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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: VRYY1

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2089491.085642
FMO2-HF: Nuclear repulsion 2012277.069954
FMO2-HF: Total energy -77214.015687
FMO2-MP2: Total energy -77432.205516


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.
-3.512-1.4550.051-0.867-1.2420
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 : -0.009 / q_NPA : -0.015
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].
3A23ALA0-0.039-0.0233.779-1.489-0.2360.005-0.524-0.7340.002
4A24ILE00.0190.0033.339-1.589-0.8880.047-0.332-0.417-0.002
5A25SER00.0140.0184.5830.1800.283-0.001-0.011-0.0910.000
6A26ASP-1-0.948-0.9785.9930.1420.1420.0000.0000.0000.000
7A27PRO00.0100.0049.708-0.067-0.0670.0000.0000.0000.000
8A28GLU-1-0.761-0.8849.703-0.279-0.2790.0000.0000.0000.000
9A29GLU-1-0.880-0.91313.397-0.121-0.1210.0000.0000.0000.000
10A30THR00.0340.01016.041-0.006-0.0060.0000.0000.0000.000
11A31LEU0-0.118-0.06517.9300.0160.0160.0000.0000.0000.000
12A32MET0-0.023-0.02620.0320.0100.0100.0000.0000.0000.000
13A33ASP-1-0.756-0.86217.403-0.241-0.2410.0000.0000.0000.000
14A34SER00.0330.02320.4480.0030.0030.0000.0000.0000.000
15A35THR0-0.055-0.04718.9170.0060.0060.0000.0000.0000.000
16A36THR0-0.040-0.02520.5370.0050.0050.0000.0000.0000.000
17A37ALA0-0.041-0.00223.2200.0110.0110.0000.0000.0000.000
18A38THR00.0540.02226.5230.0000.0000.0000.0000.0000.000
19A39ALA0-0.035-0.02529.2740.0020.0020.0000.0000.0000.000
20A40GLU-1-0.931-0.97130.343-0.079-0.0790.0000.0000.0000.000
21A41LEU00.0130.00225.8830.0030.0030.0000.0000.0000.000
22A42GLY00.0100.02329.9760.0030.0030.0000.0000.0000.000
23A43TRP0-0.037-0.02923.3890.0030.0030.0000.0000.0000.000
24A44MET0-0.044-0.00531.2050.0040.0040.0000.0000.0000.000
25A45VAL00.0660.03732.667-0.002-0.0020.0000.0000.0000.000
26A46HIS10.8160.94334.4040.0470.0470.0000.0000.0000.000
27A47PRO00.026-0.00235.4840.0000.0000.0000.0000.0000.000
28A48PRO00.040-0.01037.003-0.002-0.0020.0000.0000.0000.000
29A49SER00.0160.02038.352-0.001-0.0010.0000.0000.0000.000
30A50GLY00.0350.03735.1920.0000.0000.0000.0000.0000.000
31A51TRP0-0.050-0.04926.043-0.004-0.0040.0000.0000.0000.000
32A52GLU-1-0.860-0.92232.117-0.073-0.0730.0000.0000.0000.000
33A53GLU-1-0.790-0.88830.047-0.098-0.0980.0000.0000.0000.000
34A54VAL00.0100.00230.0270.0040.0040.0000.0000.0000.000
35A55SER0-0.034-0.01729.104-0.008-0.0080.0000.0000.0000.000
36A56GLY00.0300.01427.8110.0060.0060.0000.0000.0000.000
37A57TYR0-0.072-0.01626.391-0.004-0.0040.0000.0000.0000.000
38A58ASP-1-0.796-0.89922.329-0.197-0.1970.0000.0000.0000.000
39A59GLU-1-0.884-0.93819.388-0.261-0.2610.0000.0000.0000.000
40A60ASN0-0.111-0.05521.2100.0120.0120.0000.0000.0000.000
41A61MET0-0.059-0.03025.3540.0130.0130.0000.0000.0000.000
42A62ASN0-0.0290.00222.5990.0210.0210.0000.0000.0000.000
43A63THR00.025-0.01625.9820.0010.0010.0000.0000.0000.000
44A64ILE0-0.0090.01421.0960.0000.0000.0000.0000.0000.000
45A65ARG10.8260.93925.2340.1160.1160.0000.0000.0000.000
46A66THR0-0.041-0.02224.268-0.008-0.0080.0000.0000.0000.000
47A67TYR0-0.019-0.05126.2290.0110.0110.0000.0000.0000.000
48A68GLN0-0.066-0.02727.041-0.015-0.0150.0000.0000.0000.000
49A69VAL00.0460.02329.2730.0060.0060.0000.0000.0000.000
50A70CYS0-0.093-0.05329.458-0.003-0.0030.0000.0000.0000.000
51A71ASN00.0120.00933.2080.0000.0000.0000.0000.0000.000
52A72VAL00.0090.00733.3850.0030.0030.0000.0000.0000.000
53A73PHE0-0.069-0.04335.9700.0030.0030.0000.0000.0000.000
54A74GLU-1-0.913-0.94238.917-0.044-0.0440.0000.0000.0000.000
55A75SER00.0100.00039.171-0.001-0.0010.0000.0000.0000.000
56A76SER0-0.094-0.06339.3600.0000.0000.0000.0000.0000.000
57A77GLN00.0660.06035.339-0.003-0.0030.0000.0000.0000.000
58A78ASN00.0520.02434.390-0.001-0.0010.0000.0000.0000.000
59A79ASN0-0.058-0.03432.6600.0050.0050.0000.0000.0000.000
60A80TRP0-0.075-0.02930.503-0.005-0.0050.0000.0000.0000.000
61A81LEU00.0080.03126.8600.0010.0010.0000.0000.0000.000
62A82ARG10.8740.92428.6330.0480.0480.0000.0000.0000.000
63A83THR00.0250.02124.5950.0000.0000.0000.0000.0000.000
64A84LYS10.8750.92528.0710.0820.0820.0000.0000.0000.000
65A85PHE0-0.0110.01328.152-0.003-0.0030.0000.0000.0000.000
66A86ILE0-0.024-0.00423.180-0.005-0.0050.0000.0000.0000.000
67A87ARG10.9190.95526.6630.0590.0590.0000.0000.0000.000
68A88ARG10.8850.90923.9380.0060.0060.0000.0000.0000.000
69A89ARG10.8480.92323.5450.0800.0800.0000.0000.0000.000
70A90GLY00.0380.01723.924-0.002-0.0020.0000.0000.0000.000
71A91ALA00.0030.03320.0220.0110.0110.0000.0000.0000.000
72A92HIS00.0340.01721.124-0.001-0.0010.0000.0000.0000.000
73A93ARG10.9060.94616.261-0.008-0.0080.0000.0000.0000.000
74A94ILE0-0.0250.00018.356-0.009-0.0090.0000.0000.0000.000
75A95HIS0-0.019-0.00512.655-0.007-0.0070.0000.0000.0000.000
76A96VAL00.017-0.00515.467-0.003-0.0030.0000.0000.0000.000
77A97GLU-1-0.819-0.89312.029-0.403-0.4030.0000.0000.0000.000
78A98MET0-0.015-0.00714.5650.0220.0220.0000.0000.0000.000
79A99LYS10.9220.97413.0430.3690.3690.0000.0000.0000.000
80A100PHE00.0180.00216.8370.0230.0230.0000.0000.0000.000
81A101SER0-0.015-0.01119.581-0.012-0.0120.0000.0000.0000.000
82A102VAL00.0130.00122.2400.0100.0100.0000.0000.0000.000
83A103ARG10.8220.90824.5590.0790.0790.0000.0000.0000.000
84A104ASP-1-0.855-0.91525.314-0.097-0.0970.0000.0000.0000.000
85A105CYS00.0230.02427.9280.0010.0010.0000.0000.0000.000
86A106SER0-0.0070.00229.7340.0020.0020.0000.0000.0000.000
87A107SER0-0.023-0.01230.0150.0010.0010.0000.0000.0000.000
88A108ILE0-0.0260.00231.733-0.001-0.0010.0000.0000.0000.000
89A109PRO00.016-0.00734.6580.0040.0040.0000.0000.0000.000
90A110SER0-0.029-0.03338.2640.0000.0000.0000.0000.0000.000
91A111VAL00.0150.03534.3520.0020.0020.0000.0000.0000.000
92A112PRO00.0160.01937.2600.0030.0030.0000.0000.0000.000
93A113GLY00.027-0.00537.105-0.002-0.0020.0000.0000.0000.000
94A114SER0-0.016-0.00636.7000.0010.0010.0000.0000.0000.000
95A116LYS10.8380.90229.5180.0470.0470.0000.0000.0000.000
96A117GLU-1-0.804-0.91025.953-0.076-0.0760.0000.0000.0000.000
97A118THR0-0.022-0.01223.789-0.006-0.0060.0000.0000.0000.000
98A119PHE00.0110.00820.2860.0060.0060.0000.0000.0000.000
99A120ASN0-0.0520.01923.941-0.004-0.0040.0000.0000.0000.000
100A121LEU00.0530.03319.652-0.004-0.0040.0000.0000.0000.000
101A122TYR0-0.051-0.05423.6590.0100.0100.0000.0000.0000.000
102A123TYR00.000-0.00724.080-0.007-0.0070.0000.0000.0000.000
103A124TYR00.0140.01226.1640.0070.0070.0000.0000.0000.000
104A125GLU-1-0.793-0.90327.616-0.018-0.0180.0000.0000.0000.000
105A126ALA0-0.011-0.01329.8050.0020.0020.0000.0000.0000.000
106A127ASP-1-0.815-0.90931.821-0.018-0.0180.0000.0000.0000.000
107A128PHE00.000-0.01334.1710.0000.0000.0000.0000.0000.000
108A129ASP-1-0.850-0.89733.964-0.049-0.0490.0000.0000.0000.000
109A130LEU00.0100.00634.9410.0010.0010.0000.0000.0000.000
110A131ALA0-0.0330.00034.5570.0020.0020.0000.0000.0000.000
111A132THR00.0330.00236.587-0.001-0.0010.0000.0000.0000.000
112A133LYS10.9700.96937.9180.0390.0390.0000.0000.0000.000
113A134THR0-0.046-0.02039.523-0.001-0.0010.0000.0000.0000.000
114A135PHE00.0360.06138.0650.0010.0010.0000.0000.0000.000
115A136PRO00.0400.01033.657-0.002-0.0020.0000.0000.0000.000
116A137ASN00.0350.00436.762-0.002-0.0020.0000.0000.0000.000
117A138TRP0-0.032-0.03432.682-0.001-0.0010.0000.0000.0000.000
118A139MET0-0.009-0.00534.1890.0000.0000.0000.0000.0000.000
119A140GLU-1-0.847-0.93530.125-0.023-0.0230.0000.0000.0000.000
120A141ASN0-0.052-0.00232.5840.0030.0030.0000.0000.0000.000
121A142PRO0-0.026-0.02134.6370.0000.0000.0000.0000.0000.000
122A143TRP0-0.050-0.02928.238-0.002-0.0020.0000.0000.0000.000
123A144VAL00.0410.01625.9780.0030.0030.0000.0000.0000.000
124A145LYS10.9090.96325.1170.0280.0280.0000.0000.0000.000
125A146VAL0-0.089-0.04219.6650.0060.0060.0000.0000.0000.000
126A147ASP-1-0.767-0.88219.421-0.051-0.0510.0000.0000.0000.000
127A148THR0-0.095-0.07022.204-0.002-0.0020.0000.0000.0000.000
128A149ILE0-0.024-0.01018.292-0.001-0.0010.0000.0000.0000.000
129A150ALA00.0410.00119.5450.0070.0070.0000.0000.0000.000
130A151ALA0-0.023-0.00918.600-0.017-0.0170.0000.0000.0000.000
131A152ASP-1-0.834-0.89614.211-0.206-0.2060.0000.0000.0000.000
132A153GLU-1-0.943-0.96216.333-0.101-0.1010.0000.0000.0000.000
133A154SER0-0.108-0.06911.725-0.034-0.0340.0000.0000.0000.000
134A155ILE0-0.050-0.02213.842-0.003-0.0030.0000.0000.0000.000
135A156SER0-0.023-0.01412.920-0.035-0.0350.0000.0000.0000.000
136A157GLN0-0.013-0.03714.9580.0590.0590.0000.0000.0000.000
137A158VAL00.0290.02917.407-0.026-0.0260.0000.0000.0000.000
138A159ASP-1-0.874-0.94519.783-0.156-0.1560.0000.0000.0000.000
139A160LEU0-0.008-0.00522.419-0.003-0.0030.0000.0000.0000.000
140A161GLY0-0.025-0.02325.6330.0100.0100.0000.0000.0000.000
141A162GLY0-0.049-0.03128.810-0.002-0.0020.0000.0000.0000.000
142A163ARG10.9520.97927.5570.1080.1080.0000.0000.0000.000
143A164VAL00.0780.04021.484-0.007-0.0070.0000.0000.0000.000
144A165MET0-0.076-0.02422.1490.0110.0110.0000.0000.0000.000
145A166LYS10.9340.95319.6990.1700.1700.0000.0000.0000.000
146A167ILE0-0.0180.00716.2570.0220.0220.0000.0000.0000.000
147A168ASN00.0690.04415.528-0.036-0.0360.0000.0000.0000.000
148A169THR00.001-0.02411.476-0.002-0.0020.0000.0000.0000.000
149A170GLU-1-0.796-0.85512.748-0.200-0.2000.0000.0000.0000.000
150A171VAL0-0.014-0.01510.1090.0060.0060.0000.0000.0000.000
151A172ARG10.7500.85713.0300.1500.1500.0000.0000.0000.000
152A173SER00.0320.00914.6560.0020.0020.0000.0000.0000.000
153A174PHE0-0.020-0.01216.5410.0120.0120.0000.0000.0000.000
154A175GLY00.0220.01720.083-0.004-0.0040.0000.0000.0000.000
155A176PRO0-0.045-0.02522.4020.0060.0060.0000.0000.0000.000
156A177VAL0-0.0100.00823.217-0.003-0.0030.0000.0000.0000.000
157A178SER0-0.064-0.05425.6690.0030.0030.0000.0000.0000.000
158A179ARG10.9070.96428.7760.0120.0120.0000.0000.0000.000
159A180ASN0-0.021-0.01628.9470.0000.0000.0000.0000.0000.000
160A181GLY0-0.005-0.00627.714-0.005-0.0050.0000.0000.0000.000
161A182PHE0-0.011-0.00522.0270.0060.0060.0000.0000.0000.000
162A183TYR0-0.056-0.03127.411-0.003-0.0030.0000.0000.0000.000
163A184LEU00.0290.00521.2590.0040.0040.0000.0000.0000.000
164A185ALA0-0.009-0.01525.6320.0010.0010.0000.0000.0000.000
165A186PHE00.0320.01221.534-0.001-0.0010.0000.0000.0000.000
166A187GLN00.0320.02126.4370.0030.0030.0000.0000.0000.000
167A188ASP-1-0.705-0.85027.926-0.069-0.0690.0000.0000.0000.000
168A189TYR0-0.050-0.04126.9590.0040.0040.0000.0000.0000.000
169A190GLY00.0150.00232.4950.0040.0040.0000.0000.0000.000
170A191GLY00.0100.01029.9370.0020.0020.0000.0000.0000.000
171A193MET0-0.0310.00125.256-0.008-0.0080.0000.0000.0000.000
172A194SER00.0330.01325.0740.0030.0030.0000.0000.0000.000
173A195LEU0-0.045-0.02720.979-0.011-0.0110.0000.0000.0000.000
174A196ILE0-0.005-0.02420.5310.0050.0050.0000.0000.0000.000
175A197ALA00.0490.01218.1990.0000.0000.0000.0000.0000.000
176A198VAL0-0.039-0.01318.511-0.003-0.0030.0000.0000.0000.000
177A199ARG10.8440.92410.9440.3510.3510.0000.0000.0000.000
178A200VAL0-0.027-0.01716.408-0.001-0.0010.0000.0000.0000.000
179A201PHE00.0280.01411.1930.0040.0040.0000.0000.0000.000
180A202TYR0-0.012-0.00515.6330.0190.0190.0000.0000.0000.000
181A203ARG10.9310.9568.6480.1420.1420.0000.0000.0000.000
182A204LYS10.8510.92514.0600.1270.1270.0000.0000.0000.000
183A205CYS0-0.003-0.02115.0620.0200.0200.0000.0000.0000.000
184A206PRO00.0160.01416.391-0.001-0.0010.0000.0000.0000.000
185A207ARG10.9400.98319.199-0.021-0.0210.0000.0000.0000.000