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: PZ5NX

Calculation Name: 2YJD-B-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: 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 -3035662.239084
FMO2-HF: Nuclear repulsion 2939240.144556
FMO2-HF: Total energy -96422.094528
FMO2-MP2: Total energy -96692.453612


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.
-82.011-53.28362.315-26.316-64.7310.054


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


Summations of interaction energy for fragment #235(B: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.
-82.011-53.28362.315-26.316-64.731-0.054
Interaction energy analysis for fragmet #235(B:1498:YJD)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.066
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].
1B264SER10.8630.91529.4320.1010.1010.0000.0000.0000.000
2B265PRO00.1670.06826.310-0.017-0.0170.0000.0000.0000.000
3B266GLU-1-0.922-0.94525.178-0.104-0.1040.0000.0000.0000.000
4B267GLN00.008-0.00525.298-0.009-0.0090.0000.0000.0000.000
5B268LEU00.0350.03222.145-0.022-0.0220.0000.0000.0000.000
6B269VAL00.0350.01320.569-0.027-0.0270.0000.0000.0000.000
7B270LEU0-0.015-0.00220.463-0.029-0.0290.0000.0000.0000.000
8B271THR0-0.016-0.02321.248-0.034-0.0340.0000.0000.0000.000
9B272LEU0-0.005-0.00317.010-0.047-0.0470.0000.0000.0000.000
10B273LEU0-0.017-0.02016.436-0.058-0.0580.0000.0000.0000.000
11B274GLU-1-0.974-0.99216.978-0.400-0.4000.0000.0000.0000.000
12B275ALA0-0.055-0.02016.081-0.056-0.0560.0000.0000.0000.000
13B276GLU-1-0.902-0.95711.848-0.802-0.8020.0000.0000.0000.000
14B277PRO0-0.0340.0038.911-0.010-0.0100.0000.0000.0000.000
15B278PRO0-0.015-0.00110.8980.0990.0990.0000.0000.0000.000
16B279HIS00.020-0.0028.316-0.427-0.4270.0000.0000.0000.000
17B280VAL0-0.019-0.0016.0510.3800.3800.0000.0000.0000.000
18B281LEU0-0.0020.0077.8030.0360.0360.0000.0000.0000.000
19B282ILE00.0250.0006.726-0.239-0.2390.0000.0000.0000.000
20B283SER0-0.062-0.0199.178-0.004-0.0040.0000.0000.0000.000
21B284ARG10.9620.96712.0480.2360.2360.0000.0000.0000.000
22B285PRO00.0220.02314.4500.0740.0740.0000.0000.0000.000
23B286SER0-0.010-0.01417.3920.0750.0750.0000.0000.0000.000
24B287ALA00.0160.00616.310-0.022-0.0220.0000.0000.0000.000
25B288PRO00.0000.00115.971-0.005-0.0050.0000.0000.0000.000
26B289PHE00.0150.01010.052-0.009-0.0090.0000.0000.0000.000
27B290THR00.0020.00212.8810.0580.0580.0000.0000.0000.000
28B291GLU-1-0.858-0.94610.0860.7160.7160.0000.0000.0000.000
29B292ALA00.0920.0368.6540.1000.1000.0000.0000.0000.000
30B293SER0-0.052-0.0138.882-0.205-0.2050.0000.0000.0000.000
31B294MET00.0280.0076.398-0.059-0.0590.0000.0000.0000.000
32B295MET00.0680.0412.524-0.768-0.2421.042-0.184-1.3830.000
33B296MET0-0.0060.0034.217-1.463-1.2880.000-0.028-0.1470.000
34B297SER0-0.041-0.0326.618-0.655-0.6550.0000.0000.0000.000
35B298LEU00.0030.0082.460-4.852-1.2571.415-0.929-4.0820.004
36B299THR00.0030.0022.266-7.142-4.6583.112-1.887-3.710-0.019
37B300LYS10.8880.9593.6861.8302.0070.0190.089-0.2850.000
38B301LEU0-0.078-0.0372.352-0.1591.1751.351-0.636-2.0500.005
39B302ALA00.0490.0172.267-2.308-1.6183.489-1.501-2.6790.001
40B303ASP-1-0.828-0.9153.822-1.592-1.2540.011-0.090-0.2600.000
41B304LYS10.9300.9596.2223.1683.1680.0000.0000.0000.000
42B305GLU-1-0.821-0.9091.700-40.647-42.65415.556-8.034-5.516-0.096
43B306LEU00.0030.0134.9551.1211.1210.0000.0000.0000.000
44B307VAL00.0140.0198.3110.6150.6150.0000.0000.0000.000
45B308HIS0-0.029-0.0268.7130.6090.6090.0000.0000.0000.000
46B309MET0-0.0320.0057.0630.4850.4850.0000.0000.0000.000
47B310ILE00.0730.04010.0120.3660.3660.0000.0000.0000.000
48B311SER0-0.066-0.04213.2840.2400.2400.0000.0000.0000.000
49B312TRP0-0.019-0.01511.6200.1330.1330.0000.0000.0000.000
50B313ALA00.0640.02313.7620.1360.1360.0000.0000.0000.000
51B314LYS10.9110.95515.4660.7060.7060.0000.0000.0000.000
52B315LYS10.9120.96816.2490.8470.8470.0000.0000.0000.000
53B316ILE00.0100.02215.1970.0570.0570.0000.0000.0000.000
54B317PRO0-0.027-0.02419.4220.0150.0150.0000.0000.0000.000
55B318GLY00.0550.02523.2750.0270.0270.0000.0000.0000.000
56B319PHE00.0100.00117.5560.0190.0190.0000.0000.0000.000
57B320VAL0-0.009-0.01721.582-0.003-0.0030.0000.0000.0000.000
58B321GLU-1-0.928-0.96223.520-0.217-0.2170.0000.0000.0000.000
59B322LEU0-0.081-0.02021.6350.0330.0330.0000.0000.0000.000
60B323SER00.0180.02025.505-0.022-0.0220.0000.0000.0000.000
61B324LEU00.0820.02021.529-0.003-0.0030.0000.0000.0000.000
62B325PHE0-0.0070.01021.178-0.018-0.0180.0000.0000.0000.000
63B326ASP-1-0.796-0.90520.497-0.072-0.0720.0000.0000.0000.000
64B327GLN0-0.101-0.05419.737-0.041-0.0410.0000.0000.0000.000
65B328VAL00.0210.00516.210-0.041-0.0410.0000.0000.0000.000
66B329ARG10.8520.91615.607-0.003-0.0030.0000.0000.0000.000
67B330LEU0-0.049-0.00715.5080.0370.0370.0000.0000.0000.000
68B331LEU0-0.001-0.00312.5970.0280.0280.0000.0000.0000.000
69B332GLU-1-0.851-0.93611.177-0.359-0.3590.0000.0000.0000.000
70B333SER0-0.075-0.03510.7850.1360.1360.0000.0000.0000.000
71B334CYS0-0.097-0.03311.4180.1490.1490.0000.0000.0000.000
72B335TRP00.0720.0322.904-0.6670.1240.155-0.124-0.8220.000
73B336MET00.0270.0262.306-3.394-0.3691.515-1.075-3.4650.006
74B337GLU-1-0.865-0.9655.1100.9631.119-0.001-0.007-0.1480.000
75B338VAL0-0.031-0.0206.607-0.058-0.0580.0000.0000.0000.000
76B339LEU0-0.027-0.0062.764-3.062-0.3522.124-1.187-3.6480.007
77B340MET0-0.0170.0072.372-2.5840.2112.867-1.690-3.971-0.011
78B341MET00.0060.0223.2440.7150.5210.0080.398-0.2120.000
79B342GLY00.0100.0065.415-0.026-0.0260.0000.0000.0000.000
80B343LEU0-0.033-0.0112.295-3.045-1.0063.266-1.198-4.1070.009
81B344MET0-0.014-0.0194.204-0.502-0.3150.001-0.048-0.1390.000
82B345TRP0-0.027-0.0177.156-0.078-0.0780.0000.0000.0000.000
83B346ARG10.8660.9402.410-3.130-1.5220.797-0.934-1.4710.012
84B347SER00.0110.0147.559-0.036-0.0360.0000.0000.0000.000
85B348ILE0-0.054-0.00510.1770.0160.0160.0000.0000.0000.000
86B349ASP-1-0.939-0.97012.8190.1860.1860.0000.0000.0000.000
87B350HIS0-0.033-0.02112.790-0.026-0.0260.0000.0000.0000.000
88B351PRO0-0.043-0.03612.8550.1250.1250.0000.0000.0000.000
89B352GLY0-0.005-0.00111.753-0.043-0.0430.0000.0000.0000.000
90B353LYS10.9360.97510.048-0.529-0.5290.0000.0000.0000.000
91B354LEU00.0070.0073.406-0.368-0.0170.010-0.054-0.3080.000
92B355ILE0-0.014-0.0187.549-0.016-0.0160.0000.0000.0000.000
93B356PHE00.0180.0072.254-5.228-1.3403.129-1.606-5.4110.019
94B357ALA00.0340.0075.073-1.583-1.519-0.001-0.005-0.0580.000
95B358PRO0-0.026-0.0117.8440.4040.4040.0000.0000.0000.000
96B359ASP-1-0.881-0.94711.404-0.920-0.9200.0000.0000.0000.000
97B360LEU0-0.070-0.0396.371-0.056-0.0560.0000.0000.0000.000
98B361VAL0-0.006-0.0079.0150.2050.2050.0000.0000.0000.000
99B362LEU0-0.0180.0076.1260.0360.0360.0000.0000.0000.000
100B363ASP-1-0.887-0.9458.7250.8770.8770.0000.0000.0000.000
101B364ARG10.9090.9448.295-0.826-0.8260.0000.0000.0000.000
102B365ASP-1-0.947-0.9929.3120.9080.9080.0000.0000.0000.000
103B366GLU-1-0.816-0.9169.5590.8160.8160.0000.0000.0000.000
104B367GLY00.0330.0136.8860.1140.1140.0000.0000.0000.000
105B368LYS10.8350.9177.457-0.819-0.8190.0000.0000.0000.000
106B369CYS0-0.078-0.0209.561-0.178-0.1780.0000.0000.0000.000
107B370VAL00.0070.0066.370-0.155-0.1550.0000.0000.0000.000
108B371GLU-1-0.897-0.9407.7250.9400.9400.0000.0000.0000.000
109B372GLY00.002-0.0127.2900.0740.0740.0000.0000.0000.000
110B373ILE0-0.026-0.0042.403-1.521-1.1344.393-0.988-3.7930.008
111B374LEU0-0.026-0.0093.558-1.059-0.2630.012-0.378-0.430-0.003
112B375GLU-1-0.905-0.9526.3151.5841.5840.0000.0000.0000.000
113B376ILE00.0380.0152.034-1.799-1.0814.605-1.265-4.0580.004
114B377PHE00.001-0.0112.369-2.596-1.1053.433-1.024-3.9000.003
115B378ASP-1-0.811-0.9044.3051.1681.2310.000-0.021-0.0420.000
116B379MET0-0.0260.0036.741-0.064-0.0640.0000.0000.0000.000
117B380LEU00.0330.0082.274-1.255-0.9302.370-0.580-2.1150.002
118B381LEU00.0040.0216.341-0.393-0.3930.0000.0000.0000.000
119B382ALA0-0.027-0.0058.453-0.219-0.2190.0000.0000.0000.000
120B383THR00.011-0.0099.744-0.201-0.2010.0000.0000.0000.000
121B384THR0-0.018-0.0208.697-0.168-0.1680.0000.0000.0000.000
122B385SER0-0.043-0.02311.343-0.165-0.1650.0000.0000.0000.000
123B386ARG10.9811.00513.924-0.557-0.5570.0000.0000.0000.000
124B387PHE00.025-0.00411.024-0.111-0.1110.0000.0000.0000.000
125B388ARG10.9290.97412.598-0.727-0.7270.0000.0000.0000.000
126B389GLU-1-0.979-0.99616.6590.4090.4090.0000.0000.0000.000
127B390LEU0-0.056-0.02817.861-0.052-0.0520.0000.0000.0000.000
128B391LYS10.9530.99118.897-0.261-0.2610.0000.0000.0000.000
129B392LEU0-0.0050.00913.168-0.042-0.0420.0000.0000.0000.000
130B393GLN0-0.026-0.01517.124-0.046-0.0460.0000.0000.0000.000
131B394HIS00.0500.02014.4960.0590.0590.0000.0000.0000.000
132B395LYS10.9990.98216.1370.0890.0890.0000.0000.0000.000
133B396GLU-1-0.740-0.81617.4960.1420.1420.0000.0000.0000.000
134B397TYR00.0210.0158.9880.0540.0540.0000.0000.0000.000
135B398LEU0-0.039-0.00413.267-0.008-0.0080.0000.0000.0000.000
136B399CYS0-0.057-0.01615.212-0.031-0.0310.0000.0000.0000.000
137B400VAL00.0470.00812.4800.0000.0000.0000.0000.0000.000
138B401LYS10.8920.9589.0040.6500.6500.0000.0000.0000.000
139B402ALA00.0100.00911.922-0.026-0.0260.0000.0000.0000.000
140B403MET0-0.035-0.02214.8990.0070.0070.0000.0000.0000.000
141B404ILE00.0010.0139.6080.0020.0020.0000.0000.0000.000
142B405LEU0-0.001-0.02413.2400.0230.0230.0000.0000.0000.000
143B406LEU0-0.039-0.02614.0690.0160.0160.0000.0000.0000.000
144B407ASN0-0.034-0.02816.686-0.025-0.0250.0000.0000.0000.000
145B408SER0-0.0290.00114.5750.0460.0460.0000.0000.0000.000
146B409SER0-0.019-0.01416.4610.0480.0480.0000.0000.0000.000
147B410MET00.0100.00518.666-0.014-0.0140.0000.0000.0000.000
148B411TYR0-0.030-0.03020.6470.0450.0450.0000.0000.0000.000
149B412PRO00.0280.01924.124-0.024-0.0240.0000.0000.0000.000
150B413LEU00.009-0.00227.2320.0110.0110.0000.0000.0000.000
151B414VAL00.001-0.00930.097-0.013-0.0130.0000.0000.0000.000
152B415THR0-0.018-0.01430.646-0.010-0.0100.0000.0000.0000.000
153B416ALA0-0.0140.02327.184-0.003-0.0030.0000.0000.0000.000
154B417THR00.045-0.00128.4920.0010.0010.0000.0000.0000.000
155B418GLN0-0.044-0.04423.672-0.021-0.0210.0000.0000.0000.000
156B419ASP-1-0.718-0.82923.5650.0820.0820.0000.0000.0000.000
157B420ALA0-0.0150.01726.3760.0000.0000.0000.0000.0000.000
158B421ASP-1-0.905-0.93330.142-0.038-0.0380.0000.0000.0000.000
159B422SER0-0.0140.00526.014-0.015-0.0150.0000.0000.0000.000
160B423SER00.017-0.01226.4880.0030.0030.0000.0000.0000.000
161B424ARG10.8200.91427.6750.0280.0280.0000.0000.0000.000
162B425LYS10.9670.98127.3990.1330.1330.0000.0000.0000.000
163B426LEU00.0700.04620.929-0.013-0.0130.0000.0000.0000.000
164B427ALA00.005-0.00824.1250.0080.0080.0000.0000.0000.000
165B428HIS0-0.025-0.00426.3440.0180.0180.0000.0000.0000.000
166B429LEU00.0170.00021.3180.0070.0070.0000.0000.0000.000
167B430LEU00.0240.01219.525-0.004-0.0040.0000.0000.0000.000
168B431ASN0-0.035-0.00922.4640.0120.0120.0000.0000.0000.000
169B432ALA00.0490.03124.6400.0060.0060.0000.0000.0000.000
170B433VAL0-0.007-0.01318.233-0.002-0.0020.0000.0000.0000.000
171B434THR0-0.020-0.02021.5720.0240.0240.0000.0000.0000.000
172B435ASP-1-0.889-0.94422.7600.0180.0180.0000.0000.0000.000
173B436ALA0-0.111-0.04622.3480.0020.0020.0000.0000.0000.000
174B437LEU00.0270.01418.7720.0020.0020.0000.0000.0000.000
175B438VAL00.0020.00221.9720.0130.0130.0000.0000.0000.000
176B439TRP00.002-0.00824.962-0.001-0.0010.0000.0000.0000.000
177B440VAL0-0.038-0.03721.024-0.003-0.0030.0000.0000.0000.000
178B441ILE0-0.029-0.00621.8060.0050.0050.0000.0000.0000.000
179B442ALA00.0260.02925.0290.0050.0050.0000.0000.0000.000
180B443LYS10.9000.95826.7330.0210.0210.0000.0000.0000.000
181B444SER0-0.058-0.03825.915-0.001-0.0010.0000.0000.0000.000
182B445GLY0-0.0060.00327.9880.0040.0040.0000.0000.0000.000
183B446ILE0-0.035-0.00226.6070.0050.0050.0000.0000.0000.000
184B447SER00.0540.02030.840-0.005-0.0050.0000.0000.0000.000
185B448SER00.0950.03731.2090.0050.0050.0000.0000.0000.000
186B449GLN00.0200.00931.2680.0020.0020.0000.0000.0000.000
187B450GLN00.015-0.00728.3280.0150.0150.0000.0000.0000.000
188B451GLN0-0.040-0.02427.2440.0110.0110.0000.0000.0000.000
189B452SER00.0130.00626.2850.0060.0060.0000.0000.0000.000
190B453MET0-0.0040.00526.2100.0180.0180.0000.0000.0000.000
191B454ARG10.7290.81720.150-0.158-0.1580.0000.0000.0000.000
192B455LEU00.0400.02021.6650.0250.0250.0000.0000.0000.000
193B456ALA00.0180.01121.4050.0220.0220.0000.0000.0000.000
194B457ASN0-0.034-0.03420.8330.0570.0570.0000.0000.0000.000
195B458LEU0-0.039-0.02016.7370.0520.0520.0000.0000.0000.000
196B459LEU00.004-0.00816.6020.0460.0460.0000.0000.0000.000
197B460MET0-0.0060.00117.9020.0430.0430.0000.0000.0000.000
198B461LEU0-0.026-0.01513.9920.0680.0680.0000.0000.0000.000
199B462LEU00.0340.02713.3260.1210.1210.0000.0000.0000.000
200B463SER00.0070.00513.1930.0860.0860.0000.0000.0000.000
201B464HIS0-0.030-0.00712.1010.1620.1620.0000.0000.0000.000
202B465VAL0-0.0130.0077.9510.2930.2930.0000.0000.0000.000
203B466ARG10.9610.9828.827-0.303-0.3030.0000.0000.0000.000
204B467HIS0-0.013-0.00210.6600.2560.2560.0000.0000.0000.000
205B468ALA00.0420.0106.2050.1730.1730.0000.0000.0000.000
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