FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 8G5QY

Calculation Name: 1QB2-A-Xray540

Preferred Name: Signal recognition particle 54 kDa protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1QB2

Chain ID: A

ChEMBL ID: CHEMBL4295786

UniProt ID: P61011

Base Structure: X-ray

Registration Date: 2025-07-14

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -757972.49036
FMO2-HF: Nuclear repulsion 713700.857449
FMO2-HF: Total energy -44271.632911
FMO2-MP2: Total energy -44393.212352


3D Structure Molmil
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(A:326:GLN)


Summations of interaction energy for fragment #1(A:326:GLN)
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.
-0.8240.591-0.014-0.763-0.6380.002
Interaction energy analysis for fragmet #1(A:326:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / 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].
4A327PHE0-0.1000.1064.4330.1780.5050.001-0.165-0.1640.000
5A328THR00.019-0.0763.8210.2251.358-0.013-0.587-0.5330.002
6A328THR0-0.0530.0594.6340.5380.576-0.001-0.005-0.0310.000
7A329LEU00.128-0.0886.3920.4940.4940.0000.0000.0000.000
8A329LEU0-0.0560.11710.4090.0140.0140.0000.0000.0000.000
9A330ARG00.112-0.0929.5540.3210.3210.0000.0000.0000.000
10A330ARG10.8711.0789.9481.1511.1510.0000.0000.0000.000
11A331ASP00.180-0.1067.4620.3880.3880.0000.0000.0000.000
12A331ASP-1-0.928-0.8025.562-4.141-4.224-0.001-0.0060.0900.000
13A332MET00.078-0.1068.9480.3190.3190.0000.0000.0000.000
14A332MET0-0.1070.10110.0800.0580.0580.0000.0000.0000.000
15A333TYR00.060-0.09510.8800.1780.1780.0000.0000.0000.000
16A333TYR0-0.1120.06113.6440.0120.0120.0000.0000.0000.000
17A334GLU00.054-0.14912.5950.1640.1640.0000.0000.0000.000
18A334GLU-1-0.982-0.81011.028-1.223-1.2230.0000.0000.0000.000
19A335GLN00.063-0.12112.2690.0590.0590.0000.0000.0000.000
20A335GLN0-0.0570.1149.9390.1630.1630.0000.0000.0000.000
21A336PHE00.047-0.11213.3430.0940.0940.0000.0000.0000.000
22A336PHE0-0.0420.10914.6690.0010.0010.0000.0000.0000.000
23A337GLN00.078-0.10816.3500.0600.0600.0000.0000.0000.000
24A337GLN0-0.0890.10616.924-0.048-0.0480.0000.0000.0000.000
25A338ASN00.102-0.10616.5310.0300.0300.0000.0000.0000.000
26A338ASN0-0.1250.08414.344-0.014-0.0140.0000.0000.0000.000
27A339ILE00.073-0.08917.4140.0200.0200.0000.0000.0000.000
28A339ILE0-0.0650.11015.6160.0060.0060.0000.0000.0000.000
29A340MET00.038-0.12118.9770.0300.0300.0000.0000.0000.000
30A340MET0-0.0710.10320.912-0.011-0.0110.0000.0000.0000.000
31A341LYS00.112-0.08221.1760.0170.0170.0000.0000.0000.000
32A341LYS10.8351.06619.6200.1430.1430.0000.0000.0000.000
33A342MET00.032-0.13821.666-0.002-0.0020.0000.0000.0000.000
34A342MET0-0.0860.12820.664-0.009-0.0090.0000.0000.0000.000
35A343GLY00.059-0.06323.1790.0230.0230.0000.0000.0000.000
36A344PRO00.008-0.01725.1940.0140.0140.0000.0000.0000.000
37A345PHE00.1500.02627.0920.0070.0070.0000.0000.0000.000
38A345PHE0-0.0750.09226.110-0.002-0.0020.0000.0000.0000.000
39A346SER0-0.008-0.12225.9290.0030.0030.0000.0000.0000.000
40A346SER0-0.0180.08824.4140.0100.0100.0000.0000.0000.000
41A347GLN00.141-0.04927.1610.0140.0140.0000.0000.0000.000
42A347GLN0-0.1040.08229.5270.0060.0060.0000.0000.0000.000
43A348ILE00.084-0.12630.1650.0060.0060.0000.0000.0000.000
44A348ILE0-0.1010.10131.591-0.001-0.0010.0000.0000.0000.000
45A349LEU00.008-0.13930.103-0.001-0.0010.0000.0000.0000.000
46A349LEU0-0.0620.13027.4750.0000.0000.0000.0000.0000.000
47A350GLY00.023-0.08331.1340.0050.0050.0000.0000.0000.000
48A351MET00.036-0.01232.3800.0050.0050.0000.0000.0000.000
49A351MET0-0.0930.10134.514-0.002-0.0020.0000.0000.0000.000
50A352ILE00.033-0.12434.880-0.003-0.0030.0000.0000.0000.000
51A352ILE0-0.1210.11134.135-0.001-0.0010.0000.0000.0000.000
52A353PRO0-0.025-0.11535.6530.0070.0070.0000.0000.0000.000
53A354GLY00.0430.00536.425-0.002-0.0020.0000.0000.0000.000
54A355PHE00.023-0.03632.4240.0090.0090.0000.0000.0000.000
55A355PHE0-0.0500.17030.178-0.001-0.0010.0000.0000.0000.000
56A356GLY00.023-0.12031.2160.0120.0120.0000.0000.0000.000
57A357THR00.0950.03732.489-0.005-0.0050.0000.0000.0000.000
58A357THR0-0.0620.05734.1750.0010.0010.0000.0000.0000.000
59A358ASP00.105-0.07830.583-0.012-0.0120.0000.0000.0000.000
60A358ASP-1-1.015-0.86029.6840.1250.1250.0000.0000.0000.000
61A359PHE00.140-0.07528.3910.0210.0210.0000.0000.0000.000
62A359PHE0-0.1010.08325.9630.0000.0000.0000.0000.0000.000
63A360MET0-0.004-0.12524.221-0.009-0.0090.0000.0000.0000.000
64A360MET0-0.1320.09121.1430.0050.0050.0000.0000.0000.000
65A361SER00.088-0.04723.927-0.001-0.0010.0000.0000.0000.000
66A361SER0-0.0670.05627.2170.0000.0000.0000.0000.0000.000
67A362LYS00.203-0.03623.3860.0170.0170.0000.0000.0000.000
68A362LYS10.8041.02523.252-0.208-0.2080.0000.0000.0000.000
69A363GLY0-0.108-0.14423.358-0.017-0.0170.0000.0000.0000.000
70A364ASN00.0870.04424.9850.0200.0200.0000.0000.0000.000
71A364ASN0-0.0940.07626.935-0.002-0.0020.0000.0000.0000.000
72A365GLU00.173-0.08221.090-0.032-0.0320.0000.0000.0000.000
73A365GLU-1-0.921-0.81919.9470.2980.2980.0000.0000.0000.000
74A366GLN00.121-0.08321.764-0.010-0.0100.0000.0000.0000.000
75A366GLN0-0.0660.09618.660-0.013-0.0130.0000.0000.0000.000
76A367GLU00.034-0.17822.598-0.003-0.0030.0000.0000.0000.000
77A367GLU-1-0.904-0.76625.6050.2460.2460.0000.0000.0000.000
78A368SER00.000-0.13625.475-0.015-0.0150.0000.0000.0000.000
79A368SER0-0.0420.07924.517-0.011-0.0110.0000.0000.0000.000
80A369MET00.095-0.09621.947-0.035-0.0350.0000.0000.0000.000
81A369MET0-0.1050.10518.4610.0050.0050.0000.0000.0000.000
82A370ALA00.115-0.10623.390-0.013-0.0130.0000.0000.0000.000
83A370ALA0-0.0910.11625.6460.0010.0010.0000.0000.0000.000
84A371ARG00.036-0.12725.754-0.012-0.0120.0000.0000.0000.000
85A371ARG10.7801.03428.019-0.127-0.1270.0000.0000.0000.000
86A372LEU00.060-0.12225.543-0.013-0.0130.0000.0000.0000.000
87A372LEU0-0.0390.13323.666-0.002-0.0020.0000.0000.0000.000
88A373LYS00.153-0.05825.006-0.020-0.0200.0000.0000.0000.000
89A373LYS10.8831.07923.031-0.185-0.1850.0000.0000.0000.000
90A374LYS00.094-0.08125.757-0.007-0.0070.0000.0000.0000.000
91A374LYS10.8451.06229.843-0.105-0.1050.0000.0000.0000.000
92A375LEU00.058-0.12929.403-0.007-0.0070.0000.0000.0000.000
93A375LEU0-0.0540.12529.444-0.001-0.0010.0000.0000.0000.000
94A376MET00.093-0.08526.701-0.016-0.0160.0000.0000.0000.000
95A376MET0-0.0930.08822.7990.0070.0070.0000.0000.0000.000
96A377THR00.058-0.02628.242-0.011-0.0110.0000.0000.0000.000
97A377THR0-0.0940.01227.5080.0060.0060.0000.0000.0000.000
98A378ILE00.067-0.07529.633-0.004-0.0040.0000.0000.0000.000
99A378ILE0-0.1070.05032.9820.0000.0000.0000.0000.0000.000
100A379MET00.039-0.11131.387-0.005-0.0050.0000.0000.0000.000
101A379MET0-0.0930.07930.3390.0010.0010.0000.0000.0000.000
102A380ASP00.120-0.08830.234-0.013-0.0130.0000.0000.0000.000
103A380ASP-1-0.969-0.83928.0490.0720.0720.0000.0000.0000.000
104A381SER0-0.012-0.07631.128-0.004-0.0040.0000.0000.0000.000
105A381SER0-0.0670.06434.0230.0010.0010.0000.0000.0000.000
106A382MET00.022-0.13934.339-0.002-0.0020.0000.0000.0000.000
107A382MET0-0.0820.10134.784-0.002-0.0020.0000.0000.0000.000
108A383ASN00.100-0.00235.1690.0000.0000.0000.0000.0000.000
109A383ASN0-0.1150.01238.508-0.003-0.0030.0000.0000.0000.000
110A384ASP00.198-0.13935.4970.0040.0040.0000.0000.0000.000
111A384ASP-1-0.976-0.79434.527-0.018-0.0180.0000.0000.0000.000
112A385GLN00.127-0.05536.481-0.004-0.0040.0000.0000.0000.000
113A385GLN0-0.1180.07741.0270.0030.0030.0000.0000.0000.000
114A386GLU00.006-0.12438.853-0.004-0.0040.0000.0000.0000.000
115A386GLU-1-0.823-0.75938.0380.0180.0180.0000.0000.0000.000
116A387LEU00.052-0.12034.1750.0020.0020.0000.0000.0000.000
117A387LEU0-0.0840.11532.1430.0000.0000.0000.0000.0000.000
118A388ASP00.099-0.11034.9060.0000.0000.0000.0000.0000.000
119A388ASP-1-1.004-0.84334.091-0.033-0.0330.0000.0000.0000.000
120A389SER00.030-0.06836.338-0.006-0.0060.0000.0000.0000.000
121A389SER0-0.0780.03540.0010.0000.0000.0000.0000.0000.000
122A390THR00.003-0.04138.5050.0020.0020.0000.0000.0000.000
123A390THR0-0.0630.01740.152-0.001-0.0010.0000.0000.0000.000
124A391ASP00.135-0.08239.5780.0000.0000.0000.0000.0000.000
125A391ASP-1-0.975-0.85142.0610.0010.0010.0000.0000.0000.000
126A392GLY00.033-0.08838.9190.0010.0010.0000.0000.0000.000
127A393ALA00.109-0.00939.9620.0040.0040.0000.0000.0000.000
128A393ALA0-0.0500.13341.4760.0000.0000.0000.0000.0000.000
129A394LYS00.054-0.10142.1940.0030.0030.0000.0000.0000.000
130A394LYS10.8601.05245.2730.0040.0040.0000.0000.0000.000
131A395VAL00.054-0.13243.278-0.001-0.0010.0000.0000.0000.000
132A395VAL0-0.0320.13541.9970.0000.0000.0000.0000.0000.000
133A396PHE00.012-0.11243.562-0.001-0.0010.0000.0000.0000.000
134A396PHE0-0.0290.11838.8850.0010.0010.0000.0000.0000.000
135A397SER00.054-0.09644.6590.0020.0020.0000.0000.0000.000
136A397SER0-0.0300.09747.298-0.001-0.0010.0000.0000.0000.000
137A398LYS00.034-0.08747.7840.0010.0010.0000.0000.0000.000
138A398LYS10.8771.06748.3520.0030.0030.0000.0000.0000.000
139A399GLN00.014-0.09747.944-0.001-0.0010.0000.0000.0000.000
140A399GLN0-0.0570.09447.295-0.002-0.0020.0000.0000.0000.000
141A400PRO00.093-0.06346.9160.0010.0010.0000.0000.0000.000
142A401GLY0-0.009-0.00746.9960.0030.0030.0000.0000.0000.000
143A402ARG00.040-0.04343.8450.0030.0030.0000.0000.0000.000
144A402ARG10.7210.99042.562-0.007-0.0070.0000.0000.0000.000
145A403ILE00.106-0.07242.2090.0020.0020.0000.0000.0000.000
146A403ILE0-0.0370.11542.5230.0000.0000.0000.0000.0000.000
147A404GLN00.175-0.08842.1330.0050.0050.0000.0000.0000.000
148A404GLN0-0.1210.09745.6890.0000.0000.0000.0000.0000.000
149A405ARG00.048-0.12342.5380.0050.0050.0000.0000.0000.000
150A405ARG10.6740.96738.582-0.024-0.0240.0000.0000.0000.000
151A406VAL00.090-0.08938.4660.0030.0030.0000.0000.0000.000
152A406VAL0-0.0760.11736.6430.0000.0000.0000.0000.0000.000
153A407ALA00.138-0.08137.9730.0050.0050.0000.0000.0000.000
154A407ALA0-0.0910.10640.8550.0000.0000.0000.0000.0000.000
155A408ARG0-0.012-0.10839.2660.0060.0060.0000.0000.0000.000
156A408ARG10.8781.03441.920-0.048-0.0480.0000.0000.0000.000
157A409GLY0-0.066-0.10637.6900.0030.0030.0000.0000.0000.000
158A410SER00.0410.01234.4040.0030.0030.0000.0000.0000.000
159A410SER0-0.0400.08733.9600.0010.0010.0000.0000.0000.000
160A411GLY0-0.037-0.10134.7310.0090.0090.0000.0000.0000.000
161A412VAL00.0230.01836.6530.0070.0070.0000.0000.0000.000
162A412VAL0-0.0950.08335.4320.0010.0010.0000.0000.0000.000
163A413SER00.092-0.08137.758-0.006-0.0060.0000.0000.0000.000
164A413SER0-0.0650.06340.232-0.002-0.0020.0000.0000.0000.000
165A414THR00.107-0.06840.1320.0010.0010.0000.0000.0000.000
166A414THR0-0.0310.05743.5680.0010.0010.0000.0000.0000.000
167A415ARG00.055-0.09042.251-0.005-0.0050.0000.0000.0000.000
168A415ARG10.8891.07741.495-0.061-0.0610.0000.0000.0000.000
169A416ASP00.104-0.07437.843-0.004-0.0040.0000.0000.0000.000
170A416ASP-1-0.894-0.82736.7880.0860.0860.0000.0000.0000.000
171A417VAL00.110-0.08137.7120.0010.0010.0000.0000.0000.000
172A417VAL0-0.0720.10737.924-0.001-0.0010.0000.0000.0000.000
173A418GLN00.091-0.09138.904-0.004-0.0040.0000.0000.0000.000
174A418GLN0-0.1050.07842.828-0.001-0.0010.0000.0000.0000.000
175A419GLU00.033-0.13039.054-0.007-0.0070.0000.0000.0000.000
176A419GLU-1-0.987-0.84036.1120.0790.0790.0000.0000.0000.000
177A420LEU00.203-0.07735.779-0.002-0.0020.0000.0000.0000.000
178A420LEU0-0.0990.11533.1440.0000.0000.0000.0000.0000.000
179A421LEU00.043-0.13736.511-0.003-0.0030.0000.0000.0000.000
180A421LEU0-0.0700.12838.316-0.001-0.0010.0000.0000.0000.000
181A422THR00.002-0.09438.972-0.006-0.0060.0000.0000.0000.000
182A422THR0-0.1080.03340.460-0.001-0.0010.0000.0000.0000.000
183A423GLN00.034-0.13636.049-0.006-0.0060.0000.0000.0000.000
184A423GLN0-0.0940.11635.0820.0000.0000.0000.0000.0000.000
185A424TYR00.108-0.09835.364-0.002-0.0020.0000.0000.0000.000
186A424TYR0-0.0670.11534.8550.0010.0010.0000.0000.0000.000
187A425THR00.048-0.06036.346-0.006-0.0060.0000.0000.0000.000
188A425THR0-0.0600.05240.843-0.001-0.0010.0000.0000.0000.000
189A426LYS00.103-0.06139.085-0.005-0.0050.0000.0000.0000.000
190A426LYS10.8011.03138.023-0.033-0.0330.0000.0000.0000.000
191A427PHE00.180-0.07134.730-0.003-0.0030.0000.0000.0000.000
192A427PHE0-0.1200.07530.4860.0010.0010.0000.0000.0000.000
193A428ALA00.085-0.11535.978-0.004-0.0040.0000.0000.0000.000
194A428ALA0-0.0710.11737.0620.0000.0000.0000.0000.0000.000
195A429GLN0-0.019-0.11537.155-0.006-0.0060.0000.0000.0000.000
196A429GLN0-0.1040.06040.7600.0040.0040.0000.0000.0000.000
197A430MET00.030-0.10737.326-0.003-0.0030.0000.0000.0000.000
198A430MET0-0.1010.09836.4970.0020.0020.0000.0000.0000.000
199A431VAL0-0.056-0.10334.778-0.005-0.0050.0000.0000.0000.000
200A431VAL00.0110.01132.918-0.001-0.0010.0000.0000.0000.000