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: K9273

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 OptAll
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 -1959970.644595
FMO2-HF: Nuclear repulsion 1886238.993516
FMO2-HF: Total energy -73731.65108
FMO2-MP2: Total energy -73947.294677


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.
-16.524-7.7754.256-3.159-9.8470.009
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 : 0.014 / q_NPA : -0.003
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-1-0.754-0.8563.484-0.3152.813-0.001-1.488-1.6390.004
4A489PRO00.0660.0535.361-0.516-0.435-0.001-0.009-0.0710.000
5A490ARG10.9060.9498.367-1.972-1.9720.0000.0000.0000.000
6A491LYS10.7950.8774.446-4.538-4.341-0.001-0.016-0.1800.000
7A492SER00.002-0.0215.567-0.312-0.3120.0000.0000.0000.000
8A493GLU-1-0.819-0.8777.525-0.423-0.4230.0000.0000.0000.000
9A494LEU0-0.012-0.0069.027-0.013-0.0130.0000.0000.0000.000
10A495TYR00.024-0.01210.4720.0080.0080.0000.0000.0000.000
11A496VAL0-0.030-0.02212.9270.0090.0090.0000.0000.0000.000
12A497VAL0-0.0030.00114.638-0.001-0.0010.0000.0000.0000.000
13A498GLU-1-0.816-0.90717.304-0.094-0.0940.0000.0000.0000.000
14A499GLY00.0330.01421.071-0.015-0.0150.0000.0000.0000.000
15A500ASP-1-0.926-0.96523.032-0.098-0.0980.0000.0000.0000.000
16A513MET00.0320.0252.682-0.5410.6400.232-0.482-0.931-0.004
17A514PHE0-0.065-0.0302.645-6.601-1.8943.864-2.217-6.3540.006
18A515GLN0-0.023-0.0423.7200.060-0.4850.1631.053-0.6720.003
19A516ALA0-0.0050.0156.169-0.230-0.2300.0000.0000.0000.000
20A517ILE00.0180.0008.4800.0100.0100.0000.0000.0000.000
21A518LEU0-0.031-0.00711.3580.0080.0080.0000.0000.0000.000
22A519PRO0-0.0040.01014.943-0.008-0.0080.0000.0000.0000.000
23A520LEU0-0.002-0.00418.2670.0270.0270.0000.0000.0000.000
24A521ARG10.8390.90821.4850.1130.1130.0000.0000.0000.000
25A522GLY00.0910.05824.7840.0130.0130.0000.0000.0000.000
26A523LYS10.8430.92327.9950.0810.0810.0000.0000.0000.000
27A533ASP-1-0.805-0.91232.285-0.001-0.0010.0000.0000.0000.000
28A534ARG10.9140.94232.9720.0110.0110.0000.0000.0000.000
29A535VAL00.0630.03628.534-0.001-0.0010.0000.0000.0000.000
30A536LEU00.0290.02127.113-0.006-0.0060.0000.0000.0000.000
31A537LYS10.8960.94827.773-0.002-0.0020.0000.0000.0000.000
32A538ASN00.0170.02825.398-0.008-0.0080.0000.0000.0000.000
33A539THR00.0670.01622.9680.0060.0060.0000.0000.0000.000
34A540GLU-1-0.816-0.89720.731-0.114-0.1140.0000.0000.0000.000
35A541VAL00.0400.02420.5350.0020.0020.0000.0000.0000.000
36A542GLN0-0.001-0.00621.9960.0070.0070.0000.0000.0000.000
37A543ALA0-0.0050.01917.5580.0190.0190.0000.0000.0000.000
38A544ILE00.0240.00717.2710.0190.0190.0000.0000.0000.000
39A545ILE00.008-0.00817.9530.0280.0280.0000.0000.0000.000
40A546THR0-0.057-0.03617.8500.0290.0290.0000.0000.0000.000
41A547ALA0-0.049-0.02113.7450.0380.0380.0000.0000.0000.000
42A548LEU00.024-0.00214.5100.0620.0620.0000.0000.0000.000
43A549GLY0-0.0140.00416.2960.0570.0570.0000.0000.0000.000
44A550THR0-0.026-0.02317.2710.0010.0010.0000.0000.0000.000
45A551GLY00.0270.03719.965-0.004-0.0040.0000.0000.0000.000
46A552ILE0-0.035-0.03322.999-0.002-0.0020.0000.0000.0000.000
47A553HIS0-0.002-0.00426.1140.0010.0010.0000.0000.0000.000
48A554ASP-1-0.878-0.93328.7970.0850.0850.0000.0000.0000.000
49A555GLU-1-0.969-0.99327.0100.0930.0930.0000.0000.0000.000
50A556PHE0-0.098-0.03222.0400.0210.0210.0000.0000.0000.000
51A557ASP-1-0.794-0.89521.7690.2710.2710.0000.0000.0000.000
52A558ILE00.019-0.00119.6810.0200.0200.0000.0000.0000.000
53A559GLY0-0.023-0.01018.3670.0420.0420.0000.0000.0000.000
54A560LYS10.8050.88816.585-0.189-0.1890.0000.0000.0000.000
55A561LEU0-0.0160.00314.976-0.012-0.0120.0000.0000.0000.000
56A562ARG10.8100.9017.051-0.706-0.7060.0000.0000.0000.000
57A563TYR0-0.024-0.0218.4980.1430.1430.0000.0000.0000.000
58A564HIS00.0100.01910.931-0.090-0.0900.0000.0000.0000.000
59A565LYS10.9210.97912.165-0.102-0.1020.0000.0000.0000.000
60A566ILE00.0440.02313.061-0.002-0.0020.0000.0000.0000.000
61A567VAL0-0.020-0.00613.1540.0090.0090.0000.0000.0000.000
62A568LEU00.0350.02515.619-0.037-0.0370.0000.0000.0000.000
63A569MET0-0.009-0.00414.793-0.011-0.0110.0000.0000.0000.000
64A570ALA00.0510.03218.738-0.004-0.0040.0000.0000.0000.000
65A571ASP-1-0.780-0.89422.239-0.172-0.1720.0000.0000.0000.000
66A572ALA0-0.018-0.01025.1880.0130.0130.0000.0000.0000.000
67A573ASP-1-0.872-0.92927.505-0.114-0.1140.0000.0000.0000.000
68A574VAL00.009-0.00628.2340.0040.0040.0000.0000.0000.000
69A575ASP-1-0.850-0.92029.768-0.083-0.0830.0000.0000.0000.000
70A576GLY0-0.064-0.03730.7930.0080.0080.0000.0000.0000.000
71A577GLN0-0.024-0.00825.871-0.004-0.0040.0000.0000.0000.000
72A578HIS00.0350.02428.0220.0080.0080.0000.0000.0000.000
73A579ILE0-0.008-0.00123.9310.0100.0100.0000.0000.0000.000
74A580SER00.020-0.01122.8950.0110.0110.0000.0000.0000.000
75A581THR0-0.050-0.01725.0150.0130.0130.0000.0000.0000.000
76A582LEU0-0.0180.01126.5770.0100.0100.0000.0000.0000.000
77A583LEU0-0.003-0.00820.1470.0100.0100.0000.0000.0000.000
78A584LEU00.020-0.00123.2400.0170.0170.0000.0000.0000.000
79A585THR0-0.0050.01625.7170.0140.0140.0000.0000.0000.000
80A586LEU0-0.015-0.01526.0130.0110.0110.0000.0000.0000.000
81A587LEU0-0.015-0.01821.3020.0150.0150.0000.0000.0000.000
82A588PHE00.020-0.00125.4490.0150.0150.0000.0000.0000.000
83A589ARG10.7700.85628.717-0.002-0.0020.0000.0000.0000.000
84A590PHE00.0040.01027.6400.0000.0000.0000.0000.0000.000
85A591MET0-0.034-0.00821.2710.0030.0030.0000.0000.0000.000
86A592ARG10.8920.97324.488-0.041-0.0410.0000.0000.0000.000
87A593PRO00.0530.02723.867-0.001-0.0010.0000.0000.0000.000
88A594LEU00.0000.00019.0970.0190.0190.0000.0000.0000.000
89A595ILE0-0.014-0.00521.3430.0000.0000.0000.0000.0000.000
90A596GLU-1-0.872-0.94823.8410.0910.0910.0000.0000.0000.000
91A597ASN0-0.109-0.05621.2870.0140.0140.0000.0000.0000.000
92A598GLY00.0010.00520.4810.0240.0240.0000.0000.0000.000
93A599HIS10.8160.89515.946-0.254-0.2540.0000.0000.0000.000
94A600VAL00.0090.01417.123-0.021-0.0210.0000.0000.0000.000
95A601PHE0-0.013-0.02216.8200.0020.0020.0000.0000.0000.000
96A602LEU00.0210.02518.956-0.005-0.0050.0000.0000.0000.000
97A603ALA00.005-0.00716.043-0.004-0.0040.0000.0000.0000.000
98A604GLN00.005-0.01418.1810.0100.0100.0000.0000.0000.000
99A605PRO00.0380.01519.746-0.024-0.0240.0000.0000.0000.000
100A606PRO00.0000.00919.5920.0230.0230.0000.0000.0000.000
101A607LEU00.0090.00922.7610.0040.0040.0000.0000.0000.000
102A608TYR0-0.095-0.08325.8480.0140.0140.0000.0000.0000.000
103A609LYS10.8460.91823.2460.2240.2240.0000.0000.0000.000
104A610LEU0-0.047-0.02126.1080.0150.0150.0000.0000.0000.000
105A611LYS10.8390.90427.6410.1360.1360.0000.0000.0000.000
106A612TRP0-0.037-0.04327.5660.0190.0190.0000.0000.0000.000
107A613GLN0-0.019-0.02329.990-0.002-0.0020.0000.0000.0000.000
108A614ARG10.8800.92630.9590.1100.1100.0000.0000.0000.000
109A615SER0-0.039-0.01927.8130.0090.0090.0000.0000.0000.000
110A616ASP-1-0.852-0.90822.563-0.227-0.2270.0000.0000.0000.000
111A617PRO0-0.044-0.01822.2920.0140.0140.0000.0000.0000.000
112A618GLU-1-0.801-0.87322.971-0.174-0.1740.0000.0000.0000.000
113A619PHE00.021-0.00420.6450.0090.0090.0000.0000.0000.000
114A620ALA0-0.030-0.00523.5960.0060.0060.0000.0000.0000.000
115A621TYR00.010-0.01618.2110.0040.0040.0000.0000.0000.000
116A622SER0-0.004-0.00124.8670.0170.0170.0000.0000.0000.000
117A623ASP-1-0.772-0.85328.589-0.103-0.1030.0000.0000.0000.000
118A624ARG10.9860.98831.8050.0680.0680.0000.0000.0000.000
119A625GLU-1-0.831-0.90224.412-0.158-0.1580.0000.0000.0000.000
120A626ARG10.8070.87129.1960.0980.0980.0000.0000.0000.000
121A627ASP-1-0.848-0.89730.227-0.091-0.0910.0000.0000.0000.000
122A628GLY00.0060.00331.7360.0040.0040.0000.0000.0000.000
123A629LEU00.0310.00825.3810.0030.0030.0000.0000.0000.000
124A630LEU0-0.022-0.01030.0200.0000.0000.0000.0000.0000.000
125A631GLU-1-0.876-0.92033.048-0.068-0.0680.0000.0000.0000.000
126A632ALA00.005-0.00531.1350.0040.0040.0000.0000.0000.000
127A633GLY0-0.006-0.01032.1370.0000.0000.0000.0000.0000.000
128A634LEU0-0.030-0.02032.6620.0040.0040.0000.0000.0000.000
129A635LYS10.7960.87536.3830.0750.0750.0000.0000.0000.000
130A636ALA0-0.0230.01433.3670.0040.0040.0000.0000.0000.000
131A637GLY0-0.031-0.01235.297-0.002-0.0020.0000.0000.0000.000
132A638LYS10.8250.92528.1420.1420.1420.0000.0000.0000.000
133A639LYS10.9520.96734.2030.0860.0860.0000.0000.0000.000
134A640ILE00.0300.02131.327-0.007-0.0070.0000.0000.0000.000
135A641ASN0-0.022-0.01934.8050.0120.0120.0000.0000.0000.000
136A642LYS10.8510.90736.0640.0720.0720.0000.0000.0000.000
137A643GLU-1-0.875-0.92438.158-0.076-0.0760.0000.0000.0000.000
138A644ASP-1-0.805-0.88733.492-0.124-0.1240.0000.0000.0000.000
139A645GLY00.0080.02132.572-0.008-0.0080.0000.0000.0000.000
140A646ILE0-0.006-0.00830.727-0.010-0.0100.0000.0000.0000.000
141A647GLN00.0130.00926.2090.0090.0090.0000.0000.0000.000
142A648ARG10.9160.95128.2660.1020.1020.0000.0000.0000.000
143A649TYR0-0.0090.00222.5820.0000.0000.0000.0000.0000.000
144A650LYS10.7720.84927.4350.1270.1270.0000.0000.0000.000
145A651GLY00.0470.05126.287-0.001-0.0010.0000.0000.0000.000
146A652LEU00.0040.00419.148-0.016-0.0160.0000.0000.0000.000
147A653GLY0-0.015-0.00719.6150.0060.0060.0000.0000.0000.000
148A654GLU-1-0.980-0.98520.653-0.173-0.1730.0000.0000.0000.000
149A655MET0-0.054-0.03519.805-0.003-0.0030.0000.0000.0000.000
150A656ASP-1-0.771-0.87618.464-0.351-0.3510.0000.0000.0000.000
151A657ALA0-0.024-0.00615.700-0.019-0.0190.0000.0000.0000.000
152A658LYS10.8150.89813.9250.3050.3050.0000.0000.0000.000
153A659GLU-1-0.770-0.86714.643-0.309-0.3090.0000.0000.0000.000
154A660LEU00.0480.01714.800-0.003-0.0030.0000.0000.0000.000
155A661TRP00.0090.0116.5760.0490.0490.0000.0000.0000.000
156A662GLU-1-0.899-0.97712.396-0.540-0.5400.0000.0000.0000.000
157A663THR0-0.0010.01413.7720.0410.0410.0000.0000.0000.000
158A664THR0-0.049-0.03014.3630.0500.0500.0000.0000.0000.000
159A665MET0-0.0560.0118.7880.0880.0880.0000.0000.0000.000
160A666ASP-1-0.742-0.8469.902-0.794-0.7940.0000.0000.0000.000
161A667PRO0-0.059-0.0497.7280.1290.1290.0000.0000.0000.000
162A668SER0-0.097-0.06610.7200.1080.1080.0000.0000.0000.000
163A669VAL0-0.025-0.01713.6210.0740.0740.0000.0000.0000.000
164A670ARG10.7370.87610.7290.4670.4670.0000.0000.0000.000
165A671VAL00.0220.01815.7860.0370.0370.0000.0000.0000.000
166A672LEU0-0.027-0.02314.342-0.002-0.0020.0000.0000.0000.000
167A673ARG10.7650.85418.4490.0640.0640.0000.0000.0000.000
168A674GLN0-0.0090.00520.4850.0000.0000.0000.0000.0000.000
169A675VAL0-0.014-0.00721.382-0.008-0.0080.0000.0000.0000.000
170A676THR0-0.015-0.03023.8590.0180.0180.0000.0000.0000.000
171A677LEU00.024-0.01226.922-0.003-0.0030.0000.0000.0000.000
172A678ASP-1-0.881-0.93429.5100.0180.0180.0000.0000.0000.000
173A679ASP-1-0.760-0.82827.221-0.024-0.0240.0000.0000.0000.000
174A680ALA0-0.003-0.00127.281-0.005-0.0050.0000.0000.0000.000
175A681ALA0-0.0060.00429.155-0.001-0.0010.0000.0000.0000.000
176A682ALA00.0160.01132.475-0.002-0.0020.0000.0000.0000.000
177A683ALA00.0020.00529.477-0.004-0.0040.0000.0000.0000.000
178A684ASP-1-0.822-0.91531.4820.0080.0080.0000.0000.0000.000
179A685GLU-1-0.926-0.95533.484-0.007-0.0070.0000.0000.0000.000
180A686LEU00.0100.00532.412-0.002-0.0020.0000.0000.0000.000
181A687PHE0-0.024-0.03032.516-0.003-0.0030.0000.0000.0000.000
182A688SER0-0.035-0.02534.5710.0010.0010.0000.0000.0000.000
183A689ILE0-0.018-0.00238.0040.0000.0000.0000.0000.0000.000
184A690LEU0-0.095-0.03534.284-0.002-0.0020.0000.0000.0000.000
185A691MET0-0.116-0.05135.642-0.001-0.0010.0000.0000.0000.000