Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5N9JZ

Calculation Name: 1EBA-A-Xray372

Preferred Name: Erythropoietin receptor

Target Type: SINGLE PROTEIN

Ligand Name: 3,5 dibromotyrosine

ligand 3-letter code: DBY

PDB ID: 1EBA

Chain ID: A

ChEMBL ID: CHEMBL1817

UniProt ID: P19235

Base Structure: X-ray

Registration Date: 2023-09-26

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

DOI:


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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240516.808626
FMO2-HF: Nuclear repulsion 2157368.92814
FMO2-HF: Total energy -83147.880486
FMO2-MP2: Total energy -83390.561348


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:10:LYS)


Summations of interaction energy for fragment #1(A:10:LYS)
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.
6.3068.3867.831-3.889-6.021-0.018
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.030 / q_NPA : 1.002
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].
3A12GLU-1-0.829-0.9253.378-26.032-23.9380.004-0.844-1.2540.002
4A13SER0-0.0030.0002.336-2.370-1.6813.935-2.109-2.514-0.018
5A14LYS10.9220.9441.84764.78264.0793.892-0.936-2.253-0.002
6A15ALA00.0040.0125.7532.9562.9560.0000.0000.0000.000
7A16ALA00.0290.0187.7012.5282.5280.0000.0000.0000.000
8A17LEU0-0.080-0.0467.5641.4581.4580.0000.0000.0000.000
9A18LEU0-0.030-0.0189.3541.3401.3400.0000.0000.0000.000
10A19ALA0-0.0210.02512.2481.4271.4270.0000.0000.0000.000
11A20ALA0-0.030-0.02114.2670.3210.3210.0000.0000.0000.000
12A21ARG10.9650.99017.08315.76215.7620.0000.0000.0000.000
13A22GLY00.005-0.00219.3290.2010.2010.0000.0000.0000.000
14A23PRO0-0.027-0.02423.074-0.245-0.2450.0000.0000.0000.000
15A24GLU-1-0.940-0.96323.247-11.718-11.7180.0000.0000.0000.000
16A25GLU-1-0.899-0.96123.927-9.933-9.9330.0000.0000.0000.000
17A26LEU0-0.0390.00324.491-0.325-0.3250.0000.0000.0000.000
18A27LEU00.0050.00220.3800.2360.2360.0000.0000.0000.000
19A28CYS0-0.063-0.02924.1510.0340.0340.0000.0000.0000.000
20A29PHE0-0.034-0.01319.369-0.095-0.0950.0000.0000.0000.000
21A30THR00.0150.02924.1900.1000.1000.0000.0000.0000.000
22A31GLU-1-0.916-0.97720.106-12.547-12.5470.0000.0000.0000.000
23A32ARG10.8410.91821.46311.13711.1370.0000.0000.0000.000
24A33LEU0-0.050-0.02526.5260.0350.0350.0000.0000.0000.000
25A34GLU-1-0.968-0.97429.090-8.492-8.4920.0000.0000.0000.000
26A35ASP-1-0.788-0.89425.881-10.253-10.2530.0000.0000.0000.000
27A36LEU00.034-0.01026.8220.0750.0750.0000.0000.0000.000
28A37VAL0-0.0160.00022.2350.0840.0840.0000.0000.0000.000
29A39PHE0-0.029-0.04118.858-0.218-0.2180.0000.0000.0000.000
30A40TRP0-0.0100.01222.9390.2580.2580.0000.0000.0000.000
31A41GLU-1-0.926-0.99517.255-15.999-15.9990.0000.0000.0000.000
32A42GLU-1-0.762-0.87821.659-10.651-10.6510.0000.0000.0000.000
33A43ALA0-0.024-0.01521.828-0.642-0.6420.0000.0000.0000.000
34A44ALA00.0280.01622.3240.3560.3560.0000.0000.0000.000
35A45SER00.031-0.00524.0110.3980.3980.0000.0000.0000.000
36A46ALA0-0.0130.00027.6840.0760.0760.0000.0000.0000.000
37A47GLY0-0.014-0.01128.9850.2560.2560.0000.0000.0000.000
38A48VAL0-0.0230.00328.0960.3530.3530.0000.0000.0000.000
39A49GLY00.0210.02427.852-0.423-0.4230.0000.0000.0000.000
40A50PRO00.003-0.01527.1760.1890.1890.0000.0000.0000.000
41A51GLY0-0.018-0.00229.3250.2120.2120.0000.0000.0000.000
42A52ASN0-0.026-0.01131.7520.1510.1510.0000.0000.0000.000
43A53TYR0-0.026-0.01328.8750.3170.3170.0000.0000.0000.000
44A54SER0-0.0120.00433.0190.0550.0550.0000.0000.0000.000
45A55PHE00.0360.00929.012-0.004-0.0040.0000.0000.0000.000
46A56SER0-0.022-0.02333.4140.0230.0230.0000.0000.0000.000
47A57TYR0-0.056-0.04534.579-0.200-0.2000.0000.0000.0000.000
48A58GLN00.0590.04536.7020.1710.1710.0000.0000.0000.000
49A59LEU00.017-0.02537.010-0.210-0.2100.0000.0000.0000.000
50A60GLU-1-0.894-0.94639.710-6.633-6.6330.0000.0000.0000.000
51A61ASP-1-0.927-0.96442.449-6.072-6.0720.0000.0000.0000.000
52A62GLU-1-0.998-0.97442.287-6.716-6.7160.0000.0000.0000.000
53A63PRO0-0.054-0.02843.781-0.040-0.0400.0000.0000.0000.000
54A64TRP0-0.028-0.00638.050-0.234-0.2340.0000.0000.0000.000
55A65LYS10.8920.95738.3877.5177.5170.0000.0000.0000.000
56A66LEU0-0.016-0.01935.473-0.118-0.1180.0000.0000.0000.000
57A67CYS0-0.0070.02024.7120.1020.1020.0000.0000.0000.000
58A68ARG10.9430.96830.9039.0809.0800.0000.0000.0000.000
59A69LEU00.0170.01527.451-0.227-0.2270.0000.0000.0000.000
60A70HIS0-0.039-0.01224.5310.2150.2150.0000.0000.0000.000
61A71GLN00.0320.00222.7210.2290.2290.0000.0000.0000.000
62A72ALA0-0.036-0.00718.310-0.107-0.1070.0000.0000.0000.000
63A73PRO00.0170.01615.8980.1470.1470.0000.0000.0000.000
64A74THR0-0.002-0.04614.060-0.682-0.6820.0000.0000.0000.000
65A75ALA00.010-0.0079.269-0.162-0.1620.0000.0000.0000.000
66A76ARG10.9240.96211.35615.64015.6400.0000.0000.0000.000
67A77GLY0-0.023-0.00213.3910.6820.6820.0000.0000.0000.000
68A78ALA0-0.0330.00116.2720.9410.9410.0000.0000.0000.000
69A79VAL00.0060.03417.727-0.742-0.7420.0000.0000.0000.000
70A80ARG10.9290.97514.70215.94415.9440.0000.0000.0000.000
71A81PHE0-0.030-0.01620.874-0.029-0.0290.0000.0000.0000.000
72A82TRP00.022-0.00321.5330.0110.0110.0000.0000.0000.000
73A84SER0-0.010-0.00225.644-0.136-0.1360.0000.0000.0000.000
74A85LEU0-0.005-0.00127.4800.1640.1640.0000.0000.0000.000
75A86PRO0-0.032-0.00630.395-0.153-0.1530.0000.0000.0000.000
76A87THR00.0840.02631.8440.1250.1250.0000.0000.0000.000
77A88ALA0-0.054-0.02733.3340.0390.0390.0000.0000.0000.000
78A89ASP-1-0.819-0.89435.169-7.467-7.4670.0000.0000.0000.000
79A90THR0-0.045-0.04730.933-0.149-0.1490.0000.0000.0000.000
80A91SER00.0460.02133.725-0.048-0.0480.0000.0000.0000.000
81A92SER0-0.026-0.02433.300-0.137-0.1370.0000.0000.0000.000
82A93PHE0-0.031-0.01634.864-0.054-0.0540.0000.0000.0000.000
83A94VAL0-0.0120.02737.4210.1030.1030.0000.0000.0000.000
84A95PRO0-0.044-0.02136.926-0.196-0.1960.0000.0000.0000.000
85A96LEU00.0440.02432.6370.0980.0980.0000.0000.0000.000
86A97GLU-1-0.895-0.94535.276-7.443-7.4430.0000.0000.0000.000
87A98LEU0-0.010-0.01830.447-0.071-0.0710.0000.0000.0000.000
88A99ARG10.8650.92134.4697.5547.5540.0000.0000.0000.000
89A100VAL00.0350.03030.511-0.068-0.0680.0000.0000.0000.000
90A101THR0-0.037-0.01833.8250.0140.0140.0000.0000.0000.000
91A102ALA00.0410.02534.561-0.177-0.1770.0000.0000.0000.000
92A103ALA00.0340.00035.4470.2290.2290.0000.0000.0000.000
93A104SER0-0.089-0.03637.8170.1770.1770.0000.0000.0000.000
94A105GLY00.0100.00439.6570.1610.1610.0000.0000.0000.000
95A106ALA0-0.019-0.00537.6320.0370.0370.0000.0000.0000.000
96A107PRO00.0240.00336.907-0.184-0.1840.0000.0000.0000.000
97A108ARG10.8910.95427.79110.01510.0150.0000.0000.0000.000
98A109TYR00.011-0.00326.567-0.152-0.1520.0000.0000.0000.000
99A110HIS0-0.041-0.01932.8100.3690.3690.0000.0000.0000.000
100A111ARG10.8920.93826.5909.6599.6590.0000.0000.0000.000
101A112VAL00.0280.02233.4520.0300.0300.0000.0000.0000.000
102A113ILE0-0.032-0.01029.579-0.113-0.1130.0000.0000.0000.000
103A114HIS00.0590.04232.3550.0730.0730.0000.0000.0000.000
104A115ILE00.0500.02229.432-0.207-0.2070.0000.0000.0000.000
105A116ASN00.0110.00229.373-0.284-0.2840.0000.0000.0000.000
106A117GLU-1-0.919-0.97030.161-8.385-8.3850.0000.0000.0000.000
107A118VAL0-0.090-0.03325.755-0.246-0.2460.0000.0000.0000.000
108A119VAL00.0390.01024.554-0.249-0.2490.0000.0000.0000.000
109A120LEU0-0.083-0.03817.486-0.187-0.1870.0000.0000.0000.000
110A121LEU00.0060.00720.507-0.207-0.2070.0000.0000.0000.000
111A122ASP-1-0.799-0.87617.872-13.134-13.1340.0000.0000.0000.000
112A123ALA0-0.061-0.04515.0660.3510.3510.0000.0000.0000.000
113A124PRO0-0.025-0.01617.1500.2360.2360.0000.0000.0000.000
114A125VAL00.0330.01417.797-0.669-0.6690.0000.0000.0000.000
115A126GLY0-0.010-0.00919.7370.4120.4120.0000.0000.0000.000
116A127LEU00.0000.01317.7480.4520.4520.0000.0000.0000.000
117A128VAL0-0.021-0.00620.402-0.301-0.3010.0000.0000.0000.000
118A129ALA0-0.010-0.02222.5370.1330.1330.0000.0000.0000.000
119A130ARG10.9490.97924.3248.8738.8730.0000.0000.0000.000
120A131LEU00.006-0.00427.617-0.125-0.1250.0000.0000.0000.000
121A132ALA0-0.060-0.02230.3490.1090.1090.0000.0000.0000.000
122A133ASP-1-0.902-0.94833.543-7.970-7.9700.0000.0000.0000.000
123A134GLU-1-0.938-0.97036.474-7.511-7.5110.0000.0000.0000.000
124A135SER0-0.046-0.03835.588-0.150-0.1500.0000.0000.0000.000
125A136GLY00.0580.04133.607-0.042-0.0420.0000.0000.0000.000
126A137HIS0-0.032-0.02231.247-0.410-0.4100.0000.0000.0000.000
127A138VAL00.0010.01624.713-0.038-0.0380.0000.0000.0000.000
128A139VAL0-0.026-0.01528.1500.0660.0660.0000.0000.0000.000
129A140LEU0-0.029-0.02922.085-0.230-0.2300.0000.0000.0000.000
130A141ARG10.9290.96324.9179.1309.1300.0000.0000.0000.000
131A142TRP00.0050.00422.177-0.437-0.4370.0000.0000.0000.000
132A143LEU0-0.0020.00123.3370.4720.4720.0000.0000.0000.000
133A144PRO00.0150.00322.972-0.369-0.3690.0000.0000.0000.000
134A145PRO00.0080.01920.963-0.078-0.0780.0000.0000.0000.000
135A146PRO00.026-0.00520.7170.4320.4320.0000.0000.0000.000
136A147GLU-1-0.956-0.97823.614-10.247-10.2470.0000.0000.0000.000
137A148THR00.0230.01724.427-0.059-0.0590.0000.0000.0000.000
138A149PRO0-0.017-0.00326.9040.1590.1590.0000.0000.0000.000
139A150MET00.007-0.00829.455-0.061-0.0610.0000.0000.0000.000
140A151THR00.0830.02928.6140.0310.0310.0000.0000.0000.000
141A152SER0-0.056-0.03429.632-0.166-0.1660.0000.0000.0000.000
142A153HIS00.0470.02331.2280.0620.0620.0000.0000.0000.000
143A154ILE0-0.0030.01524.755-0.117-0.1170.0000.0000.0000.000
144A155ARG10.9780.99926.0649.4529.4520.0000.0000.0000.000
145A156TYR00.000-0.02222.195-0.443-0.4430.0000.0000.0000.000
146A157GLU-1-0.851-0.93520.376-11.520-11.5200.0000.0000.0000.000
147A158VAL0-0.027-0.01320.133-0.437-0.4370.0000.0000.0000.000
148A159ASP-1-0.880-0.93416.025-14.131-14.1310.0000.0000.0000.000
149A160VAL0-0.021-0.01418.465-0.127-0.1270.0000.0000.0000.000
150A161SER00.0290.02316.197-0.143-0.1430.0000.0000.0000.000
151A162ALA00.008-0.01618.1350.2120.2120.0000.0000.0000.000
152A163GLY0-0.001-0.00417.652-0.388-0.3880.0000.0000.0000.000
153A164ASN0-0.079-0.06518.6730.0150.0150.0000.0000.0000.000
154A165GLY00.0590.04020.983-0.104-0.1040.0000.0000.0000.000
155A166ALA00.0020.01918.8720.1770.1770.0000.0000.0000.000
156A167GLY0-0.013-0.02119.9100.5500.5500.0000.0000.0000.000
157A168SER0-0.064-0.02521.674-0.046-0.0460.0000.0000.0000.000
158A169VAL00.0420.02119.817-0.296-0.2960.0000.0000.0000.000
159A170GLN00.0020.01121.0040.3380.3380.0000.0000.0000.000
160A171ARG10.8880.92815.53713.37213.3720.0000.0000.0000.000
161A172VAL0-0.0220.00522.5220.3390.3390.0000.0000.0000.000
162A173GLU-1-0.897-0.94024.336-9.363-9.3630.0000.0000.0000.000
163A174ILE0-0.056-0.02925.2720.2040.2040.0000.0000.0000.000
164A175LEU00.0220.00127.815-0.033-0.0330.0000.0000.0000.000
165A176GLU-1-0.845-0.94129.330-8.455-8.4550.0000.0000.0000.000
166A177GLY0-0.038-0.00729.5420.2970.2970.0000.0000.0000.000
167A178ARG10.8380.92830.4258.0088.0080.0000.0000.0000.000
168A179THR0-0.0040.00626.534-0.090-0.0900.0000.0000.0000.000
169A180GLU-1-0.928-0.97627.145-8.739-8.7390.0000.0000.0000.000
170A181CYS0-0.040-0.01225.1870.1220.1220.0000.0000.0000.000
171A182VAL00.0090.02727.518-0.202-0.2020.0000.0000.0000.000
172A183LEU00.0060.00324.1500.0750.0750.0000.0000.0000.000
173A184SER00.038-0.00628.7390.0100.0100.0000.0000.0000.000
174A185ASN0-0.033-0.00227.8820.0550.0550.0000.0000.0000.000
175A186LEU0-0.033-0.01325.202-0.213-0.2130.0000.0000.0000.000
176A187ARG10.9710.99225.23711.32211.3220.0000.0000.0000.000
177A188GLY00.0990.05328.359-0.180-0.1800.0000.0000.0000.000
178A189ARG10.9110.96528.5889.3079.3070.0000.0000.0000.000
179A190THR0-0.051-0.04123.325-0.242-0.2420.0000.0000.0000.000
180A191ARG10.9290.97217.59914.20614.2060.0000.0000.0000.000
181A192TYR00.0300.01120.209-0.132-0.1320.0000.0000.0000.000
182A193THR0-0.033-0.01913.9930.0190.0190.0000.0000.0000.000
183A194PHE00.0210.00617.3650.1790.1790.0000.0000.0000.000
184A195ALA00.0550.01214.488-0.511-0.5110.0000.0000.0000.000
185A196VAL0-0.0090.00916.4570.2430.2430.0000.0000.0000.000
186A197ARG10.8500.93816.49612.64512.6450.0000.0000.0000.000
187A198ALA00.037-0.00418.5270.5110.5110.0000.0000.0000.000
188A199ARG10.9370.97121.04310.09310.0930.0000.0000.0000.000
189A200MET00.0050.02923.8070.2850.2850.0000.0000.0000.000
190A201ALA0-0.018-0.00627.132-0.090-0.0900.0000.0000.0000.000
191A202GLU-1-0.877-0.90330.059-8.674-8.6740.0000.0000.0000.000
192A203PRO0-0.088-0.07532.9270.0810.0810.0000.0000.0000.000
193A204SER0-0.020-0.02035.0350.0560.0560.0000.0000.0000.000
194A205PHE0-0.014-0.01229.8110.0140.0140.0000.0000.0000.000
195A206GLY00.1020.06228.9110.0710.0710.0000.0000.0000.000
196A207GLY0-0.0110.00125.370-0.070-0.0700.0000.0000.0000.000
197A208PHE0-0.084-0.04720.300-0.117-0.1170.0000.0000.0000.000
198A209TRP0-0.060-0.02818.6560.0690.0690.0000.0000.0000.000
199A210SER00.0750.04217.200-0.169-0.1690.0000.0000.0000.000
200A211ALA0-0.038-0.01512.054-0.301-0.3010.0000.0000.0000.000
201A212TRP0-0.001-0.02211.3820.8610.8610.0000.0000.0000.000
202A213SER00.0450.03112.927-0.287-0.2870.0000.0000.0000.000
203A214GLU-1-0.963-0.97811.246-18.887-18.8870.0000.0000.0000.000
204A215PRO0-0.026-0.01411.4790.8330.8330.0000.0000.0000.000
205A216VAL00.0090.01314.3780.0560.0560.0000.0000.0000.000
206A217SER0-0.033-0.02615.935-0.230-0.2300.0000.0000.0000.000
207A218LEU0-0.018-0.00518.4330.1830.1830.0000.0000.0000.000
208A219LEU0-0.049-0.02722.136-0.207-0.2070.0000.0000.0000.000
209A220THR00.0400.04024.8040.1380.1380.0000.0000.0000.000
210A221PRO00.0510.01927.836-0.082-0.0820.0000.0000.0000.000
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