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: 1XMZP

Calculation Name: 3ERD-B-Xray7

Preferred Name: Estrogen receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ERD

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.
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 238
LigandCharge DES=0
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3155795.554907
FMO2-HF: Nuclear repulsion 3057581.945588
FMO2-HF: Total energy -98213.609319
FMO2-MP2: Total energy -98490.695344


3D Structure
Snapshot
 
Ligand structure

DES

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.
-123.467-112.742101.613-47.928-64.4100.134


Interactive mode: IFIE and PIEDA for fragment #237(B:800:DES)


Summations of interaction energy for fragment #237(B:800:DES)
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.
-123.467-112.742101.613-47.928-64.41-0.134
Interaction energy analysis for fragmet #237(B:800:DES)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.133 / 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].
1B309SER10.84530.372-0.020-0.0200.0000.0000.0000.000
2B310LEU00.13925.6010.0000.0000.0000.0000.0000.000
3B311THR00.01929.5760.0060.0060.0000.0000.0000.000
4B312ALA00.04926.9740.0010.0010.0000.0000.0000.000
5B313ASP-1-0.80125.8740.1100.1100.0000.0000.0000.000
6B314GLN0-0.00925.9460.0020.0020.0000.0000.0000.000
7B315MET0-0.03122.438-0.007-0.0070.0000.0000.0000.000
8B316VAL00.04821.3390.0030.0030.0000.0000.0000.000
9B317SER0-0.01220.9830.0110.0110.0000.0000.0000.000
10B318ALA00.00421.411-0.005-0.0050.0000.0000.0000.000
11B319LEU0-0.03217.342-0.012-0.0120.0000.0000.0000.000
12B320LEU0-0.02016.6750.0110.0110.0000.0000.0000.000
13B321ASP-1-0.91617.0520.0420.0420.0000.0000.0000.000
14B322ALA0-0.07516.102-0.042-0.0420.0000.0000.0000.000
15B323GLU-1-0.78711.8290.3700.3700.0000.0000.0000.000
16B324PRO0-0.0558.660-0.069-0.0690.0000.0000.0000.000
17B325PRO00.01210.4000.1210.1210.0000.0000.0000.000
18B326ILE00.0037.810-0.149-0.1490.0000.0000.0000.000
19B327LEU0-0.0326.5040.1380.1380.0000.0000.0000.000
20B328TYR00.0257.9710.2250.2250.0000.0000.0000.000
21B329SER00.0207.556-0.443-0.4430.0000.0000.0000.000
22B330GLU-1-0.8858.833-0.480-0.4800.0000.0000.0000.000
23B331TYR0-0.05811.8550.1270.1270.0000.0000.0000.000
24B332ASP-1-0.79214.7380.0680.0680.0000.0000.0000.000
25B333PRO0-0.08515.7480.0430.0430.0000.0000.0000.000
26B334THR0-0.05116.8660.0340.0340.0000.0000.0000.000
27B335ARG10.88111.873-0.494-0.4940.0000.0000.0000.000
28B336PRO0-0.01315.391-0.023-0.0230.0000.0000.0000.000
29B337PHE00.03710.8550.0060.0060.0000.0000.0000.000
30B338SER00.01412.0470.0200.0200.0000.0000.0000.000
31B339GLU-1-0.6917.7200.3120.3120.0000.0000.0000.000
32B340ALA00.0507.2900.1850.1850.0000.0000.0000.000
33B341SER0-0.0328.252-0.033-0.0330.0000.0000.0000.000
34B342MET0-0.0136.099-0.171-0.1710.0000.0000.0000.000
35B343MET00.0302.585-2.923-1.6213.265-1.179-3.3870.010
36B344GLY00.0234.563-0.629-0.463-0.001-0.010-0.1560.000
37B345LEU0-0.0337.309-0.350-0.3500.0000.0000.0000.000
38B346LEU0-0.0262.543-3.883-0.8261.084-0.707-3.4340.002
39B347THR00.0042.717-7.829-3.6281.019-1.905-3.315-0.018
40B348ASN00.0203.724-0.554-0.4030.0020.068-0.2210.000
41B349LEU0-0.0402.918-0.4760.7130.160-0.263-1.0860.001
42B350ALA00.0302.369-2.440-1.5543.675-1.359-3.2020.000
43B351ASP-1-0.8273.651-0.414-0.1320.029-0.036-0.2750.000
44B352ARG10.8556.4561.9171.9170.0000.0000.0000.000
45B353GLU-1-0.7731.449-37.419-52.77038.592-18.268-4.974-0.124
46B354LEU00.0185.0780.9200.9200.0000.0000.0000.000
47B355VAL00.0088.0340.3940.3940.0000.0000.0000.000
48B356HIS0-0.0408.6040.3500.3500.0000.0000.0000.000
49B357MET0-0.0376.8380.2370.2370.0000.0000.0000.000
50B358ILE00.0679.6980.1940.1940.0000.0000.0000.000
51B359ASN0-0.04913.0560.1090.1090.0000.0000.0000.000
52B360TRP0-0.00911.6840.0760.0760.0000.0000.0000.000
53B361ALA00.04913.4550.0580.0580.0000.0000.0000.000
54B362LYS10.90415.1220.2660.2660.0000.0000.0000.000
55B363ARG10.80113.8940.1740.1740.0000.0000.0000.000
56B364VAL00.00915.8020.0290.0290.0000.0000.0000.000
57B365PRO0-0.03218.738-0.017-0.0170.0000.0000.0000.000
58B366GLY00.03722.5230.0120.0120.0000.0000.0000.000
59B367PHE00.02717.390-0.007-0.0070.0000.0000.0000.000
60B368VAL0-0.00421.376-0.015-0.0150.0000.0000.0000.000
61B369ASP-1-0.92523.241-0.040-0.0400.0000.0000.0000.000
62B370LEU0-0.06521.6730.0010.0010.0000.0000.0000.000
63B371THR00.01325.083-0.012-0.0120.0000.0000.0000.000
64B372LEU00.05520.489-0.001-0.0010.0000.0000.0000.000
65B373HIS0-0.00520.755-0.019-0.0190.0000.0000.0000.000
66B374ASP-1-0.83420.525-0.107-0.1070.0000.0000.0000.000
67B375GLN0-0.07319.030-0.019-0.0190.0000.0000.0000.000
68B376VAL00.02116.055-0.007-0.0070.0000.0000.0000.000
69B377HIS00.02915.575-0.029-0.0290.0000.0000.0000.000
70B378LEU0-0.05315.869-0.010-0.0100.0000.0000.0000.000
71B379LEU0-0.01512.5140.0220.0220.0000.0000.0000.000
72B380GLU-1-0.89111.396-0.310-0.3100.0000.0000.0000.000
73B381CYS0-0.10811.168-0.039-0.0390.0000.0000.0000.000
74B382ALA00.00411.210-0.016-0.0160.0000.0000.0000.000
75B383TRP00.0452.898-0.8090.1180.093-0.140-0.8810.000
76B384LEU00.0402.678-1.3480.2100.804-0.381-1.9810.000
77B385GLU-1-0.8345.3220.7580.7580.0000.0000.0000.000
78B386ILE0-0.0326.8110.3560.3560.0000.0000.0000.000
79B387LEU0-0.0102.642-2.8810.1641.699-1.220-3.5230.007
80B388MET0-0.0152.823-1.2481.7200.778-1.057-2.689-0.011
81B389ILE0-0.0133.6690.3310.4130.0020.053-0.1370.000
82B390GLY00.0365.527-0.259-0.2590.0000.0000.0000.000
83B391LEU0-0.0072.596-3.345-0.8611.006-0.958-2.5320.010
84B392VAL0-0.0174.544-1.136-1.0330.000-0.017-0.0860.000
85B393TRP0-0.0177.417-0.336-0.3360.0000.0000.0000.000
86B394ARG10.8002.377-8.524-6.5870.902-1.136-1.7030.014
87B395SER0-0.0307.612-0.153-0.1530.0000.0000.0000.000
88B396MET0-0.04110.287-0.192-0.1920.0000.0000.0000.000
89B397GLU-1-0.91413.2920.4160.4160.0000.0000.0000.000
90B398HIS0-0.05112.912-0.108-0.1080.0000.0000.0000.000
91B399PRO00.01813.9170.1150.1150.0000.0000.0000.000
92B400GLY0-0.05313.700-0.062-0.0620.0000.0000.0000.000
93B401LYS10.89011.295-0.751-0.7510.0000.0000.0000.000
94B402LEU00.0345.028-0.026-0.0260.0000.0000.0000.000
95B403LEU0-0.0148.194-0.122-0.1220.0000.0000.0000.000
96B404PHE00.0401.983-4.043-1.8164.902-1.700-5.4280.012
97B405ALA00.0664.960-1.086-1.016-0.001-0.006-0.0640.000
98B406PRO00.0127.6700.2470.2470.0000.0000.0000.000
99B407ASN0-0.03810.7370.0380.0380.0000.0000.0000.000
100B408LEU0-0.0336.369-0.052-0.0520.0000.0000.0000.000
101B409LEU00.0078.8670.3800.3800.0000.0000.0000.000
102B410LEU0-0.0285.990-0.245-0.2450.0000.0000.0000.000
103B411ASP-1-0.7969.6870.8810.8810.0000.0000.0000.000
104B412ARG10.8689.278-0.398-0.3980.0000.0000.0000.000
105B413ASN0-0.08210.348-0.100-0.1000.0000.0000.0000.000
106B414GLN00.02710.265-0.016-0.0160.0000.0000.0000.000
107B415GLY00.0567.3480.0850.0850.0000.0000.0000.000
108B416LYS10.8968.089-0.475-0.4750.0000.0000.0000.000
109B417CYS0-0.08510.192-0.121-0.1210.0000.0000.0000.000
110B418VAL00.0014.518-0.1430.022-0.001-0.014-0.1510.000
111B419GLU-1-0.8277.276-0.470-0.4700.0000.0000.0000.000
112B420GLY00.0486.032-0.534-0.5340.0000.0000.0000.000
113B421MET0-0.0082.716-4.032-1.8613.009-1.078-4.1020.009
114B422VAL0-0.0445.8230.5970.5970.0000.0000.0000.000
115B423GLU-1-0.8488.337-0.103-0.1030.0000.0000.0000.000
116B424ILE00.0013.028-0.7090.2110.169-0.200-0.8890.001
117B425PHE00.0362.937-0.2040.5090.065-0.115-0.6630.000
118B426ASP-1-0.7605.7100.6020.6020.0000.0000.0000.000
119B427MET0-0.0497.522-0.022-0.0220.0000.0000.0000.000
120B428LEU00.0682.652-0.625-0.0650.429-0.144-0.8450.000
121B429LEU0-0.0247.233-0.094-0.0940.0000.0000.0000.000
122B430ALA0-0.02710.035-0.119-0.1190.0000.0000.0000.000
123B431THR0-0.0139.896-0.154-0.1540.0000.0000.0000.000
124B432SER00.00910.127-0.128-0.1280.0000.0000.0000.000
125B433SER00.00111.825-0.120-0.1200.0000.0000.0000.000
126B434ARG10.92314.814-0.460-0.4600.0000.0000.0000.000
127B435PHE00.05510.545-0.082-0.0820.0000.0000.0000.000
128B436ARG10.90614.002-0.875-0.8750.0000.0000.0000.000
129B437MET0-0.05817.136-0.057-0.0570.0000.0000.0000.000
130B438MET0-0.07818.333-0.041-0.0410.0000.0000.0000.000
131B439ASN0-0.00119.338-0.013-0.0130.0000.0000.0000.000
132B440LEU0-0.06113.690-0.035-0.0350.0000.0000.0000.000
133B441GLN00.02617.3820.0160.0160.0000.0000.0000.000
134B442GLY00.06515.8820.0370.0370.0000.0000.0000.000
135B443GLU-1-0.85716.5430.2770.2770.0000.0000.0000.000
136B444GLU-1-0.76918.1290.3100.3100.0000.0000.0000.000
137B445PHE0-0.0059.2890.0220.0220.0000.0000.0000.000
138B446VAL00.02813.6950.0220.0220.0000.0000.0000.000
139B447CYS0-0.05215.203-0.051-0.0510.0000.0000.0000.000
140B448LEU00.00613.787-0.030-0.0300.0000.0000.0000.000
141B449LYS10.8479.393-0.529-0.5290.0000.0000.0000.000
142B450SER00.03012.414-0.069-0.0690.0000.0000.0000.000
143B451ILE0-0.03215.446-0.047-0.0470.0000.0000.0000.000
144B452ILE0-0.02110.211-0.036-0.0360.0000.0000.0000.000
145B453LEU0-0.02113.636-0.054-0.0540.0000.0000.0000.000
146B454LEU00.00414.542-0.050-0.0500.0000.0000.0000.000
147B455ASN00.00417.237-0.036-0.0360.0000.0000.0000.000
148B456SER0-0.06113.457-0.012-0.0120.0000.0000.0000.000
149B457GLY00.07316.468-0.034-0.0340.0000.0000.0000.000
150B458VAL00.02617.787-0.014-0.0140.0000.0000.0000.000
151B459TYR0-0.05021.149-0.002-0.0020.0000.0000.0000.000
152B460THR0-0.03417.909-0.007-0.0070.0000.0000.0000.000
153B461PHE0-0.00320.972-0.012-0.0120.0000.0000.0000.000
154B462LEU00.03022.4820.0050.0050.0000.0000.0000.000
155B463SER0-0.02924.4840.0050.0050.0000.0000.0000.000
156B464SER0-0.01827.7920.0050.0050.0000.0000.0000.000
157B465THR0-0.00329.8500.0060.0060.0000.0000.0000.000
158B466LEU00.05531.5060.0000.0000.0000.0000.0000.000
159B467LYS10.89229.8940.0570.0570.0000.0000.0000.000
160B468SER00.00027.179-0.002-0.0020.0000.0000.0000.000
161B469LEU0-0.01128.554-0.001-0.0010.0000.0000.0000.000
162B470GLU-1-0.81930.391-0.041-0.0410.0000.0000.0000.000
163B471GLU00.02125.0050.0070.0070.0000.0000.0000.000
164B472LYS10.88424.7010.0790.0790.0000.0000.0000.000
165B473ASP-1-0.94227.076-0.001-0.0010.0000.0000.0000.000
166B474HIS0-0.02425.2980.0130.0130.0000.0000.0000.000
167B475ILE00.04221.6690.0100.0100.0000.0000.0000.000
168B476HIS00.01424.1260.0150.0150.0000.0000.0000.000
169B477ARG10.94226.0430.0050.0050.0000.0000.0000.000
170B478VAL0-0.04522.4690.0110.0110.0000.0000.0000.000
171B479LEU0-0.01619.6740.0180.0180.0000.0000.0000.000
172B480ASP-1-0.87823.1430.0660.0660.0000.0000.0000.000
173B481LYS10.87825.409-0.054-0.0540.0000.0000.0000.000
174B482ILE00.00319.1390.0110.0110.0000.0000.0000.000
175B483THR00.00122.8620.0250.0250.0000.0000.0000.000
176B484ASP-1-0.93124.1930.0840.0840.0000.0000.0000.000
177B485THR0-0.10923.243-0.002-0.0020.0000.0000.0000.000
178B486LEU00.02019.2710.0100.0100.0000.0000.0000.000
179B487ILE00.01723.3680.0070.0070.0000.0000.0000.000
180B488HIS0-0.02826.794-0.001-0.0010.0000.0000.0000.000
181B489LEU00.01721.756-0.004-0.0040.0000.0000.0000.000
182B490MET0-0.03622.390-0.003-0.0030.0000.0000.0000.000
183B491ALA0-0.02526.707-0.004-0.0040.0000.0000.0000.000
184B492LYS10.87128.530-0.116-0.1160.0000.0000.0000.000
185B493ALA0-0.03026.763-0.003-0.0030.0000.0000.0000.000
186B494GLY0-0.01628.9020.0030.0030.0000.0000.0000.000
187B495LEU0-0.03726.294-0.002-0.0020.0000.0000.0000.000
188B496THR00.03730.725-0.008-0.0080.0000.0000.0000.000
189B497LEU00.06631.7060.0070.0070.0000.0000.0000.000
190B498GLN00.01131.7650.0030.0030.0000.0000.0000.000
191B499GLN0-0.00329.1530.0030.0030.0000.0000.0000.000
192B500GLN0-0.00127.5820.0120.0120.0000.0000.0000.000
193B501HIS00.08426.5710.0060.0060.0000.0000.0000.000
194B502GLN0-0.07426.579-0.007-0.0070.0000.0000.0000.000
195B503ARG10.78120.464-0.302-0.3020.0000.0000.0000.000
196B504LEU00.04121.9680.0260.0260.0000.0000.0000.000
197B505ALA00.01721.7700.0110.0110.0000.0000.0000.000
198B506GLN0-0.05221.0710.0260.0260.0000.0000.0000.000
199B507LEU0-0.00417.1970.0290.0290.0000.0000.0000.000
200B508LEU00.04316.9240.0360.0360.0000.0000.0000.000
201B509LEU0-0.01917.849-0.007-0.0070.0000.0000.0000.000
202B510ILE0-0.04413.110-0.011-0.0110.0000.0000.0000.000
203B511LEU00.04812.8820.0560.0560.0000.0000.0000.000
204B512SER0-0.04513.933-0.046-0.0460.0000.0000.0000.000
205B513HIS00.01312.771-0.063-0.0630.0000.0000.0000.000
206B514ILE00.0048.415-0.009-0.0090.0000.0000.0000.000
207B515ARG10.9229.4470.0190.0190.0000.0000.0000.000
208B516HIS0-0.06410.837-0.218-0.2180.0000.0000.0000.000
209B517MET0-0.0216.620-0.113-0.1130.0000.0000.0000.000
210B518SER00.0666.309-0.473-0.4730.0000.0000.0000.000
211B519ASN00.0146.518-0.528-0.5280.0000.0000.0000.000
212B520LYS10.9087.3830.6870.6870.0000.0000.0000.000
213B521GLY00.0193.420-1.061-0.7500.022-0.087-0.2460.000
214B522MET00.0392.874-4.715-2.8270.276-0.940-1.224-0.011
215B523GLU-1-0.9445.522-0.992-0.9920.0000.0000.0000.000
216B524HIS0-0.0321.620-21.644-36.70632.694-11.638-5.994-0.056
217B525LEU00.0492.549-5.423-0.6814.753-2.442-7.0530.007
218B526TYR00.0413.5251.5351.2790.1040.674-0.5210.002
219B527SER0-0.0035.5310.5700.5700.0000.0000.0000.000
220B528MET0-0.0332.678-1.451-0.1130.900-0.703-1.5340.006
221B529LYS10.9215.2530.0420.133-0.001-0.002-0.0880.000
222B530CYS0-0.1037.557-0.101-0.1010.0000.0000.0000.000
223B531LYS10.7398.242-0.023-0.0230.0000.0000.0000.000
224B532ASN0-0.0129.2690.0550.0550.0000.0000.0000.000
225B533VAL0-0.0306.848-0.081-0.0810.0000.0000.0000.000
226B534VAL0-0.0386.354-0.078-0.0780.0000.0000.0000.000
227B535PRO0-0.0208.5830.1190.1190.0000.0000.0000.000
228B536LEU00.0035.3900.0050.0050.0000.0000.0000.000
229B537TYR00.0067.343-0.073-0.0730.0000.0000.0000.000
230B538ASP-1-0.8668.917-0.293-0.2930.0000.0000.0000.000
231B539LEU0-0.0018.7390.0240.0240.0000.0000.0000.000
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