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

tag_button

FMODB ID: VK251

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2244091.219683
FMO2-HF: Nuclear repulsion 2160941.165397
FMO2-HF: Total energy -83150.054286
FMO2-MP2: Total energy -83392.664253


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.
-13.825-9.6011.4-2.129-3.494-0.011
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 : 1.017 / q_NPA : 0.995
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-1-0.824-0.9203.631-25.020-23.2060.002-0.755-1.0610.001
4A13SER0-0.013-0.0042.570-3.366-1.4411.398-1.270-2.052-0.012
5A14LYS10.9440.9614.16146.51547.0000.000-0.104-0.3810.000
6A15ALA00.0190.0156.1332.7412.7410.0000.0000.0000.000
7A16ALA00.0260.0107.3622.1402.1400.0000.0000.0000.000
8A17LEU0-0.060-0.0387.3241.3791.3790.0000.0000.0000.000
9A18LEU0-0.054-0.0249.8871.3521.3520.0000.0000.0000.000
10A19ALA00.0110.03412.1801.3201.3200.0000.0000.0000.000
11A20ALA0-0.038-0.03113.8260.4000.4000.0000.0000.0000.000
12A21ARG10.9240.96816.64315.51815.5180.0000.0000.0000.000
13A22GLY00.0260.01118.4210.2010.2010.0000.0000.0000.000
14A23PRO0-0.031-0.02522.195-0.224-0.2240.0000.0000.0000.000
15A24GLU-1-0.842-0.87223.214-11.058-11.0580.0000.0000.0000.000
16A25GLU-1-0.794-0.87223.843-9.728-9.7280.0000.0000.0000.000
17A26LEU0-0.057-0.01724.200-0.314-0.3140.0000.0000.0000.000
18A27LEU0-0.018-0.00319.5280.1640.1640.0000.0000.0000.000
19A28CYS0-0.042-0.00223.349-0.011-0.0110.0000.0000.0000.000
20A29PHE0-0.017-0.01619.461-0.098-0.0980.0000.0000.0000.000
21A30THR0-0.008-0.00723.7860.1610.1610.0000.0000.0000.000
22A31GLU-1-0.896-0.92820.168-12.410-12.4100.0000.0000.0000.000
23A32ARG10.7670.84020.47111.57011.5700.0000.0000.0000.000
24A33LEU0-0.013-0.00726.3740.0810.0810.0000.0000.0000.000
25A34GLU-1-0.972-0.98329.271-8.431-8.4310.0000.0000.0000.000
26A35ASP-1-0.794-0.87525.428-10.345-10.3450.0000.0000.0000.000
27A36LEU00.049-0.00426.6060.1460.1460.0000.0000.0000.000
28A37VAL0-0.027-0.00721.5340.0360.0360.0000.0000.0000.000
29A39PHE0-0.044-0.03917.911-0.155-0.1550.0000.0000.0000.000
30A40TRP00.0300.01622.4590.2170.2170.0000.0000.0000.000
31A41GLU-1-0.806-0.90516.611-16.049-16.0490.0000.0000.0000.000
32A42GLU-1-0.714-0.79621.134-10.365-10.3650.0000.0000.0000.000
33A43ALA0-0.013-0.01321.477-0.629-0.6290.0000.0000.0000.000
34A44ALA00.0290.01521.5710.3190.3190.0000.0000.0000.000
35A45SER00.005-0.01323.4270.3550.3550.0000.0000.0000.000
36A46ALA0-0.011-0.00127.081-0.005-0.0050.0000.0000.0000.000
37A47GLY00.0070.00329.0990.2570.2570.0000.0000.0000.000
38A48VAL0-0.0160.00828.0000.3190.3190.0000.0000.0000.000
39A49GLY00.0390.01327.404-0.460-0.4600.0000.0000.0000.000
40A50PRO0-0.018-0.01227.1020.2130.2130.0000.0000.0000.000
41A51GLY0-0.0010.00329.2080.2020.2020.0000.0000.0000.000
42A52ASN0-0.040-0.01731.3040.1740.1740.0000.0000.0000.000
43A53TYR0-0.058-0.05728.2360.3070.3070.0000.0000.0000.000
44A54SER0-0.018-0.00832.8250.1590.1590.0000.0000.0000.000
45A55PHE00.0430.01528.172-0.006-0.0060.0000.0000.0000.000
46A56SER0-0.031-0.01632.5980.1400.1400.0000.0000.0000.000
47A57TYR0-0.049-0.06934.228-0.208-0.2080.0000.0000.0000.000
48A58GLN00.0410.02636.3440.2610.2610.0000.0000.0000.000
49A59LEU00.0380.00536.715-0.171-0.1710.0000.0000.0000.000
50A60GLU-1-0.913-0.95739.320-6.624-6.6240.0000.0000.0000.000
51A61ASP-1-0.934-0.96442.193-6.161-6.1610.0000.0000.0000.000
52A62GLU-1-0.902-0.92741.099-6.810-6.8100.0000.0000.0000.000
53A63PRO0-0.080-0.04543.449-0.027-0.0270.0000.0000.0000.000
54A64TRP0-0.055-0.02437.597-0.191-0.1910.0000.0000.0000.000
55A65LYS10.8140.90037.7647.3527.3520.0000.0000.0000.000
56A66LEU0-0.029-0.02534.720-0.078-0.0780.0000.0000.0000.000
57A67CYS0-0.0320.00624.1750.2080.2080.0000.0000.0000.000
58A68ARG10.9160.95230.2029.2889.2880.0000.0000.0000.000
59A69LEU00.0030.01827.506-0.255-0.2550.0000.0000.0000.000
60A70HIS0-0.017-0.01124.7430.3090.3090.0000.0000.0000.000
61A71GLN00.0440.00922.5190.2980.2980.0000.0000.0000.000
62A72ALA0-0.023-0.00218.019-0.132-0.1320.0000.0000.0000.000
63A73PRO00.0230.01715.9230.2020.2020.0000.0000.0000.000
64A74THR0-0.009-0.03013.769-0.549-0.5490.0000.0000.0000.000
65A75ALA0-0.001-0.0108.901-0.122-0.1220.0000.0000.0000.000
66A76ARG10.8810.93411.02314.40914.4090.0000.0000.0000.000
67A77GLY0-0.0100.00213.1070.7920.7920.0000.0000.0000.000
68A78ALA0-0.0360.00115.8690.9110.9110.0000.0000.0000.000
69A79VAL0-0.0220.00117.495-0.629-0.6290.0000.0000.0000.000
70A80ARG10.8740.92413.84315.99015.9900.0000.0000.0000.000
71A81PHE0-0.016-0.00320.589-0.033-0.0330.0000.0000.0000.000
72A82TRP00.020-0.00421.727-0.026-0.0260.0000.0000.0000.000
73A84SER00.0130.00025.223-0.369-0.3690.0000.0000.0000.000
74A85LEU00.0080.01327.1020.1510.1510.0000.0000.0000.000
75A86PRO0-0.0100.00530.131-0.169-0.1690.0000.0000.0000.000
76A87THR00.0750.02431.5570.1230.1230.0000.0000.0000.000
77A88ALA0-0.044-0.01133.0870.0620.0620.0000.0000.0000.000
78A89ASP-1-0.810-0.86634.550-7.486-7.4860.0000.0000.0000.000
79A90THR0-0.025-0.03230.859-0.088-0.0880.0000.0000.0000.000
80A91SER00.0200.00533.481-0.076-0.0760.0000.0000.0000.000
81A92SER00.0220.00233.291-0.067-0.0670.0000.0000.0000.000
82A93PHE0-0.045-0.01334.177-0.116-0.1160.0000.0000.0000.000
83A94VAL0-0.0110.01136.8430.1340.1340.0000.0000.0000.000
84A95PRO0-0.047-0.01236.689-0.183-0.1830.0000.0000.0000.000
85A96LEU00.0490.01732.8200.1060.1060.0000.0000.0000.000
86A97GLU-1-0.847-0.91434.766-7.383-7.3830.0000.0000.0000.000
87A98LEU00.0110.00429.885-0.027-0.0270.0000.0000.0000.000
88A99ARG10.7960.87333.8967.3687.3680.0000.0000.0000.000
89A100VAL00.0130.02129.884-0.027-0.0270.0000.0000.0000.000
90A101THR00.0320.01333.1810.0660.0660.0000.0000.0000.000
91A102ALA00.0090.00234.125-0.184-0.1840.0000.0000.0000.000
92A103ALA00.0210.00135.1490.2330.2330.0000.0000.0000.000
93A104SER0-0.061-0.02737.6890.1620.1620.0000.0000.0000.000
94A105GLY00.0090.00639.2640.1760.1760.0000.0000.0000.000
95A106ALA0-0.015-0.00637.1670.0370.0370.0000.0000.0000.000
96A107PRO0-0.007-0.01436.095-0.198-0.1980.0000.0000.0000.000
97A108ARG10.7460.84826.97610.01510.0150.0000.0000.0000.000
98A109TYR00.006-0.03126.437-0.185-0.1850.0000.0000.0000.000
99A110HIS0-0.016-0.00931.9700.3850.3850.0000.0000.0000.000
100A111ARG10.8230.88126.3539.5159.5150.0000.0000.0000.000
101A112VAL00.0370.02632.6300.0040.0040.0000.0000.0000.000
102A113ILE0-0.052-0.02629.403-0.168-0.1680.0000.0000.0000.000
103A114HIS00.0740.04632.5270.0800.0800.0000.0000.0000.000
104A115ILE00.0380.02229.317-0.216-0.2160.0000.0000.0000.000
105A116ASN0-0.040-0.04329.340-0.255-0.2550.0000.0000.0000.000
106A117GLU-1-0.881-0.93430.039-8.383-8.3830.0000.0000.0000.000
107A118VAL0-0.077-0.03325.776-0.228-0.2280.0000.0000.0000.000
108A119VAL00.0360.01524.392-0.326-0.3260.0000.0000.0000.000
109A120LEU0-0.069-0.03317.411-0.160-0.1600.0000.0000.0000.000
110A121LEU0-0.0030.00720.668-0.169-0.1690.0000.0000.0000.000
111A122ASP-1-0.759-0.87817.771-13.693-13.6930.0000.0000.0000.000
112A123ALA0-0.040-0.01015.0820.2360.2360.0000.0000.0000.000
113A124PRO0-0.034-0.01917.2310.3320.3320.0000.0000.0000.000
114A125VAL00.0190.00718.133-0.696-0.6960.0000.0000.0000.000
115A126GLY00.001-0.00920.1300.4300.4300.0000.0000.0000.000
116A127LEU0-0.047-0.00717.8090.4460.4460.0000.0000.0000.000
117A128VAL0-0.026-0.00920.589-0.341-0.3410.0000.0000.0000.000
118A129ALA0-0.002-0.00722.8940.2090.2090.0000.0000.0000.000
119A130ARG10.8490.92724.6439.0069.0060.0000.0000.0000.000
120A131LEU0-0.008-0.00828.014-0.107-0.1070.0000.0000.0000.000
121A132ALA0-0.027-0.00830.7140.0730.0730.0000.0000.0000.000
122A133ASP-1-0.922-0.95933.858-8.191-8.1910.0000.0000.0000.000
123A134GLU-1-0.852-0.90736.697-7.677-7.6770.0000.0000.0000.000
124A135SER0-0.065-0.05836.659-0.007-0.0070.0000.0000.0000.000
125A136GLY0-0.039-0.01833.799-0.068-0.0680.0000.0000.0000.000
126A137HIS00.0180.00131.813-0.479-0.4790.0000.0000.0000.000
127A138VAL00.0070.01025.168-0.036-0.0360.0000.0000.0000.000
128A139VAL0-0.035-0.02428.5080.1520.1520.0000.0000.0000.000
129A140LEU0-0.013-0.00222.570-0.216-0.2160.0000.0000.0000.000
130A141ARG10.8600.89425.0639.3289.3280.0000.0000.0000.000
131A142TRP00.0100.01822.335-0.468-0.4680.0000.0000.0000.000
132A143LEU0-0.0070.00723.4100.5060.5060.0000.0000.0000.000
133A144PRO00.0300.00723.288-0.352-0.3520.0000.0000.0000.000
134A145PRO00.0090.00720.947-0.096-0.0960.0000.0000.0000.000
135A146PRO00.0240.00220.5260.4350.4350.0000.0000.0000.000
136A147GLU-1-0.959-0.97423.507-10.316-10.3160.0000.0000.0000.000
137A148THR0-0.0030.01524.3390.0320.0320.0000.0000.0000.000
138A149PRO00.0040.00526.8270.1740.1740.0000.0000.0000.000
139A150MET00.024-0.00529.399-0.077-0.0770.0000.0000.0000.000
140A151THR00.0590.02328.1630.0460.0460.0000.0000.0000.000
141A152SER0-0.028-0.02129.716-0.162-0.1620.0000.0000.0000.000
142A153HIS00.0280.00831.5190.0370.0370.0000.0000.0000.000
143A154ILE00.0200.01824.841-0.117-0.1170.0000.0000.0000.000
144A155ARG10.8250.91526.5989.3249.3240.0000.0000.0000.000
145A156TYR00.014-0.01322.489-0.474-0.4740.0000.0000.0000.000
146A157GLU-1-0.772-0.85819.567-11.970-11.9700.0000.0000.0000.000
147A158VAL0-0.002-0.00220.278-0.466-0.4660.0000.0000.0000.000
148A159ASP-1-0.843-0.91417.001-14.028-14.0280.0000.0000.0000.000
149A160VAL00.008-0.01319.0790.0250.0250.0000.0000.0000.000
150A161SER0-0.0020.01316.514-0.075-0.0750.0000.0000.0000.000
151A162ALA00.043-0.00118.5010.2600.2600.0000.0000.0000.000
152A163GLY0-0.022-0.01217.835-0.345-0.3450.0000.0000.0000.000
153A164ASN0-0.049-0.03718.6800.0220.0220.0000.0000.0000.000
154A165GLY00.0440.02721.6680.0870.0870.0000.0000.0000.000
155A166ALA00.0070.02519.1550.2330.2330.0000.0000.0000.000
156A167GLY00.020-0.00520.2620.6120.6120.0000.0000.0000.000
157A168SER0-0.032-0.00122.118-0.199-0.1990.0000.0000.0000.000
158A169VAL00.0380.00819.737-0.229-0.2290.0000.0000.0000.000
159A170GLN00.0080.02921.7650.4310.4310.0000.0000.0000.000
160A171ARG10.7950.86515.72713.15413.1540.0000.0000.0000.000
161A172VAL0-0.028-0.01422.9250.3900.3900.0000.0000.0000.000
162A173GLU-1-0.863-0.90924.432-9.593-9.5930.0000.0000.0000.000
163A174ILE0-0.072-0.04025.5140.2290.2290.0000.0000.0000.000
164A175LEU00.0220.00527.930-0.092-0.0920.0000.0000.0000.000
165A176GLU-1-0.788-0.90829.655-8.303-8.3030.0000.0000.0000.000
166A177GLY0-0.0120.00829.6480.2780.2780.0000.0000.0000.000
167A178ARG10.7450.87630.5988.1508.1500.0000.0000.0000.000
168A179THR0-0.004-0.01826.348-0.080-0.0800.0000.0000.0000.000
169A180GLU-1-0.763-0.85627.282-9.018-9.0180.0000.0000.0000.000
170A181CYS0-0.027-0.00726.4790.1470.1470.0000.0000.0000.000
171A182VAL0-0.0090.00828.408-0.146-0.1460.0000.0000.0000.000
172A183LEU0-0.020-0.01324.6870.0160.0160.0000.0000.0000.000
173A184SER00.0510.01529.201-0.092-0.0920.0000.0000.0000.000
174A185ASN0-0.051-0.02127.6930.1240.1240.0000.0000.0000.000
175A186LEU0-0.0160.00325.864-0.167-0.1670.0000.0000.0000.000
176A187ARG10.8820.93623.93911.73411.7340.0000.0000.0000.000
177A188GLY00.1280.07428.563-0.235-0.2350.0000.0000.0000.000
178A189ARG10.8760.93128.5059.2729.2720.0000.0000.0000.000
179A190THR0-0.031-0.01123.627-0.396-0.3960.0000.0000.0000.000
180A191ARG10.8850.95117.63115.07315.0730.0000.0000.0000.000
181A192TYR00.0220.01120.610-0.247-0.2470.0000.0000.0000.000
182A193THR0-0.024-0.02014.537-0.026-0.0260.0000.0000.0000.000
183A194PHE00.0210.03517.8080.0720.0720.0000.0000.0000.000
184A195ALA00.0430.01814.692-0.537-0.5370.0000.0000.0000.000
185A196VAL00.0110.00616.7170.4390.4390.0000.0000.0000.000
186A197ARG10.8350.90816.55712.33512.3350.0000.0000.0000.000
187A198ALA00.0390.00418.7030.4940.4940.0000.0000.0000.000
188A199ARG10.8510.89821.2669.4359.4350.0000.0000.0000.000
189A200MET0-0.0080.01324.0760.2740.2740.0000.0000.0000.000
190A201ALA0-0.0120.00227.394-0.049-0.0490.0000.0000.0000.000
191A202GLU-1-0.735-0.82329.644-8.896-8.8960.0000.0000.0000.000
192A203PRO0-0.071-0.05732.6860.0650.0650.0000.0000.0000.000
193A204SER0-0.012-0.01034.5340.0700.0700.0000.0000.0000.000
194A205PHE0-0.012-0.00329.6460.0230.0230.0000.0000.0000.000
195A206GLY00.0590.03228.8700.0830.0830.0000.0000.0000.000
196A207GLY00.0140.02525.294-0.105-0.1050.0000.0000.0000.000
197A208PHE0-0.079-0.04820.213-0.048-0.0480.0000.0000.0000.000
198A209TRP0-0.048-0.02118.9060.0780.0780.0000.0000.0000.000
199A210SER00.0260.01217.263-0.157-0.1570.0000.0000.0000.000
200A211ALA0-0.012-0.00912.403-0.339-0.3390.0000.0000.0000.000
201A212TRP0-0.051-0.02511.5540.8330.8330.0000.0000.0000.000
202A213SER00.0210.01213.449-0.282-0.2820.0000.0000.0000.000
203A214GLU-1-0.913-0.95311.617-19.476-19.4760.0000.0000.0000.000
204A215PRO0-0.035-0.00911.6590.9260.9260.0000.0000.0000.000
205A216VAL00.0180.00914.7480.0070.0070.0000.0000.0000.000
206A217SER0-0.053-0.04417.112-0.188-0.1880.0000.0000.0000.000
207A218LEU0-0.0060.00218.8810.2570.2570.0000.0000.0000.000
208A219LEU0-0.049-0.02622.660-0.323-0.3230.0000.0000.0000.000
209A220THR00.0330.00025.1470.1720.1720.0000.0000.0000.000
210A221PRO00.0380.01628.253-0.097-0.0970.0000.0000.0000.000
211A222SER0-0.099-0.07831.445-0.218-0.2180.0000.0000.0000.000
212A223ASP-1-0.869-0.91133.302-8.373-8.3730.0000.0000.0000.000
213A224LEU00.0070.02133.7010.1070.1070.0000.0000.0000.000