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: R9YN8

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1961427.302993
FMO2-HF: Nuclear repulsion 1887698.412598
FMO2-HF: Total energy -73728.890396
FMO2-MP2: Total energy -73944.84225


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.
-13.329-4.3631.195-3.648-6.514-0.001
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 : -0.006
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-1-0.863-0.9223.257-2.4921.049-0.024-1.730-1.7880.002
4A489PRO00.0680.0514.921-0.656-0.572-0.001-0.009-0.0740.000
5A490ARG10.9560.9887.307-0.508-0.5080.0000.0000.0000.000
6A491LYS10.8380.9054.4310.0030.168-0.001-0.011-0.1530.000
7A492SER00.031-0.0046.449-0.106-0.1060.0000.0000.0000.000
8A493GLU-1-0.778-0.8758.122-0.741-0.7410.0000.0000.0000.000
9A494LEU0-0.0050.0139.6110.0460.0460.0000.0000.0000.000
10A495TYR0-0.002-0.02210.375-0.052-0.0520.0000.0000.0000.000
11A496VAL0-0.017-0.01813.4520.0380.0380.0000.0000.0000.000
12A497VAL0-0.0080.00015.333-0.016-0.0160.0000.0000.0000.000
13A498GLU-1-0.857-0.95318.004-0.077-0.0770.0000.0000.0000.000
14A499GLY00.0050.01721.741-0.010-0.0100.0000.0000.0000.000
15A500ASP-1-0.930-0.98023.045-0.049-0.0490.0000.0000.0000.000
16A513MET0-0.014-0.0092.768-2.694-1.3860.510-0.737-1.081-0.009
17A514PHE0-0.029-0.0032.837-4.003-0.4560.692-1.125-3.1140.005
18A515GLN0-0.046-0.0314.236-0.562-0.2410.019-0.036-0.3040.001
19A516ALA00.0050.0176.672-0.132-0.1320.0000.0000.0000.000
20A517ILE00.012-0.0028.702-0.061-0.0610.0000.0000.0000.000
21A518LEU0-0.013-0.01111.7850.0590.0590.0000.0000.0000.000
22A519PRO0-0.0260.00315.108-0.024-0.0240.0000.0000.0000.000
23A520LEU00.009-0.00118.4680.0310.0310.0000.0000.0000.000
24A521ARG10.8880.95421.8940.0250.0250.0000.0000.0000.000
25A522GLY00.0690.03025.0340.0110.0110.0000.0000.0000.000
26A523LYS10.8890.95528.4700.0230.0230.0000.0000.0000.000
27A533ASP-1-0.882-0.95232.5670.0260.0260.0000.0000.0000.000
28A534ARG10.9180.95033.263-0.021-0.0210.0000.0000.0000.000
29A535VAL00.0960.04428.8220.0050.0050.0000.0000.0000.000
30A536LEU00.0070.01727.1650.0030.0030.0000.0000.0000.000
31A537LYS10.9250.95927.627-0.051-0.0510.0000.0000.0000.000
32A538ASN0-0.0040.01925.3340.0040.0040.0000.0000.0000.000
33A539THR00.056-0.00523.5090.0030.0030.0000.0000.0000.000
34A540GLU-1-0.844-0.92221.164-0.010-0.0100.0000.0000.0000.000
35A541VAL00.0370.02720.8940.0050.0050.0000.0000.0000.000
36A542GLN00.0230.01122.1610.0060.0060.0000.0000.0000.000
37A543ALA0-0.0050.04217.9280.0310.0310.0000.0000.0000.000
38A544ILE00.0190.00417.5220.0400.0400.0000.0000.0000.000
39A545ILE0-0.008-0.01418.3810.0220.0220.0000.0000.0000.000
40A546THR0-0.074-0.06518.0550.0230.0230.0000.0000.0000.000
41A547ALA0-0.049-0.02514.2610.0540.0540.0000.0000.0000.000
42A548LEU0-0.005-0.00814.8490.0710.0710.0000.0000.0000.000
43A549GLY00.003-0.00616.5910.0310.0310.0000.0000.0000.000
44A550THR00.0030.02017.6990.0060.0060.0000.0000.0000.000
45A551GLY00.0110.03419.939-0.014-0.0140.0000.0000.0000.000
46A552ILE0-0.026-0.03623.158-0.011-0.0110.0000.0000.0000.000
47A553HIS00.002-0.01026.2320.0030.0030.0000.0000.0000.000
48A554ASP-1-0.891-0.93228.8300.0830.0830.0000.0000.0000.000
49A555GLU-1-0.994-1.00026.3840.1310.1310.0000.0000.0000.000
50A556PHE0-0.085-0.03121.5280.0210.0210.0000.0000.0000.000
51A557ASP-1-0.751-0.88121.3400.2390.2390.0000.0000.0000.000
52A558ILE0-0.032-0.02818.9360.0240.0240.0000.0000.0000.000
53A559GLY0-0.020-0.01117.9530.0160.0160.0000.0000.0000.000
54A560LYS10.7890.88516.206-0.245-0.2450.0000.0000.0000.000
55A561LEU00.0100.02114.8700.0280.0280.0000.0000.0000.000
56A562ARG10.7770.8747.007-1.495-1.4950.0000.0000.0000.000
57A563TYR0-0.031-0.0149.1980.2000.2000.0000.0000.0000.000
58A564HIS00.0070.01811.422-0.018-0.0180.0000.0000.0000.000
59A565LYS10.8960.96812.4470.2880.2880.0000.0000.0000.000
60A566ILE00.0340.01513.6810.0280.0280.0000.0000.0000.000
61A567VAL0-0.017-0.00513.754-0.006-0.0060.0000.0000.0000.000
62A568LEU0-0.0140.00116.0620.0030.0030.0000.0000.0000.000
63A569MET0-0.011-0.01815.025-0.027-0.0270.0000.0000.0000.000
64A570ALA00.0470.02019.0210.0120.0120.0000.0000.0000.000
65A571ASP-1-0.819-0.90022.426-0.180-0.1800.0000.0000.0000.000
66A572ALA0-0.074-0.03825.3730.0130.0130.0000.0000.0000.000
67A573ASP-1-0.931-0.99127.639-0.131-0.1310.0000.0000.0000.000
68A574VAL0-0.026-0.00528.5770.0090.0090.0000.0000.0000.000
69A575ASP-1-0.929-0.98430.145-0.071-0.0710.0000.0000.0000.000
70A576GLY00.0120.01130.7260.0040.0040.0000.0000.0000.000
71A577GLN0-0.017-0.00626.689-0.008-0.0080.0000.0000.0000.000
72A578HIS00.0530.03528.4020.0030.0030.0000.0000.0000.000
73A579ILE00.003-0.00124.9570.0120.0120.0000.0000.0000.000
74A580SER00.0870.04523.8210.0060.0060.0000.0000.0000.000
75A581THR0-0.082-0.04925.6680.0030.0030.0000.0000.0000.000
76A582LEU0-0.0250.00926.8050.0090.0090.0000.0000.0000.000
77A583LEU0-0.012-0.02021.0200.0130.0130.0000.0000.0000.000
78A584LEU00.0130.00824.3260.0130.0130.0000.0000.0000.000
79A585THR0-0.0140.04126.2900.0130.0130.0000.0000.0000.000
80A586LEU00.013-0.00625.4610.0110.0110.0000.0000.0000.000
81A587LEU0-0.015-0.01221.9120.0130.0130.0000.0000.0000.000
82A588PHE00.0560.00125.8240.0110.0110.0000.0000.0000.000
83A589ARG10.7780.87328.872-0.005-0.0050.0000.0000.0000.000
84A590PHE00.008-0.00827.6810.0050.0050.0000.0000.0000.000
85A591MET0-0.039-0.02121.8420.0100.0100.0000.0000.0000.000
86A592ARG10.9771.02424.746-0.021-0.0210.0000.0000.0000.000
87A593PRO00.0360.02623.976-0.012-0.0120.0000.0000.0000.000
88A594LEU0-0.0090.00619.236-0.004-0.0040.0000.0000.0000.000
89A595ILE0-0.0070.00221.997-0.018-0.0180.0000.0000.0000.000
90A596GLU-1-0.908-0.96224.4900.0090.0090.0000.0000.0000.000
91A597ASN0-0.155-0.08821.262-0.010-0.0100.0000.0000.0000.000
92A598GLY00.0270.02621.217-0.005-0.0050.0000.0000.0000.000
93A599HIS10.8510.91616.758-0.047-0.0470.0000.0000.0000.000
94A600VAL00.0210.01717.777-0.022-0.0220.0000.0000.0000.000
95A601PHE0-0.010-0.01917.426-0.030-0.0300.0000.0000.0000.000
96A602LEU00.0310.03619.5690.0110.0110.0000.0000.0000.000
97A603ALA00.001-0.00716.499-0.022-0.0220.0000.0000.0000.000
98A604GLN00.003-0.00518.5890.0110.0110.0000.0000.0000.000
99A605PRO00.0310.00619.552-0.034-0.0340.0000.0000.0000.000
100A606PRO00.0250.01219.3460.0180.0180.0000.0000.0000.000
101A607LEU00.0050.00122.3190.0130.0130.0000.0000.0000.000
102A608TYR0-0.104-0.09425.5400.0260.0260.0000.0000.0000.000
103A609LYS10.8980.97223.3260.2360.2360.0000.0000.0000.000
104A610LEU0-0.043-0.03526.0570.0200.0200.0000.0000.0000.000
105A611LYS10.9150.96027.4380.1530.1530.0000.0000.0000.000
106A612TRP0-0.038-0.00627.3240.0250.0250.0000.0000.0000.000
107A613GLN0-0.029-0.03829.8100.0010.0010.0000.0000.0000.000
108A614ARG10.8800.92430.4120.1350.1350.0000.0000.0000.000
109A615SER0-0.0230.00227.6980.0050.0050.0000.0000.0000.000
110A616ASP-1-0.863-0.91322.264-0.282-0.2820.0000.0000.0000.000
111A617PRO0-0.046-0.03022.4100.0130.0130.0000.0000.0000.000
112A618GLU-1-0.858-0.93323.178-0.245-0.2450.0000.0000.0000.000
113A619PHE0-0.002-0.00520.4540.0160.0160.0000.0000.0000.000
114A620ALA00.0050.02523.494-0.001-0.0010.0000.0000.0000.000
115A621TYR0-0.007-0.00418.2510.0080.0080.0000.0000.0000.000
116A622SER00.0180.00824.8980.0180.0180.0000.0000.0000.000
117A623ASP-1-0.830-0.89428.575-0.136-0.1360.0000.0000.0000.000
118A624ARG10.9580.97331.7780.1270.1270.0000.0000.0000.000
119A625GLU-1-0.888-0.94924.932-0.245-0.2450.0000.0000.0000.000
120A626ARG10.8550.92229.4220.1310.1310.0000.0000.0000.000
121A627ASP-1-0.869-0.91930.549-0.129-0.1290.0000.0000.0000.000
122A628GLY00.0310.02532.4650.0050.0050.0000.0000.0000.000
123A629LEU00.0600.03425.7440.0040.0040.0000.0000.0000.000
124A630LEU0-0.038-0.02530.3890.0020.0020.0000.0000.0000.000
125A631GLU-1-0.978-0.99133.021-0.122-0.1220.0000.0000.0000.000
126A632ALA00.0130.00131.3450.0050.0050.0000.0000.0000.000
127A633GLY00.013-0.01032.0760.0010.0010.0000.0000.0000.000
128A634LEU0-0.030-0.02732.6230.0060.0060.0000.0000.0000.000
129A635LYS10.8710.94736.2530.1150.1150.0000.0000.0000.000
130A636ALA00.0060.02333.4890.0040.0040.0000.0000.0000.000
131A637GLY0-0.054-0.02335.197-0.002-0.0020.0000.0000.0000.000
132A638LYS10.8910.97228.4270.1980.1980.0000.0000.0000.000
133A639LYS10.9340.95134.3880.1110.1110.0000.0000.0000.000
134A640ILE00.0310.01731.784-0.007-0.0070.0000.0000.0000.000
135A641ASN00.0210.02634.9340.0100.0100.0000.0000.0000.000
136A642LYS10.9600.96536.1640.0850.0850.0000.0000.0000.000
137A643GLU-1-0.972-0.98438.490-0.088-0.0880.0000.0000.0000.000
138A644ASP-1-0.895-0.94234.506-0.123-0.1230.0000.0000.0000.000
139A645GLY0-0.014-0.00232.891-0.008-0.0080.0000.0000.0000.000
140A646ILE0-0.021-0.02330.510-0.012-0.0120.0000.0000.0000.000
141A647GLN0-0.0020.00726.3650.0090.0090.0000.0000.0000.000
142A648ARG10.9500.95028.7650.1220.1220.0000.0000.0000.000
143A649TYR0-0.011-0.00622.6840.0070.0070.0000.0000.0000.000
144A650LYS10.9310.97527.3680.1120.1120.0000.0000.0000.000
145A651GLY00.0920.06426.8940.0020.0020.0000.0000.0000.000
146A652LEU00.0720.02919.276-0.022-0.0220.0000.0000.0000.000
147A653GLY0-0.0240.01019.8950.0120.0120.0000.0000.0000.000
148A654GLU-1-1.044-1.03620.949-0.147-0.1470.0000.0000.0000.000
149A655MET0-0.086-0.02419.781-0.007-0.0070.0000.0000.0000.000
150A656ASP-1-0.751-0.91418.666-0.316-0.3160.0000.0000.0000.000
151A657ALA00.0030.01315.196-0.034-0.0340.0000.0000.0000.000
152A658LYS10.8680.90213.7190.3710.3710.0000.0000.0000.000
153A659GLU-1-0.805-0.89214.735-0.318-0.3180.0000.0000.0000.000
154A660LEU00.024-0.00215.4900.0180.0180.0000.0000.0000.000
155A661TRP0-0.0140.0246.7250.0760.0760.0000.0000.0000.000
156A662GLU-1-0.906-0.97812.551-0.587-0.5870.0000.0000.0000.000
157A663THR00.0110.02113.5670.0170.0170.0000.0000.0000.000
158A664THR0-0.039-0.02714.4020.0390.0390.0000.0000.0000.000
159A665MET0-0.087-0.0258.8060.0800.0800.0000.0000.0000.000
160A666ASP-1-0.810-0.9079.730-1.122-1.1220.0000.0000.0000.000
161A667PRO0-0.067-0.0618.3150.1430.1430.0000.0000.0000.000
162A668SER0-0.070-0.02011.4670.1100.1100.0000.0000.0000.000
163A669VAL00.0240.00713.8900.0680.0680.0000.0000.0000.000
164A670ARG10.7460.90011.0330.7350.7350.0000.0000.0000.000
165A671VAL00.0450.01816.0780.0220.0220.0000.0000.0000.000
166A672LEU0-0.039-0.02614.5510.0180.0180.0000.0000.0000.000
167A673ARG10.9230.96718.8660.1420.1420.0000.0000.0000.000
168A674GLN0-0.036-0.01921.1320.0150.0150.0000.0000.0000.000
169A675VAL0-0.0120.01121.9970.0040.0040.0000.0000.0000.000
170A676THR0-0.029-0.02624.3980.0120.0120.0000.0000.0000.000
171A677LEU00.034-0.01127.2600.0030.0030.0000.0000.0000.000
172A678ASP-1-0.909-0.93529.709-0.040-0.0400.0000.0000.0000.000
173A679ASP-1-0.827-0.91627.594-0.088-0.0880.0000.0000.0000.000
174A680ALA0-0.037-0.03427.6500.0010.0010.0000.0000.0000.000
175A681ALA00.0030.01729.3900.0060.0060.0000.0000.0000.000
176A682ALA00.0260.02032.5850.0030.0030.0000.0000.0000.000
177A683ALA0-0.0030.01129.5920.0020.0020.0000.0000.0000.000
178A684ASP-1-0.820-0.93431.5960.0030.0030.0000.0000.0000.000
179A685GLU-1-0.881-0.94433.519-0.023-0.0230.0000.0000.0000.000
180A686LEU0-0.020-0.01933.2430.0020.0020.0000.0000.0000.000
181A687PHE00.012-0.00332.8360.0020.0020.0000.0000.0000.000
182A688SER0-0.045-0.03035.0270.0050.0050.0000.0000.0000.000
183A689ILE0-0.031-0.02938.2540.0020.0020.0000.0000.0000.000
184A690LEU0-0.132-0.03034.725-0.001-0.0010.0000.0000.0000.000
185A691MET0-0.099-0.03936.7260.0020.0020.0000.0000.0000.000