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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: XYJ2P

Calculation Name: 3OLL-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 3OLL

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 -3072678.93014
FMO2-HF: Nuclear repulsion 2976282.962862
FMO2-HF: Total energy -96395.967278
FMO2-MP2: Total energy -96666.584701


3D Structure
Snapshot
 
Ligand structure

EST

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.
-87.341-65.23672.938-26.563-68.4820.101


Interactive mode: IFIE and PIEDA for fragment #235(D:600:EST)


Summations of interaction energy for fragment #235(D:600:EST)
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.
-87.341-65.23672.938-26.563-68.482-0.101
Interaction energy analysis for fragmet #235(D:600:EST)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.098 / q_NPA : -0.083
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].
1D264SER10.8510.91330.529-0.054-0.0540.0000.0000.0000.000
2D265PRO00.1710.07126.664-0.005-0.0050.0000.0000.0000.000
3D266GLU-1-0.817-0.88524.9730.1030.1030.0000.0000.0000.000
4D267GLN00.0450.01124.3440.0060.0060.0000.0000.0000.000
5D268LEU0-0.0110.02822.218-0.005-0.0050.0000.0000.0000.000
6D269VAL00.019-0.01220.6350.0050.0050.0000.0000.0000.000
7D270LEU0-0.066-0.01520.0130.0120.0120.0000.0000.0000.000
8D271THR00.0440.00420.218-0.009-0.0090.0000.0000.0000.000
9D272LEU0-0.003-0.00816.670-0.010-0.0100.0000.0000.0000.000
10D273LEU0-0.037-0.01915.6260.0160.0160.0000.0000.0000.000
11D274GLU-1-0.873-0.94416.148-0.001-0.0010.0000.0000.0000.000
12D275ALA00.0410.02115.271-0.031-0.0310.0000.0000.0000.000
13D276GLU-1-0.773-0.83610.4480.1090.1090.0000.0000.0000.000
14D277PRO0-0.0140.0088.1810.0050.0050.0000.0000.0000.000
15D278PRO0-0.039-0.02310.3450.0720.0720.0000.0000.0000.000
16D279HIS0-0.032-0.0136.457-0.273-0.2730.0000.0000.0000.000
17D280VAL0-0.044-0.0165.6210.4730.4730.0000.0000.0000.000
18D281LEU0-0.020-0.0066.7360.0120.0120.0000.0000.0000.000
19D282ILE0-0.035-0.0306.374-0.129-0.1290.0000.0000.0000.000
20D283SER00.0190.0049.3270.1230.1230.0000.0000.0000.000
21D284ARG10.7740.84910.871-0.321-0.3210.0000.0000.0000.000
22D285PRO0-0.0090.00911.471-0.053-0.0530.0000.0000.0000.000
23D286SER0-0.0050.00314.2700.0110.0110.0000.0000.0000.000
24D287ALA0-0.021-0.01916.540-0.012-0.0120.0000.0000.0000.000
25D288PRO00.0120.00716.3110.0180.0180.0000.0000.0000.000
26D289PHE00.0080.01310.2050.0070.0070.0000.0000.0000.000
27D290THR00.003-0.01312.068-0.033-0.0330.0000.0000.0000.000
28D291GLU-1-0.708-0.8587.848-0.629-0.6290.0000.0000.0000.000
29D292ALA00.0580.0338.5520.1470.1470.0000.0000.0000.000
30D293SER0-0.040-0.0289.7720.0940.0940.0000.0000.0000.000
31D294MET00.0180.0156.274-0.009-0.0090.0000.0000.0000.000
32D295MET00.0590.0362.438-2.986-1.8293.003-0.911-3.2490.008
33D296MET0-0.0070.0375.7410.1450.1450.0000.0000.0000.000
34D297SER0-0.049-0.0217.446-0.178-0.1780.0000.0000.0000.000
35D298LEU00.0230.0002.465-2.721-0.5220.753-0.453-2.4990.001
36D299THR00.002-0.0232.606-6.421-3.0321.878-1.688-3.579-0.025
37D300LYS10.8820.9484.078-0.389-0.1670.002-0.014-0.2090.000
38D301LEU0-0.0160.0022.215-1.357-0.1602.164-0.670-2.6920.003
39D302ALA00.0270.0092.255-3.208-1.4973.808-1.710-3.8080.004
40D303ASP-1-0.746-0.8613.578-0.237-0.1910.0850.237-0.3670.001
41D304LYS10.7870.8776.7230.4190.4190.0000.0000.0000.000
42D305GLU-1-0.758-0.8551.668-25.183-30.59213.871-4.983-3.478-0.057
43D306LEU00.0130.0055.7150.6140.6140.0000.0000.0000.000
44D307VAL0-0.031-0.0158.1310.1310.1310.0000.0000.0000.000
45D308HIS0-0.018-0.0248.4910.2360.2360.0000.0000.0000.000
46D309MET0-0.0140.0196.9090.1230.1230.0000.0000.0000.000
47D310ILE00.0100.0059.9790.1160.1160.0000.0000.0000.000
48D311SER0-0.032-0.02412.6780.0570.0570.0000.0000.0000.000
49D312TRP00.0010.00911.1610.0400.0400.0000.0000.0000.000
50D313ALA00.0490.01813.1150.0380.0380.0000.0000.0000.000
51D314LYS10.8670.92015.1010.0180.0180.0000.0000.0000.000
52D315LYS10.8010.91714.8050.1130.1130.0000.0000.0000.000
53D316ILE0-0.0230.00015.5750.0080.0080.0000.0000.0000.000
54D317PRO00.0230.00719.9630.0020.0020.0000.0000.0000.000
55D318GLY00.0070.00322.9720.0110.0110.0000.0000.0000.000
56D319PHE00.017-0.01517.158-0.001-0.0010.0000.0000.0000.000
57D320VAL0-0.021-0.01621.123-0.002-0.0020.0000.0000.0000.000
58D321GLU-1-0.890-0.93623.0360.0260.0260.0000.0000.0000.000
59D322LEU0-0.0200.01121.5510.0010.0010.0000.0000.0000.000
60D323SER0-0.008-0.02525.390-0.006-0.0060.0000.0000.0000.000
61D324LEU0-0.011-0.01723.1820.0040.0040.0000.0000.0000.000
62D325PHE00.0450.01522.461-0.001-0.0010.0000.0000.0000.000
63D326ASP-1-0.735-0.82521.0780.0550.0550.0000.0000.0000.000
64D327GLN0-0.061-0.02219.7480.0050.0050.0000.0000.0000.000
65D328VAL0-0.045-0.00616.735-0.004-0.0040.0000.0000.0000.000
66D329ARG10.9000.95016.329-0.029-0.0290.0000.0000.0000.000
67D330LEU0-0.012-0.01816.7680.0120.0120.0000.0000.0000.000
68D331LEU00.0010.01112.1620.0330.0330.0000.0000.0000.000
69D332GLU-1-0.902-0.96912.1420.1680.1680.0000.0000.0000.000
70D333SER0-0.016-0.00412.1070.0070.0070.0000.0000.0000.000
71D334CYS0-0.044-0.01811.039-0.009-0.0090.0000.0000.0000.000
72D335TRP00.0890.0214.392-0.1120.177-0.001-0.008-0.2800.000
73D336MET0-0.0100.0112.684-1.907-0.4651.884-0.521-2.806-0.001
74D337GLU-1-0.750-0.8794.2280.4360.6340.000-0.032-0.1670.000
75D338VAL0-0.026-0.0146.4470.2440.2440.0000.0000.0000.000
76D339LEU0-0.0190.0052.714-3.786-0.7642.345-1.308-4.0590.010
77D340MET0-0.0110.0142.285-2.1240.6325.248-1.751-6.254-0.013
78D341MET00.0030.0013.4420.1230.1030.0110.237-0.2280.000
79D342GLY0-0.0060.0054.805-0.525-0.444-0.001-0.009-0.0700.000
80D343LEU00.0170.0172.322-3.954-2.1474.128-1.388-4.5460.007
81D344MET0-0.031-0.0054.177-1.419-1.1830.002-0.059-0.1800.000
82D345TRP0-0.054-0.0267.022-0.331-0.3310.0000.0000.0000.000
83D346ARG10.7410.8262.2912.7463.8910.608-0.628-1.1260.002
84D347SER00.014-0.0047.276-0.138-0.1380.0000.0000.0000.000
85D348ILE0-0.0050.0129.896-0.150-0.1500.0000.0000.0000.000
86D349ASP-1-0.868-0.94112.6920.4000.4000.0000.0000.0000.000
87D350HIS0-0.034-0.00512.592-0.076-0.0760.0000.0000.0000.000
88D351PRO0-0.022-0.02314.0590.0340.0340.0000.0000.0000.000
89D352GLY0-0.0020.01013.175-0.039-0.0390.0000.0000.0000.000
90D353LYS10.8020.87211.100-0.407-0.4070.0000.0000.0000.000
91D354LEU00.0180.0164.765-0.169-0.031-0.001-0.003-0.1340.000
92D355ILE00.000-0.0028.305-0.054-0.0540.0000.0000.0000.000
93D356PHE00.0260.0032.138-4.966-1.3193.710-1.402-5.9560.011
94D357ALA00.0440.0304.651-1.530-1.371-0.001-0.015-0.1440.000
95D358PRO0-0.037-0.0297.3640.2470.2470.0000.0000.0000.000
96D359ASP-1-0.809-0.90810.516-0.152-0.1520.0000.0000.0000.000
97D360LEU0-0.043-0.0106.3250.0050.0050.0000.0000.0000.000
98D361VAL00.0270.0198.3960.3840.3840.0000.0000.0000.000
99D362LEU0-0.013-0.0046.249-0.186-0.1860.0000.0000.0000.000
100D363ASP-1-0.807-0.90010.0970.4670.4670.0000.0000.0000.000
101D364ARG10.8040.86110.166-0.030-0.0300.0000.0000.0000.000
102D365ASP-1-0.802-0.89510.783-0.103-0.1030.0000.0000.0000.000
103D366GLU-1-0.739-0.83210.8300.2980.2980.0000.0000.0000.000
104D367GLY00.0270.0128.186-0.041-0.0410.0000.0000.0000.000
105D368LYS10.8030.8738.669-0.160-0.1600.0000.0000.0000.000
106D369CYS0-0.077-0.02410.265-0.019-0.0190.0000.0000.0000.000
107D370VAL00.000-0.0024.507-0.0490.073-0.001-0.005-0.1160.000
108D371GLU-1-0.796-0.8857.576-1.185-1.1850.0000.0000.0000.000
109D372GLY00.0230.0086.517-0.707-0.7070.0000.0000.0000.000
110D373ILE0-0.0030.0132.236-1.102-0.8683.742-0.605-3.3710.000
111D374LEU0-0.024-0.0114.8910.3240.426-0.001-0.003-0.0980.000
112D375GLU-1-0.821-0.8956.847-0.961-0.9610.0000.0000.0000.000
113D376ILE00.0180.0072.336-1.159-0.4252.415-0.392-2.757-0.001
114D377PHE0-0.004-0.0113.8730.0630.5890.001-0.047-0.4800.000
115D378ASP-1-0.754-0.8376.6450.2220.2220.0000.0000.0000.000
116D379MET0-0.0240.0017.7070.0560.0560.0000.0000.0000.000
117D380LEU00.0440.0232.950-0.7870.0860.183-0.175-0.881-0.001
118D381LEU00.0340.0317.2460.0540.0540.0000.0000.0000.000
119D382ALA0-0.0190.0099.984-0.043-0.0430.0000.0000.0000.000
120D383THR0-0.022-0.0289.273-0.044-0.0440.0000.0000.0000.000
121D384THR0-0.008-0.0298.5830.0460.0460.0000.0000.0000.000
122D385SER0-0.055-0.04111.054-0.071-0.0710.0000.0000.0000.000
123D386ARG10.8210.91414.210-0.246-0.2460.0000.0000.0000.000
124D387PHE00.0420.0009.929-0.065-0.0650.0000.0000.0000.000
125D388ARG10.8560.92713.442-0.560-0.5600.0000.0000.0000.000
126D389GLU-1-0.876-0.92616.6130.1560.1560.0000.0000.0000.000
127D390LEU0-0.014-0.02017.237-0.034-0.0340.0000.0000.0000.000
128D391LYS10.8790.95818.963-0.225-0.2250.0000.0000.0000.000
129D392LEU0-0.0140.02013.175-0.030-0.0300.0000.0000.0000.000
130D393GLN0-0.016-0.02117.1250.0000.0000.0000.0000.0000.000
131D394HIS00.0890.04612.9520.0590.0590.0000.0000.0000.000
132D395LYS10.8560.90715.878-0.116-0.1160.0000.0000.0000.000
133D396GLU-1-0.738-0.83617.3980.2250.2250.0000.0000.0000.000
134D397TYR00.004-0.0198.8630.0460.0460.0000.0000.0000.000
135D398LEU0-0.0070.01412.9690.0340.0340.0000.0000.0000.000
136D399CYS0-0.036-0.01214.591-0.018-0.0180.0000.0000.0000.000
137D400VAL00.0230.00212.413-0.012-0.0120.0000.0000.0000.000
138D401LYS10.8380.8998.124-0.314-0.3140.0000.0000.0000.000
139D402ALA00.0040.00512.033-0.020-0.0200.0000.0000.0000.000
140D403MET0-0.032-0.01815.317-0.020-0.0200.0000.0000.0000.000
141D404ILE0-0.019-0.0059.460-0.021-0.0210.0000.0000.0000.000
142D405LEU0-0.034-0.00613.357-0.024-0.0240.0000.0000.0000.000
143D406LEU0-0.010-0.01314.696-0.040-0.0400.0000.0000.0000.000
144D407ASN0-0.033-0.01616.616-0.032-0.0320.0000.0000.0000.000
145D408SER00.0470.01514.9970.0120.0120.0000.0000.0000.000
146D409SER0-0.0160.00417.511-0.018-0.0180.0000.0000.0000.000
147D410MET0-0.0170.00019.607-0.005-0.0050.0000.0000.0000.000
148D411TYR00.0140.02221.702-0.004-0.0040.0000.0000.0000.000
149D412PRO00.0270.00125.7080.0010.0010.0000.0000.0000.000
150D413LEU00.0080.01123.608-0.003-0.0030.0000.0000.0000.000
151D414VAL0-0.005-0.00628.3090.0010.0010.0000.0000.0000.000
152D415THR00.0380.02226.0300.0000.0000.0000.0000.0000.000
153D416ALA00.0070.00727.410-0.003-0.0030.0000.0000.0000.000
154D417THR0-0.040-0.05028.740-0.001-0.0010.0000.0000.0000.000
155D418GLN0-0.054-0.03230.992-0.001-0.0010.0000.0000.0000.000
156D419ASP-1-0.787-0.86429.5740.0260.0260.0000.0000.0000.000
157D420ALA00.0570.02931.7030.0000.0000.0000.0000.0000.000
158D421ASP-1-0.892-0.95031.0960.0320.0320.0000.0000.0000.000
159D422SER00.004-0.01325.9300.0050.0050.0000.0000.0000.000
160D423SER00.028-0.00925.9370.0020.0020.0000.0000.0000.000
161D424ARG10.7860.89227.016-0.025-0.0250.0000.0000.0000.000
162D425LYS10.8410.92726.970-0.030-0.0300.0000.0000.0000.000
163D426LEU00.0340.02820.7450.0030.0030.0000.0000.0000.000
164D427ALA00.0000.00224.1440.0080.0080.0000.0000.0000.000
165D428HIS0-0.013-0.00726.1260.0050.0050.0000.0000.0000.000
166D429LEU00.0000.00121.2730.0030.0030.0000.0000.0000.000
167D430LEU00.0220.01419.7840.0100.0100.0000.0000.0000.000
168D431ASN0-0.054-0.02822.4870.0090.0090.0000.0000.0000.000
169D432ALA00.0280.02124.8830.0070.0070.0000.0000.0000.000
170D433VAL0-0.002-0.01618.5550.0020.0020.0000.0000.0000.000
171D434THR0-0.005-0.01421.2600.0210.0210.0000.0000.0000.000
172D435ASP-1-0.867-0.92822.2570.0920.0920.0000.0000.0000.000
173D436ALA0-0.061-0.03022.680-0.003-0.0030.0000.0000.0000.000
174D437LEU00.0150.01318.1650.0030.0030.0000.0000.0000.000
175D438VAL00.0140.00621.7320.0020.0020.0000.0000.0000.000
176D439TRP00.002-0.01424.975-0.003-0.0030.0000.0000.0000.000
177D440VAL0-0.027-0.01821.012-0.008-0.0080.0000.0000.0000.000
178D441ILE00.0070.01321.358-0.002-0.0020.0000.0000.0000.000
179D442ALA0-0.0050.00624.428-0.005-0.0050.0000.0000.0000.000
180D443LYS10.7820.90725.327-0.111-0.1110.0000.0000.0000.000
181D444SER0-0.043-0.02825.892-0.003-0.0030.0000.0000.0000.000
182D445GLY0-0.010-0.00127.912-0.003-0.0030.0000.0000.0000.000
183D446ILE0-0.0200.00526.801-0.007-0.0070.0000.0000.0000.000
184D447SER00.0590.02531.1040.0000.0000.0000.0000.0000.000
185D448SER00.0660.02631.1900.0070.0070.0000.0000.0000.000
186D449GLN00.0420.02530.2520.0020.0020.0000.0000.0000.000
187D450GLN00.0180.00028.8190.0110.0110.0000.0000.0000.000
188D451GLN0-0.033-0.02326.7470.0120.0120.0000.0000.0000.000
189D452SER00.015-0.00225.6690.0100.0100.0000.0000.0000.000
190D453MET0-0.0120.00325.2820.0080.0080.0000.0000.0000.000
191D454ARG10.7580.84120.216-0.206-0.2060.0000.0000.0000.000
192D455LEU00.0470.01621.2110.0210.0210.0000.0000.0000.000
193D456ALA00.0240.01220.9480.0130.0130.0000.0000.0000.000
194D457ASN0-0.023-0.02419.4710.0090.0090.0000.0000.0000.000
195D458LEU00.0320.01415.9980.0250.0250.0000.0000.0000.000
196D459LEU00.0060.01216.2580.0270.0270.0000.0000.0000.000
197D460MET0-0.020-0.00617.220-0.009-0.0090.0000.0000.0000.000
198D461LEU0-0.022-0.00913.159-0.009-0.0090.0000.0000.0000.000
199D462LEU00.0100.00612.3850.0430.0430.0000.0000.0000.000
200D463SER0-0.032-0.01312.568-0.006-0.0060.0000.0000.0000.000
201D464HIS0-0.006-0.00711.520-0.060-0.0600.0000.0000.0000.000
202D465VAL0-0.0160.0037.200-0.008-0.0080.0000.0000.0000.000
203D466ARG10.8190.8958.262-0.230-0.2300.0000.0000.0000.000
204D467HIS0-0.0070.0059.855-0.102-0.1020.0000.0000.0000.000
205D468ALA00.0320.0045.816-0.144-0.1440.0000.0000.0000.000
206D469SER0-0.029-0.0435.202-0.283-0.2830.0000.0000.0000.000
207D470ASN0-0.041-0.0216.202-0.075-0.0750.0000.0000.0000.000
208D471LYS10.7840.8886.2400.9040.9040.0000.0000.0000.000
209D472GLY00.035-0.0032.313-1.422-0.8951.461-0.839-1.1490.001
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