FMO DATABASE

FMODB ID: 5YYQZ

Calculation Name: 4B6C-A-Xray547

Preferred Name: DNA gyrase subunit B

Target Type: SINGLE PROTEIN

Ligand Name: 6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin-1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide

Ligand 3-letter code: B5U

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4B6C

Chain ID: A

ChEMBL ID: CHEMBL6059

UniProt ID: A0QNE0

Base Structure: X-ray

Registration Date: 2025-10-04

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1699145.541822
FMO2-HF: Nuclear repulsion	1632749.287072
FMO2-HF: Total energy	-66396.25475
FMO2-MP2: Total energy	-66590.074951

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:36:SER)

Summations of interaction energy for fragment #1(A:36:SER)

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.
-132.194	-128.818	0.875	-1.678	-2.572	-0.011

Interaction energy analysis for fragmet #1(A:36:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.886

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 ES EX CT+mix DI(MP2)

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].
3	A	38	GLY	0	0.085	0.064	3.470	7.970	10.918	-0.019	-1.426	-1.503	-0.009
4	A	39	GLU	-1	-0.821	-0.921	5.116	-30.001	-29.995	-0.001	-0.001	-0.004	0.000
5	A	40	ARG	1	0.947	0.966	4.306	39.113	39.247	-0.001	-0.008	-0.124	0.000
6	A	41	GLY	0	-0.060	-0.033	2.447	-2.414	-2.063	0.830	-0.674	-0.507	0.000
7	A	42	LEU	0	0.018	0.041	3.098	1.695	1.378	0.067	0.501	-0.251	-0.002
76	A	131	LEU	0	-0.073	-0.028	3.959	-3.314	-3.176	0.000	-0.036	-0.102	0.000
125	A	180	PHE	0	-0.078	-0.057	4.490	-8.414	-8.298	-0.001	-0.034	-0.081	0.000
8	A	43	HIS	0	0.016	-0.008	6.726	5.447	5.447	0.000	0.000	0.000	0.000
9	A	44	HIS	0	-0.097	-0.051	5.134	0.294	0.294	0.000	0.000	0.000	0.000
10	A	45	LEU	0	-0.004	-0.001	5.735	1.872	1.872	0.000	0.000	0.000	0.000
11	A	46	ILE	0	0.007	0.013	8.307	3.053	3.053	0.000	0.000	0.000	0.000
12	A	47	TRP	0	-0.059	-0.032	8.626	2.472	2.472	0.000	0.000	0.000	0.000
13	A	48	GLU	-1	-0.796	-0.884	8.836	-27.450	-27.450	0.000	0.000	0.000	0.000
14	A	49	VAL	0	-0.008	0.003	11.666	1.905	1.905	0.000	0.000	0.000	0.000
15	A	50	VAL	0	-0.021	-0.019	14.318	1.510	1.510	0.000	0.000	0.000	0.000
16	A	51	ASP	-1	-0.802	-0.882	13.847	-20.540	-20.540	0.000	0.000	0.000	0.000
17	A	52	ASN	0	-0.027	-0.025	14.895	1.765	1.765	0.000	0.000	0.000	0.000
18	A	53	ALA	0	-0.013	-0.002	17.904	0.924	0.924	0.000	0.000	0.000	0.000
19	A	54	VAL	0	-0.033	-0.019	19.396	0.860	0.860	0.000	0.000	0.000	0.000
20	A	55	ASP	-1	-0.867	-0.931	19.308	-15.178	-15.178	0.000	0.000	0.000	0.000
21	A	56	GLU	-1	-0.805	-0.878	22.087	-11.480	-11.480	0.000	0.000	0.000	0.000
22	A	57	ALA	0	-0.018	0.007	24.232	0.615	0.615	0.000	0.000	0.000	0.000
23	A	58	MET	0	-0.036	-0.018	22.599	0.277	0.277	0.000	0.000	0.000	0.000
24	A	59	ALA	0	-0.080	-0.037	26.072	0.441	0.441	0.000	0.000	0.000	0.000
25	A	60	GLY	0	-0.031	-0.011	28.034	0.384	0.384	0.000	0.000	0.000	0.000
26	A	61	PHE	0	-0.068	-0.043	27.788	0.447	0.447	0.000	0.000	0.000	0.000
27	A	62	ALA	0	0.001	0.010	26.258	0.168	0.168	0.000	0.000	0.000	0.000
28	A	63	THR	0	-0.087	-0.075	28.296	0.134	0.134	0.000	0.000	0.000	0.000
29	A	64	ARG	1	0.781	0.834	27.296	11.181	11.181	0.000	0.000	0.000	0.000
30	A	65	VAL	0	0.034	0.020	20.585	-0.272	-0.272	0.000	0.000	0.000	0.000
31	A	66	ASP	-1	-0.825	-0.873	23.651	-11.687	-11.687	0.000	0.000	0.000	0.000
32	A	67	VAL	0	0.003	-0.009	17.467	-0.711	-0.711	0.000	0.000	0.000	0.000
33	A	68	LYS	1	0.863	0.923	20.127	13.088	13.088	0.000	0.000	0.000	0.000
34	A	69	ILE	0	0.018	0.015	16.664	-0.741	-0.741	0.000	0.000	0.000	0.000
35	A	70	HIS	1	0.784	0.851	19.112	15.342	15.342	0.000	0.000	0.000	0.000
36	A	71	ALA	0	0.017	0.005	20.193	-0.579	-0.579	0.000	0.000	0.000	0.000
37	A	72	ASP	-1	-0.801	-0.856	20.390	-15.478	-15.478	0.000	0.000	0.000	0.000
38	A	73	GLY	0	0.028	0.018	17.341	-0.382	-0.382	0.000	0.000	0.000	0.000
39	A	74	SER	0	-0.083	-0.061	15.585	-1.257	-1.257	0.000	0.000	0.000	0.000
40	A	75	VAL	0	-0.013	-0.011	14.169	0.661	0.661	0.000	0.000	0.000	0.000
41	A	76	GLU	-1	-0.859	-0.913	16.505	-13.921	-13.921	0.000	0.000	0.000	0.000
42	A	77	VAL	0	-0.012	-0.012	16.260	0.074	0.074	0.000	0.000	0.000	0.000
43	A	78	ARG	1	0.857	0.913	19.405	11.774	11.774	0.000	0.000	0.000	0.000
44	A	79	ASP	-1	-0.784	-0.899	22.597	-13.475	-13.475	0.000	0.000	0.000	0.000
45	A	80	ASP	-1	-0.795	-0.870	24.587	-10.840	-10.840	0.000	0.000	0.000	0.000
46	A	81	GLY	0	0.057	0.035	26.552	0.337	0.337	0.000	0.000	0.000	0.000
47	A	82	ARG	1	0.798	0.853	25.549	12.076	12.076	0.000	0.000	0.000	0.000
48	A	83	GLY	0	0.025	0.034	25.926	0.297	0.297	0.000	0.000	0.000	0.000
49	A	84	ILE	0	-0.028	-0.026	19.844	0.139	0.139	0.000	0.000	0.000	0.000
50	A	85	PRO	0	0.001	-0.001	24.165	0.104	0.104	0.000	0.000	0.000	0.000
51	A	86	VAL	0	-0.009	-0.021	24.783	-0.604	-0.604	0.000	0.000	0.000	0.000
52	A	87	GLU	-1	-0.795	-0.876	26.776	-10.693	-10.693	0.000	0.000	0.000	0.000
53	A	88	MET	0	-0.055	-0.023	28.250	-0.414	-0.414	0.000	0.000	0.000	0.000
54	A	89	HIS	0	0.012	0.019	29.954	0.503	0.503	0.000	0.000	0.000	0.000
55	A	90	ALA	0	-0.003	-0.011	31.723	0.141	0.141	0.000	0.000	0.000	0.000
56	A	91	THR	0	-0.054	-0.029	30.927	0.393	0.393	0.000	0.000	0.000	0.000
57	A	92	GLY	0	0.026	0.022	32.744	-0.222	-0.222	0.000	0.000	0.000	0.000
58	A	93	MET	0	-0.094	-0.065	31.790	0.101	0.101	0.000	0.000	0.000	0.000
59	A	94	PRO	0	-0.003	0.010	27.346	-0.143	-0.143	0.000	0.000	0.000	0.000
60	A	95	THR	0	0.071	0.021	25.663	0.014	0.014	0.000	0.000	0.000	0.000
61	A	96	ILE	0	-0.033	-0.023	21.164	-0.329	-0.329	0.000	0.000	0.000	0.000
62	A	97	ASP	-1	-0.790	-0.906	23.732	-11.353	-11.353	0.000	0.000	0.000	0.000
63	A	98	VAL	0	-0.070	-0.008	24.223	0.124	0.124	0.000	0.000	0.000	0.000
64	A	99	VAL	0	0.042	0.017	21.431	-0.667	-0.667	0.000	0.000	0.000	0.000
65	A	100	MET	0	0.028	0.017	20.603	-1.138	-1.138	0.000	0.000	0.000	0.000
66	A	101	THR	0	-0.036	-0.013	19.673	-0.730	-0.730	0.000	0.000	0.000	0.000
67	A	102	GLN	0	0.000	-0.007	17.233	-0.855	-0.855	0.000	0.000	0.000	0.000
68	A	123	VAL	0	0.018	0.019	15.524	-1.344	-1.344	0.000	0.000	0.000	0.000
69	A	124	GLY	0	0.010	0.015	14.961	-1.434	-1.434	0.000	0.000	0.000	0.000
70	A	125	VAL	0	-0.027	-0.008	14.071	-0.841	-0.841	0.000	0.000	0.000	0.000
71	A	126	SER	0	-0.017	-0.006	11.681	-2.332	-2.332	0.000	0.000	0.000	0.000
72	A	127	VAL	0	0.011	-0.017	4.920	-0.907	-0.907	0.000	0.000	0.000	0.000
73	A	128	VAL	0	0.014	0.011	7.958	-2.343	-2.343	0.000	0.000	0.000	0.000
74	A	129	ASN	0	-0.019	-0.010	9.801	0.939	0.939	0.000	0.000	0.000	0.000
75	A	130	ALA	0	-0.002	-0.001	8.922	0.225	0.225	0.000	0.000	0.000	0.000
77	A	132	SER	0	0.022	-0.003	8.376	-0.749	-0.749	0.000	0.000	0.000	0.000
78	A	133	THR	0	-0.029	-0.009	11.750	1.104	1.104	0.000	0.000	0.000	0.000
79	A	134	ARG	1	0.833	0.909	15.056	15.988	15.988	0.000	0.000	0.000	0.000
80	A	135	LEU	0	0.010	0.015	13.530	-1.121	-1.121	0.000	0.000	0.000	0.000
81	A	136	GLU	-1	-0.869	-0.927	16.701	-12.983	-12.983	0.000	0.000	0.000	0.000
82	A	137	ALA	0	0.028	0.010	19.425	-0.392	-0.392	0.000	0.000	0.000	0.000
83	A	138	THR	0	-0.004	-0.008	20.979	0.628	0.628	0.000	0.000	0.000	0.000
84	A	139	VAL	0	-0.034	-0.010	24.157	-0.289	-0.289	0.000	0.000	0.000	0.000
85	A	140	LEU	0	0.008	0.015	26.472	0.425	0.425	0.000	0.000	0.000	0.000
86	A	141	ARG	1	0.902	0.916	28.432	10.514	10.514	0.000	0.000	0.000	0.000
87	A	142	ASP	-1	-0.901	-0.946	31.407	-9.485	-9.485	0.000	0.000	0.000	0.000
88	A	143	GLY	0	-0.003	0.007	34.746	0.196	0.196	0.000	0.000	0.000	0.000
89	A	144	TYR	0	-0.031	-0.015	34.174	0.270	0.270	0.000	0.000	0.000	0.000
90	A	145	GLU	-1	-0.891	-0.936	29.703	-10.693	-10.693	0.000	0.000	0.000	0.000
91	A	146	TRP	0	-0.040	-0.026	28.217	0.203	0.203	0.000	0.000	0.000	0.000
92	A	147	PHE	0	-0.029	-0.021	25.806	-0.395	-0.395	0.000	0.000	0.000	0.000
93	A	148	GLN	0	-0.023	-0.016	21.707	0.798	0.798	0.000	0.000	0.000	0.000
94	A	149	TYR	0	-0.002	-0.013	21.364	-0.277	-0.277	0.000	0.000	0.000	0.000
95	A	150	TYR	0	0.020	0.006	17.444	0.445	0.445	0.000	0.000	0.000	0.000
96	A	151	ASP	-1	-0.937	-0.967	18.735	-15.445	-15.445	0.000	0.000	0.000	0.000
97	A	152	ARG	1	0.948	0.960	14.877	19.292	19.292	0.000	0.000	0.000	0.000
98	A	153	SER	0	0.019	0.017	13.370	-0.455	-0.455	0.000	0.000	0.000	0.000
99	A	154	VAL	0	-0.034	-0.004	15.402	0.449	0.449	0.000	0.000	0.000	0.000
100	A	155	PRO	0	-0.011	0.006	19.106	0.154	0.154	0.000	0.000	0.000	0.000
101	A	156	GLY	0	0.010	0.009	21.394	0.554	0.554	0.000	0.000	0.000	0.000
102	A	157	LYS	1	0.911	0.947	24.699	9.723	9.723	0.000	0.000	0.000	0.000
103	A	158	LEU	0	0.051	0.038	26.734	-0.091	-0.091	0.000	0.000	0.000	0.000
104	A	159	LYS	1	0.819	0.920	27.636	11.699	11.699	0.000	0.000	0.000	0.000
105	A	160	GLN	0	0.003	0.015	30.026	-0.270	-0.270	0.000	0.000	0.000	0.000
106	A	161	GLY	0	-0.018	-0.014	32.724	0.125	0.125	0.000	0.000	0.000	0.000
107	A	162	GLY	0	-0.006	-0.003	33.764	0.255	0.255	0.000	0.000	0.000	0.000
108	A	163	GLU	-1	-0.921	-0.965	35.529	-7.884	-7.884	0.000	0.000	0.000	0.000
109	A	164	THR	0	-0.047	-0.036	33.293	0.060	0.060	0.000	0.000	0.000	0.000
110	A	165	LYS	1	0.854	0.918	36.792	8.608	8.608	0.000	0.000	0.000	0.000
111	A	166	GLU	-1	-0.928	-0.951	32.590	-9.233	-9.233	0.000	0.000	0.000	0.000
112	A	167	THR	0	-0.028	-0.014	30.544	0.134	0.134	0.000	0.000	0.000	0.000
113	A	168	GLY	0	0.039	0.032	27.221	0.051	0.051	0.000	0.000	0.000	0.000
114	A	169	THR	0	-0.029	-0.017	21.333	0.110	0.110	0.000	0.000	0.000	0.000
115	A	170	THR	0	-0.035	-0.021	22.129	0.098	0.098	0.000	0.000	0.000	0.000
116	A	171	ILE	0	-0.005	0.010	15.876	0.061	0.061	0.000	0.000	0.000	0.000
117	A	172	ARG	1	0.830	0.904	17.707	14.475	14.475	0.000	0.000	0.000	0.000
118	A	173	PHE	0	0.017	0.002	10.687	-0.021	-0.021	0.000	0.000	0.000	0.000
119	A	174	TRP	0	-0.021	-0.020	14.810	0.002	0.002	0.000	0.000	0.000	0.000
120	A	175	ALA	0	0.017	0.012	9.428	-0.401	-0.401	0.000	0.000	0.000	0.000
121	A	176	ASP	-1	-0.822	-0.934	10.255	-22.487	-22.487	0.000	0.000	0.000	0.000
122	A	177	PRO	0	-0.010	-0.023	10.610	-2.529	-2.529	0.000	0.000	0.000	0.000
123	A	178	GLU	-1	-0.978	-0.967	12.574	-19.518	-19.518	0.000	0.000	0.000	0.000
124	A	179	ILE	0	-0.077	-0.030	6.176	-1.815	-1.815	0.000	0.000	0.000	0.000
126	A	181	GLU	-1	-0.935	-0.960	8.571	-22.487	-22.487	0.000	0.000	0.000	0.000
127	A	182	THR	0	0.001	0.004	10.153	1.130	1.130	0.000	0.000	0.000	0.000
128	A	183	THR	0	-0.039	-0.026	10.700	2.427	2.427	0.000	0.000	0.000	0.000
129	A	184	ASP	-1	-0.858	-0.917	12.198	-17.641	-17.641	0.000	0.000	0.000	0.000
130	A	185	TYR	0	0.033	0.012	10.867	-2.096	-2.096	0.000	0.000	0.000	0.000
131	A	186	ASN	0	0.010	0.007	13.150	2.609	2.609	0.000	0.000	0.000	0.000
132	A	187	PHE	0	0.067	0.030	14.820	-0.346	-0.346	0.000	0.000	0.000	0.000
133	A	188	GLU	-1	-0.800	-0.905	17.812	-14.273	-14.273	0.000	0.000	0.000	0.000
134	A	189	THR	0	-0.097	-0.051	11.429	0.092	0.092	0.000	0.000	0.000	0.000
135	A	190	VAL	0	0.032	0.010	13.614	-0.478	-0.478	0.000	0.000	0.000	0.000
136	A	191	ALA	0	-0.001	-0.005	15.357	0.434	0.434	0.000	0.000	0.000	0.000
137	A	192	ARG	1	0.916	0.971	15.203	17.820	17.820	0.000	0.000	0.000	0.000
138	A	193	ARG	1	0.829	0.907	11.692	22.904	22.904	0.000	0.000	0.000	0.000
139	A	194	LEU	0	0.044	0.009	16.048	0.483	0.483	0.000	0.000	0.000	0.000
140	A	195	GLN	0	-0.024	-0.004	19.125	0.336	0.336	0.000	0.000	0.000	0.000
141	A	196	GLU	-1	-0.896	-0.951	18.236	-14.031	-14.031	0.000	0.000	0.000	0.000
142	A	197	MET	0	-0.034	-0.012	16.806	0.352	0.352	0.000	0.000	0.000	0.000
143	A	198	ALA	0	0.061	0.024	20.590	0.508	0.508	0.000	0.000	0.000	0.000
144	A	199	PHE	0	-0.098	-0.041	23.484	0.794	0.794	0.000	0.000	0.000	0.000
145	A	200	LEU	0	-0.033	-0.018	20.227	0.513	0.513	0.000	0.000	0.000	0.000
146	A	201	ASN	0	-0.046	-0.022	22.477	0.566	0.566	0.000	0.000	0.000	0.000
147	A	202	LYS	1	0.949	0.975	26.006	10.547	10.547	0.000	0.000	0.000	0.000
148	A	203	GLY	0	-0.026	-0.009	29.380	0.142	0.142	0.000	0.000	0.000	0.000
149	A	204	LEU	0	-0.020	0.011	23.746	0.129	0.129	0.000	0.000	0.000	0.000
150	A	205	THR	0	-0.056	-0.020	27.517	0.041	0.041	0.000	0.000	0.000	0.000
151	A	206	ILE	0	0.020	0.009	21.208	-0.292	-0.292	0.000	0.000	0.000	0.000
152	A	207	GLU	-1	-0.868	-0.907	24.104	-10.691	-10.691	0.000	0.000	0.000	0.000
153	A	208	LEU	0	-0.019	-0.001	18.695	-0.597	-0.597	0.000	0.000	0.000	0.000
154	A	209	THR	0	-0.022	-0.024	22.351	0.764	0.764	0.000	0.000	0.000	0.000
155	A	210	ASP	-1	-0.767	-0.867	19.704	-16.437	-16.437	0.000	0.000	0.000	0.000
156	A	211	GLU	-1	-0.832	-0.902	22.349	-12.116	-12.116	0.000	0.000	0.000	0.000
157	A	212	ARG	1	0.702	0.817	16.838	17.565	17.565	0.000	0.000	0.000	0.000
158	A	213	ASP	-1	-0.854	-0.931	23.279	-12.948	-12.948	0.000	0.000	0.000	0.000
159	A	246	GLY	0	-0.004	0.010	25.306	0.482	0.482	0.000	0.000	0.000	0.000
160	A	247	LYS	1	0.814	0.915	22.313	13.458	13.458	0.000	0.000	0.000	0.000
161	A	248	HIS	0	-0.047	-0.041	24.665	-0.295	-0.295	0.000	0.000	0.000	0.000
162	A	249	ARG	1	0.816	0.885	21.759	13.326	13.326	0.000	0.000	0.000	0.000
163	A	250	VAL	0	0.029	0.029	25.351	-0.265	-0.265	0.000	0.000	0.000	0.000
164	A	251	PHE	0	-0.033	-0.023	21.671	-0.011	-0.011	0.000	0.000	0.000	0.000
165	A	252	HIS	0	0.015	-0.004	25.976	0.139	0.139	0.000	0.000	0.000	0.000
166	A	253	TYR	0	-0.028	-0.005	25.227	0.146	0.146	0.000	0.000	0.000	0.000
167	A	254	PRO	0	-0.003	0.006	29.965	-0.065	-0.065	0.000	0.000	0.000	0.000
168	A	255	GLY	-1	-0.922	-0.957	33.024	-9.096	-9.096	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:36:SER)