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: QYN7Y

Calculation Name: 2ZJT-A-Xray372

Preferred Name: DNA gyrase subunit A/DNA gyrase subunit B

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZJT

Chain ID: A

ChEMBL ID: CHEMBL3430898

UniProt ID: P9WG45

Base Structure: X-ray

Registration Date: 2023-06-22

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1960223.201321
FMO2-HF: Nuclear repulsion 1886492.653728
FMO2-HF: Total energy -73730.547593
FMO2-MP2: Total energy -73946.32863


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(A:486:PHE)


Summations of interaction energy for fragment #1(A:486:PHE)
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.
-11.546-2.8662.377-3.639-7.4150.005
Interaction energy analysis for fragmet #1(A:486:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.005
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].
3A488ASP-1-0.785-0.8603.196-2.8860.523-0.019-1.653-1.7370.002
4A489PRO00.0970.0584.863-0.547-0.456-0.001-0.009-0.0800.000
5A490ARG10.8910.9307.219-0.403-0.4030.0000.0000.0000.000
6A491LYS10.7780.8664.4260.0820.251-0.001-0.012-0.1550.000
7A492SER00.010-0.0076.455-0.028-0.0280.0000.0000.0000.000
8A493GLU-1-0.803-0.8778.049-0.605-0.6050.0000.0000.0000.000
9A494LEU0-0.0080.0119.3690.0360.0360.0000.0000.0000.000
10A495TYR00.006-0.02310.738-0.035-0.0350.0000.0000.0000.000
11A496VAL0-0.016-0.01913.2180.0300.0300.0000.0000.0000.000
12A497VAL0-0.013-0.00115.032-0.012-0.0120.0000.0000.0000.000
13A498GLU-1-0.817-0.91717.745-0.070-0.0700.0000.0000.0000.000
14A499GLY00.0010.01621.477-0.009-0.0090.0000.0000.0000.000
15A500ASP-1-0.927-0.98022.767-0.055-0.0550.0000.0000.0000.000
16A513MET00.0310.0232.269-0.5330.3430.781-0.598-1.059-0.005
17A514PHE0-0.069-0.0352.635-4.597-0.7651.589-1.361-4.0590.007
18A515GLN0-0.023-0.0254.106-0.523-0.2200.028-0.006-0.3250.001
19A516ALA0-0.0010.0156.444-0.175-0.1750.0000.0000.0000.000
20A517ILE00.012-0.0058.623-0.041-0.0410.0000.0000.0000.000
21A518LEU0-0.019-0.01111.7300.0490.0490.0000.0000.0000.000
22A519PRO0-0.0130.01114.997-0.019-0.0190.0000.0000.0000.000
23A520LEU00.002-0.01018.3840.0290.0290.0000.0000.0000.000
24A521ARG10.8340.90921.8120.0300.0300.0000.0000.0000.000
25A522GLY00.0550.03224.9630.0100.0100.0000.0000.0000.000
26A523LYS10.9050.96028.3120.0260.0260.0000.0000.0000.000
27A533ASP-1-0.843-0.93932.2580.0170.0170.0000.0000.0000.000
28A534ARG10.9130.94833.090-0.017-0.0170.0000.0000.0000.000
29A535VAL00.0950.04328.6550.0040.0040.0000.0000.0000.000
30A536LEU00.0060.02027.2340.0020.0020.0000.0000.0000.000
31A537LYS10.9140.95127.410-0.045-0.0450.0000.0000.0000.000
32A538ASN0-0.0020.01825.5860.0030.0030.0000.0000.0000.000
33A539THR00.0670.00823.3180.0050.0050.0000.0000.0000.000
34A540GLU-1-0.795-0.87820.969-0.020-0.0200.0000.0000.0000.000
35A541VAL00.0350.02420.7210.0040.0040.0000.0000.0000.000
36A542GLN00.0170.01021.9780.0050.0050.0000.0000.0000.000
37A543ALA0-0.0070.02517.7420.0280.0280.0000.0000.0000.000
38A544ILE00.0160.00417.3500.0350.0350.0000.0000.0000.000
39A545ILE00.000-0.01318.2130.0210.0210.0000.0000.0000.000
40A546THR0-0.068-0.04818.1660.0230.0230.0000.0000.0000.000
41A547ALA0-0.045-0.02214.0420.0490.0490.0000.0000.0000.000
42A548LEU0-0.004-0.00914.8310.0650.0650.0000.0000.0000.000
43A549GLY0-0.002-0.00816.5250.0290.0290.0000.0000.0000.000
44A550THR00.0060.02217.6310.0070.0070.0000.0000.0000.000
45A551GLY00.0110.02819.874-0.013-0.0130.0000.0000.0000.000
46A552ILE0-0.025-0.03523.091-0.010-0.0100.0000.0000.0000.000
47A553HIS0-0.012-0.02226.1660.0000.0000.0000.0000.0000.000
48A554ASP-1-0.867-0.92028.7670.0710.0710.0000.0000.0000.000
49A555GLU-1-1.000-1.00126.3980.1150.1150.0000.0000.0000.000
50A556PHE0-0.083-0.03021.5460.0190.0190.0000.0000.0000.000
51A557ASP-1-0.761-0.88221.4070.2060.2060.0000.0000.0000.000
52A558ILE0-0.033-0.02519.0540.0220.0220.0000.0000.0000.000
53A559GLY0-0.016-0.00517.9000.0140.0140.0000.0000.0000.000
54A560LYS10.7920.87716.144-0.207-0.2070.0000.0000.0000.000
55A561LEU00.0040.02314.7680.0270.0270.0000.0000.0000.000
56A562ARG10.8020.8957.133-1.353-1.3530.0000.0000.0000.000
57A563TYR0-0.024-0.0198.8370.1930.1930.0000.0000.0000.000
58A564HIS00.0100.02111.344-0.023-0.0230.0000.0000.0000.000
59A565LYS10.9220.98312.4650.1940.1940.0000.0000.0000.000
60A566ILE00.0310.01113.5390.0260.0260.0000.0000.0000.000
61A567VAL0-0.020-0.00613.553-0.004-0.0040.0000.0000.0000.000
62A568LEU00.0010.00715.9360.0000.0000.0000.0000.0000.000
63A569MET0-0.017-0.02015.023-0.021-0.0210.0000.0000.0000.000
64A570ALA00.0550.02918.8640.0080.0080.0000.0000.0000.000
65A571ASP-1-0.798-0.89922.260-0.158-0.1580.0000.0000.0000.000
66A572ALA0-0.070-0.04025.2400.0110.0110.0000.0000.0000.000
67A573ASP-1-0.881-0.95527.562-0.111-0.1110.0000.0000.0000.000
68A574VAL0-0.027-0.00728.5260.0070.0070.0000.0000.0000.000
69A575ASP-1-0.922-0.97829.955-0.063-0.0630.0000.0000.0000.000
70A576GLY00.0270.02230.5340.0040.0040.0000.0000.0000.000
71A577GLN0-0.014-0.00926.344-0.005-0.0050.0000.0000.0000.000
72A578HIS00.0440.03428.2080.0050.0050.0000.0000.0000.000
73A579ILE00.005-0.00424.6660.0110.0110.0000.0000.0000.000
74A580SER00.033-0.00723.1030.0040.0040.0000.0000.0000.000
75A581THR0-0.109-0.04425.4580.0020.0020.0000.0000.0000.000
76A582LEU0-0.0170.01426.9140.0080.0080.0000.0000.0000.000
77A583LEU0-0.012-0.01620.5410.0120.0120.0000.0000.0000.000
78A584LEU00.0120.00823.9540.0120.0120.0000.0000.0000.000
79A585THR00.0000.04526.0830.0110.0110.0000.0000.0000.000
80A586LEU0-0.016-0.01925.7620.0100.0100.0000.0000.0000.000
81A587LEU0-0.005-0.01421.5240.0110.0110.0000.0000.0000.000
82A588PHE00.0660.00725.5920.0100.0100.0000.0000.0000.000
83A589ARG10.7590.86828.675-0.004-0.0040.0000.0000.0000.000
84A590PHE00.016-0.00227.5830.0040.0040.0000.0000.0000.000
85A591MET0-0.054-0.02021.3300.0080.0080.0000.0000.0000.000
86A592ARG10.9541.01424.690-0.017-0.0170.0000.0000.0000.000
87A593PRO00.0360.03123.842-0.010-0.0100.0000.0000.0000.000
88A594LEU0-0.014-0.00619.250-0.004-0.0040.0000.0000.0000.000
89A595ILE0-0.009-0.01121.951-0.015-0.0150.0000.0000.0000.000
90A596GLU-1-0.881-0.94924.3810.0110.0110.0000.0000.0000.000
91A597ASN0-0.152-0.08021.220-0.006-0.0060.0000.0000.0000.000
92A598GLY00.0140.02121.182-0.005-0.0050.0000.0000.0000.000
93A599HIS10.8350.90516.579-0.043-0.0430.0000.0000.0000.000
94A600VAL00.0100.01517.665-0.017-0.0170.0000.0000.0000.000
95A601PHE00.007-0.01217.369-0.022-0.0220.0000.0000.0000.000
96A602LEU00.0360.04119.5090.0090.0090.0000.0000.0000.000
97A603ALA00.005-0.00416.434-0.017-0.0170.0000.0000.0000.000
98A604GLN00.006-0.00718.5540.0140.0140.0000.0000.0000.000
99A605PRO00.0350.01119.536-0.028-0.0280.0000.0000.0000.000
100A606PRO00.0100.01219.4040.0140.0140.0000.0000.0000.000
101A607LEU0-0.013-0.01022.3550.0100.0100.0000.0000.0000.000
102A608TYR0-0.111-0.09225.5900.0190.0190.0000.0000.0000.000
103A609LYS10.8370.91223.4280.2050.2050.0000.0000.0000.000
104A610LEU0-0.051-0.03526.1400.0170.0170.0000.0000.0000.000
105A611LYS10.8550.92427.5890.1230.1230.0000.0000.0000.000
106A612TRP0-0.059-0.04127.5980.0210.0210.0000.0000.0000.000
107A613GLN0-0.018-0.03029.9810.0000.0000.0000.0000.0000.000
108A614ARG10.8690.92030.6220.1130.1130.0000.0000.0000.000
109A615SER0-0.0100.00527.8830.0050.0050.0000.0000.0000.000
110A616ASP-1-0.868-0.91722.468-0.233-0.2330.0000.0000.0000.000
111A617PRO0-0.036-0.02622.6860.0100.0100.0000.0000.0000.000
112A618GLU-1-0.811-0.88623.371-0.200-0.2000.0000.0000.0000.000
113A619PHE00.0150.00320.0070.0150.0150.0000.0000.0000.000
114A620ALA0-0.0220.00923.6300.0000.0000.0000.0000.0000.000
115A621TYR00.010-0.01718.1950.0050.0050.0000.0000.0000.000
116A622SER00.0210.01124.9840.0160.0160.0000.0000.0000.000
117A623ASP-1-0.790-0.86728.663-0.116-0.1160.0000.0000.0000.000
118A624ARG10.9650.97631.8930.1050.1050.0000.0000.0000.000
119A625GLU-1-0.846-0.91624.750-0.203-0.2030.0000.0000.0000.000
120A626ARG10.8410.89229.4870.1120.1120.0000.0000.0000.000
121A627ASP-1-0.871-0.91130.694-0.109-0.1090.0000.0000.0000.000
122A628GLY00.0240.01632.4380.0040.0040.0000.0000.0000.000
123A629LEU00.0610.03125.7690.0030.0030.0000.0000.0000.000
124A630LEU0-0.029-0.01230.4530.0010.0010.0000.0000.0000.000
125A631GLU-1-0.899-0.93133.216-0.096-0.0960.0000.0000.0000.000
126A632ALA00.010-0.00531.3360.0050.0050.0000.0000.0000.000
127A633GLY00.008-0.00832.1370.0010.0010.0000.0000.0000.000
128A634LEU0-0.024-0.02032.6950.0050.0050.0000.0000.0000.000
129A635LYS10.7780.88936.3890.0980.0980.0000.0000.0000.000
130A636ALA00.0010.01633.4500.0030.0030.0000.0000.0000.000
131A637GLY0-0.057-0.02635.232-0.001-0.0010.0000.0000.0000.000
132A638LYS10.8410.94328.4570.1670.1670.0000.0000.0000.000
133A639LYS10.9490.95734.6070.0940.0940.0000.0000.0000.000
134A640ILE00.0330.01831.619-0.006-0.0060.0000.0000.0000.000
135A641ASN0-0.005-0.00635.0980.0090.0090.0000.0000.0000.000
136A642LYS10.9520.96536.2750.0720.0720.0000.0000.0000.000
137A643GLU-1-0.965-0.97138.603-0.076-0.0760.0000.0000.0000.000
138A644ASP-1-0.835-0.91634.092-0.111-0.1110.0000.0000.0000.000
139A645GLY00.0120.02332.984-0.007-0.0070.0000.0000.0000.000
140A646ILE0-0.025-0.02730.496-0.010-0.0100.0000.0000.0000.000
141A647GLN0-0.0010.01326.3950.0080.0080.0000.0000.0000.000
142A648ARG10.9580.95428.7970.1040.1040.0000.0000.0000.000
143A649TYR0-0.012-0.00622.5460.0070.0070.0000.0000.0000.000
144A650LYS10.8710.93827.3250.1070.1070.0000.0000.0000.000
145A651GLY00.0640.05026.7620.0020.0020.0000.0000.0000.000
146A652LEU00.0580.01819.444-0.019-0.0190.0000.0000.0000.000
147A653GLY0-0.0160.01819.7280.0100.0100.0000.0000.0000.000
148A654GLU-1-1.036-1.02920.782-0.134-0.1340.0000.0000.0000.000
149A655MET0-0.079-0.02819.746-0.006-0.0060.0000.0000.0000.000
150A656ASP-1-0.717-0.87218.799-0.287-0.2870.0000.0000.0000.000
151A657ALA0-0.0160.01115.076-0.030-0.0300.0000.0000.0000.000
152A658LYS10.8360.87413.7390.3240.3240.0000.0000.0000.000
153A659GLU-1-0.738-0.83714.732-0.264-0.2640.0000.0000.0000.000
154A660LEU00.002-0.00715.1590.0170.0170.0000.0000.0000.000
155A661TRP0-0.019-0.0016.6410.0530.0530.0000.0000.0000.000
156A662GLU-1-0.899-0.96312.609-0.514-0.5140.0000.0000.0000.000
157A663THR00.0000.01313.6910.0190.0190.0000.0000.0000.000
158A664THR0-0.029-0.01914.4490.0350.0350.0000.0000.0000.000
159A665MET0-0.083-0.0149.0250.0710.0710.0000.0000.0000.000
160A666ASP-1-0.758-0.8509.836-0.906-0.9060.0000.0000.0000.000
161A667PRO0-0.073-0.0568.3310.1130.1130.0000.0000.0000.000
162A668SER0-0.098-0.06111.4490.0810.0810.0000.0000.0000.000
163A669VAL0-0.007-0.00713.9330.0600.0600.0000.0000.0000.000
164A670ARG10.7440.87911.1380.5910.5910.0000.0000.0000.000
165A671VAL00.0400.01416.1210.0200.0200.0000.0000.0000.000
166A672LEU0-0.047-0.02614.7970.0150.0150.0000.0000.0000.000
167A673ARG10.8060.87718.7770.1160.1160.0000.0000.0000.000
168A674GLN0-0.031-0.02220.552-0.003-0.0030.0000.0000.0000.000
169A675VAL0-0.0110.00421.9190.0040.0040.0000.0000.0000.000
170A676THR0-0.015-0.02624.2860.0110.0110.0000.0000.0000.000
171A677LEU00.040-0.00527.1780.0020.0020.0000.0000.0000.000
172A678ASP-1-0.913-0.94129.613-0.034-0.0340.0000.0000.0000.000
173A679ASP-1-0.749-0.83727.542-0.077-0.0770.0000.0000.0000.000
174A680ALA0-0.030-0.02627.4890.0010.0010.0000.0000.0000.000
175A681ALA00.0060.01629.2610.0050.0050.0000.0000.0000.000
176A682ALA00.0180.01732.5150.0020.0020.0000.0000.0000.000
177A683ALA0-0.0040.01029.4310.0020.0020.0000.0000.0000.000
178A684ASP-1-0.791-0.91831.4290.0030.0030.0000.0000.0000.000
179A685GLU-1-0.909-0.95633.324-0.020-0.0200.0000.0000.0000.000
180A686LEU0-0.013-0.01232.9200.0010.0010.0000.0000.0000.000
181A687PHE0-0.012-0.01532.7240.0010.0010.0000.0000.0000.000
182A688SER0-0.059-0.03834.7970.0040.0040.0000.0000.0000.000
183A689ILE0-0.019-0.02438.0200.0010.0010.0000.0000.0000.000
184A690LEU0-0.116-0.02534.722-0.001-0.0010.0000.0000.0000.000
185A691MET0-0.081-0.03035.9960.0030.0030.0000.0000.0000.000