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: M3G9Z

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 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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2495054.943299
FMO2-HF: Nuclear repulsion 2406873.945617
FMO2-HF: Total energy -88180.997682
FMO2-MP2: Total energy -88436.616751


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.
-1.6121.4911.653-1.746-3.009-0.004
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 : 0.038 / q_NPA : 0.012
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].
3J34PRO00.0730.0153.517-2.783-1.0530.011-0.925-0.8150.000
4J35VAL00.0290.0256.0750.2900.2900.0000.0000.0000.000
5J36MET00.0350.0122.5960.1080.6940.439-0.321-0.7040.000
6J37LEU0-0.013-0.0012.2190.1470.8941.204-0.487-1.464-0.004
7J38ALA00.0140.0274.7010.4320.472-0.001-0.013-0.0260.000
8J39PHE00.0620.0308.0280.2140.2140.0000.0000.0000.000
9J40LYS10.8100.9046.277-0.488-0.4880.0000.0000.0000.000
10J41SER0-0.066-0.0458.4020.0770.0770.0000.0000.0000.000
11J42PHE00.0400.00610.5750.0020.0020.0000.0000.0000.000
12J43GLN00.004-0.01111.4790.1270.1270.0000.0000.0000.000
13J44GLN00.0030.00710.9950.1390.1390.0000.0000.0000.000
14J45GLU-1-0.865-0.90814.223-0.023-0.0230.0000.0000.0000.000
15J46LEU0-0.005-0.01515.704-0.006-0.0060.0000.0000.0000.000
16J47ASP-1-0.801-0.89416.4580.0710.0710.0000.0000.0000.000
17J48ALA00.0000.01718.423-0.002-0.0020.0000.0000.0000.000
18J49ARG10.8290.89920.2920.0050.0050.0000.0000.0000.000
19J50HIS0-0.002-0.00520.167-0.005-0.0050.0000.0000.0000.000
20J51ASP-1-0.867-0.93422.6470.0830.0830.0000.0000.0000.000
21J52LYS10.7060.85824.511-0.049-0.0490.0000.0000.0000.000
22J53TYR00.010-0.00326.313-0.006-0.0060.0000.0000.0000.000
23J54GLU-1-0.807-0.91127.1330.0180.0180.0000.0000.0000.000
24J55ARG10.8260.91424.836-0.065-0.0650.0000.0000.0000.000
25J56LEU00.0090.00430.098-0.003-0.0030.0000.0000.0000.000
26J57VAL00.0300.01432.045-0.003-0.0030.0000.0000.0000.000
27J58LYS10.7490.86730.808-0.029-0.0290.0000.0000.0000.000
28J59LEU00.0330.02134.044-0.001-0.0010.0000.0000.0000.000
29J60SER00.0220.01936.509-0.002-0.0020.0000.0000.0000.000
30J61ARG10.9310.98838.042-0.009-0.0090.0000.0000.0000.000
31J62ASP-1-0.816-0.90339.3520.0230.0230.0000.0000.0000.000
32J63ILE0-0.024-0.00539.388-0.001-0.0010.0000.0000.0000.000
33J64THR0-0.018-0.02541.845-0.002-0.0020.0000.0000.0000.000
34J65VAL0-0.045-0.02244.013-0.001-0.0010.0000.0000.0000.000
35J66GLU-1-0.781-0.88245.7340.0140.0140.0000.0000.0000.000
36J67SER00.0260.02046.2260.0000.0000.0000.0000.0000.000
37J68LYS10.8160.89048.461-0.002-0.0020.0000.0000.0000.000
38J69ARG10.8130.89847.870-0.014-0.0140.0000.0000.0000.000
39J70THR0-0.003-0.00850.9830.0000.0000.0000.0000.0000.000
40J71ILE00.0020.01851.9070.0000.0000.0000.0000.0000.000
41J72PHE0-0.039-0.03852.5810.0000.0000.0000.0000.0000.000
42J73LEU0-0.082-0.02255.9950.0000.0000.0000.0000.0000.000
43J74LEU00.0310.01256.0710.0000.0000.0000.0000.0000.000
44J75HIS0-0.073-0.05557.8700.0000.0000.0000.0000.0000.000
45J76ARG10.8780.95857.598-0.009-0.0090.0000.0000.0000.000
46J77ILE0-0.0220.00262.1280.0000.0000.0000.0000.0000.000
47J78THR0-0.009-0.00765.1490.0000.0000.0000.0000.0000.000
48J79SER0-0.003-0.00968.5610.0000.0000.0000.0000.0000.000
49J80ALA0-0.0090.01769.7690.0000.0000.0000.0000.0000.000
50J81PRO00.008-0.00869.7350.0000.0000.0000.0000.0000.000
51J82ASP-1-0.870-0.93566.9450.0070.0070.0000.0000.0000.000
52J83MET0-0.010-0.00765.0540.0000.0000.0000.0000.0000.000
53J84GLU-1-0.885-0.94264.2100.0080.0080.0000.0000.0000.000
54J85ASP-1-0.892-0.93863.2880.0100.0100.0000.0000.0000.000
55J86ILE0-0.028-0.01860.7500.0010.0010.0000.0000.0000.000
56J87LEU0-0.0040.00359.5510.0000.0000.0000.0000.0000.000
57J88THR0-0.0040.00658.7930.0010.0010.0000.0000.0000.000
58J89GLU-1-0.921-0.97356.3760.0120.0120.0000.0000.0000.000
59J90SER0-0.038-0.05555.3360.0010.0010.0000.0000.0000.000
60J91GLU-1-0.763-0.85753.9330.0110.0110.0000.0000.0000.000
61J92ILE00.0220.01952.8110.0010.0010.0000.0000.0000.000
62J93LYS10.8050.89750.859-0.012-0.0120.0000.0000.0000.000
63J94LEU00.0010.00349.3420.0010.0010.0000.0000.0000.000
64J95ASP-1-0.805-0.88748.3690.0170.0170.0000.0000.0000.000
65J96GLY0-0.038-0.00646.7290.0020.0020.0000.0000.0000.000
66J97VAL0-0.059-0.03244.5530.0020.0020.0000.0000.0000.000
67J98ARG10.7830.84843.682-0.013-0.0130.0000.0000.0000.000
68J99GLN00.0130.00642.5370.0030.0030.0000.0000.0000.000
69J100LYS10.8450.90839.528-0.025-0.0250.0000.0000.0000.000
70J101ILE00.0130.00738.9940.0010.0010.0000.0000.0000.000
71J102PHE00.0050.01438.7230.0010.0010.0000.0000.0000.000
72J103GLN00.005-0.00435.9140.0000.0000.0000.0000.0000.000
73J104VAL0-0.005-0.00234.8150.0020.0020.0000.0000.0000.000
74J105ALA0-0.023-0.01734.4400.0000.0000.0000.0000.0000.000
75J106GLN0-0.038-0.01633.7470.0040.0040.0000.0000.0000.000
76J107GLU-1-0.819-0.89128.5610.0580.0580.0000.0000.0000.000
77J108LEU0-0.009-0.01429.6860.0010.0010.0000.0000.0000.000
78J109SER0-0.063-0.03431.318-0.002-0.0020.0000.0000.0000.000
79J110GLY0-0.019-0.01728.2490.0050.0050.0000.0000.0000.000
80J111GLU-1-0.831-0.88825.6820.0310.0310.0000.0000.0000.000
81J112ASP-1-0.900-0.95027.244-0.008-0.0080.0000.0000.0000.000
82J113MET0-0.028-0.03230.128-0.002-0.0020.0000.0000.0000.000
83J114HIS0-0.017-0.01233.208-0.001-0.0010.0000.0000.0000.000
84J115GLN0-0.0340.00625.793-0.010-0.0100.0000.0000.0000.000
85J116PHE00.0310.00525.399-0.003-0.0030.0000.0000.0000.000
86J117HIS0-0.019-0.01930.9530.0000.0000.0000.0000.0000.000
87J118ARG10.9460.95830.3140.0260.0260.0000.0000.0000.000
88J119ALA0-0.0070.02031.848-0.001-0.0010.0000.0000.0000.000
89J120ILE00.019-0.01433.9850.0020.0020.0000.0000.0000.000
90J121THR0-0.038-0.01637.0390.0000.0000.0000.0000.0000.000
91J122THR00.0270.00339.6480.0000.0000.0000.0000.0000.000
92J123GLY00.0340.02840.4990.0000.0000.0000.0000.0000.000
93J124LEU0-0.026-0.02239.2080.0010.0010.0000.0000.0000.000
94J125GLN0-0.056-0.03542.3120.0000.0000.0000.0000.0000.000
95J126GLU-1-0.803-0.89145.2280.0030.0030.0000.0000.0000.000
96J127TYR00.0530.01645.3900.0010.0010.0000.0000.0000.000
97J128VAL0-0.006-0.00246.7990.0000.0000.0000.0000.0000.000
98J129GLU-1-0.855-0.90149.0500.0010.0010.0000.0000.0000.000
99J130ALA0-0.005-0.00850.2810.0000.0000.0000.0000.0000.000
100J131VAL00.003-0.00450.0380.0000.0000.0000.0000.0000.000
101J132SER0-0.034-0.04552.7140.0000.0000.0000.0000.0000.000
102J133PHE0-0.004-0.00554.7610.0000.0000.0000.0000.0000.000
103J134GLN00.003-0.01055.6920.0000.0000.0000.0000.0000.000
104J135HIS00.0210.00856.4820.0010.0010.0000.0000.0000.000
105J136PHE0-0.0160.00758.3380.0000.0000.0000.0000.0000.000
106J137ILE0-0.021-0.02459.5850.0000.0000.0000.0000.0000.000
107J138LYS10.8410.92857.329-0.009-0.0090.0000.0000.0000.000
108J139THR0-0.046-0.01861.1840.0000.0000.0000.0000.0000.000
109J140ARG10.7870.86863.825-0.003-0.0030.0000.0000.0000.000
110J141SER0-0.042-0.03261.238-0.001-0.0010.0000.0000.0000.000
111J142LEU0-0.002-0.02055.2120.0000.0000.0000.0000.0000.000
112J143ILE00.0020.03653.1710.0000.0000.0000.0000.0000.000
113J144SER00.013-0.02553.578-0.001-0.0010.0000.0000.0000.000
114J145MET0-0.005-0.00847.1090.0010.0010.0000.0000.0000.000
115J146ASP-1-0.834-0.91648.6690.0070.0070.0000.0000.0000.000
116J147GLU-1-0.811-0.86050.0490.0050.0050.0000.0000.0000.000
117J148ILE00.0010.00347.3410.0010.0010.0000.0000.0000.000
118J149ASN00.0270.00145.1770.0020.0020.0000.0000.0000.000
119J150LYS10.7930.89246.382-0.006-0.0060.0000.0000.0000.000
120J151GLN00.0090.01948.4810.0010.0010.0000.0000.0000.000
121J152LEU0-0.070-0.02642.9930.0010.0010.0000.0000.0000.000
122J153ILE0-0.0130.00142.6880.0010.0010.0000.0000.0000.000
123J154PHE00.0310.01541.1800.0000.0000.0000.0000.0000.000
124J155THR0-0.020-0.00241.9710.0000.0000.0000.0000.0000.000
125J180LEU0-0.011-0.01336.9890.0000.0000.0000.0000.0000.000
126J181ARG10.9070.95039.206-0.009-0.0090.0000.0000.0000.000
127J182VAL00.0270.02340.805-0.001-0.0010.0000.0000.0000.000
128J183THR0-0.028-0.04639.577-0.001-0.0010.0000.0000.0000.000
129J184PRO00.062-0.01242.7990.0000.0000.0000.0000.0000.000
130J185VAL00.0220.02242.5990.0000.0000.0000.0000.0000.000
131J186ASP-1-0.727-0.80641.576-0.002-0.0020.0000.0000.0000.000
132J187TYR0-0.008-0.03144.4820.0000.0000.0000.0000.0000.000
133J188LEU00.003-0.00147.9110.0000.0000.0000.0000.0000.000
134J189LEU0-0.047-0.02344.3040.0000.0000.0000.0000.0000.000
135J190GLY00.0970.04148.0330.0000.0000.0000.0000.0000.000
136J191VAL00.017-0.00249.3860.0000.0000.0000.0000.0000.000
137J192ALA0-0.021-0.00351.7230.0000.0000.0000.0000.0000.000
138J193ASP-1-0.821-0.86949.255-0.005-0.0050.0000.0000.0000.000
139J194LEU00.0210.03252.7730.0000.0000.0000.0000.0000.000
140J195THR0-0.031-0.03855.0250.0000.0000.0000.0000.0000.000
141J196GLY0-0.005-0.00956.4430.0000.0000.0000.0000.0000.000
142J197GLU-1-0.742-0.83455.0680.0010.0010.0000.0000.0000.000
143J198LEU00.0400.02158.0800.0000.0000.0000.0000.0000.000
144J199MET0-0.054-0.01860.4710.0000.0000.0000.0000.0000.000
145J200ARG10.8120.86955.5170.0010.0010.0000.0000.0000.000
146J201MET00.0150.02262.0230.0000.0000.0000.0000.0000.000
147J202CYS0-0.0670.01163.8490.0000.0000.0000.0000.0000.000
148J203ILE00.0140.00565.9190.0000.0000.0000.0000.0000.000
149J204ASN0-0.010-0.01062.8190.0000.0000.0000.0000.0000.000
150J205SER0-0.003-0.00167.2130.0000.0000.0000.0000.0000.000
151J206VAL0-0.013-0.01269.5160.0000.0000.0000.0000.0000.000
152J207GLY0-0.044-0.01470.7210.0000.0000.0000.0000.0000.000
153J208ASN0-0.040-0.03269.9560.0000.0000.0000.0000.0000.000
154J209GLY0-0.0140.00272.8660.0000.0000.0000.0000.0000.000
155J210ASP-1-0.793-0.86871.2560.0020.0020.0000.0000.0000.000
156J211ILE0-0.041-0.03473.9770.0000.0000.0000.0000.0000.000
157J212ASP-1-0.930-0.95673.7520.0010.0010.0000.0000.0000.000
158J213THR00.005-0.03367.4120.0000.0000.0000.0000.0000.000
159J214PRO0-0.033-0.03868.7320.0000.0000.0000.0000.0000.000
160J215PHE00.032-0.00469.285-0.001-0.0010.0000.0000.0000.000
161J216GLU-1-0.782-0.85268.1680.0010.0010.0000.0000.0000.000
162J217VAL0-0.007-0.00563.7800.0000.0000.0000.0000.0000.000
163J218SER0-0.032-0.02365.314-0.001-0.0010.0000.0000.0000.000
164J219GLN0-0.063-0.03866.9900.0000.0000.0000.0000.0000.000
165J220PHE00.0400.02159.0830.0000.0000.0000.0000.0000.000
166J221LEU00.003-0.01760.7970.0000.0000.0000.0000.0000.000
167J222ARG10.8320.91162.4390.0030.0030.0000.0000.0000.000
168J223GLN00.0350.02362.9510.0000.0000.0000.0000.0000.000
169J224VAL00.0050.00857.2680.0000.0000.0000.0000.0000.000
170J225TYR00.0120.00358.708-0.001-0.0010.0000.0000.0000.000
171J226ASP-1-0.878-0.93659.968-0.007-0.0070.0000.0000.0000.000
172J227GLY0-0.0110.00158.593-0.001-0.0010.0000.0000.0000.000
173J228PHE0-0.024-0.03252.093-0.001-0.0010.0000.0000.0000.000
174J229SER0-0.067-0.04856.125-0.001-0.0010.0000.0000.0000.000
175J230PHE0-0.061-0.02357.217-0.001-0.0010.0000.0000.0000.000
176J231ILE0-0.0120.01551.718-0.001-0.0010.0000.0000.0000.000
177J232GLY00.0490.01354.536-0.001-0.0010.0000.0000.0000.000
178J233ASN0-0.053-0.04151.980-0.001-0.0010.0000.0000.0000.000
179J234THR0-0.047-0.00650.682-0.001-0.0010.0000.0000.0000.000
180J235GLY00.011-0.00348.0180.0010.0010.0000.0000.0000.000
181J236PRO00.0030.00944.051-0.001-0.0010.0000.0000.0000.000
182J237TYR00.0830.04744.3690.0010.0010.0000.0000.0000.000
183J238GLU-1-0.890-0.96442.716-0.017-0.0170.0000.0000.0000.000
184J239VAL00.0130.00046.2630.0010.0010.0000.0000.0000.000
185J240SER00.024-0.00249.2490.0010.0010.0000.0000.0000.000
186J241LYS10.8530.93245.8960.0180.0180.0000.0000.0000.000
187J242LYS10.7790.87948.3010.0070.0070.0000.0000.0000.000
188J243LEU00.0110.01852.3880.0010.0010.0000.0000.0000.000
189J244TYR0-0.0040.00555.1340.0010.0010.0000.0000.0000.000
190J245THR00.018-0.01053.6160.0000.0000.0000.0000.0000.000
191J246LEU00.0340.04356.3230.0010.0010.0000.0000.0000.000
192J247LYS10.9250.96657.9690.0100.0100.0000.0000.0000.000
193J248GLN0-0.006-0.00759.2640.0010.0010.0000.0000.0000.000
194J249SER0-0.004-0.00658.5490.0000.0000.0000.0000.0000.000
195J250LEU00.0130.01761.4850.0000.0000.0000.0000.0000.000
196J251ALA00.0580.02863.8550.0000.0000.0000.0000.0000.000
197J252LYS10.8740.94561.6150.0060.0060.0000.0000.0000.000
198J253VAL00.0610.03964.6360.0000.0000.0000.0000.0000.000
199J254GLU-1-0.828-0.89867.395-0.004-0.0040.0000.0000.0000.000
200J255ASN0-0.069-0.05069.5810.0000.0000.0000.0000.0000.000
201J256ALA00.0130.01769.9950.0000.0000.0000.0000.0000.000
202J257CYS0-0.0140.00770.5720.0000.0000.0000.0000.0000.000
203J258TYR0-0.009-0.00773.4140.0000.0000.0000.0000.0000.000
204J259ALA0-0.022-0.01974.8500.0000.0000.0000.0000.0000.000
205J260LEU00.0130.01773.6960.0000.0000.0000.0000.0000.000
206J261LYS10.9260.96077.4330.0020.0020.0000.0000.0000.000
207J262VAL0-0.0200.00079.3980.0000.0000.0000.0000.0000.000
208J263ARG10.9480.97277.9790.0020.0020.0000.0000.0000.000
209J264GLY00.0070.01281.5510.0000.0000.0000.0000.0000.000
210J265SER0-0.084-0.05983.0150.0000.0000.0000.0000.0000.000
211J266GLU-1-0.928-0.95585.524-0.002-0.0020.0000.0000.0000.000
212J267ILE0-0.019-0.01287.9580.0000.0000.0000.0000.0000.000
213J268PRO00.0210.01989.6440.0000.0000.0000.0000.0000.000
214J269LYS10.9230.95791.8600.0020.0020.0000.0000.0000.000
215J270HIS0-0.023-0.02694.1350.0000.0000.0000.0000.0000.000
216J271MET00.0080.01993.5200.0000.0000.0000.0000.0000.000
217J272LEU0-0.033-0.02689.3970.0000.0000.0000.0000.0000.000
218J273ALA0-0.0060.00993.9130.0000.0000.0000.0000.0000.000
219J274ASP-1-0.960-0.97296.4770.0000.0000.0000.0000.0000.000