FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 4JN3N

Calculation Name: 3D24-A-Xray372

Preferred Name: Estrogen-related receptor alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3D24

Chain ID: A

ChEMBL ID: CHEMBL3429

UniProt ID: P11474

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2420488.393518
FMO2-HF: Nuclear repulsion 2339892.595573
FMO2-HF: Total energy -80595.797945
FMO2-MP2: Total energy -80832.549299


3D Structure
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:194:VAL)


Summations of interaction energy for fragment #1(A:194:VAL)
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.
-4.902-0.4671.265-2.285-3.416-0.007
Interaction energy analysis for fragmet #1(A:194:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.006
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].
3A196ALA00.0220.0022.772-2.6660.5050.490-1.734-1.928-0.003
4A197LEU00.0420.0174.8680.3020.420-0.001-0.004-0.1130.000
5A198VAL00.0250.0074.1740.1100.297-0.001-0.017-0.1690.000
6A199SER0-0.006-0.0102.457-0.2990.4940.779-0.517-1.056-0.004
7A200HIS0-0.042-0.0184.9850.2070.244-0.001-0.005-0.0300.000
8A201LEU0-0.009-0.0148.2840.1640.1640.0000.0000.0000.000
9A202LEU0-0.054-0.0255.3740.1160.1160.0000.0000.0000.000
10A203VAL0-0.048-0.0198.4350.0890.0890.0000.0000.0000.000
11A204VAL0-0.042-0.01510.8170.0560.0560.0000.0000.0000.000
12A205GLU-1-0.842-0.90612.664-0.094-0.0940.0000.0000.0000.000
13A206PRO0-0.047-0.02314.4270.0180.0180.0000.0000.0000.000
14A207GLU-1-0.911-0.94317.341-0.018-0.0180.0000.0000.0000.000
15A208LYS10.7640.86619.327-0.065-0.0650.0000.0000.0000.000
16A209LEU0-0.0260.00221.307-0.006-0.0060.0000.0000.0000.000
17A210TYR00.006-0.00224.0920.0100.0100.0000.0000.0000.000
18A211ALA00.004-0.00828.025-0.008-0.0080.0000.0000.0000.000
19A212MET0-0.0250.04331.4180.0000.0000.0000.0000.0000.000
20A223PRO00.015-0.01041.6500.0000.0000.0000.0000.0000.000
21A224ALA0-0.0010.00938.8640.0010.0010.0000.0000.0000.000
22A225VAL00.0610.03037.834-0.002-0.0020.0000.0000.0000.000
23A226ALA00.0260.01037.867-0.003-0.0030.0000.0000.0000.000
24A227THR00.0220.01434.494-0.003-0.0030.0000.0000.0000.000
25A228LEU00.0060.01432.002-0.002-0.0020.0000.0000.0000.000
26A229CYS0-0.0300.00033.179-0.004-0.0040.0000.0000.0000.000
27A230ASP-1-0.829-0.92634.527-0.033-0.0330.0000.0000.0000.000
28A231LEU0-0.040-0.03328.885-0.004-0.0040.0000.0000.0000.000
29A232PHE00.026-0.00629.426-0.005-0.0050.0000.0000.0000.000
30A233ASP-1-0.780-0.87829.703-0.062-0.0620.0000.0000.0000.000
31A234ARG10.8590.89528.6940.0230.0230.0000.0000.0000.000
32A235GLU-1-0.797-0.91024.553-0.046-0.0460.0000.0000.0000.000
33A236ILE00.0070.03125.240-0.013-0.0130.0000.0000.0000.000
34A237VAL0-0.014-0.00826.426-0.011-0.0110.0000.0000.0000.000
35A238VAL0-0.012-0.00421.485-0.011-0.0110.0000.0000.0000.000
36A239THR0-0.004-0.00721.756-0.018-0.0180.0000.0000.0000.000
37A240ILE00.0030.00421.903-0.020-0.0200.0000.0000.0000.000
38A241SER0-0.094-0.04622.159-0.015-0.0150.0000.0000.0000.000
39A242TRP00.0390.01814.947-0.016-0.0160.0000.0000.0000.000
40A243ALA00.0470.01617.727-0.033-0.0330.0000.0000.0000.000
41A244LYS10.9310.96618.9080.1370.1370.0000.0000.0000.000
42A245SER0-0.032-0.01516.044-0.012-0.0120.0000.0000.0000.000
43A246ILE0-0.0010.01114.164-0.062-0.0620.0000.0000.0000.000
44A247PRO0-0.033-0.02311.5880.0350.0350.0000.0000.0000.000
45A248GLY00.0710.03514.888-0.026-0.0260.0000.0000.0000.000
46A249PHE00.0150.01517.8770.0350.0350.0000.0000.0000.000
47A250SER0-0.019-0.03019.7720.0310.0310.0000.0000.0000.000
48A251SER0-0.123-0.05020.9980.0110.0110.0000.0000.0000.000
49A252LEU00.0380.03622.3870.0130.0130.0000.0000.0000.000
50A253SER00.0510.03724.8120.0050.0050.0000.0000.0000.000
51A254LEU00.032-0.01027.735-0.001-0.0010.0000.0000.0000.000
52A255SER0-0.001-0.03029.4610.0010.0010.0000.0000.0000.000
53A256ASP-1-0.737-0.85827.011-0.151-0.1510.0000.0000.0000.000
54A257GLN0-0.095-0.05124.2420.0030.0030.0000.0000.0000.000
55A258MET0-0.039-0.02626.5260.0040.0040.0000.0000.0000.000
56A259SER00.0430.02529.5120.0090.0090.0000.0000.0000.000
57A260VAL00.0070.02323.2370.0070.0070.0000.0000.0000.000
58A261LEU0-0.010-0.00823.5700.0070.0070.0000.0000.0000.000
59A262GLN0-0.013-0.03026.6100.0080.0080.0000.0000.0000.000
60A263SER0-0.029-0.00928.6170.0060.0060.0000.0000.0000.000
61A264VAL0-0.0070.01123.5340.0050.0050.0000.0000.0000.000
62A265TRP00.0180.00825.0190.0040.0040.0000.0000.0000.000
63A266MET0-0.0070.01225.6820.0050.0050.0000.0000.0000.000
64A267GLU-1-0.847-0.91423.797-0.087-0.0870.0000.0000.0000.000
65A268VAL00.0030.00020.0580.0060.0060.0000.0000.0000.000
66A269LEU0-0.0010.01421.9210.0070.0070.0000.0000.0000.000
67A270VAL00.004-0.01724.2640.0110.0110.0000.0000.0000.000
68A271LEU00.002-0.00418.1010.0130.0130.0000.0000.0000.000
69A272GLY0-0.0080.00520.3450.0120.0120.0000.0000.0000.000
70A273VAL00.0020.00521.3890.0150.0150.0000.0000.0000.000
71A274ALA00.0010.00422.5230.0130.0130.0000.0000.0000.000
72A275GLN00.003-0.00516.5610.0110.0110.0000.0000.0000.000
73A276ARG10.7790.87520.0540.0300.0300.0000.0000.0000.000
74A277SER0-0.001-0.01622.1050.0070.0070.0000.0000.0000.000
75A278LEU0-0.055-0.00318.5810.0080.0080.0000.0000.0000.000
76A279PRO0-0.040-0.01821.1310.0090.0090.0000.0000.0000.000
77A280LEU0-0.0200.01623.5850.0040.0040.0000.0000.0000.000
78A281GLN0-0.044-0.04627.0520.0080.0080.0000.0000.0000.000
79A282ASP-1-0.882-0.92929.8150.0460.0460.0000.0000.0000.000
80A283GLU-1-0.890-0.95030.1900.0480.0480.0000.0000.0000.000
81A284LEU0-0.043-0.01828.5440.0010.0010.0000.0000.0000.000
82A285ALA00.0330.01425.831-0.002-0.0020.0000.0000.0000.000
83A286PHE00.022-0.00526.268-0.005-0.0050.0000.0000.0000.000
84A287ALA00.0030.00026.465-0.009-0.0090.0000.0000.0000.000
85A288GLU-1-0.827-0.89422.1770.0580.0580.0000.0000.0000.000
86A289ASP-1-0.847-0.90926.3380.0200.0200.0000.0000.0000.000
87A290LEU0-0.061-0.03629.597-0.003-0.0030.0000.0000.0000.000
88A291VAL00.004-0.00129.003-0.002-0.0020.0000.0000.0000.000
89A292LEU0-0.047-0.01631.603-0.001-0.0010.0000.0000.0000.000
90A293ASP-1-0.768-0.86933.6460.0260.0260.0000.0000.0000.000
91A294GLU-1-0.888-0.97735.1600.0190.0190.0000.0000.0000.000
92A295GLU-1-0.988-0.97936.5540.0170.0170.0000.0000.0000.000
93A296GLY00.0530.00938.979-0.003-0.0030.0000.0000.0000.000
94A297ALA0-0.026-0.01035.832-0.004-0.0040.0000.0000.0000.000
95A298ARG10.8490.89937.713-0.011-0.0110.0000.0000.0000.000
96A299ALA00.0020.01041.086-0.003-0.0030.0000.0000.0000.000
97A300ALA0-0.089-0.04338.790-0.002-0.0020.0000.0000.0000.000
98A301GLY0-0.019-0.02040.711-0.003-0.0030.0000.0000.0000.000
99A302LEU0-0.032-0.01935.410-0.003-0.0030.0000.0000.0000.000
100A303GLY00.0100.00638.4320.0000.0000.0000.0000.0000.000
101A304GLU-1-0.802-0.90438.0170.0100.0100.0000.0000.0000.000
102A305LEU0-0.0130.00434.0100.0000.0000.0000.0000.0000.000
103A306GLY00.0430.02133.4570.0000.0000.0000.0000.0000.000
104A307ALA00.0880.05433.0380.0030.0030.0000.0000.0000.000
105A308ALA0-0.098-0.04933.1340.0010.0010.0000.0000.0000.000
106A309LEU00.015-0.00528.435-0.001-0.0010.0000.0000.0000.000
107A310LEU00.0530.02828.4900.0030.0030.0000.0000.0000.000
108A311GLN0-0.093-0.03129.1730.0030.0030.0000.0000.0000.000
109A312LEU0-0.008-0.00723.7690.0030.0030.0000.0000.0000.000
110A313VAL00.0250.02124.6450.0040.0040.0000.0000.0000.000
111A314ARG10.9400.97124.628-0.024-0.0240.0000.0000.0000.000
112A315ARG10.8220.92424.3270.0030.0030.0000.0000.0000.000
113A316LEU00.013-0.00519.6000.0080.0080.0000.0000.0000.000
114A317GLN0-0.011-0.01220.8040.0120.0120.0000.0000.0000.000
115A318ALA0-0.047-0.01122.3760.0210.0210.0000.0000.0000.000
116A319LEU0-0.057-0.02918.8780.0150.0150.0000.0000.0000.000
117A320ARG10.8750.93817.885-0.153-0.1530.0000.0000.0000.000
118A321LEU0-0.0100.01414.9790.0320.0320.0000.0000.0000.000
119A322GLU-1-0.836-0.89910.5260.6120.6120.0000.0000.0000.000
120A323ARG10.9500.97310.049-0.095-0.0950.0000.0000.0000.000
121A324GLU-1-0.825-0.9335.7210.3290.3290.0000.0000.0000.000
122A325GLU-1-0.710-0.7828.5070.0700.0700.0000.0000.0000.000
123A326TYR0-0.005-0.00211.449-0.069-0.0690.0000.0000.0000.000
124A327VAL0-0.002-0.0069.150-0.026-0.0260.0000.0000.0000.000
125A328LEU00.0100.0148.385-0.043-0.0430.0000.0000.0000.000
126A329LEU0-0.035-0.01011.886-0.012-0.0120.0000.0000.0000.000
127A330LYS10.8380.90615.2060.1180.1180.0000.0000.0000.000
128A331ALA00.0030.00213.8300.0030.0030.0000.0000.0000.000
129A332LEU0-0.012-0.00715.4550.0050.0050.0000.0000.0000.000
130A333ALA0-0.018-0.02017.2260.0120.0120.0000.0000.0000.000
131A334LEU0-0.036-0.01218.5950.0090.0090.0000.0000.0000.000
132A335ALA00.001-0.00918.5030.0080.0080.0000.0000.0000.000
133A336ASN0-0.030-0.01220.473-0.010-0.0100.0000.0000.0000.000
134A337SER0-0.0090.00122.8780.0190.0190.0000.0000.0000.000
135A338ASP-1-0.839-0.89825.843-0.124-0.1240.0000.0000.0000.000
136A339SER0-0.054-0.02628.9950.0130.0130.0000.0000.0000.000
137A340VAL0-0.008-0.02231.050-0.005-0.0050.0000.0000.0000.000
138A341HIS0-0.029-0.02033.1200.0000.0000.0000.0000.0000.000
139A342ILE0-0.050-0.00827.219-0.002-0.0020.0000.0000.0000.000
140A343GLU-1-0.922-0.93730.750-0.118-0.1180.0000.0000.0000.000
141A344ASP-1-0.882-0.94827.963-0.189-0.1890.0000.0000.0000.000
142A345ALA0-0.008-0.02527.153-0.014-0.0140.0000.0000.0000.000
143A346GLU-1-0.922-0.95626.284-0.183-0.1830.0000.0000.0000.000
144A347ALA0-0.0190.00323.743-0.025-0.0250.0000.0000.0000.000
145A348VAL0-0.014-0.01822.124-0.028-0.0280.0000.0000.0000.000
146A349GLU-1-0.841-0.89121.454-0.212-0.2120.0000.0000.0000.000
147A350GLN00.0000.00019.211-0.049-0.0490.0000.0000.0000.000
148A351LEU0-0.036-0.01316.025-0.051-0.0510.0000.0000.0000.000
149A352ARG10.8210.89116.5920.1610.1610.0000.0000.0000.000
150A353GLU-1-0.932-0.98117.013-0.320-0.3200.0000.0000.0000.000
151A354ALA0-0.0060.01613.642-0.055-0.0550.0000.0000.0000.000
152A355LEU0-0.021-0.01711.971-0.118-0.1180.0000.0000.0000.000
153A356HIS0-0.026-0.01212.452-0.013-0.0130.0000.0000.0000.000
154A357GLU-1-0.896-0.95211.374-0.555-0.5550.0000.0000.0000.000
155A358ALA0-0.011-0.0038.440-0.096-0.0960.0000.0000.0000.000
156A359LEU0-0.044-0.0208.092-0.011-0.0110.0000.0000.0000.000
157A360LEU0-0.038-0.0269.8790.1600.1600.0000.0000.0000.000
158A361GLU-1-0.854-0.9306.124-2.327-2.3270.0000.0000.0000.000
159A362TYR0-0.103-0.0724.5660.0450.174-0.001-0.008-0.1200.000
160A363GLH0-0.053-0.0766.3440.4700.4700.0000.0000.0000.000
161A364ALA0-0.123-0.0407.7850.1490.1490.0000.0000.0000.000
162A365GLY0-0.046-0.0127.0140.0240.0240.0000.0000.0000.000
163A374GLU-1-0.725-0.83411.462-0.094-0.0940.0000.0000.0000.000
164A375ARG10.9660.95313.5010.1350.1350.0000.0000.0000.000
165A376ARG10.8230.89414.766-0.145-0.1450.0000.0000.0000.000
166A377ARG10.7370.82513.815-0.212-0.2120.0000.0000.0000.000
167A378ALA00.1000.05213.8430.0010.0010.0000.0000.0000.000
168A379GLY00.0380.02215.423-0.015-0.0150.0000.0000.0000.000
169A380ARG10.8940.93818.964-0.079-0.0790.0000.0000.0000.000
170A381LEU00.0460.03914.0830.0000.0000.0000.0000.0000.000
171A382LEU00.0660.04517.5680.0010.0010.0000.0000.0000.000
172A383LEU0-0.035-0.01919.9950.0020.0020.0000.0000.0000.000
173A384THR0-0.091-0.05420.7300.0080.0080.0000.0000.0000.000
174A385LEU00.0760.03419.6430.0040.0040.0000.0000.0000.000
175A386PRO0-0.0150.00023.4270.0010.0010.0000.0000.0000.000
176A387LEU0-0.031-0.01126.4890.0020.0020.0000.0000.0000.000
177A388LEU00.0220.03821.6030.0060.0060.0000.0000.0000.000
178A389ARG10.8420.88025.5470.1080.1080.0000.0000.0000.000
179A390GLN0-0.017-0.01027.7330.0070.0070.0000.0000.0000.000
180A391THR0-0.043-0.04428.1620.0050.0050.0000.0000.0000.000
181A392ALA00.0300.01327.4730.0030.0030.0000.0000.0000.000
182A393GLY00.0360.01729.5410.0000.0000.0000.0000.0000.000
183A394LYS10.8760.93332.8360.0190.0190.0000.0000.0000.000
184A395VAL00.0290.00430.5940.0030.0030.0000.0000.0000.000
185A396LEU00.0210.01731.5220.0020.0020.0000.0000.0000.000
186A397ALA00.006-0.00334.6030.0010.0010.0000.0000.0000.000
187A398HIS0-0.034-0.00636.7950.0040.0040.0000.0000.0000.000
188A399PHE00.032-0.01534.6430.0020.0020.0000.0000.0000.000
189A400TYR0-0.007-0.01337.9600.0010.0010.0000.0000.0000.000
190A401GLY00.013-0.00539.7320.0000.0000.0000.0000.0000.000
191A402VAL0-0.036-0.02039.6670.0020.0020.0000.0000.0000.000
192A403LYS10.8330.92840.4070.0400.0400.0000.0000.0000.000
193A404LEU0-0.067-0.02842.8260.0000.0000.0000.0000.0000.000
194A405GLU-1-0.845-0.91044.820-0.012-0.0120.0000.0000.0000.000
195A406GLY0-0.0200.00546.1170.0010.0010.0000.0000.0000.000
196A407LYS10.7570.85946.8690.0120.0120.0000.0000.0000.000
197A408VAL0-0.0120.00440.7270.0010.0010.0000.0000.0000.000
198A409PRO0-0.0150.00741.977-0.002-0.0020.0000.0000.0000.000
199A410MET00.007-0.01038.132-0.001-0.0010.0000.0000.0000.000
200A411HIS0-0.037-0.02536.209-0.005-0.0050.0000.0000.0000.000
201A412LYS10.8430.93634.3400.0540.0540.0000.0000.0000.000
202A413LEU00.0390.01330.423-0.001-0.0010.0000.0000.0000.000
203A414PHE00.0740.01532.515-0.002-0.0020.0000.0000.0000.000
204A415LEU0-0.013-0.00634.5780.0000.0000.0000.0000.0000.000
205A416GLU-1-0.978-0.98835.046-0.073-0.0730.0000.0000.0000.000
206A417MET0-0.006-0.02429.249-0.003-0.0030.0000.0000.0000.000
207A418LEU0-0.073-0.03233.961-0.001-0.0010.0000.0000.0000.000
208A419GLU-1-0.840-0.90535.867-0.041-0.0410.0000.0000.0000.000
209A420ALA0-0.0770.00234.351-0.002-0.0020.0000.0000.0000.000