FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: LJ879

Calculation Name: 3PJA-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PJA

Chain ID: J

ChEMBL ID:

UniProt ID: Q99598

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:

Apendix: None


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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2486827.311722
FMO2-HF: Nuclear repulsion 2398648.2443
FMO2-HF: Total energy -88179.067422
FMO2-MP2: Total energy -88434.824873


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:32:SER)


Summations of interaction energy for fragment #1(J:32:SER)
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.
-0.2292.6422.544-1.744-3.671-0.004
Interaction energy analysis for fragmet #1(J:32:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.004
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].
3J34PRO00.0690.0243.810-1.819-0.428-0.006-0.707-0.6790.002
4J35VAL00.0440.0166.2620.3110.3110.0000.0000.0000.000
5J36MET00.0280.0122.2960.3580.6141.571-0.509-1.318-0.002
6J37LEU0-0.020-0.0082.3670.1651.3450.980-0.522-1.637-0.004
7J38ALA00.0150.0264.7680.4140.458-0.001-0.006-0.0370.000
8J39PHE00.0540.0057.5570.2430.2430.0000.0000.0000.000
9J40LYS10.8640.9615.886-0.171-0.1710.0000.0000.0000.000
10J41SER0-0.034-0.0257.9800.1190.1190.0000.0000.0000.000
11J42PHE00.0310.01610.670-0.003-0.0030.0000.0000.0000.000
12J43GLN0-0.015-0.00611.0780.0980.0980.0000.0000.0000.000
13J44GLN0-0.031-0.03211.5440.0400.0400.0000.0000.0000.000
14J45GLU-1-0.919-0.94314.043-0.069-0.0690.0000.0000.0000.000
15J46LEU0-0.036-0.02915.9430.0080.0080.0000.0000.0000.000
16J47ASP-1-0.854-0.93216.307-0.066-0.0660.0000.0000.0000.000
17J48ALA00.0280.02918.1800.0100.0100.0000.0000.0000.000
18J49ARG10.9230.95620.0920.0850.0850.0000.0000.0000.000
19J50HIS00.014-0.00119.8660.0060.0060.0000.0000.0000.000
20J51ASP-1-0.884-0.93521.5610.0110.0110.0000.0000.0000.000
21J52LYS10.7940.90724.190-0.017-0.0170.0000.0000.0000.000
22J53TYR00.003-0.00425.9350.0000.0000.0000.0000.0000.000
23J54GLU-1-0.906-0.96526.891-0.035-0.0350.0000.0000.0000.000
24J55ARG10.8150.91424.968-0.023-0.0230.0000.0000.0000.000
25J56LEU00.0060.00129.9990.0010.0010.0000.0000.0000.000
26J57VAL00.0460.03331.2870.0000.0000.0000.0000.0000.000
27J58LYS10.8820.94430.2820.0110.0110.0000.0000.0000.000
28J59LEU00.0150.01134.1680.0010.0010.0000.0000.0000.000
29J60SER00.0220.02836.1790.0010.0010.0000.0000.0000.000
30J61ARG10.9350.97637.6060.0160.0160.0000.0000.0000.000
31J62ASP-1-0.863-0.94939.1890.0000.0000.0000.0000.0000.000
32J63ILE0-0.014-0.00439.5390.0010.0010.0000.0000.0000.000
33J64THR00.0040.00141.569-0.001-0.0010.0000.0000.0000.000
34J65VAL0-0.074-0.03843.5470.0000.0000.0000.0000.0000.000
35J66GLU-1-0.881-0.96245.2650.0010.0010.0000.0000.0000.000
36J67SER00.0400.03146.0630.0010.0010.0000.0000.0000.000
37J68LYS11.0111.01048.0720.0150.0150.0000.0000.0000.000
38J69ARG10.8500.92648.8430.0040.0040.0000.0000.0000.000
39J70THR00.0170.00650.6930.0010.0010.0000.0000.0000.000
40J71ILE00.0470.03451.5030.0010.0010.0000.0000.0000.000
41J72PHE0-0.059-0.04752.3300.0000.0000.0000.0000.0000.000
42J73LEU0-0.048-0.01555.7990.0000.0000.0000.0000.0000.000
43J74LEU00.0640.03155.9850.0000.0000.0000.0000.0000.000
44J75HIS0-0.113-0.07257.3370.0000.0000.0000.0000.0000.000
45J76ARG10.8700.94257.5500.0030.0030.0000.0000.0000.000
46J77ILE00.0020.01561.7680.0000.0000.0000.0000.0000.000
47J78THR0-0.003-0.00364.909-0.001-0.0010.0000.0000.0000.000
48J79SER00.0000.01968.4130.0000.0000.0000.0000.0000.000
49J80ALA0-0.027-0.02669.3320.0000.0000.0000.0000.0000.000
50J81PRO00.0170.00369.8980.0000.0000.0000.0000.0000.000
51J82ASP-1-0.886-0.94766.5510.0000.0000.0000.0000.0000.000
52J83MET0-0.002-0.00365.4290.0000.0000.0000.0000.0000.000
53J84GLU-1-0.919-0.95264.3600.0010.0010.0000.0000.0000.000
54J85ASP-1-0.889-0.93263.3710.0030.0030.0000.0000.0000.000
55J86ILE0-0.010-0.00560.5440.0000.0000.0000.0000.0000.000
56J87LEU00.0240.00659.7060.0000.0000.0000.0000.0000.000
57J88THR0-0.0130.00558.7520.0000.0000.0000.0000.0000.000
58J89GLU-1-0.926-0.96856.5630.0020.0020.0000.0000.0000.000
59J90SER0-0.085-0.07555.2940.0000.0000.0000.0000.0000.000
60J91GLU-1-0.887-0.96053.8620.0030.0030.0000.0000.0000.000
61J92ILE0-0.0200.01152.7580.0010.0010.0000.0000.0000.000
62J93LYS10.8640.93150.9390.0000.0000.0000.0000.0000.000
63J94LEU0-0.002-0.00349.2910.0000.0000.0000.0000.0000.000
64J95ASP-1-0.821-0.88948.3440.0070.0070.0000.0000.0000.000
65J96GLY0-0.024-0.00846.7890.0010.0010.0000.0000.0000.000
66J97VAL0-0.059-0.03544.6100.0010.0010.0000.0000.0000.000
67J98ARG10.8990.93143.639-0.003-0.0030.0000.0000.0000.000
68J99GLN0-0.0090.00342.6940.0030.0030.0000.0000.0000.000
69J100LYS10.9170.95740.118-0.005-0.0050.0000.0000.0000.000
70J101ILE0-0.004-0.00138.9270.0000.0000.0000.0000.0000.000
71J102PHE0-0.0230.00338.9780.0010.0010.0000.0000.0000.000
72J103GLN0-0.008-0.01135.9560.0000.0000.0000.0000.0000.000
73J104VAL00.0020.00634.7650.0010.0010.0000.0000.0000.000
74J105ALA0-0.009-0.01034.314-0.001-0.0010.0000.0000.0000.000
75J106GLN0-0.047-0.02433.8500.0030.0030.0000.0000.0000.000
76J107GLU-1-0.869-0.93629.3090.0290.0290.0000.0000.0000.000
77J108LEU0-0.018-0.02429.733-0.002-0.0020.0000.0000.0000.000
78J109SER0-0.055-0.01731.156-0.001-0.0010.0000.0000.0000.000
79J110GLY0-0.028-0.01828.7490.0050.0050.0000.0000.0000.000
80J111GLU-1-0.885-0.94125.570-0.006-0.0060.0000.0000.0000.000
81J112ASP-1-0.939-0.96227.856-0.030-0.0300.0000.0000.0000.000
82J113MET0-0.017-0.03330.236-0.003-0.0030.0000.0000.0000.000
83J114HIS00.004-0.01033.030-0.003-0.0030.0000.0000.0000.000
84J115GLN00.0000.02025.359-0.014-0.0140.0000.0000.0000.000
85J116PHE00.007-0.00125.369-0.007-0.0070.0000.0000.0000.000
86J117HIS0-0.025-0.01030.6430.0000.0000.0000.0000.0000.000
87J118ARG10.9460.95530.0640.0700.0700.0000.0000.0000.000
88J119ALA00.0100.02231.5370.0000.0000.0000.0000.0000.000
89J120ILE00.002-0.01733.4840.0030.0030.0000.0000.0000.000
90J121THR0-0.065-0.00736.5680.0020.0020.0000.0000.0000.000
91J122THR00.027-0.00139.0620.0020.0020.0000.0000.0000.000
92J123GLY00.0540.03839.9990.0020.0020.0000.0000.0000.000
93J124LEU0-0.026-0.01739.0800.0020.0020.0000.0000.0000.000
94J125GLN0-0.041-0.03241.8770.0020.0020.0000.0000.0000.000
95J126GLU-1-0.874-0.93444.677-0.014-0.0140.0000.0000.0000.000
96J127TYR00.0290.01045.2560.0020.0020.0000.0000.0000.000
97J128VAL0-0.038-0.01746.2700.0010.0010.0000.0000.0000.000
98J129GLU-1-0.850-0.91848.651-0.014-0.0140.0000.0000.0000.000
99J130ALA0-0.033-0.02150.0870.0010.0010.0000.0000.0000.000
100J131VAL0-0.001-0.00449.8720.0010.0010.0000.0000.0000.000
101J132SER0-0.031-0.03552.5700.0000.0000.0000.0000.0000.000
102J133PHE00.0210.01354.4490.0000.0000.0000.0000.0000.000
103J134GLN0-0.010-0.02655.4030.0000.0000.0000.0000.0000.000
104J135HIS0-0.014-0.00856.3890.0010.0010.0000.0000.0000.000
105J136PHE0-0.006-0.00658.2150.0000.0000.0000.0000.0000.000
106J137ILE0-0.028-0.01859.7800.0000.0000.0000.0000.0000.000
107J138LYS10.9300.97158.8050.0000.0000.0000.0000.0000.000
108J139THR0-0.0230.00661.0250.0000.0000.0000.0000.0000.000
109J140ARG10.8230.91963.4660.0050.0050.0000.0000.0000.000
110J141SER0-0.048-0.03861.297-0.001-0.0010.0000.0000.0000.000
111J142LEU0-0.013-0.01954.8950.0000.0000.0000.0000.0000.000
112J143ILE00.0060.03652.9850.0000.0000.0000.0000.0000.000
113J144SER00.0180.00353.953-0.001-0.0010.0000.0000.0000.000
114J145MET00.0180.01247.1870.0000.0000.0000.0000.0000.000
115J146ASP-1-0.965-0.99249.100-0.004-0.0040.0000.0000.0000.000
116J147GLU-1-0.850-0.92250.284-0.003-0.0030.0000.0000.0000.000
117J148ILE0-0.0110.01147.7300.0010.0010.0000.0000.0000.000
118J149ASN00.033-0.00345.4620.0010.0010.0000.0000.0000.000
119J150LYS10.9370.98746.5410.0000.0000.0000.0000.0000.000
120J151GLN00.009-0.00148.6780.0010.0010.0000.0000.0000.000
121J152LEU0-0.086-0.02443.3650.0010.0010.0000.0000.0000.000
122J153ILE0-0.007-0.00543.3300.0000.0000.0000.0000.0000.000
123J154PHE00.0300.01041.4360.0000.0000.0000.0000.0000.000
124J155THR0-0.0250.00042.3050.0020.0020.0000.0000.0000.000
125J180LEU0-0.007-0.01137.7180.0000.0000.0000.0000.0000.000
126J181ARG10.9220.96139.8780.0040.0040.0000.0000.0000.000
127J182VAL00.0390.02640.932-0.002-0.0020.0000.0000.0000.000
128J183THR0-0.053-0.01239.565-0.001-0.0010.0000.0000.0000.000
129J184PRO00.097-0.01042.7560.0000.0000.0000.0000.0000.000
130J185VAL00.0260.01642.7800.0010.0010.0000.0000.0000.000
131J186ASP-1-0.761-0.88241.137-0.024-0.0240.0000.0000.0000.000
132J187TYR0-0.020-0.03544.2050.0000.0000.0000.0000.0000.000
133J188LEU00.004-0.00247.6290.0000.0000.0000.0000.0000.000
134J189LEU0-0.045-0.02644.0270.0000.0000.0000.0000.0000.000
135J190GLY00.0710.03747.7640.0000.0000.0000.0000.0000.000
136J191VAL00.0320.01449.0170.0010.0010.0000.0000.0000.000
137J192ALA0-0.035-0.02551.1380.0000.0000.0000.0000.0000.000
138J193ASP-1-0.856-0.88449.157-0.021-0.0210.0000.0000.0000.000
139J194LEU00.0150.02952.4080.0010.0010.0000.0000.0000.000
140J195THR0-0.064-0.05654.6980.0010.0010.0000.0000.0000.000
141J196GLY00.0080.00255.9970.0000.0000.0000.0000.0000.000
142J197GLU-1-0.768-0.88254.737-0.012-0.0120.0000.0000.0000.000
143J198LEU00.0210.01357.5750.0010.0010.0000.0000.0000.000
144J199MET0-0.076-0.02660.4400.0000.0000.0000.0000.0000.000
145J200ARG10.8320.90855.5180.0140.0140.0000.0000.0000.000
146J201MET00.0420.03061.8150.0000.0000.0000.0000.0000.000
147J202CYS0-0.0380.01063.5460.0010.0010.0000.0000.0000.000
148J203ILE0-0.025-0.01765.5480.0000.0000.0000.0000.0000.000
149J204ASN00.0080.00363.0450.0000.0000.0000.0000.0000.000
150J205SER0-0.034-0.00867.0370.0000.0000.0000.0000.0000.000
151J206VAL0-0.010-0.01569.4220.0000.0000.0000.0000.0000.000
152J207GLY0-0.048-0.01570.5400.0000.0000.0000.0000.0000.000
153J208ASN0-0.069-0.04669.9180.0000.0000.0000.0000.0000.000
154J209GLY0-0.0110.00772.8800.0000.0000.0000.0000.0000.000
155J210ASP-1-0.784-0.87371.301-0.005-0.0050.0000.0000.0000.000
156J211ILE0-0.043-0.04273.998-0.001-0.0010.0000.0000.0000.000
157J212ASP-1-0.925-0.94473.517-0.005-0.0050.0000.0000.0000.000
158J213THR0-0.023-0.03467.4160.0000.0000.0000.0000.0000.000
159J214PRO0-0.021-0.02268.939-0.001-0.0010.0000.0000.0000.000
160J215PHE00.037-0.01569.132-0.001-0.0010.0000.0000.0000.000
161J216GLU-1-0.822-0.88668.216-0.006-0.0060.0000.0000.0000.000
162J217VAL0-0.004-0.00763.7340.0000.0000.0000.0000.0000.000
163J218SER0-0.023-0.02765.144-0.001-0.0010.0000.0000.0000.000
164J219GLN0-0.035-0.00966.814-0.001-0.0010.0000.0000.0000.000
165J220PHE00.0330.00958.727-0.001-0.0010.0000.0000.0000.000
166J221LEU00.007-0.01060.444-0.001-0.0010.0000.0000.0000.000
167J222ARG10.8810.93662.3250.0110.0110.0000.0000.0000.000
168J223GLN0-0.0020.00862.7850.0000.0000.0000.0000.0000.000
169J224VAL00.0230.01157.042-0.001-0.0010.0000.0000.0000.000
170J225TYR0-0.020-0.00958.444-0.002-0.0020.0000.0000.0000.000
171J226ASP-1-0.866-0.94259.746-0.016-0.0160.0000.0000.0000.000
172J227GLY0-0.025-0.00258.192-0.001-0.0010.0000.0000.0000.000
173J228PHE0-0.044-0.04051.657-0.001-0.0010.0000.0000.0000.000
174J229SER0-0.060-0.03555.885-0.002-0.0020.0000.0000.0000.000
175J230PHE0-0.062-0.01557.274-0.001-0.0010.0000.0000.0000.000
176J231ILE0-0.0240.00251.649-0.001-0.0010.0000.0000.0000.000
177J232GLY00.0260.00654.732-0.001-0.0010.0000.0000.0000.000
178J233ASN0-0.032-0.02851.748-0.002-0.0020.0000.0000.0000.000
179J234THR0-0.070-0.02250.201-0.002-0.0020.0000.0000.0000.000
180J235GLY00.0170.01548.3270.0000.0000.0000.0000.0000.000
181J236PRO00.0110.00543.834-0.001-0.0010.0000.0000.0000.000
182J237TYR00.0400.02144.1830.0010.0010.0000.0000.0000.000
183J238GLU-1-0.887-0.96342.138-0.038-0.0380.0000.0000.0000.000
184J239VAL00.0390.01745.8970.0020.0020.0000.0000.0000.000
185J240SER00.0450.01348.8230.0020.0020.0000.0000.0000.000
186J241LYS10.8840.95045.6120.0380.0380.0000.0000.0000.000
187J242LYS10.8320.90847.7690.0260.0260.0000.0000.0000.000
188J243LEU00.0350.02551.6410.0010.0010.0000.0000.0000.000
189J244TYR00.0050.01554.4890.0010.0010.0000.0000.0000.000
190J245THR00.024-0.01053.4650.0010.0010.0000.0000.0000.000
191J246LEU00.0280.03755.8350.0010.0010.0000.0000.0000.000
192J247LYS10.9470.96657.4470.0220.0220.0000.0000.0000.000
193J248GLN0-0.049-0.02159.0450.0020.0020.0000.0000.0000.000
194J249SER0-0.011-0.00758.3330.0010.0010.0000.0000.0000.000
195J250LEU00.0380.02961.1930.0010.0010.0000.0000.0000.000
196J251ALA00.0310.02163.4740.0010.0010.0000.0000.0000.000
197J252LYS10.9440.95960.9250.0170.0170.0000.0000.0000.000
198J253VAL00.0420.03464.1310.0010.0010.0000.0000.0000.000
199J254GLU-1-0.873-0.93766.937-0.013-0.0130.0000.0000.0000.000
200J255ASN0-0.074-0.04569.1380.0010.0010.0000.0000.0000.000
201J256ALA00.0150.01969.4520.0000.0000.0000.0000.0000.000
202J257CYS0-0.0170.00470.2430.0010.0010.0000.0000.0000.000
203J258TYR0-0.0160.00172.9930.0000.0000.0000.0000.0000.000
204J259ALA0-0.010-0.01174.5920.0000.0000.0000.0000.0000.000
205J260LEU0-0.0090.00473.7700.0000.0000.0000.0000.0000.000
206J261LYS10.9470.98677.1480.0080.0080.0000.0000.0000.000
207J262VAL00.0160.01079.1660.0000.0000.0000.0000.0000.000
208J263ARG10.9620.97878.0560.0090.0090.0000.0000.0000.000
209J264GLY00.0100.01581.1850.0000.0000.0000.0000.0000.000
210J265SER0-0.132-0.07782.4700.0000.0000.0000.0000.0000.000
211J266GLU-1-0.941-0.96884.823-0.008-0.0080.0000.0000.0000.000
212J267ILE0-0.028-0.00887.3730.0000.0000.0000.0000.0000.000
213J268PRO00.0150.02189.6780.0000.0000.0000.0000.0000.000
214J269LYS10.9470.96391.6680.0070.0070.0000.0000.0000.000
215J270HIS0-0.011-0.02993.7290.0000.0000.0000.0000.0000.000
216J271MET0-0.0190.00993.3260.0000.0000.0000.0000.0000.000
217J272LEU0-0.001-0.01189.3940.0000.0000.0000.0000.0000.000
218J273ALA0-0.021-0.00193.8420.0000.0000.0000.0000.0000.000
219J274ASP-1-0.949-0.96495.907-0.004-0.0040.0000.0000.0000.000