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: 1499Z

Calculation Name: 3ETP-A-Xray372

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: 2023-03-14

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2086233.874569
FMO2-HF: Nuclear repulsion 2009018.890894
FMO2-HF: Total energy -77214.983676
FMO2-MP2: Total energy -77433.083717


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.
-4.191-2.0680.065-0.992-1.196-0.001
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 : 0.006 / q_NPA : -0.013
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].
3A23ALA0-0.030-0.0103.435-1.923-0.4600.013-0.671-0.8050.001
4A24ILE00.007-0.0033.341-1.964-1.3040.052-0.321-0.391-0.002
5A25SER00.0140.0155.2830.3140.3140.0000.0000.0000.000
6A26ASP-1-0.914-0.9636.4000.0590.0590.0000.0000.0000.000
7A27PRO00.002-0.00410.059-0.083-0.0830.0000.0000.0000.000
8A28GLU-1-0.745-0.8559.994-0.392-0.3920.0000.0000.0000.000
9A29GLU-1-0.837-0.89713.806-0.136-0.1360.0000.0000.0000.000
10A30THR00.003-0.00815.982-0.005-0.0050.0000.0000.0000.000
11A31LEU0-0.070-0.03418.1000.0160.0160.0000.0000.0000.000
12A32MET0-0.011-0.01620.4340.0150.0150.0000.0000.0000.000
13A33ASP-1-0.780-0.87317.450-0.271-0.2710.0000.0000.0000.000
14A34SER00.0370.02520.5330.0050.0050.0000.0000.0000.000
15A35THR0-0.026-0.03818.8190.0090.0090.0000.0000.0000.000
16A36THR0-0.058-0.03820.8650.0080.0080.0000.0000.0000.000
17A37ALA0-0.026-0.00123.4780.0120.0120.0000.0000.0000.000
18A38THR00.0440.02326.8280.0010.0010.0000.0000.0000.000
19A39ALA0-0.032-0.01129.5400.0040.0040.0000.0000.0000.000
20A40GLU-1-0.837-0.93330.378-0.089-0.0890.0000.0000.0000.000
21A41LEU0-0.009-0.00325.7410.0000.0000.0000.0000.0000.000
22A42GLY0-0.0100.00929.7620.0030.0030.0000.0000.0000.000
23A43TRP0-0.048-0.04023.3930.0030.0030.0000.0000.0000.000
24A44MET0-0.036-0.01031.2580.0040.0040.0000.0000.0000.000
25A45VAL00.0490.02932.973-0.001-0.0010.0000.0000.0000.000
26A46HIS10.8370.94334.6290.0590.0590.0000.0000.0000.000
27A47PRO00.0450.01735.664-0.001-0.0010.0000.0000.0000.000
28A48PRO0-0.002-0.03137.255-0.003-0.0030.0000.0000.0000.000
29A49SER00.0320.02338.9900.0000.0000.0000.0000.0000.000
30A50GLY00.0180.02835.3470.0000.0000.0000.0000.0000.000
31A51TRP0-0.056-0.04626.330-0.004-0.0040.0000.0000.0000.000
32A52GLU-1-0.860-0.91632.385-0.082-0.0820.0000.0000.0000.000
33A53GLU-1-0.770-0.87329.896-0.110-0.1100.0000.0000.0000.000
34A54VAL0-0.005-0.00129.7920.0050.0050.0000.0000.0000.000
35A55SER0-0.026-0.00828.762-0.009-0.0090.0000.0000.0000.000
36A56GLY00.017-0.00227.9590.0070.0070.0000.0000.0000.000
37A57TYR0-0.086-0.03426.493-0.005-0.0050.0000.0000.0000.000
38A58ASP-1-0.732-0.85222.195-0.203-0.2030.0000.0000.0000.000
39A59GLU-1-0.911-0.97219.792-0.259-0.2590.0000.0000.0000.000
40A60ASN0-0.103-0.05521.2140.0120.0120.0000.0000.0000.000
41A61MET0-0.070-0.03425.3390.0140.0140.0000.0000.0000.000
42A62ASN0-0.039-0.01623.1430.0200.0200.0000.0000.0000.000
43A63THR0-0.026-0.02525.970-0.001-0.0010.0000.0000.0000.000
44A64ILE00.0330.03620.8970.0020.0020.0000.0000.0000.000
45A65ARG10.8280.92524.9620.1260.1260.0000.0000.0000.000
46A66THR0-0.039-0.02124.211-0.009-0.0090.0000.0000.0000.000
47A67TYR0-0.008-0.04325.9870.0120.0120.0000.0000.0000.000
48A68GLN0-0.062-0.03726.957-0.015-0.0150.0000.0000.0000.000
49A69VAL00.0360.01929.3510.0070.0070.0000.0000.0000.000
50A70CYS0-0.103-0.05629.655-0.003-0.0030.0000.0000.0000.000
51A71ASN00.0200.00733.368-0.001-0.0010.0000.0000.0000.000
52A72VAL0-0.018-0.00733.2010.0040.0040.0000.0000.0000.000
53A73PHE0-0.046-0.03135.8120.0030.0030.0000.0000.0000.000
54A74GLU-1-0.875-0.91238.846-0.052-0.0520.0000.0000.0000.000
55A75SER00.000-0.00939.2240.0000.0000.0000.0000.0000.000
56A76SER0-0.058-0.05339.730-0.001-0.0010.0000.0000.0000.000
57A77GLN00.0030.03535.515-0.003-0.0030.0000.0000.0000.000
58A78ASN00.0450.01034.710-0.002-0.0020.0000.0000.0000.000
59A79ASN0-0.045-0.02332.8840.0050.0050.0000.0000.0000.000
60A80TRP0-0.054-0.01530.601-0.006-0.0060.0000.0000.0000.000
61A81LEU00.0030.02127.1750.0020.0020.0000.0000.0000.000
62A82ARG10.8760.93229.0570.0610.0610.0000.0000.0000.000
63A83THR0-0.0040.00225.0290.0020.0020.0000.0000.0000.000
64A84LYS10.8340.91828.4540.0950.0950.0000.0000.0000.000
65A85PHE0-0.0230.00228.594-0.005-0.0050.0000.0000.0000.000
66A86ILE0-0.0210.00423.481-0.005-0.0050.0000.0000.0000.000
67A87ARG10.9450.97026.8940.0730.0730.0000.0000.0000.000
68A88ARG10.8720.88824.6200.0270.0270.0000.0000.0000.000
69A89ARG10.8260.91823.5020.1040.1040.0000.0000.0000.000
70A90GLY00.0450.02923.937-0.003-0.0030.0000.0000.0000.000
71A91ALA00.0080.02620.7120.0090.0090.0000.0000.0000.000
72A92HIS00.0140.01521.6180.0040.0040.0000.0000.0000.000
73A93ARG10.8560.91616.7790.0470.0470.0000.0000.0000.000
74A94ILE0-0.0150.01418.618-0.008-0.0080.0000.0000.0000.000
75A95HIS0-0.010-0.01213.189-0.013-0.0130.0000.0000.0000.000
76A96VAL00.014-0.00315.6270.0020.0020.0000.0000.0000.000
77A97GLU-1-0.797-0.87412.077-0.474-0.4740.0000.0000.0000.000
78A98MET0-0.029-0.01314.7160.0330.0330.0000.0000.0000.000
79A99LYS10.9100.95812.5450.4230.4230.0000.0000.0000.000
80A100PHE00.010-0.00117.0110.0230.0230.0000.0000.0000.000
81A101SER00.0150.00519.801-0.009-0.0090.0000.0000.0000.000
82A102VAL0-0.004-0.01322.3840.0090.0090.0000.0000.0000.000
83A103ARG10.8230.91424.7950.0860.0860.0000.0000.0000.000
84A104ASP-1-0.830-0.91225.234-0.110-0.1100.0000.0000.0000.000
85A105CYS0-0.0030.02927.9300.0010.0010.0000.0000.0000.000
86A106SER0-0.004-0.00329.0780.0030.0030.0000.0000.0000.000
87A107SER0-0.026-0.01429.7220.0020.0020.0000.0000.0000.000
88A108ILE0-0.0170.00131.824-0.001-0.0010.0000.0000.0000.000
89A109PRO0-0.003-0.01534.6760.0040.0040.0000.0000.0000.000
90A110SER0-0.023-0.02438.3450.0000.0000.0000.0000.0000.000
91A111VAL00.0180.02934.4150.0010.0010.0000.0000.0000.000
92A112PRO00.0160.02737.4400.0030.0030.0000.0000.0000.000
93A113GLY00.0280.00037.031-0.002-0.0020.0000.0000.0000.000
94A114SER0-0.007-0.01336.4530.0000.0000.0000.0000.0000.000
95A116LYS10.7970.88229.2800.0590.0590.0000.0000.0000.000
96A117GLU-1-0.805-0.90626.005-0.087-0.0870.0000.0000.0000.000
97A118THR0-0.023-0.01723.935-0.007-0.0070.0000.0000.0000.000
98A119PHE0-0.014-0.00520.3880.0060.0060.0000.0000.0000.000
99A120ASN0-0.0270.02023.906-0.006-0.0060.0000.0000.0000.000
100A121LEU00.0290.01519.796-0.005-0.0050.0000.0000.0000.000
101A122TYR0-0.026-0.02923.8880.0100.0100.0000.0000.0000.000
102A123TYR0-0.002-0.00324.378-0.008-0.0080.0000.0000.0000.000
103A124TYR00.0150.01026.4390.0080.0080.0000.0000.0000.000
104A125GLU-1-0.747-0.86928.235-0.040-0.0400.0000.0000.0000.000
105A126ALA0-0.019-0.01930.3720.0030.0030.0000.0000.0000.000
106A127ASP-1-0.794-0.90132.234-0.034-0.0340.0000.0000.0000.000
107A128PHE0-0.024-0.01634.6390.0010.0010.0000.0000.0000.000
108A129ASP-1-0.830-0.88833.952-0.064-0.0640.0000.0000.0000.000
109A130LEU00.0090.00435.2600.0030.0030.0000.0000.0000.000
110A131ALA0-0.0210.00834.9160.0020.0020.0000.0000.0000.000
111A132THR00.0230.00736.914-0.001-0.0010.0000.0000.0000.000
112A133LYS10.9950.98138.0460.0470.0470.0000.0000.0000.000
113A134THR0-0.059-0.02039.904-0.001-0.0010.0000.0000.0000.000
114A135PHE00.0450.05138.4090.0010.0010.0000.0000.0000.000
115A136PRO00.0460.01533.931-0.002-0.0020.0000.0000.0000.000
116A137ASN00.029-0.00436.426-0.003-0.0030.0000.0000.0000.000
117A138TRP0-0.031-0.03332.894-0.001-0.0010.0000.0000.0000.000
118A139MET0-0.027-0.01334.6280.0010.0010.0000.0000.0000.000
119A140GLU-1-0.859-0.94230.119-0.045-0.0450.0000.0000.0000.000
120A141ASN0-0.044-0.00132.6650.0040.0040.0000.0000.0000.000
121A142PRO0-0.032-0.02134.6850.0010.0010.0000.0000.0000.000
122A143TRP0-0.053-0.02628.625-0.003-0.0030.0000.0000.0000.000
123A144VAL00.0420.02426.4210.0030.0030.0000.0000.0000.000
124A145LYS10.8880.94125.1590.0520.0520.0000.0000.0000.000
125A146VAL0-0.086-0.04019.8300.0050.0050.0000.0000.0000.000
126A147ASP-1-0.763-0.87619.296-0.096-0.0960.0000.0000.0000.000
127A148THR0-0.086-0.07022.1620.0050.0050.0000.0000.0000.000
128A149ILE0-0.0070.01417.979-0.001-0.0010.0000.0000.0000.000
129A150ALA00.0480.00919.4890.0120.0120.0000.0000.0000.000
130A151ALA0-0.009-0.00518.848-0.019-0.0190.0000.0000.0000.000
131A152ASP-1-0.832-0.89714.162-0.238-0.2380.0000.0000.0000.000
132A153GLU-1-0.918-0.96516.320-0.136-0.1360.0000.0000.0000.000
133A154SER0-0.101-0.05111.297-0.029-0.0290.0000.0000.0000.000
134A155ILE0-0.100-0.04813.290-0.030-0.0300.0000.0000.0000.000
135A156SER0-0.026-0.00812.913-0.038-0.0380.0000.0000.0000.000
136A157GLN0-0.001-0.03114.9350.0630.0630.0000.0000.0000.000
137A158VAL00.0460.03517.318-0.028-0.0280.0000.0000.0000.000
138A159ASP-1-0.864-0.94219.795-0.148-0.1480.0000.0000.0000.000
139A160LEU00.002-0.00523.013-0.005-0.0050.0000.0000.0000.000
140A161GLY0-0.006-0.00225.8290.0100.0100.0000.0000.0000.000
141A162GLY0-0.016-0.00728.5430.0080.0080.0000.0000.0000.000
142A163ARG10.8940.93927.4620.1220.1220.0000.0000.0000.000
143A164VAL00.0210.03721.554-0.007-0.0070.0000.0000.0000.000
144A165MET0-0.044-0.01722.3850.0140.0140.0000.0000.0000.000
145A166LYS10.9210.94819.7530.1690.1690.0000.0000.0000.000
146A167ILE0-0.0310.00016.4700.0230.0230.0000.0000.0000.000
147A168ASN00.0810.04515.904-0.033-0.0330.0000.0000.0000.000
148A169THR0-0.004-0.02011.353-0.004-0.0040.0000.0000.0000.000
149A170GLU-1-0.762-0.84012.719-0.246-0.2460.0000.0000.0000.000
150A171VAL0-0.038-0.02110.057-0.002-0.0020.0000.0000.0000.000
151A172ARG10.7420.83812.9780.2020.2020.0000.0000.0000.000
152A173SER00.0260.01214.8480.0000.0000.0000.0000.0000.000
153A174PHE0-0.0050.00316.7480.0160.0160.0000.0000.0000.000
154A175GLY00.0360.00820.376-0.005-0.0050.0000.0000.0000.000
155A176PRO0-0.031-0.01622.6920.0060.0060.0000.0000.0000.000
156A177VAL0-0.0350.00023.312-0.004-0.0040.0000.0000.0000.000
157A178SER0-0.083-0.05825.9990.0040.0040.0000.0000.0000.000
158A179ARG10.9240.96629.2730.0290.0290.0000.0000.0000.000
159A180ASN0-0.039-0.02529.526-0.002-0.0020.0000.0000.0000.000
160A181GLY0-0.010-0.01628.034-0.006-0.0060.0000.0000.0000.000
161A182PHE0-0.031-0.00322.4920.0060.0060.0000.0000.0000.000
162A183TYR0-0.041-0.03827.811-0.002-0.0020.0000.0000.0000.000
163A184LEU00.0260.00321.3620.0020.0020.0000.0000.0000.000
164A185ALA0-0.016-0.01325.8050.0030.0030.0000.0000.0000.000
165A186PHE00.0310.00821.917-0.004-0.0040.0000.0000.0000.000
166A187GLN00.0040.01226.6020.0040.0040.0000.0000.0000.000
167A188ASP-1-0.666-0.83428.121-0.082-0.0820.0000.0000.0000.000
168A189TYR0-0.063-0.04627.0510.0040.0040.0000.0000.0000.000
169A190GLY0-0.0010.00232.6120.0040.0040.0000.0000.0000.000
170A191GLY00.0360.02029.9130.0020.0020.0000.0000.0000.000
171A193MET0-0.0210.00325.378-0.008-0.0080.0000.0000.0000.000
172A194SER00.0330.01025.2100.0040.0040.0000.0000.0000.000
173A195LEU0-0.017-0.00521.056-0.015-0.0150.0000.0000.0000.000
174A196ILE00.007-0.01220.5390.0070.0070.0000.0000.0000.000
175A197ALA00.0420.01418.086-0.001-0.0010.0000.0000.0000.000
176A198VAL0-0.028-0.01318.510-0.004-0.0040.0000.0000.0000.000
177A199ARG10.8070.90611.1340.4130.4130.0000.0000.0000.000
178A200VAL0-0.004-0.00716.9750.0000.0000.0000.0000.0000.000
179A201PHE00.009-0.00711.8630.0090.0090.0000.0000.0000.000
180A202TYR0-0.012-0.01515.9280.0180.0180.0000.0000.0000.000
181A203ARG10.8990.9439.0930.2910.2910.0000.0000.0000.000
182A204LYS10.8470.92114.2950.1540.1540.0000.0000.0000.000
183A205CYS0-0.031-0.02815.6860.0160.0160.0000.0000.0000.000
184A206PRO00.0290.01916.2140.0000.0000.0000.0000.0000.000
185A207ARG10.9250.97219.2280.0030.0030.0000.0000.0000.000