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: 3945L

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 OptH
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 -2446329.719414
FMO2-HF: Nuclear repulsion 2358165.412761
FMO2-HF: Total energy -88164.306653
FMO2-MP2: Total energy -88418.018394


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.
-2.850.0579999999999990.068-1.438-1.538-0.003
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 : -0.031 / q_NPA : -0.023
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].
3H3GLN0-0.035-0.0113.8110.9282.412-0.024-0.659-0.8020.003
4H4LEU0-0.003-0.0096.2110.1930.1930.0000.0000.0000.000
5H5VAL00.0170.0179.9520.2380.2380.0000.0000.0000.000
6H6GLN0-0.001-0.04012.3440.0310.0310.0000.0000.0000.000
7H7SER00.0110.01115.9140.0460.0460.0000.0000.0000.000
8H8GLY0-0.036-0.01819.161-0.004-0.0040.0000.0000.0000.000
9H9ALA00.002-0.00121.0620.0030.0030.0000.0000.0000.000
10H10GLN0-0.011-0.01023.7390.0520.0520.0000.0000.0000.000
11H11MET00.0510.03826.973-0.003-0.0030.0000.0000.0000.000
12H12LYS10.8570.93229.1320.3160.3160.0000.0000.0000.000
13H13ASN00.0760.04232.8660.0000.0000.0000.0000.0000.000
14H14PRO0-0.009-0.02335.986-0.010-0.0100.0000.0000.0000.000
15H15GLY0-0.0050.00736.9550.0100.0100.0000.0000.0000.000
16H16ALA0-0.046-0.00534.5190.0000.0000.0000.0000.0000.000
17H17SER0-0.010-0.01432.171-0.006-0.0060.0000.0000.0000.000
18H18VAL00.004-0.00326.2730.0040.0040.0000.0000.0000.000
19H19LYS10.9780.99024.4550.3950.3950.0000.0000.0000.000
20H20VAL0-0.034-0.00119.8020.0040.0040.0000.0000.0000.000
21H21SER00.0130.00218.9150.0000.0000.0000.0000.0000.000
22H22CYS0-0.070-0.04014.182-0.032-0.0320.0000.0000.0000.000
23H23ALA00.0370.03513.3660.0300.0300.0000.0000.0000.000
24H24PRO0-0.016-0.01010.021-0.139-0.1390.0000.0000.0000.000
25H25SER0-0.0130.0127.1180.1180.1180.0000.0000.0000.000
26H26GLY00.0670.0153.435-0.933-0.6720.018-0.153-0.1250.000
27H27TYR0-0.017-0.0143.082-3.582-2.4190.074-0.626-0.611-0.006
28H28THR00.0260.0245.8860.3740.3740.0000.0000.0000.000
29H29PHE00.0170.0059.5430.2100.2100.0000.0000.0000.000
30H30THR0-0.017-0.02711.9490.0710.0710.0000.0000.0000.000
31H31ASP-1-0.836-0.90511.403-0.865-0.8650.0000.0000.0000.000
32H32PHE0-0.024-0.0088.7560.1350.1350.0000.0000.0000.000
33H33TYR0-0.028-0.00613.9440.0160.0160.0000.0000.0000.000
34H34ILE00.0100.01713.937-0.114-0.1140.0000.0000.0000.000
35H35HIS00.0260.03316.4870.1520.1520.0000.0000.0000.000
36H36TRP00.0330.01117.744-0.070-0.0700.0000.0000.0000.000
37H37LEU0-0.0210.00018.0470.0720.0720.0000.0000.0000.000
38H38ARG10.8590.90621.3660.3300.3300.0000.0000.0000.000
39H39GLN00.0290.01121.6700.0040.0040.0000.0000.0000.000
40H40ALA00.0470.02824.4160.0000.0000.0000.0000.0000.000
41H41PRO00.023-0.00328.0320.0020.0020.0000.0000.0000.000
42H42GLY0-0.0090.01328.9440.0150.0150.0000.0000.0000.000
43H43GLN00.0040.00728.7940.0120.0120.0000.0000.0000.000
44H44GLY00.0220.00325.501-0.009-0.0090.0000.0000.0000.000
45H45LEU0-0.051-0.02619.304-0.004-0.0040.0000.0000.0000.000
46H46GLN00.0110.01223.6730.0300.0300.0000.0000.0000.000
47H47TRP0-0.016-0.02321.1870.0030.0030.0000.0000.0000.000
48H48MET0-0.077-0.03923.2490.0290.0290.0000.0000.0000.000
49H49GLY00.026-0.00823.0840.0420.0420.0000.0000.0000.000
50H50TRP00.0150.02721.100-0.053-0.0530.0000.0000.0000.000
51H51MET00.0240.00118.3050.0710.0710.0000.0000.0000.000
52H52ASN00.0450.04119.421-0.079-0.0790.0000.0000.0000.000
53H53PRO00.0520.04015.5360.0950.0950.0000.0000.0000.000
54H54GLN00.0790.05318.3010.0060.0060.0000.0000.0000.000
55H55THR0-0.086-0.06419.5550.0540.0540.0000.0000.0000.000
56H56GLY0-0.022-0.01922.1430.0330.0330.0000.0000.0000.000
57H57ARG10.9000.96923.1720.4180.4180.0000.0000.0000.000
58H58THR0-0.004-0.01323.967-0.038-0.0380.0000.0000.0000.000
59H59ASN00.0210.00925.5320.0520.0520.0000.0000.0000.000
60H60THR00.0220.01325.962-0.038-0.0380.0000.0000.0000.000
61H61ALA00.0060.02027.7860.0190.0190.0000.0000.0000.000
62H62ARG11.0030.98729.3780.2300.2300.0000.0000.0000.000
63H63ASN0-0.010-0.01332.1500.0150.0150.0000.0000.0000.000
64H64PHE0-0.012-0.01428.3190.0050.0050.0000.0000.0000.000
65H65GLN00.0090.01031.628-0.004-0.0040.0000.0000.0000.000
66H66GLY00.0500.02933.0540.0000.0000.0000.0000.0000.000
67H67ARG10.7660.86532.1600.2810.2810.0000.0000.0000.000
68H68VAL00.0640.02926.502-0.008-0.0080.0000.0000.0000.000
69H69THR0-0.0110.01428.0880.0210.0210.0000.0000.0000.000
70H70MET0-0.0300.00823.036-0.031-0.0310.0000.0000.0000.000
71H71THR0-0.027-0.01123.4530.0220.0220.0000.0000.0000.000
72H72ARG10.9090.91318.9660.4720.4720.0000.0000.0000.000
73H73ASP-1-0.797-0.82319.522-0.461-0.4610.0000.0000.0000.000
74H74THR0-0.013-0.02617.580-0.071-0.0710.0000.0000.0000.000
75H75SER0-0.092-0.08317.133-0.041-0.0410.0000.0000.0000.000
76H76ILE00.0020.00016.603-0.002-0.0020.0000.0000.0000.000
77H77GLY0-0.0190.00913.963-0.120-0.1200.0000.0000.0000.000
78H78THR0-0.051-0.03514.152-0.144-0.1440.0000.0000.0000.000
79H79ALA00.0030.00716.7130.1090.1090.0000.0000.0000.000
80H80TYR0-0.013-0.02818.549-0.009-0.0090.0000.0000.0000.000
81H81MET0-0.0120.01921.7860.0360.0360.0000.0000.0000.000
82H82GLU-1-0.917-0.96723.800-0.325-0.3250.0000.0000.0000.000
83H83LEU00.0110.00427.3710.0080.0080.0000.0000.0000.000
84H84ARG10.8480.88929.5070.3080.3080.0000.0000.0000.000
85H85SER00.000-0.00633.213-0.002-0.0020.0000.0000.0000.000
86H86LEU0-0.0310.00530.5100.0000.0000.0000.0000.0000.000
87H87THR00.0710.03034.3420.0170.0170.0000.0000.0000.000
88H88SER00.0480.00534.137-0.010-0.0100.0000.0000.0000.000
89H89ASP-1-0.883-0.93233.884-0.232-0.2320.0000.0000.0000.000
90H90ASP-1-0.802-0.86430.428-0.313-0.3130.0000.0000.0000.000
91H91THR00.0040.04629.136-0.026-0.0260.0000.0000.0000.000
92H92ALA00.0170.00225.9840.0080.0080.0000.0000.0000.000
93H93ILE0-0.0010.01220.505-0.007-0.0070.0000.0000.0000.000
94H94TYR0-0.055-0.07021.608-0.001-0.0010.0000.0000.0000.000
95H95TYR00.0140.02016.003-0.037-0.0370.0000.0000.0000.000
96H97THR00.0290.01413.059-0.104-0.1040.0000.0000.0000.000
97H98THR00.0450.0189.512-0.036-0.0360.0000.0000.0000.000
98H99GLY0-0.027-0.01912.7470.0990.0990.0000.0000.0000.000
99H100GLY00.0510.03314.017-0.061-0.0610.0000.0000.0000.000
100H101TRP00.0500.01712.991-0.065-0.0650.0000.0000.0000.000
101H102ILE0-0.084-0.04815.6210.1060.1060.0000.0000.0000.000
102H103SER0-0.005-0.00717.8310.0210.0210.0000.0000.0000.000
103H104LEU0-0.034-0.01920.5140.0020.0020.0000.0000.0000.000
104H105TYR0-0.0120.00321.6050.0130.0130.0000.0000.0000.000
105H106TYR00.000-0.01420.106-0.025-0.0250.0000.0000.0000.000
106H107ASP-1-0.802-0.89323.759-0.409-0.4090.0000.0000.0000.000
107H108SER0-0.006-0.01319.2910.0010.0010.0000.0000.0000.000
108H109SER0-0.071-0.03920.388-0.047-0.0470.0000.0000.0000.000
109H110TYR0-0.034-0.02521.589-0.034-0.0340.0000.0000.0000.000
110H111TYR00.0060.00219.3630.0350.0350.0000.0000.0000.000
111H112PRO0-0.0450.00419.003-0.063-0.0630.0000.0000.0000.000
112H113ASN0-0.014-0.02515.2350.0360.0360.0000.0000.0000.000
113H114PHE0-0.004-0.02213.692-0.047-0.0470.0000.0000.0000.000
114H115ASP-1-0.898-0.9368.542-1.026-1.0260.0000.0000.0000.000
115H116HIS0-0.007-0.0024.979-0.405-0.4050.0000.0000.0000.000
116H117TRP00.004-0.0199.0220.2870.2870.0000.0000.0000.000
117H118GLY00.0260.01310.620-0.199-0.1990.0000.0000.0000.000
118H119GLN0-0.0010.00112.945-0.045-0.0450.0000.0000.0000.000
119H120GLY00.0040.02014.0810.1050.1050.0000.0000.0000.000
120H121THR0-0.054-0.03717.607-0.009-0.0090.0000.0000.0000.000
121H122LEU0-0.022-0.00520.5940.0180.0180.0000.0000.0000.000
122H123LEU0-0.028-0.00223.9060.0130.0130.0000.0000.0000.000
123H124THR00.016-0.00226.9910.0130.0130.0000.0000.0000.000
124H125VAL0-0.017-0.01230.4460.0040.0040.0000.0000.0000.000
125H126SER00.001-0.01233.3250.0130.0130.0000.0000.0000.000
126H127GLY00.0500.02636.533-0.002-0.0020.0000.0000.0000.000
127H128ALA0-0.0260.00137.8570.0080.0080.0000.0000.0000.000
128H129SER0-0.003-0.01138.160-0.003-0.0030.0000.0000.0000.000
129H130THR0-0.052-0.01333.2780.0000.0000.0000.0000.0000.000
130H131LYS10.9690.97635.1850.1560.1560.0000.0000.0000.000
131H132GLY00.0520.03233.645-0.012-0.0120.0000.0000.0000.000
132H133PRO0-0.024-0.00631.2210.0080.0080.0000.0000.0000.000
133H134SER0-0.0040.00834.4560.0080.0080.0000.0000.0000.000
134H135VAL0-0.008-0.00932.154-0.003-0.0030.0000.0000.0000.000
135H136PHE0-0.022-0.02235.1770.0090.0090.0000.0000.0000.000
136H137PRO00.0060.00935.400-0.006-0.0060.0000.0000.0000.000
137H138LEU0-0.038-0.01534.3780.0050.0050.0000.0000.0000.000
138H139ALA00.0350.00436.2860.0010.0010.0000.0000.0000.000
139H140PRO00.010-0.00736.384-0.002-0.0020.0000.0000.0000.000
140H141SER0-0.030-0.00937.7130.0060.0060.0000.0000.0000.000
141H142SER00.0560.01338.260-0.004-0.0040.0000.0000.0000.000
142H143LYS10.9100.96140.0180.0490.0490.0000.0000.0000.000
143H144SER00.0170.00837.8970.0020.0020.0000.0000.0000.000
144H145THR0-0.028-0.01535.246-0.006-0.0060.0000.0000.0000.000
145H146SER00.0300.01034.0650.0020.0020.0000.0000.0000.000
146H147GLY00.0310.05535.8610.0040.0040.0000.0000.0000.000
147H148GLY00.0570.02938.045-0.004-0.0040.0000.0000.0000.000
148H149THR0-0.075-0.07833.3730.0010.0010.0000.0000.0000.000
149H150ALA0-0.0050.01635.055-0.002-0.0020.0000.0000.0000.000
150H151ALA00.0200.00933.678-0.003-0.0030.0000.0000.0000.000
151H152LEU00.0050.02731.4790.0030.0030.0000.0000.0000.000
152H153GLY00.035-0.00331.571-0.007-0.0070.0000.0000.0000.000
153H154CYS0-0.105-0.02427.4910.0000.0000.0000.0000.0000.000
154H155LEU00.0250.03232.461-0.007-0.0070.0000.0000.0000.000
155H156VAL0-0.008-0.01029.8570.0040.0040.0000.0000.0000.000
156H157LYS10.8620.91733.1950.1170.1170.0000.0000.0000.000
157H158ASP-1-0.803-0.89936.279-0.132-0.1320.0000.0000.0000.000
158H159TYR0-0.021-0.01429.5150.0060.0060.0000.0000.0000.000
159H160PHE00.0080.01433.264-0.003-0.0030.0000.0000.0000.000
160H161PRO00.010-0.00230.0400.0070.0070.0000.0000.0000.000
161H162GLU-1-0.785-0.87526.815-0.259-0.2590.0000.0000.0000.000
162H163PRO0-0.009-0.02623.510-0.010-0.0100.0000.0000.0000.000
163H164VAL0-0.010-0.01025.9770.0020.0020.0000.0000.0000.000
164H165THR0-0.028-0.01220.521-0.020-0.0200.0000.0000.0000.000
165H166VAL0-0.004-0.01323.2850.0180.0180.0000.0000.0000.000
166H167SER0-0.0090.00621.113-0.022-0.0220.0000.0000.0000.000
167H168TRP00.0250.00322.7530.0220.0220.0000.0000.0000.000
168H169ASN0-0.016-0.01023.4880.0000.0000.0000.0000.0000.000
169H170SER00.000-0.01222.5670.0100.0100.0000.0000.0000.000
170H171GLY0-0.020-0.00819.248-0.010-0.0100.0000.0000.0000.000
171H172ALA0-0.0180.00219.2820.0050.0050.0000.0000.0000.000
172H173LEU0-0.051-0.01921.3840.0220.0220.0000.0000.0000.000
173H174THR00.023-0.00217.723-0.014-0.0140.0000.0000.0000.000
174H175SER0-0.022-0.01121.001-0.018-0.0180.0000.0000.0000.000
175H176GLY00.0780.03723.1100.0060.0060.0000.0000.0000.000
176H177VAL0-0.036-0.01523.0140.0020.0020.0000.0000.0000.000
177H178HIS00.0200.01524.143-0.022-0.0220.0000.0000.0000.000
178H179THR00.022-0.00224.0500.0210.0210.0000.0000.0000.000
179H180PHE0-0.035-0.01026.031-0.013-0.0130.0000.0000.0000.000
180H181PRO00.012-0.00627.421-0.008-0.0080.0000.0000.0000.000
181H182ALA00.0030.01028.9500.0160.0160.0000.0000.0000.000
182H183VAL0-0.017-0.00231.323-0.001-0.0010.0000.0000.0000.000
183H184LEU0-0.012-0.01234.887-0.003-0.0030.0000.0000.0000.000
184H185GLN0-0.056-0.02736.4090.0150.0150.0000.0000.0000.000
185H186SER00.0370.01439.789-0.005-0.0050.0000.0000.0000.000
186H187SER00.000-0.00641.2160.0000.0000.0000.0000.0000.000
187H188GLY00.0120.01439.6720.0000.0000.0000.0000.0000.000
188H189LEU0-0.060-0.02136.860-0.010-0.0100.0000.0000.0000.000
189H190TYR00.0210.00932.5620.0040.0040.0000.0000.0000.000
190H191SER00.003-0.02034.1510.0090.0090.0000.0000.0000.000
191H192LEU00.0080.03127.611-0.001-0.0010.0000.0000.0000.000
192H193SER00.020-0.00231.1450.0150.0150.0000.0000.0000.000
193H194SER0-0.048-0.01426.371-0.008-0.0080.0000.0000.0000.000
194H195VAL00.0130.00428.8490.0120.0120.0000.0000.0000.000
195H196VAL00.0330.01427.138-0.008-0.0080.0000.0000.0000.000
196H197THR0-0.023-0.01329.0380.0080.0080.0000.0000.0000.000
197H198VAL0-0.019-0.00229.5520.0030.0030.0000.0000.0000.000
198H199PRO00.0460.02030.909-0.001-0.0010.0000.0000.0000.000
199H200SER00.002-0.01833.890-0.004-0.0040.0000.0000.0000.000
200H201SER0-0.009-0.00936.977-0.003-0.0030.0000.0000.0000.000
201H202SER00.0470.03633.8000.0020.0020.0000.0000.0000.000
202H203LEU00.0250.02035.361-0.003-0.0030.0000.0000.0000.000
203H204GLY0-0.0250.00037.2620.0040.0040.0000.0000.0000.000
204H205THR0-0.059-0.03335.9010.0030.0030.0000.0000.0000.000
205H206GLN00.0000.00529.4010.0060.0060.0000.0000.0000.000
206H207THR0-0.043-0.02331.179-0.006-0.0060.0000.0000.0000.000
207H208TYR00.0340.01029.3310.0000.0000.0000.0000.0000.000
208H209ILE00.0340.01628.940-0.001-0.0010.0000.0000.0000.000
209H211ASN00.016-0.02624.3860.0050.0050.0000.0000.0000.000
210H212VAL00.0130.01025.215-0.022-0.0220.0000.0000.0000.000
211H213ASN0-0.045-0.03422.6250.0090.0090.0000.0000.0000.000
212H214HIS00.0740.09525.559-0.010-0.0100.0000.0000.0000.000
213H215LYS10.9760.97120.4250.4120.4120.0000.0000.0000.000
214H216PRO0-0.0060.01026.0810.0040.0040.0000.0000.0000.000
215H217SER0-0.016-0.07528.7700.0100.0100.0000.0000.0000.000
216H218ASN0-0.093-0.03828.6380.0030.0030.0000.0000.0000.000
217H219THR00.0310.02629.4420.0200.0200.0000.0000.0000.000
218H220LYS10.9220.95123.7480.2460.2460.0000.0000.0000.000
219H221VAL00.0050.00428.8760.0140.0140.0000.0000.0000.000
220H222ASP-1-0.829-0.87927.877-0.156-0.1560.0000.0000.0000.000
221H223LYS10.9220.96030.4900.1080.1080.0000.0000.0000.000
222H224ARG10.9470.97532.1030.0370.0370.0000.0000.0000.000
223H225VAL0-0.032-0.02132.7950.0000.0000.0000.0000.0000.000
224H226GLU-1-0.906-0.95335.161-0.038-0.0380.0000.0000.0000.000
225H227PRO0-0.012-0.01737.947-0.004-0.0040.0000.0000.0000.000
226H228LYS10.9901.01940.6180.0420.0420.0000.0000.0000.000
227H229SER0-0.002-0.02243.8950.0040.0040.0000.0000.0000.000
228H230CYS0-0.0020.01047.533-0.002-0.0020.0000.0000.0000.000