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: QYQJY

Calculation Name: 2B34-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B34

Chain ID: A

ChEMBL ID:

UniProt ID: Q20062

Base Structure: X-ray

Registration Date: 2023-09-20

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2113744.127353
FMO2-HF: Nuclear repulsion 2040409.437688
FMO2-HF: Total energy -73334.689664
FMO2-MP2: Total energy -73550.464089


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:8:ALA)


Summations of interaction energy for fragment #1(A:8: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.
-7.282-2.1733.606-3.462-5.253-0.022
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.012
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].
3A10ILE00.0240.0283.812-1.2540.627-0.028-0.880-0.9730.001
4A11ASN00.0400.0326.1640.1340.1340.0000.0000.0000.000
5A12PRO00.022-0.0089.629-0.056-0.0560.0000.0000.0000.000
6A13THR0-0.046-0.02911.524-0.001-0.0010.0000.0000.0000.000
7A14ASN00.0260.0195.914-0.202-0.2020.0000.0000.0000.000
8A15SER00.014-0.0088.123-0.163-0.1630.0000.0000.0000.000
9A16ALA00.0310.0189.4680.0730.0730.0000.0000.0000.000
10A17LEU0-0.052-0.00710.986-0.077-0.0770.0000.0000.0000.000
11A18PHE00.025-0.01713.2030.0400.0400.0000.0000.0000.000
12A19VAL00.020-0.00314.960-0.022-0.0220.0000.0000.0000.000
13A20CYS00.0350.02417.7770.0000.0000.0000.0000.0000.000
14A21ASP-1-0.719-0.84519.610-0.173-0.1730.0000.0000.0000.000
15A22LEU00.0340.02820.3830.0070.0070.0000.0000.0000.000
16A23GLN0-0.033-0.04224.0700.0000.0000.0000.0000.0000.000
17A24GLU-1-0.841-0.93227.722-0.084-0.0840.0000.0000.0000.000
18A25LYS10.8360.91831.1260.0810.0810.0000.0000.0000.000
19A26PHE00.0030.00826.8610.0010.0010.0000.0000.0000.000
20A27ALA0-0.0030.00529.814-0.003-0.0030.0000.0000.0000.000
21A28SER0-0.010-0.00330.8900.0000.0000.0000.0000.0000.000
22A29ASN0-0.098-0.05331.1730.0050.0050.0000.0000.0000.000
23A30ILE00.0160.00824.988-0.007-0.0070.0000.0000.0000.000
24A31LYS10.8480.93326.0460.1280.1280.0000.0000.0000.000
25A32TYR00.0440.03424.772-0.015-0.0150.0000.0000.0000.000
26A33PHE00.0660.04925.427-0.008-0.0080.0000.0000.0000.000
27A34PRO00.0270.00426.084-0.004-0.0040.0000.0000.0000.000
28A35GLU-1-0.819-0.91524.568-0.125-0.1250.0000.0000.0000.000
29A36ILE00.0120.01920.844-0.007-0.0070.0000.0000.0000.000
30A37ILE0-0.0060.01921.691-0.011-0.0110.0000.0000.0000.000
31A38THR0-0.023-0.01323.4550.0030.0030.0000.0000.0000.000
32A39THR0-0.005-0.01418.2930.0090.0090.0000.0000.0000.000
33A40SER00.010-0.02018.639-0.020-0.0200.0000.0000.0000.000
34A41ARG10.7670.87519.5300.0880.0880.0000.0000.0000.000
35A42ARG10.8760.94219.4270.1370.1370.0000.0000.0000.000
36A43LEU00.0110.00113.4340.0020.0020.0000.0000.0000.000
37A44ILE00.0020.01616.9470.0030.0030.0000.0000.0000.000
38A45ASP-1-0.783-0.86219.224-0.078-0.0780.0000.0000.0000.000
39A46ALA0-0.002-0.00716.4240.0160.0160.0000.0000.0000.000
40A47ALA0-0.003-0.00215.6940.0140.0140.0000.0000.0000.000
41A48ARG10.8240.89516.8760.0920.0920.0000.0000.0000.000
42A49ILE0-0.086-0.03519.9820.0150.0150.0000.0000.0000.000
43A50LEU0-0.051-0.03314.6850.0220.0220.0000.0000.0000.000
44A51SER0-0.037-0.00817.0280.0170.0170.0000.0000.0000.000
45A52ILE0-0.0300.00212.2290.0060.0060.0000.0000.0000.000
46A53PRO0-0.003-0.00514.224-0.006-0.0060.0000.0000.0000.000
47A54THR0-0.0020.00115.100-0.037-0.0370.0000.0000.0000.000
48A55ILE0-0.008-0.00116.7960.0210.0210.0000.0000.0000.000
49A56VAL00.0150.01418.169-0.021-0.0210.0000.0000.0000.000
50A57THR0-0.030-0.02320.2350.0040.0040.0000.0000.0000.000
51A58GLU-1-0.747-0.84122.397-0.103-0.1030.0000.0000.0000.000
52A59GLN00.0390.02125.4150.0020.0020.0000.0000.0000.000
53A60TYR00.022-0.00326.9420.0090.0090.0000.0000.0000.000
54A61PRO00.1000.04129.1780.0030.0030.0000.0000.0000.000
55A62LYS10.9050.97531.5050.0690.0690.0000.0000.0000.000
56A63GLY0-0.043-0.01934.0290.0040.0040.0000.0000.0000.000
57A64LEU0-0.034-0.02728.7220.0030.0030.0000.0000.0000.000
58A65GLY00.0190.02531.493-0.003-0.0030.0000.0000.0000.000
59A66HIS0-0.035-0.03429.724-0.001-0.0010.0000.0000.0000.000
60A67THR0-0.056-0.07224.571-0.005-0.0050.0000.0000.0000.000
61A68VAL00.007-0.00226.8540.0090.0090.0000.0000.0000.000
62A69PRO00.0410.01427.672-0.004-0.0040.0000.0000.0000.000
63A70THR00.0470.02527.293-0.001-0.0010.0000.0000.0000.000
64A71LEU0-0.029-0.00622.434-0.001-0.0010.0000.0000.0000.000
65A72LYS10.8910.93624.5720.0900.0900.0000.0000.0000.000
66A73GLU-1-0.903-0.94826.774-0.069-0.0690.0000.0000.0000.000
67A74GLY0-0.0190.00224.5770.0060.0060.0000.0000.0000.000
68A75LEU0-0.033-0.00621.602-0.003-0.0030.0000.0000.0000.000
69A76ALA00.0150.00421.1400.0110.0110.0000.0000.0000.000
70A77GLU-1-0.925-0.95223.130-0.033-0.0330.0000.0000.0000.000
71A78ASN0-0.038-0.01424.5380.0020.0020.0000.0000.0000.000
72A79THR0-0.041-0.03121.177-0.006-0.0060.0000.0000.0000.000
73A80PRO0-0.0150.00021.1240.0030.0030.0000.0000.0000.000
74A81ILE0-0.010-0.01622.566-0.012-0.0120.0000.0000.0000.000
75A82PHE0-0.011-0.00521.0210.0090.0090.0000.0000.0000.000
76A83ASP-1-0.919-0.95424.944-0.098-0.0980.0000.0000.0000.000
77A84LYS10.7740.87821.3850.1700.1700.0000.0000.0000.000
78A85THR0-0.006-0.01426.7470.0000.0000.0000.0000.0000.000
79A86LYS10.8870.95820.4400.1790.1790.0000.0000.0000.000
80A87PHE00.0750.01922.695-0.002-0.0020.0000.0000.0000.000
81A88SER0-0.060-0.05318.338-0.012-0.0120.0000.0000.0000.000
82A89MET0-0.007-0.00316.8410.0060.0060.0000.0000.0000.000
83A90CYS0-0.0460.00715.6160.0050.0050.0000.0000.0000.000
84A91ILE0-0.020-0.00418.2180.0140.0140.0000.0000.0000.000
85A92PRO00.0760.02620.830-0.003-0.0030.0000.0000.0000.000
86A93PRO00.0060.00422.1690.0030.0030.0000.0000.0000.000
87A94THR0-0.051-0.02817.444-0.003-0.0030.0000.0000.0000.000
88A95GLU-1-0.861-0.92817.343-0.136-0.1360.0000.0000.0000.000
89A96ASP-1-0.847-0.93317.422-0.053-0.0530.0000.0000.0000.000
90A97THR0-0.048-0.02714.8350.0160.0160.0000.0000.0000.000
91A98LEU00.011-0.00412.0710.0010.0010.0000.0000.0000.000
92A99LYS10.8600.93812.8420.0590.0590.0000.0000.0000.000
93A100LYS10.9060.96314.5920.0400.0400.0000.0000.0000.000
94A101VAL0-0.070-0.0169.8630.0400.0400.0000.0000.0000.000
95A102GLN00.0220.0026.0150.1070.1070.0000.0000.0000.000
96A103ASN0-0.026-0.0043.453-1.329-0.6440.024-0.265-0.444-0.002
97A104VAL00.0280.0196.0450.1720.1720.0000.0000.0000.000
98A105ILE0-0.0060.0087.853-0.130-0.1300.0000.0000.0000.000
99A106LEU0-0.014-0.0039.7240.0930.0930.0000.0000.0000.000
100A107VAL00.0010.00012.435-0.013-0.0130.0000.0000.0000.000
101A108GLY00.0260.01015.8170.0130.0130.0000.0000.0000.000
102A109ILE0-0.027-0.03819.148-0.012-0.0120.0000.0000.0000.000
103A110GLU-1-0.872-0.93121.489-0.169-0.1690.0000.0000.0000.000
104A111ALA00.0390.00818.699-0.014-0.0140.0000.0000.0000.000
105A112HIS00.0410.01618.491-0.036-0.0360.0000.0000.0000.000
106A113VAL0-0.027-0.01621.0070.0090.0090.0000.0000.0000.000
107A115VAL00.0140.02914.907-0.020-0.0200.0000.0000.0000.000
108A116LEU0-0.0040.02115.287-0.047-0.0470.0000.0000.0000.000
109A117GLN0-0.016-0.01516.055-0.022-0.0220.0000.0000.0000.000
110A118THR00.002-0.01613.9180.0080.0080.0000.0000.0000.000
111A119THR0-0.024-0.02610.815-0.040-0.0400.0000.0000.0000.000
112A120TYR00.015-0.00512.011-0.058-0.0580.0000.0000.0000.000
113A121ASP-1-0.713-0.81613.916-0.236-0.2360.0000.0000.0000.000
114A122LEU0-0.030-0.03410.2300.0200.0200.0000.0000.0000.000
115A123LEU0-0.022-0.0167.605-0.014-0.0140.0000.0000.0000.000
116A124GLU-1-0.964-0.96810.284-0.250-0.2500.0000.0000.0000.000
117A125ARG10.7780.88612.7210.2550.2550.0000.0000.0000.000
118A126GLY0-0.0140.0049.3910.0620.0620.0000.0000.0000.000
119A127LEU0-0.077-0.0157.537-0.004-0.0040.0000.0000.0000.000
120A128ASN0-0.034-0.0292.582-3.451-1.5862.003-1.646-2.222-0.018
121A129VAL00.0150.0074.5820.2200.232-0.001-0.009-0.0020.000
122A130HIS0-0.014-0.0082.527-0.3810.1820.486-0.292-0.757-0.001
123A131VAL00.0330.0017.1620.1770.1770.0000.0000.0000.000
124A132VAL00.0060.00710.793-0.012-0.0120.0000.0000.0000.000
125A133VAL00.0350.00713.0860.0580.0580.0000.0000.0000.000
126A134ASP-1-0.792-0.86915.403-0.256-0.2560.0000.0000.0000.000
127A135ALA0-0.029-0.02916.4930.0320.0320.0000.0000.0000.000
128A136VAL00.0370.03915.1840.0070.0070.0000.0000.0000.000
129A137SER00.002-0.03718.3830.0030.0030.0000.0000.0000.000
130A138SER00.011-0.00721.663-0.008-0.0080.0000.0000.0000.000
131A139ARG11.0021.01624.3490.1250.1250.0000.0000.0000.000
132A140SER0-0.036-0.01527.2360.0090.0090.0000.0000.0000.000
133A141HIS00.1110.03225.504-0.003-0.0030.0000.0000.0000.000
134A142THR00.0260.01224.399-0.013-0.0130.0000.0000.0000.000
135A143ASP-1-0.871-0.94324.027-0.171-0.1710.0000.0000.0000.000
136A144ARG10.7930.88219.7110.2120.2120.0000.0000.0000.000
137A145HIS0-0.017-0.00519.674-0.029-0.0290.0000.0000.0000.000
138A146PHE00.032-0.00819.372-0.020-0.0200.0000.0000.0000.000
139A147ALA0-0.0100.03118.363-0.015-0.0150.0000.0000.0000.000
140A148PHE00.0550.01014.814-0.032-0.0320.0000.0000.0000.000
141A149LYS10.8740.93914.3830.2770.2770.0000.0000.0000.000
142A150GLN0-0.012-0.02115.557-0.016-0.0160.0000.0000.0000.000
143A151MET0-0.030-0.00212.130-0.032-0.0320.0000.0000.0000.000
144A152GLU-1-0.850-0.91910.596-0.532-0.5320.0000.0000.0000.000
145A153GLN0-0.095-0.04911.398-0.032-0.0320.0000.0000.0000.000
146A154ALA0-0.0200.00012.3110.0100.0100.0000.0000.0000.000
147A155GLY00.0180.0198.393-0.009-0.0090.0000.0000.0000.000
148A156ALA0-0.051-0.0176.602-0.335-0.3350.0000.0000.0000.000
149A157ILE0-0.017-0.0162.395-0.407-0.3041.122-0.370-0.855-0.002
150A158LEU0-0.0320.0006.7800.1420.1420.0000.0000.0000.000
151A159THR00.0050.0018.2790.0400.0400.0000.0000.0000.000
152A160THR00.0490.01210.3380.0750.0750.0000.0000.0000.000
153A161SER0-0.020-0.04512.795-0.022-0.0220.0000.0000.0000.000
154A162GLU-1-0.946-0.97314.720-0.140-0.1400.0000.0000.0000.000
155A163ALA00.0190.01111.2580.0240.0240.0000.0000.0000.000
156A164THR0-0.033-0.0329.489-0.051-0.0510.0000.0000.0000.000
157A165ILE0-0.024-0.01611.2770.0270.0270.0000.0000.0000.000
158A166LEU00.0210.00214.2720.0410.0410.0000.0000.0000.000
159A167GLY0-0.022-0.00410.2920.0620.0620.0000.0000.0000.000
160A168LEU0-0.059-0.0219.6960.0770.0770.0000.0000.0000.000
161A169VAL0-0.012-0.00911.5570.0730.0730.0000.0000.0000.000
162A170GLY0-0.024-0.00212.9060.0510.0510.0000.0000.0000.000
163A171GLY00.014-0.00813.7040.0310.0310.0000.0000.0000.000
164A172SER0-0.035-0.03217.409-0.018-0.0180.0000.0000.0000.000
165A173ASP-1-0.903-0.94920.6280.0840.0840.0000.0000.0000.000
166A174HIS0-0.0020.02316.076-0.007-0.0070.0000.0000.0000.000
167A175PRO00.0220.00119.676-0.017-0.0170.0000.0000.0000.000
168A176LYS10.8620.91620.004-0.011-0.0110.0000.0000.0000.000
169A177PHE00.0050.01919.377-0.018-0.0180.0000.0000.0000.000
170A178LYS10.9120.92921.104-0.018-0.0180.0000.0000.0000.000
171A179GLU-1-0.830-0.90322.888-0.015-0.0150.0000.0000.0000.000
172A180VAL00.0430.01217.850-0.010-0.0100.0000.0000.0000.000
173A181GLN00.0420.03120.725-0.005-0.0050.0000.0000.0000.000
174A182LYS10.9140.95322.4460.0230.0230.0000.0000.0000.000
175A183LEU0-0.023-0.00419.934-0.001-0.0010.0000.0000.0000.000
176A184ILE0-0.030-0.01518.502-0.012-0.0120.0000.0000.0000.000
177A185LEU0-0.0290.01221.9650.0040.0040.0000.0000.0000.000
178A186THR00.0080.00825.4210.0010.0010.0000.0000.0000.000
179A187SER00.0800.03722.454-0.004-0.0040.0000.0000.0000.000
180A188ALA0-0.031-0.00520.1710.0070.0070.0000.0000.0000.000
181A189PRO0-0.007-0.00922.1540.0030.0030.0000.0000.0000.000
182A190ASP-1-0.835-0.91823.028-0.166-0.1660.0000.0000.0000.000
183A191THR0-0.042-0.01621.282-0.003-0.0030.0000.0000.0000.000
184A192GLY00.0360.01923.602-0.008-0.0080.0000.0000.0000.000
185A193LEU0-0.070-0.02717.910-0.001-0.0010.0000.0000.0000.000
186A194VAL00.0010.00720.610-0.012-0.0120.0000.0000.0000.000
187A195PRO0-0.013-0.00922.1450.0130.0130.0000.0000.0000.000
188A196LEU0-0.017-0.00125.3430.0040.0040.0000.0000.0000.000
189A197SER00.000-0.00927.9640.0010.0010.0000.0000.0000.000
190A198LYN00.0150.00629.8380.0050.0050.0000.0000.0000.000
191A199LEU00.0020.01833.289-0.001-0.0010.0000.0000.0000.000