FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 896NY

Calculation Name: 1QZQ-B-Xray372

Preferred Name: Tyrosyl-DNA phosphodiesterase 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1QZQ

Chain ID: B

ChEMBL ID: CHEMBL1075138

UniProt ID: Q9NUW8

Base Structure: X-ray

Registration Date: 2023-09-23

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 448
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8881808.905253
FMO2-HF: Nuclear repulsion 8705685.706526
FMO2-HF: Total energy -176123.198727
FMO2-MP2: Total energy -176642.52744


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(B:161:GLY)


Summations of interaction energy for fragment #1(B:161:GLY)
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.
-1.1891.8210.175-1.496-1.69-0.002
Interaction energy analysis for fragmet #1(B:161:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.001
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].
3B163PRO00.0910.0373.8351.4932.802-0.016-0.707-0.5860.002
4B164PHE0-0.023-0.0127.0220.1700.1700.0000.0000.0000.000
5B165GLN00.0730.0553.085-2.427-1.7870.051-0.256-0.4350.001
6B166PHE0-0.020-0.0065.908-0.061-0.0610.0000.0000.0000.000
7B167TYR0-0.074-0.0573.084-1.233-0.1720.140-0.533-0.669-0.005
8B168LEU00.0030.0017.9940.0020.0020.0000.0000.0000.000
9B169THR00.0460.02610.5300.0320.0320.0000.0000.0000.000
10B170ARG10.8980.95012.246-0.053-0.0530.0000.0000.0000.000
11B171VAL00.0020.01314.1180.0070.0070.0000.0000.0000.000
12B172SER0-0.0040.00517.391-0.014-0.0140.0000.0000.0000.000
13B173GLY00.0510.01520.3220.0020.0020.0000.0000.0000.000
14B174VAL00.0020.02616.968-0.006-0.0060.0000.0000.0000.000
15B175LYS10.9560.96718.4030.1180.1180.0000.0000.0000.000
16B176PRO00.1030.03315.644-0.007-0.0070.0000.0000.0000.000
17B177LYS10.9600.99013.1130.2360.2360.0000.0000.0000.000
18B178TYR0-0.002-0.00212.150-0.038-0.0380.0000.0000.0000.000
19B179ASN00.022-0.00812.0820.0240.0240.0000.0000.0000.000
20B180SER0-0.046-0.0069.1570.0400.0400.0000.0000.0000.000
21B181GLY00.0640.0305.637-0.118-0.1180.0000.0000.0000.000
22B182ALA0-0.065-0.0216.5900.0710.0710.0000.0000.0000.000
23B183LEU00.0100.0036.8430.0220.0220.0000.0000.0000.000
24B184HIS0-0.029-0.01910.131-0.041-0.0410.0000.0000.0000.000
25B185ILE00.0210.01013.2160.0380.0380.0000.0000.0000.000
26B186LYS10.9290.96015.463-0.067-0.0670.0000.0000.0000.000
27B187ASP-1-0.864-0.92010.6720.1740.1740.0000.0000.0000.000
28B188ILE0-0.054-0.02610.9920.0450.0450.0000.0000.0000.000
29B189LEU0-0.051-0.02512.4890.0260.0260.0000.0000.0000.000
30B190SER00.0130.01412.596-0.029-0.0290.0000.0000.0000.000
31B191PRO00.0530.01014.3260.0400.0400.0000.0000.0000.000
32B192LEU0-0.0280.00011.0170.0080.0080.0000.0000.0000.000
33B193PHE0-0.080-0.0397.8800.1060.1060.0000.0000.0000.000
34B194GLY00.0380.02611.7960.0510.0510.0000.0000.0000.000
35B195THR0-0.011-0.00615.102-0.032-0.0320.0000.0000.0000.000
36B196LEU0-0.082-0.04218.585-0.001-0.0010.0000.0000.0000.000
37B197VAL0-0.003-0.00120.004-0.024-0.0240.0000.0000.0000.000
38B198SER00.002-0.01922.306-0.020-0.0200.0000.0000.0000.000
39B199SER0-0.0040.01220.8300.0240.0240.0000.0000.0000.000
40B200ALA00.0230.01321.750-0.021-0.0210.0000.0000.0000.000
41B201GLN00.002-0.01718.9630.0190.0190.0000.0000.0000.000
42B202PHE0-0.0080.00722.090-0.019-0.0190.0000.0000.0000.000
43B203ASN00.035-0.00621.123-0.003-0.0030.0000.0000.0000.000
44B204TYR0-0.0260.01224.516-0.006-0.0060.0000.0000.0000.000
45B205CYS0-0.020-0.01326.486-0.006-0.0060.0000.0000.0000.000
46B206PHE0-0.010-0.01925.6110.0090.0090.0000.0000.0000.000
47B207ASP-1-0.857-0.91026.7730.0540.0540.0000.0000.0000.000
48B208VAL00.0200.00327.0920.0060.0060.0000.0000.0000.000
49B209ASP-1-0.782-0.86327.8230.0640.0640.0000.0000.0000.000
50B210TRP0-0.062-0.03820.1350.0050.0050.0000.0000.0000.000
51B211LEU00.007-0.00422.0030.0060.0060.0000.0000.0000.000
52B212VAL00.0490.02723.2860.0120.0120.0000.0000.0000.000
53B213LYS10.8870.93924.646-0.057-0.0570.0000.0000.0000.000
54B214GLN0-0.066-0.04719.4900.0010.0010.0000.0000.0000.000
55B215TYR00.0300.01419.5580.0160.0160.0000.0000.0000.000
56B216PRO00.0300.02718.130-0.021-0.0210.0000.0000.0000.000
57B217PRO0-0.016-0.03120.9420.0010.0010.0000.0000.0000.000
58B218GLU-1-0.828-0.90620.9220.1120.1120.0000.0000.0000.000
59B219PHE0-0.019-0.02817.597-0.002-0.0020.0000.0000.0000.000
60B220ARG10.8390.93023.256-0.092-0.0920.0000.0000.0000.000
61B221LYS10.9660.98225.693-0.080-0.0800.0000.0000.0000.000
62B222LYS10.9080.98423.793-0.135-0.1350.0000.0000.0000.000
63B223PRO00.0430.02526.672-0.002-0.0020.0000.0000.0000.000
64B224ILE0-0.0130.00624.7880.0130.0130.0000.0000.0000.000
65B225LEU0-0.0200.00525.997-0.011-0.0110.0000.0000.0000.000
66B226LEU00.0110.01325.9270.0110.0110.0000.0000.0000.000
67B227VAL0-0.017-0.01426.296-0.009-0.0090.0000.0000.0000.000
68B228HIS00.0780.03127.2660.0010.0010.0000.0000.0000.000
69B229GLY00.0320.00429.8300.0000.0000.0000.0000.0000.000
70B230ASP-1-0.882-0.92832.6060.0570.0570.0000.0000.0000.000
71B231LYS10.8490.90034.886-0.049-0.0490.0000.0000.0000.000
72B232ARG10.8900.94338.644-0.037-0.0370.0000.0000.0000.000
73B233GLU-1-0.773-0.89740.8570.0360.0360.0000.0000.0000.000
74B234ALA00.0150.02536.0460.0010.0010.0000.0000.0000.000
75B235LYS10.9230.96836.302-0.055-0.0550.0000.0000.0000.000
76B236ALA00.0060.00237.2070.0030.0030.0000.0000.0000.000
77B237HIS00.0280.01235.1090.0000.0000.0000.0000.0000.000
78B238LEU00.0040.00730.7870.0010.0010.0000.0000.0000.000
79B239HIS0-0.028-0.03234.4500.0020.0020.0000.0000.0000.000
80B240ALA0-0.015-0.00236.5480.0010.0010.0000.0000.0000.000
81B241GLN00.002-0.00631.5340.0010.0010.0000.0000.0000.000
82B242ALA0-0.007-0.01232.7040.0020.0020.0000.0000.0000.000
83B243LYS10.9160.96833.689-0.050-0.0500.0000.0000.0000.000
84B244PRO0-0.021-0.00934.7720.0000.0000.0000.0000.0000.000
85B245TYR0-0.060-0.04130.9500.0010.0010.0000.0000.0000.000
86B246GLU-1-0.871-0.94433.4690.0630.0630.0000.0000.0000.000
87B247ASN0-0.098-0.04028.045-0.006-0.0060.0000.0000.0000.000
88B248ILE00.001-0.00128.6080.0090.0090.0000.0000.0000.000
89B249SER0-0.0210.00030.424-0.007-0.0070.0000.0000.0000.000
90B250LEU00.007-0.00830.5090.0050.0050.0000.0000.0000.000
91B251CYS0-0.034-0.01930.431-0.004-0.0040.0000.0000.0000.000
92B252GLN0-0.025-0.00531.5990.0010.0010.0000.0000.0000.000
93B253ALA00.0230.01530.789-0.002-0.0020.0000.0000.0000.000
94B254LYS10.9070.97832.920-0.074-0.0740.0000.0000.0000.000
95B255LEU0-0.006-0.00132.7290.0020.0020.0000.0000.0000.000
96B256ASP-1-0.881-0.94136.5320.0500.0500.0000.0000.0000.000
97B257ILE0-0.045-0.01837.415-0.003-0.0030.0000.0000.0000.000
98B258ALA0-0.020-0.00838.4690.0010.0010.0000.0000.0000.000
99B259PHE00.019-0.01338.0430.0000.0000.0000.0000.0000.000
100B260GLY00.0610.06134.5700.0000.0000.0000.0000.0000.000
101B261THR0-0.012-0.01230.7030.0010.0010.0000.0000.0000.000
102B262HIS00.0890.03625.8330.0050.0050.0000.0000.0000.000
103B263HIS0-0.042-0.02425.0650.0000.0000.0000.0000.0000.000
104B264THR00.016-0.00322.1050.0000.0000.0000.0000.0000.000
105B265LYS10.8160.94119.760-0.099-0.0990.0000.0000.0000.000
106B266MET0-0.012-0.00518.0850.0190.0190.0000.0000.0000.000
107B267MET0-0.055-0.00515.733-0.015-0.0150.0000.0000.0000.000
108B268LEU0-0.0170.00717.3970.0390.0390.0000.0000.0000.000
109B269LEU00.014-0.00614.738-0.031-0.0310.0000.0000.0000.000
110B270LEU00.0040.00418.0220.0260.0260.0000.0000.0000.000
111B271TYR00.0410.00314.1380.0090.0090.0000.0000.0000.000
112B272GLU-1-0.949-0.97319.2310.1540.1540.0000.0000.0000.000
113B273GLU-1-0.824-0.92116.5190.2660.2660.0000.0000.0000.000
114B274GLY0-0.024-0.00817.3700.0260.0260.0000.0000.0000.000
115B275LEU0-0.031-0.01517.207-0.026-0.0260.0000.0000.0000.000
116B276ARG10.8940.9838.996-0.857-0.8570.0000.0000.0000.000
117B277VAL0-0.004-0.00714.227-0.082-0.0820.0000.0000.0000.000
118B278VAL00.0070.00612.3440.0770.0770.0000.0000.0000.000
119B279ILE00.0060.01013.674-0.068-0.0680.0000.0000.0000.000
120B280HIS0-0.008-0.01113.9710.0120.0120.0000.0000.0000.000
121B281THR00.0300.00815.683-0.018-0.0180.0000.0000.0000.000
122B282SER0-0.0110.00117.398-0.021-0.0210.0000.0000.0000.000
123B283ASN00.028-0.02519.4280.0170.0170.0000.0000.0000.000
124B284LEU0-0.059-0.02420.0590.0040.0040.0000.0000.0000.000
125B285ILE00.0410.01922.983-0.005-0.0050.0000.0000.0000.000
126B286HIS00.0430.00923.0040.0090.0090.0000.0000.0000.000
127B287ALA00.0490.00722.663-0.001-0.0010.0000.0000.0000.000
128B288ASP-1-0.804-0.88120.9160.0580.0580.0000.0000.0000.000
129B289TRP0-0.029-0.02114.1950.0090.0090.0000.0000.0000.000
130B290HIS00.0050.01918.6640.0010.0010.0000.0000.0000.000
131B291GLN0-0.018-0.03519.963-0.005-0.0050.0000.0000.0000.000
132B292LYS10.8740.94119.874-0.030-0.0300.0000.0000.0000.000
133B293THR0-0.029-0.01915.933-0.004-0.0040.0000.0000.0000.000
134B294GLN00.022-0.01515.7450.0050.0050.0000.0000.0000.000
135B295GLY00.007-0.01213.022-0.016-0.0160.0000.0000.0000.000
136B296ILE0-0.011-0.0179.9740.0090.0090.0000.0000.0000.000
137B297TRP00.0200.0119.765-0.022-0.0220.0000.0000.0000.000
138B298LEU0-0.016-0.0156.368-0.105-0.1050.0000.0000.0000.000
139B299SER00.0090.0248.9670.1510.1510.0000.0000.0000.000
140B300PRO00.0170.0079.5690.1510.1510.0000.0000.0000.000
141B301LEU0-0.031-0.01110.591-0.134-0.1340.0000.0000.0000.000
142B302TYR00.014-0.01312.603-0.010-0.0100.0000.0000.0000.000
143B303PRO00.0760.05515.984-0.037-0.0370.0000.0000.0000.000
144B304ARG11.0040.98618.336-0.201-0.2010.0000.0000.0000.000
145B305ILE0-0.059-0.04021.987-0.001-0.0010.0000.0000.0000.000
146B306ALA00.005-0.01124.428-0.010-0.0100.0000.0000.0000.000
147B307ASP-1-0.866-0.94026.6620.1160.1160.0000.0000.0000.000
148B308GLY00.0180.02029.475-0.006-0.0060.0000.0000.0000.000
149B309THR0-0.061-0.02628.555-0.008-0.0080.0000.0000.0000.000
150B310HIS0-0.024-0.01029.9090.0110.0110.0000.0000.0000.000
151B311LYS10.9900.97323.709-0.174-0.1740.0000.0000.0000.000
152B312SER0-0.0060.02725.7470.0040.0040.0000.0000.0000.000
153B313GLY00.020-0.00422.9800.0030.0030.0000.0000.0000.000
154B314GLU-1-0.799-0.89421.6760.2160.2160.0000.0000.0000.000
155B315SER00.0240.01618.524-0.007-0.0070.0000.0000.0000.000
156B316PRO00.000-0.00218.996-0.022-0.0220.0000.0000.0000.000
157B317THR0-0.075-0.05517.893-0.015-0.0150.0000.0000.0000.000
158B318HIS0-0.017-0.00620.925-0.006-0.0060.0000.0000.0000.000
159B319PHE00.0210.02117.1310.0000.0000.0000.0000.0000.000
160B320LYS10.8200.91520.652-0.204-0.2040.0000.0000.0000.000
161B321ALA00.001-0.00322.409-0.009-0.0090.0000.0000.0000.000
162B322ASP-1-0.828-0.92222.9960.1260.1260.0000.0000.0000.000
163B323LEU0-0.037-0.01719.715-0.009-0.0090.0000.0000.0000.000
164B324ILE0-0.003-0.00823.280-0.012-0.0120.0000.0000.0000.000
165B325SER0-0.002-0.00526.398-0.013-0.0130.0000.0000.0000.000
166B326TYR0-0.030-0.03124.581-0.012-0.0120.0000.0000.0000.000
167B327LEU0-0.019-0.02623.880-0.009-0.0090.0000.0000.0000.000
168B328MET0-0.0190.00527.587-0.008-0.0080.0000.0000.0000.000
169B329ALA0-0.0060.01430.483-0.008-0.0080.0000.0000.0000.000
170B330TYR0-0.033-0.02826.825-0.005-0.0050.0000.0000.0000.000
171B331ASN0-0.088-0.04132.207-0.004-0.0040.0000.0000.0000.000
172B332ALA00.0150.00532.266-0.005-0.0050.0000.0000.0000.000
173B333PRO00.0470.01133.2420.0050.0050.0000.0000.0000.000
174B334SER00.0580.01731.1010.0040.0040.0000.0000.0000.000
175B335LEU00.0210.01027.1750.0080.0080.0000.0000.0000.000
176B336LYS10.9270.97928.988-0.094-0.0940.0000.0000.0000.000
177B337GLU-1-0.842-0.92430.3260.1100.1100.0000.0000.0000.000
178B338TRP0-0.023-0.01822.0690.0140.0140.0000.0000.0000.000
179B339ILE0-0.062-0.03325.7850.0130.0130.0000.0000.0000.000
180B340ASP-1-0.846-0.92927.2710.1250.1250.0000.0000.0000.000
181B341VAL0-0.022-0.00222.9600.0050.0050.0000.0000.0000.000
182B342ILE0-0.0080.00521.9820.0150.0150.0000.0000.0000.000
183B343HIS00.001-0.00323.7790.0140.0140.0000.0000.0000.000
184B344LYS10.8830.97025.523-0.143-0.1430.0000.0000.0000.000
185B345HIS0-0.037-0.02919.8950.0080.0080.0000.0000.0000.000
186B346ASP-1-0.841-0.90519.5960.2540.2540.0000.0000.0000.000
187B347LEU0-0.025-0.02517.5920.0390.0390.0000.0000.0000.000
188B348SER0-0.020-0.02117.9240.0210.0210.0000.0000.0000.000
189B349GLU-1-0.915-0.96011.4080.7970.7970.0000.0000.0000.000
190B350THR0-0.104-0.05513.8350.0800.0800.0000.0000.0000.000
191B351ASN00.0530.02010.780-0.070-0.0700.0000.0000.0000.000
192B352VAL00.0070.02512.882-0.055-0.0550.0000.0000.0000.000
193B353TYR00.0440.02115.6730.0050.0050.0000.0000.0000.000
194B354LEU00.0070.02618.897-0.002-0.0020.0000.0000.0000.000
195B355ILE00.000-0.01120.451-0.021-0.0210.0000.0000.0000.000
196B356GLY00.0360.01922.5950.0050.0050.0000.0000.0000.000
197B357SER0-0.056-0.04124.893-0.009-0.0090.0000.0000.0000.000
198B358THR00.0390.01828.0820.0040.0040.0000.0000.0000.000
199B359PRO0-0.022-0.00930.702-0.005-0.0050.0000.0000.0000.000
200B360GLY00.0200.00334.1260.0020.0020.0000.0000.0000.000
201B361ARG10.9210.96136.907-0.041-0.0410.0000.0000.0000.000
202B362PHE00.0290.01734.147-0.001-0.0010.0000.0000.0000.000
203B363GLN00.0310.00138.071-0.003-0.0030.0000.0000.0000.000
204B364GLY00.0310.01239.5970.0020.0020.0000.0000.0000.000
205B365SER00.0520.01736.6770.0000.0000.0000.0000.0000.000
206B366GLN00.0430.01535.0180.0060.0060.0000.0000.0000.000
207B367LYS10.8300.93434.339-0.038-0.0380.0000.0000.0000.000
208B368ASP-1-0.909-0.96831.7730.0500.0500.0000.0000.0000.000
209B369ASN0-0.018-0.00230.0210.0050.0050.0000.0000.0000.000
210B370TRP00.013-0.00127.1530.0090.0090.0000.0000.0000.000
211B371GLY00.0490.03028.366-0.007-0.0070.0000.0000.0000.000
212B372HIS10.7900.87128.067-0.034-0.0340.0000.0000.0000.000
213B373PHE0-0.006-0.01029.450-0.005-0.0050.0000.0000.0000.000
214B374ARG10.8620.95223.328-0.116-0.1160.0000.0000.0000.000
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