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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7XV1P

Calculation Name: 1XPC-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2s,3r)-3-(4-hydroxyphenyl)-2-(4-{[(2r)-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol

ligand 3-letter code: AIT

PDB ID: 1XPC

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 AIT=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3172971.641505
FMO2-HF: Nuclear repulsion 3073811.24586
FMO2-HF: Total energy -99160.395645
FMO2-MP2: Total energy -99439.275019


3D Structure
Snapshot
 
Ligand structure

AIT

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.
-350.594-302.809104.413-49.065-103.1360.259


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


Summations of interaction energy for fragment #237(A:600:AIT)
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.
-350.594-302.809104.413-49.065-103.136-0.259
Interaction energy analysis for fragmet #237(A:600:AIT)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.744 / 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].
1A309SER10.85430.4229.5529.5520.0000.0000.0000.000
2A310LEU00.13325.2880.2670.2670.0000.0000.0000.000
3A311THR0-0.01329.223-0.020-0.0200.0000.0000.0000.000
4A312ALA00.11026.921-0.318-0.3180.0000.0000.0000.000
5A313ASP-1-0.88725.788-9.263-9.2630.0000.0000.0000.000
6A314GLN0-0.01225.947-0.239-0.2390.0000.0000.0000.000
7A315MET00.00422.045-0.424-0.4240.0000.0000.0000.000
8A316VAL00.00921.168-0.480-0.4800.0000.0000.0000.000
9A317SER00.03620.749-0.214-0.2140.0000.0000.0000.000
10A318ALA0-0.01621.211-0.263-0.2630.0000.0000.0000.000
11A319LEU0-0.00616.963-0.528-0.5280.0000.0000.0000.000
12A320LEU0-0.04416.358-0.592-0.5920.0000.0000.0000.000
13A321ASP-1-0.94917.029-11.944-11.9440.0000.0000.0000.000
14A322ALA0-0.08415.906-0.382-0.3820.0000.0000.0000.000
15A323GLU-1-0.80811.531-18.054-18.0540.0000.0000.0000.000
16A324PRO0-0.0258.4610.0590.0590.0000.0000.0000.000
17A325PRO0-0.00610.0260.8530.8530.0000.0000.0000.000
18A326ILE00.0167.751-1.596-1.5960.0000.0000.0000.000
19A327LEU0-0.0456.3541.0021.0020.0000.0000.0000.000
20A328TYR00.0487.4760.4820.4820.0000.0000.0000.000
21A329SER0-0.0037.428-2.535-2.5350.0000.0000.0000.000
22A330GLU-1-0.9098.390-21.805-21.8050.0000.0000.0000.000
23A331TYR0-0.09210.411-0.469-0.4690.0000.0000.0000.000
24A332ASP-1-0.81012.968-13.294-13.2940.0000.0000.0000.000
25A333PRO0-0.01315.9460.1370.1370.0000.0000.0000.000
26A334THR0-0.06317.2180.7320.7320.0000.0000.0000.000
27A335ARG10.83818.47913.93613.9360.0000.0000.0000.000
28A336PRO0-0.02018.489-0.134-0.1340.0000.0000.0000.000
29A337PHE00.05710.973-0.556-0.5560.0000.0000.0000.000
30A338SER0-0.04515.185-0.685-0.6850.0000.0000.0000.000
31A339GLU-1-0.83716.656-13.893-13.8930.0000.0000.0000.000
32A340ALA00.00312.183-0.645-0.6450.0000.0000.0000.000
33A341SER0-0.0089.108-1.017-1.0170.0000.0000.0000.000
34A342MET00.0826.364-1.239-1.2390.0000.0000.0000.000
35A343MET00.0493.264-3.794-2.0310.385-0.499-1.6490.002
36A344GLY0-0.0294.443-5.128-4.911-0.001-0.016-0.2000.000
37A345LEU00.0216.817-2.566-2.5660.0000.0000.0000.000
38A346LEU0-0.0142.342-7.601-3.9684.032-1.877-5.7880.011
39A347THR0-0.0172.268-12.855-7.9204.816-3.203-6.548-0.015
40A348ASN0-0.0143.275-8.624-8.3700.0450.511-0.810-0.002
41A349LEU0-0.0632.483-1.5850.1601.302-0.579-2.4680.003
42A350ALA00.0332.703-4.949-1.1462.362-1.509-4.6570.007
43A351ASP-1-0.8611.940-118.777-111.9719.264-7.866-8.204-0.095
44A352ARG10.8803.24935.77935.6640.0110.478-0.374-0.001
45A353GLU-1-0.7581.691-65.993-67.20016.616-9.234-6.175-0.116
46A354LEU00.0092.2042.5132.7072.868-0.542-2.520-0.005
47A355VAL00.0294.7153.9954.067-0.001-0.008-0.0640.000
48A356HIS0-0.0237.8673.8283.8280.0000.0000.0000.000
49A357MET0-0.0515.5932.2582.2580.0000.0000.0000.000
50A358ILE00.0508.1312.2682.2680.0000.0000.0000.000
51A359ASN0-0.03310.3611.9461.9460.0000.0000.0000.000
52A360TRP0-0.00711.3730.8410.8410.0000.0000.0000.000
53A361ALA00.05511.9911.2851.2850.0000.0000.0000.000
54A362LYS10.93213.83219.57319.5730.0000.0000.0000.000
55A363ARG10.89416.45315.32615.3260.0000.0000.0000.000
56A364VAL0-0.02615.6910.8180.8180.0000.0000.0000.000
57A365PRO0-0.03218.5240.1620.1620.0000.0000.0000.000
58A366GLY00.02721.699-0.071-0.0710.0000.0000.0000.000
59A367PHE00.05113.1620.0330.0330.0000.0000.0000.000
60A368VAL0-0.01318.151-0.207-0.2070.0000.0000.0000.000
61A369ASP-1-0.96519.954-11.546-11.5460.0000.0000.0000.000
62A370LEU0-0.05717.7650.3300.3300.0000.0000.0000.000
63A371THR0-0.07220.082-0.261-0.2610.0000.0000.0000.000
64A372LEU00.04614.745-0.334-0.3340.0000.0000.0000.000
65A373HIS0-0.08115.394-0.614-0.6140.0000.0000.0000.000
66A374ASP-1-0.79015.175-15.630-15.6300.0000.0000.0000.000
67A375GLN0-0.05814.195-1.490-1.4900.0000.0000.0000.000
68A376VAL00.01710.061-1.549-1.5490.0000.0000.0000.000
69A377HIS0-0.00910.393-2.594-2.5940.0000.0000.0000.000
70A378LEU0-0.04511.539-0.923-0.9230.0000.0000.0000.000
71A379LEU00.0167.999-0.986-0.9860.0000.0000.0000.000
72A380GLU-1-0.9466.781-32.242-32.2420.0000.0000.0000.000
73A381CYS0-0.0907.541-1.299-1.2990.0000.0000.0000.000
74A382ALA00.0159.430-0.126-0.1260.0000.0000.0000.000
75A383TRP00.0372.229-13.845-8.5624.170-2.381-7.072-0.022
76A384LEU00.0062.264-2.864-0.7131.679-0.573-3.257-0.004
77A385GLU-1-0.8265.397-17.261-17.044-0.001-0.004-0.2120.000
78A386ILE0-0.0087.1072.1592.1590.0000.0000.0000.000
79A387LEU0-0.0262.626-2.4271.4761.613-1.374-4.1420.009
80A388MET0-0.0442.7632.0575.3370.681-0.990-2.971-0.003
81A389ILE00.0243.8502.0392.1820.0010.000-0.1430.000
82A390GLY00.0435.4941.1281.1280.0000.0000.0000.000
83A391LEU0-0.0222.803-2.2620.4411.172-0.792-3.0830.005
84A392VAL0-0.0374.8630.2450.354-0.001-0.012-0.0970.000
85A393TRP00.0287.7370.7810.7810.0000.0000.0000.000
86A394ARG10.7842.22416.63718.5761.894-1.562-2.2700.020
87A395SER0-0.0177.6800.2500.2500.0000.0000.0000.000
88A396MET0-0.01710.3950.5920.5920.0000.0000.0000.000
89A397GLU-1-0.98213.299-10.815-10.8150.0000.0000.0000.000
90A398HIS0-0.03812.5670.4600.4600.0000.0000.0000.000
91A399PRO0-0.00914.253-0.282-0.2820.0000.0000.0000.000
92A400GLY0-0.04214.3480.1080.1080.0000.0000.0000.000
93A401LYS10.91911.45111.66711.6670.0000.0000.0000.000
94A402LEU00.0305.3020.0970.0970.0000.0000.0000.000
95A403LEU0-0.0068.738-0.270-0.2700.0000.0000.0000.000
96A404PHE00.0282.286-5.706-1.7973.903-1.398-6.4150.010
97A405ALA00.0494.607-3.192-2.966-0.001-0.013-0.2120.000
98A406PRO00.0197.1311.0861.0860.0000.0000.0000.000
99A407ASN00.00010.0420.1780.1780.0000.0000.0000.000
100A408LEU0-0.0315.699-0.246-0.2460.0000.0000.0000.000
101A409LEU00.0118.385-0.229-0.2290.0000.0000.0000.000
102A410LEU0-0.0326.6410.2180.2180.0000.0000.0000.000
103A411ASP-1-0.8249.893-12.819-12.8190.0000.0000.0000.000
104A412ARG10.8549.82712.36412.3640.0000.0000.0000.000
105A413ASN0-0.02110.470-0.616-0.6160.0000.0000.0000.000
106A414GLN00.06510.305-0.061-0.0610.0000.0000.0000.000
107A415GLY00.0866.929-0.976-0.9760.0000.0000.0000.000
108A416LYS10.8687.44311.77311.7730.0000.0000.0000.000
109A417CYS0-0.0968.9870.4120.4120.0000.0000.0000.000
110A418VAL0-0.0355.080-0.381-0.3810.0000.0000.0000.000
111A419GLU-1-0.8997.080-18.801-18.8010.0000.0000.0000.000
112A420GLY00.0876.346-2.187-2.1870.0000.0000.0000.000
113A421MET0-0.0502.210-4.339-3.1381.830-0.580-2.4500.000
114A422VAL0-0.0474.4251.5511.659-0.001-0.004-0.1030.000
115A423GLU-1-0.8347.175-15.551-15.5510.0000.0000.0000.000
116A424ILE0-0.0062.711-2.3090.7081.234-1.150-3.1010.014
117A425PHE00.0283.1310.4301.2190.024-0.098-0.7150.000
118A426ASP-1-0.7636.813-12.841-12.8410.0000.0000.0000.000
119A427MET0-0.0487.4000.7250.7250.0000.0000.0000.000
120A428LEU00.0464.019-0.3280.4340.055-0.131-0.6860.000
121A429LEU0-0.0148.4030.4280.4280.0000.0000.0000.000
122A430ALA0-0.01511.0340.4950.4950.0000.0000.0000.000
123A431THR0-0.00810.0580.3610.3610.0000.0000.0000.000
124A432SER0-0.00910.2890.4020.4020.0000.0000.0000.000
125A433SER0-0.02311.9560.4680.4680.0000.0000.0000.000
126A434ARG10.93815.06610.94210.9420.0000.0000.0000.000
127A435PHE00.02310.6190.3470.3470.0000.0000.0000.000
128A436ARG10.97714.61811.54011.5400.0000.0000.0000.000
129A437MET0-0.06917.3700.3490.3490.0000.0000.0000.000
130A438MET0-0.07318.6820.2080.2080.0000.0000.0000.000
131A439ASN00.01419.772-0.002-0.0020.0000.0000.0000.000
132A440LEU0-0.05814.1240.1130.1130.0000.0000.0000.000
133A441GLN00.01717.816-0.045-0.0450.0000.0000.0000.000
134A442GLY00.05215.690-0.368-0.3680.0000.0000.0000.000
135A443GLU-1-0.88116.390-11.267-11.2670.0000.0000.0000.000
136A444GLU-1-0.74618.364-10.672-10.6720.0000.0000.0000.000
137A445PHE00.0068.966-0.413-0.4130.0000.0000.0000.000
138A446VAL00.02813.737-0.655-0.6550.0000.0000.0000.000
139A447CYS0-0.03814.896-0.282-0.2820.0000.0000.0000.000
140A448LEU0-0.01414.250-0.303-0.3030.0000.0000.0000.000
141A449LYS10.8209.04418.30918.3090.0000.0000.0000.000
142A450SER00.04012.686-1.029-1.0290.0000.0000.0000.000
143A451ILE0-0.02115.569-0.145-0.1450.0000.0000.0000.000
144A452ILE0-0.03010.574-0.100-0.1000.0000.0000.0000.000
145A453LEU0-0.02211.939-0.480-0.4800.0000.0000.0000.000
146A454LEU00.00714.094-0.221-0.2210.0000.0000.0000.000
147A455ASN0-0.00417.1720.8000.8000.0000.0000.0000.000
148A456SER0-0.08613.2610.8440.8440.0000.0000.0000.000
149A457GLY00.06114.492-0.051-0.0510.0000.0000.0000.000
150A458VAL00.01815.2090.4700.4700.0000.0000.0000.000
151A459TYR0-0.07618.7590.7190.7190.0000.0000.0000.000
152A460THR0-0.00415.7230.4250.4250.0000.0000.0000.000
153A461PHE00.00416.950-0.226-0.2260.0000.0000.0000.000
154A462LEU0-0.00118.5380.6120.6120.0000.0000.0000.000
155A463SER00.00521.5990.6950.6950.0000.0000.0000.000
156A464SER00.00524.4330.0970.0970.0000.0000.0000.000
157A465THR00.00225.7580.3640.3640.0000.0000.0000.000
158A466LEU00.06228.120-0.102-0.1020.0000.0000.0000.000
159A467LYS10.97024.31811.73611.7360.0000.0000.0000.000
160A468SER00.01623.073-0.081-0.0810.0000.0000.0000.000
161A469LEU0-0.03024.777-0.175-0.1750.0000.0000.0000.000
162A470GLU-1-0.91727.305-9.882-9.8820.0000.0000.0000.000
163A471GLU-1-0.76621.159-13.232-13.2320.0000.0000.0000.000
164A472LYS10.92222.60411.64711.6470.0000.0000.0000.000
165A473ASP-1-0.85823.976-9.905-9.9050.0000.0000.0000.000
166A474HIS0-0.05022.6980.5670.5670.0000.0000.0000.000
167A475ILE00.03119.136-0.003-0.0030.0000.0000.0000.000
168A476HIS00.00022.792-0.033-0.0330.0000.0000.0000.000
169A477ARG10.90825.24510.28110.2810.0000.0000.0000.000
170A478VAL0-0.06322.2430.2200.2200.0000.0000.0000.000
171A479LEU00.00019.930-0.028-0.0280.0000.0000.0000.000
172A480ASP-1-0.86723.507-10.007-10.0070.0000.0000.0000.000
173A481LYS10.84525.45210.03410.0340.0000.0000.0000.000
174A482ILE0-0.01219.3480.1510.1510.0000.0000.0000.000
175A483THR0-0.02023.2220.0780.0780.0000.0000.0000.000
176A484ASP-1-0.90524.810-9.165-9.1650.0000.0000.0000.000
177A485THR0-0.06723.0350.2920.2920.0000.0000.0000.000
178A486LEU00.01819.7200.1730.1730.0000.0000.0000.000
179A487ILE0-0.01323.7800.2330.2330.0000.0000.0000.000
180A488HIS0-0.01927.2970.3230.3230.0000.0000.0000.000
181A489LEU0-0.04521.7630.2290.2290.0000.0000.0000.000
182A490MET0-0.03522.7950.2780.2780.0000.0000.0000.000
183A491ALA00.02127.1820.2160.2160.0000.0000.0000.000
184A492LYS10.93426.0089.4009.4000.0000.0000.0000.000
185A493ALA0-0.04327.0620.1570.1570.0000.0000.0000.000
186A494GLY0-0.01629.2080.1350.1350.0000.0000.0000.000
187A495LEU0-0.02126.4690.1380.1380.0000.0000.0000.000
188A496THR00.02831.1910.0270.0270.0000.0000.0000.000
189A497LEU00.07732.033-0.188-0.1880.0000.0000.0000.000
190A498GLN0-0.00732.118-0.131-0.1310.0000.0000.0000.000
191A499GLN00.04829.384-0.197-0.1970.0000.0000.0000.000
192A500GLN0-0.00828.041-0.357-0.3570.0000.0000.0000.000
193A501HIS00.01927.005-0.137-0.1370.0000.0000.0000.000
194A502GLN0-0.05626.988-0.283-0.2830.0000.0000.0000.000
195A503ARG10.77320.8079.7969.7960.0000.0000.0000.000
196A504LEU00.03722.562-0.369-0.3690.0000.0000.0000.000
197A505ALA00.02122.135-0.393-0.3930.0000.0000.0000.000
198A506GLN0-0.05921.265-0.437-0.4370.0000.0000.0000.000
199A507LEU0-0.00417.590-0.363-0.3630.0000.0000.0000.000
200A508LEU00.03017.304-0.566-0.5660.0000.0000.0000.000
201A509LEU0-0.01018.265-0.408-0.4080.0000.0000.0000.000
202A510ILE0-0.03813.388-0.285-0.2850.0000.0000.0000.000
203A511LEU00.05213.248-0.604-0.6040.0000.0000.0000.000
204A512SER0-0.02314.213-0.737-0.7370.0000.0000.0000.000
205A513HIS0-0.02513.506-0.610-0.6100.0000.0000.0000.000
206A514ILE00.0068.532-0.478-0.4780.0000.0000.0000.000
207A515ARG10.9739.29616.64316.6430.0000.0000.0000.000
208A516HIS0-0.0559.639-1.122-1.1220.0000.0000.0000.000
209A517MET00.0086.734-0.412-0.4120.0000.0000.0000.000
210A518SER00.0505.275-1.836-1.8360.0000.0000.0000.000
211A519ASN00.0175.500-2.545-2.5450.0000.0000.0000.000
212A520LYS10.9256.64516.19616.1960.0000.0000.0000.000
213A521GLY00.0332.423-1.552-0.5661.928-1.343-1.5710.008
214A522MET0-0.0153.070-3.850-3.8150.2340.868-1.138-0.004
215A523GLU-1-0.9495.233-19.769-19.689-0.001-0.006-0.0730.000
216A524HIS0-0.0291.730-28.517-36.75423.153-8.385-6.531-0.068
217A525LEU00.0122.748-8.929-3.2852.174-1.608-6.2100.013
218A526TYR0-0.0344.549-2.738-2.4590.000-0.024-0.2540.000
219A527SER0-0.0516.3363.0323.0320.0000.0000.0000.000
220A528MET0-0.0294.0891.6381.793-0.001-0.013-0.1410.000
221A529LYS10.8746.16828.91228.9120.0000.0000.0000.000
222A530CYS0-0.0252.676-5.208-8.8747.891-0.813-3.412-0.009
223A531LYS10.9782.22347.79945.4666.857-0.967-3.558-0.004
224A532ASN00.0212.645-9.798-8.7680.630-0.159-1.502-0.016
225A533VAL0-0.0045.4934.4534.4530.0000.0000.0000.000
226A534VAL00.0057.355-2.616-2.6160.0000.0000.0000.000
227A535PRO00.0166.852-4.357-4.3570.0000.0000.0000.000
228A536LEU00.0093.037-2.048-1.1170.205-0.197-0.939-0.002
229A537TYR00.0486.0031.0731.0730.0000.0000.0000.000
230A538ASP-1-0.8149.133-22.432-22.4320.0000.0000.0000.000
231A539LEU0-0.0473.503-0.1940.0480.006-0.043-0.2040.000
232A540LEU0-0.0265.5400.4250.4250.0000.0000.0000.000
233A541LEU0-0.0387.8492.0612.0610.0000.0000.0000.000
234A542GLU-1-0.99710.382-19.148-19.1480.0000.0000.0000.000
235A543MET0-0.1135.3030.3330.3330.0000.0000.0000.000
236A544LEU-1-0.94910.933-17.475-17.4750.0000.0000.0000.000
238A1010HOH0-0.0262.352-0.2880.5111.386-0.969-1.2170.005