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: 5J93Z

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 OptAll
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 -2426107.60271
FMO2-HF: Nuclear repulsion 2345511.23719
FMO2-HF: Total energy -80596.36552
FMO2-MP2: Total energy -80833.033824


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.
-4.055-0.30.908-1.9-2.762-0.004
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 : 0.022 / q_NPA : 0.010
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].
3A196ALA00.0230.0123.214-1.7860.6910.082-1.304-1.2540.001
4A197LEU00.0310.0215.0410.3600.468-0.001-0.003-0.1040.000
5A198VAL00.0280.0054.5450.1660.313-0.001-0.008-0.1380.000
6A199SER0-0.025-0.0272.544-0.4710.3280.830-0.565-1.064-0.005
7A200HIS0-0.044-0.0244.9430.2410.287-0.001-0.007-0.0380.000
8A201LEU00.000-0.0138.4690.1830.1830.0000.0000.0000.000
9A202LEU0-0.059-0.0315.1010.1420.1420.0000.0000.0000.000
10A203VAL0-0.034-0.0158.5080.1100.1100.0000.0000.0000.000
11A204VAL0-0.024-0.00911.0090.0590.0590.0000.0000.0000.000
12A205GLU-1-0.842-0.90512.811-0.113-0.1130.0000.0000.0000.000
13A206PRO0-0.057-0.03114.4590.0160.0160.0000.0000.0000.000
14A207GLU-1-0.889-0.94517.523-0.039-0.0390.0000.0000.0000.000
15A208LYS10.7480.87019.180-0.042-0.0420.0000.0000.0000.000
16A209LEU0-0.0200.00521.358-0.005-0.0050.0000.0000.0000.000
17A210TYR00.0010.00324.2640.0100.0100.0000.0000.0000.000
18A211ALA00.0610.01627.981-0.009-0.0090.0000.0000.0000.000
19A212MET0-0.0540.03431.407-0.004-0.0040.0000.0000.0000.000
20A223PRO00.0600.00441.4240.0010.0010.0000.0000.0000.000
21A224ALA0-0.0060.02338.312-0.002-0.0020.0000.0000.0000.000
22A225VAL00.0640.03237.528-0.002-0.0020.0000.0000.0000.000
23A226ALA00.0460.02537.733-0.003-0.0030.0000.0000.0000.000
24A227THR0-0.028-0.02234.704-0.003-0.0030.0000.0000.0000.000
25A228LEU0-0.0080.00231.941-0.002-0.0020.0000.0000.0000.000
26A229CYS0-0.043-0.00933.142-0.005-0.0050.0000.0000.0000.000
27A230ASP-1-0.822-0.93234.247-0.041-0.0410.0000.0000.0000.000
28A231LEU0-0.027-0.01528.672-0.005-0.0050.0000.0000.0000.000
29A232PHE00.021-0.00129.297-0.005-0.0050.0000.0000.0000.000
30A233ASP-1-0.764-0.86529.685-0.072-0.0720.0000.0000.0000.000
31A234ARG10.8180.87228.3410.0330.0330.0000.0000.0000.000
32A235GLU-1-0.762-0.87624.149-0.058-0.0580.0000.0000.0000.000
33A236ILE0-0.0030.03125.199-0.013-0.0130.0000.0000.0000.000
34A237VAL0-0.004-0.00526.335-0.013-0.0130.0000.0000.0000.000
35A238VAL0-0.0090.00021.684-0.013-0.0130.0000.0000.0000.000
36A239THR0-0.005-0.00221.926-0.021-0.0210.0000.0000.0000.000
37A240ILE00.007-0.00222.153-0.021-0.0210.0000.0000.0000.000
38A241SER0-0.095-0.05322.266-0.016-0.0160.0000.0000.0000.000
39A242TRP00.0320.01715.013-0.016-0.0160.0000.0000.0000.000
40A243ALA00.0420.01617.868-0.036-0.0360.0000.0000.0000.000
41A244LYS10.9380.96519.1170.1560.1560.0000.0000.0000.000
42A245SER0-0.026-0.00716.272-0.011-0.0110.0000.0000.0000.000
43A246ILE0-0.0030.00614.265-0.068-0.0680.0000.0000.0000.000
44A247PRO0-0.037-0.02611.7290.0360.0360.0000.0000.0000.000
45A248GLY00.0610.03715.037-0.012-0.0120.0000.0000.0000.000
46A249PHE00.0560.04018.0660.0430.0430.0000.0000.0000.000
47A250SER0-0.044-0.04720.0070.0350.0350.0000.0000.0000.000
48A251SER0-0.142-0.07621.1950.0060.0060.0000.0000.0000.000
49A252LEU00.0490.04322.7210.0120.0120.0000.0000.0000.000
50A253SER00.0150.00225.1430.0020.0020.0000.0000.0000.000
51A254LEU0-0.001-0.02228.143-0.002-0.0020.0000.0000.0000.000
52A255SER0-0.002-0.02829.8410.0030.0030.0000.0000.0000.000
53A256ASP-1-0.721-0.85227.164-0.157-0.1570.0000.0000.0000.000
54A257GLN0-0.076-0.04424.5380.0030.0030.0000.0000.0000.000
55A258MET0-0.025-0.01526.7980.0040.0040.0000.0000.0000.000
56A259SER00.0100.00029.8590.0080.0080.0000.0000.0000.000
57A260VAL00.0080.02423.6140.0080.0080.0000.0000.0000.000
58A261LEU0-0.014-0.01324.0020.0080.0080.0000.0000.0000.000
59A262GLN0-0.035-0.04427.0630.0080.0080.0000.0000.0000.000
60A263SER0-0.028-0.01329.0320.0070.0070.0000.0000.0000.000
61A264VAL00.0020.01023.9750.0060.0060.0000.0000.0000.000
62A265TRP00.0150.00325.1610.0010.0010.0000.0000.0000.000
63A266MET0-0.0100.01825.6870.0040.0040.0000.0000.0000.000
64A267GLU-1-0.829-0.90823.830-0.083-0.0830.0000.0000.0000.000
65A268VAL00.0150.00420.1220.0060.0060.0000.0000.0000.000
66A269LEU00.0070.01621.8300.0070.0070.0000.0000.0000.000
67A270VAL0-0.010-0.01324.3350.0120.0120.0000.0000.0000.000
68A271LEU00.008-0.00118.1090.0140.0140.0000.0000.0000.000
69A272GLY0-0.0040.00820.4780.0110.0110.0000.0000.0000.000
70A273VAL00.0140.00421.4980.0150.0150.0000.0000.0000.000
71A274ALA0-0.0170.00122.6190.0130.0130.0000.0000.0000.000
72A275GLN0-0.002-0.01216.5770.0180.0180.0000.0000.0000.000
73A276ARG10.7400.83820.0940.0440.0440.0000.0000.0000.000
74A277SER00.013-0.00622.0090.0070.0070.0000.0000.0000.000
75A278LEU0-0.053-0.01318.7120.0090.0090.0000.0000.0000.000
76A279PRO0-0.045-0.01921.0780.0130.0130.0000.0000.0000.000
77A280LEU0-0.0020.02623.5020.0040.0040.0000.0000.0000.000
78A281GLN0-0.053-0.05227.2130.0130.0130.0000.0000.0000.000
79A282ASP-1-0.856-0.91129.9170.0510.0510.0000.0000.0000.000
80A283GLU-1-0.895-0.94930.2460.0460.0460.0000.0000.0000.000
81A284LEU0-0.053-0.03328.5800.0020.0020.0000.0000.0000.000
82A285ALA00.0380.02125.608-0.004-0.0040.0000.0000.0000.000
83A286PHE00.018-0.00926.258-0.006-0.0060.0000.0000.0000.000
84A287ALA0-0.010-0.00126.458-0.010-0.0100.0000.0000.0000.000
85A288GLU-1-0.805-0.88721.9790.0430.0430.0000.0000.0000.000
86A289ASP-1-0.846-0.91526.3200.0080.0080.0000.0000.0000.000
87A290LEU0-0.067-0.03029.637-0.002-0.0020.0000.0000.0000.000
88A291VAL00.0240.01028.846-0.002-0.0020.0000.0000.0000.000
89A292LEU0-0.055-0.01731.475-0.002-0.0020.0000.0000.0000.000
90A293ASP-1-0.741-0.86033.2080.0270.0270.0000.0000.0000.000
91A294GLU-1-0.808-0.91534.8840.0250.0250.0000.0000.0000.000
92A295GLU-1-0.997-0.98336.4560.0180.0180.0000.0000.0000.000
93A296GLY00.0460.00538.469-0.004-0.0040.0000.0000.0000.000
94A297ALA0-0.021-0.02135.507-0.004-0.0040.0000.0000.0000.000
95A298ARG10.8300.89037.486-0.013-0.0130.0000.0000.0000.000
96A299ALA0-0.012-0.00540.885-0.003-0.0030.0000.0000.0000.000
97A300ALA0-0.047-0.01738.606-0.002-0.0020.0000.0000.0000.000
98A301GLY0-0.011-0.00740.588-0.003-0.0030.0000.0000.0000.000
99A302LEU0-0.039-0.01835.152-0.004-0.0040.0000.0000.0000.000
100A303GLY00.0400.01138.2130.0000.0000.0000.0000.0000.000
101A304GLU-1-0.830-0.89637.7880.0140.0140.0000.0000.0000.000
102A305LEU0-0.007-0.00433.9320.0000.0000.0000.0000.0000.000
103A306GLY00.0420.03233.4140.0010.0010.0000.0000.0000.000
104A307ALA00.0630.02633.0700.0020.0020.0000.0000.0000.000
105A308ALA0-0.071-0.03533.2080.0020.0020.0000.0000.0000.000
106A309LEU00.0190.00628.457-0.001-0.0010.0000.0000.0000.000
107A310LEU00.0400.02228.4380.0040.0040.0000.0000.0000.000
108A311GLN0-0.076-0.03029.3650.0040.0040.0000.0000.0000.000
109A312LEU0-0.009-0.00623.6940.0050.0050.0000.0000.0000.000
110A313VAL00.0140.01824.6390.0060.0060.0000.0000.0000.000
111A314ARG10.8260.89924.740-0.028-0.0280.0000.0000.0000.000
112A315ARG10.8110.90824.054-0.019-0.0190.0000.0000.0000.000
113A316LEU00.010-0.00419.6020.0100.0100.0000.0000.0000.000
114A317GLN0-0.025-0.02921.0030.0160.0160.0000.0000.0000.000
115A318ALA0-0.033-0.00422.4440.0210.0210.0000.0000.0000.000
116A319LEU0-0.049-0.02519.0300.0200.0200.0000.0000.0000.000
117A320ARG10.8670.93718.118-0.181-0.1810.0000.0000.0000.000
118A321LEU0-0.0130.01715.0350.0410.0410.0000.0000.0000.000
119A322GLU-1-0.835-0.89410.1040.7350.7350.0000.0000.0000.000
120A323ARG10.9130.96610.214-0.025-0.0250.0000.0000.0000.000
121A324GLU-1-0.820-0.9325.9360.2480.2480.0000.0000.0000.000
122A325GLU-1-0.695-0.7848.5050.1230.1230.0000.0000.0000.000
123A326TYR0-0.0070.00411.364-0.077-0.0770.0000.0000.0000.000
124A327VAL0-0.012-0.0069.266-0.028-0.0280.0000.0000.0000.000
125A328LEU00.0000.0118.254-0.040-0.0400.0000.0000.0000.000
126A329LEU0-0.031-0.01211.979-0.008-0.0080.0000.0000.0000.000
127A330LYS10.8330.90015.3720.1370.1370.0000.0000.0000.000
128A331ALA00.0210.00813.9770.0050.0050.0000.0000.0000.000
129A332LEU0-0.027-0.01315.1200.0060.0060.0000.0000.0000.000
130A333ALA0-0.022-0.01917.1890.0150.0150.0000.0000.0000.000
131A334LEU0-0.037-0.01019.1220.0100.0100.0000.0000.0000.000
132A335ALA0-0.014-0.00818.6800.0080.0080.0000.0000.0000.000
133A336ASN0-0.021-0.00720.666-0.007-0.0070.0000.0000.0000.000
134A337SER00.0090.01623.1890.0230.0230.0000.0000.0000.000
135A338ASP-1-0.865-0.91726.134-0.122-0.1220.0000.0000.0000.000
136A339SER0-0.049-0.02429.1260.0130.0130.0000.0000.0000.000
137A340VAL0-0.002-0.02131.313-0.005-0.0050.0000.0000.0000.000
138A341HIS0-0.021-0.00333.3480.0000.0000.0000.0000.0000.000
139A342ILE0-0.0280.00627.644-0.004-0.0040.0000.0000.0000.000
140A343GLU-1-0.899-0.90130.830-0.122-0.1220.0000.0000.0000.000
141A344ASP-1-0.885-0.95027.898-0.193-0.1930.0000.0000.0000.000
142A345ALA00.012-0.01427.196-0.014-0.0140.0000.0000.0000.000
143A346GLU-1-0.925-0.95226.474-0.181-0.1810.0000.0000.0000.000
144A347ALA0-0.014-0.00523.701-0.025-0.0250.0000.0000.0000.000
145A348VAL0-0.025-0.01922.261-0.030-0.0300.0000.0000.0000.000
146A349GLU-1-0.848-0.89521.913-0.196-0.1960.0000.0000.0000.000
147A350GLN0-0.005-0.00819.607-0.046-0.0460.0000.0000.0000.000
148A351LEU0-0.025-0.00516.542-0.052-0.0520.0000.0000.0000.000
149A352ARG10.8080.88017.0180.1490.1490.0000.0000.0000.000
150A353GLU-1-0.942-0.97917.013-0.292-0.2920.0000.0000.0000.000
151A354ALA0-0.009-0.00114.273-0.049-0.0490.0000.0000.0000.000
152A355LEU0-0.025-0.01712.369-0.130-0.1300.0000.0000.0000.000
153A356HIS0-0.009-0.00712.3540.0060.0060.0000.0000.0000.000
154A357GLU-1-0.891-0.94911.209-0.446-0.4460.0000.0000.0000.000
155A358ALA0-0.0150.0008.559-0.093-0.0930.0000.0000.0000.000
156A359LEU0-0.034-0.0157.785-0.017-0.0170.0000.0000.0000.000
157A360LEU0-0.062-0.0439.5810.1860.1860.0000.0000.0000.000
158A361GLU-1-0.866-0.9385.523-2.533-2.5330.0000.0000.0000.000
159A362TYR0-0.093-0.0614.2790.1120.290-0.001-0.013-0.1640.000
160A363GLH0-0.069-0.0736.0480.5890.5890.0000.0000.0000.000
161A364ALA0-0.064-0.0227.3680.0660.0660.0000.0000.0000.000
162A365GLY0-0.059-0.0146.538-0.010-0.0100.0000.0000.0000.000
163A374GLU-1-0.730-0.83910.9060.0220.0220.0000.0000.0000.000
164A375ARG10.9480.95512.8710.0780.0780.0000.0000.0000.000
165A376ARG10.8470.89613.625-0.291-0.2910.0000.0000.0000.000
166A377ARG10.7150.82313.573-0.275-0.2750.0000.0000.0000.000
167A378ALA00.1130.04913.654-0.012-0.0120.0000.0000.0000.000
168A379GLY00.0310.01315.330-0.022-0.0220.0000.0000.0000.000
169A380ARG10.8680.93018.806-0.133-0.1330.0000.0000.0000.000
170A381LEU00.0600.04113.997-0.005-0.0050.0000.0000.0000.000
171A382LEU00.0620.05117.668-0.006-0.0060.0000.0000.0000.000
172A383LEU0-0.029-0.01319.968-0.002-0.0020.0000.0000.0000.000
173A384THR0-0.081-0.05420.6560.0080.0080.0000.0000.0000.000
174A385LEU00.0840.04519.6270.0030.0030.0000.0000.0000.000
175A386PRO00.0070.00323.594-0.001-0.0010.0000.0000.0000.000
176A387LEU0-0.035-0.00926.7100.0010.0010.0000.0000.0000.000
177A388LEU00.0060.02221.9660.0050.0050.0000.0000.0000.000
178A389ARG10.8340.88025.8220.1010.1010.0000.0000.0000.000
179A390GLN0-0.021-0.00928.1270.0050.0050.0000.0000.0000.000
180A391THR0-0.022-0.03928.6950.0040.0040.0000.0000.0000.000
181A392ALA00.0350.01727.7560.0020.0020.0000.0000.0000.000
182A393GLY00.0430.02429.831-0.001-0.0010.0000.0000.0000.000
183A394LYS10.8290.92232.0980.0110.0110.0000.0000.0000.000
184A395VAL00.0310.00730.7440.0020.0020.0000.0000.0000.000
185A396LEU00.0280.01531.6410.0010.0010.0000.0000.0000.000
186A397ALA00.0040.00134.7670.0010.0010.0000.0000.0000.000
187A398HIS0-0.016-0.00236.8950.0040.0040.0000.0000.0000.000
188A399PHE00.009-0.02234.7790.0020.0020.0000.0000.0000.000
189A400TYR0-0.005-0.01338.0180.0010.0010.0000.0000.0000.000
190A401GLY00.0020.00040.0680.0010.0010.0000.0000.0000.000
191A402VAL0-0.039-0.02739.5310.0010.0010.0000.0000.0000.000
192A403LYS10.8120.90340.1060.0420.0420.0000.0000.0000.000
193A404LEU0-0.047-0.01342.7860.0000.0000.0000.0000.0000.000
194A405GLU-1-0.831-0.89145.051-0.014-0.0140.0000.0000.0000.000
195A406GLY0-0.0010.00946.2490.0020.0020.0000.0000.0000.000
196A407LYS10.7300.83447.1230.0140.0140.0000.0000.0000.000
197A408VAL0-0.0190.00440.7540.0010.0010.0000.0000.0000.000
198A409PRO0-0.0150.00542.419-0.002-0.0020.0000.0000.0000.000
199A410MET00.004-0.00538.178-0.001-0.0010.0000.0000.0000.000
200A411HIS00.0050.00136.055-0.005-0.0050.0000.0000.0000.000
201A412LYS10.7720.86934.6780.0610.0610.0000.0000.0000.000
202A413LEU00.0290.02930.685-0.001-0.0010.0000.0000.0000.000
203A414PHE00.0660.00032.543-0.001-0.0010.0000.0000.0000.000
204A415LEU0-0.007-0.00434.5910.0010.0010.0000.0000.0000.000
205A416GLU-1-0.930-0.96534.994-0.082-0.0820.0000.0000.0000.000
206A417MET00.000-0.01229.148-0.002-0.0020.0000.0000.0000.000
207A418LEU0-0.046-0.01333.9480.0000.0000.0000.0000.0000.000
208A419GLU-1-0.839-0.90036.242-0.043-0.0430.0000.0000.0000.000
209A420ALA0-0.089-0.02334.535-0.002-0.0020.0000.0000.0000.000