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: XQZYP

Calculation Name: 1X78-B-Xray11

Preferred Name: Estrogen receptor beta

Target Type: SINGLE PROTEIN

Ligand Name: [5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]acetonitrile

ligand 3-letter code: 244

PDB ID: 1X78

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 -3074264.632382
FMO2-HF: Nuclear repulsion 2977824.741781
FMO2-HF: Total energy -96439.890601
FMO2-MP2: Total energy -96710.511013


3D Structure
Snapshot
 
Ligand structure

244

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.
-121.340-103.97882.451-35.152-64.6590.096


Interactive mode: IFIE and PIEDA for fragment #235(B:202:244)


Summations of interaction energy for fragment #235(B:202:244)
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.
-121.34-103.97882.451-35.152-64.659-0.096
Interaction energy analysis for fragmet #235(B:202:244)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.094 / q_NPA : -0.114
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].
1B264SER10.8650.92129.276-0.008-0.0080.0000.0000.0000.000
2B265PRO00.2230.08626.154-0.013-0.0130.0000.0000.0000.000
3B266GLU-1-0.894-0.93124.8620.0800.0800.0000.0000.0000.000
4B267GLN00.0100.00024.866-0.001-0.0010.0000.0000.0000.000
5B268LEU00.0080.03221.844-0.017-0.0170.0000.0000.0000.000
6B269VAL00.010-0.01320.329-0.005-0.0050.0000.0000.0000.000
7B270LEU0-0.048-0.04120.1780.0060.0060.0000.0000.0000.000
8B271THR00.0250.00620.287-0.017-0.0170.0000.0000.0000.000
9B272LEU0-0.025-0.01216.386-0.038-0.0380.0000.0000.0000.000
10B273LEU0-0.050-0.02415.909-0.006-0.0060.0000.0000.0000.000
11B274GLU-1-0.970-0.97916.516-0.185-0.1850.0000.0000.0000.000
12B275ALA0-0.068-0.04415.653-0.057-0.0570.0000.0000.0000.000
13B276GLU-1-0.830-0.89710.707-0.083-0.0830.0000.0000.0000.000
14B277PRO0-0.044-0.0048.301-0.037-0.0370.0000.0000.0000.000
15B278PRO0-0.0140.00010.4190.1450.1450.0000.0000.0000.000
16B279HIS00.0420.0017.815-0.540-0.5400.0000.0000.0000.000
17B280VAL0-0.0040.0055.9060.3670.3670.0000.0000.0000.000
18B281LEU0-0.018-0.0117.6370.0910.0910.0000.0000.0000.000
19B282ILE0-0.043-0.0236.341-0.189-0.1890.0000.0000.0000.000
20B283SER0-0.059-0.0259.4870.2710.2710.0000.0000.0000.000
21B284ARG10.8950.93911.829-1.499-1.4990.0000.0000.0000.000
22B285PRO0-0.060-0.00811.911-0.128-0.1280.0000.0000.0000.000
23B286SER00.021-0.00214.8060.1000.1000.0000.0000.0000.000
24B287ALA0-0.034-0.00718.3290.0390.0390.0000.0000.0000.000
25B288PRO00.005-0.01017.0070.0780.0780.0000.0000.0000.000
26B289PHE0-0.027-0.01310.838-0.074-0.0740.0000.0000.0000.000
27B290THR00.0190.01012.911-0.075-0.0750.0000.0000.0000.000
28B291GLU-1-0.794-0.9088.484-0.393-0.3930.0000.0000.0000.000
29B292ALA00.0470.0138.6860.1000.1000.0000.0000.0000.000
30B293SER00.0030.0039.5330.0500.0500.0000.0000.0000.000
31B294MET00.0300.0217.3130.1510.1510.0000.0000.0000.000
32B295MET00.0480.0283.876-1.3470.2460.198-0.496-1.2950.004
33B296MET00.0080.0365.152-0.797-0.639-0.001-0.003-0.1540.000
34B297SER0-0.022-0.0267.473-0.617-0.6170.0000.0000.0000.000
35B298LEU0-0.0020.0102.511-5.632-1.8871.971-1.380-4.3360.011
36B299THR00.004-0.0252.753-9.698-6.2620.607-1.598-2.445-0.021
37B300LYS10.9240.9644.4250.6030.746-0.001-0.013-0.1300.000
38B301LEU0-0.064-0.0162.112-0.6810.8181.632-0.803-2.3280.003
39B302ALA00.0510.0122.153-3.129-1.5551.935-1.198-2.3100.000
40B303ASP-1-0.906-0.9503.615-0.676-0.5480.0490.060-0.2370.000
41B304LYS10.9680.9726.6372.2682.2680.0000.0000.0000.000
42B305GLU-1-0.826-0.8991.549-39.817-50.05328.029-12.078-5.716-0.118
43B306LEU00.0260.0295.8431.1131.1130.0000.0000.0000.000
44B307VAL00.0120.0158.0720.5760.5760.0000.0000.0000.000
45B308HIS0-0.020-0.0238.1880.4920.4920.0000.0000.0000.000
46B309MET0-0.0200.0177.8270.3450.3450.0000.0000.0000.000
47B310ILE00.0330.0209.6950.3160.3160.0000.0000.0000.000
48B311SER0-0.042-0.03013.0020.1980.1980.0000.0000.0000.000
49B312TRP0-0.020-0.01511.3850.1270.1270.0000.0000.0000.000
50B313ALA00.0500.02113.4260.1210.1210.0000.0000.0000.000
51B314LYS10.9000.94515.0670.5300.5300.0000.0000.0000.000
52B315LYS10.9240.97415.8020.4820.4820.0000.0000.0000.000
53B316ILE0-0.0080.01215.0110.0610.0610.0000.0000.0000.000
54B317PRO0-0.015-0.02018.896-0.010-0.0100.0000.0000.0000.000
55B318GLY00.0630.03222.7170.0140.0140.0000.0000.0000.000
56B319PHE00.0240.01317.699-0.004-0.0040.0000.0000.0000.000
57B320VAL0-0.016-0.02021.236-0.014-0.0140.0000.0000.0000.000
58B321GLU-1-1.005-0.99722.957-0.141-0.1410.0000.0000.0000.000
59B322LEU0-0.052-0.00921.5020.0170.0170.0000.0000.0000.000
60B323SER00.004-0.02425.345-0.015-0.0150.0000.0000.0000.000
61B324LEU00.016-0.00722.591-0.010-0.0100.0000.0000.0000.000
62B325PHE00.029-0.00422.637-0.027-0.0270.0000.0000.0000.000
63B326ASP-1-0.799-0.86822.843-0.243-0.2430.0000.0000.0000.000
64B327GLN0-0.065-0.03819.500-0.044-0.0440.0000.0000.0000.000
65B328VAL0-0.0050.00418.070-0.031-0.0310.0000.0000.0000.000
66B329ARG10.9611.01017.8470.2420.2420.0000.0000.0000.000
67B330LEU0-0.058-0.03217.154-0.006-0.0060.0000.0000.0000.000
68B331LEU0-0.004-0.01012.6040.0080.0080.0000.0000.0000.000
69B332GLU-1-0.861-0.94413.040-0.544-0.5440.0000.0000.0000.000
70B333SER0-0.041-0.00813.274-0.007-0.0070.0000.0000.0000.000
71B334CYS0-0.042-0.00811.6380.0090.0090.0000.0000.0000.000
72B335TRP00.0460.0035.2070.2230.2230.0000.0000.0000.000
73B336MET00.0400.0263.182-2.9260.1600.831-0.729-3.1870.006
74B337GLU-1-0.875-0.9445.2910.6410.6410.0000.0000.0000.000
75B338VAL0-0.031-0.0126.7510.4190.4190.0000.0000.0000.000
76B339LEU0-0.0070.0032.741-2.901-0.0992.520-1.295-4.0270.011
77B340MET0-0.0330.0042.654-1.2681.4431.019-1.083-2.647-0.009
78B341MET0-0.0140.0053.5060.5650.6330.0040.132-0.2040.000
79B342GLY0-0.012-0.0105.214-0.116-0.1160.0000.0000.0000.000
80B343LEU0-0.0070.0032.298-2.403-0.5721.318-0.873-2.2770.006
81B344MET0-0.016-0.0084.194-0.979-0.7470.001-0.045-0.1880.000
82B345TRP0-0.021-0.0037.188-0.332-0.3320.0000.0000.0000.000
83B346ARG10.8350.9202.010-7.279-7.8694.694-1.673-2.4310.020
84B347SER0-0.018-0.0067.434-0.018-0.0180.0000.0000.0000.000
85B348ILE0-0.0050.02410.064-0.090-0.0900.0000.0000.0000.000
86B349ASP-1-0.946-0.96012.6810.9360.9360.0000.0000.0000.000
87B350HIS0-0.036-0.01913.055-0.101-0.1010.0000.0000.0000.000
88B351PRO00.0290.00613.8040.3080.3080.0000.0000.0000.000
89B352GLY0-0.036-0.01512.797-0.095-0.0950.0000.0000.0000.000
90B353LYS10.8510.90811.460-1.790-1.7900.0000.0000.0000.000
91B354LEU00.0080.0144.767-0.146-0.008-0.001-0.005-0.1320.000
92B355ILE0-0.004-0.0168.4120.0100.0100.0000.0000.0000.000
93B356PHE00.0460.0132.894-6.039-1.7241.662-1.433-4.5430.019
94B357ALA00.021-0.0014.536-2.041-1.910-0.001-0.012-0.1180.000
95B358PRO0-0.023-0.0157.2260.4270.4270.0000.0000.0000.000
96B359ASP-1-0.869-0.93810.9090.6870.6870.0000.0000.0000.000
97B360LEU00.005-0.0026.174-0.169-0.1690.0000.0000.0000.000
98B361VAL0-0.022-0.0079.0110.7560.7560.0000.0000.0000.000
99B362LEU0-0.034-0.0156.379-0.351-0.3510.0000.0000.0000.000
100B363ASP-1-0.827-0.9019.7892.2732.2730.0000.0000.0000.000
101B364ARG10.9050.9549.017-1.620-1.6200.0000.0000.0000.000
102B365ASP-1-0.890-0.9629.6541.9641.9640.0000.0000.0000.000
103B366GLU-1-0.730-0.85510.2721.9221.9220.0000.0000.0000.000
104B367GLY0-0.0030.0037.7340.0770.0770.0000.0000.0000.000
105B368LYS10.8620.9228.322-1.761-1.7610.0000.0000.0000.000
106B369CYS0-0.093-0.02110.884-0.353-0.3530.0000.0000.0000.000
107B370VAL00.0470.0124.944-0.235-0.2350.0000.0000.0000.000
108B371GLU-1-0.904-0.9518.225-1.108-1.1080.0000.0000.0000.000
109B372GLY00.016-0.0016.819-0.920-0.9200.0000.0000.0000.000
110B373ILE0-0.0020.0083.108-3.523-1.2950.586-0.713-2.1010.007
111B374LEU0-0.040-0.0205.1382.4152.498-0.001-0.001-0.0810.000
112B375GLU-1-0.905-0.9447.243-0.501-0.5010.0000.0000.0000.000
113B376ILE00.0430.0042.224-1.525-2.1106.018-1.151-4.282-0.003
114B377PHE00.022-0.0062.427-0.966-0.7863.721-0.816-3.0850.013
115B378ASP-1-0.807-0.9004.9171.4641.5240.000-0.010-0.0490.000
116B379MET0-0.0380.0006.865-0.416-0.4160.0000.0000.0000.000
117B380LEU00.0170.0092.796-1.204-0.8431.654-0.402-1.6120.007
118B381LEU00.0220.0197.002-0.871-0.8710.0000.0000.0000.000
119B382ALA0-0.032-0.0099.511-0.560-0.5600.0000.0000.0000.000
120B383THR0-0.001-0.01310.422-0.447-0.4470.0000.0000.0000.000
121B384THR00.006-0.0099.441-0.260-0.2600.0000.0000.0000.000
122B385SER0-0.027-0.02511.680-0.299-0.2990.0000.0000.0000.000
123B386ARG10.9110.98914.965-0.889-0.8890.0000.0000.0000.000
124B387PHE00.0670.00211.165-0.188-0.1880.0000.0000.0000.000
125B388ARG10.8690.93013.909-1.763-1.7630.0000.0000.0000.000
126B389GLU-1-0.953-0.97216.6580.6150.6150.0000.0000.0000.000
127B390LEU0-0.053-0.02517.889-0.110-0.1100.0000.0000.0000.000
128B391LYS10.9050.96318.869-0.627-0.6270.0000.0000.0000.000
129B392LEU0-0.0240.00213.120-0.086-0.0860.0000.0000.0000.000
130B393GLN0-0.026-0.01917.048-0.012-0.0120.0000.0000.0000.000
131B394HIS00.0940.03713.8050.0790.0790.0000.0000.0000.000
132B395LYS10.9470.95916.216-0.205-0.2050.0000.0000.0000.000
133B396GLU-1-0.785-0.88317.6840.4290.4290.0000.0000.0000.000
134B397TYR00.0540.0269.0490.0120.0120.0000.0000.0000.000
135B398LEU0-0.034-0.00313.544-0.012-0.0120.0000.0000.0000.000
136B399CYS0-0.030-0.00214.895-0.068-0.0680.0000.0000.0000.000
137B400VAL00.0400.01112.805-0.050-0.0500.0000.0000.0000.000
138B401LYS10.8220.9008.514-0.082-0.0820.0000.0000.0000.000
139B402ALA00.0350.01412.220-0.086-0.0860.0000.0000.0000.000
140B403MET0-0.054-0.02615.167-0.035-0.0350.0000.0000.0000.000
141B404ILE0-0.020-0.00310.138-0.033-0.0330.0000.0000.0000.000
142B405LEU00.0280.00413.395-0.056-0.0560.0000.0000.0000.000
143B406LEU0-0.022-0.01414.525-0.044-0.0440.0000.0000.0000.000
144B407ASN0-0.017-0.01817.195-0.040-0.0400.0000.0000.0000.000
145B408SER0-0.052-0.01215.101-0.014-0.0140.0000.0000.0000.000
146B409SER00.0170.01217.164-0.046-0.0460.0000.0000.0000.000
147B410MET0-0.074-0.00718.5810.0010.0010.0000.0000.0000.000
148B411TYR0-0.046-0.01417.8030.0130.0130.0000.0000.0000.000
149B412PRO00.0050.02113.5010.0110.0110.0000.0000.0000.000
150B413LEU0-0.035-0.04315.5440.0350.0350.0000.0000.0000.000
151B414VAL00.1290.05816.990-0.023-0.0230.0000.0000.0000.000
152B415THR00.014-0.01718.8240.0410.0410.0000.0000.0000.000
153B416ALA0-0.0060.00722.6040.0060.0060.0000.0000.0000.000
154B417THR0-0.041-0.01523.7820.0290.0290.0000.0000.0000.000
155B418GLN00.015-0.00225.1110.0110.0110.0000.0000.0000.000
156B419ASP-1-0.816-0.86027.757-0.205-0.2050.0000.0000.0000.000
157B420ALA0-0.018-0.03129.6580.0150.0150.0000.0000.0000.000
158B421ASP-1-0.832-0.88932.280-0.109-0.1090.0000.0000.0000.000
159B422SER0-0.025-0.03726.4660.0080.0080.0000.0000.0000.000
160B423SER0-0.024-0.01927.3500.0110.0110.0000.0000.0000.000
161B424ARG10.8410.86827.7220.1230.1230.0000.0000.0000.000
162B425LYS10.9230.97926.7820.1620.1620.0000.0000.0000.000
163B426LEU00.0330.02021.1640.0060.0060.0000.0000.0000.000
164B427ALA00.0070.00224.2980.0160.0160.0000.0000.0000.000
165B428HIS0-0.019-0.01026.2950.0230.0230.0000.0000.0000.000
166B429LEU00.0020.00322.5060.0160.0160.0000.0000.0000.000
167B430LEU00.0150.01419.8110.0190.0190.0000.0000.0000.000
168B431ASN00.0250.03322.7030.0410.0410.0000.0000.0000.000
169B432ALA00.0150.02725.0150.0210.0210.0000.0000.0000.000
170B433VAL00.014-0.00218.6830.0180.0180.0000.0000.0000.000
171B434THR0-0.022-0.03721.8610.0420.0420.0000.0000.0000.000
172B435ASP-1-0.973-0.99322.8910.0900.0900.0000.0000.0000.000
173B436ALA0-0.053-0.02222.5200.0120.0120.0000.0000.0000.000
174B437LEU0-0.016-0.00918.9800.0230.0230.0000.0000.0000.000
175B438VAL00.015-0.00222.1270.0270.0270.0000.0000.0000.000
176B439TRP00.0380.01724.8780.0120.0120.0000.0000.0000.000
177B440VAL0-0.058-0.03521.2070.0050.0050.0000.0000.0000.000
178B441ILE00.0170.01321.9850.0130.0130.0000.0000.0000.000
179B442ALA00.0310.04725.0020.0070.0070.0000.0000.0000.000
180B443LYS10.8140.92825.171-0.190-0.1900.0000.0000.0000.000
181B444SER0-0.062-0.05725.7530.0080.0080.0000.0000.0000.000
182B445GLY00.0030.00127.7070.0050.0050.0000.0000.0000.000
183B446ILE0-0.0290.01126.891-0.006-0.0060.0000.0000.0000.000
184B447SER00.0430.01031.001-0.011-0.0110.0000.0000.0000.000
185B448SER00.0690.02431.5230.0090.0090.0000.0000.0000.000
186B449GLN00.0460.00231.4070.0150.0150.0000.0000.0000.000
187B450GLN00.0660.03029.0480.0000.0000.0000.0000.0000.000
188B451GLN0-0.048-0.01327.3200.0190.0190.0000.0000.0000.000
189B452SER00.0020.01026.3980.0080.0080.0000.0000.0000.000
190B453MET00.006-0.00526.3370.0120.0120.0000.0000.0000.000
191B454ARG10.7840.88620.474-0.450-0.4500.0000.0000.0000.000
192B455LEU00.0300.00921.8280.0400.0400.0000.0000.0000.000
193B456ALA00.0100.00321.6120.0140.0140.0000.0000.0000.000
194B457ASN0-0.023-0.03021.0880.0130.0130.0000.0000.0000.000
195B458LEU0-0.0020.00216.6400.0640.0640.0000.0000.0000.000
196B459LEU00.0150.00216.8100.0500.0500.0000.0000.0000.000
197B460MET0-0.035-0.00417.889-0.017-0.0170.0000.0000.0000.000
198B461LEU0-0.014-0.00614.0740.0060.0060.0000.0000.0000.000
199B462LEU00.0110.00713.4430.0960.0960.0000.0000.0000.000
200B463SER00.0060.01313.406-0.059-0.0590.0000.0000.0000.000
201B464HIS00.0210.00812.099-0.158-0.1580.0000.0000.0000.000
202B465VAL00.0020.0088.3470.0580.0580.0000.0000.0000.000
203B466ARG10.9480.9588.670-0.004-0.0040.0000.0000.0000.000
204B467HIS0-0.062-0.0249.842-0.330-0.3300.0000.0000.0000.000
205B468ALA00.0620.0085.559-0.380-0.3800.0000.0000.0000.000
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