Manual

About

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: P29RX

Calculation Name: 1X7B-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 2-(3-fluoro-4-hydroxyphenyl)-7-vinyl-1,3-benzoxazol-5-ol

ligand 3-letter code: 041

PDB ID: 1X7B

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 -3050025.993798
FMO2-HF: Nuclear repulsion 2953525.238903
FMO2-HF: Total energy -96500.754894
FMO2-MP2: Total energy -96771.36662


3D Structure
Snapshot
 
Ligand structure

041

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.
-121.662-112.54298.112-42.699-64.5310.084


Interactive mode: IFIE and PIEDA for fragment #235(B:202:041)


Summations of interaction energy for fragment #235(B:202:041)
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.
-121.662-112.54298.112-42.699-64.531-0.084
Interaction energy analysis for fragmet #235(B:202:041)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.145
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].
1B264SER10.8710.92429.245-0.083-0.0830.0000.0000.0000.000
2B265PRO00.1890.07126.428-0.005-0.0050.0000.0000.0000.000
3B266GLU-1-0.893-0.93725.2030.1050.1050.0000.0000.0000.000
4B267GLN00.006-0.00825.2410.0040.0040.0000.0000.0000.000
5B268LEU00.0110.04021.991-0.014-0.0140.0000.0000.0000.000
6B269VAL00.0280.00120.5180.0020.0020.0000.0000.0000.000
7B270LEU0-0.035-0.02620.4170.0040.0040.0000.0000.0000.000
8B271THR00.0180.00420.475-0.019-0.0190.0000.0000.0000.000
9B272LEU0-0.021-0.01816.726-0.027-0.0270.0000.0000.0000.000
10B273LEU0-0.051-0.03816.175-0.002-0.0020.0000.0000.0000.000
11B274GLU-1-0.975-0.97616.654-0.086-0.0860.0000.0000.0000.000
12B275ALA0-0.068-0.03615.965-0.053-0.0530.0000.0000.0000.000
13B276GLU-1-0.787-0.88310.8980.1620.1620.0000.0000.0000.000
14B277PRO0-0.048-0.0048.469-0.062-0.0620.0000.0000.0000.000
15B278PRO0-0.014-0.00310.4460.0920.0920.0000.0000.0000.000
16B279HIS0-0.001-0.0227.907-0.129-0.1290.0000.0000.0000.000
17B280VAL00.0180.0175.9010.3750.3750.0000.0000.0000.000
18B281LEU0-0.020-0.0117.8560.0410.0410.0000.0000.0000.000
19B282ILE0-0.051-0.0366.413-0.083-0.0830.0000.0000.0000.000
20B283SER0-0.0040.0019.6720.0860.0860.0000.0000.0000.000
21B284ARG10.8330.91911.599-0.361-0.3610.0000.0000.0000.000
22B285PRO0-0.053-0.00811.924-0.044-0.0440.0000.0000.0000.000
23B286SER00.015-0.01114.8610.0190.0190.0000.0000.0000.000
24B287ALA0-0.035-0.00618.5250.0090.0090.0000.0000.0000.000
25B288PRO00.009-0.00616.6290.0270.0270.0000.0000.0000.000
26B289PHE0-0.009-0.00110.5900.0210.0210.0000.0000.0000.000
27B290THR00.0080.01213.449-0.032-0.0320.0000.0000.0000.000
28B291GLU-1-0.790-0.9248.408-0.450-0.4500.0000.0000.0000.000
29B292ALA00.0540.0178.5800.2350.2350.0000.0000.0000.000
30B293SER0-0.043-0.0069.7050.1890.1890.0000.0000.0000.000
31B294MET00.0430.0296.9940.0360.0360.0000.0000.0000.000
32B295MET00.0570.0342.330-1.775-1.8094.332-1.011-3.2880.012
33B296MET0-0.0140.0125.4850.4300.4300.0000.0000.0000.000
34B297SER0-0.021-0.0317.427-0.408-0.4080.0000.0000.0000.000
35B298LEU0-0.019-0.0022.786-6.371-1.8991.588-1.284-4.7750.015
36B299THR00.001-0.0082.793-5.911-3.4510.304-1.018-1.745-0.013
37B300LYS10.9400.9645.150-1.012-0.867-0.001-0.006-0.1380.000
38B301LEU0-0.052-0.0082.218-1.0300.9411.215-0.869-2.3160.002
39B302ALA00.0660.0212.338-3.773-2.1051.058-0.921-1.8040.000
40B303ASP-1-0.900-0.9483.5320.1870.3360.0370.030-0.2140.000
41B304LYS10.9570.9726.5541.7411.7410.0000.0000.0000.000
42B305GLU-1-0.827-0.8951.515-41.493-56.97535.806-14.577-5.747-0.115
43B306LEU00.0170.0255.6981.1501.1500.0000.0000.0000.000
44B307VAL00.0170.0158.0430.4920.4920.0000.0000.0000.000
45B308HIS0-0.026-0.0228.0860.4720.4720.0000.0000.0000.000
46B309MET0-0.0350.0057.8120.3340.3340.0000.0000.0000.000
47B310ILE00.0310.0179.6720.2790.2790.0000.0000.0000.000
48B311SER0-0.044-0.02912.9570.1460.1460.0000.0000.0000.000
49B312TRP0-0.025-0.01711.5010.1100.1100.0000.0000.0000.000
50B313ALA00.0720.03213.5020.0910.0910.0000.0000.0000.000
51B314LYS10.8920.94315.1530.1880.1880.0000.0000.0000.000
52B315LYS10.9390.97615.8710.2670.2670.0000.0000.0000.000
53B316ILE0-0.0030.01715.0600.0300.0300.0000.0000.0000.000
54B317PRO0-0.026-0.02318.996-0.005-0.0050.0000.0000.0000.000
55B318GLY00.0670.02422.8080.0190.0190.0000.0000.0000.000
56B319PHE00.0300.01917.541-0.001-0.0010.0000.0000.0000.000
57B320VAL0-0.027-0.02421.199-0.002-0.0020.0000.0000.0000.000
58B321GLU-1-0.991-0.99222.9810.0280.0280.0000.0000.0000.000
59B322LEU0-0.047-0.00121.6440.0050.0050.0000.0000.0000.000
60B323SER0-0.004-0.00625.345-0.014-0.0140.0000.0000.0000.000
61B324LEU00.0310.00422.2180.0080.0080.0000.0000.0000.000
62B325PHE00.0450.01122.3890.0020.0020.0000.0000.0000.000
63B326ASP-1-0.708-0.81322.6460.1180.1180.0000.0000.0000.000
64B327GLN0-0.080-0.03419.4520.0070.0070.0000.0000.0000.000
65B328VAL00.0120.00218.0630.0110.0110.0000.0000.0000.000
66B329ARG10.9060.98117.831-0.129-0.1290.0000.0000.0000.000
67B330LEU0-0.075-0.04117.2430.0450.0450.0000.0000.0000.000
68B331LEU00.005-0.01412.4600.0690.0690.0000.0000.0000.000
69B332GLU-1-0.842-0.93713.0890.3150.3150.0000.0000.0000.000
70B333SER0-0.033-0.01413.2390.1050.1050.0000.0000.0000.000
71B334CYS0-0.081-0.02311.6580.0720.0720.0000.0000.0000.000
72B335TRP00.0680.0175.3600.3160.514-0.001-0.003-0.1940.000
73B336MET00.0380.0322.889-3.362-0.6801.048-0.724-3.0060.007
74B337GLU-1-0.835-0.9365.2551.7431.817-0.001-0.003-0.0710.000
75B338VAL0-0.057-0.0276.7950.3400.3400.0000.0000.0000.000
76B339LEU0-0.013-0.0082.793-3.215-0.0862.313-1.425-4.0170.008
77B340MET0-0.0090.0072.478-0.3433.7013.419-2.306-5.1570.015
78B341MET00.0040.0163.339-0.938-0.9740.0440.365-0.3730.002
79B342GLY0-0.016-0.0105.525-0.500-0.5000.0000.0000.0000.000
80B343LEU0-0.0080.0132.377-3.851-1.6291.987-1.449-2.7600.013
81B344MET0-0.0200.0034.298-2.107-1.9010.000-0.027-0.1790.000
82B345TRP0-0.021-0.0057.281-0.581-0.5810.0000.0000.0000.000
83B346ARG10.8230.9042.408-6.495-4.5350.746-1.046-1.6600.015
84B347SER0-0.014-0.0227.441-0.304-0.3040.0000.0000.0000.000
85B348ILE0-0.0090.02010.119-0.184-0.1840.0000.0000.0000.000
86B349ASP-1-0.940-0.96312.7130.4450.4450.0000.0000.0000.000
87B350HIS0-0.034-0.01712.900-0.108-0.1080.0000.0000.0000.000
88B351PRO0-0.002-0.00713.7890.1020.1020.0000.0000.0000.000
89B352GLY0-0.020-0.01112.562-0.060-0.0600.0000.0000.0000.000
90B353LYS10.9200.96111.584-0.545-0.5450.0000.0000.0000.000
91B354LEU00.0120.0105.0740.1160.1160.0000.0000.0000.000
92B355ILE0-0.004-0.0018.424-0.152-0.1520.0000.0000.0000.000
93B356PHE00.0530.0193.035-3.4870.2291.034-1.102-3.6480.014
94B357ALA00.0220.0084.534-1.728-1.614-0.001-0.013-0.1010.000
95B358PRO0-0.015-0.0127.2450.3530.3530.0000.0000.0000.000
96B359ASP-1-0.879-0.94510.9570.0360.0360.0000.0000.0000.000
97B360LEU0-0.0090.0065.992-0.042-0.0420.0000.0000.0000.000
98B361VAL0-0.008-0.0058.9970.3060.3060.0000.0000.0000.000
99B362LEU0-0.020-0.0035.937-0.132-0.1320.0000.0000.0000.000
100B363ASP-1-0.856-0.9449.6620.5720.5720.0000.0000.0000.000
101B364ARG10.8250.9078.699-0.088-0.0880.0000.0000.0000.000
102B365ASP-1-0.889-0.9439.4640.2370.2370.0000.0000.0000.000
103B366GLU-1-0.726-0.88010.1230.4280.4280.0000.0000.0000.000
104B367GLY0-0.007-0.0077.4810.0410.0410.0000.0000.0000.000
105B368LYS10.8940.9198.201-0.255-0.2550.0000.0000.0000.000
106B369CYS0-0.121-0.03111.037-0.091-0.0910.0000.0000.0000.000
107B370VAL00.0330.0064.9370.0510.0510.0000.0000.0000.000
108B371GLU-1-0.909-0.9467.542-1.217-1.2170.0000.0000.0000.000
109B372GLY00.0130.0026.874-0.749-0.7490.0000.0000.0000.000
110B373ILE0-0.0100.0092.745-3.316-1.0060.760-0.739-2.3310.007
111B374LEU0-0.0170.0044.5200.5750.718-0.001-0.008-0.1340.000
112B375GLU-1-0.894-0.9436.780-1.056-1.0560.0000.0000.0000.000
113B376ILE00.008-0.0112.065-0.108-1.0295.264-0.945-3.397-0.002
114B377PHE00.004-0.0132.491-0.9550.2691.401-0.584-2.0410.003
115B378ASP-1-0.785-0.8764.4940.3870.4290.000-0.012-0.0310.000
116B379MET0-0.037-0.0036.3050.2040.2040.0000.0000.0000.000
117B380LEU00.0310.0162.620-0.5450.0490.541-0.226-0.9090.000
118B381LEU00.0200.0266.5650.1470.1470.0000.0000.0000.000
119B382ALA0-0.037-0.0079.227-0.063-0.0630.0000.0000.0000.000
120B383THR00.007-0.0119.886-0.099-0.0990.0000.0000.0000.000
121B384THR0-0.008-0.0189.4070.0470.0470.0000.0000.0000.000
122B385SER0-0.020-0.01511.565-0.125-0.1250.0000.0000.0000.000
123B386ARG10.8970.98314.632-0.515-0.5150.0000.0000.0000.000
124B387PHE00.043-0.00510.931-0.094-0.0940.0000.0000.0000.000
125B388ARG10.8690.92614.045-0.802-0.8020.0000.0000.0000.000
126B389GLU-1-0.957-0.98116.7150.2970.2970.0000.0000.0000.000
127B390LEU0-0.052-0.01717.580-0.059-0.0590.0000.0000.0000.000
128B391LYS10.9060.95918.893-0.333-0.3330.0000.0000.0000.000
129B392LEU0-0.0200.00313.168-0.042-0.0420.0000.0000.0000.000
130B393GLN0-0.033-0.02117.237-0.032-0.0320.0000.0000.0000.000
131B394HIS00.0880.03814.1300.0900.0900.0000.0000.0000.000
132B395LYS10.9470.95916.318-0.169-0.1690.0000.0000.0000.000
133B396GLU-1-0.759-0.86217.6220.3820.3820.0000.0000.0000.000
134B397TYR00.0300.0169.1730.0970.0970.0000.0000.0000.000
135B398LEU0-0.0290.00013.4700.0540.0540.0000.0000.0000.000
136B399CYS0-0.0320.00115.078-0.038-0.0380.0000.0000.0000.000
137B400VAL00.0500.00913.013-0.018-0.0180.0000.0000.0000.000
138B401LYS10.8230.9068.766-0.470-0.4700.0000.0000.0000.000
139B402ALA00.0240.00812.154-0.024-0.0240.0000.0000.0000.000
140B403MET0-0.058-0.02715.045-0.033-0.0330.0000.0000.0000.000
141B404ILE0-0.025-0.00510.084-0.036-0.0360.0000.0000.0000.000
142B405LEU00.003-0.00713.414-0.028-0.0280.0000.0000.0000.000
143B406LEU0-0.031-0.02514.505-0.043-0.0430.0000.0000.0000.000
144B407ASN0-0.0010.00217.126-0.079-0.0790.0000.0000.0000.000
145B408SER0-0.0350.00715.007-0.005-0.0050.0000.0000.0000.000
146B409SER00.0040.00717.155-0.029-0.0290.0000.0000.0000.000
147B410MET0-0.068-0.03916.756-0.015-0.0150.0000.0000.0000.000
148B411TYR00.008-0.01719.659-0.014-0.0140.0000.0000.0000.000
149B412PRO00.0380.03919.393-0.023-0.0230.0000.0000.0000.000
150B413LEU0-0.004-0.00222.7220.0010.0010.0000.0000.0000.000
151B414VAL00.0030.01424.4360.0040.0040.0000.0000.0000.000
152B415THR0-0.021-0.04825.991-0.014-0.0140.0000.0000.0000.000
153B416ALA00.0150.00228.3070.0040.0040.0000.0000.0000.000
154B417THR0-0.0250.00230.223-0.003-0.0030.0000.0000.0000.000
155B418GLN0-0.014-0.01932.5790.0000.0000.0000.0000.0000.000
156B419ASP-1-0.836-0.90033.6140.0580.0580.0000.0000.0000.000
157B420ALA00.0180.01134.1510.0030.0030.0000.0000.0000.000
158B421ASP-1-0.873-0.94332.6070.0630.0630.0000.0000.0000.000
159B422SER0-0.045-0.03826.6990.0020.0020.0000.0000.0000.000
160B423SER00.0260.01027.2050.0120.0120.0000.0000.0000.000
161B424ARG10.8200.87227.785-0.058-0.0580.0000.0000.0000.000
162B425LYS10.9320.97727.153-0.046-0.0460.0000.0000.0000.000
163B426LEU00.0330.01721.1680.0020.0020.0000.0000.0000.000
164B427ALA00.0130.01524.1620.0170.0170.0000.0000.0000.000
165B428HIS0-0.010-0.00625.9700.0160.0160.0000.0000.0000.000
166B429LEU00.0200.01322.6680.0030.0030.0000.0000.0000.000
167B430LEU00.0000.00820.0110.0130.0130.0000.0000.0000.000
168B431ASN00.015-0.00222.7430.0290.0290.0000.0000.0000.000
169B432ALA00.0260.03124.8580.0040.0040.0000.0000.0000.000
170B433VAL0-0.001-0.00618.5940.0000.0000.0000.0000.0000.000
171B434THR0-0.013-0.00621.9150.0290.0290.0000.0000.0000.000
172B435ASP-1-0.905-0.96323.0090.1510.1510.0000.0000.0000.000
173B436ALA0-0.102-0.04222.532-0.006-0.0060.0000.0000.0000.000
174B437LEU00.003-0.00219.0230.0030.0030.0000.0000.0000.000
175B438VAL00.0160.00222.1800.0040.0040.0000.0000.0000.000
176B439TRP00.007-0.00225.084-0.005-0.0050.0000.0000.0000.000
177B440VAL0-0.033-0.02921.339-0.010-0.0100.0000.0000.0000.000
178B441ILE00.0130.01421.866-0.002-0.0020.0000.0000.0000.000
179B442ALA00.0260.06025.026-0.008-0.0080.0000.0000.0000.000
180B443LYS10.8390.93225.959-0.179-0.1790.0000.0000.0000.000
181B444SER0-0.091-0.07825.763-0.005-0.0050.0000.0000.0000.000
182B445GLY0-0.004-0.00227.780-0.004-0.0040.0000.0000.0000.000
183B446ILE0-0.0230.01427.019-0.009-0.0090.0000.0000.0000.000
184B447SER00.0490.01031.158-0.002-0.0020.0000.0000.0000.000
185B448SER00.0700.01931.6800.0130.0130.0000.0000.0000.000
186B449GLN00.0400.00431.5440.0110.0110.0000.0000.0000.000
187B450GLN00.0540.02029.1360.0070.0070.0000.0000.0000.000
188B451GLN0-0.042-0.01227.4290.0220.0220.0000.0000.0000.000
189B452SER00.0050.00426.4660.0170.0170.0000.0000.0000.000
190B453MET0-0.005-0.00426.4030.0170.0170.0000.0000.0000.000
191B454ARG10.7850.87520.311-0.339-0.3390.0000.0000.0000.000
192B455LEU00.0350.01821.8990.0390.0390.0000.0000.0000.000
193B456ALA00.0230.00821.5270.0330.0330.0000.0000.0000.000
194B457ASN0-0.026-0.02821.0950.0210.0210.0000.0000.0000.000
195B458LEU0-0.0080.00016.9890.0490.0490.0000.0000.0000.000
196B459LEU00.0240.00716.6880.0730.0730.0000.0000.0000.000
197B460MET0-0.043-0.01117.5400.0200.0200.0000.0000.0000.000
198B461LEU00.0000.00014.165-0.018-0.0180.0000.0000.0000.000
199B462LEU00.0100.00612.7470.1220.1220.0000.0000.0000.000
200B463SER0-0.0070.00413.3880.0600.0600.0000.0000.0000.000
201B464HIS00.0170.00412.147-0.018-0.0180.0000.0000.0000.000
202B465VAL00.0010.0097.8210.0650.0650.0000.0000.0000.000
203B466ARG10.9300.9648.956-0.446-0.4460.0000.0000.0000.000
204B467HIS0-0.051-0.01710.0760.0180.0180.0000.0000.0000.000
205B468ALA00.0460.0025.605-0.270-0.2700.0000.0000.0000.000
206B469SER00.011-0.0015.2830.3030.3030.0000.0000.0000.000
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