Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: GQK61

Calculation Name: 3ETP-A-Xray308

Preferred Name: Ephrin type-B receptor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ETP

Chain ID: A

ChEMBL ID: CHEMBL5961

UniProt ID: P54763

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 185
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2087333.165683
FMO2-HF: Nuclear repulsion 2010121.256585
FMO2-HF: Total energy -77211.909098
FMO2-MP2: Total energy -77430.198793


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:21:ALA )


Summations of interaction energy for fragment #1(A:21:ALA )
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.
-3.908-1.80.057-0.908-1.255-0.001
Interaction energy analysis for fragmet #1(A:21:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.008
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].
3A23ALA 0-0.039-0.0233.769-1.582-0.3250.007-0.544-0.7200.002
4A24ILE 00.0140.0013.325-1.694-0.9510.050-0.353-0.438-0.003
5A25SER 00.0150.0164.5290.1830.2910.000-0.011-0.0970.000
6A26ASP -1-0.944-0.9765.9830.1610.1610.0000.0000.0000.000
7A27PRO 0-0.0040.0029.701-0.079-0.0790.0000.0000.0000.000
8A28GLU -1-0.864-0.9449.474-0.348-0.3480.0000.0000.0000.000
9A29GLU -1-0.987-0.99313.379-0.134-0.1340.0000.0000.0000.000
10A30THR 00.0490.01615.924-0.006-0.0060.0000.0000.0000.000
11A31LEU 0-0.117-0.06917.9230.0180.0180.0000.0000.0000.000
12A32MET 0-0.051-0.02620.0470.0090.0090.0000.0000.0000.000
13A33ASP -1-0.743-0.84917.844-0.256-0.2560.0000.0000.0000.000
14A34SER 00.0320.01920.4580.0040.0040.0000.0000.0000.000
15A35THR 0-0.062-0.06518.9440.0070.0070.0000.0000.0000.000
16A36THR 0-0.037-0.01720.4980.0070.0070.0000.0000.0000.000
17A37ALA 0-0.0370.00023.2060.0130.0130.0000.0000.0000.000
18A38THR 00.0340.01326.5180.0010.0010.0000.0000.0000.000
19A39ALA 0-0.026-0.01929.2580.0020.0020.0000.0000.0000.000
20A40GLU -1-0.903-0.94930.347-0.086-0.0860.0000.0000.0000.000
21A41LEU 0-0.010-0.00925.9110.0030.0030.0000.0000.0000.000
22A42GLY 0-0.012-0.00829.9970.0040.0040.0000.0000.0000.000
23A43TRP 0-0.063-0.03823.5280.0040.0040.0000.0000.0000.000
24A44MET 0-0.064-0.02031.1480.0040.0040.0000.0000.0000.000
25A45VAL 00.0710.04432.591-0.002-0.0020.0000.0000.0000.000
26A46HIS 10.8100.93834.3720.0490.0490.0000.0000.0000.000
27A47PRO 00.021-0.01035.4620.0000.0000.0000.0000.0000.000
28A48PRO 00.050-0.00736.967-0.002-0.0020.0000.0000.0000.000
29A49SER 00.0170.02638.305-0.001-0.0010.0000.0000.0000.000
30A50GLY 00.0330.02935.1610.0000.0000.0000.0000.0000.000
31A51TRP 0-0.061-0.04526.164-0.004-0.0040.0000.0000.0000.000
32A52GLU -1-0.908-0.96132.082-0.074-0.0740.0000.0000.0000.000
33A53GLU -1-0.825-0.92530.147-0.104-0.1040.0000.0000.0000.000
34A54VAL 00.0040.00029.9130.0040.0040.0000.0000.0000.000
35A55SER 0-0.043-0.02729.135-0.009-0.0090.0000.0000.0000.000
36A56GLY 00.0280.01227.8320.0060.0060.0000.0000.0000.000
37A57TYR 00.012-0.02526.400-0.005-0.0050.0000.0000.0000.000
38A58ASP -1-0.845-0.93421.969-0.210-0.2100.0000.0000.0000.000
39A59GLU -1-0.854-0.92419.424-0.278-0.2780.0000.0000.0000.000
40A60ASN 0-0.102-0.05321.1560.0110.0110.0000.0000.0000.000
41A61MET 0-0.070-0.03225.3160.0140.0140.0000.0000.0000.000
42A62ASN 0-0.0160.02223.7580.0080.0080.0000.0000.0000.000
43A63THR 0-0.067-0.01725.9690.0010.0010.0000.0000.0000.000
44A64ILE 00.0010.02321.5870.0000.0000.0000.0000.0000.000
45A65ARG 10.8310.92225.2410.1240.1240.0000.0000.0000.000
46A66THR 0-0.037-0.00924.412-0.008-0.0080.0000.0000.0000.000
47A67TYR 00.0310.01126.1660.0110.0110.0000.0000.0000.000
48A68GLN 0-0.018-0.00426.983-0.017-0.0170.0000.0000.0000.000
49A69VAL 00.0500.02429.2210.0070.0070.0000.0000.0000.000
50A192CYS 0-0.113-0.05629.441-0.003-0.0030.0000.0000.0000.000
51A71ASN 00.0280.01833.1720.0010.0010.0000.0000.0000.000
52A72VAL 0-0.0020.00033.4240.0030.0030.0000.0000.0000.000
53A73PHE 0-0.070-0.04435.9520.0040.0040.0000.0000.0000.000
54A74GLU -1-0.925-0.94838.905-0.046-0.0460.0000.0000.0000.000
55A75SER 0-0.016-0.01439.162-0.001-0.0010.0000.0000.0000.000
56A76SER 0-0.055-0.04139.4100.0000.0000.0000.0000.0000.000
57A77GLN 00.0750.07335.205-0.003-0.0030.0000.0000.0000.000
58A78ASN 00.0530.02734.356-0.002-0.0020.0000.0000.0000.000
59A79ASN 0-0.077-0.04632.6000.0050.0050.0000.0000.0000.000
60A80TRP 0-0.068-0.01830.619-0.005-0.0050.0000.0000.0000.000
61A81LEU 00.0140.03426.7150.0010.0010.0000.0000.0000.000
62A82ARG 10.8870.92828.6040.0510.0510.0000.0000.0000.000
63A83THR 00.0170.01124.5410.0000.0000.0000.0000.0000.000
64A84LYS 10.9290.96528.0260.0850.0850.0000.0000.0000.000
65A85PHE 0-0.0080.01828.108-0.003-0.0030.0000.0000.0000.000
66A86ILE 0-0.0110.00323.029-0.005-0.0050.0000.0000.0000.000
67A87ARG 10.9010.94326.6220.0640.0640.0000.0000.0000.000
68A88ARG 10.9540.96924.0550.0090.0090.0000.0000.0000.000
69A89ARG 10.8980.94023.5230.0790.0790.0000.0000.0000.000
70A90GLY 00.0430.02423.897-0.001-0.0010.0000.0000.0000.000
71A91ALA 00.0220.03219.9560.0120.0120.0000.0000.0000.000
72A92HIS 0-0.002-0.00221.1220.0040.0040.0000.0000.0000.000
73A93ARG 10.9240.95416.261-0.018-0.0180.0000.0000.0000.000
74A94ILE 0-0.0310.00118.334-0.010-0.0100.0000.0000.0000.000
75A95HIS 0-0.020-0.00412.972-0.005-0.0050.0000.0000.0000.000
76A96VAL 00.011-0.00915.465-0.005-0.0050.0000.0000.0000.000
77A97GLU -1-0.895-0.95211.322-0.444-0.4440.0000.0000.0000.000
78A98MET 0-0.016-0.00214.5260.0230.0230.0000.0000.0000.000
79A99LYS 10.9841.00713.2300.3950.3950.0000.0000.0000.000
80A100PHE 00.0160.00217.0830.0250.0250.0000.0000.0000.000
81A101SER 0-0.0190.00019.586-0.014-0.0140.0000.0000.0000.000
82A102VAL 00.0440.01322.2460.0110.0110.0000.0000.0000.000
83A103ARG 10.8250.90224.5830.0820.0820.0000.0000.0000.000
84A104ASP -1-0.865-0.90725.619-0.096-0.0960.0000.0000.0000.000
85A115CYS 0-0.017-0.00427.9710.0010.0010.0000.0000.0000.000
86A106SER 0-0.014-0.00329.9170.0020.0020.0000.0000.0000.000
87A107SER 0-0.019-0.01630.0760.0000.0000.0000.0000.0000.000
88A108ILE 0-0.0320.00031.893-0.001-0.0010.0000.0000.0000.000
89A109PRO 00.025-0.00734.6900.0040.0040.0000.0000.0000.000
90A110SER 0-0.021-0.02838.2960.0010.0010.0000.0000.0000.000
91A111VAL 0-0.0100.02334.4450.0020.0020.0000.0000.0000.000
92A112PRO 00.0320.02337.3370.0040.0040.0000.0000.0000.000
93A113GLY 00.011-0.01337.113-0.002-0.0020.0000.0000.0000.000
94A114SER 0-0.068-0.03036.7210.0010.0010.0000.0000.0000.000
95A116LYS 10.9430.96029.6120.0440.0440.0000.0000.0000.000
96A117GLU -1-0.797-0.89826.082-0.081-0.0810.0000.0000.0000.000
97A118THR 0-0.0120.01223.961-0.006-0.0060.0000.0000.0000.000
98A119PHE 00.0250.01720.2470.0050.0050.0000.0000.0000.000
99A120ASN 0-0.0210.02723.952-0.003-0.0030.0000.0000.0000.000
100A121LEU 00.0510.03119.559-0.004-0.0040.0000.0000.0000.000
101A122TYR 0-0.062-0.04823.6640.0120.0120.0000.0000.0000.000
102A123TYR 00.005-0.00724.100-0.008-0.0080.0000.0000.0000.000
103A124TYR 00.0070.00526.1680.0080.0080.0000.0000.0000.000
104A125GLU -1-0.842-0.93427.764-0.018-0.0180.0000.0000.0000.000
105A126ALA 0-0.003-0.01129.8080.0020.0020.0000.0000.0000.000
106A127ASP -1-0.835-0.91931.809-0.019-0.0190.0000.0000.0000.000
107A128PHE 00.000-0.01634.131-0.001-0.0010.0000.0000.0000.000
108A129ASP -1-0.861-0.89133.809-0.051-0.0510.0000.0000.0000.000
109A130LEU 00.0140.01034.9070.0010.0010.0000.0000.0000.000
110A131ALA 0-0.032-0.00134.5360.0020.0020.0000.0000.0000.000
111A132THR 00.0360.01036.561-0.001-0.0010.0000.0000.0000.000
112A133LYS 10.9650.95737.8880.0410.0410.0000.0000.0000.000
113A134THR 0-0.058-0.02139.497-0.001-0.0010.0000.0000.0000.000
114A135PHE 00.0380.05937.6600.0020.0020.0000.0000.0000.000
115A136PRO 00.0530.01133.746-0.003-0.0030.0000.0000.0000.000
116A137ASN 00.0310.01036.755-0.003-0.0030.0000.0000.0000.000
117A138TRP 0-0.029-0.03132.618-0.001-0.0010.0000.0000.0000.000
118A139MET 0-0.025-0.01434.2090.0000.0000.0000.0000.0000.000
119A140GLU -1-0.856-0.93530.486-0.021-0.0210.0000.0000.0000.000
120A141ASN 0-0.053-0.00232.6100.0020.0020.0000.0000.0000.000
121A142PRO 0-0.022-0.02234.6580.0000.0000.0000.0000.0000.000
122A143TRP 0-0.060-0.02728.179-0.002-0.0020.0000.0000.0000.000
123A144VAL 00.0460.01225.9650.0030.0030.0000.0000.0000.000
124A145LYS 10.9420.98125.3410.0250.0250.0000.0000.0000.000
125A146VAL 0-0.089-0.04219.7030.0070.0070.0000.0000.0000.000
126A147ASP -1-0.779-0.88019.456-0.044-0.0440.0000.0000.0000.000
127A148THR 0-0.097-0.07522.243-0.003-0.0030.0000.0000.0000.000
128A149ILE 0-0.047-0.02218.2130.0000.0000.0000.0000.0000.000
129A150ALA 00.026-0.01119.5590.0070.0070.0000.0000.0000.000
130A151ALA 0-0.023-0.00918.612-0.017-0.0170.0000.0000.0000.000
131A152ASP -1-0.830-0.87813.534-0.226-0.2260.0000.0000.0000.000
132A153GLU -1-0.977-1.00316.425-0.103-0.1030.0000.0000.0000.000
133A154SER 0-0.087-0.04811.849-0.034-0.0340.0000.0000.0000.000
134A155ILE 0-0.037-0.01113.885-0.001-0.0010.0000.0000.0000.000
135A156SER 0-0.031-0.01712.953-0.039-0.0390.0000.0000.0000.000
136A157GLN 0-0.051-0.06314.9320.0660.0660.0000.0000.0000.000
137A158VAL 00.0250.02617.344-0.028-0.0280.0000.0000.0000.000
138A159ASP -1-0.876-0.94619.723-0.165-0.1650.0000.0000.0000.000
139A160LEU 00.0030.00222.392-0.003-0.0030.0000.0000.0000.000
140A161GLY 0-0.034-0.02525.6310.0110.0110.0000.0000.0000.000
141A162GLY 0-0.048-0.02728.789-0.002-0.0020.0000.0000.0000.000
142A163ARG 10.9370.96727.5750.1150.1150.0000.0000.0000.000
143A164VAL 00.1040.05721.808-0.008-0.0080.0000.0000.0000.000
144A165MET 0-0.088-0.03222.1090.0130.0130.0000.0000.0000.000
145A166LYS 10.9730.97519.6770.1720.1720.0000.0000.0000.000
146A167ILE 0-0.019-0.00616.1420.0200.0200.0000.0000.0000.000
147A168ASN 00.0590.03515.521-0.043-0.0430.0000.0000.0000.000
148A169THR 0-0.002-0.01911.366-0.005-0.0050.0000.0000.0000.000
149A170GLU -1-0.813-0.87512.729-0.224-0.2240.0000.0000.0000.000
150A171VAL 00.010-0.0039.9960.0080.0080.0000.0000.0000.000
151A172ARG 10.7690.87113.0310.1580.1580.0000.0000.0000.000
152A173SER 00.000-0.00814.6250.0010.0010.0000.0000.0000.000
153A174PHE 0-0.008-0.00416.5720.0130.0130.0000.0000.0000.000
154A175GLY 00.0130.01120.121-0.004-0.0040.0000.0000.0000.000
155A176PRO 0-0.030-0.02122.4430.0070.0070.0000.0000.0000.000
156A177VAL 0-0.0070.01023.950-0.004-0.0040.0000.0000.0000.000
157A178SER 0-0.052-0.04525.6920.0030.0030.0000.0000.0000.000
158A179ARG 10.8860.95728.7950.0120.0120.0000.0000.0000.000
159A180ASN 0-0.022-0.02428.945-0.001-0.0010.0000.0000.0000.000
160A181GLY 0-0.011-0.01627.686-0.005-0.0050.0000.0000.0000.000
161A182PHE 0-0.005-0.00221.9910.0070.0070.0000.0000.0000.000
162A183TYR 0-0.062-0.03827.385-0.004-0.0040.0000.0000.0000.000
163A184LEU 00.0290.00721.2480.0040.0040.0000.0000.0000.000
164A185ALA 0-0.001-0.00925.6140.0010.0010.0000.0000.0000.000
165A186PHE 00.0270.01021.311-0.001-0.0010.0000.0000.0000.000
166A187GLN 00.0440.01126.4200.0030.0030.0000.0000.0000.000
167A188ASP -1-0.689-0.84927.923-0.072-0.0720.0000.0000.0000.000
168A189TYR 0-0.089-0.06527.0580.0070.0070.0000.0000.0000.000
169A190GLY 00.008-0.00532.5680.0040.0040.0000.0000.0000.000
170A191GLY 00.0140.01129.9270.0020.0020.0000.0000.0000.000
171A193MET 0-0.025-0.00225.200-0.009-0.0090.0000.0000.0000.000
172A194SER 00.0140.00625.0310.0020.0020.0000.0000.0000.000
173A195LEU 0-0.021-0.01720.975-0.012-0.0120.0000.0000.0000.000
174A196ILE 0-0.004-0.02220.1400.0050.0050.0000.0000.0000.000
175A197ALA 00.0250.00118.2280.0000.0000.0000.0000.0000.000
176A198VAL 0-0.028-0.00318.503-0.002-0.0020.0000.0000.0000.000
177A199ARG 10.8820.95711.1110.3840.3840.0000.0000.0000.000
178A200VAL 0-0.041-0.01916.3580.0000.0000.0000.0000.0000.000
179A201PHE 00.0380.02010.9160.0060.0060.0000.0000.0000.000
180A202TYR 0-0.007-0.00915.6060.0240.0240.0000.0000.0000.000
181A203ARG 11.0100.9979.212-0.010-0.0100.0000.0000.0000.000
182A204LYS 10.9360.97914.0490.1300.1300.0000.0000.0000.000
183A205CYS 0-0.018-0.02714.8160.0230.0230.0000.0000.0000.000
184A206PRO 0-0.051-0.01816.313-0.004-0.0040.0000.0000.0000.000
185A207ARG 00.0630.05519.2000.0650.0650.0000.0000.0000.000