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

tag_button

FMODB ID: 9PJ9X

Calculation Name: 1ERR-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: raloxifene

ligand 3-letter code: RAL

PDB ID: 1ERR

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 RAL=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3207557.660583
FMO2-HF: Nuclear repulsion 3108361.856231
FMO2-HF: Total energy -99195.804352
FMO2-MP2: Total energy -99475.196733


3D Structure
Snapshot
 
Ligand structure

RAL

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.
-372.016-364.898175.935-80.892-102.1660.300


Interactive mode: IFIE and PIEDA for fragment #237(A:600:RAL)


Summations of interaction energy for fragment #237(A:600:RAL)
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.
-372.016-364.898175.935-80.892-102.166-0.3
Interaction energy analysis for fragmet #237(A:600:RAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.699 / 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].
1A309SER10.87429.7009.7599.7590.0000.0000.0000.000
2A310LEU00.05525.4820.2530.2530.0000.0000.0000.000
3A311THR00.02829.227-0.066-0.0660.0000.0000.0000.000
4A312ALA00.07427.296-0.266-0.2660.0000.0000.0000.000
5A313ASP-1-0.83126.032-9.373-9.3730.0000.0000.0000.000
6A314GLN00.00725.945-0.202-0.2020.0000.0000.0000.000
7A315MET0-0.01221.783-0.291-0.2910.0000.0000.0000.000
8A316VAL00.05121.383-0.483-0.4830.0000.0000.0000.000
9A317SER0-0.02620.820-0.419-0.4190.0000.0000.0000.000
10A318ALA00.00420.962-0.399-0.3990.0000.0000.0000.000
11A319LEU0-0.03417.394-0.463-0.4630.0000.0000.0000.000
12A320LEU0-0.02516.825-0.623-0.6230.0000.0000.0000.000
13A321ASP-1-0.92616.808-12.632-12.6320.0000.0000.0000.000
14A322ALA0-0.09315.992-0.454-0.4540.0000.0000.0000.000
15A323GLU-1-0.82511.562-18.512-18.5120.0000.0000.0000.000
16A324PRO0-0.0148.433-0.120-0.1200.0000.0000.0000.000
17A325PRO00.0049.6300.9760.9760.0000.0000.0000.000
18A326ILE0-0.0027.313-1.492-1.4920.0000.0000.0000.000
19A327LEU0-0.0466.1121.0201.0200.0000.0000.0000.000
20A328TYR00.0577.4350.6810.6810.0000.0000.0000.000
21A329SER00.0117.867-2.849-2.8490.0000.0000.0000.000
22A330GLU-1-0.8688.771-24.418-24.4180.0000.0000.0000.000
23A331TYR0-0.04611.4440.7690.7690.0000.0000.0000.000
24A332ASP-1-0.85213.800-14.598-14.5980.0000.0000.0000.000
25A333PRO00.00113.5650.8540.8540.0000.0000.0000.000
26A334THR0-0.02315.4810.8330.8330.0000.0000.0000.000
27A335ARG10.83013.46413.57113.5710.0000.0000.0000.000
28A336PRO00.01616.0700.5210.5210.0000.0000.0000.000
29A337PHE00.01011.203-0.035-0.0350.0000.0000.0000.000
30A338SER00.01612.6010.2940.2940.0000.0000.0000.000
31A339GLU-1-0.8299.352-20.008-20.0080.0000.0000.0000.000
32A340ALA00.0158.453-1.403-1.4030.0000.0000.0000.000
33A341SER0-0.0048.691-1.648-1.6480.0000.0000.0000.000
34A342MET00.0336.311-1.023-1.0230.0000.0000.0000.000
35A343MET00.0482.669-2.281-0.7000.437-0.415-1.6030.002
36A344GLY00.0024.192-7.245-6.9820.000-0.048-0.2150.000
37A345LEU0-0.0156.618-2.912-2.9120.0000.0000.0000.000
38A346LEU0-0.0162.567-7.330-3.9812.201-1.343-4.2060.014
39A347THR0-0.0682.098-15.319-11.4125.090-3.345-5.652-0.016
40A348ASN00.0393.331-4.654-5.0100.0320.771-0.4470.000
41A349LEU00.0042.673-1.994-0.6050.193-0.279-1.3030.000
42A350ALA00.0522.319-3.466-0.2642.317-1.460-4.0590.002
43A351ASP-1-0.7381.619-117.338-122.25622.766-10.839-7.009-0.106
44A352ARG10.7763.90135.83636.3130.002-0.108-0.3710.000
45A353GLU-1-0.7441.312-79.015-105.88964.788-33.806-4.108-0.158
46A354LEU0-0.0042.1383.8731.8586.032-0.823-3.194-0.005
47A355VAL00.0165.1683.9584.058-0.001-0.003-0.0960.000
48A356HIS0-0.0278.0213.9353.9350.0000.0000.0000.000
49A357MET0-0.0265.8232.5082.5080.0000.0000.0000.000
50A358ILE00.0966.3462.3822.3820.0000.0000.0000.000
51A359ASN0-0.01110.1981.9681.9680.0000.0000.0000.000
52A360TRP00.01411.4450.9500.9500.0000.0000.0000.000
53A361ALA00.04011.6091.2731.2730.0000.0000.0000.000
54A362LYS10.85413.59619.47319.4730.0000.0000.0000.000
55A363ARG10.86415.92717.40517.4050.0000.0000.0000.000
56A364VAL0-0.03415.4650.9120.9120.0000.0000.0000.000
57A365PRO0-0.02618.4450.1810.1810.0000.0000.0000.000
58A366GLY00.05021.292-0.041-0.0410.0000.0000.0000.000
59A367PHE00.00212.279-0.067-0.0670.0000.0000.0000.000
60A368VAL0-0.06117.847-0.336-0.3360.0000.0000.0000.000
61A369ASP-1-0.83319.195-11.782-11.7820.0000.0000.0000.000
62A370LEU0-0.06416.7780.2870.2870.0000.0000.0000.000
63A371THR00.01018.951-0.345-0.3450.0000.0000.0000.000
64A372LEU00.04813.424-0.240-0.2400.0000.0000.0000.000
65A373HIS0-0.00114.092-0.416-0.4160.0000.0000.0000.000
66A374ASP-1-0.79914.287-16.295-16.2950.0000.0000.0000.000
67A375GLN0-0.06213.144-1.386-1.3860.0000.0000.0000.000
68A376VAL00.0338.952-1.294-1.2940.0000.0000.0000.000
69A377HIS00.0279.789-1.398-1.3980.0000.0000.0000.000
70A378LEU0-0.04311.490-0.826-0.8260.0000.0000.0000.000
71A379LEU0-0.0227.266-1.163-1.1630.0000.0000.0000.000
72A380GLU-1-0.9426.748-31.249-31.2490.0000.0000.0000.000
73A381CYS0-0.0877.311-2.097-2.0970.0000.0000.0000.000
74A382ALA00.0629.607-0.457-0.4570.0000.0000.0000.000
75A383TRP00.0232.031-9.966-7.5676.101-1.950-6.550-0.018
76A384LEU00.0172.897-1.7700.3920.332-0.415-2.0790.000
77A385GLU-1-0.7435.813-16.909-16.9090.0000.0000.0000.000
78A386ILE0-0.0327.2342.2512.2510.0000.0000.0000.000
79A387LEU0-0.0152.799-2.5710.9652.893-1.332-5.0970.007
80A388MET0-0.0342.826-1.7972.4522.302-1.687-4.863-0.008
81A389ILE0-0.0264.1311.6491.8140.001-0.012-0.1540.000
82A390GLY00.0605.6751.2601.2600.0000.0000.0000.000
83A391LEU0-0.0342.087-0.8670.7773.389-1.140-3.8940.001
84A392VAL00.0024.1651.0191.2090.000-0.048-0.1420.000
85A393TRP00.0437.2581.0331.0330.0000.0000.0000.000
86A394ARG10.7502.02012.15412.5844.087-1.852-2.6660.024
87A395SER00.0106.9700.4750.4750.0000.0000.0000.000
88A396MET0-0.0499.6410.6230.6230.0000.0000.0000.000
89A397GLU-1-0.94812.674-9.534-9.5340.0000.0000.0000.000
90A398HIS0-0.01212.2770.4320.4320.0000.0000.0000.000
91A399PRO00.04513.487-0.251-0.2510.0000.0000.0000.000
92A400GLY0-0.06113.3130.1810.1810.0000.0000.0000.000
93A401LYS10.90311.01711.25811.2580.0000.0000.0000.000
94A402LEU00.0234.555-0.192-0.009-0.001-0.012-0.1700.000
95A403LEU0-0.0108.171-0.194-0.1940.0000.0000.0000.000
96A404PHE00.0272.766-5.779-1.8123.705-1.425-6.2470.004
97A405ALA00.0554.584-2.198-2.082-0.001-0.016-0.1000.000
98A406PRO00.0147.3261.0921.0920.0000.0000.0000.000
99A407ASN0-0.04010.5830.2010.2010.0000.0000.0000.000
100A408LEU0-0.0327.1130.0610.0610.0000.0000.0000.000
101A409LEU00.0089.120-0.218-0.2180.0000.0000.0000.000
102A410LEU0-0.0367.4640.4710.4710.0000.0000.0000.000
103A411ASP-1-0.8319.986-11.669-11.6690.0000.0000.0000.000
104A412ARG11.0148.99610.92210.9220.0000.0000.0000.000
105A413ASN0-0.0749.529-0.435-0.4350.0000.0000.0000.000
106A414GLN00.08610.723-0.115-0.1150.0000.0000.0000.000
107A415GLY00.0386.915-0.572-0.5720.0000.0000.0000.000
108A416LYS10.9197.06111.71511.7150.0000.0000.0000.000
109A417CYS0-0.0749.593-0.021-0.0210.0000.0000.0000.000
110A418VAL0-0.0025.465-0.710-0.7100.0000.0000.0000.000
111A419GLU-1-0.7667.020-20.043-20.0430.0000.0000.0000.000
112A420GLY0-0.0205.098-1.788-1.779-0.001-0.005-0.0040.000
113A421MET00.0522.322-6.145-3.2816.312-2.548-6.6290.026
114A422VAL0-0.0933.6731.2321.5380.0080.104-0.4180.001
115A423GLU-1-0.8115.905-12.568-12.5680.0000.0000.0000.000
116A424ILE00.0422.289-3.224-1.4503.634-1.520-3.8880.016
117A425PHE0-0.0193.839-1.692-0.8240.010-0.200-0.679-0.001
118A426ASP-1-0.8884.383-11.899-11.8090.000-0.020-0.0700.000
119A427MET0-0.0626.2810.0270.0270.0000.0000.0000.000
120A428LEU00.0282.714-1.605-0.2090.687-0.408-1.6750.000
121A429LEU0-0.0626.9140.2010.2010.0000.0000.0000.000
122A430ALA0-0.0209.4290.2850.2850.0000.0000.0000.000
123A431THR0-0.0049.7450.1950.1950.0000.0000.0000.000
124A432SER00.04710.0580.2000.2000.0000.0000.0000.000
125A433SER0-0.01311.6420.4690.4690.0000.0000.0000.000
126A434ARG10.95214.52810.77810.7780.0000.0000.0000.000
127A435PHE00.03710.5650.2560.2560.0000.0000.0000.000
128A436ARG10.88914.29011.01311.0130.0000.0000.0000.000
129A437MET0-0.04816.9790.2410.2410.0000.0000.0000.000
130A438MET0-0.10218.5770.1770.1770.0000.0000.0000.000
131A439ASN00.00719.260-0.059-0.0590.0000.0000.0000.000
132A440LEU0-0.06013.6430.0720.0720.0000.0000.0000.000
133A441GLN0-0.01317.4540.0270.0270.0000.0000.0000.000
134A442GLY00.04015.693-0.323-0.3230.0000.0000.0000.000
135A443GLU-1-0.85016.322-11.370-11.3700.0000.0000.0000.000
136A444GLU-1-0.70417.830-10.572-10.5720.0000.0000.0000.000
137A445PHE0-0.0279.158-0.456-0.4560.0000.0000.0000.000
138A446VAL00.02113.744-0.730-0.7300.0000.0000.0000.000
139A447CYS0-0.03215.228-0.260-0.2600.0000.0000.0000.000
140A448LEU00.01113.962-0.252-0.2520.0000.0000.0000.000
141A449LYS10.8099.17118.30918.3090.0000.0000.0000.000
142A450SER0-0.00412.942-0.809-0.8090.0000.0000.0000.000
143A451ILE00.01316.127-0.213-0.2130.0000.0000.0000.000
144A452ILE0-0.02910.793-0.065-0.0650.0000.0000.0000.000
145A453LEU0-0.04211.571-0.603-0.6030.0000.0000.0000.000
146A454LEU0-0.00213.973-0.235-0.2350.0000.0000.0000.000
147A455ASN00.01117.1460.7980.7980.0000.0000.0000.000
148A456SER0-0.13713.4460.7750.7750.0000.0000.0000.000
149A457GLY00.07214.851-0.223-0.2230.0000.0000.0000.000
150A458VAL00.01115.6120.3950.3950.0000.0000.0000.000
151A459TYR0-0.07918.8190.7480.7480.0000.0000.0000.000
152A460THR0-0.09615.423-0.021-0.0210.0000.0000.0000.000
153A461PHE00.05816.509-0.335-0.3350.0000.0000.0000.000
154A462LEU0-0.01216.0720.7570.7570.0000.0000.0000.000
155A463SER00.05119.6370.8360.8360.0000.0000.0000.000
156A464SER0-0.03022.6090.0010.0010.0000.0000.0000.000
157A465THR00.02526.0940.4200.4200.0000.0000.0000.000
158A466LEU00.03328.111-0.125-0.1250.0000.0000.0000.000
159A467LYS10.89223.97011.75811.7580.0000.0000.0000.000
160A468SER00.01223.443-0.248-0.2480.0000.0000.0000.000
161A469LEU0-0.05425.269-0.215-0.2150.0000.0000.0000.000
162A470GLU-1-0.90128.058-9.572-9.5720.0000.0000.0000.000
163A471GLU-1-0.80221.963-12.434-12.4340.0000.0000.0000.000
164A472LYS10.85223.01112.10312.1030.0000.0000.0000.000
165A473ASP-1-0.82524.757-9.974-9.9740.0000.0000.0000.000
166A474HIS0-0.04823.1740.4400.4400.0000.0000.0000.000
167A475ILE00.03319.293-0.014-0.0140.0000.0000.0000.000
168A476HIS00.03223.275-0.187-0.1870.0000.0000.0000.000
169A477ARG10.86025.62110.37110.3710.0000.0000.0000.000
170A478VAL0-0.05722.0470.2150.2150.0000.0000.0000.000
171A479LEU0-0.01920.296-0.020-0.0200.0000.0000.0000.000
172A480ASP-1-0.91523.755-10.057-10.0570.0000.0000.0000.000
173A481LYS10.87426.1519.9399.9390.0000.0000.0000.000
174A482ILE00.02019.8120.1910.1910.0000.0000.0000.000
175A483THR00.01423.2170.0860.0860.0000.0000.0000.000
176A484ASP-1-0.91924.529-9.230-9.2300.0000.0000.0000.000
177A485THR0-0.10023.5060.2610.2610.0000.0000.0000.000
178A486LEU00.00719.3560.1420.1420.0000.0000.0000.000
179A487ILE0-0.00623.4000.2680.2680.0000.0000.0000.000
180A488HIS0-0.02726.8340.3670.3670.0000.0000.0000.000
181A489LEU0-0.03021.6830.2690.2690.0000.0000.0000.000
182A490MET0-0.04522.7120.2620.2620.0000.0000.0000.000
183A491ALA00.02626.8340.2350.2350.0000.0000.0000.000
184A492LYS10.91926.7869.1329.1320.0000.0000.0000.000
185A493ALA0-0.00526.8450.1200.1200.0000.0000.0000.000
186A494GLY0-0.03728.9730.1290.1290.0000.0000.0000.000
187A495LEU0-0.07926.3880.1570.1570.0000.0000.0000.000
188A496THR00.05430.6500.0430.0430.0000.0000.0000.000
189A497LEU00.06031.768-0.167-0.1670.0000.0000.0000.000
190A498GLN0-0.00631.925-0.093-0.0930.0000.0000.0000.000
191A499GLN00.03529.233-0.154-0.1540.0000.0000.0000.000
192A500GLN00.00027.747-0.306-0.3060.0000.0000.0000.000
193A501HIS00.07026.717-0.134-0.1340.0000.0000.0000.000
194A502GLN0-0.10026.807-0.246-0.2460.0000.0000.0000.000
195A503ARG10.78920.2849.7749.7740.0000.0000.0000.000
196A504LEU00.01622.378-0.342-0.3420.0000.0000.0000.000
197A505ALA00.02022.024-0.398-0.3980.0000.0000.0000.000
198A506GLN0-0.07521.358-0.365-0.3650.0000.0000.0000.000
199A507LEU00.00717.124-0.337-0.3370.0000.0000.0000.000
200A508LEU00.05717.423-0.495-0.4950.0000.0000.0000.000
201A509LEU0-0.02718.030-0.481-0.4810.0000.0000.0000.000
202A510ILE0-0.04213.409-0.193-0.1930.0000.0000.0000.000
203A511LEU00.03513.539-0.548-0.5480.0000.0000.0000.000
204A512SER0-0.00814.019-0.950-0.9500.0000.0000.0000.000
205A513HIS00.01212.117-0.619-0.6190.0000.0000.0000.000
206A514ILE00.0118.914-0.501-0.5010.0000.0000.0000.000
207A515ARG10.9399.86316.76016.7600.0000.0000.0000.000
208A516HIS0-0.05510.350-1.063-1.0630.0000.0000.0000.000
209A517MET0-0.0056.117-0.432-0.4320.0000.0000.0000.000
210A518SER00.0686.490-1.801-1.8010.0000.0000.0000.000
211A519ASN00.0287.126-3.156-3.1560.0000.0000.0000.000
212A520LYS10.8796.14016.51416.5140.0000.0000.0000.000
213A521GLY00.0163.394-1.682-0.8860.093-0.325-0.5630.001
214A522MET0-0.0183.634-6.437-5.7230.008-0.162-0.560-0.001
215A523GLU-1-0.8836.257-20.321-20.3210.0000.0000.0000.000
216A524HIS00.0411.726-25.255-32.66921.778-8.530-5.834-0.077
217A525LEU0-0.0252.540-3.428-0.7954.542-1.200-5.9750.005
218A526TYR0-0.0394.961-2.630-2.377-0.001-0.008-0.2450.000
219A527SER0-0.0867.1842.1372.1370.0000.0000.0000.000
220A528MET0-0.0434.3241.9202.1990.000-0.010-0.2680.000
221A529LYS10.8338.12021.79521.7950.0000.0000.0000.000
222A530CYS0-0.0613.6570.2270.8030.012-0.095-0.4930.000
223A531LYS10.8531.92559.39459.8144.009-1.373-3.057-0.001
224A532ASN00.0292.512-16.003-14.1631.603-1.226-2.217-0.015
225A533VAL0-0.0444.8195.0055.0050.0000.0000.0000.000
226A534VAL00.0234.589-4.925-4.743-0.001-0.008-0.1730.000
227A535PRO00.0275.040-5.263-5.155-0.001-0.002-0.1050.000
228A536LEU00.0212.096-1.097-1.8753.051-0.374-1.899-0.003
229A537TYR00.0445.0100.6980.761-0.001-0.001-0.0610.000
230A538ASP-1-0.8558.161-23.536-23.5360.0000.0000.0000.000
231A539LEU00.0122.297-1.302-1.1291.453-0.252-1.374-0.003
232A540LEU0-0.0324.4141.1691.299-0.001-0.007-0.1220.000
233A541LEU0-0.0486.8472.5962.5960.0000.0000.0000.000
234A542GLU-1-1.0029.127-25.443-25.4430.0000.0000.0000.000
235A543MET0-0.1184.113-0.186-0.0590.000-0.012-0.1150.000
236A544LEU-1-0.9859.487-18.283-18.2830.0000.0000.0000.000
238A3HOH0-0.0052.312-1.345-0.7822.076-1.123-1.5170.009