Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 94262

Calculation Name: 5TQA-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TQA

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446880.40838
FMO2-HF: Nuclear repulsion 2358714.608508
FMO2-HF: Total energy -88165.799872
FMO2-MP2: Total energy -88419.446759


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1: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.
-3.217-0.0580000000000010.922-1.774-2.307-0.011
Interaction energy analysis for fragmet #1(H:1:GLN)
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 : -0.028
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].
3H3GLN0-0.0040.0063.8722.6103.884-0.015-0.542-0.7160.001
4H4LEU0-0.0010.0186.424-0.393-0.3930.0000.0000.0000.000
5H5VAL00.0090.00810.2090.2920.2920.0000.0000.0000.000
6H6GLN00.008-0.01712.583-0.035-0.0350.0000.0000.0000.000
7H7SER0-0.0180.01216.1830.0450.0450.0000.0000.0000.000
8H8GLY00.000-0.01019.5270.0190.0190.0000.0000.0000.000
9H9ALA0-0.008-0.00221.110-0.004-0.0040.0000.0000.0000.000
10H10GLN0-0.020-0.00523.8100.0270.0270.0000.0000.0000.000
11H11MET00.0330.03627.2340.0060.0060.0000.0000.0000.000
12H12LYS10.8340.90629.2610.1900.1900.0000.0000.0000.000
13H13ASN00.0570.03533.4370.0030.0030.0000.0000.0000.000
14H14PRO00.0430.00236.364-0.009-0.0090.0000.0000.0000.000
15H15GLY0-0.027-0.00438.0370.0040.0040.0000.0000.0000.000
16H16ALA0-0.0170.00235.265-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.004-0.00632.355-0.001-0.0010.0000.0000.0000.000
18H18VAL0-0.025-0.01326.7650.0070.0070.0000.0000.0000.000
19H19LYS10.8920.93925.1140.3050.3050.0000.0000.0000.000
20H20VAL0-0.0150.00820.5450.0160.0160.0000.0000.0000.000
21H21SER00.0340.00719.270-0.006-0.0060.0000.0000.0000.000
22H22CYS0-0.031-0.01614.890-0.021-0.0210.0000.0000.0000.000
23H23ALA00.0600.04413.0030.0070.0070.0000.0000.0000.000
24H24PRO0-0.012-0.0099.972-0.060-0.0600.0000.0000.0000.000
25H25SER0-0.035-0.0137.0950.1070.1070.0000.0000.0000.000
26H26GLY00.0590.0123.002-0.3780.0190.139-0.243-0.2930.001
27H27TYR0-0.010-0.0062.619-6.018-4.5300.798-0.989-1.298-0.013
28H28THR00.000-0.0255.4490.6010.6010.0000.0000.0000.000
29H29PHE0-0.009-0.0059.1780.2720.2720.0000.0000.0000.000
30H30THR0-0.022-0.02811.3940.1510.1510.0000.0000.0000.000
31H31ASP-1-0.809-0.86711.208-1.263-1.2630.0000.0000.0000.000
32H32PHE0-0.004-0.0049.5930.0480.0480.0000.0000.0000.000
33H33TYR0-0.067-0.03313.7270.0310.0310.0000.0000.0000.000
34H34ILE0-0.0180.00213.158-0.105-0.1050.0000.0000.0000.000
35H35HIS00.0150.00716.6400.1380.1380.0000.0000.0000.000
36H36TRP00.0250.00418.471-0.030-0.0300.0000.0000.0000.000
37H37LEU0-0.022-0.00619.0990.0440.0440.0000.0000.0000.000
38H38ARG10.8160.88122.1500.1940.1940.0000.0000.0000.000
39H39GLN00.0470.04122.0120.0020.0020.0000.0000.0000.000
40H40ALA00.0410.02825.3650.0000.0000.0000.0000.0000.000
41H41PRO00.006-0.02128.7980.0060.0060.0000.0000.0000.000
42H42GLY0-0.0010.00829.6010.0030.0030.0000.0000.0000.000
43H43GLN0-0.0200.00929.6580.0070.0070.0000.0000.0000.000
44H44GLY00.0290.01226.9980.0010.0010.0000.0000.0000.000
45H45LEU0-0.032-0.01820.587-0.007-0.0070.0000.0000.0000.000
46H46GLN00.0280.02024.8550.0090.0090.0000.0000.0000.000
47H47TRP00.002-0.00522.3320.0090.0090.0000.0000.0000.000
48H48MET0-0.049-0.02424.4590.0230.0230.0000.0000.0000.000
49H49GLY00.0390.00524.2280.0230.0230.0000.0000.0000.000
50H50TRP0-0.0170.01421.221-0.036-0.0360.0000.0000.0000.000
51H51MET00.010-0.00618.2910.0640.0640.0000.0000.0000.000
52H52ASN00.0690.05619.068-0.080-0.0800.0000.0000.0000.000
53H53PRO00.0300.01815.1160.0890.0890.0000.0000.0000.000
54H54GLN00.0450.03217.5640.0040.0040.0000.0000.0000.000
55H55THR0-0.051-0.04318.8210.0660.0660.0000.0000.0000.000
56H56GLY0-0.009-0.01121.8910.0360.0360.0000.0000.0000.000
57H57ARG10.8300.92123.2450.4380.4380.0000.0000.0000.000
58H58THR0-0.008-0.02123.455-0.036-0.0360.0000.0000.0000.000
59H59ASN00.0130.01525.3610.0440.0440.0000.0000.0000.000
60H60THR00.0300.00526.125-0.027-0.0270.0000.0000.0000.000
61H61ALA0-0.0010.01228.5340.0160.0160.0000.0000.0000.000
62H62ARG11.0070.99130.2960.1640.1640.0000.0000.0000.000
63H63ASN0-0.034-0.02332.7070.0020.0020.0000.0000.0000.000
64H64PHE00.0030.00229.0170.0060.0060.0000.0000.0000.000
65H65GLN0-0.0100.00632.5680.0020.0020.0000.0000.0000.000
66H66GLY00.0760.04633.610-0.002-0.0020.0000.0000.0000.000
67H67ARG10.7520.85133.2490.1820.1820.0000.0000.0000.000
68H68VAL00.0730.03527.094-0.004-0.0040.0000.0000.0000.000
69H69THR0-0.068-0.03027.9080.0160.0160.0000.0000.0000.000
70H70MET0-0.0140.01422.702-0.015-0.0150.0000.0000.0000.000
71H71THR0-0.011-0.00622.8640.0170.0170.0000.0000.0000.000
72H72ARG10.8620.91018.3450.5290.5290.0000.0000.0000.000
73H73ASP-1-0.817-0.87419.190-0.482-0.4820.0000.0000.0000.000
74H74THR0-0.003-0.02016.897-0.069-0.0690.0000.0000.0000.000
75H75SER0-0.062-0.04116.408-0.066-0.0660.0000.0000.0000.000
76H76ILE00.0010.00015.831-0.007-0.0070.0000.0000.0000.000
77H77GLY0-0.0050.01413.061-0.081-0.0810.0000.0000.0000.000
78H78THR0-0.024-0.01513.444-0.119-0.1190.0000.0000.0000.000
79H79ALA0-0.006-0.00616.1530.0920.0920.0000.0000.0000.000
80H80TYR0-0.016-0.02917.9390.0180.0180.0000.0000.0000.000
81H81MET0-0.0130.00921.3220.0150.0150.0000.0000.0000.000
82H82GLU-1-0.854-0.91123.832-0.253-0.2530.0000.0000.0000.000
83H83LEU00.0240.00827.5270.0000.0000.0000.0000.0000.000
84H84ARG10.8360.88029.9140.2470.2470.0000.0000.0000.000
85H85SER00.0100.00133.6750.0000.0000.0000.0000.0000.000
86H86LEU0-0.033-0.00130.8720.0030.0030.0000.0000.0000.000
87H87THR00.024-0.00234.6200.0130.0130.0000.0000.0000.000
88H88SER00.057-0.00134.606-0.005-0.0050.0000.0000.0000.000
89H89ASP-1-0.877-0.91334.138-0.127-0.1270.0000.0000.0000.000
90H90ASP-1-0.777-0.84030.983-0.192-0.1920.0000.0000.0000.000
91H91THR00.0050.02029.700-0.014-0.0140.0000.0000.0000.000
92H92ALA00.003-0.00626.5630.0090.0090.0000.0000.0000.000
93H93ILE00.0030.01520.792-0.008-0.0080.0000.0000.0000.000
94H94TYR0-0.018-0.03522.163-0.004-0.0040.0000.0000.0000.000
95H95TYR00.001-0.01916.902-0.006-0.0060.0000.0000.0000.000
96H97THR00.0230.00514.046-0.019-0.0190.0000.0000.0000.000
97H98THR00.0370.02310.269-0.063-0.0630.0000.0000.0000.000
98H99GLY00.0100.00013.6300.1540.1540.0000.0000.0000.000
99H100GLY00.0350.01014.504-0.110-0.1100.0000.0000.0000.000
100H101TRP00.0260.01312.9450.0270.0270.0000.0000.0000.000
101H102ILE0-0.061-0.01515.3200.1540.1540.0000.0000.0000.000
102H103SER00.0020.00217.606-0.013-0.0130.0000.0000.0000.000
103H104LEU0-0.021-0.01420.3900.0150.0150.0000.0000.0000.000
104H105TYR0-0.019-0.00521.0090.0430.0430.0000.0000.0000.000
105H106TYR00.0190.01119.842-0.020-0.0200.0000.0000.0000.000
106H107ASP-1-0.713-0.80323.459-0.452-0.4520.0000.0000.0000.000
107H108SER00.025-0.01218.9140.0350.0350.0000.0000.0000.000
108H109SER0-0.063-0.05220.766-0.016-0.0160.0000.0000.0000.000
109H110TYR0-0.051-0.04822.035-0.008-0.0080.0000.0000.0000.000
110H111TYR00.0050.01319.4130.0320.0320.0000.0000.0000.000
111H112PRO0-0.026-0.00519.451-0.050-0.0500.0000.0000.0000.000
112H113ASN0-0.007-0.01215.1510.0630.0630.0000.0000.0000.000
113H114PHE0-0.015-0.01214.647-0.086-0.0860.0000.0000.0000.000
114H115ASP-1-0.896-0.9479.575-0.582-0.5820.0000.0000.0000.000
115H116HIS00.0130.0075.3990.2030.2030.0000.0000.0000.000
116H117TRP0-0.003-0.02510.139-0.054-0.0540.0000.0000.0000.000
117H118GLY00.0150.01310.890-0.056-0.0560.0000.0000.0000.000
118H119GLN0-0.031-0.01713.0010.0280.0280.0000.0000.0000.000
119H120GLY00.0140.02214.3170.0680.0680.0000.0000.0000.000
120H121THR0-0.082-0.05317.824-0.019-0.0190.0000.0000.0000.000
121H122LEU0-0.0120.00520.9070.0060.0060.0000.0000.0000.000
122H123LEU0-0.025-0.00624.084-0.004-0.0040.0000.0000.0000.000
123H124THR00.0170.00027.2530.0130.0130.0000.0000.0000.000
124H125VAL0-0.018-0.01130.821-0.004-0.0040.0000.0000.0000.000
125H126SER00.008-0.00733.9020.0090.0090.0000.0000.0000.000
126H127GLY00.0330.00937.206-0.004-0.0040.0000.0000.0000.000
127H128ALA0-0.0260.00438.4500.0040.0040.0000.0000.0000.000
128H129SER0-0.004-0.01338.201-0.004-0.0040.0000.0000.0000.000
129H130THR0-0.036-0.02833.0710.0050.0050.0000.0000.0000.000
130H131LYS10.9410.95935.0270.0710.0710.0000.0000.0000.000
131H132GLY00.0580.03833.610-0.003-0.0030.0000.0000.0000.000
132H133PRO0-0.035-0.00731.2100.0040.0040.0000.0000.0000.000
133H134SER00.0130.02134.5300.0030.0030.0000.0000.0000.000
134H135VAL0-0.003-0.01032.3450.0010.0010.0000.0000.0000.000
135H136PHE0-0.007-0.00835.4100.0020.0020.0000.0000.0000.000
136H137PRO00.0370.02735.5190.0000.0000.0000.0000.0000.000
137H138LEU0-0.049-0.01934.609-0.001-0.0010.0000.0000.0000.000
138H139ALA00.0250.00136.3750.0040.0040.0000.0000.0000.000
139H140PRO00.002-0.00236.4780.0000.0000.0000.0000.0000.000
140H141SER0-0.0150.00237.872-0.002-0.0020.0000.0000.0000.000
141H142SER00.0450.01138.3520.0010.0010.0000.0000.0000.000
142H143LYS10.9060.95640.129-0.021-0.0210.0000.0000.0000.000
143H144SER00.0040.00838.285-0.003-0.0030.0000.0000.0000.000
144H145THR0-0.003-0.01135.105-0.002-0.0020.0000.0000.0000.000
145H146SER00.0340.01633.852-0.001-0.0010.0000.0000.0000.000
146H147GLY00.0130.02136.1630.0050.0050.0000.0000.0000.000
147H148GLY00.0130.01437.809-0.003-0.0030.0000.0000.0000.000
148H149THR0-0.049-0.03832.7970.0030.0030.0000.0000.0000.000
149H150ALA00.0040.01735.067-0.005-0.0050.0000.0000.0000.000
150H151ALA00.0160.01533.6520.0040.0040.0000.0000.0000.000
151H152LEU0-0.0020.01531.203-0.004-0.0040.0000.0000.0000.000
152H153GLY00.049-0.00331.7380.0020.0020.0000.0000.0000.000
153H154CYS0-0.077-0.00627.5360.0020.0020.0000.0000.0000.000
154H155LEU00.0150.03532.352-0.002-0.0020.0000.0000.0000.000
155H156VAL0-0.003-0.01430.197-0.002-0.0020.0000.0000.0000.000
156H157LYS10.8330.87633.5730.0320.0320.0000.0000.0000.000
157H158ASP-1-0.808-0.88736.520-0.043-0.0430.0000.0000.0000.000
158H159TYR0-0.009-0.01929.8790.0010.0010.0000.0000.0000.000
159H160PHE00.0270.00733.8600.0000.0000.0000.0000.0000.000
160H161PRO00.0080.01330.3340.0000.0000.0000.0000.0000.000
161H162GLU-1-0.752-0.86527.260-0.077-0.0770.0000.0000.0000.000
162H163PRO0-0.042-0.02323.836-0.012-0.0120.0000.0000.0000.000
163H164VAL0-0.032-0.01726.546-0.007-0.0070.0000.0000.0000.000
164H165THR0-0.057-0.02821.100-0.005-0.0050.0000.0000.0000.000
165H166VAL00.020-0.00923.3150.0000.0000.0000.0000.0000.000
166H167SER0-0.0160.01321.1040.0010.0010.0000.0000.0000.000
167H168TRP00.0260.00122.906-0.004-0.0040.0000.0000.0000.000
168H169ASN0-0.004-0.01723.4220.0010.0010.0000.0000.0000.000
169H170SER0-0.019-0.01823.2640.0110.0110.0000.0000.0000.000
170H171GLY00.0060.00919.426-0.008-0.0080.0000.0000.0000.000
171H172ALA0-0.034-0.00919.5210.0210.0210.0000.0000.0000.000
172H173LEU0-0.049-0.01521.6780.0140.0140.0000.0000.0000.000
173H174THR00.021-0.00118.117-0.013-0.0130.0000.0000.0000.000
174H175SER00.0300.00821.327-0.006-0.0060.0000.0000.0000.000
175H176GLY00.0460.01923.041-0.009-0.0090.0000.0000.0000.000
176H177VAL0-0.047-0.00623.275-0.012-0.0120.0000.0000.0000.000
177H178HIS00.0150.01424.3810.0070.0070.0000.0000.0000.000
178H179THR00.003-0.00524.632-0.003-0.0030.0000.0000.0000.000
179H180PHE0-0.0150.00726.429-0.001-0.0010.0000.0000.0000.000
180H181PRO00.025-0.00427.773-0.007-0.0070.0000.0000.0000.000
181H182ALA0-0.0120.00529.2630.0050.0050.0000.0000.0000.000
182H183VAL0-0.007-0.00131.749-0.001-0.0010.0000.0000.0000.000
183H184LEU0-0.015-0.01035.094-0.002-0.0020.0000.0000.0000.000
184H185GLN0-0.044-0.03136.5010.0080.0080.0000.0000.0000.000
185H186SER00.0310.00840.008-0.004-0.0040.0000.0000.0000.000
186H187SER0-0.0020.00041.375-0.001-0.0010.0000.0000.0000.000
187H188GLY00.0130.01240.205-0.002-0.0020.0000.0000.0000.000
188H189LEU0-0.067-0.02337.284-0.006-0.0060.0000.0000.0000.000
189H190TYR00.0400.02532.1960.0020.0020.0000.0000.0000.000
190H191SER0-0.010-0.01634.3690.0030.0030.0000.0000.0000.000
191H192LEU00.0180.03227.9340.0010.0010.0000.0000.0000.000
192H193SER0-0.004-0.02131.3090.0030.0030.0000.0000.0000.000
193H194SER0-0.0260.00126.5850.0020.0020.0000.0000.0000.000
194H195VAL00.008-0.00928.792-0.001-0.0010.0000.0000.0000.000
195H196VAL00.0290.00927.0110.0040.0040.0000.0000.0000.000
196H197THR0-0.030-0.00329.190-0.004-0.0040.0000.0000.0000.000
197H198VAL00.0100.00329.5770.0090.0090.0000.0000.0000.000
198H199PRO00.0560.02130.960-0.005-0.0050.0000.0000.0000.000
199H200SER00.036-0.00833.957-0.003-0.0030.0000.0000.0000.000
200H201SER0-0.023-0.01037.094-0.003-0.0030.0000.0000.0000.000
201H202SER00.0030.00533.9600.0030.0030.0000.0000.0000.000
202H203LEU0-0.0110.00135.512-0.002-0.0020.0000.0000.0000.000
203H204GLY0-0.0200.00037.3590.0000.0000.0000.0000.0000.000
204H205THR0-0.007-0.00436.695-0.001-0.0010.0000.0000.0000.000
205H206GLN0-0.0090.00929.5070.0060.0060.0000.0000.0000.000
206H207THR0-0.016-0.00331.200-0.010-0.0100.0000.0000.0000.000
207H208TYR00.0390.00729.7030.0090.0090.0000.0000.0000.000
208H209ILE00.0220.00528.979-0.006-0.0060.0000.0000.0000.000
209H211ASN00.024-0.01124.5370.0040.0040.0000.0000.0000.000
210H212VAL00.0110.00825.372-0.008-0.0080.0000.0000.0000.000
211H213ASN0-0.007-0.00623.530-0.021-0.0210.0000.0000.0000.000
212H214HIS00.0540.03525.584-0.004-0.0040.0000.0000.0000.000
213H215LYS10.9610.96520.6190.1840.1840.0000.0000.0000.000
214H216PRO00.0390.02726.491-0.004-0.0040.0000.0000.0000.000
215H217SER0-0.0070.00129.3390.0060.0060.0000.0000.0000.000
216H218ASN0-0.050-0.02728.180-0.002-0.0020.0000.0000.0000.000
217H219THR00.0170.01129.5140.0050.0050.0000.0000.0000.000
218H220LYS10.8840.93325.7090.1060.1060.0000.0000.0000.000
219H221VAL0-0.006-0.00729.3670.0040.0040.0000.0000.0000.000
220H222ASP-1-0.846-0.89827.710-0.025-0.0250.0000.0000.0000.000
221H223LYS10.8750.93630.4160.0190.0190.0000.0000.0000.000
222H224ARG10.8470.89032.184-0.030-0.0300.0000.0000.0000.000
223H225VAL0-0.030-0.01932.915-0.005-0.0050.0000.0000.0000.000
224H226GLU-1-0.832-0.88535.0950.0340.0340.0000.0000.0000.000
225H227PRO0-0.001-0.01537.849-0.003-0.0030.0000.0000.0000.000
226H228LYS10.9620.99740.956-0.015-0.0150.0000.0000.0000.000
227H229SER00.0170.00543.9640.0020.0020.0000.0000.0000.000
228H230CYS00.0100.00947.555-0.002-0.0020.0000.0000.0000.000