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: KGR33

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 OptH
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 -2420053.201285
FMO2-HF: Nuclear repulsion 2339458.730576
FMO2-HF: Total energy -80594.470709
FMO2-MP2: Total energy -80831.28136


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.
-1.0832.2811.831-1.84-3.355-0.012
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 : -0.009 / q_NPA : -0.018
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].
3A196ALA00.0280.0012.654-2.404-0.2530.886-1.243-1.795-0.009
4A197LEU00.0410.0194.6910.1420.259-0.001-0.004-0.1130.000
5A198VAL00.0250.0063.914-0.0410.1720.001-0.024-0.1890.000
6A199SER00.002-0.0022.323-0.5900.1360.947-0.557-1.116-0.003
7A200HIS0-0.046-0.0245.0240.1480.188-0.001-0.005-0.0330.000
8A201LEU0-0.009-0.0168.2600.1430.1430.0000.0000.0000.000
9A202LEU0-0.045-0.0225.4250.1050.1050.0000.0000.0000.000
10A203VAL0-0.050-0.0168.3770.0720.0720.0000.0000.0000.000
11A204VAL0-0.045-0.01710.7440.0660.0660.0000.0000.0000.000
12A205GLU-1-0.860-0.92912.685-0.099-0.0990.0000.0000.0000.000
13A206PRO0-0.052-0.02414.4430.0030.0030.0000.0000.0000.000
14A207GLU-1-0.924-0.95117.170-0.197-0.1970.0000.0000.0000.000
15A208LYS10.9170.95519.2100.0700.0700.0000.0000.0000.000
16A209LEU0-0.0020.01521.402-0.005-0.0050.0000.0000.0000.000
17A210TYR0-0.036-0.01824.1600.0050.0050.0000.0000.0000.000
18A211ALA00.000-0.01028.124-0.003-0.0030.0000.0000.0000.000
19A212MET0-0.0470.02331.506-0.003-0.0030.0000.0000.0000.000
20A223PRO0-0.005-0.02441.6750.0010.0010.0000.0000.0000.000
21A224ALA00.0120.02238.933-0.001-0.0010.0000.0000.0000.000
22A225VAL00.0520.02937.881-0.003-0.0030.0000.0000.0000.000
23A226ALA00.0290.00637.891-0.002-0.0020.0000.0000.0000.000
24A227THR00.0200.01834.416-0.003-0.0030.0000.0000.0000.000
25A228LEU00.0090.01232.281-0.004-0.0040.0000.0000.0000.000
26A229CYS0-0.030-0.00433.195-0.002-0.0020.0000.0000.0000.000
27A230ASP-1-0.840-0.92934.526-0.041-0.0410.0000.0000.0000.000
28A231LEU0-0.035-0.03728.780-0.006-0.0060.0000.0000.0000.000
29A232PHE00.025-0.00429.398-0.005-0.0050.0000.0000.0000.000
30A233ASP-1-0.794-0.89829.686-0.060-0.0600.0000.0000.0000.000
31A234ARG10.8630.90328.7560.0570.0570.0000.0000.0000.000
32A235GLU-1-0.829-0.93824.987-0.060-0.0600.0000.0000.0000.000
33A236ILE00.0090.02425.215-0.010-0.0100.0000.0000.0000.000
34A237VAL0-0.018-0.00826.372-0.008-0.0080.0000.0000.0000.000
35A238VAL0-0.014-0.00721.413-0.012-0.0120.0000.0000.0000.000
36A239THR00.0040.00121.703-0.016-0.0160.0000.0000.0000.000
37A240ILE0-0.0030.00221.907-0.013-0.0130.0000.0000.0000.000
38A241SER0-0.098-0.05022.053-0.014-0.0140.0000.0000.0000.000
39A242TRP00.0450.02814.806-0.006-0.0060.0000.0000.0000.000
40A243ALA00.0490.01617.712-0.026-0.0260.0000.0000.0000.000
41A244LYS10.9220.96018.8580.1340.1340.0000.0000.0000.000
42A245SER0-0.034-0.01715.991-0.015-0.0150.0000.0000.0000.000
43A246ILE00.0000.01214.068-0.063-0.0630.0000.0000.0000.000
44A247PRO0-0.039-0.02411.4770.0310.0310.0000.0000.0000.000
45A248GLY00.0810.04014.7780.0060.0060.0000.0000.0000.000
46A249PHE00.0110.02317.7550.0320.0320.0000.0000.0000.000
47A250SER0-0.012-0.02619.6840.0240.0240.0000.0000.0000.000
48A251SER0-0.128-0.05620.8750.0090.0090.0000.0000.0000.000
49A252LEU00.0440.03722.2960.0120.0120.0000.0000.0000.000
50A253SER00.0740.04724.697-0.005-0.0050.0000.0000.0000.000
51A254LEU00.040-0.00627.638-0.001-0.0010.0000.0000.0000.000
52A255SER00.0290.01829.372-0.002-0.0020.0000.0000.0000.000
53A256ASP-1-0.711-0.83727.081-0.065-0.0650.0000.0000.0000.000
54A257GLN0-0.096-0.05624.2220.0000.0000.0000.0000.0000.000
55A258MET0-0.043-0.02826.4540.0020.0020.0000.0000.0000.000
56A259SER00.0300.01629.4620.0060.0060.0000.0000.0000.000
57A260VAL0-0.0070.01023.1930.0060.0060.0000.0000.0000.000
58A261LEU0-0.006-0.01523.5720.0050.0050.0000.0000.0000.000
59A262GLN00.003-0.01826.5820.0080.0080.0000.0000.0000.000
60A263SER0-0.0490.00228.3190.0070.0070.0000.0000.0000.000
61A264VAL00.0180.01823.5370.0060.0060.0000.0000.0000.000
62A265TRP00.011-0.00124.9220.0000.0000.0000.0000.0000.000
63A266MET00.0060.02225.617-0.001-0.0010.0000.0000.0000.000
64A267GLU-1-0.857-0.93023.8160.0030.0030.0000.0000.0000.000
65A268VAL00.0090.00420.0400.0050.0050.0000.0000.0000.000
66A269LEU0-0.0190.00921.8910.0010.0010.0000.0000.0000.000
67A270VAL00.003-0.01624.2600.0050.0050.0000.0000.0000.000
68A271LEU0-0.007-0.00117.9130.0090.0090.0000.0000.0000.000
69A272GLY00.0010.00320.4010.0060.0060.0000.0000.0000.000
70A273VAL0-0.0030.00121.4060.0050.0050.0000.0000.0000.000
71A274ALA0-0.011-0.00622.4350.0060.0060.0000.0000.0000.000
72A275GLN0-0.004-0.00617.0290.0240.0240.0000.0000.0000.000
73A276ARG10.8630.93320.1120.0440.0440.0000.0000.0000.000
74A277SER0-0.006-0.01222.1950.0000.0000.0000.0000.0000.000
75A278LEU0-0.067-0.00718.7210.0100.0100.0000.0000.0000.000
76A279PRO0-0.047-0.02621.2310.0100.0100.0000.0000.0000.000
77A280LEU0-0.0030.02023.7240.0010.0010.0000.0000.0000.000
78A281GLN0-0.007-0.01927.1650.0060.0060.0000.0000.0000.000
79A282ASP-1-0.948-0.96329.9270.0440.0440.0000.0000.0000.000
80A283GLU-1-0.920-0.96930.2780.0170.0170.0000.0000.0000.000
81A284LEU0-0.052-0.02828.7090.0030.0030.0000.0000.0000.000
82A285ALA00.0400.01625.898-0.004-0.0040.0000.0000.0000.000
83A286PHE0-0.005-0.01826.343-0.003-0.0030.0000.0000.0000.000
84A287ALA0-0.002-0.01226.565-0.008-0.0080.0000.0000.0000.000
85A288GLU-1-0.913-0.95822.257-0.028-0.0280.0000.0000.0000.000
86A289ASP-1-0.847-0.90226.460-0.032-0.0320.0000.0000.0000.000
87A290LEU0-0.056-0.03429.7040.0010.0010.0000.0000.0000.000
88A291VAL00.0120.00129.1210.0000.0000.0000.0000.0000.000
89A292LEU0-0.048-0.01531.708-0.001-0.0010.0000.0000.0000.000
90A293ASP-1-0.745-0.85133.7300.0160.0160.0000.0000.0000.000
91A294GLU-1-0.922-0.98835.6090.0290.0290.0000.0000.0000.000
92A295GLU-1-0.976-0.97936.6230.0130.0130.0000.0000.0000.000
93A296GLY00.034-0.00539.032-0.002-0.0020.0000.0000.0000.000
94A297ALA0-0.036-0.01635.956-0.003-0.0030.0000.0000.0000.000
95A298ARG10.8770.92337.769-0.019-0.0190.0000.0000.0000.000
96A299ALA0-0.0030.00941.133-0.002-0.0020.0000.0000.0000.000
97A300ALA0-0.083-0.04538.834-0.002-0.0020.0000.0000.0000.000
98A301GLY0-0.020-0.01840.752-0.002-0.0020.0000.0000.0000.000
99A302LEU0-0.031-0.02035.301-0.002-0.0020.0000.0000.0000.000
100A303GLY00.0080.00438.4450.0020.0020.0000.0000.0000.000
101A304GLU-1-0.836-0.93138.2250.0210.0210.0000.0000.0000.000
102A305LEU0-0.041-0.01034.0360.0030.0030.0000.0000.0000.000
103A306GLY00.0580.03233.4670.0020.0020.0000.0000.0000.000
104A307ALA00.0980.05933.0710.0040.0040.0000.0000.0000.000
105A308ALA0-0.093-0.04733.0500.0050.0050.0000.0000.0000.000
106A309LEU00.0280.00128.4590.0050.0050.0000.0000.0000.000
107A310LEU00.0340.02428.5090.0070.0070.0000.0000.0000.000
108A311GLN0-0.088-0.02929.2080.0050.0050.0000.0000.0000.000
109A312LEU0-0.001-0.01123.9210.0100.0100.0000.0000.0000.000
110A313VAL00.0310.02124.6910.0110.0110.0000.0000.0000.000
111A314ARG11.0081.00724.673-0.045-0.0450.0000.0000.0000.000
112A315ARG10.8670.94924.391-0.098-0.0980.0000.0000.0000.000
113A316LEU00.014-0.00419.6820.0190.0190.0000.0000.0000.000
114A317GLN0-0.017-0.01220.8470.0210.0210.0000.0000.0000.000
115A318ALA0-0.059-0.01922.4490.0170.0170.0000.0000.0000.000
116A319LEU0-0.092-0.03818.8890.0220.0220.0000.0000.0000.000
117A320ARG10.9480.97517.691-0.178-0.1780.0000.0000.0000.000
118A321LEU0-0.0080.00914.9890.0410.0410.0000.0000.0000.000
119A322GLU-1-0.835-0.89810.8130.6060.6060.0000.0000.0000.000
120A323ARG10.9550.9699.9810.0810.0810.0000.0000.0000.000
121A324GLU-1-0.831-0.9335.5980.1220.1220.0000.0000.0000.000
122A325GLU-1-0.707-0.7788.5400.4160.4160.0000.0000.0000.000
123A326TYR0-0.021-0.00211.428-0.049-0.0490.0000.0000.0000.000
124A327VAL0-0.001-0.0028.954-0.016-0.0160.0000.0000.0000.000
125A328LEU00.0160.0138.273-0.029-0.0290.0000.0000.0000.000
126A329LEU0-0.029-0.00311.776-0.003-0.0030.0000.0000.0000.000
127A330LYS10.8670.93615.1440.1150.1150.0000.0000.0000.000
128A331ALA00.0050.00113.744-0.006-0.0060.0000.0000.0000.000
129A332LEU0-0.013-0.01414.5340.0020.0020.0000.0000.0000.000
130A333ALA0-0.036-0.02217.0690.0040.0040.0000.0000.0000.000
131A334LEU0-0.037-0.00818.7050.0010.0010.0000.0000.0000.000
132A335ALA00.001-0.00818.4570.0010.0010.0000.0000.0000.000
133A336ASN0-0.050-0.02220.4150.0070.0070.0000.0000.0000.000
134A337SER0-0.025-0.01722.7010.0100.0100.0000.0000.0000.000
135A338ASP-1-0.827-0.89825.6800.0040.0040.0000.0000.0000.000
136A339SER0-0.056-0.02728.9160.0040.0040.0000.0000.0000.000
137A340VAL0-0.002-0.02130.989-0.001-0.0010.0000.0000.0000.000
138A341HIS0-0.037-0.02633.0930.0000.0000.0000.0000.0000.000
139A342ILE0-0.047-0.00326.997-0.005-0.0050.0000.0000.0000.000
140A343GLU-1-0.978-1.00030.767-0.053-0.0530.0000.0000.0000.000
141A344ASP-1-0.895-0.95227.682-0.072-0.0720.0000.0000.0000.000
142A345ALA0-0.021-0.03327.032-0.005-0.0050.0000.0000.0000.000
143A346GLU-1-0.914-0.95426.166-0.042-0.0420.0000.0000.0000.000
144A347ALA0-0.0190.00723.610-0.007-0.0070.0000.0000.0000.000
145A348VAL0-0.017-0.01921.996-0.012-0.0120.0000.0000.0000.000
146A349GLU-1-0.948-0.96821.348-0.017-0.0170.0000.0000.0000.000
147A350GLN00.0040.00618.876-0.024-0.0240.0000.0000.0000.000
148A351LEU0-0.032-0.01115.968-0.017-0.0170.0000.0000.0000.000
149A352ARG10.9290.95916.4860.0000.0000.0000.0000.0000.000
150A353GLU-1-0.940-0.98716.9220.0160.0160.0000.0000.0000.000
151A354ALA00.0070.02513.4370.0200.0200.0000.0000.0000.000
152A355LEU0-0.021-0.02011.952-0.018-0.0180.0000.0000.0000.000
153A356HIS0-0.029-0.01812.4060.0720.0720.0000.0000.0000.000
154A357GLU-1-0.905-0.95111.4070.2680.2680.0000.0000.0000.000
155A358ALA0-0.011-0.0108.3860.1200.1200.0000.0000.0000.000
156A359LEU0-0.056-0.0258.1040.2430.2430.0000.0000.0000.000
157A360LEU0-0.073-0.0409.8950.1890.1890.0000.0000.0000.000
158A361GLU-1-0.862-0.9486.6350.3100.3100.0000.0000.0000.000
159A362TYR0-0.109-0.0704.7080.6110.728-0.001-0.007-0.1090.000
160A363GLH0-0.078-0.1036.3630.3180.3180.0000.0000.0000.000
161A364ALA0-0.132-0.0378.550-0.112-0.1120.0000.0000.0000.000
162A365GLY0-0.053-0.0187.613-0.129-0.1290.0000.0000.0000.000
163A374GLU-1-0.769-0.89911.8670.5880.5880.0000.0000.0000.000
164A375ARG11.0140.98113.558-0.338-0.3380.0000.0000.0000.000
165A376ARG10.8510.94815.257-0.592-0.5920.0000.0000.0000.000
166A377ARG10.7500.81713.723-0.434-0.4340.0000.0000.0000.000
167A378ALA00.1000.06013.928-0.041-0.0410.0000.0000.0000.000
168A379GLY00.0390.02215.439-0.051-0.0510.0000.0000.0000.000
169A380ARG10.8880.93618.982-0.291-0.2910.0000.0000.0000.000
170A381LEU00.0510.03813.919-0.031-0.0310.0000.0000.0000.000
171A382LEU00.0580.04217.211-0.034-0.0340.0000.0000.0000.000
172A383LEU0-0.056-0.02920.000-0.023-0.0230.0000.0000.0000.000
173A384THR0-0.104-0.06320.669-0.017-0.0170.0000.0000.0000.000
174A385LEU00.0710.02819.505-0.012-0.0120.0000.0000.0000.000
175A386PRO0-0.023-0.00223.330-0.012-0.0120.0000.0000.0000.000
176A387LEU0-0.0050.00426.426-0.006-0.0060.0000.0000.0000.000
177A388LEU00.0140.03521.537-0.005-0.0050.0000.0000.0000.000
178A389ARG10.8580.91425.557-0.010-0.0100.0000.0000.0000.000
179A390GLN0-0.047-0.02627.640-0.002-0.0020.0000.0000.0000.000
180A391THR0-0.053-0.05128.070-0.002-0.0020.0000.0000.0000.000
181A392ALA00.0310.01427.445-0.004-0.0040.0000.0000.0000.000
182A393GLY00.0380.01629.479-0.004-0.0040.0000.0000.0000.000
183A394LYS10.9110.94932.759-0.027-0.0270.0000.0000.0000.000
184A395VAL00.0400.00730.471-0.001-0.0010.0000.0000.0000.000
185A396LEU00.0110.01031.454-0.002-0.0020.0000.0000.0000.000
186A397ALA00.007-0.00334.544-0.001-0.0010.0000.0000.0000.000
187A398HIS0-0.041-0.00636.7980.0010.0010.0000.0000.0000.000
188A399PHE00.042-0.01134.027-0.001-0.0010.0000.0000.0000.000
189A400TYR00.0250.02637.929-0.002-0.0020.0000.0000.0000.000
190A401GLY00.005-0.01339.678-0.001-0.0010.0000.0000.0000.000
191A402VAL0-0.0070.00339.3420.0000.0000.0000.0000.0000.000
192A403LYS10.9360.98040.3930.0190.0190.0000.0000.0000.000
193A404LEU0-0.103-0.04542.791-0.001-0.0010.0000.0000.0000.000
194A405GLU-1-0.915-0.95044.666-0.009-0.0090.0000.0000.0000.000
195A406GLY0-0.0220.00246.0810.0000.0000.0000.0000.0000.000
196A407LYS10.8560.90846.8560.0080.0080.0000.0000.0000.000
197A408VAL0-0.0100.00740.786-0.001-0.0010.0000.0000.0000.000
198A409PRO0-0.0220.00241.894-0.001-0.0010.0000.0000.0000.000
199A410MET00.028-0.00138.1970.0000.0000.0000.0000.0000.000
200A411HIS0-0.050-0.02336.187-0.003-0.0030.0000.0000.0000.000
201A412LYS10.9210.96834.1090.0610.0610.0000.0000.0000.000
202A413LEU00.0000.00630.3940.0010.0010.0000.0000.0000.000
203A414PHE00.0600.01532.7040.0020.0020.0000.0000.0000.000
204A415LEU0-0.020-0.01234.5310.0030.0030.0000.0000.0000.000
205A416GLU-1-0.953-0.97435.127-0.051-0.0510.0000.0000.0000.000
206A417MET0-0.032-0.03729.5040.0010.0010.0000.0000.0000.000
207A418LEU0-0.090-0.03533.8760.0030.0030.0000.0000.0000.000
208A419GLU-1-0.976-0.99435.791-0.023-0.0230.0000.0000.0000.000
209A420ALA0-0.0620.00534.2090.0020.0020.0000.0000.0000.000