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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: YYRR2

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2087541.669999
FMO2-HF: Nuclear repulsion 2010329.114976
FMO2-HF: Total energy -77212.555022
FMO2-MP2: Total energy -77430.854539


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.
-3.889-1.7820.053-0.897-1.2640
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 : -0.009
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].
3A23ALA0-0.041-0.0243.769-1.558-0.2900.004-0.543-0.7300.003
4A24ILE00.0160.0023.325-1.619-0.8900.050-0.343-0.436-0.003
5A25SER00.0170.0174.5290.1830.293-0.001-0.011-0.0980.000
6A26ASP-1-0.953-0.9805.9830.1670.1670.0000.0000.0000.000
7A27PRO0-0.0030.0029.701-0.074-0.0740.0000.0000.0000.000
8A28GLU-1-0.864-0.9459.474-0.326-0.3260.0000.0000.0000.000
9A29GLU-1-0.989-0.99413.379-0.128-0.1280.0000.0000.0000.000
10A30THR00.0510.01815.924-0.005-0.0050.0000.0000.0000.000
11A31LEU0-0.120-0.07017.9230.0160.0160.0000.0000.0000.000
12A32MET0-0.048-0.02520.0460.0090.0090.0000.0000.0000.000
13A33ASP-1-0.745-0.84917.843-0.248-0.2480.0000.0000.0000.000
14A34SER00.0330.02120.4580.0040.0040.0000.0000.0000.000
15A35THR0-0.064-0.06518.9430.0070.0070.0000.0000.0000.000
16A36THR0-0.034-0.01620.4980.0060.0060.0000.0000.0000.000
17A37ALA0-0.039-0.00123.2060.0120.0120.0000.0000.0000.000
18A38THR00.0350.01326.5180.0000.0000.0000.0000.0000.000
19A39ALA0-0.027-0.01929.2580.0020.0020.0000.0000.0000.000
20A40GLU-1-0.900-0.94930.347-0.084-0.0840.0000.0000.0000.000
21A41LEU0-0.011-0.00925.9100.0030.0030.0000.0000.0000.000
22A42GLY0-0.010-0.00729.9960.0040.0040.0000.0000.0000.000
23A43TRP0-0.063-0.03923.5270.0040.0040.0000.0000.0000.000
24A44MET0-0.064-0.02031.1480.0040.0040.0000.0000.0000.000
25A45VAL00.0680.04232.591-0.002-0.0020.0000.0000.0000.000
26A46HIS10.8140.94034.3710.0470.0470.0000.0000.0000.000
27A47PRO00.022-0.00835.4620.0000.0000.0000.0000.0000.000
28A48PRO00.048-0.00936.967-0.002-0.0020.0000.0000.0000.000
29A49SER00.0200.02638.305-0.001-0.0010.0000.0000.0000.000
30A50GLY00.0300.02935.1610.0000.0000.0000.0000.0000.000
31A51TRP0-0.058-0.04426.164-0.004-0.0040.0000.0000.0000.000
32A52GLU-1-0.909-0.96132.082-0.073-0.0730.0000.0000.0000.000
33A53GLU-1-0.825-0.92430.146-0.101-0.1010.0000.0000.0000.000
34A54VAL00.0040.00029.9120.0040.0040.0000.0000.0000.000
35A55SER0-0.042-0.02729.134-0.008-0.0080.0000.0000.0000.000
36A56GLY00.0280.01327.8310.0060.0060.0000.0000.0000.000
37A57TYR00.010-0.02526.399-0.004-0.0040.0000.0000.0000.000
38A58ASP-1-0.841-0.93421.968-0.207-0.2070.0000.0000.0000.000
39A59GLU-1-0.856-0.92519.423-0.276-0.2760.0000.0000.0000.000
40A60ASN0-0.102-0.05321.1550.0100.0100.0000.0000.0000.000
41A61MET0-0.068-0.03125.3150.0140.0140.0000.0000.0000.000
42A62ASN0-0.0160.02223.7570.0080.0080.0000.0000.0000.000
43A63THR0-0.070-0.01725.9690.0010.0010.0000.0000.0000.000
44A64ILE00.0040.02421.5860.0000.0000.0000.0000.0000.000
45A65ARG10.8300.92225.2400.1210.1210.0000.0000.0000.000
46A66THR0-0.035-0.00924.411-0.008-0.0080.0000.0000.0000.000
47A67TYR00.0270.01026.1660.0110.0110.0000.0000.0000.000
48A68GLN0-0.021-0.00526.983-0.017-0.0170.0000.0000.0000.000
49A69VAL00.0490.02329.2210.0070.0070.0000.0000.0000.000
50A70CYS0-0.106-0.05429.441-0.003-0.0030.0000.0000.0000.000
51A71ASN00.0240.01833.1720.0000.0000.0000.0000.0000.000
52A72VAL00.0010.00133.4240.0030.0030.0000.0000.0000.000
53A73PHE0-0.068-0.04435.9520.0030.0030.0000.0000.0000.000
54A74GLU-1-0.926-0.94738.905-0.045-0.0450.0000.0000.0000.000
55A75SER0-0.016-0.01339.162-0.001-0.0010.0000.0000.0000.000
56A76SER0-0.052-0.04039.4100.0000.0000.0000.0000.0000.000
57A77GLN00.0720.07135.205-0.003-0.0030.0000.0000.0000.000
58A78ASN00.0550.02834.356-0.002-0.0020.0000.0000.0000.000
59A79ASN0-0.077-0.04632.6000.0050.0050.0000.0000.0000.000
60A80TRP0-0.069-0.01830.619-0.005-0.0050.0000.0000.0000.000
61A81LEU00.0150.03326.7150.0010.0010.0000.0000.0000.000
62A82ARG10.8850.92828.6040.0490.0490.0000.0000.0000.000
63A83THR00.0190.01224.5410.0010.0010.0000.0000.0000.000
64A84LYS10.9320.96828.0260.0820.0820.0000.0000.0000.000
65A85PHE0-0.0110.01728.108-0.003-0.0030.0000.0000.0000.000
66A86ILE0-0.0120.00223.029-0.005-0.0050.0000.0000.0000.000
67A87ARG10.9010.94426.6220.0610.0610.0000.0000.0000.000
68A88ARG10.9570.97024.0540.0060.0060.0000.0000.0000.000
69A89ARG10.9000.94123.5230.0750.0750.0000.0000.0000.000
70A90GLY00.0400.02223.897-0.001-0.0010.0000.0000.0000.000
71A91ALA00.0180.02919.9560.0120.0120.0000.0000.0000.000
72A92HIS0-0.009-0.00521.1210.0030.0030.0000.0000.0000.000
73A93ARG10.9240.95416.261-0.024-0.0240.0000.0000.0000.000
74A94ILE0-0.0290.00318.334-0.008-0.0080.0000.0000.0000.000
75A95HIS0-0.024-0.00512.972-0.004-0.0040.0000.0000.0000.000
76A96VAL00.012-0.01015.465-0.004-0.0040.0000.0000.0000.000
77A97GLU-1-0.897-0.95211.322-0.428-0.4280.0000.0000.0000.000
78A98MET0-0.013-0.00114.5260.0210.0210.0000.0000.0000.000
79A99LYS10.9851.00713.2290.3870.3870.0000.0000.0000.000
80A100PHE00.0120.00017.0830.0240.0240.0000.0000.0000.000
81A101SER0-0.0140.00119.586-0.014-0.0140.0000.0000.0000.000
82A102VAL00.0440.01322.2460.0100.0100.0000.0000.0000.000
83A103ARG10.8230.90324.5830.0810.0810.0000.0000.0000.000
84A104ASP-1-0.863-0.90525.619-0.096-0.0960.0000.0000.0000.000
85A105CYS0-0.017-0.00527.9700.0010.0010.0000.0000.0000.000
86A106SER0-0.017-0.00529.9370.0020.0020.0000.0000.0000.000
87A107SER0-0.019-0.01630.0760.0000.0000.0000.0000.0000.000
88A108ILE0-0.0300.00131.893-0.002-0.0020.0000.0000.0000.000
89A109PRO00.021-0.00934.6890.0040.0040.0000.0000.0000.000
90A110SER0-0.019-0.02738.2960.0010.0010.0000.0000.0000.000
91A111VAL0-0.0070.02334.4440.0020.0020.0000.0000.0000.000
92A112PRO00.0290.02337.3370.0030.0030.0000.0000.0000.000
93A113GLY00.013-0.01337.113-0.002-0.0020.0000.0000.0000.000
94A114SER0-0.066-0.03036.7210.0010.0010.0000.0000.0000.000
95A116LYS10.9450.96129.6120.0430.0430.0000.0000.0000.000
96A117GLU-1-0.796-0.89726.082-0.079-0.0790.0000.0000.0000.000
97A118THR0-0.0130.01223.961-0.006-0.0060.0000.0000.0000.000
98A119PHE00.0250.01720.2470.0050.0050.0000.0000.0000.000
99A120ASN0-0.0240.02623.952-0.002-0.0020.0000.0000.0000.000
100A121LEU00.0540.03219.559-0.004-0.0040.0000.0000.0000.000
101A122TYR0-0.061-0.04823.6640.0120.0120.0000.0000.0000.000
102A123TYR00.002-0.00924.100-0.008-0.0080.0000.0000.0000.000
103A124TYR00.0050.00526.1680.0070.0070.0000.0000.0000.000
104A125GLU-1-0.841-0.93527.764-0.014-0.0140.0000.0000.0000.000
105A126ALA0-0.001-0.00929.8080.0020.0020.0000.0000.0000.000
106A127ASP-1-0.833-0.91931.809-0.016-0.0160.0000.0000.0000.000
107A128PHE00.000-0.01634.131-0.001-0.0010.0000.0000.0000.000
108A129ASP-1-0.863-0.89233.809-0.049-0.0490.0000.0000.0000.000
109A130LEU00.0200.01234.9070.0010.0010.0000.0000.0000.000
110A131ALA0-0.032-0.00134.5360.0020.0020.0000.0000.0000.000
111A132THR00.0310.01036.561-0.001-0.0010.0000.0000.0000.000
112A133LYS10.9670.95837.8880.0390.0390.0000.0000.0000.000
113A134THR0-0.056-0.02139.497-0.001-0.0010.0000.0000.0000.000
114A135PHE00.0380.06037.6600.0020.0020.0000.0000.0000.000
115A136PRO00.0450.00933.746-0.003-0.0030.0000.0000.0000.000
116A137ASN00.0350.01136.755-0.003-0.0030.0000.0000.0000.000
117A138TRP0-0.031-0.03332.618-0.001-0.0010.0000.0000.0000.000
118A139MET0-0.020-0.01234.2090.0000.0000.0000.0000.0000.000
119A140GLU-1-0.856-0.93530.486-0.019-0.0190.0000.0000.0000.000
120A141ASN0-0.055-0.00232.6100.0020.0020.0000.0000.0000.000
121A142PRO0-0.021-0.02134.6580.0000.0000.0000.0000.0000.000
122A143TRP0-0.058-0.02728.179-0.002-0.0020.0000.0000.0000.000
123A144VAL00.0440.01125.9650.0030.0030.0000.0000.0000.000
124A145LYS10.9400.98125.3410.0230.0230.0000.0000.0000.000
125A146VAL0-0.089-0.04319.7020.0070.0070.0000.0000.0000.000
126A147ASP-1-0.782-0.88219.456-0.040-0.0400.0000.0000.0000.000
127A148THR0-0.095-0.07422.243-0.003-0.0030.0000.0000.0000.000
128A149ILE0-0.048-0.02318.2130.0000.0000.0000.0000.0000.000
129A150ALA00.025-0.01019.5590.0070.0070.0000.0000.0000.000
130A151ALA0-0.019-0.00818.612-0.016-0.0160.0000.0000.0000.000
131A152ASP-1-0.833-0.87913.534-0.223-0.2230.0000.0000.0000.000
132A153GLU-1-0.975-1.00216.426-0.104-0.1040.0000.0000.0000.000
133A154SER0-0.088-0.04811.848-0.034-0.0340.0000.0000.0000.000
134A155ILE0-0.034-0.01013.8850.0000.0000.0000.0000.0000.000
135A156SER0-0.033-0.01812.953-0.039-0.0390.0000.0000.0000.000
136A157GLN0-0.048-0.06314.9310.0650.0650.0000.0000.0000.000
137A158VAL00.0220.02517.344-0.027-0.0270.0000.0000.0000.000
138A159ASP-1-0.875-0.94619.723-0.164-0.1640.0000.0000.0000.000
139A160LEU00.0020.00222.391-0.003-0.0030.0000.0000.0000.000
140A161GLY0-0.034-0.02425.6320.0110.0110.0000.0000.0000.000
141A162GLY0-0.047-0.02828.789-0.002-0.0020.0000.0000.0000.000
142A163ARG10.9390.96827.5750.1140.1140.0000.0000.0000.000
143A164VAL00.1030.05721.808-0.007-0.0070.0000.0000.0000.000
144A165MET0-0.090-0.03322.1090.0120.0120.0000.0000.0000.000
145A166LYS10.9750.97619.6760.1730.1730.0000.0000.0000.000
146A167ILE0-0.019-0.00616.1420.0200.0200.0000.0000.0000.000
147A168ASN00.0600.03615.521-0.042-0.0420.0000.0000.0000.000
148A169THR0-0.006-0.02111.366-0.004-0.0040.0000.0000.0000.000
149A170GLU-1-0.809-0.87312.729-0.218-0.2180.0000.0000.0000.000
150A171VAL00.007-0.0049.9960.0080.0080.0000.0000.0000.000
151A172ARG10.7730.87313.0310.1500.1500.0000.0000.0000.000
152A173SER0-0.002-0.01014.6250.0010.0010.0000.0000.0000.000
153A174PHE0-0.004-0.00216.5720.0120.0120.0000.0000.0000.000
154A175GLY00.0160.01120.121-0.004-0.0040.0000.0000.0000.000
155A176PRO0-0.036-0.02322.4430.0070.0070.0000.0000.0000.000
156A177VAL0-0.0020.01223.950-0.004-0.0040.0000.0000.0000.000
157A178SER0-0.057-0.04725.6920.0030.0030.0000.0000.0000.000
158A179ARG10.8890.96028.7950.0090.0090.0000.0000.0000.000
159A180ASN0-0.022-0.02428.9450.0000.0000.0000.0000.0000.000
160A181GLY0-0.017-0.01927.687-0.005-0.0050.0000.0000.0000.000
161A182PHE0-0.007-0.00221.9910.0070.0070.0000.0000.0000.000
162A183TYR0-0.058-0.03727.385-0.004-0.0040.0000.0000.0000.000
163A184LEU00.0290.00721.2480.0050.0050.0000.0000.0000.000
164A185ALA0-0.005-0.01025.6140.0010.0010.0000.0000.0000.000
165A186PHE00.0290.01021.311-0.001-0.0010.0000.0000.0000.000
166A187GLN00.0440.01126.4200.0030.0030.0000.0000.0000.000
167A188ASP-1-0.688-0.84827.923-0.070-0.0700.0000.0000.0000.000
168A189TYR0-0.086-0.06527.0590.0060.0060.0000.0000.0000.000
169A190GLY00.004-0.00632.5680.0040.0040.0000.0000.0000.000
170A191GLY00.0140.01129.9270.0020.0020.0000.0000.0000.000
171A193MET0-0.026-0.00225.200-0.008-0.0080.0000.0000.0000.000
172A194SER00.0150.00625.0310.0020.0020.0000.0000.0000.000
173A195LEU0-0.026-0.01920.975-0.011-0.0110.0000.0000.0000.000
174A196ILE0-0.002-0.02220.1390.0050.0050.0000.0000.0000.000
175A197ALA00.0300.00218.2280.0000.0000.0000.0000.0000.000
176A198VAL0-0.030-0.00318.504-0.002-0.0020.0000.0000.0000.000
177A199ARG10.8820.95811.1110.3690.3690.0000.0000.0000.000
178A200VAL0-0.041-0.01916.3580.0000.0000.0000.0000.0000.000
179A201PHE00.0410.02010.9160.0070.0070.0000.0000.0000.000
180A202TYR0-0.011-0.00915.6060.0240.0240.0000.0000.0000.000
181A203ARG11.0171.0019.212-0.027-0.0270.0000.0000.0000.000
182A204LYS10.9440.98514.0490.1220.1220.0000.0000.0000.000
183A205CYS0-0.001-0.01714.8130.0250.0250.0000.0000.0000.000
184A206PRO0-0.0120.00516.312-0.003-0.0030.0000.0000.0000.000
185A207ARG10.9861.00919.200-0.030-0.0300.0000.0000.0000.000