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: ZYJQN

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2306697.480719
FMO2-HF: Nuclear repulsion 2224743.458264
FMO2-HF: Total energy -81954.022455
FMO2-MP2: Total energy -82191.963756


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.
-17.998-11.3134.321-4.65-6.357-0.014
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 : 0.056 / 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].
3A7GLU-1-0.925-0.9732.283-14.500-9.3551.286-3.054-3.377-0.011
4A8GLU-1-0.873-0.9372.126-1.641-0.3843.028-1.509-2.777-0.003
5A9ALA0-0.0030.0173.8670.0680.3510.007-0.087-0.2030.000
6A10GLN00.0260.0156.348-0.257-0.2570.0000.0000.0000.000
7A11GLU-1-0.895-0.9516.860-1.979-1.9790.0000.0000.0000.000
8A12THR0-0.021-0.0337.2260.3460.3460.0000.0000.0000.000
9A13ARG10.8800.9489.607-0.018-0.0180.0000.0000.0000.000
10A14ALA00.0370.02011.7220.0310.0310.0000.0000.0000.000
11A15GLN00.0120.00912.4360.1170.1170.0000.0000.0000.000
12A16ILE00.000-0.00712.6310.0570.0570.0000.0000.0000.000
13A17ILE00.0270.02115.6360.0250.0250.0000.0000.0000.000
14A18GLU-1-0.782-0.86317.143-0.285-0.2850.0000.0000.0000.000
15A19ALA0-0.037-0.01018.1910.0160.0160.0000.0000.0000.000
16A20ALA00.0260.00019.6940.0230.0230.0000.0000.0000.000
17A21GLU-1-0.741-0.84221.623-0.189-0.1890.0000.0000.0000.000
18A22ARG10.8610.92217.8930.2540.2540.0000.0000.0000.000
19A23ALA00.000-0.00223.8650.0120.0120.0000.0000.0000.000
20A24PHE00.021-0.00824.0170.0120.0120.0000.0000.0000.000
21A25TYR00.0550.04027.2840.0060.0060.0000.0000.0000.000
22A26LYS10.8980.94128.6360.0830.0830.0000.0000.0000.000
23A27ARG10.7430.85627.4760.0380.0380.0000.0000.0000.000
24A28GLY00.0270.03430.3080.0080.0080.0000.0000.0000.000
25A29VAL00.0270.01327.8690.0040.0040.0000.0000.0000.000
26A30ALA00.0280.03629.2970.0090.0090.0000.0000.0000.000
27A31ARG10.8250.88731.2710.0310.0310.0000.0000.0000.000
28A32THR00.0080.01025.288-0.008-0.0080.0000.0000.0000.000
29A33THR0-0.042-0.02924.8650.0130.0130.0000.0000.0000.000
30A34LEU00.0750.02919.888-0.017-0.0170.0000.0000.0000.000
31A35ALA00.0230.00320.358-0.005-0.0050.0000.0000.0000.000
32A36ASP-1-0.773-0.86721.426-0.022-0.0220.0000.0000.0000.000
33A37ILE00.0060.00418.582-0.020-0.0200.0000.0000.0000.000
34A38ALA00.0100.01116.912-0.027-0.0270.0000.0000.0000.000
35A39GLU-1-0.761-0.85317.260-0.001-0.0010.0000.0000.0000.000
36A40LEU0-0.082-0.02819.644-0.028-0.0280.0000.0000.0000.000
37A41ALA0-0.008-0.01115.063-0.037-0.0370.0000.0000.0000.000
38A42GLY0-0.0250.00415.227-0.060-0.0600.0000.0000.0000.000
39A43VAL0-0.024-0.01011.712-0.027-0.0270.0000.0000.0000.000
40A44THR0-0.010-0.01312.3120.0390.0390.0000.0000.0000.000
41A45ARG10.8360.87114.2160.0020.0020.0000.0000.0000.000
42A46GLY00.0090.00015.896-0.002-0.0020.0000.0000.0000.000
43A47ALA00.0310.01210.9560.0380.0380.0000.0000.0000.000
44A48ILE0-0.0010.00212.8500.0390.0390.0000.0000.0000.000
45A49TYR0-0.017-0.01815.265-0.018-0.0180.0000.0000.0000.000
46A50TRP0-0.048-0.0059.4660.1080.1080.0000.0000.0000.000
47A51HIS0-0.028-0.0079.082-0.013-0.0130.0000.0000.0000.000
48A52PHE00.0230.00313.885-0.064-0.0640.0000.0000.0000.000
49A53ASN0-0.041-0.02017.7500.0280.0280.0000.0000.0000.000
50A54ASN0-0.044-0.03820.441-0.015-0.0150.0000.0000.0000.000
51A55LYS10.8210.89922.132-0.025-0.0250.0000.0000.0000.000
52A56ALA00.0030.01324.302-0.018-0.0180.0000.0000.0000.000
53A57GLU-1-0.767-0.88318.7990.1480.1480.0000.0000.0000.000
54A58LEU0-0.027-0.00818.684-0.018-0.0180.0000.0000.0000.000
55A59VAL0-0.029-0.02421.501-0.026-0.0260.0000.0000.0000.000
56A60GLN0-0.042-0.02924.296-0.012-0.0120.0000.0000.0000.000
57A61ALA00.0290.01419.473-0.013-0.0130.0000.0000.0000.000
58A62LEU0-0.063-0.02921.617-0.029-0.0290.0000.0000.0000.000
59A63LEU0-0.016-0.00423.165-0.016-0.0160.0000.0000.0000.000
60A64ASP-1-0.849-0.92522.528-0.049-0.0490.0000.0000.0000.000
61A65SER0-0.032-0.01921.081-0.015-0.0150.0000.0000.0000.000
62A66LEU0-0.026-0.01322.705-0.015-0.0150.0000.0000.0000.000
63A67ALA0-0.020-0.01225.5370.0030.0030.0000.0000.0000.000
64A68GLU-1-0.949-0.97719.442-0.287-0.2870.0000.0000.0000.000
65A69THR0-0.049-0.04423.788-0.012-0.0120.0000.0000.0000.000
66A70HIS0-0.033-0.02425.7660.0060.0060.0000.0000.0000.000
67A71ASP-1-0.829-0.88026.135-0.120-0.1200.0000.0000.0000.000
68A72HIS00.0230.01327.8720.0070.0070.0000.0000.0000.000
69A73LEU0-0.018-0.01029.5380.0110.0110.0000.0000.0000.000
70A74ALA00.0070.00931.2960.0100.0100.0000.0000.0000.000
71A75ARG10.8160.87028.8610.1040.1040.0000.0000.0000.000
72A76ALA00.0000.01632.6780.0070.0070.0000.0000.0000.000
73A77SER0-0.080-0.05035.0500.0090.0090.0000.0000.0000.000
74A78GLU-1-0.835-0.92334.113-0.061-0.0610.0000.0000.0000.000
75A79SER00.0140.02036.0270.0090.0090.0000.0000.0000.000
76A80GLU-1-0.815-0.90137.814-0.042-0.0420.0000.0000.0000.000
77A81ASP-1-0.906-0.94238.422-0.055-0.0550.0000.0000.0000.000
78A82GLU-1-0.877-0.91538.041-0.086-0.0860.0000.0000.0000.000
79A83VAL0-0.029-0.02940.5120.0060.0060.0000.0000.0000.000
80A84ASP-1-0.839-0.91941.614-0.074-0.0740.0000.0000.0000.000
81A85PRO00.0450.04340.309-0.005-0.0050.0000.0000.0000.000
82A86LEU00.016-0.00340.664-0.002-0.0020.0000.0000.0000.000
83A87GLY00.0400.01742.073-0.002-0.0020.0000.0000.0000.000
84A88CYS0-0.088-0.04237.009-0.008-0.0080.0000.0000.0000.000
85A89MET00.0530.02637.286-0.005-0.0050.0000.0000.0000.000
86A90ARG10.6880.79638.6940.0770.0770.0000.0000.0000.000
87A91LYS10.8590.92036.2470.0920.0920.0000.0000.0000.000
88A92LEU0-0.0030.01433.178-0.007-0.0070.0000.0000.0000.000
89A93LEU00.014-0.00234.725-0.005-0.0050.0000.0000.0000.000
90A94LEU0-0.013-0.00437.024-0.002-0.0020.0000.0000.0000.000
91A95GLN0-0.034-0.01429.196-0.007-0.0070.0000.0000.0000.000
92A96VAL00.0130.00532.274-0.008-0.0080.0000.0000.0000.000
93A97PHE0-0.009-0.01933.448-0.001-0.0010.0000.0000.0000.000
94A98ASN0-0.030-0.03033.613-0.004-0.0040.0000.0000.0000.000
95A99GLU-1-0.811-0.87827.260-0.180-0.1800.0000.0000.0000.000
96A100LEU0-0.0040.00030.734-0.005-0.0050.0000.0000.0000.000
97A101VAL00.0180.01132.4280.0010.0010.0000.0000.0000.000
98A102LEU0-0.0210.00631.208-0.003-0.0030.0000.0000.0000.000
99A103ASP-1-0.798-0.88325.732-0.239-0.2390.0000.0000.0000.000
100A104ALA0-0.040-0.03126.3350.0150.0150.0000.0000.0000.000
101A105ARG10.8140.88418.1530.3030.3030.0000.0000.0000.000
102A106THR00.0460.00225.1690.0210.0210.0000.0000.0000.000
103A107ARG10.8290.92627.6020.1700.1700.0000.0000.0000.000
104A108ARG10.7230.83422.3770.2310.2310.0000.0000.0000.000
105A109ILE00.0210.01023.5460.0190.0190.0000.0000.0000.000
106A110ASN00.002-0.01027.7690.0230.0230.0000.0000.0000.000
107A111GLU-1-0.761-0.87431.366-0.065-0.0650.0000.0000.0000.000
108A112ILE0-0.080-0.04526.5770.0120.0120.0000.0000.0000.000
109A113LEU0-0.013-0.01428.2270.0140.0140.0000.0000.0000.000
110A114HIS0-0.047-0.02231.6650.0070.0070.0000.0000.0000.000
111A115HIS0-0.064-0.05234.5930.0140.0140.0000.0000.0000.000
112A116LYS10.8350.93531.6040.0790.0790.0000.0000.0000.000
113A117CYS0-0.0360.00930.5400.0060.0060.0000.0000.0000.000
114A118GLU-1-0.846-0.91132.296-0.013-0.0130.0000.0000.0000.000
115A119PHE0-0.021-0.00833.5540.0030.0030.0000.0000.0000.000
116A120THR0-0.024-0.04534.597-0.002-0.0020.0000.0000.0000.000
117A121ASP-1-0.896-0.95635.8480.0210.0210.0000.0000.0000.000
118A122ASP-1-0.893-0.93533.4460.0360.0360.0000.0000.0000.000
119A123MET0-0.031-0.00129.1830.0060.0060.0000.0000.0000.000
120A124CYS0-0.0040.00432.147-0.003-0.0030.0000.0000.0000.000
121A125GLU-1-0.821-0.90727.1880.0750.0750.0000.0000.0000.000
122A126ILE00.0340.01228.892-0.007-0.0070.0000.0000.0000.000
123A127ARG10.8980.94430.836-0.009-0.0090.0000.0000.0000.000
124A128GLN00.004-0.00232.411-0.001-0.0010.0000.0000.0000.000
125A129GLN00.0260.02726.999-0.010-0.0100.0000.0000.0000.000
126A130ARG10.9020.93730.5380.0270.0270.0000.0000.0000.000
127A131GLN0-0.021-0.01732.419-0.003-0.0030.0000.0000.0000.000
128A132SER0-0.018-0.01231.3730.0000.0000.0000.0000.0000.000
129A133ALA00.0930.04929.937-0.004-0.0040.0000.0000.0000.000
130A134VAL0-0.038-0.01431.850-0.007-0.0070.0000.0000.0000.000
131A135LEU0-0.036-0.02135.403-0.002-0.0020.0000.0000.0000.000
132A136ASP-1-0.884-0.93731.460-0.019-0.0190.0000.0000.0000.000
133A137CYS0-0.027-0.01633.576-0.007-0.0070.0000.0000.0000.000
134A138HIS0-0.075-0.03634.868-0.005-0.0050.0000.0000.0000.000
135A139LYS10.8410.91036.9700.0180.0180.0000.0000.0000.000
136A140GLY00.0710.04935.6240.0000.0000.0000.0000.0000.000
137A141ILE00.008-0.00336.571-0.001-0.0010.0000.0000.0000.000
138A142THR0-0.050-0.04339.1690.0010.0010.0000.0000.0000.000
139A143LEU0-0.037-0.00937.7490.0020.0020.0000.0000.0000.000
140A144ALA00.0590.03238.4540.0000.0000.0000.0000.0000.000
141A145LEU0-0.032-0.02240.4760.0000.0000.0000.0000.0000.000
142A146ALA0-0.015-0.00943.8320.0010.0010.0000.0000.0000.000
143A147ASN00.0160.01140.1050.0070.0070.0000.0000.0000.000
144A148ALA00.0020.00544.1430.0000.0000.0000.0000.0000.000
145A149VAL0-0.069-0.03345.6800.0010.0010.0000.0000.0000.000
146A150ARG10.8080.88443.8940.0370.0370.0000.0000.0000.000
147A151ARG10.7330.85243.5870.0520.0520.0000.0000.0000.000
148A152GLY0-0.030-0.00748.504-0.001-0.0010.0000.0000.0000.000
149A153GLN0-0.038-0.02445.0230.0000.0000.0000.0000.0000.000
150A154LEU0-0.018-0.00646.121-0.001-0.0010.0000.0000.0000.000
151A155PRO0-0.024-0.01650.3930.0020.0020.0000.0000.0000.000
152A156GLY00.0480.02252.6320.0000.0000.0000.0000.0000.000
153A157GLU-1-0.863-0.92053.731-0.020-0.0200.0000.0000.0000.000
154A158LEU0-0.003-0.00748.4550.0010.0010.0000.0000.0000.000
155A159ASP-1-0.848-0.91250.171-0.020-0.0200.0000.0000.0000.000
156A160ALA00.0420.02145.629-0.001-0.0010.0000.0000.0000.000
157A161GLU-1-0.744-0.84844.214-0.022-0.0220.0000.0000.0000.000
158A162ARG10.7990.85645.7030.0200.0200.0000.0000.0000.000
159A163ALA0-0.011-0.00547.230-0.001-0.0010.0000.0000.0000.000
160A164ALA00.0520.02841.847-0.003-0.0030.0000.0000.0000.000
161A165VAL00.0020.00242.608-0.003-0.0030.0000.0000.0000.000
162A166ALA0-0.030-0.01444.159-0.002-0.0020.0000.0000.0000.000
163A167MET0-0.0160.00641.300-0.003-0.0030.0000.0000.0000.000
164A168PHE00.0320.00935.895-0.003-0.0030.0000.0000.0000.000
165A169ALA0-0.004-0.00640.692-0.003-0.0030.0000.0000.0000.000
166A170TYR0-0.078-0.05143.1590.0000.0000.0000.0000.0000.000
167A171VAL00.0160.00837.566-0.003-0.0030.0000.0000.0000.000
168A172ASP-1-0.881-0.92137.516-0.058-0.0580.0000.0000.0000.000
169A173GLY00.0190.00439.232-0.002-0.0020.0000.0000.0000.000
170A174LEU0-0.038-0.01541.5800.0000.0000.0000.0000.0000.000
171A175ILE00.0240.01435.081-0.003-0.0030.0000.0000.0000.000
172A176ARG10.8990.95838.4590.0450.0450.0000.0000.0000.000
173A177ARG10.8720.92839.4150.0570.0570.0000.0000.0000.000
174A178TRP00.0010.00635.072-0.002-0.0020.0000.0000.0000.000
175A179LEU0-0.028-0.02134.247-0.002-0.0020.0000.0000.0000.000
176A180LEU0-0.045-0.01038.0570.0000.0000.0000.0000.0000.000
177A181LEU0-0.058-0.02940.9020.0030.0030.0000.0000.0000.000
178A182PRO00.0770.06139.0910.0010.0010.0000.0000.0000.000
179A183ASP-1-0.916-0.96441.480-0.082-0.0820.0000.0000.0000.000
180A184SER0-0.118-0.07144.6050.0040.0040.0000.0000.0000.000
181A185VAL0-0.029-0.02943.3810.0040.0040.0000.0000.0000.000
182A186ASP-1-0.792-0.88042.490-0.096-0.0960.0000.0000.0000.000
183A187LEU0-0.035-0.02038.1960.0010.0010.0000.0000.0000.000
184A188LEU00.0040.00236.487-0.004-0.0040.0000.0000.0000.000
185A189GLY00.001-0.00739.706-0.002-0.0020.0000.0000.0000.000
186A190ASP-1-0.798-0.88442.920-0.070-0.0700.0000.0000.0000.000
187A191VAL0-0.029-0.00538.5370.0040.0040.0000.0000.0000.000
188A192GLU-1-0.780-0.89041.767-0.090-0.0900.0000.0000.0000.000
189A193LYS10.8350.90444.2520.0730.0730.0000.0000.0000.000
190A194TRP0-0.0330.00542.6700.0070.0070.0000.0000.0000.000
191A195VAL00.0370.03340.2390.0030.0030.0000.0000.0000.000
192A196ASP-1-0.780-0.85843.365-0.065-0.0650.0000.0000.0000.000
193A197THR0-0.057-0.04346.9120.0050.0050.0000.0000.0000.000
194A198GLY00.0050.00445.1270.0030.0030.0000.0000.0000.000
195A199LEU00.027-0.00542.9280.0030.0030.0000.0000.0000.000
196A200ASP-1-0.837-0.90046.774-0.049-0.0490.0000.0000.0000.000
197A201MET0-0.041-0.00547.0380.0040.0040.0000.0000.0000.000
198A202LEU0-0.013-0.02044.8950.0040.0040.0000.0000.0000.000
199A203ARG10.8520.89849.5670.0530.0530.0000.0000.0000.000
200A204LEU0-0.008-0.00651.6130.0030.0030.0000.0000.0000.000
201A205SER00.0020.00953.4520.0030.0030.0000.0000.0000.000
202A206PRO0-0.004-0.02355.2830.0010.0010.0000.0000.0000.000
203A207ALA00.0110.01455.8110.0010.0010.0000.0000.0000.000
204A208LEU0-0.0140.01449.7210.0020.0020.0000.0000.0000.000
205A209ARG10.8660.94952.5890.0310.0310.0000.0000.0000.000
206A210LYS10.8350.92652.8230.0240.0240.0000.0000.0000.000