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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: P5VZX

Calculation Name: 2YJD-A-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: 4-(2-propan-2-yloxybenzimidazol-1-yl)phenol

ligand 3-letter code: YJD

PDB ID: 2YJD

Chain ID: A

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 -3086227.373783
FMO2-HF: Nuclear repulsion 2989803.227214
FMO2-HF: Total energy -96424.146569
FMO2-MP2: Total energy -96694.787709


3D Structure
Snapshot
 
Ligand structure

YJD

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.
-67.309-46.19966.412-24.043-63.4860.035


Interactive mode: IFIE and PIEDA for fragment #235(C:1498:YJD)


Summations of interaction energy for fragment #235(C:1498:YJD)
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.
-67.309-46.19966.412-24.043-63.486-0.035
Interaction energy analysis for fragmet #235(C:1498:YJD)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.052
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].
1C264SER10.7590.85328.1160.0500.0500.0000.0000.0000.000
2C265PRO00.0910.05426.126-0.014-0.0140.0000.0000.0000.000
3C266GLU-1-0.764-0.86925.426-0.083-0.0830.0000.0000.0000.000
4C267GLN00.0120.01425.438-0.006-0.0060.0000.0000.0000.000
5C268LEU00.0230.03321.726-0.021-0.0210.0000.0000.0000.000
6C269VAL00.022-0.00620.705-0.017-0.0170.0000.0000.0000.000
7C270LEU0-0.063-0.01720.624-0.018-0.0180.0000.0000.0000.000
8C271THR00.035-0.00321.107-0.023-0.0230.0000.0000.0000.000
9C272LEU0-0.022-0.01516.570-0.036-0.0360.0000.0000.0000.000
10C273LEU0-0.037-0.01516.460-0.040-0.0400.0000.0000.0000.000
11C274GLU-1-0.886-0.96117.035-0.301-0.3010.0000.0000.0000.000
12C275ALA00.0260.00816.043-0.056-0.0560.0000.0000.0000.000
13C276GLU-1-0.816-0.86911.599-0.556-0.5560.0000.0000.0000.000
14C277PRO0-0.0220.0038.555-0.004-0.0040.0000.0000.0000.000
15C278PRO00.0050.00010.2130.0040.0040.0000.0000.0000.000
16C279HIS00.0150.0007.334-0.162-0.1620.0000.0000.0000.000
17C280VAL0-0.0070.0016.2030.2400.2400.0000.0000.0000.000
18C281LEU00.0160.0278.2710.1970.1970.0000.0000.0000.000
19C282ILE0-0.003-0.0196.393-0.243-0.2430.0000.0000.0000.000
20C283SER0-0.048-0.0099.5430.1100.1100.0000.0000.0000.000
21C284ARG10.8280.89512.661-0.019-0.0190.0000.0000.0000.000
22C285PRO00.0380.02315.4400.0230.0230.0000.0000.0000.000
23C286SER00.0150.01017.4650.0210.0210.0000.0000.0000.000
24C287ALA00.0040.00516.810-0.007-0.0070.0000.0000.0000.000
25C288PRO00.0250.02416.6700.0270.0270.0000.0000.0000.000
26C289PHE00.0280.00411.302-0.014-0.0140.0000.0000.0000.000
27C290THR00.0340.00412.0560.0060.0060.0000.0000.0000.000
28C291GLU-1-0.679-0.8148.9400.9780.9780.0000.0000.0000.000
29C292ALA00.0610.0338.2810.1630.1630.0000.0000.0000.000
30C293SER0-0.061-0.0448.960-0.161-0.1610.0000.0000.0000.000
31C294MET00.0060.0136.548-0.027-0.0270.0000.0000.0000.000
32C295MET00.0590.0372.539-0.3640.0961.529-0.272-1.7180.001
33C296MET00.0010.0234.463-1.308-1.1600.000-0.012-0.1360.000
34C297SER0-0.083-0.0657.143-0.634-0.6340.0000.0000.0000.000
35C298LEU00.0240.0162.317-5.550-1.3812.895-1.389-5.6750.008
36C299THR00.0220.0032.772-6.068-3.5330.602-1.215-1.922-0.014
37C300LYS10.8190.9084.1430.9241.0540.000-0.007-0.1230.000
38C301LEU0-0.045-0.0152.270-0.3430.9332.145-0.754-2.6680.004
39C302ALA00.0500.0102.495-2.288-0.7392.077-1.015-2.6120.002
40C303ASP-1-0.836-0.8983.976-1.428-1.1270.006-0.057-0.2500.000
41C304LYS10.8610.9266.8002.7452.7450.0000.0000.0000.000
42C305GLU-1-0.781-0.8711.581-31.156-40.36120.967-7.688-4.074-0.071
43C306LEU00.0460.0395.4430.8910.8910.0000.0000.0000.000
44C307VAL00.0070.0118.3120.4570.4570.0000.0000.0000.000
45C308HIS0-0.059-0.0267.4030.5130.5130.0000.0000.0000.000
46C309MET0-0.0170.0076.7490.4140.4140.0000.0000.0000.000
47C310ILE00.0490.0239.4830.3100.3100.0000.0000.0000.000
48C311SER0-0.082-0.06012.4630.2290.2290.0000.0000.0000.000
49C312TRP00.0160.01211.4980.0660.0660.0000.0000.0000.000
50C313ALA00.0440.00613.4640.1030.1030.0000.0000.0000.000
51C314LYS10.8730.91915.3840.8030.8030.0000.0000.0000.000
52C315LYS10.7760.91715.1650.6550.6550.0000.0000.0000.000
53C316ILE0-0.0050.01215.4530.0420.0420.0000.0000.0000.000
54C317PRO00.0280.00619.9370.0100.0100.0000.0000.0000.000
55C318GLY00.0470.01522.6270.0080.0080.0000.0000.0000.000
56C319PHE0-0.025-0.02016.9090.0110.0110.0000.0000.0000.000
57C320VAL00.002-0.00221.338-0.002-0.0020.0000.0000.0000.000
58C321GLU-1-0.843-0.90123.251-0.125-0.1250.0000.0000.0000.000
59C322LEU0-0.064-0.01521.5970.0250.0250.0000.0000.0000.000
60C323SER0-0.010-0.03124.387-0.023-0.0230.0000.0000.0000.000
61C324LEU00.0430.00519.699-0.005-0.0050.0000.0000.0000.000
62C325PHE00.0340.02419.945-0.026-0.0260.0000.0000.0000.000
63C326ASP-1-0.770-0.86119.697-0.116-0.1160.0000.0000.0000.000
64C327GLN0-0.045-0.03118.594-0.031-0.0310.0000.0000.0000.000
65C328VAL00.0060.00715.066-0.030-0.0300.0000.0000.0000.000
66C329ARG10.9120.95914.723-0.002-0.0020.0000.0000.0000.000
67C330LEU0-0.064-0.02415.4220.0540.0540.0000.0000.0000.000
68C331LEU00.001-0.00111.9180.0350.0350.0000.0000.0000.000
69C332GLU-1-0.854-0.95410.790-0.245-0.2450.0000.0000.0000.000
70C333SER0-0.050-0.02410.7330.0990.0990.0000.0000.0000.000
71C334CYS0-0.050-0.01311.3960.0750.0750.0000.0000.0000.000
72C335TRP00.0430.0132.279-0.533-0.0781.297-0.230-1.523-0.001
73C336MET00.0100.0202.467-0.7990.7700.395-0.364-1.6010.000
74C337GLU-1-0.805-0.9204.9410.9271.104-0.001-0.006-0.1690.000
75C338VAL0-0.015-0.0176.281-0.046-0.0460.0000.0000.0000.000
76C339LEU0-0.026-0.0062.652-3.962-1.1383.346-1.490-4.6800.011
77C340MET0-0.0180.0052.268-2.2180.7602.677-1.599-4.055-0.004
78C341MET0-0.0060.0053.1190.8120.3330.0170.665-0.2030.000
79C342GLY00.0110.0085.222-0.187-0.1870.0000.0000.0000.000
80C343LEU0-0.0190.0052.281-3.661-1.7573.985-1.367-4.5230.009
81C344MET0-0.0140.0074.239-0.570-0.3730.001-0.053-0.1440.000
82C345TRP0-0.0050.0027.035-0.066-0.0660.0000.0000.0000.000
83C346ARG10.7090.8212.6994.2624.9600.091-0.253-0.5360.000
84C347SER0-0.005-0.0207.4670.0250.0250.0000.0000.0000.000
85C348ILE0-0.0240.01510.1430.0180.0180.0000.0000.0000.000
86C349ASP-1-0.778-0.90612.5240.2680.2680.0000.0000.0000.000
87C350HIS00.0020.01512.6420.0220.0220.0000.0000.0000.000
88C351PRO00.006-0.00113.7700.0650.0650.0000.0000.0000.000
89C352GLY00.0230.03212.5990.0050.0050.0000.0000.0000.000
90C353LYS10.7780.8559.730-0.687-0.6870.0000.0000.0000.000
91C354LEU0-0.0030.0113.867-0.375-0.1130.001-0.032-0.2320.000
92C355ILE0-0.032-0.0247.5810.1610.1610.0000.0000.0000.000
93C356PHE00.0300.0172.131-5.449-2.5856.404-1.958-7.3100.020
94C357ALA00.0500.0254.973-2.057-1.995-0.001-0.005-0.0560.000
95C358PRO00.004-0.0047.7950.4290.4290.0000.0000.0000.000
96C359ASP-1-0.777-0.88410.654-0.738-0.7380.0000.0000.0000.000
97C360LEU0-0.038-0.0225.932-0.008-0.0080.0000.0000.0000.000
98C361VAL00.0290.0188.9100.3320.3320.0000.0000.0000.000
99C362LEU00.0330.0286.426-0.087-0.0870.0000.0000.0000.000
100C363ASP-1-0.877-0.9458.7690.8290.8290.0000.0000.0000.000
101C364ARG10.8660.9007.849-0.635-0.6350.0000.0000.0000.000
102C365ASP-1-0.816-0.8898.8580.7630.7630.0000.0000.0000.000
103C366GLU-1-0.777-0.87910.1760.9150.9150.0000.0000.0000.000
104C367GLY00.0440.0207.0710.1070.1070.0000.0000.0000.000
105C368LYS10.8100.8757.722-0.693-0.6930.0000.0000.0000.000
106C369CYS0-0.119-0.0409.852-0.176-0.1760.0000.0000.0000.000
107C370VAL0-0.028-0.0275.911-0.044-0.0440.0000.0000.0000.000
108C371GLU-1-0.782-0.8688.7380.7100.7100.0000.0000.0000.000
109C372GLY00.0110.0176.5100.3120.3120.0000.0000.0000.000
110C373ILE0-0.024-0.0222.302-1.387-1.1934.367-1.067-3.4950.006
111C374LEU0-0.027-0.0013.469-1.313-0.4370.016-0.396-0.496-0.003
112C375GLU-1-0.823-0.9216.3031.0271.0270.0000.0000.0000.000
113C376ILE00.0300.0182.211-1.934-0.9434.006-1.013-3.9840.001
114C377PHE0-0.017-0.0152.318-2.352-0.5511.800-0.801-2.8000.006
115C378ASP-1-0.804-0.8854.5520.8780.911-0.001-0.013-0.0200.000
116C379MET0-0.044-0.0116.741-0.014-0.0140.0000.0000.0000.000
117C380LEU00.0420.0162.620-1.207-0.2190.400-0.310-1.0780.000
118C381LEU00.0250.0296.586-0.160-0.1600.0000.0000.0000.000
119C382ALA0-0.0090.0198.906-0.129-0.1290.0000.0000.0000.000
120C383THR0-0.023-0.0339.645-0.110-0.1100.0000.0000.0000.000
121C384THR0-0.033-0.0358.943-0.082-0.0820.0000.0000.0000.000
122C385SER0-0.051-0.03511.558-0.102-0.1020.0000.0000.0000.000
123C386ARG10.8320.89214.207-0.416-0.4160.0000.0000.0000.000
124C387PHE00.029-0.0069.827-0.068-0.0680.0000.0000.0000.000
125C388ARG10.8080.90813.156-0.536-0.5360.0000.0000.0000.000
126C389GLU-1-0.842-0.89916.7710.3130.3130.0000.0000.0000.000
127C390LEU0-0.032-0.01117.517-0.034-0.0340.0000.0000.0000.000
128C391LYS10.7780.88018.283-0.253-0.2530.0000.0000.0000.000
129C392LEU0-0.0150.02113.095-0.032-0.0320.0000.0000.0000.000
130C393GLN0-0.009-0.02016.990-0.036-0.0360.0000.0000.0000.000
131C394HIS00.0610.02713.6340.0460.0460.0000.0000.0000.000
132C395LYS10.8850.91416.5140.0770.0770.0000.0000.0000.000
133C396GLU-1-0.728-0.82517.5970.1080.1080.0000.0000.0000.000
134C397TYR0-0.009-0.0179.2820.0180.0180.0000.0000.0000.000
135C398LEU0-0.053-0.00813.3960.0020.0020.0000.0000.0000.000
136C399CYS0-0.034-0.01015.328-0.019-0.0190.0000.0000.0000.000
137C400VAL00.0410.00612.6110.0040.0040.0000.0000.0000.000
138C401LYS10.8320.9088.8010.4320.4320.0000.0000.0000.000
139C402ALA00.0140.01212.054-0.020-0.0200.0000.0000.0000.000
140C403MET0-0.033-0.03215.1960.0080.0080.0000.0000.0000.000
141C404ILE00.0060.0129.5000.0030.0030.0000.0000.0000.000
142C405LEU00.0080.00013.0900.0110.0110.0000.0000.0000.000
143C406LEU0-0.0230.00014.003-0.006-0.0060.0000.0000.0000.000
144C407ASN0-0.007-0.01816.908-0.017-0.0170.0000.0000.0000.000
145C408SER0-0.011-0.01214.6610.0230.0230.0000.0000.0000.000
146C409SER00.0140.01616.4230.0220.0220.0000.0000.0000.000
147C410MET00.0000.00818.9980.0200.0200.0000.0000.0000.000
148C411TYR0-0.061-0.02021.8510.0080.0080.0000.0000.0000.000
149C412PRO0-0.012-0.00519.0860.0010.0010.0000.0000.0000.000
150C413LEU00.0180.01716.5760.0140.0140.0000.0000.0000.000
151C414VAL0-0.001-0.00521.172-0.014-0.0140.0000.0000.0000.000
152C415THR0-0.020-0.02623.151-0.012-0.0120.0000.0000.0000.000
153C416ALA00.0070.00721.551-0.007-0.0070.0000.0000.0000.000
154C417THR0-0.064-0.03619.9290.0090.0090.0000.0000.0000.000
155C418GLN00.0550.03518.271-0.008-0.0080.0000.0000.0000.000
156C419ASP-1-0.854-0.91221.979-0.063-0.0630.0000.0000.0000.000
157C420ALA0-0.025-0.01324.3840.0090.0090.0000.0000.0000.000
158C421ASP-1-0.705-0.81324.242-0.056-0.0560.0000.0000.0000.000
159C422SER0-0.021-0.03025.5000.0030.0030.0000.0000.0000.000
160C423SER0-0.034-0.05024.3330.0020.0020.0000.0000.0000.000
161C424ARG10.8170.88626.1570.0500.0500.0000.0000.0000.000
162C425LYS10.8390.91727.2040.1260.1260.0000.0000.0000.000
163C426LEU00.0160.03320.350-0.003-0.0030.0000.0000.0000.000
164C427ALA00.0090.01423.8640.0110.0110.0000.0000.0000.000
165C428HIS0-0.053-0.03226.3570.0190.0190.0000.0000.0000.000
166C429LEU00.0360.02720.7800.0080.0080.0000.0000.0000.000
167C430LEU00.0220.01319.4380.0020.0020.0000.0000.0000.000
168C431ASN0-0.040-0.02322.3340.0250.0250.0000.0000.0000.000
169C432ALA00.0030.00724.9300.0070.0070.0000.0000.0000.000
170C433VAL00.0140.00018.382-0.003-0.0030.0000.0000.0000.000
171C434THR0-0.007-0.00121.5680.0200.0200.0000.0000.0000.000
172C435ASP-1-0.809-0.91023.255-0.023-0.0230.0000.0000.0000.000
173C436ALA0-0.021-0.01122.3350.0010.0010.0000.0000.0000.000
174C437LEU00.0190.01118.6490.0010.0010.0000.0000.0000.000
175C438VAL00.003-0.00222.0130.0090.0090.0000.0000.0000.000
176C439TRP00.0290.00725.439-0.002-0.0020.0000.0000.0000.000
177C440VAL0-0.034-0.02621.143-0.006-0.0060.0000.0000.0000.000
178C441ILE0-0.0180.00521.7340.0050.0050.0000.0000.0000.000
179C442ALA0-0.031-0.00624.8670.0020.0020.0000.0000.0000.000
180C443LYS10.8150.92226.1090.0290.0290.0000.0000.0000.000
181C444SER0-0.052-0.02726.0000.0010.0010.0000.0000.0000.000
182C445GLY00.0270.01628.1060.0000.0000.0000.0000.0000.000
183C446ILE0-0.034-0.01726.9300.0060.0060.0000.0000.0000.000
184C447SER00.0510.02031.218-0.003-0.0030.0000.0000.0000.000
185C448SER00.0770.01531.4960.0060.0060.0000.0000.0000.000
186C449GLN00.0110.03631.0620.0090.0090.0000.0000.0000.000
187C450GLN00.0390.01028.9460.0080.0080.0000.0000.0000.000
188C451GLN0-0.015-0.01127.0270.0080.0080.0000.0000.0000.000
189C452SER00.011-0.00726.0840.0050.0050.0000.0000.0000.000
190C453MET00.0060.00325.7510.0180.0180.0000.0000.0000.000
191C454ARG10.7620.84920.345-0.111-0.1110.0000.0000.0000.000
192C455LEU00.0280.00621.5220.0170.0170.0000.0000.0000.000
193C456ALA00.0210.00821.3390.0170.0170.0000.0000.0000.000
194C457ASN0-0.031-0.02520.0070.0460.0460.0000.0000.0000.000
195C458LEU00.0010.00116.2260.0380.0380.0000.0000.0000.000
196C459LEU0-0.006-0.00716.5990.0240.0240.0000.0000.0000.000
197C460MET0-0.019-0.00818.0570.0270.0270.0000.0000.0000.000
198C461LEU00.0060.01113.9530.0420.0420.0000.0000.0000.000
199C462LEU0-0.0030.00813.3080.0800.0800.0000.0000.0000.000
200C463SER0-0.025-0.02213.2660.0610.0610.0000.0000.0000.000
201C464HIS00.0050.00711.7440.0660.0660.0000.0000.0000.000
202C465VAL00.0030.0117.6340.1880.1880.0000.0000.0000.000
203C466ARG10.8560.9188.938-0.196-0.1960.0000.0000.0000.000
204C467HIS0-0.0140.00410.8250.0900.0900.0000.0000.0000.000
205C468ALA00.0330.0036.2500.1190.1190.0000.0000.0000.000
206C469SER0-0.070-0.0426.7980.7380.7380.0000.0000.0000.000
207C470ASN00.0260.0088.1510.0940.0940.0000.0000.0000.000
208C471LYS10.8140.9056.180-1.271-1.2710.0000.0000.0000.000
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