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: YNQZ2

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241033.911227
FMO2-HF: Nuclear repulsion 2157884.680137
FMO2-HF: Total energy -83149.23109
FMO2-MP2: Total energy -83391.85893


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.
-7.755-2.8941.124-2.288-3.698-0.008
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 : 1.026 / q_NPA : 0.999
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-1-0.822-0.9213.318-25.682-23.5550.005-0.873-1.2600.002
4A13SER0-0.012-0.0062.642-2.281-0.3451.101-1.220-1.817-0.010
5A14LYS10.9320.9513.37451.93452.7320.018-0.195-0.6210.000
6A15ALA00.0110.0146.0402.8862.8860.0000.0000.0000.000
7A16ALA00.0220.0157.6792.4462.4460.0000.0000.0000.000
8A17LEU0-0.074-0.0427.3861.4431.4430.0000.0000.0000.000
9A18LEU0-0.041-0.0229.6291.3211.3210.0000.0000.0000.000
10A19ALA0-0.0110.02812.3391.3741.3740.0000.0000.0000.000
11A20ALA0-0.028-0.02114.2510.3450.3450.0000.0000.0000.000
12A21ARG10.9640.99517.18215.28315.2830.0000.0000.0000.000
13A22GLY00.012-0.00219.3070.2230.2230.0000.0000.0000.000
14A23PRO0-0.027-0.02423.058-0.220-0.2200.0000.0000.0000.000
15A24GLU-1-0.883-0.92723.509-11.312-11.3120.0000.0000.0000.000
16A25GLU-1-0.796-0.89323.942-9.736-9.7360.0000.0000.0000.000
17A26LEU0-0.0370.00424.496-0.346-0.3460.0000.0000.0000.000
18A27LEU0-0.025-0.01220.3000.1650.1650.0000.0000.0000.000
19A28CYS0-0.045-0.01724.1570.0090.0090.0000.0000.0000.000
20A29PHE0-0.017-0.01019.718-0.108-0.1080.0000.0000.0000.000
21A30THR00.0060.00824.2000.0900.0900.0000.0000.0000.000
22A31GLU-1-0.899-0.94220.414-12.424-12.4240.0000.0000.0000.000
23A32ARG10.7920.86620.96211.43711.4370.0000.0000.0000.000
24A33LEU0-0.051-0.02826.5430.0370.0370.0000.0000.0000.000
25A34GLU-1-0.972-0.98029.110-8.447-8.4470.0000.0000.0000.000
26A35ASP-1-0.792-0.89425.701-10.364-10.3640.0000.0000.0000.000
27A36LEU00.0410.00126.8360.0920.0920.0000.0000.0000.000
28A37VAL0-0.025-0.00422.3660.0920.0920.0000.0000.0000.000
29A39PHE0-0.031-0.03918.653-0.233-0.2330.0000.0000.0000.000
30A40TRP00.0110.00922.9530.2180.2180.0000.0000.0000.000
31A41GLU-1-0.828-0.91817.182-16.080-16.0800.0000.0000.0000.000
32A42GLU-1-0.702-0.78921.637-10.364-10.3640.0000.0000.0000.000
33A43ALA0-0.021-0.01221.814-0.608-0.6080.0000.0000.0000.000
34A44ALA00.0250.01322.2620.3550.3550.0000.0000.0000.000
35A45SER00.0440.00024.0040.3860.3860.0000.0000.0000.000
36A46ALA0-0.021-0.00127.6790.0680.0680.0000.0000.0000.000
37A47GLY00.003-0.00129.1110.2530.2530.0000.0000.0000.000
38A48VAL0-0.023-0.00528.4740.3390.3390.0000.0000.0000.000
39A49GLY00.0220.02327.841-0.427-0.4270.0000.0000.0000.000
40A50PRO0-0.002-0.01527.2660.1890.1890.0000.0000.0000.000
41A51GLY0-0.029-0.00529.3080.2090.2090.0000.0000.0000.000
42A52ASN0-0.039-0.01631.7610.2170.2170.0000.0000.0000.000
43A53TYR0-0.057-0.05328.5540.3300.3300.0000.0000.0000.000
44A54SER0-0.0050.00632.9980.0540.0540.0000.0000.0000.000
45A55PHE00.0410.01128.7800.0100.0100.0000.0000.0000.000
46A56SER0-0.011-0.02133.4050.1200.1200.0000.0000.0000.000
47A57TYR0-0.070-0.08034.577-0.197-0.1970.0000.0000.0000.000
48A58GLN00.0370.03636.7210.2140.2140.0000.0000.0000.000
49A59LEU00.008-0.02536.712-0.201-0.2010.0000.0000.0000.000
50A60GLU-1-0.887-0.95039.726-6.641-6.6410.0000.0000.0000.000
51A61ASP-1-0.925-0.95742.462-6.129-6.1290.0000.0000.0000.000
52A62GLU-1-0.984-0.96842.536-6.691-6.6910.0000.0000.0000.000
53A63PRO0-0.061-0.04343.799-0.044-0.0440.0000.0000.0000.000
54A64TRP0-0.051-0.01237.939-0.223-0.2230.0000.0000.0000.000
55A65LYS10.8500.92138.5347.4757.4750.0000.0000.0000.000
56A66LEU0-0.035-0.02635.406-0.114-0.1140.0000.0000.0000.000
57A67CYS0-0.0110.01824.6970.0970.0970.0000.0000.0000.000
58A68ARG10.9430.96830.6439.1829.1820.0000.0000.0000.000
59A69LEU00.0040.01127.655-0.232-0.2320.0000.0000.0000.000
60A70HIS0-0.032-0.01324.6180.2840.2840.0000.0000.0000.000
61A71GLN00.0540.01522.7150.3480.3480.0000.0000.0000.000
62A72ALA0-0.025-0.00118.341-0.136-0.1360.0000.0000.0000.000
63A73PRO00.0150.01015.9330.1690.1690.0000.0000.0000.000
64A74THR00.002-0.03014.032-0.704-0.7040.0000.0000.0000.000
65A75ALA00.000-0.0089.239-0.134-0.1340.0000.0000.0000.000
66A76ARG10.8900.94211.34714.93614.9360.0000.0000.0000.000
67A77GLY0-0.015-0.00113.3830.6980.6980.0000.0000.0000.000
68A78ALA0-0.049-0.00716.2720.9250.9250.0000.0000.0000.000
69A79VAL0-0.0060.01017.715-0.652-0.6520.0000.0000.0000.000
70A80ARG10.8730.92514.38116.12216.1220.0000.0000.0000.000
71A81PHE0-0.010-0.01020.853-0.031-0.0310.0000.0000.0000.000
72A82TRP00.0270.00221.5880.0030.0030.0000.0000.0000.000
73A84SER0-0.0070.00225.673-0.243-0.2430.0000.0000.0000.000
74A85LEU00.001-0.00227.5090.1720.1720.0000.0000.0000.000
75A86PRO0-0.025-0.00230.424-0.173-0.1730.0000.0000.0000.000
76A87THR00.0790.02431.7370.1220.1220.0000.0000.0000.000
77A88ALA0-0.042-0.01833.3620.0450.0450.0000.0000.0000.000
78A89ASP-1-0.788-0.84135.070-7.453-7.4530.0000.0000.0000.000
79A90THR0-0.022-0.03630.839-0.153-0.1530.0000.0000.0000.000
80A91SER00.0350.01833.745-0.055-0.0550.0000.0000.0000.000
81A92SER0-0.001-0.01733.260-0.133-0.1330.0000.0000.0000.000
82A93PHE0-0.036-0.01734.874-0.046-0.0460.0000.0000.0000.000
83A94VAL0-0.0200.02137.4270.0940.0940.0000.0000.0000.000
84A95PRO0-0.035-0.01636.934-0.190-0.1900.0000.0000.0000.000
85A96LEU00.0330.02232.7990.0980.0980.0000.0000.0000.000
86A97GLU-1-0.817-0.89335.284-7.372-7.3720.0000.0000.0000.000
87A98LEU0-0.001-0.00830.412-0.060-0.0600.0000.0000.0000.000
88A99ARG10.8050.87334.4827.4957.4950.0000.0000.0000.000
89A100VAL00.0240.02630.480-0.064-0.0640.0000.0000.0000.000
90A101THR0-0.001-0.00333.7980.0700.0700.0000.0000.0000.000
91A102ALA00.0110.01134.459-0.171-0.1710.0000.0000.0000.000
92A103ALA00.0370.00435.4280.2280.2280.0000.0000.0000.000
93A104SER0-0.086-0.03437.8010.1680.1680.0000.0000.0000.000
94A105GLY00.0050.00139.6520.1590.1590.0000.0000.0000.000
95A106ALA0-0.018-0.00437.6300.0330.0330.0000.0000.0000.000
96A107PRO00.0270.00436.860-0.172-0.1720.0000.0000.0000.000
97A108ARG10.7640.86127.42910.04310.0430.0000.0000.0000.000
98A109TYR0-0.023-0.01626.869-0.181-0.1810.0000.0000.0000.000
99A110HIS0-0.016-0.01032.8170.3320.3320.0000.0000.0000.000
100A111ARG10.8280.89626.6419.5949.5940.0000.0000.0000.000
101A112VAL00.0260.01733.4570.0320.0320.0000.0000.0000.000
102A113ILE0-0.034-0.01529.519-0.105-0.1050.0000.0000.0000.000
103A114HIS00.0630.03632.3410.0680.0680.0000.0000.0000.000
104A115ILE00.0470.02529.546-0.202-0.2020.0000.0000.0000.000
105A116ASN0-0.029-0.02329.379-0.258-0.2580.0000.0000.0000.000
106A117GLU-1-0.904-0.95730.161-8.394-8.3940.0000.0000.0000.000
107A118VAL0-0.086-0.03325.799-0.227-0.2270.0000.0000.0000.000
108A119VAL00.0270.00724.541-0.250-0.2500.0000.0000.0000.000
109A120LEU0-0.078-0.03217.512-0.186-0.1860.0000.0000.0000.000
110A121LEU00.0110.01120.517-0.218-0.2180.0000.0000.0000.000
111A122ASP-1-0.788-0.85917.882-13.304-13.3040.0000.0000.0000.000
112A123ALA0-0.061-0.04115.0420.3530.3530.0000.0000.0000.000
113A124PRO0-0.020-0.01417.1550.2430.2430.0000.0000.0000.000
114A125VAL00.0220.00717.803-0.690-0.6900.0000.0000.0000.000
115A126GLY0-0.010-0.00819.7450.4230.4230.0000.0000.0000.000
116A127LEU0-0.0160.01017.4930.4730.4730.0000.0000.0000.000
117A128VAL0-0.023-0.00920.404-0.327-0.3270.0000.0000.0000.000
118A129ALA0-0.011-0.01922.4810.1510.1510.0000.0000.0000.000
119A130ARG10.8560.93824.3168.9648.9640.0000.0000.0000.000
120A131LEU00.003-0.00627.633-0.112-0.1120.0000.0000.0000.000
121A132ALA0-0.064-0.02330.3580.0970.0970.0000.0000.0000.000
122A133ASP-1-0.907-0.95433.524-8.064-8.0640.0000.0000.0000.000
123A134GLU-1-0.849-0.90436.493-7.676-7.6760.0000.0000.0000.000
124A135SER0-0.084-0.07535.692-0.155-0.1550.0000.0000.0000.000
125A136GLY00.0320.02633.585-0.047-0.0470.0000.0000.0000.000
126A137HIS0-0.034-0.02131.228-0.445-0.4450.0000.0000.0000.000
127A138VAL00.0130.01724.670-0.048-0.0480.0000.0000.0000.000
128A139VAL0-0.051-0.02728.1260.0820.0820.0000.0000.0000.000
129A140LEU0-0.027-0.01422.395-0.224-0.2240.0000.0000.0000.000
130A141ARG10.8830.92124.9209.2579.2570.0000.0000.0000.000
131A142TRP0-0.0050.00522.185-0.441-0.4410.0000.0000.0000.000
132A143LEU0-0.0020.00923.3460.4900.4900.0000.0000.0000.000
133A144PRO00.0300.00422.975-0.380-0.3800.0000.0000.0000.000
134A145PRO00.0150.00720.935-0.075-0.0750.0000.0000.0000.000
135A146PRO0-0.007-0.00720.7130.4210.4210.0000.0000.0000.000
136A147GLU-1-0.962-0.98023.633-10.279-10.2790.0000.0000.0000.000
137A148THR00.0430.03324.372-0.027-0.0270.0000.0000.0000.000
138A149PRO0-0.017-0.00626.9190.1620.1620.0000.0000.0000.000
139A150MET00.008-0.01029.463-0.066-0.0660.0000.0000.0000.000
140A151THR00.0910.03328.1460.0290.0290.0000.0000.0000.000
141A152SER0-0.058-0.03529.631-0.165-0.1650.0000.0000.0000.000
142A153HIS00.0350.01531.2250.0810.0810.0000.0000.0000.000
143A154ILE00.0050.01524.809-0.099-0.0990.0000.0000.0000.000
144A155ARG10.8330.91426.3269.3719.3710.0000.0000.0000.000
145A156TYR00.002-0.01922.329-0.462-0.4620.0000.0000.0000.000
146A157GLU-1-0.789-0.87919.693-11.882-11.8820.0000.0000.0000.000
147A158VAL0-0.015-0.00820.097-0.455-0.4550.0000.0000.0000.000
148A159ASP-1-0.844-0.89416.437-14.123-14.1230.0000.0000.0000.000
149A160VAL0-0.016-0.01318.433-0.148-0.1480.0000.0000.0000.000
150A161SER00.0430.02716.001-0.170-0.1700.0000.0000.0000.000
151A162ALA00.005-0.01618.0930.1660.1660.0000.0000.0000.000
152A163GLY0-0.009-0.00817.624-0.391-0.3910.0000.0000.0000.000
153A164ASN0-0.054-0.05518.6460.0570.0570.0000.0000.0000.000
154A165GLY00.0380.03021.2130.0630.0630.0000.0000.0000.000
155A166ALA00.0110.02418.8730.2190.2190.0000.0000.0000.000
156A167GLY0-0.014-0.02019.9070.5370.5370.0000.0000.0000.000
157A168SER0-0.059-0.01921.639-0.043-0.0430.0000.0000.0000.000
158A169VAL00.0370.01419.785-0.278-0.2780.0000.0000.0000.000
159A170GLN00.0190.01720.9510.4800.4800.0000.0000.0000.000
160A171ARG10.8170.88115.33913.39813.3980.0000.0000.0000.000
161A172VAL0-0.0240.00222.4850.3540.3540.0000.0000.0000.000
162A173GLU-1-0.853-0.91424.308-9.541-9.5410.0000.0000.0000.000
163A174ILE0-0.065-0.03625.2070.2100.2100.0000.0000.0000.000
164A175LEU00.0300.00827.793-0.037-0.0370.0000.0000.0000.000
165A176GLU-1-0.816-0.91829.318-8.417-8.4170.0000.0000.0000.000
166A177GLY0-0.0340.00129.5310.3130.3130.0000.0000.0000.000
167A178ARG10.7850.89230.4258.0588.0580.0000.0000.0000.000
168A179THR00.000-0.00526.292-0.074-0.0740.0000.0000.0000.000
169A180GLU-1-0.769-0.88127.137-8.964-8.9640.0000.0000.0000.000
170A181CYS0-0.025-0.01325.8310.1130.1130.0000.0000.0000.000
171A182VAL0-0.0130.01627.497-0.202-0.2020.0000.0000.0000.000
172A183LEU0-0.0060.00024.0330.0890.0890.0000.0000.0000.000
173A184SER00.035-0.00428.7090.0040.0040.0000.0000.0000.000
174A185ASN0-0.038-0.00527.6090.0850.0850.0000.0000.0000.000
175A186LEU0-0.012-0.00125.146-0.204-0.2040.0000.0000.0000.000
176A187ARG10.9570.98424.55611.43411.4340.0000.0000.0000.000
177A188GLY00.1010.06128.339-0.202-0.2020.0000.0000.0000.000
178A189ARG10.9070.95528.5519.3709.3700.0000.0000.0000.000
179A190THR0-0.062-0.03123.577-0.274-0.2740.0000.0000.0000.000
180A191ARG10.9220.97517.45714.64514.6450.0000.0000.0000.000
181A192TYR00.0170.00620.172-0.236-0.2360.0000.0000.0000.000
182A193THR0-0.014-0.00813.9290.1740.1740.0000.0000.0000.000
183A194PHE00.0300.01717.3350.2190.2190.0000.0000.0000.000
184A195ALA00.0560.01314.446-0.544-0.5440.0000.0000.0000.000
185A196VAL0-0.0120.00616.4360.2740.2740.0000.0000.0000.000
186A197ARG10.8200.89316.49012.39612.3960.0000.0000.0000.000
187A198ALA00.034-0.00318.5140.5120.5120.0000.0000.0000.000
188A199ARG10.8420.90521.0349.5189.5180.0000.0000.0000.000
189A200MET00.0110.02323.7980.2960.2960.0000.0000.0000.000
190A201ALA0-0.0090.00127.127-0.054-0.0540.0000.0000.0000.000
191A202GLU-1-0.731-0.82029.439-8.965-8.9650.0000.0000.0000.000
192A203PRO0-0.058-0.05232.9150.0630.0630.0000.0000.0000.000
193A204SER0-0.010-0.01234.8980.0240.0240.0000.0000.0000.000
194A205PHE00.0070.00229.8840.0130.0130.0000.0000.0000.000
195A206GLY00.0690.04628.8980.0770.0770.0000.0000.0000.000
196A207GLY0-0.0030.00425.364-0.062-0.0620.0000.0000.0000.000
197A208PHE0-0.070-0.03720.310-0.076-0.0760.0000.0000.0000.000
198A209TRP0-0.047-0.01718.7510.0080.0080.0000.0000.0000.000
199A210SER00.0580.03217.063-0.172-0.1720.0000.0000.0000.000
200A211ALA0-0.041-0.01512.041-0.299-0.2990.0000.0000.0000.000
201A212TRP0-0.001-0.02011.3720.7920.7920.0000.0000.0000.000
202A213SER00.0380.02912.925-0.285-0.2850.0000.0000.0000.000
203A214GLU-1-0.948-0.96911.088-19.562-19.5620.0000.0000.0000.000
204A215PRO0-0.027-0.01911.3480.8710.8710.0000.0000.0000.000
205A216VAL00.0040.00814.3660.0370.0370.0000.0000.0000.000
206A217SER0-0.055-0.04116.464-0.232-0.2320.0000.0000.0000.000
207A218LEU0-0.018-0.00818.4600.1900.1900.0000.0000.0000.000
208A219LEU0-0.043-0.03022.166-0.189-0.1890.0000.0000.0000.000
209A220THR00.0410.01924.8390.1170.1170.0000.0000.0000.000
210A221PRO00.0530.01727.853-0.084-0.0840.0000.0000.0000.000
211A222SER0-0.097-0.08431.372-0.211-0.2110.0000.0000.0000.000
212A223ASP-1-0.892-0.93233.052-8.241-8.2410.0000.0000.0000.000
213A224LEU00.0130.02833.2290.1110.1110.0000.0000.0000.000