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: KPZNP

Calculation Name: 2IOK-B-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: n-[(1r)-3-(4-hydroxyphenyl)-1-methylpropyl]-2-(2-phenyl-1h-indol-3-yl)acetamide

ligand 3-letter code: IOK

PDB ID: 2IOK

Chain ID: B

ChEMBL ID: CHEMBL206

UniProt ID: P03372

Base Structure: X-ray

Registration Date: 2017-02-24

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement BioStationViewer:StructureComplemation (agonist templeate: 1A52)
Water A bridging water among Glu353, Arg394 and ligand are complementated by template structure (PDBID: 2YJA).
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandCharge IOK=0
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3152242.932697
FMO2-HF: Nuclear repulsion 3053617.788784
FMO2-HF: Total energy -98625.143913
FMO2-MP2: Total energy -98903.749338


3D Structure
Snapshot
 
Ligand structure

IOK

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.
-120.179-99.916125.860-59.767-86.3520.048


Interactive mode: IFIE and PIEDA for fragment #237(B:600:IOK)


Summations of interaction energy for fragment #237(B:600:IOK)
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.
-120.179-99.916125.86-59.767-86.352-0.048
Interaction energy analysis for fragmet #237(B:600:IOK)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : ******
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].
1B309SER10.88830.497-0.111-0.1110.0000.0000.0000.000
2B310LEU00.11825.309-0.001-0.0010.0000.0000.0000.000
3B311THR0-0.00928.9750.0070.0070.0000.0000.0000.000
4B312ALA00.05426.674-0.001-0.0010.0000.0000.0000.000
5B313ASP-1-0.84925.9240.1020.1020.0000.0000.0000.000
6B314GLN0-0.05926.429-0.014-0.0140.0000.0000.0000.000
7B315MET0-0.02922.086-0.011-0.0110.0000.0000.0000.000
8B316VAL00.03421.231-0.010-0.0100.0000.0000.0000.000
9B317SER00.02520.784-0.019-0.0190.0000.0000.0000.000
10B318ALA00.04621.500-0.023-0.0230.0000.0000.0000.000
11B319LEU0-0.04017.366-0.014-0.0140.0000.0000.0000.000
12B320LEU0-0.05116.878-0.038-0.0380.0000.0000.0000.000
13B321ASP-1-0.96117.359-0.103-0.1030.0000.0000.0000.000
14B322ALA0-0.09016.445-0.035-0.0350.0000.0000.0000.000
15B323GLU-1-0.84312.335-0.406-0.4060.0000.0000.0000.000
16B324PRO0-0.0088.9370.0030.0030.0000.0000.0000.000
17B325PRO0-0.0219.8810.0590.0590.0000.0000.0000.000
18B326ILE00.0059.308-0.235-0.2350.0000.0000.0000.000
19B327LEU0-0.0095.5160.1780.1780.0000.0000.0000.000
20B328TYR0-0.0078.0030.0520.0520.0000.0000.0000.000
21B329SER0-0.0098.136-0.062-0.0620.0000.0000.0000.000
22B330GLU-1-0.8159.182-0.457-0.4570.0000.0000.0000.000
23B331TYR0-0.06711.398-0.073-0.0730.0000.0000.0000.000
24B332ASP-1-0.84913.332-0.248-0.2480.0000.0000.0000.000
25B333PRO00.00516.9440.0300.0300.0000.0000.0000.000
26B334THR0-0.05519.0120.0240.0240.0000.0000.0000.000
27B335ARG10.91819.1300.2420.2420.0000.0000.0000.000
28B336PRO00.02020.6770.0300.0300.0000.0000.0000.000
29B337PHE0-0.00112.699-0.029-0.0290.0000.0000.0000.000
30B338SER0-0.01915.6530.0490.0490.0000.0000.0000.000
31B339GLU-1-0.97615.331-0.334-0.3340.0000.0000.0000.000
32B340ALA00.01613.289-0.019-0.0190.0000.0000.0000.000
33B341SER0-0.0259.299-0.244-0.2440.0000.0000.0000.000
34B342MET00.0175.107-0.017-0.0170.0000.0000.0000.000
35B343MET00.0552.639-5.184-2.5563.087-1.642-4.0730.016
36B344GLY00.0324.201-0.661-0.4190.000-0.040-0.2020.000
37B345LEU0-0.0026.6370.1270.1270.0000.0000.0000.000
38B346LEU0-0.0772.233-4.148-0.5346.239-2.145-7.7070.015
39B347THR00.0072.771-6.695-2.5690.638-1.856-2.909-0.022
40B348ASN00.0043.8770.4560.6580.0040.002-0.2090.000
41B349LEU00.0152.769-2.395-0.3560.718-0.827-1.9300.008
42B350ALA00.0342.185-3.069-0.4783.175-1.872-3.8940.006
43B351ASP-1-0.8853.520-2.184-2.1120.0820.304-0.4570.002
44B352ARG10.8516.8000.5430.5430.0000.0000.0000.000
45B353GLU-1-0.7571.285-38.283-73.08071.367-33.546-3.025-0.110
46B354LEU00.0224.9450.0430.184-0.001-0.003-0.1370.000
47B355VAL00.0237.4860.1150.1150.0000.0000.0000.000
48B356HIS0-0.0748.6790.2310.2310.0000.0000.0000.000
49B357MET00.0107.0820.1710.1710.0000.0000.0000.000
50B358ILE00.06410.0620.1320.1320.0000.0000.0000.000
51B359ASN0-0.06312.9270.1060.1060.0000.0000.0000.000
52B360TRP00.04211.8220.0240.0240.0000.0000.0000.000
53B361ALA00.01413.5360.0730.0730.0000.0000.0000.000
54B362LYS10.95815.2200.1530.1530.0000.0000.0000.000
55B363ARG10.84017.0210.1180.1180.0000.0000.0000.000
56B364VAL0-0.02016.1620.0160.0160.0000.0000.0000.000
57B365PRO0-0.01519.1260.0090.0090.0000.0000.0000.000
58B366GLY0-0.01822.6700.0290.0290.0000.0000.0000.000
59B367PHE00.03117.3550.0160.0160.0000.0000.0000.000
60B368VAL00.02521.4980.0020.0020.0000.0000.0000.000
61B369ASP-1-0.96723.3930.1020.1020.0000.0000.0000.000
62B370LEU0-0.08221.5360.0070.0070.0000.0000.0000.000
63B371THR0-0.00424.668-0.031-0.0310.0000.0000.0000.000
64B372LEU00.04320.9160.0220.0220.0000.0000.0000.000
65B373HIS0-0.05721.2900.0340.0340.0000.0000.0000.000
66B374ASP-1-0.83120.9710.2870.2870.0000.0000.0000.000
67B375GLN0-0.11219.4360.0380.0380.0000.0000.0000.000
68B376VAL00.01116.5200.0290.0290.0000.0000.0000.000
69B377HIS00.01515.8650.0570.0570.0000.0000.0000.000
70B378LEU00.02715.5920.1260.1260.0000.0000.0000.000
71B379LEU00.03512.4330.1860.1860.0000.0000.0000.000
72B380GLU-1-0.90111.1990.6150.6150.0000.0000.0000.000
73B381CYS0-0.10611.7080.1990.1990.0000.0000.0000.000
74B382ALA0-0.00911.0820.3820.3820.0000.0000.0000.000
75B383TRP00.0193.065-0.5160.4270.055-0.177-0.8200.001
76B384LEU0-0.0032.318-4.037-1.3382.781-1.294-4.1850.013
77B385GLU-1-0.8735.2042.8112.8110.0000.0000.0000.000
78B386ILE0-0.0147.517-0.477-0.4770.0000.0000.0000.000
79B387LEU0-0.0062.553-4.122-1.1593.545-1.615-4.8930.008
80B388MET0-0.0222.650-5.995-3.4381.164-0.855-2.8660.005
81B389ILE0-0.0084.021-0.469-0.3310.000-0.003-0.1350.000
82B390GLY00.0425.736-0.037-0.0370.0000.0000.0000.000
83B391LEU0-0.0072.601-1.7170.1090.648-0.600-1.8740.004
84B392VAL0-0.0375.0420.3300.399-0.001-0.005-0.0640.000
85B393TRP00.0077.5690.1180.1180.0000.0000.0000.000
86B394ARG10.7682.9083.2623.7530.026-0.138-0.3780.001
87B395SER00.0067.5790.1500.1500.0000.0000.0000.000
88B396MET0-0.00310.2990.0890.0890.0000.0000.0000.000
89B397GLU-1-0.94713.4250.2090.2090.0000.0000.0000.000
90B398HIS0-0.01112.865-0.002-0.0020.0000.0000.0000.000
91B399PRO00.00912.9510.1290.1290.0000.0000.0000.000
92B400GLY0-0.03812.322-0.064-0.0640.0000.0000.0000.000
93B401LYS10.84510.390-0.504-0.5040.0000.0000.0000.000
94B402LEU00.0013.902-0.223-0.0100.001-0.020-0.1940.000
95B403LEU00.0237.9850.1030.1030.0000.0000.0000.000
96B404PHE00.0272.543-4.653-1.2111.331-1.102-3.6710.013
97B405ALA00.0625.843-1.083-1.0830.0000.0000.0000.000
98B406PRO00.0208.0050.2200.2200.0000.0000.0000.000
99B407ASN0-0.03711.2640.0100.0100.0000.0000.0000.000
100B408LEU0-0.0107.106-0.011-0.0110.0000.0000.0000.000
101B409LEU00.0139.2740.2810.2810.0000.0000.0000.000
102B410LEU00.0016.544-0.048-0.0480.0000.0000.0000.000
103B411ASP-1-0.8239.2260.5930.5930.0000.0000.0000.000
104B412ARG10.9218.844-0.772-0.7720.0000.0000.0000.000
105B413ASN0-0.0489.1630.0120.0120.0000.0000.0000.000
106B414GLN00.0168.436-0.114-0.1140.0000.0000.0000.000
107B415GLY00.0505.836-0.078-0.0780.0000.0000.0000.000
108B416LYS10.8736.142-0.296-0.2960.0000.0000.0000.000
109B417CYS0-0.0558.502-0.212-0.2120.0000.0000.0000.000
110B418VAL0-0.0013.086-1.893-0.2840.559-0.680-1.4880.008
111B419GLU-1-0.9082.817-4.849-3.6460.096-0.443-0.8560.002
112B420GLY00.0902.608-5.445-3.1440.858-1.270-1.888-0.016
113B421MET0-0.0392.172-3.359-1.3477.090-1.864-7.2380.016
114B422VAL0-0.0413.6800.6381.0350.017-0.058-0.3560.000
115B423GLU-1-0.8526.4811.1111.1110.0000.0000.0000.000
116B424ILE00.0242.287-3.898-0.7731.568-1.143-3.5500.009
117B425PHE00.0373.536-0.8000.2100.042-0.185-0.8660.000
118B426ASP-1-0.7814.6560.9120.959-0.001-0.004-0.0420.000
119B427MET0-0.0446.131-0.318-0.3180.0000.0000.0000.000
120B428LEU00.0642.425-1.128-0.9562.288-0.390-2.0700.000
121B429LEU0-0.0436.602-0.512-0.5120.0000.0000.0000.000
122B430ALA0-0.0389.069-0.267-0.2670.0000.0000.0000.000
123B431THR0-0.0149.927-0.163-0.1630.0000.0000.0000.000
124B432SER00.02610.080-0.239-0.2390.0000.0000.0000.000
125B433SER0-0.03011.781-0.205-0.2050.0000.0000.0000.000
126B434ARG10.89714.330-0.806-0.8060.0000.0000.0000.000
127B435PHE00.07610.781-0.103-0.1030.0000.0000.0000.000
128B436ARG10.89513.500-0.722-0.7220.0000.0000.0000.000
129B437MET0-0.10317.007-0.062-0.0620.0000.0000.0000.000
130B438MET0-0.06718.833-0.024-0.0240.0000.0000.0000.000
131B439ASN00.05019.474-0.036-0.0360.0000.0000.0000.000
132B440LEU0-0.04114.041-0.022-0.0220.0000.0000.0000.000
133B441GLN00.02417.518-0.062-0.0620.0000.0000.0000.000
134B442GLY00.06415.8230.0170.0170.0000.0000.0000.000
135B443GLU-1-0.90016.5630.1060.1060.0000.0000.0000.000
136B444GLU-1-0.82418.2410.3410.3410.0000.0000.0000.000
137B445PHE0-0.0229.2980.0430.0430.0000.0000.0000.000
138B446VAL00.02913.8160.0280.0280.0000.0000.0000.000
139B447CYS0-0.04715.2590.0110.0110.0000.0000.0000.000
140B448LEU0-0.00514.3700.0380.0380.0000.0000.0000.000
141B449LYS10.9089.3700.5350.5350.0000.0000.0000.000
142B450SER00.01812.8720.0350.0350.0000.0000.0000.000
143B451ILE0-0.03915.9610.0460.0460.0000.0000.0000.000
144B452ILE0-0.03410.5690.0440.0440.0000.0000.0000.000
145B453LEU0-0.02514.0080.1220.1220.0000.0000.0000.000
146B454LEU00.03015.1820.0290.0290.0000.0000.0000.000
147B455ASN0-0.04217.3360.0600.0600.0000.0000.0000.000
148B456SER0-0.04914.3780.1050.1050.0000.0000.0000.000
149B457GLY00.07116.0050.0840.0840.0000.0000.0000.000
150B458VAL00.05218.261-0.088-0.0880.0000.0000.0000.000
151B459TYR0-0.03821.075-0.052-0.0520.0000.0000.0000.000
152B460THR0-0.11919.6910.0510.0510.0000.0000.0000.000
153B461PHE00.02721.0230.0000.0000.0000.0000.0000.000
154B462LEU00.10423.081-0.011-0.0110.0000.0000.0000.000
155B463SER0-0.01825.659-0.004-0.0040.0000.0000.0000.000
156B464SER0-0.02528.9030.0180.0180.0000.0000.0000.000
157B465THR0-0.02631.122-0.008-0.0080.0000.0000.0000.000
158B466LEU00.04233.3400.0040.0040.0000.0000.0000.000
159B467LYS11.03530.565-0.126-0.1260.0000.0000.0000.000
160B468SER0-0.02227.9780.0140.0140.0000.0000.0000.000
161B469LEU0-0.01728.8110.0240.0240.0000.0000.0000.000
162B470GLU-1-0.88031.3160.1460.1460.0000.0000.0000.000
163B471GLU-1-0.81626.2320.1890.1890.0000.0000.0000.000
164B472LYS10.84925.061-0.343-0.3430.0000.0000.0000.000
165B473ASP-1-0.96727.5510.2140.2140.0000.0000.0000.000
166B474HIS00.01826.166-0.001-0.0010.0000.0000.0000.000
167B475ILE00.02822.257-0.001-0.0010.0000.0000.0000.000
168B476HIS0-0.02224.9970.0430.0430.0000.0000.0000.000
169B477ARG10.95626.585-0.194-0.1940.0000.0000.0000.000
170B478VAL0-0.01122.958-0.008-0.0080.0000.0000.0000.000
171B479LEU0-0.02120.119-0.003-0.0030.0000.0000.0000.000
172B480ASP-1-0.90023.5880.3030.3030.0000.0000.0000.000
173B481LYS10.88926.249-0.174-0.1740.0000.0000.0000.000
174B482ILE0-0.04120.011-0.017-0.0170.0000.0000.0000.000
175B483THR00.00123.3990.0150.0150.0000.0000.0000.000
176B484ASP-1-0.92524.6750.2210.2210.0000.0000.0000.000
177B485THR0-0.03322.988-0.023-0.0230.0000.0000.0000.000
178B486LEU00.06019.773-0.009-0.0090.0000.0000.0000.000
179B487ILE0-0.00123.814-0.008-0.0080.0000.0000.0000.000
180B488HIS0-0.03427.148-0.005-0.0050.0000.0000.0000.000
181B489LEU0-0.01522.148-0.014-0.0140.0000.0000.0000.000
182B490MET0-0.04222.394-0.004-0.0040.0000.0000.0000.000
183B491ALA0-0.02826.959-0.006-0.0060.0000.0000.0000.000
184B492LYS10.93428.213-0.127-0.1270.0000.0000.0000.000
185B493ALA0-0.03627.280-0.008-0.0080.0000.0000.0000.000
186B494GLY00.01029.404-0.003-0.0030.0000.0000.0000.000
187B495LEU0-0.04826.9120.0040.0040.0000.0000.0000.000
188B496THR00.03731.4720.0000.0000.0000.0000.0000.000
189B497LEU00.09232.2140.0130.0130.0000.0000.0000.000
190B498GLN0-0.00931.8360.0000.0000.0000.0000.0000.000
191B499GLN0-0.05429.2510.0290.0290.0000.0000.0000.000
192B500GLN00.02327.7150.0270.0270.0000.0000.0000.000
193B501HIS00.03526.7770.0150.0150.0000.0000.0000.000
194B502GLN00.01127.1260.0100.0100.0000.0000.0000.000
195B503ARG10.73220.999-0.314-0.3140.0000.0000.0000.000
196B504LEU00.06922.2960.0430.0430.0000.0000.0000.000
197B505ALA00.02921.9470.0440.0440.0000.0000.0000.000
198B506GLN00.00320.8820.0830.0830.0000.0000.0000.000
199B507LEU0-0.01617.4410.0870.0870.0000.0000.0000.000
200B508LEU00.03717.0430.0980.0980.0000.0000.0000.000
201B509LEU0-0.04418.7810.0710.0710.0000.0000.0000.000
202B510ILE0-0.06113.1440.1180.1180.0000.0000.0000.000
203B511LEU00.04813.5700.2480.2480.0000.0000.0000.000
204B512SER00.00913.2640.2150.2150.0000.0000.0000.000
205B513HIS0-0.03210.9460.3710.3710.0000.0000.0000.000
206B514ILE00.0497.9880.4800.4800.0000.0000.0000.000
207B515ARG10.9608.321-0.598-0.5980.0000.0000.0000.000
208B516HIS0-0.0629.1310.2970.2970.0000.0000.0000.000
209B517MET0-0.0215.5070.2790.2790.0000.0000.0000.000
210B518SER00.0734.8402.9543.196-0.001-0.009-0.2320.000
211B519ASN00.0285.5650.5880.659-0.001-0.001-0.0690.000
212B520LYS10.9195.739-2.806-2.8060.0000.0000.0000.000
213B521GLY00.0172.618-1.637-0.3702.259-1.508-2.0170.009
214B522MET0-0.0132.778-5.345-5.3090.6410.953-1.631-0.011
215B523GLU-1-0.9834.895-0.230-0.128-0.001-0.006-0.0950.000
216B524HIS00.0042.765-7.629-4.4975.270-2.077-6.325-0.015
217B525LEU0-0.0292.281-8.354-4.6158.960-2.086-10.6130.007
218B526TYR00.0284.380-0.859-0.5360.001-0.030-0.2940.000
219B527SER0-0.0695.0120.0590.0590.0000.0000.0000.000
220B528MET0-0.0936.380-0.486-0.4860.0000.0000.0000.000
221B529LYS10.9222.7423.4604.1640.100-0.125-0.6790.000
222B530CYS0-0.0522.980-2.063-0.9320.185-0.278-1.038-0.001
223B531LYS10.9546.1431.0951.0950.0000.0000.0000.000
224B532ASN00.0399.0900.3280.3280.0000.0000.0000.000
225B533VAL0-0.00811.7710.0870.0870.0000.0000.0000.000
226B534VAL0-0.01914.033-0.062-0.0620.0000.0000.0000.000
227B535PRO0-0.01913.713-0.030-0.0300.0000.0000.0000.000
228B536LEU00.0738.489-0.019-0.0190.0000.0000.0000.000
229B537TYR00.02812.830-0.044-0.0440.0000.0000.0000.000
230B538ASP-1-0.90416.008-0.050-0.0500.0000.0000.0000.000
231B539LEU0-0.04811.373-0.040-0.0400.0000.0000.0000.000
232B540LEU0-0.01011.822-0.028-0.0280.0000.0000.0000.000
233B541LEU0-0.01315.762-0.011-0.0110.0000.0000.0000.000
234B542GLU-1-0.94817.251-0.224-0.2240.0000.0000.0000.000
235B543MET0-0.11713.433-0.030-0.0300.0000.0000.0000.000
236B544LEU-1-0.99216.873-0.023-0.0230.0000.0000.0000.000
238B2025HOH0-0.0752.515-2.754-1.3131.071-1.129-1.382-0.016