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: 9GJM2

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 OptHSide
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 -2487710.003124
FMO2-HF: Nuclear repulsion 2399529.47916
FMO2-HF: Total energy -88180.523964
FMO2-MP2: Total energy -88436.210549


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.
-0.5662.5872.26-1.946-3.467-0.002
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 : 0.032 / q_NPA : 0.001
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].
3J34PRO00.0770.0203.810-1.984-0.525-0.008-0.784-0.6670.003
4J35VAL00.0350.0226.2640.2920.2920.0000.0000.0000.000
5J36MET00.0330.0122.2590.1820.6311.645-0.784-1.310-0.002
6J37LEU0-0.021-0.0072.6560.1151.3140.624-0.372-1.451-0.003
7J38ALA00.0130.0264.7900.4430.489-0.001-0.006-0.0390.000
8J39PHE00.0640.0157.5350.2570.2570.0000.0000.0000.000
9J40LYS10.8520.9445.893-0.181-0.1810.0000.0000.0000.000
10J41SER0-0.040-0.0297.9800.1190.1190.0000.0000.0000.000
11J42PHE00.0180.00210.6730.0040.0040.0000.0000.0000.000
12J43GLN0-0.004-0.01210.9610.1120.1120.0000.0000.0000.000
13J44GLN0-0.044-0.03110.8110.0720.0720.0000.0000.0000.000
14J45GLU-1-0.868-0.91514.053-0.089-0.0890.0000.0000.0000.000
15J46LEU0-0.013-0.01615.6060.0090.0090.0000.0000.0000.000
16J47ASP-1-0.806-0.89216.072-0.053-0.0530.0000.0000.0000.000
17J48ALA00.0070.01618.1920.0100.0100.0000.0000.0000.000
18J49ARG10.8570.91720.0250.0810.0810.0000.0000.0000.000
19J50HIS00.015-0.00119.7490.0060.0060.0000.0000.0000.000
20J51ASP-1-0.884-0.93422.1830.0230.0230.0000.0000.0000.000
21J52LYS10.6870.83624.191-0.010-0.0100.0000.0000.0000.000
22J53TYR00.006-0.00125.936-0.001-0.0010.0000.0000.0000.000
23J54GLU-1-0.854-0.93426.937-0.025-0.0250.0000.0000.0000.000
24J55ARG10.8230.90124.676-0.024-0.0240.0000.0000.0000.000
25J56LEU00.0130.00429.9690.0010.0010.0000.0000.0000.000
26J57VAL00.0410.02631.6830.0000.0000.0000.0000.0000.000
27J58LYS10.8210.91229.9680.0090.0090.0000.0000.0000.000
28J59LEU00.0200.01233.8620.0000.0000.0000.0000.0000.000
29J60SER00.0230.02836.1810.0010.0010.0000.0000.0000.000
30J61ARG10.9470.98837.6020.0130.0130.0000.0000.0000.000
31J62ASP-1-0.824-0.90439.1980.0020.0020.0000.0000.0000.000
32J63ILE0-0.016-0.00539.2530.0000.0000.0000.0000.0000.000
33J64THR0-0.024-0.01941.443-0.001-0.0010.0000.0000.0000.000
34J65VAL0-0.038-0.02143.5780.0000.0000.0000.0000.0000.000
35J66GLU-1-0.809-0.91045.2650.0010.0010.0000.0000.0000.000
36J67SER00.0140.00945.9230.0010.0010.0000.0000.0000.000
37J68LYS10.8840.92948.0710.0140.0140.0000.0000.0000.000
38J69ARG10.8110.90948.0720.0020.0020.0000.0000.0000.000
39J70THR0-0.003-0.00950.6460.0010.0010.0000.0000.0000.000
40J71ILE00.0110.02351.2360.0000.0000.0000.0000.0000.000
41J72PHE0-0.042-0.03652.2380.0000.0000.0000.0000.0000.000
42J73LEU0-0.060-0.01655.7980.0000.0000.0000.0000.0000.000
43J74LEU00.0510.02355.8320.0000.0000.0000.0000.0000.000
44J75HIS0-0.099-0.05657.3270.0000.0000.0000.0000.0000.000
45J76ARG10.8820.94757.4680.0020.0020.0000.0000.0000.000
46J77ILE0-0.0090.00662.0430.0000.0000.0000.0000.0000.000
47J78THR0-0.008-0.00564.9100.0000.0000.0000.0000.0000.000
48J79SER0-0.0010.01768.4120.0000.0000.0000.0000.0000.000
49J80ALA0-0.025-0.02169.3390.0000.0000.0000.0000.0000.000
50J81PRO00.0210.00169.9030.0000.0000.0000.0000.0000.000
51J82ASP-1-0.882-0.93966.7610.0000.0000.0000.0000.0000.000
52J83MET0-0.020-0.01365.1400.0000.0000.0000.0000.0000.000
53J84GLU-1-0.913-0.95364.4210.0010.0010.0000.0000.0000.000
54J85ASP-1-0.889-0.94263.3830.0030.0030.0000.0000.0000.000
55J86ILE0-0.007-0.00860.5410.0000.0000.0000.0000.0000.000
56J87LEU00.0140.01659.7150.0000.0000.0000.0000.0000.000
57J88THR00.0100.01658.7630.0000.0000.0000.0000.0000.000
58J89GLU-1-0.928-0.97356.5230.0020.0020.0000.0000.0000.000
59J90SER0-0.045-0.06155.2950.0000.0000.0000.0000.0000.000
60J91GLU-1-0.792-0.88953.8720.0010.0010.0000.0000.0000.000
61J92ILE0-0.0090.00852.8780.0010.0010.0000.0000.0000.000
62J93LYS10.8270.91050.6360.0000.0000.0000.0000.0000.000
63J94LEU00.008-0.00149.3020.0000.0000.0000.0000.0000.000
64J95ASP-1-0.797-0.87148.3570.0060.0060.0000.0000.0000.000
65J96GLY0-0.031-0.00446.8040.0010.0010.0000.0000.0000.000
66J97VAL0-0.062-0.03944.6140.0010.0010.0000.0000.0000.000
67J98ARG10.8210.87643.651-0.003-0.0030.0000.0000.0000.000
68J99GLN0-0.0040.00542.7520.0020.0020.0000.0000.0000.000
69J100LYS10.8600.91039.770-0.006-0.0060.0000.0000.0000.000
70J101ILE0-0.004-0.00538.9410.0000.0000.0000.0000.0000.000
71J102PHE0-0.0060.00938.9950.0000.0000.0000.0000.0000.000
72J103GLN0-0.006-0.00835.888-0.001-0.0010.0000.0000.0000.000
73J104VAL0-0.0030.00134.7730.0010.0010.0000.0000.0000.000
74J105ALA0-0.002-0.00934.331-0.001-0.0010.0000.0000.0000.000
75J106GLN0-0.046-0.02333.9560.0020.0020.0000.0000.0000.000
76J107GLU-1-0.837-0.90828.8020.0250.0250.0000.0000.0000.000
77J108LEU0-0.007-0.00929.753-0.002-0.0020.0000.0000.0000.000
78J109SER0-0.059-0.02031.177-0.002-0.0020.0000.0000.0000.000
79J110GLY0-0.019-0.01428.7790.0040.0040.0000.0000.0000.000
80J111GLU-1-0.832-0.89125.673-0.009-0.0090.0000.0000.0000.000
81J112ASP-1-0.933-0.95727.679-0.037-0.0370.0000.0000.0000.000
82J113MET0-0.016-0.03630.250-0.002-0.0020.0000.0000.0000.000
83J114HIS0-0.016-0.01433.037-0.002-0.0020.0000.0000.0000.000
84J115GLN00.0080.02525.604-0.014-0.0140.0000.0000.0000.000
85J116PHE00.013-0.00125.354-0.006-0.0060.0000.0000.0000.000
86J117HIS0-0.033-0.02030.6420.0000.0000.0000.0000.0000.000
87J118ARG10.9500.95629.9020.0660.0660.0000.0000.0000.000
88J119ALA0-0.0040.02131.3460.0000.0000.0000.0000.0000.000
89J120ILE00.020-0.01533.4760.0030.0030.0000.0000.0000.000
90J121THR0-0.060-0.01136.5660.0020.0020.0000.0000.0000.000
91J122THR00.0410.00739.0570.0010.0010.0000.0000.0000.000
92J123GLY00.0390.03439.9850.0020.0020.0000.0000.0000.000
93J124LEU0-0.010-0.01239.0590.0020.0020.0000.0000.0000.000
94J125GLN0-0.047-0.03541.8050.0010.0010.0000.0000.0000.000
95J126GLU-1-0.800-0.88544.653-0.012-0.0120.0000.0000.0000.000
96J127TYR00.0570.01445.1700.0020.0020.0000.0000.0000.000
97J128VAL0-0.024-0.00946.2890.0010.0010.0000.0000.0000.000
98J129GLU-1-0.897-0.93848.653-0.013-0.0130.0000.0000.0000.000
99J130ALA0-0.023-0.01550.0580.0010.0010.0000.0000.0000.000
100J131VAL00.009-0.00149.8920.0010.0010.0000.0000.0000.000
101J132SER0-0.023-0.03352.5690.0000.0000.0000.0000.0000.000
102J133PHE00.0050.00454.4520.0000.0000.0000.0000.0000.000
103J134GLN00.001-0.01355.5970.0000.0000.0000.0000.0000.000
104J135HIS00.0070.00156.4240.0010.0010.0000.0000.0000.000
105J136PHE0-0.014-0.00458.2220.0000.0000.0000.0000.0000.000
106J137ILE0-0.026-0.02059.4600.0000.0000.0000.0000.0000.000
107J138LYS10.8360.92757.6610.0010.0010.0000.0000.0000.000
108J139THR0-0.027-0.01261.0700.0000.0000.0000.0000.0000.000
109J140ARG10.7900.88163.4780.0050.0050.0000.0000.0000.000
110J141SER0-0.042-0.02761.252-0.001-0.0010.0000.0000.0000.000
111J142LEU0-0.005-0.01455.0420.0000.0000.0000.0000.0000.000
112J143ILE00.0020.03353.2590.0000.0000.0000.0000.0000.000
113J144SER00.002-0.03053.961-0.001-0.0010.0000.0000.0000.000
114J145MET00.0100.00047.3450.0000.0000.0000.0000.0000.000
115J146ASP-1-0.880-0.94249.111-0.005-0.0050.0000.0000.0000.000
116J147GLU-1-0.831-0.88350.300-0.004-0.0040.0000.0000.0000.000
117J148ILE0-0.0080.00947.4510.0010.0010.0000.0000.0000.000
118J149ASN00.025-0.00445.4560.0010.0010.0000.0000.0000.000
119J150LYS10.8560.93846.5600.0040.0040.0000.0000.0000.000
120J151GLN00.0250.01348.7000.0010.0010.0000.0000.0000.000
121J152LEU0-0.087-0.02843.3140.0010.0010.0000.0000.0000.000
122J153ILE0-0.020-0.01043.3510.0000.0000.0000.0000.0000.000
123J154PHE00.0360.01641.4870.0000.0000.0000.0000.0000.000
124J155THR0-0.0170.00242.3370.0000.0000.0000.0000.0000.000
125J180LEU0-0.013-0.01537.2860.0000.0000.0000.0000.0000.000
126J181ARG10.9210.96139.7550.0070.0070.0000.0000.0000.000
127J182VAL00.0200.01740.941-0.002-0.0020.0000.0000.0000.000
128J183THR0-0.042-0.04739.548-0.001-0.0010.0000.0000.0000.000
129J184PRO00.077-0.00642.7590.0010.0010.0000.0000.0000.000
130J185VAL00.0240.01542.7450.0010.0010.0000.0000.0000.000
131J186ASP-1-0.748-0.82441.254-0.023-0.0230.0000.0000.0000.000
132J187TYR0-0.005-0.03344.2020.0000.0000.0000.0000.0000.000
133J188LEU00.0030.00347.6280.0010.0010.0000.0000.0000.000
134J189LEU0-0.035-0.02044.0560.0000.0000.0000.0000.0000.000
135J190GLY00.0830.03647.7730.0000.0000.0000.0000.0000.000
136J191VAL00.0290.00949.0120.0010.0010.0000.0000.0000.000
137J192ALA0-0.022-0.01551.1280.0010.0010.0000.0000.0000.000
138J193ASP-1-0.803-0.85748.903-0.020-0.0200.0000.0000.0000.000
139J194LEU00.0190.03652.3970.0010.0010.0000.0000.0000.000
140J195THR0-0.052-0.04654.6910.0010.0010.0000.0000.0000.000
141J196GLY0-0.028-0.01455.9870.0000.0000.0000.0000.0000.000
142J197GLU-1-0.729-0.83354.673-0.011-0.0110.0000.0000.0000.000
143J198LEU00.0270.01757.5660.0010.0010.0000.0000.0000.000
144J199MET0-0.050-0.02460.1320.0000.0000.0000.0000.0000.000
145J200ARG10.8030.86955.2930.0130.0130.0000.0000.0000.000
146J201MET00.0260.02061.8070.0000.0000.0000.0000.0000.000
147J202CYS0-0.0700.01963.5390.0000.0000.0000.0000.0000.000
148J203ILE00.017-0.00465.6040.0000.0000.0000.0000.0000.000
149J204ASN0-0.008-0.00462.8250.0000.0000.0000.0000.0000.000
150J205SER0-0.024-0.00667.0280.0000.0000.0000.0000.0000.000
151J206VAL0-0.018-0.01769.4160.0000.0000.0000.0000.0000.000
152J207GLY0-0.041-0.01370.5300.0000.0000.0000.0000.0000.000
153J208ASN0-0.064-0.04069.6680.0000.0000.0000.0000.0000.000
154J209GLY0-0.0050.00972.8730.0000.0000.0000.0000.0000.000
155J210ASP-1-0.780-0.86071.126-0.005-0.0050.0000.0000.0000.000
156J211ILE0-0.036-0.03973.9930.0000.0000.0000.0000.0000.000
157J212ASP-1-0.932-0.95673.593-0.005-0.0050.0000.0000.0000.000
158J213THR0-0.017-0.04267.3590.0000.0000.0000.0000.0000.000
159J214PRO0-0.031-0.04568.935-0.001-0.0010.0000.0000.0000.000
160J215PHE00.037-0.00469.124-0.001-0.0010.0000.0000.0000.000
161J216GLU-1-0.770-0.84168.057-0.006-0.0060.0000.0000.0000.000
162J217VAL0-0.013-0.01263.572-0.001-0.0010.0000.0000.0000.000
163J218SER0-0.020-0.02265.137-0.001-0.0010.0000.0000.0000.000
164J219GLN0-0.065-0.03166.8060.0000.0000.0000.0000.0000.000
165J220PHE00.0400.01358.747-0.001-0.0010.0000.0000.0000.000
166J221LEU00.001-0.01260.362-0.001-0.0010.0000.0000.0000.000
167J222ARG10.8320.90362.3160.0100.0100.0000.0000.0000.000
168J223GLN00.0150.01662.8020.0000.0000.0000.0000.0000.000
169J224VAL00.0210.00956.989-0.001-0.0010.0000.0000.0000.000
170J225TYR0-0.015-0.00858.435-0.002-0.0020.0000.0000.0000.000
171J226ASP-1-0.863-0.93459.734-0.016-0.0160.0000.0000.0000.000
172J227GLY0-0.025-0.00158.185-0.001-0.0010.0000.0000.0000.000
173J228PHE0-0.040-0.04351.697-0.001-0.0010.0000.0000.0000.000
174J229SER0-0.064-0.04055.871-0.002-0.0020.0000.0000.0000.000
175J230PHE0-0.059-0.01657.314-0.001-0.0010.0000.0000.0000.000
176J231ILE0-0.029-0.00151.686-0.001-0.0010.0000.0000.0000.000
177J232GLY00.0350.01654.718-0.001-0.0010.0000.0000.0000.000
178J233ASN0-0.046-0.03851.718-0.001-0.0010.0000.0000.0000.000
179J234THR0-0.057-0.01050.236-0.002-0.0020.0000.0000.0000.000
180J235GLY00.0150.00648.3050.0000.0000.0000.0000.0000.000
181J236PRO00.007-0.00143.727-0.001-0.0010.0000.0000.0000.000
182J237TYR00.0420.02744.0210.0010.0010.0000.0000.0000.000
183J238GLU-1-0.888-0.96742.589-0.036-0.0360.0000.0000.0000.000
184J239VAL00.0390.01345.8770.0020.0020.0000.0000.0000.000
185J240SER00.0540.01548.8070.0020.0020.0000.0000.0000.000
186J241LYS10.8820.94945.6420.0350.0350.0000.0000.0000.000
187J242LYS10.7740.87047.7400.0230.0230.0000.0000.0000.000
188J243LEU00.0210.02351.6220.0010.0010.0000.0000.0000.000
189J244TYR0-0.0070.00754.4600.0010.0010.0000.0000.0000.000
190J245THR00.018-0.01253.4420.0010.0010.0000.0000.0000.000
191J246LEU00.0340.04055.8190.0010.0010.0000.0000.0000.000
192J247LYS10.9520.97657.4300.0210.0210.0000.0000.0000.000
193J248GLN0-0.025-0.01659.0340.0020.0020.0000.0000.0000.000
194J249SER00.0170.00358.2420.0010.0010.0000.0000.0000.000
195J250LEU00.0280.02861.1760.0010.0010.0000.0000.0000.000
196J251ALA00.0340.02063.4580.0010.0010.0000.0000.0000.000
197J252LYS10.9070.95061.0230.0160.0160.0000.0000.0000.000
198J253VAL00.0450.03264.2160.0010.0010.0000.0000.0000.000
199J254GLU-1-0.816-0.89166.923-0.012-0.0120.0000.0000.0000.000
200J255ASN0-0.084-0.05568.9810.0010.0010.0000.0000.0000.000
201J256ALA00.0130.02069.4140.0000.0000.0000.0000.0000.000
202J257CYS0-0.0230.00070.1220.0010.0010.0000.0000.0000.000
203J258TYR0-0.013-0.00272.9810.0000.0000.0000.0000.0000.000
204J259ALA0-0.006-0.01074.5780.0000.0000.0000.0000.0000.000
205J260LEU0-0.0090.00673.5290.0000.0000.0000.0000.0000.000
206J261LYS10.9070.95777.1360.0080.0080.0000.0000.0000.000
207J262VAL00.0020.00179.1520.0000.0000.0000.0000.0000.000
208J263ARG10.9710.98577.6220.0080.0080.0000.0000.0000.000
209J264GLY00.0190.01881.1720.0000.0000.0000.0000.0000.000
210J265SER0-0.112-0.05982.5410.0000.0000.0000.0000.0000.000
211J266GLU-1-0.925-0.96584.812-0.007-0.0070.0000.0000.0000.000
212J267ILE0-0.034-0.01087.3600.0000.0000.0000.0000.0000.000
213J268PRO00.0200.02389.5120.0000.0000.0000.0000.0000.000
214J269LYS10.9400.95991.6540.0060.0060.0000.0000.0000.000
215J270HIS00.002-0.01793.6270.0000.0000.0000.0000.0000.000
216J271MET0-0.026-0.00393.3400.0000.0000.0000.0000.0000.000
217J272LEU0-0.012-0.01289.2990.0000.0000.0000.0000.0000.000
218J273ALA0-0.0200.00093.8260.0000.0000.0000.0000.0000.000
219J274ASP-1-0.944-0.96195.892-0.004-0.0040.0000.0000.0000.000