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: ZYQQN

Calculation Name: 5J09-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J09

Chain ID: J

ChEMBL ID:

UniProt ID: A0A023

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1857544.870762
FMO2-HF: Nuclear repulsion 1788048.505524
FMO2-HF: Total energy -69496.365237
FMO2-MP2: Total energy -69703.912327


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(J:46:ARG)


Summations of interaction energy for fragment #1(J:46:ARG)
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.
102.878110.66715.405-8.515-14.679-0.076
Interaction energy analysis for fragmet #1(J:46:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.978
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].
3J48TYR00.0060.0051.837-45.519-41.26914.857-7.206-11.901-0.066
4J49THR0-0.061-0.0643.9789.4809.6480.000-0.037-0.1310.000
5J50LEU00.0620.0506.864-0.904-0.9040.0000.0000.0000.000
6J51ARG10.9330.9739.87020.76220.7620.0000.0000.0000.000
7J52LEU00.0520.04112.7190.9160.9160.0000.0000.0000.000
8J53THR0-0.057-0.06115.7150.2350.2350.0000.0000.0000.000
9J54ARG10.9250.98219.27412.62512.6250.0000.0000.0000.000
10J55GLN00.028-0.00722.959-0.395-0.3950.0000.0000.0000.000
11J56PHE00.0110.00726.454-0.012-0.0120.0000.0000.0000.000
12J57GLN00.0330.02230.0430.0380.0380.0000.0000.0000.000
13J58PHE0-0.016-0.01433.083-0.117-0.1170.0000.0000.0000.000
14J59LYS10.9320.95834.9407.6087.6080.0000.0000.0000.000
15J60ILE0-0.0240.01437.646-0.066-0.0660.0000.0000.0000.000
16J61ASN00.011-0.01540.8980.0580.0580.0000.0000.0000.000
17J62LYS10.8780.94444.2966.1796.1790.0000.0000.0000.000
18J63GLN00.0300.01347.4540.0080.0080.0000.0000.0000.000
19J64THR0-0.050-0.03149.5920.0670.0670.0000.0000.0000.000
20J65THR00.024-0.00250.6040.1400.1400.0000.0000.0000.000
21J66SER00.001-0.01652.791-0.035-0.0350.0000.0000.0000.000
22J67VAL00.0100.00953.725-0.030-0.0300.0000.0000.0000.000
23J68GLY00.0310.03053.5630.1140.1140.0000.0000.0000.000
24J69ASN0-0.071-0.02654.1840.0540.0540.0000.0000.0000.000
25J70LEU0-0.010-0.00147.207-0.108-0.1080.0000.0000.0000.000
26J71ILE0-0.0030.01147.9950.0310.0310.0000.0000.0000.000
27J72PHE0-0.029-0.02542.736-0.142-0.1420.0000.0000.0000.000
28J73ASN00.0170.01441.8870.0520.0520.0000.0000.0000.000
29J74ALA0-0.026-0.02237.326-0.126-0.1260.0000.0000.0000.000
30J75ASP-1-0.760-0.86034.867-8.717-8.7170.0000.0000.0000.000
31J76TYR0-0.045-0.02430.846-0.296-0.2960.0000.0000.0000.000
32J77ILE0-0.007-0.00226.013-0.041-0.0410.0000.0000.0000.000
33J78THR0-0.0010.00026.323-0.227-0.2270.0000.0000.0000.000
34J79PHE0-0.039-0.02721.320-0.073-0.0730.0000.0000.0000.000
35J80ALA00.0300.02821.2880.0840.0840.0000.0000.0000.000
36J81LEU00.0140.00615.150-0.106-0.1060.0000.0000.0000.000
37J82ASP-1-0.722-0.87618.773-14.327-14.3270.0000.0000.0000.000
38J83ASP-1-0.811-0.86321.530-12.437-12.4370.0000.0000.0000.000
39J84PHE0-0.090-0.06618.5620.4030.4030.0000.0000.0000.000
40J85LEU0-0.012-0.00115.980-0.544-0.5440.0000.0000.0000.000
41J86GLN00.0020.01819.527-0.094-0.0940.0000.0000.0000.000
42J87ALA0-0.0010.00420.4830.3980.3980.0000.0000.0000.000
43J88VAL0-0.043-0.02514.692-0.701-0.7010.0000.0000.0000.000
44J89PRO00.0580.04415.9670.5140.5140.0000.0000.0000.000
45J90ASN00.0370.00216.345-1.791-1.7910.0000.0000.0000.000
46J91PRO00.0420.00412.084-0.126-0.1260.0000.0000.0000.000
47J92HIS00.0400.03212.740-1.487-1.4870.0000.0000.0000.000
48J93THR0-0.047-0.02614.8140.1240.1240.0000.0000.0000.000
49J94LEU0-0.0170.0059.483-0.649-0.6490.0000.0000.0000.000
50J95ASN00.0100.0039.4611.6061.6060.0000.0000.0000.000
51J96PHE0-0.091-0.0485.206-2.244-2.2440.0000.0000.0000.000
52J97GLU-1-0.824-0.8999.450-17.951-17.9510.0000.0000.0000.000
53J98ASP-1-0.856-0.9089.905-19.873-19.8730.0000.0000.0000.000
54J99TYR0-0.041-0.05310.348-2.698-2.6980.0000.0000.0000.000
55J100ARG10.8950.9379.97623.94823.9480.0000.0000.0000.000
56J101ILE00.0010.01412.878-1.420-1.4200.0000.0000.0000.000
57J102LYS10.9130.98211.49621.79621.7960.0000.0000.0000.000
58J103LEU0-0.059-0.04513.9920.9210.9210.0000.0000.0000.000
59J104ALA00.0210.02116.218-0.661-0.6610.0000.0000.0000.000
60J105LYS10.8820.93518.63915.51815.5180.0000.0000.0000.000
61J106MET00.0240.03621.282-0.189-0.1890.0000.0000.0000.000
62J107GLU-1-0.826-0.89724.721-11.682-11.6820.0000.0000.0000.000
63J108MET0-0.0180.02126.786-0.105-0.1050.0000.0000.0000.000
64J109ARG10.8300.90128.75510.17010.1700.0000.0000.0000.000
65J110PRO00.0720.04332.711-0.064-0.0640.0000.0000.0000.000
66J111THR0-0.010-0.01535.472-0.098-0.0980.0000.0000.0000.000
67J112GLY0-0.002-0.00637.4650.1500.1500.0000.0000.0000.000
68J113GLY00.0180.01640.5470.1720.1720.0000.0000.0000.000
69J114HIS0-0.068-0.02840.6930.1160.1160.0000.0000.0000.000
70J115TYR00.0400.02340.961-0.202-0.2020.0000.0000.0000.000
71J116THR0-0.007-0.01537.3950.0910.0910.0000.0000.0000.000
72J117VAL00.001-0.00340.543-0.062-0.0620.0000.0000.0000.000
73J118GLN00.0130.02443.7320.1510.1510.0000.0000.0000.000
74J119SER0-0.007-0.00843.713-0.216-0.2160.0000.0000.0000.000
75J120ASP-1-0.795-0.89143.008-6.955-6.9550.0000.0000.0000.000
76J121GLY00.0350.01843.939-0.057-0.0570.0000.0000.0000.000
77J122PHE0-0.055-0.05539.962-0.204-0.2040.0000.0000.0000.000
78J123GLY00.0870.05739.0410.1880.1880.0000.0000.0000.000
79J124HIS0-0.081-0.05736.066-0.157-0.1570.0000.0000.0000.000
80J125THR00.0070.01530.831-0.230-0.2300.0000.0000.0000.000
81J126ALA00.0460.01631.3480.0410.0410.0000.0000.0000.000
82J127VAL0-0.037-0.03125.198-0.277-0.2770.0000.0000.0000.000
83J128ILE00.0110.01528.4310.1270.1270.0000.0000.0000.000
84J129GLN0-0.081-0.05122.9640.0830.0830.0000.0000.0000.000
85J130ASP-1-0.769-0.86426.497-9.848-9.8480.0000.0000.0000.000
86J131SER00.0740.02429.1320.0180.0180.0000.0000.0000.000
87J132ARG10.8940.94031.5419.4499.4490.0000.0000.0000.000
88J133ILE0-0.042-0.01829.5350.1850.1850.0000.0000.0000.000
89J134THR0-0.010-0.02833.2970.1950.1950.0000.0000.0000.000
90J135ARG10.9150.97335.1378.0128.0120.0000.0000.0000.000
91J136PHE0-0.041-0.03035.5000.2080.2080.0000.0000.0000.000
92J137LYS10.8320.90835.4458.6748.6740.0000.0000.0000.000
93J138THR0-0.036-0.02038.1840.0300.0300.0000.0000.0000.000
94J139THR0-0.011-0.00741.7610.0340.0340.0000.0000.0000.000
95J140ALA0-0.012-0.00344.3740.1580.1580.0000.0000.0000.000
96J141ASP-1-0.790-0.86145.893-6.693-6.6930.0000.0000.0000.000
97J142GLN0-0.029-0.02143.539-0.086-0.0860.0000.0000.0000.000
98J143THR00.0630.01147.471-0.042-0.0420.0000.0000.0000.000
99J144GLN0-0.0070.00846.0200.1120.1120.0000.0000.0000.000
100J145ASP-1-0.734-0.82839.927-8.048-8.0480.0000.0000.0000.000
101J146PRO00.0000.00039.664-0.041-0.0410.0000.0000.0000.000
102J147LEU0-0.046-0.04134.591-0.174-0.1740.0000.0000.0000.000
103J148ALA0-0.038-0.01237.064-0.192-0.1920.0000.0000.0000.000
104J149PRO00.0070.00338.995-0.063-0.0630.0000.0000.0000.000
105J150PHE0-0.042-0.01633.679-0.070-0.0700.0000.0000.0000.000
106J151ASP-1-0.827-0.91231.095-9.687-9.6870.0000.0000.0000.000
107J152GLY0-0.046-0.02330.579-0.236-0.2360.0000.0000.0000.000
108J153ALA00.0320.03831.373-0.300-0.3000.0000.0000.0000.000
109J154LYS10.8550.91528.71010.15110.1510.0000.0000.0000.000
110J155LYS10.9670.99533.5967.8847.8840.0000.0000.0000.000
111J156TRP0-0.083-0.02233.898-0.313-0.3130.0000.0000.0000.000
112J157PHE00.0560.01035.8880.1830.1830.0000.0000.0000.000
113J158VAL00.0780.04337.604-0.220-0.2200.0000.0000.0000.000
114J159SER0-0.0110.00538.487-0.239-0.2390.0000.0000.0000.000
115J160ARG10.9440.96936.1787.7747.7740.0000.0000.0000.000
116J161GLY00.0010.01433.611-0.287-0.2870.0000.0000.0000.000
117J162PHE0-0.031-0.02428.753-0.044-0.0440.0000.0000.0000.000
118J163LYS10.8530.90023.68711.85011.8500.0000.0000.0000.000
119J164ARG10.8120.90625.66710.75810.7580.0000.0000.0000.000
120J165LEU00.0090.00519.329-0.348-0.3480.0000.0000.0000.000
121J166LEU0-0.012-0.00321.1190.5560.5560.0000.0000.0000.000
122J167ARG10.9610.97018.25613.43213.4320.0000.0000.0000.000
123J168PRO00.0100.02519.2590.4300.4300.0000.0000.0000.000
124J169LYS10.9480.96818.55813.77313.7730.0000.0000.0000.000
125J170PRO00.0080.01119.1500.7610.7610.0000.0000.0000.000
126J189ASN00.1290.05013.2710.3940.3940.0000.0000.0000.000
127J190SER00.012-0.00516.182-0.093-0.0930.0000.0000.0000.000
128J191ALA00.0080.00717.214-0.325-0.3250.0000.0000.0000.000
129J192ARG10.9260.97115.80914.16114.1610.0000.0000.0000.000
130J193THR0-0.057-0.03913.204-0.554-0.5540.0000.0000.0000.000
131J194GLY00.009-0.00514.109-1.099-1.0990.0000.0000.0000.000
132J195TRP0-0.054-0.0207.684-0.841-0.8410.0000.0000.0000.000
133J196ILE00.0050.01213.0431.3241.3240.0000.0000.0000.000
134J197PRO00.0830.04314.265-1.078-1.0780.0000.0000.0000.000
135J198LEU0-0.013-0.00912.0170.7720.7720.0000.0000.0000.000
136J199GLN00.0350.01815.9771.4501.4500.0000.0000.0000.000
137J200GLY0-0.0080.00219.4120.6110.6110.0000.0000.0000.000
138J201GLY00.0550.03321.2500.6640.6640.0000.0000.0000.000
139J202PRO00.0210.00823.752-0.420-0.4200.0000.0000.0000.000
140J203ASN0-0.033-0.03725.2700.3980.3980.0000.0000.0000.000
141J204SER00.0350.01522.1810.1030.1030.0000.0000.0000.000
142J205ALA00.0060.02422.838-0.153-0.1530.0000.0000.0000.000
143J206GLY00.0410.02119.5970.1000.1000.0000.0000.0000.000
144J207THR0-0.059-0.05017.295-0.430-0.4300.0000.0000.0000.000
145J208LYS10.8990.95419.78411.52911.5290.0000.0000.0000.000
146J209VAL0-0.0060.01321.0030.5750.5750.0000.0000.0000.000
147J210ARG10.8010.88522.51111.58811.5880.0000.0000.0000.000
148J211HIS0-0.037-0.01819.053-0.575-0.5750.0000.0000.0000.000
149J212TYR00.0470.01223.5340.1810.1810.0000.0000.0000.000
150J213GLY00.1010.01824.791-0.391-0.3910.0000.0000.0000.000
151J214ILE0-0.102-0.03326.272-0.111-0.1110.0000.0000.0000.000
152J215ALA00.0470.03028.1910.0650.0650.0000.0000.0000.000
153J216PHE0-0.011-0.02731.816-0.164-0.1640.0000.0000.0000.000
154J217SER00.055-0.00534.0880.0300.0300.0000.0000.0000.000
155J218PHE0-0.033-0.02837.370-0.186-0.1860.0000.0000.0000.000
156J219PRO00.0410.03640.3620.0660.0660.0000.0000.0000.000
157J220GLN00.000-0.01743.378-0.192-0.1920.0000.0000.0000.000
158J221PRO00.0050.01843.2640.1250.1250.0000.0000.0000.000
159J222GLU-1-0.832-0.92346.102-5.995-5.9950.0000.0000.0000.000
160J223GLN0-0.003-0.00447.3370.0860.0860.0000.0000.0000.000
161J224THR0-0.012-0.01043.426-0.114-0.1140.0000.0000.0000.000
162J225ILE00.0360.05339.403-0.060-0.0600.0000.0000.0000.000
163J226THR0-0.014-0.01837.785-0.073-0.0730.0000.0000.0000.000
164J227TYR0-0.014-0.03633.910-0.031-0.0310.0000.0000.0000.000
165J228VAL00.0180.01529.540-0.039-0.0390.0000.0000.0000.000
166J229THR00.008-0.00427.7890.0150.0150.0000.0000.0000.000
167J230LYS10.9300.96622.44112.71412.7140.0000.0000.0000.000
168J231LEU00.0190.02822.508-0.007-0.0070.0000.0000.0000.000
169J232THR0-0.084-0.05316.553-0.133-0.1330.0000.0000.0000.000
170J233LEU00.0110.01515.9330.2810.2810.0000.0000.0000.000
171J234TYR00.002-0.01212.248-0.098-0.0980.0000.0000.0000.000
172J235VAL00.0180.01112.0460.0450.0450.0000.0000.0000.000
173J236GLN00.0180.0118.181-0.478-0.4780.0000.0000.0000.000
174J237PHE00.0590.0237.2493.5613.5610.0000.0000.0000.000
175J238ARG10.8210.8854.55218.31418.439-0.001-0.045-0.0780.000
176J239GLN00.1100.0762.457-10.883-7.6370.549-1.227-2.569-0.010