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: G86V1

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 OptAll
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 -760147.346718
FMO2-HF: Nuclear repulsion 715873.822846
FMO2-HF: Total energy -44273.523872
FMO2-MP2: Total energy -44394.999324


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.
-2.0390.568-0.012-1.458-1.1350.006
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 : 0.115 / q_NPA : 0.008
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].
4A327PHE0-0.1020.1024.284-0.0160.5060.003-0.261-0.2630.001
5A328THR0-0.087-0.1013.869-0.4731.587-0.014-1.195-0.8510.005
6A328THR0-0.0650.0175.0520.3390.364-0.001-0.002-0.0210.000
7A329LEU00.159-0.0826.9300.1490.1490.0000.0000.0000.000
8A329LEU0-0.0430.10810.4820.0260.0260.0000.0000.0000.000
9A330ARG00.085-0.07610.0680.2440.2440.0000.0000.0000.000
10A330ARG10.8201.0379.9521.1201.1200.0000.0000.0000.000
11A331ASP00.090-0.1298.0240.4310.4310.0000.0000.0000.000
12A331ASP-1-0.808-0.7285.891-4.212-4.2120.0000.0000.0000.000
13A332MET00.145-0.0649.5270.1890.1890.0000.0000.0000.000
14A332MET0-0.1110.09810.1980.0450.0450.0000.0000.0000.000
15A333TYR00.094-0.07111.2850.1560.1560.0000.0000.0000.000
16A333TYR0-0.1020.07414.1220.0250.0250.0000.0000.0000.000
17A334GLU00.084-0.13013.2360.1700.1700.0000.0000.0000.000
18A334GLU-1-0.924-0.79712.447-1.242-1.2420.0000.0000.0000.000
19A335GLN00.015-0.12112.9580.0950.0950.0000.0000.0000.000
20A335GLN0-0.0630.08111.0470.1310.1310.0000.0000.0000.000
21A336PHE00.037-0.08714.1850.0960.0960.0000.0000.0000.000
22A336PHE0-0.0470.09215.086-0.001-0.0010.0000.0000.0000.000
23A337GLN00.128-0.09417.1090.0790.0790.0000.0000.0000.000
24A337GLN0-0.0830.10517.789-0.034-0.0340.0000.0000.0000.000
25A338ASN00.074-0.07217.3670.0680.0680.0000.0000.0000.000
26A338ASN0-0.1260.06215.9800.0630.0630.0000.0000.0000.000
27A339ILE00.106-0.08318.2290.0440.0440.0000.0000.0000.000
28A339ILE0-0.0800.09615.8890.0040.0040.0000.0000.0000.000
29A340MET00.069-0.10719.6860.0430.0430.0000.0000.0000.000
30A340MET0-0.0980.08521.432-0.006-0.0060.0000.0000.0000.000
31A341LYS00.104-0.08422.0310.0380.0380.0000.0000.0000.000
32A341LYS10.7721.02719.6750.3770.3770.0000.0000.0000.000
33A342MET00.044-0.12822.3240.0250.0250.0000.0000.0000.000
34A342MET0-0.0860.12121.179-0.006-0.0060.0000.0000.0000.000
35A343GLY00.059-0.05823.7040.0250.0250.0000.0000.0000.000
36A344PRO00.030-0.00525.5930.0200.0200.0000.0000.0000.000
37A345PHE00.1400.04327.5070.0180.0180.0000.0000.0000.000
38A345PHE0-0.0850.08226.419-0.004-0.0040.0000.0000.0000.000
39A346SER00.023-0.11426.2520.0150.0150.0000.0000.0000.000
40A346SER0-0.0460.06225.0040.0000.0000.0000.0000.0000.000
41A347GLN00.145-0.04727.5470.0140.0140.0000.0000.0000.000
42A347GLN0-0.1020.08229.715-0.007-0.0070.0000.0000.0000.000
43A348ILE00.058-0.11730.4330.0120.0120.0000.0000.0000.000
44A348ILE0-0.1020.10332.1030.0000.0000.0000.0000.0000.000
45A349LEU00.028-0.11830.4010.0100.0100.0000.0000.0000.000
46A349LEU0-0.0740.09927.9560.0000.0000.0000.0000.0000.000
47A350GLY00.028-0.10131.1190.0090.0090.0000.0000.0000.000
48A351MET00.032-0.00332.3590.0080.0080.0000.0000.0000.000
49A351MET0-0.0790.09834.9380.0010.0010.0000.0000.0000.000
50A352ILE00.064-0.10835.0060.0060.0060.0000.0000.0000.000
51A352ILE0-0.1220.11534.3890.0000.0000.0000.0000.0000.000
52A353PRO0-0.039-0.13636.0050.0020.0020.0000.0000.0000.000
53A354GLY00.0560.02136.473-0.001-0.0010.0000.0000.0000.000
54A355PHE00.021-0.02632.2860.0080.0080.0000.0000.0000.000
55A355PHE0-0.0500.13430.260-0.002-0.0020.0000.0000.0000.000
56A356GLY00.000-0.11831.6240.0030.0030.0000.0000.0000.000
57A357THR00.0550.01732.531-0.009-0.0090.0000.0000.0000.000
58A357THR0-0.0610.04034.2540.0020.0020.0000.0000.0000.000
59A358ASP00.085-0.06030.631-0.008-0.0080.0000.0000.0000.000
60A358ASP-1-0.929-0.81129.809-0.045-0.0450.0000.0000.0000.000
61A359PHE00.154-0.05328.2630.0000.0000.0000.0000.0000.000
62A359PHE0-0.0970.08026.577-0.001-0.0010.0000.0000.0000.000
63A360MET0-0.012-0.11124.126-0.003-0.0030.0000.0000.0000.000
64A360MET0-0.1160.09022.482-0.003-0.0030.0000.0000.0000.000
65A361SER00.068-0.08624.030-0.022-0.0220.0000.0000.0000.000
66A361SER0-0.0690.04627.2070.0060.0060.0000.0000.0000.000
67A362LYS00.159-0.06022.8910.0040.0040.0000.0000.0000.000
68A362LYS10.7220.99622.4730.0470.0470.0000.0000.0000.000
69A363GLY0-0.034-0.12523.1350.0120.0120.0000.0000.0000.000
70A364ASN00.0800.06524.5050.0150.0150.0000.0000.0000.000
71A364ASN0-0.0790.07226.6320.0070.0070.0000.0000.0000.000
72A365GLU00.141-0.10321.144-0.002-0.0020.0000.0000.0000.000
73A365GLU-1-0.853-0.77820.329-0.078-0.0780.0000.0000.0000.000
74A366GLN00.094-0.06821.489-0.016-0.0160.0000.0000.0000.000
75A366GLN0-0.0690.09418.548-0.006-0.0060.0000.0000.0000.000
76A367GLU00.032-0.15522.347-0.001-0.0010.0000.0000.0000.000
77A367GLU-1-0.879-0.78125.203-0.011-0.0110.0000.0000.0000.000
78A368SER00.003-0.12125.2330.0040.0040.0000.0000.0000.000
79A368SER0-0.0350.05824.385-0.004-0.0040.0000.0000.0000.000
80A369MET00.110-0.10121.727-0.010-0.0100.0000.0000.0000.000
81A369MET0-0.0980.10418.150-0.012-0.0120.0000.0000.0000.000
82A370ALA00.094-0.09623.176-0.006-0.0060.0000.0000.0000.000
83A370ALA0-0.0890.10625.1800.0030.0030.0000.0000.0000.000
84A371ARG00.026-0.12225.5990.0050.0050.0000.0000.0000.000
85A371ARG10.7711.03527.9720.0390.0390.0000.0000.0000.000
86A372LEU00.059-0.09825.5870.0070.0070.0000.0000.0000.000
87A372LEU0-0.0500.10923.775-0.003-0.0030.0000.0000.0000.000
88A373LYS00.154-0.05924.684-0.005-0.0050.0000.0000.0000.000
89A373LYS10.8431.06423.3250.0330.0330.0000.0000.0000.000
90A374LYS00.062-0.09225.7560.0040.0040.0000.0000.0000.000
91A374LYS10.7951.00029.8190.0260.0260.0000.0000.0000.000
92A375LEU00.085-0.10529.4460.0060.0060.0000.0000.0000.000
93A375LEU0-0.0790.10529.791-0.001-0.0010.0000.0000.0000.000
94A376MET00.122-0.09127.0870.0020.0020.0000.0000.0000.000
95A376MET0-0.1140.09323.039-0.003-0.0030.0000.0000.0000.000
96A377THR0-0.013-0.04028.616-0.003-0.0030.0000.0000.0000.000
97A377THR0-0.0440.03328.2610.0030.0030.0000.0000.0000.000
98A378ILE00.148-0.06030.1690.0060.0060.0000.0000.0000.000
99A378ILE0-0.1160.05333.1460.0010.0010.0000.0000.0000.000
100A379MET00.084-0.10531.7190.0060.0060.0000.0000.0000.000
101A379MET0-0.1050.07830.701-0.003-0.0030.0000.0000.0000.000
102A380ASP00.065-0.10030.348-0.004-0.0040.0000.0000.0000.000
103A380ASP-1-0.966-0.84328.257-0.065-0.0650.0000.0000.0000.000
104A381SER00.033-0.06731.3430.0030.0030.0000.0000.0000.000
105A381SER0-0.0430.07134.0560.0040.0040.0000.0000.0000.000
106A382MET00.065-0.09534.7260.0070.0070.0000.0000.0000.000
107A382MET0-0.1340.07335.034-0.002-0.0020.0000.0000.0000.000
108A383ASN00.052-0.04035.8850.0010.0010.0000.0000.0000.000
109A383ASN0-0.1180.01538.644-0.002-0.0020.0000.0000.0000.000
110A384ASP00.138-0.11535.945-0.002-0.0020.0000.0000.0000.000
111A384ASP-1-0.888-0.80235.537-0.072-0.0720.0000.0000.0000.000
112A385GLN00.130-0.06136.947-0.005-0.0050.0000.0000.0000.000
113A385GLN0-0.1030.08641.5970.0040.0040.0000.0000.0000.000
114A386GLU00.020-0.12139.200-0.001-0.0010.0000.0000.0000.000
115A386GLU-1-0.832-0.74138.592-0.046-0.0460.0000.0000.0000.000
116A387LEU00.029-0.11434.6970.0020.0020.0000.0000.0000.000
117A387LEU0-0.0820.10232.5740.0000.0000.0000.0000.0000.000
118A388ASP00.143-0.10235.491-0.005-0.0050.0000.0000.0000.000
119A388ASP-1-1.016-0.84034.358-0.103-0.1030.0000.0000.0000.000
120A389SER0-0.013-0.09336.675-0.002-0.0020.0000.0000.0000.000
121A389SER0-0.0520.04040.3660.0010.0010.0000.0000.0000.000
122A390THR00.003-0.07339.004-0.003-0.0030.0000.0000.0000.000
123A390THR0-0.0330.05640.5870.0020.0020.0000.0000.0000.000
124A391ASP00.091-0.08940.628-0.003-0.0030.0000.0000.0000.000
125A391ASP-1-0.963-0.84243.006-0.063-0.0630.0000.0000.0000.000
126A392GLY00.086-0.05539.5890.0040.0040.0000.0000.0000.000
127A393ALA00.1200.00440.6130.0050.0050.0000.0000.0000.000
128A393ALA0-0.0670.12141.8080.0000.0000.0000.0000.0000.000
129A394LYS00.016-0.10442.7930.0050.0050.0000.0000.0000.000
130A394LYS10.8461.04545.4900.0560.0560.0000.0000.0000.000
131A395VAL00.029-0.14043.8040.0020.0020.0000.0000.0000.000
132A395VAL0-0.0590.11942.6520.0000.0000.0000.0000.0000.000
133A396PHE00.071-0.09543.8290.0030.0030.0000.0000.0000.000
134A396PHE0-0.0690.09839.3370.0010.0010.0000.0000.0000.000
135A397SER00.037-0.09344.9060.0040.0040.0000.0000.0000.000
136A397SER0-0.0370.07447.4620.0000.0000.0000.0000.0000.000
137A398LYS00.070-0.09448.0620.0030.0030.0000.0000.0000.000
138A398LYS10.8711.07448.3830.0480.0480.0000.0000.0000.000
139A399GLN0-0.019-0.08648.4760.0020.0020.0000.0000.0000.000
140A399GLN0-0.0280.11947.792-0.002-0.0020.0000.0000.0000.000
141A400PRO00.109-0.06647.4930.0000.0000.0000.0000.0000.000
142A401GLY00.011-0.00346.9270.0010.0010.0000.0000.0000.000
143A402ARG00.052-0.02444.2210.0030.0030.0000.0000.0000.000
144A402ARG10.7330.96543.0130.0450.0450.0000.0000.0000.000
145A403ILE00.118-0.06342.455-0.001-0.0010.0000.0000.0000.000
146A403ILE0-0.0650.10242.7280.0000.0000.0000.0000.0000.000
147A404GLN00.173-0.05942.3530.0000.0000.0000.0000.0000.000
148A404GLN0-0.1300.07845.8600.0010.0010.0000.0000.0000.000
149A405ARG00.045-0.11942.8670.0040.0040.0000.0000.0000.000
150A405ARG10.6520.92938.8690.0390.0390.0000.0000.0000.000
151A406VAL00.080-0.09738.7760.0030.0030.0000.0000.0000.000
152A406VAL0-0.0910.10337.0340.0000.0000.0000.0000.0000.000
153A407ALA00.180-0.03438.2420.0000.0000.0000.0000.0000.000
154A407ALA0-0.1220.06941.5710.0000.0000.0000.0000.0000.000
155A408ARG00.024-0.09939.2730.0020.0020.0000.0000.0000.000
156A408ARG10.8641.03842.3780.0080.0080.0000.0000.0000.000
157A409GLY0-0.061-0.11637.9910.0040.0040.0000.0000.0000.000
158A410SER00.0460.02534.6730.0030.0030.0000.0000.0000.000
159A410SER0-0.0500.07134.331-0.001-0.0010.0000.0000.0000.000
160A411GLY0-0.043-0.11434.9620.0020.0020.0000.0000.0000.000
161A412VAL00.0340.00537.0730.0050.0050.0000.0000.0000.000
162A412VAL0-0.0900.10235.9360.0000.0000.0000.0000.0000.000
163A413SER00.078-0.08638.2000.0000.0000.0000.0000.0000.000
164A413SER0-0.0790.03940.7190.0000.0000.0000.0000.0000.000
165A414THR00.103-0.07940.554-0.003-0.0030.0000.0000.0000.000
166A414THR0-0.0450.07044.0920.0010.0010.0000.0000.0000.000
167A415ARG00.080-0.07742.642-0.004-0.0040.0000.0000.0000.000
168A415ARG10.7661.00039.7420.0250.0250.0000.0000.0000.000
169A416ASP00.059-0.11038.025-0.003-0.0030.0000.0000.0000.000
170A416ASP-1-0.794-0.75336.981-0.018-0.0180.0000.0000.0000.000
171A417VAL00.090-0.07137.913-0.005-0.0050.0000.0000.0000.000
172A417VAL0-0.0720.10438.4630.0000.0000.0000.0000.0000.000
173A418GLN00.113-0.08739.350-0.006-0.0060.0000.0000.0000.000
174A418GLN0-0.1010.08543.1520.0020.0020.0000.0000.0000.000
175A419GLU00.053-0.09138.913-0.004-0.0040.0000.0000.0000.000
176A419GLU-1-0.931-0.79836.469-0.032-0.0320.0000.0000.0000.000
177A420LEU00.180-0.07536.067-0.004-0.0040.0000.0000.0000.000
178A420LEU0-0.1050.11433.2100.0000.0000.0000.0000.0000.000
179A421LEU00.075-0.11636.807-0.007-0.0070.0000.0000.0000.000
180A421LEU0-0.0880.10438.6540.0000.0000.0000.0000.0000.000
181A422THR0-0.005-0.10339.390-0.004-0.0040.0000.0000.0000.000
182A422THR0-0.0920.03340.9500.0010.0010.0000.0000.0000.000
183A423GLN00.070-0.10736.487-0.001-0.0010.0000.0000.0000.000
184A423GLN0-0.1030.09035.074-0.003-0.0030.0000.0000.0000.000
185A424TYR00.123-0.06335.787-0.006-0.0060.0000.0000.0000.000
186A424TYR0-0.1040.10235.2000.0030.0030.0000.0000.0000.000
187A425THR00.093-0.07936.772-0.007-0.0070.0000.0000.0000.000
188A425THR0-0.0660.05741.5610.0020.0020.0000.0000.0000.000
189A426LYS00.052-0.08939.447-0.002-0.0020.0000.0000.0000.000
190A426LYS10.7791.03138.3820.0620.0620.0000.0000.0000.000
191A427PHE00.165-0.05735.0790.0000.0000.0000.0000.0000.000
192A427PHE0-0.1130.07730.975-0.001-0.0010.0000.0000.0000.000
193A428ALA00.106-0.09936.376-0.007-0.0070.0000.0000.0000.000
194A428ALA0-0.0830.10037.8800.0010.0010.0000.0000.0000.000
195A429GLN0-0.022-0.11238.070-0.003-0.0030.0000.0000.0000.000
196A429GLN0-0.0660.07341.2580.0020.0020.0000.0000.0000.000
197A430MET00.021-0.09838.1050.0040.0040.0000.0000.0000.000
198A430MET0-0.0950.09036.8540.0010.0010.0000.0000.0000.000
199A431VAL0-0.064-0.11935.476-0.003-0.0030.0000.0000.0000.000
200A431VAL00.0390.02333.664-0.002-0.0020.0000.0000.0000.000