0-0.0150.0152.404-0.8780.6781.474-0.692-2.3390.003
39D302ALA00.015-0.0052.162-1.903-0.7212.207-1.199-2.1900.003
40D303ASP-1-0.825-0.9143.375-1.168-1.1740.0420.148-0.1840.000
41D304LYS10.8740.9326.8002.9722.9720.0000.0000.0000.000
42D305GLU-1-0.799-0.8841.698-26.198-31.08512.332-4.370-3.076-0.054
43D306LEU00.0230.0185.8400.9930.9930.0000.0000.0000.000
44D307VAL0-0.0010.0008.2170.5190.5190.0000.0000.0000.000
45D308HIS0-0.022-0.0188.5750.4120.4120.0000.0000.0000.000
46D309MET0-0.0290.0118.2610.3140.3140.0000.0000.0000.000
47D310ILE00.0100.01210.1830.2970.2970.0000.0000.0000.000
48D311SER0-0.010-0.01513.2560.2020.2020.0000.0000.0000.000
49D312TRP0-0.042-0.03811.0430.1810.1810.0000.0000.0000.000
50D313ALA00.0230.01113.1290.1380.1380.0000.0000.0000.000
51D314LYS10.8770.92515.2330.5560.5560.0000.0000.0000.000
52D315LYS10.8450.92315.9640.5980.5980.0000.0000.0000.000
53D316ILE0-0.0370.00015.9870.0610.0610.0000.0000.0000.000
54D317PRO0-0.008-0.01819.7740.0000.0000.0000.0000.0000.000
55D318GLY00.0490.02623.6520.0230.0230.0000.0000.0000.000
56D319PHE00.0380.01017.4360.0070.0070.0000.0000.0000.000
57D320VAL0-0.038-0.03021.551-0.010-0.0100.0000.0000.0000.000
58D321GLU-1-0.863-0.92023.524-0.133-0.1330.0000.0000.0000.000
59D322LEU0-0.0510.00321.8370.0200.0200.0000.0000.0000.000
60D323SER00.010-0.01925.229-0.035-0.0350.0000.0000.0000.000
61D324LEU00.0430.01722.513-0.010-0.0100.0000.0000.0000.000
62D325PHE00.0380.00622.459-0.032-0.0320.0000.0000.0000.000
63D326ASP-1-0.775-0.83322.505-0.122-0.1220.0000.0000.0000.000
64D327GLN0-0.041-0.03319.819-0.049-0.0490.0000.0000.0000.000
65D328VAL00.0050.01717.578-0.050-0.0500.0000.0000.0000.000
66D329ARG10.9190.96517.3280.0940.0940.0000.0000.0000.000
67D330LEU0-0.100-0.05116.8040.0340.0340.0000.0000.0000.000
68D331LEU0-0.012-0.01912.587-0.048-0.0480.0000.0000.0000.000
69D332GLU-1-0.750-0.91012.968-0.320-0.3200.0000.0000.0000.000
70D333SER0-0.007-0.01113.0520.0560.0560.0000.0000.0000.000
71D334CYS0-0.036-0.00811.1690.1120.1120.0000.0000.0000.000
72D335TRP00.0690.0234.788-0.0110.182-0.001-0.006-0.1860.000
73D336MET00.0290.0213.080-2.1390.3390.730-0.528-2.6790.005
74D337GLU-1-0.810-0.8805.2401.4721.4720.0000.0000.0000.000
75D338VAL0-0.018-0.0196.5350.2640.2640.0000.0000.0000.000
76D339LEU00.0070.0152.736-3.998-1.3083.033-1.316-4.4080.011
77D340MET0-0.039-0.0082.402-1.1091.5392.011-1.314-3.345-0.009
78D341MET0-0.009-0.0033.2390.7680.5290.0070.463-0.2310.000
79D342GLY0-0.0050.0034.843-0.317-0.231-0.001-0.008-0.0770.000
80D343LEU00.0030.0122.443-2.603-0.9002.211-1.003-2.9100.005
81D344MET0-0.0200.0044.085-0.515-0.2560.002-0.062-0.2000.000
82D345TRP0-0.040-0.0237.025-0.208-0.2080.0000.0000.0000.000
83D346ARG10.7540.8392.4321.9273.0360.853-0.669-1.2930.005
84D347SER00.008-0.0017.3730.1070.1070.0000.0000.0000.000
85D348ILE0-0.0120.0049.9830.0260.0260.0000.0000.0000.000
86D349ASP-1-0.851-0.90912.7271.0201.0200.0000.0000.0000.000
87D350HIS00.009-0.01312.911-0.019-0.0190.0000.0000.0000.000
88D351PRO0-0.028-0.00315.0000.1730.1730.0000.0000.0000.000
89D352GLY00.007-0.00813.139-0.076-0.0760.0000.0000.0000.000
90D353LYS10.7980.89311.350-1.306-1.3060.0000.0000.0000.000
91D354LEU00.0060.0164.781-0.217-0.057-0.001-0.006-0.1530.000
92D355ILE0-0.001-0.0088.045-0.173-0.1730.0000.0000.0000.000
93D356PHE00.0470.0052.602-6.687-2.3833.356-1.666-5.9930.017
94D357ALA00.0270.0063.870-1.826-1.3900.012-0.128-0.3210.000
95D358PRO0-0.021-0.0186.4120.5730.5730.0000.0000.0000.000
96D359ASP-1-0.847-0.9139.7280.2970.2970.0000.0000.0000.000
97D360LEU0-0.027-0.0085.095-0.320-0.3200.0000.0000.0000.000
98D361VAL00.0160.0198.2450.8240.8240.0000.0000.0000.000
99D362LEU00.0110.0086.690-0.272-0.2720.0000.0000.0000.000
100D363ASP-1-0.812-0.90610.0942.0672.0670.0000.0000.0000.000
101D364ARG10.8030.8599.684-1.853-1.8530.0000.0000.0000.000
102D365ASP-1-0.822-0.8919.0732.0932.0930.0000.0000.0000.000
103D366GLU-1-0.749-0.83610.0051.0951.0950.0000.0000.0000.000
104D367GLY00.0310.0117.722-0.277-0.2770.0000.0000.0000.000
105D368LYS10.8270.8878.416-1.776-1.7760.0000.0000.0000.000
106D369CYS0-0.125-0.02811.151-0.274-0.2740.0000.0000.0000.000
107D370VAL00.015-0.0185.400-0.282-0.2820.0000.0000.0000.000
108D371GLU-1-0.816-0.8787.450-1.379-1.3790.0000.0000.0000.000
109D372GLY00.0240.0126.609-1.055-1.0550.0000.0000.0000.000
110D373ILE0-0.015-0.0012.570-1.6780.1351.733-0.757-2.7900.008
111D374LEU00.0000.0034.7413.4243.534-0.001-0.004-0.1050.000
112D375GLU-1-0.838-0.9137.3681.6271.6270.0000.0000.0000.000
113D376ILE00.0260.0052.700-2.119-0.4681.498-0.664-2.4850.007
114D377PHE00.003-0.0132.779-2.675-1.0761.299-0.631-2.2670.011
115D378ASP-1-0.757-0.8485.0941.4141.462-0.001-0.005-0.0420.000
116D379MET0-0.0490.0046.912-0.663-0.6630.0000.0000.0000.000
117D380LEU00.0480.0293.436-1.726-1.0290.073-0.182-0.5880.001
118D381LEU00.0340.0267.498-1.085-1.0850.0000.0000.0000.000
119D382ALA0-0.0170.0099.923-0.652-0.6520.0000.0000.0000.000
120D383THR0-0.024-0.03210.378-0.518-0.5180.0000.0000.0000.000
121D384THR0-0.018-0.0239.476-0.383-0.3830.0000.0000.0000.000
122D385SER0-0.046-0.03811.635-0.398-0.3980.0000.0000.0000.000
123D386ARG10.8020.87415.072-1.152-1.1520.0000.0000.0000.000
124D387PHE00.0440.0029.594-0.213-0.2130.0000.0000.0000.000
125D388ARG10.8020.89613.538-1.674-1.6740.0000.0000.0000.000
126D389GLU-1-0.884-0.90816.7760.7590.7590.0000.0000.0000.000
127D390LEU0-0.044-0.02817.598-0.112-0.1120.0000.0000.0000.000
128D391LYS10.9110.96419.107-0.595-0.5950.0000.0000.0000.000
129D392LEU00.0100.02713.017-0.100-0.1000.0000.0000.0000.000
130D393GLN0-0.048-0.03417.063-0.040-0.0400.0000.0000.0000.000
131D394HIS00.0920.05112.7060.1030.1030.0000.0000.0000.000
132D395LYS10.8430.89715.873-0.147-0.1470.0000.0000.0000.000
133D396GLU-1-0.731-0.86917.2820.4650.4650.0000.0000.0000.000
134D397TYR0-0.021-0.0378.7720.0080.0080.0000.0000.0000.000
135D398LEU0-0.0130.01212.6670.0100.0100.0000.0000.0000.000
136D399CYS0-0.013-0.00514.438-0.056-0.0560.0000.0000.0000.000
137D400VAL00.0320.00612.783-0.021-0.0210.0000.0000.0000.000
138D401LYS10.8280.9208.1510.4560.4560.0000.0000.0000.000
139D402ALA00.0350.01912.034-0.074-0.0740.0000.0000.0000.000
140D403MET0-0.043-0.01915.247-0.015-0.0150.0000.0000.0000.000
141D404ILE0-0.012-0.0039.762-0.015-0.0150.0000.0000.0000.000
142D405LEU00.0060.00812.781-0.037-0.0370.0000.0000.0000.000
143D406LEU0-0.0130.00114.505-0.035-0.0350.0000.0000.0000.000
144D407ASN00.003-0.00217.284-0.004-0.0040.0000.0000.0000.000
145D408SER0-0.039-0.01814.854-0.015-0.0150.0000.0000.0000.000
146D409SER00.0260.01516.936-0.073-0.0730.0000.0000.0000.000
147D410MET0-0.112-0.05717.6260.0360.0360.0000.0000.0000.000
148D411TYR00.021-0.03414.790-0.023-0.0230.0000.0000.0000.000
149D412PRO0-0.063-0.00814.112-0.036-0.0360.0000.0000.0000.000
150D413LEU0-0.033-0.01316.103-0.014-0.0140.0000.0000.0000.000
151D414VAL00.0160.01817.5530.0130.0130.0000.0000.0000.000
152D415THR0-0.038-0.01020.2520.0120.0120.0000.0000.0000.000
153D416ALA00.009-0.01023.2430.0310.0310.0000.0000.0000.000
154D417THR0-0.053-0.03525.918-0.022-0.0220.0000.0000.0000.000
155D418GLN0-0.018-0.00827.5940.0100.0100.0000.0000.0000.000
156D419ASP-1-0.769-0.86629.369-0.069-0.0690.0000.0000.0000.000
157D420ALA00.0140.01431.4250.0140.0140.0000.0000.0000.000
158D421ASP-1-0.847-0.91330.509-0.072-0.0720.0000.0000.0000.000
159D422SER00.013-0.03927.0430.0100.0100.0000.0000.0000.000
160D423SER00.0000.02527.1250.0150.0150.0000.0000.0000.000
161D424ARG10.7940.87327.9100.0670.0670.0000.0000.0000.000
162D425LYS10.8260.90026.3400.1210.1210.0000.0000.0000.000
163D426LEU00.0230.01221.0040.0010.0010.0000.0000.0000.000
164D427ALA00.0180.01324.0550.0220.0220.0000.0000.0000.000
165D428HIS0-0.028-0.01126.1390.0260.0260.0000.0000.0000.000
166D429LEU0-0.009-0.01021.5550.0110.0110.0000.0000.0000.000
167D430LEU00.0060.00719.7060.0140.0140.0000.0000.0000.000
168D431ASN0-0.0080.01722.4480.0470.0470.0000.0000.0000.000
169D432ALA00.0620.03624.8680.0190.0190.0000.0000.0000.000
170D433VAL0-0.027-0.01918.2960.0030.0030.0000.0000.0000.000
171D434THR0-0.001-0.01421.4240.0510.0510.0000.0000.0000.000
172D435ASP-1-0.906-0.96022.8350.1300.1300.0000.0000.0000.000
173D436ALA0-0.076-0.04622.3760.0060.0060.0000.0000.0000.000
174D437LEU00.0090.00618.5910.0110.0110.0000.0000.0000.000
175D438VAL00.0350.01521.8920.0240.0240.0000.0000.0000.000
176D439TRP00.0120.00425.3190.0020.0020.0000.0000.0000.000
177D440VAL0-0.047-0.02721.194-0.010-0.0100.0000.0000.0000.000
178D441ILE00.0210.01520.7110.0090.0090.0000.0000.0000.000
179D442ALA0-0.0250.00424.6080.0110.0110.0000.0000.0000.000
180D443LYS10.8240.91127.045-0.171-0.1710.0000.0000.0000.000
181D444SER0-0.027-0.01924.0340.0070.0070.0000.0000.0000.000
182D445GLY0-0.0130.00225.7900.0300.0300.0000.0000.0000.000
183D446ILE0-0.028-0.00925.203-0.013-0.0130.0000.0000.0000.000
184D447SER00.0480.01729.125-0.010-0.0100.0000.0000.0000.000
185D448SER00.0530.02330.6600.0210.0210.0000.0000.0000.000
186D449GLN00.0280.01730.3680.0150.0150.0000.0000.0000.000
187D450GLN00.0650.02528.0560.0290.0290.0000.0000.0000.000
188D451GLN0-0.061-0.02526.2540.0240.0240.0000.0000.0000.000
189D452SER00.013-0.00725.4790.0140.0140.0000.0000.0000.000
190D453MET0-0.0070.01325.1620.0320.0320.0000.0000.0000.000
191D454ARG10.8320.90720.144-0.452-0.4520.0000.0000.0000.000
192D455LEU00.0230.00921.0280.0520.0520.0000.0000.0000.000
193D456ALA00.0240.01021.0390.0330.0330.0000.0000.0000.000
194D457ASN0-0.035-0.03420.2760.0840.0840.0000.0000.0000.000
195D458LEU00.0130.00315.8110.1000.1000.0000.0000.0000.000
196D459LEU0-0.004-0.00116.1580.0660.0660.0000.0000.0000.000
197D460MET0-0.009-0.00117.7420.0220.0220.0000.0000.0000.000
198D461LEU00.0060.01613.9980.0530.0530.0000.0000.0000.000
199D462LEU00.0050.00812.7520.2200.2200.0000.0000.0000.000
200D463SER0-0.027-0.01613.784-0.009-0.0090.0000.0000.0000.000
201D464HIS00.001-0.00111.752-0.024-0.0240.0000.0000.0000.000
202D465VAL00.0070.0068.0460.4230.4230.0000.0000.0000.000
203D466ARG10.8320.8959.295-0.338-0.3380.0000.0000.0000.000
204D467HIS0-0.009-0.01010.941-0.178-0.1780.0000.0000.0000.000
205D468ALA00.0850.0146.150-0.060-0.0600.0000.0000.0000.000
206D469SER0-0.0130.0066.4790.2050.2050.0000.0000.0000.000
207D470ASN00.0000.0168.511-0.467-0.4670.0000.0000.0000.000
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