FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: LRYG9

Calculation Name: 1AB4-A-Xray549

Preferred Name: DNA gyrase subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AB4

Chain ID: A

ChEMBL ID: CHEMBL1858

UniProt ID: P0AES4

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 493
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -8878852.863091
FMO2-HF: Nuclear repulsion 8685625.481416
FMO2-HF: Total energy -193227.381675
FMO2-MP2: Total energy -193794.162637


3D Structure Molmil
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:30:VAL)


Summations of interaction energy for fragment #1(A:30:VAL)
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.
-29.411-24.990.084-1.82-2.686-0.005
Interaction energy analysis for fragmet #1(A:30:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.901 / q_NPA : 0.928
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].
3A32ARG10.8820.9413.31740.66543.904-0.012-1.495-1.732-0.003
4A33ALA0-0.0280.0083.6665.6476.1110.001-0.124-0.341-0.001
149A178MET0-0.063-0.0392.844-0.0670.5670.096-0.192-0.539-0.001
308A337LEU0-0.050-0.0154.582-1.799-1.715-0.001-0.009-0.0740.000
5A34LEU00.0400.0194.8906.2166.2160.0000.0000.0000.000
6A35PRO0-0.0020.0157.189-1.451-1.4510.0000.0000.0000.000
7A36ASP-1-0.793-0.8949.956-25.872-25.8720.0000.0000.0000.000
8A37VAL0-0.020-0.03611.3261.6031.6030.0000.0000.0000.000
9A38ARG10.8480.93512.26722.08522.0850.0000.0000.0000.000
10A39ASP-1-0.683-0.83714.505-20.197-20.1970.0000.0000.0000.000
11A40GLY00.0100.00314.7050.8240.8240.0000.0000.0000.000
12A41LEU0-0.076-0.02313.964-0.429-0.4290.0000.0000.0000.000
13A42LYS10.8360.9088.28628.81028.8100.0000.0000.0000.000
14A43PRO00.017-0.0107.1221.8371.8370.0000.0000.0000.000
15A44VAL0-0.0070.00410.4501.5021.5020.0000.0000.0000.000
16A45HIS00.0770.02512.3120.6930.6930.0000.0000.0000.000
17A46ARG10.8080.92710.42825.12925.1290.0000.0000.0000.000
18A47ARG10.9480.9679.82025.78025.7800.0000.0000.0000.000
19A48VAL0-0.011-0.00315.9791.1051.1050.0000.0000.0000.000
20A49LEU00.0270.00318.7010.9220.9220.0000.0000.0000.000
21A50TYR00.0630.02518.3260.8520.8520.0000.0000.0000.000
22A51ALA00.0240.00920.0260.7140.7140.0000.0000.0000.000
23A52MET0-0.085-0.03421.8760.5870.5870.0000.0000.0000.000
24A53ASN00.0300.00723.3650.7320.7320.0000.0000.0000.000
25A54VAL00.0180.01522.6670.5160.5160.0000.0000.0000.000
26A55LEU0-0.065-0.02925.4890.5380.5380.0000.0000.0000.000
27A56GLY00.0310.02027.9030.4570.4570.0000.0000.0000.000
28A57ASN0-0.098-0.06427.3490.7570.7570.0000.0000.0000.000
29A58ASP-1-0.790-0.89929.157-10.417-10.4170.0000.0000.0000.000
30A59TRP00.0380.01830.9730.2820.2820.0000.0000.0000.000
31A60ASN0-0.016-0.00532.5280.0260.0260.0000.0000.0000.000
32A61LYS10.8360.91133.6419.5749.5740.0000.0000.0000.000
33A62ALA00.0040.00535.607-0.019-0.0190.0000.0000.0000.000
34A63TYR0-0.054-0.04131.771-0.082-0.0820.0000.0000.0000.000
35A64LYS10.9040.97829.59410.31110.3110.0000.0000.0000.000
36A65LYS10.8280.89830.7528.8648.8640.0000.0000.0000.000
37A66SER00.015-0.00126.092-0.260-0.2600.0000.0000.0000.000
38A67ALA0-0.002-0.01526.019-0.444-0.4440.0000.0000.0000.000
39A68ARG10.8030.89526.70010.87810.8780.0000.0000.0000.000
40A69VAL00.0480.02922.723-0.096-0.0960.0000.0000.0000.000
41A70VAL00.000-0.00121.313-0.477-0.4770.0000.0000.0000.000
42A71GLY00.0220.00721.904-0.523-0.5230.0000.0000.0000.000
43A72ASP-1-0.798-0.88323.590-12.455-12.4550.0000.0000.0000.000
44A73VAL0-0.0020.00117.599-0.466-0.4660.0000.0000.0000.000
45A74ILE0-0.057-0.02718.626-0.729-0.7290.0000.0000.0000.000
46A75GLY00.0110.00919.517-0.322-0.3220.0000.0000.0000.000
47A76LYS10.8920.97519.89313.07613.0760.0000.0000.0000.000
48A77TYR00.024-0.00415.868-0.606-0.6060.0000.0000.0000.000
49A78HIS0-0.045-0.04010.630-2.391-2.3910.0000.0000.0000.000
50A79PRO00.0500.05614.6300.2560.2560.0000.0000.0000.000
51A80HIS0-0.051-0.04111.545-1.667-1.6670.0000.0000.0000.000
52A81GLY00.0290.01915.214-0.289-0.2890.0000.0000.0000.000
53A82ASP-1-0.844-0.93818.096-14.127-14.1270.0000.0000.0000.000
54A83SER00.0080.00119.978-0.383-0.3830.0000.0000.0000.000
55A84ALA00.0740.04215.0370.0050.0050.0000.0000.0000.000
56A85VAL0-0.0160.00316.208-0.624-0.6240.0000.0000.0000.000
57A86TYR00.003-0.00618.0110.3480.3480.0000.0000.0000.000
58A87ASP-1-0.873-0.94318.131-15.101-15.1010.0000.0000.0000.000
59A88THR0-0.097-0.05915.580-0.529-0.5290.0000.0000.0000.000
60A89ILE0-0.004-0.00817.7430.2230.2230.0000.0000.0000.000
61A90VAL0-0.0100.00021.2180.4690.4690.0000.0000.0000.000
62A91ARG10.8720.93917.08016.92416.9240.0000.0000.0000.000
63A92MET0-0.022-0.01518.860-0.169-0.1690.0000.0000.0000.000
64A93ALA00.0450.03321.5270.4120.4120.0000.0000.0000.000
65A94GLN0-0.007-0.00623.4270.0990.0990.0000.0000.0000.000
66A95PRO00.0360.00225.262-0.378-0.3780.0000.0000.0000.000
67A96PHE00.0070.01325.2680.1190.1190.0000.0000.0000.000
68A97SER0-0.039-0.03321.448-0.424-0.4240.0000.0000.0000.000
69A98LEU0-0.0370.00119.321-0.771-0.7710.0000.0000.0000.000
70A99ARG10.7610.86323.10811.50911.5090.0000.0000.0000.000
71A100TYR0-0.003-0.02224.6240.4810.4810.0000.0000.0000.000
72A101MET0-0.0320.00824.370-0.407-0.4070.0000.0000.0000.000
73A102LEU00.016-0.00119.9020.0950.0950.0000.0000.0000.000
74A103VAL0-0.042-0.02722.9880.0720.0720.0000.0000.0000.000
75A104ASP-1-0.774-0.84625.659-9.718-9.7180.0000.0000.0000.000
76A105GLY00.037-0.00528.942-0.087-0.0870.0000.0000.0000.000
77A106GLN0-0.025-0.00529.7040.3280.3280.0000.0000.0000.000
78A107GLY00.023-0.00932.745-0.045-0.0450.0000.0000.0000.000
79A108ASN0-0.010-0.00631.329-0.152-0.1520.0000.0000.0000.000
80A109PHE00.0440.01225.966-0.259-0.2590.0000.0000.0000.000
81A110GLY00.0510.03326.690-0.527-0.5270.0000.0000.0000.000
82A111SER0-0.068-0.07828.5200.0620.0620.0000.0000.0000.000
83A112ILE00.0550.02127.915-0.370-0.3700.0000.0000.0000.000
84A113ASP-1-0.779-0.87029.091-9.593-9.5930.0000.0000.0000.000
85A114GLY0-0.032-0.01826.812-0.056-0.0560.0000.0000.0000.000
86A115ASP-1-0.873-0.88027.749-9.846-9.8460.0000.0000.0000.000
87A116SER0-0.023-0.01726.650-0.520-0.5200.0000.0000.0000.000
88A117ALA00.0000.00526.2250.3940.3940.0000.0000.0000.000
89A118ALA00.0020.00127.9670.1140.1140.0000.0000.0000.000
90A119ALA00.0200.00928.661-0.371-0.3710.0000.0000.0000.000
91A120MET00.0530.03425.3930.2430.2430.0000.0000.0000.000
92A121ARG10.9410.96528.2539.5069.5060.0000.0000.0000.000
93A122TYR0-0.040-0.02031.5930.2850.2850.0000.0000.0000.000
94A123THR00.0160.01428.4020.2380.2380.0000.0000.0000.000
95A124GLU-1-0.798-0.87731.003-9.016-9.0160.0000.0000.0000.000
96A125ILE0-0.004-0.00725.275-0.152-0.1520.0000.0000.0000.000
97A126ARG10.8220.91328.9539.5529.5520.0000.0000.0000.000
98A127LEU00.0160.00723.993-0.324-0.3240.0000.0000.0000.000
99A128ALA00.0210.01826.7500.4960.4960.0000.0000.0000.000
100A129LYS10.9030.94028.2589.7929.7920.0000.0000.0000.000
101A130ILE00.0620.03425.9360.0090.0090.0000.0000.0000.000
102A131ALA0-0.024-0.00923.932-0.377-0.3770.0000.0000.0000.000
103A132HIS00.0090.00424.400-0.195-0.1950.0000.0000.0000.000
104A133GLU-1-0.802-0.91026.444-10.681-10.6810.0000.0000.0000.000
105A134LEU0-0.039-0.02019.845-0.309-0.3090.0000.0000.0000.000
106A135MET0-0.038-0.02521.163-0.671-0.6710.0000.0000.0000.000
107A136ALA00.0290.02823.3130.2690.2690.0000.0000.0000.000
108A137ASP-1-0.772-0.88825.337-10.931-10.9310.0000.0000.0000.000
109A138LEU0-0.0560.00419.988-0.186-0.1860.0000.0000.0000.000
110A139GLU-1-0.903-0.96023.339-11.385-11.3850.0000.0000.0000.000
111A140LYS10.7790.90826.03610.23810.2380.0000.0000.0000.000
112A141GLU-1-0.764-0.86823.725-10.893-10.8930.0000.0000.0000.000
113A142THR0-0.046-0.03922.988-0.422-0.4220.0000.0000.0000.000
114A143VAL0-0.029-0.01017.570-0.387-0.3870.0000.0000.0000.000
115A144ASP-1-0.807-0.87715.553-15.602-15.6020.0000.0000.0000.000
116A145PHE00.015-0.00715.980-0.742-0.7420.0000.0000.0000.000
117A146VAL0-0.032-0.00210.6570.0850.0850.0000.0000.0000.000
118A147ASP-1-0.821-0.90013.798-15.702-15.7020.0000.0000.0000.000
119A148ASN0-0.053-0.05213.095-1.693-1.6930.0000.0000.0000.000
120A149TYR0-0.108-0.07613.728-0.837-0.8370.0000.0000.0000.000
121A150ASP-1-0.832-0.88014.680-14.991-14.9910.0000.0000.0000.000
122A151GLY00.0000.01317.2890.5620.5620.0000.0000.0000.000
123A152THR0-0.090-0.06218.5680.7150.7150.0000.0000.0000.000
124A153GLU-1-0.872-0.94018.941-12.937-12.9370.0000.0000.0000.000
125A154LYS10.8670.91617.30214.95014.9500.0000.0000.0000.000
126A155ILE0-0.063-0.03413.5050.3070.3070.0000.0000.0000.000
127A156PRO00.0030.02415.072-0.555-0.5550.0000.0000.0000.000
128A157ASP-1-0.897-0.95510.999-24.896-24.8960.0000.0000.0000.000
129A158VAL0-0.070-0.05311.997-1.886-1.8860.0000.0000.0000.000
130A159MET0-0.013-0.00614.7231.0081.0080.0000.0000.0000.000
131A160PRO00.0380.04018.180-0.427-0.4270.0000.0000.0000.000
132A161THR0-0.030-0.01219.7530.9220.9220.0000.0000.0000.000
133A162LYS10.8650.92222.32911.02511.0250.0000.0000.0000.000
134A163ILE00.0350.02123.6410.3060.3060.0000.0000.0000.000
135A164PRO00.0740.05221.888-0.838-0.8380.0000.0000.0000.000
136A165ASN0-0.035-0.03918.0810.4630.4630.0000.0000.0000.000
137A166LEU00.0100.01114.105-0.334-0.3340.0000.0000.0000.000
138A167LEU0-0.0060.00717.596-0.292-0.2920.0000.0000.0000.000
139A168VAL00.0120.01620.4340.1820.1820.0000.0000.0000.000
140A169ASN00.033-0.01820.0120.8700.8700.0000.0000.0000.000
141A170GLY00.0190.04118.2840.0040.0040.0000.0000.0000.000
142A171SER0-0.037-0.03812.890-1.562-1.5620.0000.0000.0000.000
143A172SER00.0240.01113.5380.5430.5430.0000.0000.0000.000
144A173GLY0-0.022-0.0189.566-1.460-1.4600.0000.0000.0000.000
145A174ILE00.0160.00810.0640.1380.1380.0000.0000.0000.000
146A175ALA00.0090.0195.209-0.065-0.0650.0000.0000.0000.000
147A176VAL00.0240.0004.8632.0882.0880.0000.0000.0000.000
148A177GLY00.0310.0346.342-4.735-4.7350.0000.0000.0000.000
150A179ALA0-0.011-0.0096.209-1.057-1.0570.0000.0000.0000.000
151A180THR0-0.019-0.0299.604-0.614-0.6140.0000.0000.0000.000
152A181ASN0-0.089-0.05311.508-0.038-0.0380.0000.0000.0000.000
153A182ILE00.0310.03713.9730.8660.8660.0000.0000.0000.000
154A183PRO00.0120.01417.076-0.341-0.3410.0000.0000.0000.000
155A184PRO0-0.006-0.00320.516-0.171-0.1710.0000.0000.0000.000
156A185HIS00.0010.01621.2850.6120.6120.0000.0000.0000.000
157A186ASN00.0430.02025.2020.0230.0230.0000.0000.0000.000
158A187LEU00.005-0.00426.588-0.196-0.1960.0000.0000.0000.000
159A188THR00.010-0.00428.475-0.006-0.0060.0000.0000.0000.000
160A189GLU-1-0.813-0.86129.487-10.264-10.2640.0000.0000.0000.000
161A190VAL00.002-0.01423.942-0.057-0.0570.0000.0000.0000.000
162A191ILE0-0.0060.00727.352-0.226-0.2260.0000.0000.0000.000
163A192ASN00.0470.03529.2370.1770.1770.0000.0000.0000.000
164A193GLY00.0580.02928.6640.1430.1430.0000.0000.0000.000
165A194CYS0-0.120-0.07225.765-0.354-0.3540.0000.0000.0000.000
166A195LEU0-0.0100.00227.976-0.020-0.0200.0000.0000.0000.000
167A196ALA00.0490.03131.3080.1170.1170.0000.0000.0000.000
168A197TYR0-0.086-0.06025.854-0.157-0.1570.0000.0000.0000.000
169A198ILE0-0.072-0.04228.389-0.114-0.1140.0000.0000.0000.000
170A199ASP-1-0.829-0.89930.796-8.831-8.8310.0000.0000.0000.000
171A200ASP-1-0.923-0.98033.077-8.991-8.9910.0000.0000.0000.000
172A201GLU-1-0.856-0.90627.388-11.327-11.3270.0000.0000.0000.000
173A202ASP-1-0.939-0.98729.234-10.183-10.1830.0000.0000.0000.000
174A203ILE0-0.0180.03029.239-0.067-0.0670.0000.0000.0000.000
175A204SER00.010-0.00229.762-0.454-0.4540.0000.0000.0000.000
176A205ILE0-0.008-0.03225.078-0.095-0.0950.0000.0000.0000.000
177A206GLU-1-0.966-0.97828.627-8.989-8.9890.0000.0000.0000.000
178A207GLY00.0730.03332.0220.0860.0860.0000.0000.0000.000
179A208LEU0-0.009-0.00725.803-0.057-0.0570.0000.0000.0000.000
180A209MET0-0.068-0.03928.692-0.215-0.2150.0000.0000.0000.000
181A210GLU-1-0.972-0.96430.681-8.502-8.5020.0000.0000.0000.000
182A211HIS0-0.0040.00730.9970.0530.0530.0000.0000.0000.000
183A212ILE0-0.058-0.02525.879-0.144-0.1440.0000.0000.0000.000
184A213PRO00.0510.03428.982-0.244-0.2440.0000.0000.0000.000
185A214GLY00.005-0.01827.542-0.001-0.0010.0000.0000.0000.000
186A215PRO0-0.033-0.00324.125-0.031-0.0310.0000.0000.0000.000
187A216ASP-1-0.731-0.84725.902-10.051-10.0510.0000.0000.0000.000
188A217PHE00.000-0.01122.765-0.550-0.5500.0000.0000.0000.000
189A218PRO0-0.0190.00124.5730.4150.4150.0000.0000.0000.000
190A219THR0-0.012-0.01427.5570.2460.2460.0000.0000.0000.000
191A220ALA0-0.040-0.01127.9460.3050.3050.0000.0000.0000.000
192A221ALA00.0780.06729.922-0.003-0.0030.0000.0000.0000.000
193A222ILE00.0070.01932.4060.0980.0980.0000.0000.0000.000
194A223ILE0-0.026-0.01127.030-0.391-0.3910.0000.0000.0000.000
195A224ASN0-0.004-0.00331.3860.1710.1710.0000.0000.0000.000
196A225GLY0-0.017-0.00230.2700.1330.1330.0000.0000.0000.000
197A226ARG10.9110.93629.5718.6668.6660.0000.0000.0000.000
198A227ARG10.9740.97529.33210.11510.1150.0000.0000.0000.000
199A228GLY0-0.048-0.02126.773-0.245-0.2450.0000.0000.0000.000
200A229ILE0-0.020-0.00625.171-0.660-0.6600.0000.0000.0000.000
201A230GLU-1-0.841-0.92425.594-10.235-10.2350.0000.0000.0000.000
202A231GLU-1-0.853-0.90924.958-11.502-11.5020.0000.0000.0000.000
203A232ALA0-0.0140.00321.355-0.471-0.4710.0000.0000.0000.000
204A233TYR00.010-0.04021.456-0.626-0.6260.0000.0000.0000.000
205A234ARG10.9030.94723.48411.34911.3490.0000.0000.0000.000
206A235THR0-0.069-0.05121.459-0.289-0.2890.0000.0000.0000.000
207A236GLY00.0460.03817.864-0.727-0.7270.0000.0000.0000.000
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