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: 2211R

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1858705.190523
FMO2-HF: Nuclear repulsion 1789209.779325
FMO2-HF: Total energy -69495.411198
FMO2-MP2: Total energy -69702.998654


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.
124.429131.9457.196-4.381-10.331-0.03
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 : 0.984 / q_NPA : 0.997
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].
3J48TYR0-0.010-0.0062.473-22.015-16.6347.043-3.730-8.694-0.026
4J49THR0-0.019-0.0264.7998.3168.424-0.001-0.009-0.0990.000
5J50LEU00.0430.0337.798-0.994-0.9940.0000.0000.0000.000
6J51ARG10.9160.95810.60820.05120.0510.0000.0000.0000.000
7J52LEU00.0390.03013.5800.2650.2650.0000.0000.0000.000
8J53THR0-0.071-0.05116.8550.3990.3990.0000.0000.0000.000
9J54ARG11.0241.03420.34412.01312.0130.0000.0000.0000.000
10J55GLN00.000-0.02123.950-0.533-0.5330.0000.0000.0000.000
11J56PHE0-0.013-0.00427.3180.0140.0140.0000.0000.0000.000
12J57GLN00.0390.02630.886-0.049-0.0490.0000.0000.0000.000
13J58PHE0-0.009-0.00734.168-0.065-0.0650.0000.0000.0000.000
14J59LYS10.9590.97035.9167.4507.4500.0000.0000.0000.000
15J60ILE00.0050.02838.740-0.044-0.0440.0000.0000.0000.000
16J61ASN0-0.012-0.01541.7690.0700.0700.0000.0000.0000.000
17J62LYS10.9641.00045.2666.0586.0580.0000.0000.0000.000
18J63GLN00.004-0.01048.297-0.064-0.0640.0000.0000.0000.000
19J64THR0-0.053-0.02950.3470.0800.0800.0000.0000.0000.000
20J65THR00.0170.01752.2520.1240.1240.0000.0000.0000.000
21J66SER00.0220.00453.605-0.029-0.0290.0000.0000.0000.000
22J67VAL00.005-0.00254.353-0.060-0.0600.0000.0000.0000.000
23J68GLY00.0380.02754.7500.1110.1110.0000.0000.0000.000
24J69ASN0-0.038-0.00754.5840.0550.0550.0000.0000.0000.000
25J70LEU00.0050.00847.448-0.098-0.0980.0000.0000.0000.000
26J71ILE00.0040.01048.3370.0290.0290.0000.0000.0000.000
27J72PHE0-0.027-0.02843.254-0.144-0.1440.0000.0000.0000.000
28J73ASN00.007-0.00642.6480.0590.0590.0000.0000.0000.000
29J74ALA0-0.036-0.03037.978-0.125-0.1250.0000.0000.0000.000
30J75ASP-1-0.798-0.90135.680-8.588-8.5880.0000.0000.0000.000
31J76TYR0-0.055-0.03531.252-0.299-0.2990.0000.0000.0000.000
32J77ILE0-0.0040.00526.948-0.048-0.0480.0000.0000.0000.000
33J78THR0-0.0190.00426.737-0.236-0.2360.0000.0000.0000.000
34J79PHE0-0.044-0.03721.859-0.095-0.0950.0000.0000.0000.000
35J80ALA00.0460.03321.656-0.038-0.0380.0000.0000.0000.000
36J81LEU00.0120.00715.392-0.037-0.0370.0000.0000.0000.000
37J82ASP-1-0.853-0.94919.310-13.253-13.2530.0000.0000.0000.000
38J83ASP-1-0.843-0.90622.007-11.974-11.9740.0000.0000.0000.000
39J84PHE0-0.128-0.08919.5070.3440.3440.0000.0000.0000.000
40J85LEU0-0.011-0.00616.612-0.701-0.7010.0000.0000.0000.000
41J86GLN00.0340.03420.382-0.078-0.0780.0000.0000.0000.000
42J87ALA0-0.019-0.00920.7630.2060.2060.0000.0000.0000.000
43J88VAL0-0.043-0.02215.295-0.617-0.6170.0000.0000.0000.000
44J89PRO00.0510.03816.2430.5290.5290.0000.0000.0000.000
45J90ASN00.0490.01816.963-1.546-1.5460.0000.0000.0000.000
46J91PRO00.025-0.01312.053-0.252-0.2520.0000.0000.0000.000
47J92HIS00.0350.01312.813-1.803-1.8030.0000.0000.0000.000
48J93THR0-0.045-0.00814.977-0.158-0.1580.0000.0000.0000.000
49J94LEU0-0.016-0.00110.153-0.725-0.7250.0000.0000.0000.000
50J95ASN00.0300.0279.7661.9621.9620.0000.0000.0000.000
51J96PHE0-0.100-0.0625.251-2.453-2.4530.0000.0000.0000.000
52J97GLU-1-0.849-0.9069.478-17.708-17.7080.0000.0000.0000.000
53J98ASP-1-0.833-0.9249.810-18.729-18.7290.0000.0000.0000.000
54J99TYR0-0.066-0.08210.163-2.486-2.4860.0000.0000.0000.000
55J100ARG10.8860.9329.47623.43123.4310.0000.0000.0000.000
56J101ILE00.0230.02512.812-1.417-1.4170.0000.0000.0000.000
57J102LYS10.8910.97612.09820.59820.5980.0000.0000.0000.000
58J103LEU0-0.065-0.05214.3800.9900.9900.0000.0000.0000.000
59J104ALA00.0440.03517.106-0.538-0.5380.0000.0000.0000.000
60J105LYS10.9080.94819.83815.02015.0200.0000.0000.0000.000
61J106MET00.0150.03322.091-0.190-0.1900.0000.0000.0000.000
62J107GLU-1-0.905-0.95425.662-11.386-11.3860.0000.0000.0000.000
63J108MET0-0.0170.02127.598-0.100-0.1000.0000.0000.0000.000
64J109ARG10.8500.91029.35810.13010.1300.0000.0000.0000.000
65J110PRO00.0420.03033.220-0.073-0.0730.0000.0000.0000.000
66J111THR00.016-0.00635.889-0.068-0.0680.0000.0000.0000.000
67J112GLY0-0.017-0.01337.8570.1530.1530.0000.0000.0000.000
68J113GLY00.0040.00840.7830.1690.1690.0000.0000.0000.000
69J114HIS0-0.0180.00941.0310.1170.1170.0000.0000.0000.000
70J115TYR00.0250.01541.635-0.176-0.1760.0000.0000.0000.000
71J116THR00.026-0.00438.3400.0670.0670.0000.0000.0000.000
72J117VAL0-0.030-0.01741.369-0.037-0.0370.0000.0000.0000.000
73J118GLN0-0.0060.01044.5010.1200.1200.0000.0000.0000.000
74J119SER0-0.040-0.03244.822-0.169-0.1690.0000.0000.0000.000
75J120ASP-1-0.795-0.90143.905-6.812-6.8120.0000.0000.0000.000
76J121GLY00.0050.00644.504-0.054-0.0540.0000.0000.0000.000
77J122PHE0-0.050-0.05140.267-0.201-0.2010.0000.0000.0000.000
78J123GLY00.0890.06339.4990.1700.1700.0000.0000.0000.000
79J124HIS0-0.077-0.07736.445-0.121-0.1210.0000.0000.0000.000
80J125THR00.0110.02331.297-0.216-0.2160.0000.0000.0000.000
81J126ALA00.0430.01131.6080.0240.0240.0000.0000.0000.000
82J127VAL0-0.045-0.02825.216-0.215-0.2150.0000.0000.0000.000
83J128ILE00.0140.01628.5550.1420.1420.0000.0000.0000.000
84J129GLN0-0.084-0.05523.0640.0390.0390.0000.0000.0000.000
85J130ASP-1-0.776-0.90026.458-9.666-9.6660.0000.0000.0000.000
86J131SER00.0430.00828.8570.0310.0310.0000.0000.0000.000
87J132ARG10.9611.00731.4209.0549.0540.0000.0000.0000.000
88J133ILE0-0.061-0.02830.0660.1980.1980.0000.0000.0000.000
89J134THR0-0.001-0.03032.6560.1880.1880.0000.0000.0000.000
90J135ARG10.9330.98634.8827.9537.9530.0000.0000.0000.000
91J136PHE0-0.053-0.03235.1980.1870.1870.0000.0000.0000.000
92J137LYS10.9220.98136.8418.3168.3160.0000.0000.0000.000
93J138THR0-0.033-0.01038.7850.0400.0400.0000.0000.0000.000
94J139THR00.0080.00042.2890.0350.0350.0000.0000.0000.000
95J140ALA0-0.025-0.00245.0810.1340.1340.0000.0000.0000.000
96J141ASP-1-0.826-0.90846.364-6.660-6.6600.0000.0000.0000.000
97J142GLN0-0.042-0.03243.760-0.067-0.0670.0000.0000.0000.000
98J143THR00.0580.02448.001-0.069-0.0690.0000.0000.0000.000
99J144GLN00.0070.01046.2640.0890.0890.0000.0000.0000.000
100J145ASP-1-0.750-0.84040.760-7.859-7.8590.0000.0000.0000.000
101J146PRO0-0.003-0.00440.370-0.051-0.0510.0000.0000.0000.000
102J147LEU0-0.036-0.03435.097-0.154-0.1540.0000.0000.0000.000
103J148ALA0-0.0390.00237.277-0.180-0.1800.0000.0000.0000.000
104J149PRO00.005-0.00738.774-0.076-0.0760.0000.0000.0000.000
105J150PHE0-0.061-0.01933.918-0.080-0.0800.0000.0000.0000.000
106J151ASP-1-0.858-0.93130.839-9.469-9.4690.0000.0000.0000.000
107J152GLY0-0.021-0.00530.770-0.271-0.2710.0000.0000.0000.000
108J153ALA00.0040.01831.687-0.308-0.3080.0000.0000.0000.000
109J154LYS10.8710.93128.58810.21610.2160.0000.0000.0000.000
110J155LYS10.9891.00434.1177.9257.9250.0000.0000.0000.000
111J156TRP0-0.102-0.02934.450-0.338-0.3380.0000.0000.0000.000
112J157PHE00.0340.00636.4290.1740.1740.0000.0000.0000.000
113J158VAL00.0960.05838.191-0.239-0.2390.0000.0000.0000.000
114J159SER00.0180.04339.274-0.211-0.2110.0000.0000.0000.000
115J160ARG10.9560.96736.4337.8447.8440.0000.0000.0000.000
116J161GLY00.0180.01734.296-0.278-0.2780.0000.0000.0000.000
117J162PHE0-0.043-0.03329.441-0.027-0.0270.0000.0000.0000.000
118J163LYS10.9780.98823.30512.32912.3290.0000.0000.0000.000
119J164ARG10.8110.90426.38310.52510.5250.0000.0000.0000.000
120J165LEU0-0.026-0.01820.009-0.350-0.3500.0000.0000.0000.000
121J166LEU00.0080.00821.8040.4730.4730.0000.0000.0000.000
122J167ARG10.9590.97118.21912.87912.8790.0000.0000.0000.000
123J168PRO0-0.0010.01419.4750.4840.4840.0000.0000.0000.000
124J169LYS10.9530.96518.07613.74613.7460.0000.0000.0000.000
125J170PRO00.0530.04918.7590.5400.5400.0000.0000.0000.000
126J189ASN00.1250.04412.9750.4380.4380.0000.0000.0000.000
127J190SER00.015-0.02116.075-0.159-0.1590.0000.0000.0000.000
128J191ALA00.0050.00917.096-0.216-0.2160.0000.0000.0000.000
129J192ARG10.9400.98815.62613.83113.8310.0000.0000.0000.000
130J193THR0-0.080-0.05112.806-0.587-0.5870.0000.0000.0000.000
131J194GLY00.010-0.01314.266-0.749-0.7490.0000.0000.0000.000
132J195TRP0-0.076-0.0347.530-0.647-0.6470.0000.0000.0000.000
133J196ILE0-0.0070.02012.9541.1601.1600.0000.0000.0000.000
134J197PRO00.0970.05114.178-1.052-1.0520.0000.0000.0000.000
135J198LEU0-0.014-0.02112.2750.7970.7970.0000.0000.0000.000
136J199GLN00.0140.01916.1401.0921.0920.0000.0000.0000.000
137J200GLY00.0260.01119.5920.4930.4930.0000.0000.0000.000
138J201GLY00.0620.03621.5730.6120.6120.0000.0000.0000.000
139J202PRO0-0.015-0.01324.131-0.370-0.3700.0000.0000.0000.000
140J203ASN0-0.042-0.03625.6360.4090.4090.0000.0000.0000.000
141J204SER00.0190.01322.4560.0000.0000.0000.0000.0000.000
142J205ALA00.0470.04022.875-0.161-0.1610.0000.0000.0000.000
143J206GLY00.0460.02219.1870.0860.0860.0000.0000.0000.000
144J207THR0-0.0100.00817.501-0.333-0.3330.0000.0000.0000.000
145J208LYS10.9580.98519.71811.07511.0750.0000.0000.0000.000
146J209VAL0-0.0270.00920.5240.5930.5930.0000.0000.0000.000
147J210ARG10.8150.88622.20711.31111.3110.0000.0000.0000.000
148J211HIS0-0.024-0.01618.849-0.492-0.4920.0000.0000.0000.000
149J212TYR00.0230.00723.2290.2890.2890.0000.0000.0000.000
150J213GLY00.1050.01924.540-0.403-0.4030.0000.0000.0000.000
151J214ILE0-0.114-0.03526.936-0.069-0.0690.0000.0000.0000.000
152J215ALA00.0600.03528.9580.0360.0360.0000.0000.0000.000
153J216PHE0-0.027-0.03532.492-0.177-0.1770.0000.0000.0000.000
154J217SER00.041-0.00634.8170.0240.0240.0000.0000.0000.000
155J218PHE0-0.014-0.02838.302-0.189-0.1890.0000.0000.0000.000
156J219PRO00.0180.02441.0570.0630.0630.0000.0000.0000.000
157J220GLN0-0.035-0.01044.525-0.154-0.1540.0000.0000.0000.000
158J221PRO00.0210.02344.3590.1070.1070.0000.0000.0000.000
159J222GLU-1-0.840-0.92647.156-5.936-5.9360.0000.0000.0000.000
160J223GLN0-0.029-0.03548.1650.0560.0560.0000.0000.0000.000
161J224THR0-0.026-0.02043.889-0.103-0.1030.0000.0000.0000.000
162J225ILE00.0210.04039.946-0.029-0.0290.0000.0000.0000.000
163J226THR0-0.014-0.01637.810-0.096-0.0960.0000.0000.0000.000
164J227TYR0-0.035-0.04834.413-0.044-0.0440.0000.0000.0000.000
165J228VAL00.0240.00730.072-0.026-0.0260.0000.0000.0000.000
166J229THR00.002-0.00328.358-0.042-0.0420.0000.0000.0000.000
167J230LYS10.9600.98721.32913.39313.3930.0000.0000.0000.000
168J231LEU00.0000.00723.673-0.059-0.0590.0000.0000.0000.000
169J232THR0-0.101-0.06317.597-0.342-0.3420.0000.0000.0000.000
170J233LEU00.0410.02716.9500.2440.2440.0000.0000.0000.000
171J234TYR0-0.019-0.02513.108-0.200-0.2000.0000.0000.0000.000
172J235VAL00.0240.00912.1330.5340.5340.0000.0000.0000.000
173J236GLN00.0170.0198.501-0.667-0.6670.0000.0000.0000.000
174J237PHE00.0820.0357.1243.3023.3020.0000.0000.0000.000
175J238ARG10.8470.9414.27717.28717.413-0.001-0.053-0.0710.000
176J239GLN00.0790.0452.776-7.996-6.0950.155-0.589-1.467-0.004