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: NN72Q

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 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 448
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8882301.44217
FMO2-HF: Nuclear repulsion 8706176.366879
FMO2-HF: Total energy -176125.075292
FMO2-MP2: Total energy -176644.352082


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.
-1.9741.5340.544-1.901-2.15-0.003
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 : 0.012 / q_NPA : 0.002
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].
3B163PRO00.0940.0473.8351.3812.718-0.016-0.722-0.5990.002
4B164PHE0-0.024-0.0096.9900.1800.1800.0000.0000.0000.000
5B165GLN00.0600.0503.192-2.678-1.7940.089-0.405-0.5670.003
6B166PHE0-0.010-0.0015.907-0.052-0.0520.0000.0000.0000.000
7B167TYR0-0.056-0.0602.825-1.721-0.4340.471-0.774-0.984-0.008
8B168LEU00.0040.0047.9950.0060.0060.0000.0000.0000.000
9B169THR00.0470.02510.5310.0260.0260.0000.0000.0000.000
10B170ARG10.8830.94311.851-0.045-0.0450.0000.0000.0000.000
11B171VAL00.0080.01214.1190.0070.0070.0000.0000.0000.000
12B172SER00.0020.00817.392-0.014-0.0140.0000.0000.0000.000
13B173GLY00.0560.02120.3230.0020.0020.0000.0000.0000.000
14B174VAL0-0.0060.02117.102-0.005-0.0050.0000.0000.0000.000
15B175LYS10.9660.97118.4240.1120.1120.0000.0000.0000.000
16B176PRO00.0950.03115.544-0.006-0.0060.0000.0000.0000.000
17B177LYS10.9310.98413.0930.2310.2310.0000.0000.0000.000
18B178TYR00.0140.00312.148-0.044-0.0440.0000.0000.0000.000
19B179ASN00.0180.00112.0860.0240.0240.0000.0000.0000.000
20B180SER0-0.0280.0128.9300.0520.0520.0000.0000.0000.000
21B181GLY00.0560.0175.635-0.108-0.1080.0000.0000.0000.000
22B182ALA0-0.073-0.0236.5880.0620.0620.0000.0000.0000.000
23B183LEU00.0190.0066.6910.0210.0210.0000.0000.0000.000
24B184HIS0-0.018-0.01410.132-0.031-0.0310.0000.0000.0000.000
25B185ILE00.0210.01313.2170.0350.0350.0000.0000.0000.000
26B186LYS10.9400.96015.464-0.056-0.0560.0000.0000.0000.000
27B187ASP-1-0.868-0.92610.6850.1460.1460.0000.0000.0000.000
28B188ILE0-0.069-0.02910.9150.0420.0420.0000.0000.0000.000
29B189LEU0-0.042-0.02312.4890.0260.0260.0000.0000.0000.000
30B190SER00.0120.01412.539-0.027-0.0270.0000.0000.0000.000
31B191PRO00.0590.01314.3010.0380.0380.0000.0000.0000.000
32B192LEU0-0.0280.00010.9810.0100.0100.0000.0000.0000.000
33B193PHE0-0.084-0.0367.9110.1020.1020.0000.0000.0000.000
34B194GLY00.0530.04011.7690.0540.0540.0000.0000.0000.000
35B195THR0-0.009-0.03115.076-0.032-0.0320.0000.0000.0000.000
36B196LEU0-0.047-0.02218.146-0.001-0.0010.0000.0000.0000.000
37B197VAL0-0.0100.00619.972-0.025-0.0250.0000.0000.0000.000
38B198SER00.017-0.01022.273-0.018-0.0180.0000.0000.0000.000
39B199SER00.0050.01220.9940.0210.0210.0000.0000.0000.000
40B200ALA00.0090.00921.753-0.019-0.0190.0000.0000.0000.000
41B201GLN0-0.005-0.02618.9690.0180.0180.0000.0000.0000.000
42B202PHE00.0030.00922.094-0.017-0.0170.0000.0000.0000.000
43B203ASN00.048-0.00621.071-0.003-0.0030.0000.0000.0000.000
44B204TYR0-0.0170.01124.516-0.006-0.0060.0000.0000.0000.000
45B205CYS0-0.018-0.00526.494-0.005-0.0050.0000.0000.0000.000
46B206PHE0-0.011-0.02625.4120.0080.0080.0000.0000.0000.000
47B207ASP-1-0.838-0.90726.7800.0490.0490.0000.0000.0000.000
48B208VAL00.0210.00427.0920.0060.0060.0000.0000.0000.000
49B209ASP-1-0.762-0.84627.8240.0570.0570.0000.0000.0000.000
50B210TRP0-0.061-0.01620.1200.0050.0050.0000.0000.0000.000
51B211LEU00.0140.00121.9400.0050.0050.0000.0000.0000.000
52B212VAL00.0520.03023.2870.0100.0100.0000.0000.0000.000
53B213LYS10.8330.90124.619-0.054-0.0540.0000.0000.0000.000
54B214GLN0-0.074-0.05419.450-0.001-0.0010.0000.0000.0000.000
55B215TYR00.0230.01519.5340.0150.0150.0000.0000.0000.000
56B216PRO00.0320.02618.084-0.019-0.0190.0000.0000.0000.000
57B217PRO0-0.018-0.02720.9210.0000.0000.0000.0000.0000.000
58B218GLU-1-0.840-0.92420.7370.1050.1050.0000.0000.0000.000
59B219PHE0-0.015-0.01617.401-0.001-0.0010.0000.0000.0000.000
60B220ARG10.8360.93723.230-0.084-0.0840.0000.0000.0000.000
61B221LYS10.9700.98425.666-0.072-0.0720.0000.0000.0000.000
62B222LYS10.8700.94723.811-0.140-0.1400.0000.0000.0000.000
63B223PRO00.0250.01226.639-0.001-0.0010.0000.0000.0000.000
64B224ILE0-0.031-0.00524.4130.0120.0120.0000.0000.0000.000
65B225LEU0-0.0130.01225.992-0.011-0.0110.0000.0000.0000.000
66B226LEU00.0170.01525.9280.0100.0100.0000.0000.0000.000
67B227VAL0-0.024-0.01326.497-0.009-0.0090.0000.0000.0000.000
68B228HIS00.0700.02727.2670.0010.0010.0000.0000.0000.000
69B229GLY00.0440.00729.8300.0000.0000.0000.0000.0000.000
70B230ASP-1-0.886-0.92832.6060.0520.0520.0000.0000.0000.000
71B231LYS10.8440.89434.887-0.046-0.0460.0000.0000.0000.000
72B232ARG10.8230.87838.645-0.034-0.0340.0000.0000.0000.000
73B233GLU-1-0.699-0.82840.8570.0340.0340.0000.0000.0000.000
74B234ALA00.0150.02636.0660.0010.0010.0000.0000.0000.000
75B235LYS10.8940.94136.303-0.052-0.0520.0000.0000.0000.000
76B236ALA00.0060.00137.2070.0020.0020.0000.0000.0000.000
77B237HIS00.0260.01234.6730.0000.0000.0000.0000.0000.000
78B238LEU00.0070.00730.6380.0010.0010.0000.0000.0000.000
79B239HIS0-0.010-0.02234.4510.0020.0020.0000.0000.0000.000
80B240ALA0-0.0060.00136.5490.0010.0010.0000.0000.0000.000
81B241GLN0-0.0060.00031.4070.0020.0020.0000.0000.0000.000
82B242ALA0-0.011-0.01432.6960.0020.0020.0000.0000.0000.000
83B243LYS10.9230.97233.690-0.046-0.0460.0000.0000.0000.000
84B244PRO0-0.017-0.00634.8100.0000.0000.0000.0000.0000.000
85B245TYR0-0.059-0.05730.9390.0020.0020.0000.0000.0000.000
86B246GLU-1-0.881-0.94533.4480.0580.0580.0000.0000.0000.000
87B247ASN0-0.098-0.03828.089-0.005-0.0050.0000.0000.0000.000
88B248ILE00.000-0.00528.5370.0080.0080.0000.0000.0000.000
89B249SER00.0000.01330.430-0.007-0.0070.0000.0000.0000.000
90B250LEU0-0.016-0.01830.5090.0050.0050.0000.0000.0000.000
91B251CYS0-0.041-0.02430.452-0.004-0.0040.0000.0000.0000.000
92B252GLN0-0.0080.01131.5990.0010.0010.0000.0000.0000.000
93B253ALA00.0200.01530.763-0.002-0.0020.0000.0000.0000.000
94B254LYS10.8780.95732.921-0.072-0.0720.0000.0000.0000.000
95B255LEU0-0.003-0.00332.6330.0020.0020.0000.0000.0000.000
96B256ASP-1-0.864-0.93236.5320.0480.0480.0000.0000.0000.000
97B257ILE0-0.026-0.00337.543-0.003-0.0030.0000.0000.0000.000
98B258ALA0-0.014-0.00838.4690.0010.0010.0000.0000.0000.000
99B259PHE00.008-0.01238.0770.0000.0000.0000.0000.0000.000
100B260GLY00.0650.06234.5720.0000.0000.0000.0000.0000.000
101B261THR0-0.023-0.02230.9110.0010.0010.0000.0000.0000.000
102B262HIS00.0490.01825.9050.0060.0060.0000.0000.0000.000
103B263HIS0-0.060-0.04524.7860.0000.0000.0000.0000.0000.000
104B264THR00.0340.01322.1930.0000.0000.0000.0000.0000.000
105B265LYS10.7900.92319.717-0.089-0.0890.0000.0000.0000.000
106B266MET0-0.015-0.00218.0870.0180.0180.0000.0000.0000.000
107B267MET0-0.040-0.00115.994-0.015-0.0150.0000.0000.0000.000
108B268LEU0-0.0210.00917.3970.0370.0370.0000.0000.0000.000
109B269LEU00.021-0.00414.712-0.030-0.0300.0000.0000.0000.000
110B270LEU0-0.0110.00017.9810.0260.0260.0000.0000.0000.000
111B271TYR00.0550.01314.0420.0120.0120.0000.0000.0000.000
112B272GLU-1-0.937-0.97119.1970.1430.1430.0000.0000.0000.000
113B273GLU-1-0.816-0.89116.4470.2490.2490.0000.0000.0000.000
114B274GLY0-0.022-0.00817.3350.0260.0260.0000.0000.0000.000
115B275LEU0-0.048-0.01917.161-0.026-0.0260.0000.0000.0000.000
116B276ARG10.8750.9509.747-0.718-0.7180.0000.0000.0000.000
117B277VAL0-0.008-0.00814.242-0.077-0.0770.0000.0000.0000.000
118B278VAL00.0070.00412.3730.0730.0730.0000.0000.0000.000
119B279ILE00.0040.01213.677-0.063-0.0630.0000.0000.0000.000
120B280HIS0-0.005-0.01313.9710.0100.0100.0000.0000.0000.000
121B281THR00.0280.00515.683-0.017-0.0170.0000.0000.0000.000
122B282SER0-0.0090.00616.901-0.020-0.0200.0000.0000.0000.000
123B283ASN00.013-0.02519.4290.0150.0150.0000.0000.0000.000
124B284LEU0-0.053-0.02320.1220.0030.0030.0000.0000.0000.000
125B285ILE00.0440.01722.983-0.005-0.0050.0000.0000.0000.000
126B286HIS00.0650.01623.0040.0080.0080.0000.0000.0000.000
127B287ALA00.0440.00422.664-0.002-0.0020.0000.0000.0000.000
128B288ASP-1-0.802-0.87520.8840.0520.0520.0000.0000.0000.000
129B289TRP0-0.024-0.02414.0490.0070.0070.0000.0000.0000.000
130B290HIS00.0020.02018.665-0.001-0.0010.0000.0000.0000.000
131B291GLN0-0.015-0.03619.963-0.005-0.0050.0000.0000.0000.000
132B292LYS10.8410.92519.879-0.024-0.0240.0000.0000.0000.000
133B293THR0-0.024-0.02115.963-0.004-0.0040.0000.0000.0000.000
134B294GLN00.011-0.00915.7030.0060.0060.0000.0000.0000.000
135B295GLY00.012-0.00913.022-0.016-0.0160.0000.0000.0000.000
136B296ILE0-0.033-0.02610.0990.0120.0120.0000.0000.0000.000
137B297TRP00.0320.0189.753-0.028-0.0280.0000.0000.0000.000
138B298LEU0-0.026-0.0186.360-0.087-0.0870.0000.0000.0000.000
139B299SER00.0170.0268.9670.1440.1440.0000.0000.0000.000
140B300PRO00.0310.0189.5290.1440.1440.0000.0000.0000.000
141B301LEU0-0.048-0.02610.549-0.133-0.1330.0000.0000.0000.000
142B302TYR00.017-0.02212.564-0.004-0.0040.0000.0000.0000.000
143B303PRO00.0810.05615.946-0.037-0.0370.0000.0000.0000.000
144B304ARG10.9740.97218.303-0.200-0.2000.0000.0000.0000.000
145B305ILE0-0.053-0.03721.9520.0000.0000.0000.0000.0000.000
146B306ALA00.014-0.00824.394-0.010-0.0100.0000.0000.0000.000
147B307ASP-1-0.841-0.90426.6330.1120.1120.0000.0000.0000.000
148B308GLY00.0300.02429.443-0.005-0.0050.0000.0000.0000.000
149B309THR0-0.061-0.02828.649-0.007-0.0070.0000.0000.0000.000
150B310HIS0-0.025-0.00829.8760.0100.0100.0000.0000.0000.000
151B311LYS10.9140.92722.242-0.200-0.2000.0000.0000.0000.000
152B312SER00.0030.03526.015-0.001-0.0010.0000.0000.0000.000
153B313GLY0-0.001-0.01222.9810.0040.0040.0000.0000.0000.000
154B314GLU-1-0.779-0.89321.6760.2120.2120.0000.0000.0000.000
155B315SER0-0.010-0.00418.089-0.009-0.0090.0000.0000.0000.000
156B316PRO00.0180.00019.051-0.021-0.0210.0000.0000.0000.000
157B317THR0-0.064-0.04417.845-0.015-0.0150.0000.0000.0000.000
158B318HIS0-0.032-0.01920.924-0.006-0.0060.0000.0000.0000.000
159B319PHE00.0230.02217.010-0.002-0.0020.0000.0000.0000.000
160B320LYS10.8030.90220.651-0.199-0.1990.0000.0000.0000.000
161B321ALA00.007-0.00622.408-0.010-0.0100.0000.0000.0000.000
162B322ASP-1-0.779-0.86823.0480.1180.1180.0000.0000.0000.000
163B323LEU0-0.020-0.01219.738-0.009-0.0090.0000.0000.0000.000
164B324ILE0-0.010-0.00923.280-0.012-0.0120.0000.0000.0000.000
165B325SER00.0090.00426.398-0.013-0.0130.0000.0000.0000.000
166B326TYR0-0.040-0.02624.504-0.011-0.0110.0000.0000.0000.000
167B327LEU0-0.013-0.01823.877-0.009-0.0090.0000.0000.0000.000
168B328MET00.0040.01127.587-0.008-0.0080.0000.0000.0000.000
169B329ALA0-0.0100.01330.482-0.008-0.0080.0000.0000.0000.000
170B330TYR0-0.033-0.03526.925-0.005-0.0050.0000.0000.0000.000
171B331ASN0-0.086-0.03432.207-0.006-0.0060.0000.0000.0000.000
172B332ALA00.0340.01832.207-0.005-0.0050.0000.0000.0000.000
173B333PRO00.0520.01233.2420.0060.0060.0000.0000.0000.000
174B334SER00.0670.02431.0500.0040.0040.0000.0000.0000.000
175B335LEU00.0090.00226.9810.0080.0080.0000.0000.0000.000
176B336LYS10.8240.92028.988-0.092-0.0920.0000.0000.0000.000
177B337GLU-1-0.868-0.94430.2630.1030.1030.0000.0000.0000.000
178B338TRP0-0.020-0.01521.7090.0140.0140.0000.0000.0000.000
179B339ILE0-0.043-0.02025.7850.0140.0140.0000.0000.0000.000
180B340ASP-1-0.761-0.87927.2710.1180.1180.0000.0000.0000.000
181B341VAL00.0020.01022.9760.0050.0050.0000.0000.0000.000
182B342ILE0-0.0010.00521.8550.0150.0150.0000.0000.0000.000
183B343HIS00.0160.00223.7360.0170.0170.0000.0000.0000.000
184B344LYS10.8290.93925.465-0.141-0.1410.0000.0000.0000.000
185B345HIS0-0.011-0.01519.7580.0090.0090.0000.0000.0000.000
186B346ASP-1-0.782-0.86019.6230.2320.2320.0000.0000.0000.000
187B347LEU0-0.022-0.01517.5870.0390.0390.0000.0000.0000.000
188B348SER0-0.015-0.03217.9240.0240.0240.0000.0000.0000.000
189B349GLU-1-0.919-0.95711.7990.7650.7650.0000.0000.0000.000
190B350THR0-0.079-0.03313.8350.0760.0760.0000.0000.0000.000
191B351ASN00.0570.04610.658-0.057-0.0570.0000.0000.0000.000
192B352VAL0-0.0060.01312.833-0.054-0.0540.0000.0000.0000.000
193B353TYR00.027-0.00115.6720.0050.0050.0000.0000.0000.000
194B354LEU0-0.0040.02018.897-0.003-0.0030.0000.0000.0000.000
195B355ILE00.000-0.00520.451-0.020-0.0200.0000.0000.0000.000
196B356GLY00.0320.01822.5950.0040.0040.0000.0000.0000.000
197B357SER0-0.052-0.04324.893-0.009-0.0090.0000.0000.0000.000
198B358THR00.0190.01128.0820.0040.0040.0000.0000.0000.000
199B359PRO0-0.007-0.00730.702-0.004-0.0040.0000.0000.0000.000
200B360GLY00.0260.00434.1260.0020.0020.0000.0000.0000.000
201B361ARG10.7880.87236.907-0.037-0.0370.0000.0000.0000.000
202B362PHE00.0170.01334.184-0.001-0.0010.0000.0000.0000.000
203B363GLN00.0470.01238.071-0.003-0.0030.0000.0000.0000.000
204B364GLY00.0450.01839.5970.0020.0020.0000.0000.0000.000
205B365SER00.0490.01336.6720.0000.0000.0000.0000.0000.000
206B366GLN00.0500.02035.0130.0050.0050.0000.0000.0000.000
207B367LYS10.8210.93534.339-0.038-0.0380.0000.0000.0000.000
208B368ASP-1-0.860-0.94031.9010.0480.0480.0000.0000.0000.000
209B369ASN0-0.0010.00730.0380.0040.0040.0000.0000.0000.000
210B370TRP00.0130.00027.0090.0080.0080.0000.0000.0000.000
211B371GLY00.0620.03528.364-0.006-0.0060.0000.0000.0000.000
212B372HIS10.8030.87728.067-0.032-0.0320.0000.0000.0000.000
213B373PHE00.003-0.00529.450-0.004-0.0040.0000.0000.0000.000
214B374ARG10.7670.88223.407-0.114-0.1140.0000.0000.0000.000
215B375LEU00.005-0.00523.4250.0030.0030.0000.0000.0000.000
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