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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: 3P8YX

Calculation Name: 1XP1-A-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name: (2s,3r)-2-(4-{2-[(3r,4r)-3,4-dimethylpyrrolidin-1-yl]ethoxy}phenyl)-3-(4-hydroxyphenyl)-2,3-dihydro-1,4-benzoxathiin-6- ol

ligand 3-letter code: AIH

PDB ID: 1XP1

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 AIH=+1
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3177598.939167
FMO2-HF: Nuclear repulsion 3078399.659932
FMO2-HF: Total energy -99199.279235
FMO2-MP2: Total energy -99478.297286


3D Structure
Snapshot
 
Ligand structure

AIH

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.
-339.690-296.177112.698-50.750-105.4640.255


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


Summations of interaction energy for fragment #237(A:600:AIH)
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.
-339.69-296.177112.698-50.75-105.464-0.255
Interaction energy analysis for fragmet #237(A:600:AIH)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.745 / 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].
1A309SER10.85729.6819.5479.5470.0000.0000.0000.000
2A310LEU00.12624.9370.2860.2860.0000.0000.0000.000
3A311THR0-0.02929.042-0.021-0.0210.0000.0000.0000.000
4A312ALA00.09626.761-0.314-0.3140.0000.0000.0000.000
5A313ASP-1-0.87725.679-9.210-9.2100.0000.0000.0000.000
6A314GLN00.01425.916-0.220-0.2200.0000.0000.0000.000
7A315MET00.00321.893-0.405-0.4050.0000.0000.0000.000
8A316VAL00.03521.309-0.462-0.4620.0000.0000.0000.000
9A317SER00.02520.721-0.221-0.2210.0000.0000.0000.000
10A318ALA0-0.02621.280-0.252-0.2520.0000.0000.0000.000
11A319LEU0-0.04017.119-0.519-0.5190.0000.0000.0000.000
12A320LEU0-0.03016.289-0.575-0.5750.0000.0000.0000.000
13A321ASP-1-0.93716.847-11.880-11.8800.0000.0000.0000.000
14A322ALA0-0.08815.774-0.328-0.3280.0000.0000.0000.000
15A323GLU-1-0.79111.357-17.812-17.8120.0000.0000.0000.000
16A324PRO0-0.0328.3450.0070.0070.0000.0000.0000.000
17A325PRO0-0.0039.8630.8630.8630.0000.0000.0000.000
18A326ILE00.0057.664-1.653-1.6530.0000.0000.0000.000
19A327LEU0-0.0366.2750.9790.9790.0000.0000.0000.000
20A328TYR00.0537.5610.6870.6870.0000.0000.0000.000
21A329SER0-0.0137.210-2.512-2.5120.0000.0000.0000.000
22A330GLU-1-0.9038.303-21.807-21.8070.0000.0000.0000.000
23A331TYR0-0.07110.421-0.571-0.5710.0000.0000.0000.000
24A332ASP-1-0.80212.995-13.215-13.2150.0000.0000.0000.000
25A333PRO0-0.02016.1020.0930.0930.0000.0000.0000.000
26A334THR0-0.08517.1880.7120.7120.0000.0000.0000.000
27A335ARG10.83118.25313.44513.4450.0000.0000.0000.000
28A336PRO0-0.01418.280-0.161-0.1610.0000.0000.0000.000
29A337PHE00.06410.915-0.517-0.5170.0000.0000.0000.000
30A338SER0-0.03015.040-0.611-0.6110.0000.0000.0000.000
31A339GLU-1-0.86516.269-14.033-14.0330.0000.0000.0000.000
32A340ALA00.01712.037-0.645-0.6450.0000.0000.0000.000
33A341SER00.0009.237-1.146-1.1460.0000.0000.0000.000
34A342MET00.0576.187-1.141-1.1410.0000.0000.0000.000
35A343MET00.0433.490-3.304-2.0340.307-0.344-1.2330.000
36A344GLY0-0.0114.414-5.165-4.975-0.001-0.017-0.1720.000
37A345LEU00.0456.957-2.469-2.4690.0000.0000.0000.000
38A346LEU0-0.0242.394-7.500-3.6053.594-1.743-5.7460.011
39A347THR0-0.0152.238-10.594-6.4024.369-2.852-5.710-0.015
40A348ASN0-0.0363.465-6.909-6.8590.0270.419-0.4950.000
41A349LEU0-0.0652.268-0.9930.5761.647-0.612-2.6040.003
42A350ALA00.0402.888-4.383-0.7671.759-1.277-4.0990.007
43A351ASP-1-0.8651.676-120.332-119.55616.573-9.538-7.812-0.109
44A352ARG10.8713.66733.89334.2920.0010.000-0.4000.000
45A353GLU-1-0.7491.699-64.792-65.14115.501-9.180-5.972-0.113
46A354LEU0-0.0012.1443.6840.6758.131-0.946-4.175-0.004
47A355VAL00.0444.4933.2933.4140.000-0.019-0.1030.000
48A356HIS0-0.0137.6253.4963.4960.0000.0000.0000.000
49A357MET0-0.0354.9812.1552.1550.0000.0000.0000.000
50A358ILE00.0627.1692.0142.0140.0000.0000.0000.000
51A359ASN0-0.0309.4902.0632.0630.0000.0000.0000.000
52A360TRP0-0.01710.8610.8740.8740.0000.0000.0000.000
53A361ALA00.04911.1641.2441.2440.0000.0000.0000.000
54A362LYS10.92513.04918.69118.6910.0000.0000.0000.000
55A363ARG10.88715.49215.07015.0700.0000.0000.0000.000
56A364VAL0-0.01515.2600.8120.8120.0000.0000.0000.000
57A365PRO0-0.04317.9860.2060.2060.0000.0000.0000.000
58A366GLY00.02821.033-0.013-0.0130.0000.0000.0000.000
59A367PHE00.01712.3270.0930.0930.0000.0000.0000.000
60A368VAL00.00817.056-0.204-0.2040.0000.0000.0000.000
61A369ASP-1-0.95718.801-11.439-11.4390.0000.0000.0000.000
62A370LEU0-0.06917.1160.3190.3190.0000.0000.0000.000
63A371THR0-0.08319.448-0.225-0.2250.0000.0000.0000.000
64A372LEU00.06814.958-0.298-0.2980.0000.0000.0000.000
65A373HIS0-0.02114.665-1.374-1.3740.0000.0000.0000.000
66A374ASP-1-0.81614.803-15.446-15.4460.0000.0000.0000.000
67A375GLN0-0.05513.397-1.424-1.4240.0000.0000.0000.000
68A376VAL00.0139.351-1.459-1.4590.0000.0000.0000.000
69A377HIS0-0.02210.232-2.455-2.4550.0000.0000.0000.000
70A378LEU0-0.04511.643-1.004-1.0040.0000.0000.0000.000
71A379LEU00.0157.268-0.988-0.9880.0000.0000.0000.000
72A380GLU-1-0.9397.053-30.871-30.8710.0000.0000.0000.000
73A381CYS0-0.1027.800-1.286-1.2860.0000.0000.0000.000
74A382ALA00.0329.601-0.171-0.1710.0000.0000.0000.000
75A383TRP00.0372.115-13.200-9.3947.116-2.312-8.610-0.026
76A384LEU0-0.0062.178-2.950-0.7681.504-0.554-3.132-0.004
77A385GLU-1-0.7955.450-17.218-17.2180.0000.0000.0000.000
78A386ILE0-0.0167.0822.1342.1340.0000.0000.0000.000
79A387LEU0-0.0262.601-2.7751.3051.788-1.418-4.4500.008
80A388MET0-0.0372.7281.8485.2200.829-1.092-3.109-0.004
81A389ILE00.0133.9022.0822.2310.000-0.002-0.1470.000
82A390GLY00.0525.2221.1451.1450.0000.0000.0000.000
83A391LEU0-0.0092.863-2.3800.3851.334-0.824-3.2760.005
84A392VAL0-0.0294.8710.2150.324-0.001-0.012-0.0970.000
85A393TRP00.0107.7400.7920.7920.0000.0000.0000.000
86A394ARG10.7662.23815.31217.6371.812-1.686-2.4510.023
87A395SER0-0.0107.7300.2300.2300.0000.0000.0000.000
88A396MET0-0.01710.4030.5680.5680.0000.0000.0000.000
89A397GLU-1-0.96113.296-10.902-10.9020.0000.0000.0000.000
90A398HIS0-0.03312.5750.4230.4230.0000.0000.0000.000
91A399PRO0-0.00414.191-0.309-0.3090.0000.0000.0000.000
92A400GLY0-0.03914.2200.1070.1070.0000.0000.0000.000
93A401LYS10.90011.36912.02312.0230.0000.0000.0000.000
94A402LEU00.0395.3660.1440.1440.0000.0000.0000.000
95A403LEU0-0.0078.697-0.323-0.3230.0000.0000.0000.000
96A404PHE00.0072.271-5.808-2.0874.919-1.566-7.0740.013
97A405ALA00.0564.417-3.186-2.9510.000-0.020-0.2140.000
98A406PRO00.0247.0200.9900.9900.0000.0000.0000.000
99A407ASN00.0009.9340.2390.2390.0000.0000.0000.000
100A408LEU0-0.0355.463-0.328-0.3280.0000.0000.0000.000
101A409LEU00.0248.178-0.210-0.2100.0000.0000.0000.000
102A410LEU0-0.0506.6620.1790.1790.0000.0000.0000.000
103A411ASP-1-0.8179.825-13.109-13.1090.0000.0000.0000.000
104A412ARG10.8619.78612.58612.5860.0000.0000.0000.000
105A413ASN0-0.04210.313-0.564-0.5640.0000.0000.0000.000
106A414GLN00.05210.262-0.146-0.1460.0000.0000.0000.000
107A415GLY00.0786.953-1.027-1.0270.0000.0000.0000.000
108A416LYS10.8867.44311.97011.9700.0000.0000.0000.000
109A417CYS0-0.0879.4760.4370.4370.0000.0000.0000.000
110A418VAL0-0.0255.093-0.409-0.4090.0000.0000.0000.000
111A419GLU-1-0.9187.122-18.992-18.9920.0000.0000.0000.000
112A420GLY00.1166.473-2.273-2.2730.0000.0000.0000.000
113A421MET0-0.0512.142-4.224-3.0721.676-0.559-2.2690.000
114A422VAL0-0.0564.3601.4721.592-0.001-0.005-0.1140.000
115A423GLU-1-0.8167.167-16.196-16.1960.0000.0000.0000.000
116A424ILE0-0.0032.571-2.3660.5501.819-1.276-3.4590.016
117A425PHE00.0203.1080.5191.3150.026-0.095-0.7260.000
118A426ASP-1-0.7516.733-13.117-13.1170.0000.0000.0000.000
119A427MET0-0.0487.2160.7690.7690.0000.0000.0000.000
120A428LEU00.0684.029-0.3610.4210.045-0.131-0.6960.000
121A429LEU0-0.0538.4560.5140.5140.0000.0000.0000.000
122A430ALA0-0.02610.8130.5200.5200.0000.0000.0000.000
123A431THR0-0.01010.1600.3880.3880.0000.0000.0000.000
124A432SER00.01110.2830.4250.4250.0000.0000.0000.000
125A433SER0-0.04711.9770.4950.4950.0000.0000.0000.000
126A434ARG10.98015.13911.08511.0850.0000.0000.0000.000
127A435PHE00.03610.7380.3570.3570.0000.0000.0000.000
128A436ARG10.95414.56711.67511.6750.0000.0000.0000.000
129A437MET0-0.06817.4420.4060.4060.0000.0000.0000.000
130A438MET0-0.08018.6270.1930.1930.0000.0000.0000.000
131A439ASN00.00419.720-0.013-0.0130.0000.0000.0000.000
132A440LEU0-0.05314.0900.1270.1270.0000.0000.0000.000
133A441GLN00.00517.872-0.002-0.0020.0000.0000.0000.000
134A442GLY00.05315.670-0.367-0.3670.0000.0000.0000.000
135A443GLU-1-0.88216.348-11.164-11.1640.0000.0000.0000.000
136A444GLU-1-0.76618.376-10.649-10.6490.0000.0000.0000.000
137A445PHE0-0.0098.901-0.401-0.4010.0000.0000.0000.000
138A446VAL00.02513.765-0.669-0.6690.0000.0000.0000.000
139A447CYS0-0.03014.888-0.304-0.3040.0000.0000.0000.000
140A448LEU0-0.01414.214-0.310-0.3100.0000.0000.0000.000
141A449LYS10.8169.10017.86517.8650.0000.0000.0000.000
142A450SER00.02312.669-0.912-0.9120.0000.0000.0000.000
143A451ILE0-0.02415.552-0.205-0.2050.0000.0000.0000.000
144A452ILE0-0.02310.505-0.076-0.0760.0000.0000.0000.000
145A453LEU0-0.01711.168-0.530-0.5300.0000.0000.0000.000
146A454LEU00.01213.443-0.208-0.2080.0000.0000.0000.000
147A455ASN00.00216.6470.7170.7170.0000.0000.0000.000
148A456SER0-0.07113.2860.7930.7930.0000.0000.0000.000
149A457GLY00.03814.612-0.087-0.0870.0000.0000.0000.000
150A458VAL00.01315.4260.4290.4290.0000.0000.0000.000
151A459TYR0-0.07318.7920.7360.7360.0000.0000.0000.000
152A460THR0-0.00715.8010.5570.5570.0000.0000.0000.000
153A461PHE0-0.01316.766-0.223-0.2230.0000.0000.0000.000
154A462LEU00.01617.7250.6630.6630.0000.0000.0000.000
155A463SER00.01020.9540.6430.6430.0000.0000.0000.000
156A464SER0-0.01924.1190.0520.0520.0000.0000.0000.000
157A465THR0-0.00225.2720.3750.3750.0000.0000.0000.000
158A466LEU00.06327.818-0.080-0.0800.0000.0000.0000.000
159A467LYS10.99423.22211.75311.7530.0000.0000.0000.000
160A468SER00.01123.354-0.058-0.0580.0000.0000.0000.000
161A469LEU0-0.01724.560-0.213-0.2130.0000.0000.0000.000
162A470GLU-1-0.88827.036-9.842-9.8420.0000.0000.0000.000
163A471GLU-1-0.77620.761-13.122-13.1220.0000.0000.0000.000
164A472LYS10.92722.53611.68711.6870.0000.0000.0000.000
165A473ASP-1-0.87423.839-9.829-9.8290.0000.0000.0000.000
166A474HIS0-0.02021.8870.5940.5940.0000.0000.0000.000
167A475ILE00.03818.6730.0080.0080.0000.0000.0000.000
168A476HIS0-0.01522.217-0.214-0.2140.0000.0000.0000.000
169A477ARG10.87824.74910.30710.3070.0000.0000.0000.000
170A478VAL0-0.04821.2180.2060.2060.0000.0000.0000.000
171A479LEU0-0.01119.8780.0240.0240.0000.0000.0000.000
172A480ASP-1-0.86823.417-9.963-9.9630.0000.0000.0000.000
173A481LYS10.87325.3459.9079.9070.0000.0000.0000.000
174A482ILE00.01419.3800.1790.1790.0000.0000.0000.000
175A483THR0-0.02023.0690.0420.0420.0000.0000.0000.000
176A484ASP-1-0.90324.704-9.138-9.1380.0000.0000.0000.000
177A485THR0-0.09423.1250.2750.2750.0000.0000.0000.000
178A486LEU00.02619.7230.1740.1740.0000.0000.0000.000
179A487ILE0-0.01723.7890.2390.2390.0000.0000.0000.000
180A488HIS0-0.02026.9520.3410.3410.0000.0000.0000.000
181A489LEU0-0.02821.7460.2150.2150.0000.0000.0000.000
182A490MET0-0.03722.7560.2830.2830.0000.0000.0000.000
183A491ALA0-0.00627.0840.2250.2250.0000.0000.0000.000
184A492LYS10.94725.8679.3609.3600.0000.0000.0000.000
185A493ALA0-0.05726.9840.1460.1460.0000.0000.0000.000
186A494GLY0-0.00629.1100.1080.1080.0000.0000.0000.000
187A495LEU0-0.02226.5290.1200.1200.0000.0000.0000.000
188A496THR00.02831.1990.0370.0370.0000.0000.0000.000
189A497LEU00.06432.091-0.178-0.1780.0000.0000.0000.000
190A498GLN00.00732.128-0.144-0.1440.0000.0000.0000.000
191A499GLN00.03029.340-0.198-0.1980.0000.0000.0000.000
192A500GLN00.00427.995-0.344-0.3440.0000.0000.0000.000
193A501HIS00.05426.990-0.119-0.1190.0000.0000.0000.000
194A502GLN0-0.06226.980-0.310-0.3100.0000.0000.0000.000
195A503ARG10.78020.9149.7639.7630.0000.0000.0000.000
196A504LEU00.02322.547-0.372-0.3720.0000.0000.0000.000
197A505ALA00.02822.066-0.417-0.4170.0000.0000.0000.000
198A506GLN0-0.04621.252-0.423-0.4230.0000.0000.0000.000
199A507LEU00.01217.569-0.375-0.3750.0000.0000.0000.000
200A508LEU00.03217.227-0.582-0.5820.0000.0000.0000.000
201A509LEU0-0.01918.231-0.440-0.4400.0000.0000.0000.000
202A510ILE0-0.05813.400-0.309-0.3090.0000.0000.0000.000
203A511LEU00.03813.329-0.631-0.6310.0000.0000.0000.000
204A512SER0-0.03514.228-0.857-0.8570.0000.0000.0000.000
205A513HIS00.01213.349-0.614-0.6140.0000.0000.0000.000
206A514ILE0-0.0058.573-0.481-0.4810.0000.0000.0000.000
207A515ARG10.9549.28516.58216.5820.0000.0000.0000.000
208A516HIS0-0.0429.607-1.181-1.1810.0000.0000.0000.000
209A517MET00.0026.711-0.401-0.4010.0000.0000.0000.000
210A518SER00.0775.170-1.984-1.9840.0000.0000.0000.000
211A519ASN0-0.0175.393-2.847-2.8470.0000.0000.0000.000
212A520LYS10.9366.50416.43116.4310.0000.0000.0000.000
213A521GLY00.0322.395-1.424-0.7242.528-1.524-1.7050.009
214A522MET0-0.0133.013-3.857-4.3070.2841.350-1.184-0.004
215A523GLU-1-0.9555.177-20.099-20.024-0.001-0.004-0.0710.000
216A524HIS0-0.0491.814-26.015-30.32017.021-6.664-6.052-0.064
217A525LEU00.0062.715-9.247-3.3042.732-1.753-6.9220.012
218A526TYR0-0.0604.647-1.551-1.3590.000-0.015-0.1770.000
219A527SER0-0.0636.5813.4203.4200.0000.0000.0000.000
220A528MET0-0.0074.9380.2290.2290.0000.0000.0000.000
221A529LYS10.9107.31327.36627.3660.0000.0000.0000.000
222A530CYS0-0.0412.490-5.366-7.7027.474-1.968-3.169-0.014
223A531LYS11.0242.18156.40658.7041.540-0.741-3.097-0.001
224A532ASN0-0.0183.780-8.102-7.4180.015-0.200-0.499-0.001
225A533VAL0-0.0275.8474.2834.2830.0000.0000.0000.000
226A534VAL0-0.0195.707-2.286-2.2860.0000.0000.0000.000
227A535PRO00.0245.765-3.848-3.8480.0000.0000.0000.000
228A536LEU00.0212.223-1.575-3.2034.273-0.424-2.221-0.007
229A537TYR00.0154.9940.6010.660-0.001-0.001-0.0570.000
230A538ASP-1-0.8308.457-22.579-22.5790.0000.0000.0000.000
231A539LEU0-0.0422.844-1.018-0.5250.294-0.119-0.668-0.001
232A540LEU0-0.0255.0620.0840.0840.0000.0000.0000.000
233A541LEU0-0.0367.1191.8611.8610.0000.0000.0000.000
234A542GLU-1-0.9969.385-19.000-19.0000.0000.0000.0000.000
235A543MET0-0.0944.8630.1320.1320.0000.0000.0000.000
236A544LEU-1-0.96010.132-17.189-17.1890.0000.0000.0000.000
238A1007HOH0-0.0172.299-0.1590.3991.765-1.026-1.2970.005