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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: PKR3X

Calculation Name: 2OUZ-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (5r,6s)-6-phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol

ligand 3-letter code: C3D

PDB ID: 2OUZ

Chain ID: A

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 (antagonist templeate: 1YIM)
Water A bridging water among Glu353, Arg394 and ligand.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandCharge C3D=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3156953.14353
FMO2-HF: Nuclear repulsion 3058300.853807
FMO2-HF: Total energy -98652.289723
FMO2-MP2: Total energy -98930.560979


3D Structure
Snapshot
 
Ligand structure

C3D

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.
-347.345-314.967112.872-57.048-88.2020.263


Interactive mode: IFIE and PIEDA for fragment #237(A:999:C3D)


Summations of interaction energy for fragment #237(A:999:C3D)
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.
-347.345-314.967112.872-57.048-88.202-0.263
Interaction energy analysis for fragmet #237(A:999:C3D)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.740 / 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].
1A309SER10.81530.5409.4659.4650.0000.0000.0000.000
2A310LEU00.11525.4840.2680.2680.0000.0000.0000.000
3A311THR00.03729.510-0.022-0.0220.0000.0000.0000.000
4A312ALA00.07627.180-0.280-0.2800.0000.0000.0000.000
5A313ASP-1-0.87625.979-9.225-9.2250.0000.0000.0000.000
6A314GLN0-0.00826.056-0.259-0.2590.0000.0000.0000.000
7A315MET0-0.00122.457-0.443-0.4430.0000.0000.0000.000
8A316VAL00.03321.370-0.475-0.4750.0000.0000.0000.000
9A317SER0-0.02521.040-0.328-0.3280.0000.0000.0000.000
10A318ALA00.02521.613-0.251-0.2510.0000.0000.0000.000
11A319LEU0-0.01617.416-0.553-0.5530.0000.0000.0000.000
12A320LEU0-0.04216.679-0.604-0.6040.0000.0000.0000.000
13A321ASP-1-0.93917.132-11.990-11.9900.0000.0000.0000.000
14A322ALA0-0.08916.142-0.335-0.3350.0000.0000.0000.000
15A323GLU-1-0.81711.897-17.781-17.7810.0000.0000.0000.000
16A324PRO0-0.0348.6610.0030.0030.0000.0000.0000.000
17A325PRO00.0029.9560.8330.8330.0000.0000.0000.000
18A326ILE00.0037.414-1.473-1.4730.0000.0000.0000.000
19A327LEU0-0.0376.1550.9420.9420.0000.0000.0000.000
20A328TYR00.0277.4940.5160.5160.0000.0000.0000.000
21A329SER00.0017.275-1.484-1.4840.0000.0000.0000.000
22A330GLU-1-0.8908.224-22.827-22.8270.0000.0000.0000.000
23A331TYR0-0.10510.868-0.314-0.3140.0000.0000.0000.000
24A332ASP-1-0.83613.666-13.574-13.5740.0000.0000.0000.000
25A333PRO0-0.00816.4560.1110.1110.0000.0000.0000.000
26A334THR0-0.09217.7300.6310.6310.0000.0000.0000.000
27A335ARG10.82518.31813.76113.7610.0000.0000.0000.000
28A336PRO0-0.02218.787-0.225-0.2250.0000.0000.0000.000
29A337PHE00.06611.470-0.438-0.4380.0000.0000.0000.000
30A338SER0-0.03215.348-0.540-0.5400.0000.0000.0000.000
31A339GLU-1-0.82016.281-14.466-14.4660.0000.0000.0000.000
32A340ALA00.00011.870-0.684-0.6840.0000.0000.0000.000
33A341SER00.0249.383-0.017-0.0170.0000.0000.0000.000
34A342MET00.0575.978-1.771-1.7710.0000.0000.0000.000
35A343MET00.0452.490-6.315-3.2621.892-0.986-3.9580.009
36A344GLY00.0154.514-6.330-6.096-0.001-0.018-0.2160.000
37A345LEU0-0.0056.710-2.765-2.7650.0000.0000.0000.000
38A346LEU0-0.0262.238-5.402-2.4962.752-1.128-4.5290.001
39A347THR00.0092.201-14.723-9.1564.146-3.467-6.246-0.029
40A348ASN00.0293.309-4.907-4.9600.0400.605-0.592-0.002
41A349LEU0-0.0462.460-0.7310.7960.499-0.402-1.6240.001
42A350ALA00.0332.482-2.6370.5003.231-1.596-4.7720.004
43A351ASP-1-0.8271.716-128.648-126.44716.578-10.362-8.416-0.123
44A352ARG10.8333.99636.07336.4200.000-0.072-0.2750.000
45A353GLU-1-0.7711.396-73.061-91.73947.544-23.584-5.282-0.142
46A354LEU0-0.0042.3802.9122.9831.652-0.278-1.445-0.001
47A355VAL00.0525.8033.5493.5490.0000.0000.0000.000
48A356HIS0-0.0388.4683.6803.6800.0000.0000.0000.000
49A357MET0-0.0476.7502.3512.3510.0000.0000.0000.000
50A358ILE00.0618.2792.0352.0350.0000.0000.0000.000
51A359ASN0-0.02111.0922.0382.0380.0000.0000.0000.000
52A360TRP0-0.00711.7120.8240.8240.0000.0000.0000.000
53A361ALA00.04112.4181.2641.2640.0000.0000.0000.000
54A362LYS10.88714.18820.05720.0570.0000.0000.0000.000
55A363ARG10.86516.85315.48915.4890.0000.0000.0000.000
56A364VAL00.01215.7450.7520.7520.0000.0000.0000.000
57A365PRO0-0.04018.7740.1800.1800.0000.0000.0000.000
58A366GLY0-0.01122.008-0.121-0.1210.0000.0000.0000.000
59A367PHE00.02013.3790.0030.0030.0000.0000.0000.000
60A368VAL0-0.00418.208-0.198-0.1980.0000.0000.0000.000
61A369ASP-1-0.92220.100-11.464-11.4640.0000.0000.0000.000
62A370LEU0-0.04818.1270.2860.2860.0000.0000.0000.000
63A371THR0-0.09720.317-0.186-0.1860.0000.0000.0000.000
64A372LEU00.04914.958-0.305-0.3050.0000.0000.0000.000
65A373HIS0-0.01215.652-1.281-1.2810.0000.0000.0000.000
66A374ASP-1-0.80615.405-15.296-15.2960.0000.0000.0000.000
67A375GLN0-0.04814.507-1.392-1.3920.0000.0000.0000.000
68A376VAL00.04110.227-1.376-1.3760.0000.0000.0000.000
69A377HIS0-0.03810.640-2.421-2.4210.0000.0000.0000.000
70A378LEU0-0.03912.044-0.810-0.8100.0000.0000.0000.000
71A379LEU00.0268.269-0.914-0.9140.0000.0000.0000.000
72A380GLU-1-0.9377.228-30.051-30.0510.0000.0000.0000.000
73A381CYS0-0.1238.109-1.203-1.2030.0000.0000.0000.000
74A382ALA00.03910.004-0.181-0.1810.0000.0000.0000.000
75A383TRP00.0222.069-9.983-7.4694.935-1.568-5.880-0.014
76A384LEU0-0.0152.189-2.846-1.0592.026-0.543-3.270-0.002
77A385GLU-1-0.8204.776-18.713-18.526-0.001-0.004-0.1830.000
78A386ILE0-0.0056.6581.7181.7180.0000.0000.0000.000
79A387LEU00.0002.630-2.6181.3261.876-1.395-4.4250.007
80A388MET0-0.0452.3560.0673.4432.397-1.495-4.278-0.014
81A389ILE00.0123.5612.0992.2270.0120.080-0.2190.000
82A390GLY00.0195.7321.3051.3050.0000.0000.0000.000
83A391LEU0-0.0182.381-1.4730.1652.832-0.934-3.5360.006
84A392VAL0-0.0124.4690.5950.7310.000-0.026-0.1110.000
85A393TRP00.0117.4930.9320.9320.0000.0000.0000.000
86A394ARG10.7992.04712.72313.1293.795-1.718-2.4840.023
87A395SER0-0.0187.4480.2300.2300.0000.0000.0000.000
88A396MET0-0.02310.1050.4230.4230.0000.0000.0000.000
89A397GLU-1-0.96413.176-11.149-11.1490.0000.0000.0000.000
90A398HIS0-0.02812.4880.3720.3720.0000.0000.0000.000
91A399PRO00.00913.358-0.350-0.3500.0000.0000.0000.000
92A400GLY0-0.04813.9690.1310.1310.0000.0000.0000.000
93A401LYS10.90711.41312.89112.8910.0000.0000.0000.000
94A402LEU00.0065.0760.0670.0670.0000.0000.0000.000
95A403LEU00.0168.237-0.393-0.3930.0000.0000.0000.000
96A404PHE00.0442.449-5.003-0.9291.364-1.090-4.3480.011
97A405ALA00.0614.682-2.045-1.861-0.001-0.011-0.1730.000
98A406PRO00.0097.3731.0231.0230.0000.0000.0000.000
99A407ASN0-0.01310.1640.1760.1760.0000.0000.0000.000
100A408LEU0-0.0126.394-0.313-0.3130.0000.0000.0000.000
101A409LEU00.0268.752-0.345-0.3450.0000.0000.0000.000
102A410LEU0-0.0356.8010.2880.2880.0000.0000.0000.000
103A411ASP-1-0.84510.401-13.092-13.0920.0000.0000.0000.000
104A412ARG11.00110.12012.46812.4680.0000.0000.0000.000
105A413ASN0-0.09910.776-0.346-0.3460.0000.0000.0000.000
106A414GLN00.03710.300-0.023-0.0230.0000.0000.0000.000
107A415GLY00.0106.951-1.010-1.0100.0000.0000.0000.000
108A416LYS10.9027.02712.14412.1440.0000.0000.0000.000
109A417CYS0-0.0868.5560.3770.3770.0000.0000.0000.000
110A418VAL00.0398.041-0.879-0.8790.0000.0000.0000.000
111A419GLU-1-0.9215.074-24.752-24.7520.0000.0000.0000.000
112A420GLY00.0195.4941.0651.0650.0000.0000.0000.000
113A421MET00.0182.0850.215-2.0478.431-1.492-4.6770.007
114A422VAL0-0.0464.1970.8280.9410.001-0.033-0.0800.000
115A423GLU-1-0.8687.861-15.697-15.6970.0000.0000.0000.000
116A424ILE00.0443.181-1.9560.1230.579-0.662-1.9970.007
117A425PHE0-0.0225.4650.1420.1420.0000.0000.0000.000
118A426ASP-1-0.8517.039-13.306-13.3060.0000.0000.0000.000
119A427MET0-0.0517.9440.3880.3880.0000.0000.0000.000
120A428LEU00.0503.059-0.6160.3430.111-0.164-0.906-0.001
121A429LEU0-0.0327.0650.5390.5390.0000.0000.0000.000
122A430ALA0-0.0139.8390.6070.6070.0000.0000.0000.000
123A431THR0-0.0089.3250.4780.4780.0000.0000.0000.000
124A432SER00.0049.5200.5130.5130.0000.0000.0000.000
125A433SER0-0.02711.3490.5540.5540.0000.0000.0000.000
126A434ARG10.92414.23011.22611.2260.0000.0000.0000.000
127A435PHE00.06610.6250.4310.4310.0000.0000.0000.000
128A436ARG10.91013.84311.99611.9960.0000.0000.0000.000
129A437MET0-0.06317.1190.4660.4660.0000.0000.0000.000
130A438MET0-0.05918.4260.2240.2240.0000.0000.0000.000
131A439ASN00.00119.5390.0110.0110.0000.0000.0000.000
132A440LEU0-0.03513.7690.1200.1200.0000.0000.0000.000
133A441GLN00.00517.5070.0350.0350.0000.0000.0000.000
134A442GLY00.05515.909-0.364-0.3640.0000.0000.0000.000
135A443GLU-1-0.84916.492-11.333-11.3330.0000.0000.0000.000
136A444GLU-1-0.73918.087-10.778-10.7780.0000.0000.0000.000
137A445PHE0-0.0269.274-0.451-0.4510.0000.0000.0000.000
138A446VAL00.02013.726-0.683-0.6830.0000.0000.0000.000
139A447CYS0-0.04815.232-0.270-0.2700.0000.0000.0000.000
140A448LEU00.00114.060-0.278-0.2780.0000.0000.0000.000
141A449LYS10.8199.40018.10218.1020.0000.0000.0000.000
142A450SER00.03512.533-0.943-0.9430.0000.0000.0000.000
143A451ILE0-0.01315.726-0.067-0.0670.0000.0000.0000.000
144A452ILE0-0.02510.167-0.026-0.0260.0000.0000.0000.000
145A453LEU00.00012.328-0.460-0.4600.0000.0000.0000.000
146A454LEU0-0.01814.397-0.087-0.0870.0000.0000.0000.000
147A455ASN0-0.00116.8140.8420.8420.0000.0000.0000.000
148A456SER0-0.10012.6550.8080.8080.0000.0000.0000.000
149A457GLY00.03314.903-0.008-0.0080.0000.0000.0000.000
150A458VAL00.03715.5840.3560.3560.0000.0000.0000.000
151A459TYR0-0.07119.2170.7550.7550.0000.0000.0000.000
152A460THR0-0.00715.9940.4290.4290.0000.0000.0000.000
153A461PHE00.04216.844-0.282-0.2820.0000.0000.0000.000
154A462LEU0-0.02019.8290.6550.6550.0000.0000.0000.000
155A463SER0-0.00221.7200.4560.4560.0000.0000.0000.000
156A464SER00.03924.529-0.187-0.1870.0000.0000.0000.000
157A465THR0-0.01626.3600.3510.3510.0000.0000.0000.000
158A466LEU00.03828.489-0.132-0.1320.0000.0000.0000.000
159A467LYS11.02524.33611.71911.7190.0000.0000.0000.000
160A468SER00.01423.492-0.126-0.1260.0000.0000.0000.000
161A469LEU0-0.02325.093-0.214-0.2140.0000.0000.0000.000
162A470GLU-1-0.91827.737-9.733-9.7330.0000.0000.0000.000
163A471GLU-1-0.76221.447-13.003-13.0030.0000.0000.0000.000
164A472LYS10.87422.85311.59111.5910.0000.0000.0000.000
165A473ASP-1-0.90224.279-9.831-9.8310.0000.0000.0000.000
166A474HIS0-0.01923.2240.4050.4050.0000.0000.0000.000
167A475ILE00.00819.4720.0050.0050.0000.0000.0000.000
168A476HIS00.00123.037-0.039-0.0390.0000.0000.0000.000
169A477ARG10.89725.5809.6359.6350.0000.0000.0000.000
170A478VAL0-0.01722.4190.2590.2590.0000.0000.0000.000
171A479LEU00.01219.533-0.003-0.0030.0000.0000.0000.000
172A480ASP-1-0.89023.288-10.011-10.0110.0000.0000.0000.000
173A481LYS10.89326.0799.6009.6000.0000.0000.0000.000
174A482ILE0-0.01819.5950.1560.1560.0000.0000.0000.000
175A483THR0-0.02423.0590.0330.0330.0000.0000.0000.000
176A484ASP-1-0.92124.464-9.142-9.1420.0000.0000.0000.000
177A485THR0-0.06123.5090.2800.2800.0000.0000.0000.000
178A486LEU00.00719.5160.1430.1430.0000.0000.0000.000
179A487ILE00.01923.5840.2340.2340.0000.0000.0000.000
180A488HIS0-0.05226.9800.5290.5290.0000.0000.0000.000
181A489LEU00.00021.8480.2430.2430.0000.0000.0000.000
182A490MET0-0.01922.4820.2870.2870.0000.0000.0000.000
183A491ALA0-0.00726.8310.2220.2220.0000.0000.0000.000
184A492LYS10.88428.6578.2588.2580.0000.0000.0000.000
185A493ALA0-0.00926.6640.1270.1270.0000.0000.0000.000
186A494GLY0-0.02328.7630.0900.0900.0000.0000.0000.000
187A495LEU0-0.04126.2710.1510.1510.0000.0000.0000.000
188A496THR00.04530.7490.0300.0300.0000.0000.0000.000
189A497LEU00.05231.654-0.179-0.1790.0000.0000.0000.000
190A498GLN0-0.02431.613-0.110-0.1100.0000.0000.0000.000
191A499GLN00.03529.009-0.181-0.1810.0000.0000.0000.000
192A500GLN00.00227.597-0.358-0.3580.0000.0000.0000.000
193A501HIS00.07026.667-0.457-0.4570.0000.0000.0000.000
194A502GLN0-0.06726.450-0.286-0.2860.0000.0000.0000.000
195A503ARG10.76620.5399.9469.9460.0000.0000.0000.000
196A504LEU00.05322.006-0.381-0.3810.0000.0000.0000.000
197A505ALA00.01121.488-0.429-0.4290.0000.0000.0000.000
198A506GLN0-0.05420.673-0.456-0.4560.0000.0000.0000.000
199A507LEU00.01817.113-0.362-0.3620.0000.0000.0000.000
200A508LEU00.03216.468-0.642-0.6420.0000.0000.0000.000
201A509LEU0-0.04117.306-0.391-0.3910.0000.0000.0000.000
202A510ILE0-0.03912.600-0.260-0.2600.0000.0000.0000.000
203A511LEU00.02212.580-0.709-0.7090.0000.0000.0000.000
204A512SER00.00512.816-0.771-0.7710.0000.0000.0000.000
205A513HIS0-0.00412.141-0.562-0.5620.0000.0000.0000.000
206A514ILE00.0287.436-0.590-0.5900.0000.0000.0000.000
207A515ARG10.9738.63516.43116.4310.0000.0000.0000.000
208A516HIS0-0.06210.170-1.026-1.0260.0000.0000.0000.000
209A517MET00.0255.831-0.464-0.4640.0000.0000.0000.000
210A518SER00.0645.876-1.998-1.9980.0000.0000.0000.000
211A519ASN0-0.0136.203-2.611-2.6110.0000.0000.0000.000
212A520LYS10.8966.99116.30616.3060.0000.0000.0000.000
213A521GLY00.0082.919-0.922-0.1780.388-0.418-0.7150.003
214A522MET0-0.0052.840-7.385-5.6950.301-0.643-1.348-0.014
215A523GLU-1-0.9105.239-19.814-19.736-0.001-0.003-0.0750.000
216A524HIS00.0022.566-1.5300.4981.292-0.886-2.434-0.013
217A525LEU00.0082.364-6.560-1.6963.169-1.648-6.3840.012
218A526TYR00.0014.981-2.059-1.897-0.001-0.007-0.1540.000
219A527SER0-0.0747.6711.4091.4090.0000.0000.0000.000
220A528MET0-0.0463.0072.3603.0010.049-0.098-0.592-0.001
221A529LYS10.9375.62629.90229.9020.0000.0000.0000.000
222A530CYS0-0.0096.4743.2633.2630.0000.0000.0000.000
223A531LYS10.9858.29219.63319.6330.0000.0000.0000.000
224A532ASN0-0.06611.1850.6610.6610.0000.0000.0000.000
225A533VAL0-0.0326.2910.4520.4520.0000.0000.0000.000
226A534VAL00.0586.6401.3841.3840.0000.0000.0000.000
227A535PRO0-0.0026.890-4.268-4.2680.0000.0000.0000.000
228A536LEU00.0192.662-2.327-1.2650.289-0.181-1.169-0.002
229A537TYR00.0095.3740.4450.480-0.0010.000-0.0340.000
230A538ASP-1-0.8468.896-21.570-21.5700.0000.0000.0000.000
231A539LEU0-0.0363.216-0.4220.0050.040-0.094-0.372-0.001
232A540LEU0-0.0305.5040.3460.3460.0000.0000.0000.000
233A541LEU0-0.0268.2811.8731.8730.0000.0000.0000.000
234A542GLU-1-1.00110.316-20.383-20.3830.0000.0000.0000.000
235A543MET0-0.0366.547-0.085-0.0850.0000.0000.0000.000
236A544LEU-1-0.98211.210-17.122-17.1220.0000.0000.0000.000
238A2HOH0-0.0202.689-0.2910.7810.657-0.727-1.0030.005