Manual

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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: PL99X

Calculation Name: 4J24-D-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: estradiol

ligand 3-letter code: EST

PDB ID: 4J24

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 -3039984.838371
FMO2-HF: Nuclear repulsion 2943590.137295
FMO2-HF: Total energy -96394.701076
FMO2-MP2: Total energy -96664.79846


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.
-102.217-68.23455.113-27.358-61.7420.113


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.
-102.217-68.23455.113-27.358-61.742-0.113
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 : -0.112 / q_NPA : -0.091
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].
1D264SER10.8560.91927.990-0.072-0.0720.0000.0000.0000.000
2D265PRO00.1660.07026.426-0.001-0.0010.0000.0000.0000.000
3D266GLU-1-0.899-0.94125.4780.0950.0950.0000.0000.0000.000
4D267GLN00.0410.03025.7960.0040.0040.0000.0000.0000.000
5D268LEU0-0.041-0.01522.002-0.005-0.0050.0000.0000.0000.000
6D269VAL00.025-0.01120.8130.0050.0050.0000.0000.0000.000
7D270LEU0-0.0100.01320.7170.0140.0140.0000.0000.0000.000
8D271THR00.013-0.01320.726-0.006-0.0060.0000.0000.0000.000
9D272LEU0-0.043-0.02816.879-0.013-0.0130.0000.0000.0000.000
10D273LEU0-0.012-0.00116.4610.0060.0060.0000.0000.0000.000
11D274GLU-1-0.955-0.98216.8790.0310.0310.0000.0000.0000.000
12D275ALA0-0.074-0.02916.179-0.033-0.0330.0000.0000.0000.000
13D276GLU-1-0.863-0.92511.6970.2770.2770.0000.0000.0000.000
14D277PRO0-0.012-0.0048.387-0.040-0.0400.0000.0000.0000.000
15D278PRO0-0.020-0.00110.9690.0990.0990.0000.0000.0000.000
16D279HIS00.007-0.0118.820-0.204-0.2040.0000.0000.0000.000
17D280VAL00.0080.0106.2760.1410.1410.0000.0000.0000.000
18D281LEU0-0.025-0.0118.1880.1220.1220.0000.0000.0000.000
19D282ILE0-0.043-0.0296.716-0.107-0.1070.0000.0000.0000.000
20D283SER0-0.009-0.00710.0840.1030.1030.0000.0000.0000.000
21D284ARG10.8000.86111.901-0.396-0.3960.0000.0000.0000.000
22D285PRO0-0.021-0.00112.205-0.045-0.0450.0000.0000.0000.000
23D286SER0-0.007-0.00715.2620.0170.0170.0000.0000.0000.000
24D287ALA0-0.019-0.00317.4600.0100.0100.0000.0000.0000.000
25D288PRO00.010-0.00716.5420.0140.0140.0000.0000.0000.000
26D289PHE0-0.0130.00510.116-0.005-0.0050.0000.0000.0000.000
27D290THR00.0210.00712.625-0.024-0.0240.0000.0000.0000.000
28D291GLU-1-0.805-0.9138.712-0.578-0.5780.0000.0000.0000.000
29D292ALA00.0460.0198.6060.0250.0250.0000.0000.0000.000
30D293SER0-0.0010.0019.5220.0630.0630.0000.0000.0000.000
31D294MET00.0070.0076.068-0.014-0.0140.0000.0000.0000.000
32D295MET00.0560.0282.581-4.654-2.1251.022-1.130-2.4210.015
33D296MET00.0100.0245.3730.1580.1580.0000.0000.0000.000
34D297SER0-0.055-0.0287.254-0.218-0.2180.0000.0000.0000.000
35D298LEU00.003-0.0012.370-3.508-0.7911.599-0.690-3.6260.001
36D299THR00.023-0.0052.615-6.802-3.6090.950-1.455-2.687-0.021
37D300LYS10.9480.9874.2690.0420.1730.000-0.008-0.1230.000
38D301LEU0-0.053-0.0242.262-0.8570.6720.973-0.600-1.9030.003
39D302ALA00.0470.0192.364-2.658-0.8621.104-0.871-2.0290.003
40D303ASP-1-0.873-0.9383.618-0.264-0.0860.0280.007-0.2130.000
41D304LYS10.9570.9666.8341.2081.2080.0000.0000.0000.000
42D305GLU-1-0.851-0.9271.714-31.215-32.96214.483-7.567-5.168-0.092
43D306LEU00.0300.0245.9270.7540.7540.0000.0000.0000.000
44D307VAL00.0020.0138.2910.3170.3170.0000.0000.0000.000
45D308HIS0-0.028-0.0228.2670.3250.3250.0000.0000.0000.000
46D309MET0-0.0350.0036.9800.2430.2430.0000.0000.0000.000
47D310ILE00.0460.02610.0090.1640.1640.0000.0000.0000.000
48D311SER0-0.049-0.03713.3380.0930.0930.0000.0000.0000.000
49D312TRP0-0.033-0.01911.7310.0700.0700.0000.0000.0000.000
50D313ALA00.0540.02313.7740.0520.0520.0000.0000.0000.000
51D314LYS10.9230.95615.4330.1430.1430.0000.0000.0000.000
52D315LYS10.9250.97316.0630.1380.1380.0000.0000.0000.000
53D316ILE0-0.0020.02015.4350.0210.0210.0000.0000.0000.000
54D317PRO0-0.004-0.00819.504-0.008-0.0080.0000.0000.0000.000
55D318GLY00.0240.00723.3210.0100.0100.0000.0000.0000.000
56D319PHE00.0300.00917.901-0.001-0.0010.0000.0000.0000.000
57D320VAL00.010-0.01221.628-0.004-0.0040.0000.0000.0000.000
58D321GLU-1-0.912-0.93823.4080.0120.0120.0000.0000.0000.000
59D322LEU0-0.055-0.01321.9380.0040.0040.0000.0000.0000.000
60D323SER00.0310.02425.606-0.009-0.0090.0000.0000.0000.000
61D324LEU00.0680.00922.8690.0030.0030.0000.0000.0000.000
62D325PHE00.0320.02123.079-0.003-0.0030.0000.0000.0000.000
63D326ASP-1-0.843-0.92922.0630.0350.0350.0000.0000.0000.000
64D327GLN0-0.098-0.06019.965-0.002-0.0020.0000.0000.0000.000
65D328VAL00.0050.00418.1530.0000.0000.0000.0000.0000.000
66D329ARG10.8880.94517.090-0.040-0.0400.0000.0000.0000.000
67D330LEU0-0.068-0.04016.6950.0180.0180.0000.0000.0000.000
68D331LEU0-0.006-0.01712.8590.0320.0320.0000.0000.0000.000
69D332GLU-1-0.863-0.93712.5880.0730.0730.0000.0000.0000.000
70D333SER0-0.039-0.01311.8090.0330.0330.0000.0000.0000.000
71D334CYS0-0.078-0.03011.5360.0280.0280.0000.0000.0000.000
72D335TRP00.0530.0254.717-0.0770.175-0.001-0.004-0.2470.000
73D336MET00.0500.0322.257-1.574-0.7122.825-0.514-3.174-0.001
74D337GLU-1-0.896-0.9704.8630.6630.788-0.001-0.003-0.1220.000
75D338VAL0-0.029-0.0167.0370.2600.2600.0000.0000.0000.000
76D339LEU0-0.0080.0062.944-2.981-0.0041.063-0.988-3.0520.009
77D340MET0-0.048-0.0112.234-1.3161.7442.690-1.364-4.386-0.007
78D341MET0-0.0030.0003.751-0.1220.0450.0030.029-0.2000.000
79D342GLY0-0.013-0.0025.452-0.282-0.2820.0000.0000.0000.000
80D343LEU0-0.0120.0002.301-2.856-1.4042.940-0.998-3.3950.004
81D344MET0-0.015-0.0094.413-1.144-0.9830.000-0.026-0.1340.000
82D345TRP0-0.001-0.0027.408-0.331-0.3310.0000.0000.0000.000
83D346ARG10.8490.9332.380-8.850-6.7890.885-1.211-1.7350.017
84D347SER0-0.0010.0057.410-0.212-0.2120.0000.0000.0000.000
85D348ILE0-0.0220.00610.050-0.189-0.1890.0000.0000.0000.000
86D349ASP-1-0.917-0.95212.6860.3980.3980.0000.0000.0000.000
87D350HIS0-0.056-0.03013.205-0.111-0.1110.0000.0000.0000.000
88D351PRO0-0.006-0.01913.3520.0810.0810.0000.0000.0000.000
89D352GLY0-0.011-0.00213.764-0.029-0.0290.0000.0000.0000.000
90D353LYS10.8870.94911.416-0.530-0.5300.0000.0000.0000.000
91D354LEU00.0080.0074.8200.0430.0430.0000.0000.0000.000
92D355ILE0-0.021-0.0108.107-0.006-0.0060.0000.0000.0000.000
93D356PHE00.0260.0012.337-4.982-1.2473.175-1.368-5.5420.014
94D357ALA00.0310.0084.880-0.979-0.861-0.001-0.004-0.1130.000
95D358PRO0-0.022-0.0097.6200.1260.1260.0000.0000.0000.000
96D359ASP-1-0.853-0.91511.2620.1650.1650.0000.0000.0000.000
97D360LEU0-0.049-0.0206.735-0.086-0.0860.0000.0000.0000.000
98D361VAL0-0.001-0.0089.1480.4290.4290.0000.0000.0000.000
99D362LEU0-0.0160.0016.735-0.222-0.2220.0000.0000.0000.000
100D363ASP-1-0.848-0.92510.2330.5410.5410.0000.0000.0000.000
101D364ARG10.8500.89910.245-0.086-0.0860.0000.0000.0000.000
102D365ASP-1-0.886-0.96810.8460.0060.0060.0000.0000.0000.000
103D366GLU-1-0.748-0.84710.9500.2920.2920.0000.0000.0000.000
104D367GLY00.0420.0118.407-0.045-0.0450.0000.0000.0000.000
105D368LYS10.8300.9208.697-0.213-0.2130.0000.0000.0000.000
106D369CYS0-0.084-0.01510.203-0.054-0.0540.0000.0000.0000.000
107D370VAL00.0280.0094.9070.0170.0170.0000.0000.0000.000
108D371GLU-1-0.878-0.9357.549-0.948-0.9480.0000.0000.0000.000
109D372GLY00.006-0.0066.840-0.540-0.5400.0000.0000.0000.000
110D373ILE0-0.0040.0122.170-1.805-0.6221.956-0.512-2.6270.000
111D374LEU0-0.021-0.0104.6030.4260.539-0.001-0.004-0.1090.000
112D375GLU-1-0.889-0.9377.824-0.387-0.3870.0000.0000.0000.000
113D376ILE00.0380.0122.482-1.221-0.0731.374-0.322-2.2010.000
114D377PHE0-0.022-0.0233.633-0.1430.5590.007-0.082-0.6270.000
115D378ASP-1-0.773-0.8746.2180.3200.3200.0000.0000.0000.000
116D379MET0-0.050-0.0147.3070.1170.1170.0000.0000.0000.000
117D380LEU00.0340.0122.417-0.8940.0200.719-0.240-1.393-0.001
118D381LEU00.0200.0216.9580.0930.0930.0000.0000.0000.000
119D382ALA0-0.0040.0109.734-0.030-0.0300.0000.0000.0000.000
120D383THR0-0.002-0.0159.334-0.055-0.0550.0000.0000.0000.000
121D384THR00.001-0.0098.3040.0490.0490.0000.0000.0000.000
122D385SER0-0.039-0.03310.899-0.066-0.0660.0000.0000.0000.000
123D386ARG10.9580.99214.148-0.332-0.3320.0000.0000.0000.000
124D387PHE00.0550.01511.154-0.056-0.0560.0000.0000.0000.000
125D388ARG10.8880.94513.252-0.635-0.6350.0000.0000.0000.000
126D389GLU-1-0.990-0.99016.6570.2190.2190.0000.0000.0000.000
127D390LEU0-0.065-0.02417.860-0.037-0.0370.0000.0000.0000.000
128D391LYS10.9630.98219.262-0.273-0.2730.0000.0000.0000.000
129D392LEU0-0.0100.01113.490-0.030-0.0300.0000.0000.0000.000
130D393GLN0-0.014-0.01317.4340.0010.0010.0000.0000.0000.000
131D394HIS00.0270.00814.569-0.022-0.0220.0000.0000.0000.000
132D395LYS10.9990.98116.520-0.157-0.1570.0000.0000.0000.000
133D396GLU-1-0.745-0.84118.0910.2740.2740.0000.0000.0000.000
134D397TYR00.0200.0129.3210.0650.0650.0000.0000.0000.000
135D398LEU0-0.031-0.00214.0070.0190.0190.0000.0000.0000.000
136D399CYS0-0.034-0.00915.548-0.028-0.0280.0000.0000.0000.000
137D400VAL00.0400.01012.941-0.019-0.0190.0000.0000.0000.000
138D401LYS10.8510.9339.038-0.415-0.4150.0000.0000.0000.000
139D402ALA00.0320.00812.629-0.029-0.0290.0000.0000.0000.000
140D403MET0-0.040-0.02515.600-0.027-0.0270.0000.0000.0000.000
141D404ILE00.0140.01310.501-0.026-0.0260.0000.0000.0000.000
142D405LEU00.0180.00313.831-0.027-0.0270.0000.0000.0000.000
143D406LEU0-0.041-0.02614.838-0.035-0.0350.0000.0000.0000.000
144D407ASN0-0.035-0.02317.107-0.023-0.0230.0000.0000.0000.000
145D408SER0-0.0310.01014.527-0.021-0.0210.0000.0000.0000.000
146D409SER00.0840.04215.835-0.014-0.0140.0000.0000.0000.000
147D410MET00.0110.02318.550-0.014-0.0140.0000.0000.0000.000
148D411TYR0-0.0090.00416.647-0.008-0.0080.0000.0000.0000.000
149D412PRO00.0070.01216.011-0.014-0.0140.0000.0000.0000.000
150D413LEU00.0260.02818.499-0.011-0.0110.0000.0000.0000.000
151D414VAL00.0380.02021.547-0.008-0.0080.0000.0000.0000.000
152D415THR0-0.052-0.04320.004-0.009-0.0090.0000.0000.0000.000
153D416ALA0-0.024-0.02218.799-0.010-0.0100.0000.0000.0000.000
154D417THR0-0.083-0.04420.832-0.002-0.0020.0000.0000.0000.000
155D418GLN0-0.090-0.02623.582-0.001-0.0010.0000.0000.0000.000
156D419ASP-1-0.843-0.92025.4980.0240.0240.0000.0000.0000.000
157D420ALA0-0.062-0.03526.3180.0050.0050.0000.0000.0000.000
158D421ASP-1-0.842-0.91322.4850.0660.0660.0000.0000.0000.000
159D422SER00.0200.00626.1100.0060.0060.0000.0000.0000.000
160D423SER00.0810.02527.364-0.008-0.0080.0000.0000.0000.000
161D424ARG10.8760.94428.528-0.040-0.0400.0000.0000.0000.000
162D425LYS10.8810.92726.694-0.020-0.0200.0000.0000.0000.000
163D426LEU00.0840.05221.6640.0020.0020.0000.0000.0000.000
164D427ALA00.0660.02824.7670.0100.0100.0000.0000.0000.000
165D428HIS0-0.097-0.04426.7770.0010.0010.0000.0000.0000.000
166D429LEU00.0120.01921.7900.0050.0050.0000.0000.0000.000
167D430LEU00.0370.01220.3540.0100.0100.0000.0000.0000.000
168D431ASN00.016-0.00123.2160.0170.0170.0000.0000.0000.000
169D432ALA0-0.0220.00625.2380.0040.0040.0000.0000.0000.000
170D433VAL00.012-0.00319.1040.0040.0040.0000.0000.0000.000
171D434THR0-0.0020.00122.3320.0210.0210.0000.0000.0000.000
172D435ASP-1-0.906-0.95723.4830.1020.1020.0000.0000.0000.000
173D436ALA0-0.080-0.04122.9800.0000.0000.0000.0000.0000.000
174D437LEU00.0260.01019.4990.0050.0050.0000.0000.0000.000
175D438VAL00.0170.00422.6840.0050.0050.0000.0000.0000.000
176D439TRP0-0.013-0.01425.548-0.003-0.0030.0000.0000.0000.000
177D440VAL0-0.029-0.02521.775-0.003-0.0030.0000.0000.0000.000
178D441ILE00.0020.00322.4050.0000.0000.0000.0000.0000.000
179D442ALA00.0060.02625.567-0.005-0.0050.0000.0000.0000.000
180D443LYS10.8830.95327.564-0.117-0.1170.0000.0000.0000.000
181D444SER0-0.065-0.04626.436-0.004-0.0040.0000.0000.0000.000
182D445GLY00.0120.01028.498-0.002-0.0020.0000.0000.0000.000
183D446ILE0-0.0240.01027.253-0.008-0.0080.0000.0000.0000.000
184D447SER00.0590.01831.449-0.003-0.0030.0000.0000.0000.000
185D448SER00.0850.02831.9900.0080.0080.0000.0000.0000.000
186D449GLN00.0440.02631.9950.0080.0080.0000.0000.0000.000
187D450GLN0-0.024-0.03129.4720.0120.0120.0000.0000.0000.000
188D451GLN0-0.024-0.01327.8590.0130.0130.0000.0000.0000.000
189D452SER0-0.0020.00126.9860.0080.0080.0000.0000.0000.000
190D453MET0-0.0080.00526.3050.0080.0080.0000.0000.0000.000
191D454ARG10.7430.84320.651-0.253-0.2530.0000.0000.0000.000
192D455LEU00.0380.02122.3250.0230.0230.0000.0000.0000.000
193D456ALA00.0220.00722.0170.0140.0140.0000.0000.0000.000
194D457ASN0-0.021-0.02821.1360.0060.0060.0000.0000.0000.000
195D458LEU0-0.022-0.00417.3360.0270.0270.0000.0000.0000.000
196D459LEU00.012-0.00117.2070.0330.0330.0000.0000.0000.000
197D460MET0-0.0090.00017.868-0.002-0.0020.0000.0000.0000.000
198D461LEU0-0.014-0.00314.106-0.008-0.0080.0000.0000.0000.000
199D462LEU00.0270.01113.2610.0570.0570.0000.0000.0000.000
200D463SER00.0040.00913.172-0.009-0.0090.0000.0000.0000.000
201D464HIS0-0.053-0.02612.411-0.046-0.0460.0000.0000.0000.000
202D465VAL00.0300.0097.862-0.001-0.0010.0000.0000.0000.000
203D466ARG10.9090.9568.527-0.181-0.1810.0000.0000.0000.000
204D467HIS0-0.049-0.0199.999-0.054-0.0540.0000.0000.0000.000
205D468ALA00.0370.0036.167-0.130-0.1300.0000.0000.0000.000
206D469SER00.0310.0075.433-0.252-0.2520.0000.0000.0000.000
207D470ASN00.0190.0066.105-0.091-0.0910.0000.0000.0000.000
208D471LYS10.9620.9846.3140.3910.3910.0000.0000.0000.000
209D472GLY00.0180.0032.432-1.467-0.7220.934-0.650-1.0280.000
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