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: LZ629

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2446223.120992
FMO2-HF: Nuclear repulsion 2358057.839468
FMO2-HF: Total energy -88165.281524
FMO2-MP2: Total energy -88418.901664


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.
-3.5550.0499999999999990.451-1.86-2.197-0.009
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 : -0.046 / q_NPA : -0.029
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].
3H3GLN0-0.025-0.0053.8112.2493.595-0.023-0.543-0.7810.002
4H4LEU0-0.0050.0006.223-0.309-0.3090.0000.0000.0000.000
5H5VAL00.0010.0049.9620.2960.2960.0000.0000.0000.000
6H6GLN00.016-0.02312.359-0.019-0.0190.0000.0000.0000.000
7H7SER0-0.0030.01315.9260.0380.0380.0000.0000.0000.000
8H8GLY0-0.031-0.02519.1760.0220.0220.0000.0000.0000.000
9H9ALA0-0.0010.00021.075-0.006-0.0060.0000.0000.0000.000
10H10GLN0-0.0020.00223.7480.0200.0200.0000.0000.0000.000
11H11MET00.0250.03026.9830.0050.0050.0000.0000.0000.000
12H12LYS10.8600.92528.9120.1830.1830.0000.0000.0000.000
13H13ASN00.0490.02932.8760.0030.0030.0000.0000.0000.000
14H14PRO00.018-0.01235.994-0.009-0.0090.0000.0000.0000.000
15H15GLY0-0.0070.00636.9510.0050.0050.0000.0000.0000.000
16H16ALA0-0.044-0.00334.592-0.004-0.0040.0000.0000.0000.000
17H17SER00.003-0.01031.946-0.002-0.0020.0000.0000.0000.000
18H18VAL0-0.029-0.01526.3520.0050.0050.0000.0000.0000.000
19H19LYS10.9070.94524.6930.3030.3030.0000.0000.0000.000
20H20VAL0-0.0320.00419.8600.0070.0070.0000.0000.0000.000
21H21SER00.0290.00719.040-0.007-0.0070.0000.0000.0000.000
22H22CYS0-0.048-0.03514.587-0.013-0.0130.0000.0000.0000.000
23H23ALA00.0560.04013.240-0.020-0.0200.0000.0000.0000.000
24H24PRO00.0040.0049.789-0.006-0.0060.0000.0000.0000.000
25H25SER0-0.0240.0006.9870.0280.0280.0000.0000.0000.000
26H26GLY00.0580.0142.916-0.528-0.0730.148-0.297-0.3060.002
27H27TYR0-0.006-0.0122.719-5.872-4.0680.326-1.020-1.110-0.013
28H28THR00.015-0.0015.5010.5880.5880.0000.0000.0000.000
29H29PHE0-0.003-0.0029.1270.3140.3140.0000.0000.0000.000
30H30THR0-0.024-0.01911.5330.1340.1340.0000.0000.0000.000
31H31ASP-1-0.826-0.88911.074-1.461-1.4610.0000.0000.0000.000
32H32PHE0-0.011-0.0109.3190.1130.1130.0000.0000.0000.000
33H33TYR0-0.039-0.00913.7530.0260.0260.0000.0000.0000.000
34H34ILE0-0.0020.01013.440-0.084-0.0840.0000.0000.0000.000
35H35HIS00.0170.01916.9110.1310.1310.0000.0000.0000.000
36H36TRP00.0290.01018.288-0.019-0.0190.0000.0000.0000.000
37H37LEU0-0.0240.00218.8890.0410.0410.0000.0000.0000.000
38H38ARG10.8500.90121.7520.1760.1760.0000.0000.0000.000
39H39GLN00.0330.02521.6890.0100.0100.0000.0000.0000.000
40H40ALA00.0490.03124.8670.0020.0020.0000.0000.0000.000
41H41PRO00.030-0.00228.1780.0070.0070.0000.0000.0000.000
42H42GLY0-0.0150.00929.3680.0010.0010.0000.0000.0000.000
43H43GLN0-0.0050.00229.5180.0090.0090.0000.0000.0000.000
44H44GLY00.0290.00826.3390.0070.0070.0000.0000.0000.000
45H45LEU0-0.052-0.02520.420-0.010-0.0100.0000.0000.0000.000
46H46GLN00.0320.02524.5980.0090.0090.0000.0000.0000.000
47H47TRP0-0.012-0.01322.0720.0070.0070.0000.0000.0000.000
48H48MET0-0.065-0.03524.0010.0170.0170.0000.0000.0000.000
49H49GLY00.023-0.01223.7640.0190.0190.0000.0000.0000.000
50H50TRP00.0170.02121.309-0.039-0.0390.0000.0000.0000.000
51H51MET00.012-0.00418.2100.0580.0580.0000.0000.0000.000
52H52ASN00.0510.03419.171-0.088-0.0880.0000.0000.0000.000
53H53PRO00.0400.03115.2360.0890.0890.0000.0000.0000.000
54H54GLN00.0620.04517.939-0.020-0.0200.0000.0000.0000.000
55H55THR0-0.038-0.04619.1770.0600.0600.0000.0000.0000.000
56H56GLY0-0.045-0.02521.7960.0390.0390.0000.0000.0000.000
57H57ARG10.8230.92623.1300.4450.4450.0000.0000.0000.000
58H58THR00.000-0.01623.666-0.033-0.0330.0000.0000.0000.000
59H59ASN00.0240.01925.4030.0430.0430.0000.0000.0000.000
60H60THR00.0160.00926.325-0.020-0.0200.0000.0000.0000.000
61H61ALA00.0090.02228.5180.0130.0130.0000.0000.0000.000
62H62ARG11.0100.98730.0800.1550.1550.0000.0000.0000.000
63H63ASN0-0.023-0.01832.7750.0030.0030.0000.0000.0000.000
64H64PHE0-0.009-0.01028.6610.0060.0060.0000.0000.0000.000
65H65GLN0-0.0070.00732.029-0.001-0.0010.0000.0000.0000.000
66H66GLY00.0560.03433.536-0.005-0.0050.0000.0000.0000.000
67H67ARG10.7640.84932.6650.1700.1700.0000.0000.0000.000
68H68VAL00.0650.03426.893-0.004-0.0040.0000.0000.0000.000
69H69THR0-0.065-0.02427.8650.0110.0110.0000.0000.0000.000
70H70MET0-0.0100.02222.799-0.016-0.0160.0000.0000.0000.000
71H71THR0-0.020-0.00923.1170.0080.0080.0000.0000.0000.000
72H72ARG10.8990.92318.4820.5340.5340.0000.0000.0000.000
73H73ASP-1-0.815-0.86919.064-0.508-0.5080.0000.0000.0000.000
74H74THR0-0.008-0.02217.089-0.069-0.0690.0000.0000.0000.000
75H75SER0-0.067-0.03816.607-0.068-0.0680.0000.0000.0000.000
76H76ILE0-0.002-0.00116.045-0.018-0.0180.0000.0000.0000.000
77H77GLY0-0.0190.00913.463-0.124-0.1240.0000.0000.0000.000
78H78THR0-0.040-0.03113.698-0.095-0.0950.0000.0000.0000.000
79H79ALA0-0.0020.00416.2800.0900.0900.0000.0000.0000.000
80H80TYR0-0.005-0.02318.1820.0220.0220.0000.0000.0000.000
81H81MET0-0.0160.01421.5460.0200.0200.0000.0000.0000.000
82H82GLU-1-0.856-0.91923.811-0.246-0.2460.0000.0000.0000.000
83H83LEU00.0270.01727.3820.0030.0030.0000.0000.0000.000
84H84ARG10.8520.88829.5150.2420.2420.0000.0000.0000.000
85H85SER00.0110.00033.2220.0000.0000.0000.0000.0000.000
86H86LEU0-0.0350.00230.4700.0030.0030.0000.0000.0000.000
87H87THR00.0600.02334.3540.0120.0120.0000.0000.0000.000
88H88SER00.0480.00934.139-0.005-0.0050.0000.0000.0000.000
89H89ASP-1-0.878-0.93633.944-0.112-0.1120.0000.0000.0000.000
90H90ASP-1-0.804-0.86530.468-0.177-0.1770.0000.0000.0000.000
91H91THR00.0130.03129.136-0.014-0.0140.0000.0000.0000.000
92H92ALA00.0140.00426.2040.0080.0080.0000.0000.0000.000
93H93ILE0-0.0050.00920.478-0.010-0.0100.0000.0000.0000.000
94H94TYR0-0.038-0.04821.618-0.007-0.0070.0000.0000.0000.000
95H95TYR0-0.001-0.00616.313-0.013-0.0130.0000.0000.0000.000
96H97THR00.0010.00013.685-0.034-0.0340.0000.0000.0000.000
97H98THR00.0380.0269.973-0.054-0.0540.0000.0000.0000.000
98H99GLY0-0.015-0.01613.2300.1420.1420.0000.0000.0000.000
99H100GLY00.0540.03114.181-0.062-0.0620.0000.0000.0000.000
100H101TRP00.0280.00512.999-0.001-0.0010.0000.0000.0000.000
101H102ILE0-0.069-0.04015.5530.1480.1480.0000.0000.0000.000
102H103SER0-0.011-0.00217.661-0.022-0.0220.0000.0000.0000.000
103H104LEU0-0.029-0.01920.3650.0240.0240.0000.0000.0000.000
104H105TYR0-0.0040.00621.3600.0380.0380.0000.0000.0000.000
105H106TYR00.0140.00419.774-0.021-0.0210.0000.0000.0000.000
106H107ASP-1-0.746-0.83023.660-0.434-0.4340.0000.0000.0000.000
107H108SER00.0390.00719.2990.0280.0280.0000.0000.0000.000
108H109SER0-0.080-0.06220.478-0.021-0.0210.0000.0000.0000.000
109H110TYR0-0.051-0.04821.883-0.001-0.0010.0000.0000.0000.000
110H111TYR00.0140.01319.5560.0360.0360.0000.0000.0000.000
111H112PRO0-0.0460.00519.411-0.049-0.0490.0000.0000.0000.000
112H113ASN0-0.021-0.03615.5450.0700.0700.0000.0000.0000.000
113H114PHE00.005-0.01214.376-0.071-0.0710.0000.0000.0000.000
114H115ASP-1-0.897-0.9369.213-0.457-0.4570.0000.0000.0000.000
115H116HIS00.0100.0005.4330.3150.3150.0000.0000.0000.000
116H117TRP0-0.004-0.0279.908-0.117-0.1170.0000.0000.0000.000
117H118GLY00.0260.02310.745-0.039-0.0390.0000.0000.0000.000
118H119GLN0-0.005-0.00112.9220.0350.0350.0000.0000.0000.000
119H120GLY00.0120.02214.0810.0640.0640.0000.0000.0000.000
120H121THR0-0.068-0.04117.607-0.018-0.0180.0000.0000.0000.000
121H122LEU0-0.011-0.00120.5980.0050.0050.0000.0000.0000.000
122H123LEU0-0.028-0.00423.908-0.001-0.0010.0000.0000.0000.000
123H124THR00.0190.00326.9950.0140.0140.0000.0000.0000.000
124H125VAL0-0.027-0.01830.449-0.003-0.0030.0000.0000.0000.000
125H126SER00.009-0.00933.3300.0090.0090.0000.0000.0000.000
126H127GLY00.0320.01336.537-0.004-0.0040.0000.0000.0000.000
127H128ALA0-0.0250.00537.8640.0040.0040.0000.0000.0000.000
128H129SER00.010-0.00638.167-0.004-0.0040.0000.0000.0000.000
129H130THR0-0.047-0.02032.9320.0050.0050.0000.0000.0000.000
130H131LYS10.9420.96835.1680.0580.0580.0000.0000.0000.000
131H132GLY00.0720.04333.652-0.003-0.0030.0000.0000.0000.000
132H133PRO0-0.025-0.00431.2170.0040.0040.0000.0000.0000.000
133H134SER0-0.0090.00734.4620.0010.0010.0000.0000.0000.000
134H135VAL00.003-0.00532.1030.0020.0020.0000.0000.0000.000
135H136PHE0-0.008-0.00835.1830.0020.0020.0000.0000.0000.000
136H137PRO00.0210.02035.4010.0010.0010.0000.0000.0000.000
137H138LEU0-0.037-0.01534.458-0.001-0.0010.0000.0000.0000.000
138H139ALA00.0260.00136.2850.0050.0050.0000.0000.0000.000
139H140PRO00.024-0.00436.3560.0000.0000.0000.0000.0000.000
140H141SER0-0.041-0.01037.704-0.003-0.0030.0000.0000.0000.000
141H142SER00.0510.00938.2530.0020.0020.0000.0000.0000.000
142H143LYS10.9040.95840.010-0.033-0.0330.0000.0000.0000.000
143H144SER00.0240.01038.088-0.001-0.0010.0000.0000.0000.000
144H145THR0-0.011-0.00834.706-0.001-0.0010.0000.0000.0000.000
145H146SER00.0120.00734.001-0.001-0.0010.0000.0000.0000.000
146H147GLY00.0340.02835.8480.0060.0060.0000.0000.0000.000
147H148GLY00.0320.01638.035-0.003-0.0030.0000.0000.0000.000
148H149THR0-0.051-0.03733.1680.0050.0050.0000.0000.0000.000
149H150ALA0-0.0250.00835.078-0.006-0.0060.0000.0000.0000.000
150H151ALA00.0300.01433.6700.0060.0060.0000.0000.0000.000
151H152LEU0-0.0040.02631.231-0.006-0.0060.0000.0000.0000.000
152H153GLY00.0470.00031.5690.0040.0040.0000.0000.0000.000
153H154CYS0-0.108-0.02427.4930.0010.0010.0000.0000.0000.000
154H155LEU00.0260.03132.4600.0000.0000.0000.0000.0000.000
155H156VAL00.000-0.00729.799-0.002-0.0020.0000.0000.0000.000
156H157LYS10.8390.88433.1970.0180.0180.0000.0000.0000.000
157H158ASP-1-0.799-0.88336.281-0.030-0.0300.0000.0000.0000.000
158H159TYR0-0.026-0.02829.5160.0010.0010.0000.0000.0000.000
159H160PHE00.0110.01333.3060.0000.0000.0000.0000.0000.000
160H161PRO00.0250.01329.929-0.001-0.0010.0000.0000.0000.000
161H162GLU-1-0.760-0.86426.905-0.055-0.0550.0000.0000.0000.000
162H163PRO0-0.024-0.02123.465-0.013-0.0130.0000.0000.0000.000
163H164VAL0-0.007-0.01426.009-0.008-0.0080.0000.0000.0000.000
164H165THR0-0.028-0.01320.438-0.002-0.0020.0000.0000.0000.000
165H166VAL0-0.010-0.01723.294-0.002-0.0020.0000.0000.0000.000
166H167SER0-0.032-0.00921.0610.0040.0040.0000.0000.0000.000
167H168TRP00.0360.00522.753-0.007-0.0070.0000.0000.0000.000
168H169ASN0-0.020-0.01523.4940.0040.0040.0000.0000.0000.000
169H170SER00.002-0.01222.6950.0100.0100.0000.0000.0000.000
170H171GLY0-0.0050.00119.2570.0000.0000.0000.0000.0000.000
171H172ALA0-0.0210.00119.2870.0240.0240.0000.0000.0000.000
172H173LEU0-0.055-0.02021.3910.0190.0190.0000.0000.0000.000
173H174THR00.0280.00217.694-0.016-0.0160.0000.0000.0000.000
174H175SER0-0.016-0.00820.997-0.005-0.0050.0000.0000.0000.000
175H176GLY00.0590.02723.103-0.011-0.0110.0000.0000.0000.000
176H177VAL0-0.033-0.01223.004-0.014-0.0140.0000.0000.0000.000
177H178HIS00.0260.01824.1330.0070.0070.0000.0000.0000.000
178H179THR00.0180.00224.217-0.006-0.0060.0000.0000.0000.000
179H180PHE0-0.025-0.00326.0220.0000.0000.0000.0000.0000.000
180H181PRO00.016-0.00527.561-0.007-0.0070.0000.0000.0000.000
181H182ALA0-0.0040.00628.9420.0040.0040.0000.0000.0000.000
182H183VAL0-0.024-0.00831.317-0.001-0.0010.0000.0000.0000.000
183H184LEU0-0.010-0.00634.881-0.003-0.0030.0000.0000.0000.000
184H185GLN0-0.048-0.03436.4050.0070.0070.0000.0000.0000.000
185H186SER00.0430.01639.785-0.004-0.0040.0000.0000.0000.000
186H187SER0-0.003-0.00641.155-0.002-0.0020.0000.0000.0000.000
187H188GLY00.0160.01539.670-0.003-0.0030.0000.0000.0000.000
188H189LEU0-0.070-0.02736.871-0.005-0.0050.0000.0000.0000.000
189H190TYR00.0250.02032.2250.0010.0010.0000.0000.0000.000
190H191SER00.010-0.01034.1470.0020.0020.0000.0000.0000.000
191H192LEU00.0060.03027.5040.0010.0010.0000.0000.0000.000
192H193SER00.008-0.00531.1680.0010.0010.0000.0000.0000.000
193H194SER0-0.041-0.01826.3730.0030.0030.0000.0000.0000.000
194H195VAL00.010-0.00128.838-0.001-0.0010.0000.0000.0000.000
195H196VAL00.0230.01026.9320.0060.0060.0000.0000.0000.000
196H197THR0-0.024-0.00329.077-0.006-0.0060.0000.0000.0000.000
197H198VAL0-0.012-0.00729.5440.0100.0100.0000.0000.0000.000
198H199PRO00.0620.02730.876-0.006-0.0060.0000.0000.0000.000
199H200SER00.017-0.02033.885-0.003-0.0030.0000.0000.0000.000
200H201SER0-0.007-0.00637.044-0.004-0.0040.0000.0000.0000.000
201H202SER00.0480.03333.8190.0000.0000.0000.0000.0000.000
202H203LEU0-0.0080.00935.501-0.001-0.0010.0000.0000.0000.000
203H204GLY0-0.0250.00037.2630.0000.0000.0000.0000.0000.000
204H205THR0-0.033-0.02336.3330.0010.0010.0000.0000.0000.000
205H206GLN0-0.0210.00129.3410.0050.0050.0000.0000.0000.000
206H207THR0-0.012-0.00830.912-0.011-0.0110.0000.0000.0000.000
207H208TYR00.0440.01529.4380.0100.0100.0000.0000.0000.000
208H209ILE00.0330.01428.996-0.008-0.0080.0000.0000.0000.000
209H211ASN00.0370.00324.3670.0030.0030.0000.0000.0000.000
210H212VAL0-0.0010.00525.223-0.003-0.0030.0000.0000.0000.000
211H213ASN0-0.044-0.03522.535-0.015-0.0150.0000.0000.0000.000
212H214HIS00.0710.05425.567-0.001-0.0010.0000.0000.0000.000
213H215LYS10.9880.97820.2910.1840.1840.0000.0000.0000.000
214H216PRO00.0110.01726.184-0.007-0.0070.0000.0000.0000.000
215H217SER0-0.041-0.04828.7810.0000.0000.0000.0000.0000.000
216H218ASN0-0.075-0.03128.274-0.001-0.0010.0000.0000.0000.000
217H219THR00.0280.02829.4490.0090.0090.0000.0000.0000.000
218H220LYS10.9290.95924.3250.0910.0910.0000.0000.0000.000
219H221VAL00.002-0.00228.8900.0030.0030.0000.0000.0000.000
220H222ASP-1-0.842-0.90227.759-0.002-0.0020.0000.0000.0000.000
221H223LYS10.8660.92430.5020.0010.0010.0000.0000.0000.000
222H224ARG10.8590.90932.110-0.043-0.0430.0000.0000.0000.000
223H225VAL0-0.029-0.01932.898-0.005-0.0050.0000.0000.0000.000
224H226GLU-1-0.842-0.90035.1650.0470.0470.0000.0000.0000.000
225H227PRO0-0.004-0.01037.951-0.003-0.0030.0000.0000.0000.000
226H228LYS10.9851.00840.619-0.025-0.0250.0000.0000.0000.000
227H229SER0-0.008-0.01543.8960.0020.0020.0000.0000.0000.000
228H230CYS00.0080.01247.534-0.002-0.0020.0000.0000.0000.000