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

tag_button

FMODB ID: 22Y1R

Calculation Name: 2XDN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XDN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9AIU0

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2302875.216469
FMO2-HF: Nuclear repulsion 2220923.525412
FMO2-HF: Total energy -81951.691057
FMO2-MP2: Total energy -82189.806734


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:5:THR)


Summations of interaction energy for fragment #1(A:5:THR)
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.
-10.724-5.3281.611-2.483-4.524-0.002
Interaction energy analysis for fragmet #1(A:5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.018
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].
3A7GLU-1-0.909-0.9722.601-6.493-3.1430.471-1.503-2.3170.000
4A8GLU-1-0.875-0.9232.362-1.888-0.0461.137-0.929-2.050-0.002
5A9ALA00.0070.0004.054-0.457-0.2530.003-0.051-0.1570.000
6A10GLN00.0060.0076.493-0.280-0.2800.0000.0000.0000.000
7A11GLU-1-0.873-0.9516.676-1.693-1.6930.0000.0000.0000.000
8A12THR0-0.040-0.0267.3090.2370.2370.0000.0000.0000.000
9A13ARG10.9921.0059.692-0.014-0.0140.0000.0000.0000.000
10A14ALA00.0030.00312.0740.0090.0090.0000.0000.0000.000
11A15GLN00.0230.01712.2400.0710.0710.0000.0000.0000.000
12A16ILE0-0.023-0.00513.0780.0380.0380.0000.0000.0000.000
13A17ILE00.010-0.00415.8100.0010.0010.0000.0000.0000.000
14A18GLU-1-0.947-0.95917.125-0.219-0.2190.0000.0000.0000.000
15A19ALA00.005-0.00718.3960.0070.0070.0000.0000.0000.000
16A20ALA00.005-0.01219.9200.0200.0200.0000.0000.0000.000
17A21GLU-1-0.778-0.86721.775-0.152-0.1520.0000.0000.0000.000
18A22ARG10.9050.94418.0500.1920.1920.0000.0000.0000.000
19A23ALA00.0040.00024.0660.0080.0080.0000.0000.0000.000
20A24PHE00.012-0.00924.3030.0090.0090.0000.0000.0000.000
21A25TYR00.0410.03327.4700.0040.0040.0000.0000.0000.000
22A26LYS10.9140.96728.8730.0600.0600.0000.0000.0000.000
23A27ARG10.7780.87627.6380.0180.0180.0000.0000.0000.000
24A28GLY00.0050.03530.7840.0060.0060.0000.0000.0000.000
25A29VAL00.030-0.00528.0480.0030.0030.0000.0000.0000.000
26A30ALA00.0000.00329.6040.0070.0070.0000.0000.0000.000
27A31ARG10.9690.97231.6920.0170.0170.0000.0000.0000.000
28A32THR0-0.0310.01025.351-0.002-0.0020.0000.0000.0000.000
29A33THR0-0.035-0.01924.7650.0100.0100.0000.0000.0000.000
30A34LEU00.1150.03820.254-0.012-0.0120.0000.0000.0000.000
31A35ALA00.027-0.00121.222-0.008-0.0080.0000.0000.0000.000
32A36ASP-1-0.814-0.90321.8110.0010.0010.0000.0000.0000.000
33A37ILE0-0.0140.00018.929-0.016-0.0160.0000.0000.0000.000
34A38ALA00.0000.00717.298-0.020-0.0200.0000.0000.0000.000
35A39GLU-1-0.771-0.86117.7630.0150.0150.0000.0000.0000.000
36A40LEU0-0.101-0.03420.302-0.021-0.0210.0000.0000.0000.000
37A41ALA0-0.033-0.02415.555-0.027-0.0270.0000.0000.0000.000
38A42GLY0-0.0130.01415.484-0.041-0.0410.0000.0000.0000.000
39A43VAL0-0.015-0.00712.060-0.028-0.0280.0000.0000.0000.000
40A44THR0-0.031-0.01512.3220.0470.0470.0000.0000.0000.000
41A45ARG10.8830.87914.414-0.027-0.0270.0000.0000.0000.000
42A46GLY0-0.008-0.01715.9760.0040.0040.0000.0000.0000.000
43A47ALA00.0190.02211.6000.0400.0400.0000.0000.0000.000
44A48ILE0-0.005-0.00313.1170.0490.0490.0000.0000.0000.000
45A49TYR0-0.014-0.02015.567-0.022-0.0220.0000.0000.0000.000
46A50TRP0-0.052-0.00210.3610.0700.0700.0000.0000.0000.000
47A51HIS0-0.070-0.0309.219-0.092-0.0920.0000.0000.0000.000
48A52PHE0-0.022-0.02114.204-0.056-0.0560.0000.0000.0000.000
49A53ASN00.0410.03218.0210.0220.0220.0000.0000.0000.000
50A54ASN0-0.015-0.00920.841-0.014-0.0140.0000.0000.0000.000
51A55LYS10.8610.93122.339-0.026-0.0260.0000.0000.0000.000
52A56ALA00.0250.01124.498-0.014-0.0140.0000.0000.0000.000
53A57GLU-1-0.808-0.88920.3560.1400.1400.0000.0000.0000.000
54A58LEU0-0.037-0.02619.111-0.014-0.0140.0000.0000.0000.000
55A59VAL0-0.049-0.03221.785-0.021-0.0210.0000.0000.0000.000
56A60GLN0-0.009-0.01924.103-0.011-0.0110.0000.0000.0000.000
57A61ALA00.0020.01519.765-0.012-0.0120.0000.0000.0000.000
58A62LEU0-0.035-0.02621.850-0.021-0.0210.0000.0000.0000.000
59A63LEU0-0.009-0.00323.587-0.013-0.0130.0000.0000.0000.000
60A64ASP-1-0.840-0.92023.046-0.033-0.0330.0000.0000.0000.000
61A65SER0-0.063-0.03821.439-0.013-0.0130.0000.0000.0000.000
62A66LEU0-0.028-0.01522.882-0.014-0.0140.0000.0000.0000.000
63A67ALA0-0.016-0.00925.869-0.001-0.0010.0000.0000.0000.000
64A68GLU-1-0.953-0.97519.860-0.207-0.2070.0000.0000.0000.000
65A69THR0-0.040-0.02724.023-0.007-0.0070.0000.0000.0000.000
66A70HIS0-0.026-0.01825.9140.0030.0030.0000.0000.0000.000
67A71ASP-1-0.853-0.89926.267-0.106-0.1060.0000.0000.0000.000
68A72HIS00.0400.02028.2250.0070.0070.0000.0000.0000.000
69A73LEU00.002-0.00629.7670.0090.0090.0000.0000.0000.000
70A74ALA00.0120.00531.2780.0080.0080.0000.0000.0000.000
71A75ARG10.8430.91628.9980.0890.0890.0000.0000.0000.000
72A76ALA00.0100.01032.6310.0050.0050.0000.0000.0000.000
73A77SER0-0.098-0.06735.1920.0080.0080.0000.0000.0000.000
74A78GLU-1-0.867-0.95334.182-0.051-0.0510.0000.0000.0000.000
75A79SER0-0.0060.01436.0270.0070.0070.0000.0000.0000.000
76A80GLU-1-0.921-0.98437.873-0.036-0.0360.0000.0000.0000.000
77A81ASP-1-0.889-0.94339.089-0.049-0.0490.0000.0000.0000.000
78A82GLU-1-0.868-0.92038.311-0.073-0.0730.0000.0000.0000.000
79A83VAL0-0.0060.01840.4320.0050.0050.0000.0000.0000.000
80A84ASP-1-0.852-0.93241.907-0.057-0.0570.0000.0000.0000.000
81A85PRO00.0300.04140.557-0.004-0.0040.0000.0000.0000.000
82A86LEU00.012-0.01940.840-0.002-0.0020.0000.0000.0000.000
83A87GLY00.0470.02942.247-0.001-0.0010.0000.0000.0000.000
84A88CYS0-0.125-0.05936.818-0.006-0.0060.0000.0000.0000.000
85A89MET00.0520.03037.625-0.003-0.0030.0000.0000.0000.000
86A90ARG10.8350.90338.7830.0610.0610.0000.0000.0000.000
87A91LYS10.9050.94336.6350.0770.0770.0000.0000.0000.000
88A92LEU00.0020.02333.621-0.006-0.0060.0000.0000.0000.000
89A93LEU00.009-0.00435.066-0.004-0.0040.0000.0000.0000.000
90A94LEU00.0260.00937.027-0.002-0.0020.0000.0000.0000.000
91A95GLN0-0.042-0.00729.998-0.005-0.0050.0000.0000.0000.000
92A96VAL00.0160.00532.575-0.005-0.0050.0000.0000.0000.000
93A97PHE00.000-0.01533.620-0.001-0.0010.0000.0000.0000.000
94A98ASN0-0.003-0.01134.0330.0010.0010.0000.0000.0000.000
95A99GLU-1-0.812-0.90826.864-0.147-0.1470.0000.0000.0000.000
96A100LEU0-0.0060.00630.848-0.004-0.0040.0000.0000.0000.000
97A101VAL0-0.024-0.01332.7460.0000.0000.0000.0000.0000.000
98A102LEU0-0.069-0.03631.378-0.002-0.0020.0000.0000.0000.000
99A103ASP-1-0.813-0.89326.029-0.186-0.1860.0000.0000.0000.000
100A104ALA0-0.043-0.02626.9540.0110.0110.0000.0000.0000.000
101A105ARG10.8820.94618.0730.2540.2540.0000.0000.0000.000
102A106THR00.0670.01925.6060.0170.0170.0000.0000.0000.000
103A107ARG10.9360.99827.7860.1240.1240.0000.0000.0000.000
104A108ARG10.8340.89824.3580.1640.1640.0000.0000.0000.000
105A109ILE00.0130.00823.7300.0140.0140.0000.0000.0000.000
106A110ASN0-0.016-0.01628.0260.0180.0180.0000.0000.0000.000
107A111GLU-1-0.807-0.90931.594-0.048-0.0480.0000.0000.0000.000
108A112ILE0-0.107-0.05526.7780.0090.0090.0000.0000.0000.000
109A113LEU0-0.039-0.03028.2320.0110.0110.0000.0000.0000.000
110A114HIS0-0.051-0.03031.8330.0050.0050.0000.0000.0000.000
111A115HIS0-0.080-0.04134.8410.0090.0090.0000.0000.0000.000
112A116LYS10.8120.90731.9460.0540.0540.0000.0000.0000.000
113A117CYS0-0.029-0.00731.0130.0040.0040.0000.0000.0000.000
114A118GLU-1-0.923-0.94932.856-0.003-0.0030.0000.0000.0000.000
115A119PHE0-0.034-0.02834.0010.0040.0040.0000.0000.0000.000
116A120THR00.0480.02434.6820.0000.0000.0000.0000.0000.000
117A121ASP-1-0.920-0.96436.1300.0190.0190.0000.0000.0000.000
118A122ASP-1-0.997-0.98934.4190.0400.0400.0000.0000.0000.000
119A123MET0-0.005-0.00727.8140.0040.0040.0000.0000.0000.000
120A124CYS00.0230.00032.823-0.003-0.0030.0000.0000.0000.000
121A125GLU-1-0.868-0.94727.5210.0670.0670.0000.0000.0000.000
122A126ILE00.0070.01729.584-0.006-0.0060.0000.0000.0000.000
123A127ARG10.9590.97631.372-0.008-0.0080.0000.0000.0000.000
124A128GLN0-0.018-0.00632.785-0.002-0.0020.0000.0000.0000.000
125A129GLN00.0560.02727.8670.0000.0000.0000.0000.0000.000
126A130ARG10.9010.96030.4340.0130.0130.0000.0000.0000.000
127A131GLN0-0.032-0.02633.125-0.002-0.0020.0000.0000.0000.000
128A132SER00.0260.01231.904-0.001-0.0010.0000.0000.0000.000
129A133ALA00.0670.05330.611-0.003-0.0030.0000.0000.0000.000
130A134VAL0-0.032-0.02932.298-0.005-0.0050.0000.0000.0000.000
131A135LEU0-0.036-0.02535.782-0.002-0.0020.0000.0000.0000.000
132A136ASP-1-0.902-0.93931.421-0.016-0.0160.0000.0000.0000.000
133A137CYS0-0.024-0.03433.788-0.005-0.0050.0000.0000.0000.000
134A138HIS0-0.0520.00234.978-0.005-0.0050.0000.0000.0000.000
135A139LYS10.9560.97736.5420.0140.0140.0000.0000.0000.000
136A140GLY00.0510.03435.774-0.001-0.0010.0000.0000.0000.000
137A141ILE0-0.017-0.00836.678-0.001-0.0010.0000.0000.0000.000
138A142THR0-0.023-0.02439.3500.0000.0000.0000.0000.0000.000
139A143LEU0-0.0120.00537.8050.0010.0010.0000.0000.0000.000
140A144ALA00.0660.04138.8770.0010.0010.0000.0000.0000.000
141A145LEU0-0.036-0.01440.8290.0000.0000.0000.0000.0000.000
142A146ALA0-0.009-0.01143.9540.0010.0010.0000.0000.0000.000
143A147ASN0-0.065-0.04140.1870.0050.0050.0000.0000.0000.000
144A148ALA00.0040.00944.3410.0000.0000.0000.0000.0000.000
145A149VAL0-0.048-0.00746.0220.0010.0010.0000.0000.0000.000
146A150ARG10.9140.97344.5280.0320.0320.0000.0000.0000.000
147A151ARG10.7410.84443.4380.0460.0460.0000.0000.0000.000
148A152GLY0-0.028-0.00548.835-0.001-0.0010.0000.0000.0000.000
149A153GLN0-0.040-0.03745.3600.0000.0000.0000.0000.0000.000
150A154LEU0-0.027-0.01146.4610.0000.0000.0000.0000.0000.000
151A155PRO0-0.057-0.02450.5110.0010.0010.0000.0000.0000.000
152A156GLY00.0570.02452.6230.0000.0000.0000.0000.0000.000
153A157GLU-1-0.927-0.96654.151-0.017-0.0170.0000.0000.0000.000
154A158LEU0-0.045-0.02548.5210.0010.0010.0000.0000.0000.000
155A159ASP-1-0.876-0.93350.649-0.017-0.0170.0000.0000.0000.000
156A160ALA00.009-0.00746.085-0.001-0.0010.0000.0000.0000.000
157A161GLU-1-0.854-0.93344.630-0.018-0.0180.0000.0000.0000.000
158A162ARG10.8700.92145.9750.0170.0170.0000.0000.0000.000
159A163ALA00.0060.00047.668-0.001-0.0010.0000.0000.0000.000
160A164ALA00.0720.03542.350-0.003-0.0030.0000.0000.0000.000
161A165VAL00.0080.01242.974-0.002-0.0020.0000.0000.0000.000
162A166ALA0-0.044-0.02444.485-0.001-0.0010.0000.0000.0000.000
163A167MET0-0.0100.00741.895-0.002-0.0020.0000.0000.0000.000
164A168PHE00.0430.01536.591-0.002-0.0020.0000.0000.0000.000
165A169ALA00.0070.00741.094-0.002-0.0020.0000.0000.0000.000
166A170TYR0-0.059-0.03343.5320.0000.0000.0000.0000.0000.000
167A171VAL00.0190.00638.165-0.002-0.0020.0000.0000.0000.000
168A172ASP-1-0.900-0.94037.990-0.043-0.0430.0000.0000.0000.000
169A173GLY0-0.006-0.01639.682-0.001-0.0010.0000.0000.0000.000
170A174LEU0-0.038-0.02041.8340.0000.0000.0000.0000.0000.000
171A175ILE00.0240.01335.302-0.002-0.0020.0000.0000.0000.000
172A176ARG10.9570.98838.7710.0310.0310.0000.0000.0000.000
173A177ARG10.9180.95039.9210.0420.0420.0000.0000.0000.000
174A178TRP0-0.0070.00535.144-0.001-0.0010.0000.0000.0000.000
175A179LEU0-0.021-0.01534.437-0.002-0.0020.0000.0000.0000.000
176A180LEU0-0.059-0.00938.4690.0010.0010.0000.0000.0000.000
177A181LEU0-0.070-0.04841.3560.0010.0010.0000.0000.0000.000
178A182PRO00.0910.06639.8140.0010.0010.0000.0000.0000.000
179A183ASP-1-0.929-0.96541.905-0.063-0.0630.0000.0000.0000.000
180A184SER0-0.146-0.08744.8900.0040.0040.0000.0000.0000.000
181A185VAL0-0.035-0.02643.3800.0020.0020.0000.0000.0000.000
182A186ASP-1-0.788-0.85043.210-0.073-0.0730.0000.0000.0000.000
183A187LEU0-0.023-0.02638.1890.0000.0000.0000.0000.0000.000
184A188LEU0-0.005-0.00836.870-0.002-0.0020.0000.0000.0000.000
185A189GLY00.013-0.01440.092-0.001-0.0010.0000.0000.0000.000
186A190ASP-1-0.913-0.96343.366-0.056-0.0560.0000.0000.0000.000
187A191VAL00.0020.00238.8880.0040.0040.0000.0000.0000.000
188A192GLU-1-0.937-0.96642.266-0.070-0.0700.0000.0000.0000.000
189A193LYS10.9450.98844.3670.0550.0550.0000.0000.0000.000
190A194TRP0-0.0130.02043.1690.0050.0050.0000.0000.0000.000
191A195VAL00.006-0.00740.3480.0030.0030.0000.0000.0000.000
192A196ASP-1-0.817-0.91143.480-0.054-0.0540.0000.0000.0000.000
193A197THR0-0.030-0.01346.9240.0040.0040.0000.0000.0000.000
194A198GLY0-0.016-0.00845.7820.0030.0030.0000.0000.0000.000
195A199LEU00.018-0.00943.0430.0030.0030.0000.0000.0000.000
196A200ASP-1-0.895-0.93846.921-0.040-0.0400.0000.0000.0000.000
197A201MET0-0.078-0.03147.2990.0030.0030.0000.0000.0000.000
198A202LEU0-0.022-0.02944.9140.0030.0030.0000.0000.0000.000
199A203ARG10.9390.94849.6400.0420.0420.0000.0000.0000.000
200A204LEU0-0.029-0.01251.8960.0020.0020.0000.0000.0000.000
201A205SER0-0.0010.01453.4770.0020.0020.0000.0000.0000.000
202A206PRO0-0.005-0.01755.3550.0000.0000.0000.0000.0000.000
203A207ALA00.0270.02655.8600.0010.0010.0000.0000.0000.000
204A208LEU0-0.041-0.01550.0740.0010.0010.0000.0000.0000.000
205A209ARG10.8680.94453.1130.0250.0250.0000.0000.0000.000
206A210LYS10.9470.99552.3680.0190.0190.0000.0000.0000.000