FMO DATABASE

FMODB ID: YZGJ2

Calculation Name: 3CGZ-A-Xray372

Preferred Name: Virulence sensor histidine kinase phoQ

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3CGZ

Chain ID: A

ChEMBL ID: CHEMBL6096

UniProt ID: P0DM80

Base Structure: X-ray

Registration Date: 2023-09-19

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1262004.497597
FMO2-HF: Nuclear repulsion	1206478.141906
FMO2-HF: Total energy	-55526.355691
FMO2-MP2: Total energy	-55687.854327

3D Structure

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:331:SER)

Summations of interaction energy for fragment #1(A:331: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.
-3.588	-1.23	0.111	-1.011	-1.458	0

Interaction energy analysis for fragmet #1(A:331:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.047

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	333	LEU	0	-0.058	-0.024	3.808	-0.185	1.513	-0.014	-0.805	-0.879	-0.001
4	A	334	LEU	0	0.041	0.045	5.987	-0.001	-0.001	0.000	0.000	0.000	0.000
5	A	335	SER	0	-0.036	-0.019	9.542	0.071	0.071	0.000	0.000	0.000	0.000
6	A	336	ARG	1	0.866	0.923	12.797	0.111	0.111	0.000	0.000	0.000	0.000
7	A	337	GLU	-1	-0.928	-0.974	15.089	-0.098	-0.098	0.000	0.000	0.000	0.000
8	A	338	LEU	0	-0.053	-0.009	18.085	0.013	0.013	0.000	0.000	0.000	0.000
9	A	339	HIS	0	0.029	0.013	21.163	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	340	PRO	0	-0.011	-0.009	24.836	0.005	0.005	0.000	0.000	0.000	0.000
11	A	341	VAL	0	0.054	0.022	27.635	0.004	0.004	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.023	0.012	29.848	0.003	0.003	0.000	0.000	0.000	0.000
13	A	343	PRO	0	-0.002	-0.018	31.221	0.003	0.003	0.000	0.000	0.000	0.000
14	A	344	LEU	0	0.001	0.011	28.102	0.003	0.003	0.000	0.000	0.000	0.000
15	A	345	LEU	0	0.005	-0.001	32.758	0.004	0.004	0.000	0.000	0.000	0.000
16	A	346	ASP	-1	-0.917	-0.944	35.282	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	347	ASN	0	0.017	-0.008	36.181	0.004	0.004	0.000	0.000	0.000	0.000
18	A	348	LEU	0	-0.021	0.003	34.619	0.002	0.002	0.000	0.000	0.000	0.000
19	A	349	ILE	0	0.048	0.023	38.595	0.002	0.002	0.000	0.000	0.000	0.000
20	A	350	SER	0	-0.036	-0.011	41.140	0.002	0.002	0.000	0.000	0.000	0.000
21	A	351	ALA	0	-0.067	-0.036	41.612	0.002	0.002	0.000	0.000	0.000	0.000
22	A	352	LEU	0	0.044	0.011	40.624	0.002	0.002	0.000	0.000	0.000	0.000
23	A	353	ASN	0	0.021	0.021	44.395	0.002	0.002	0.000	0.000	0.000	0.000
24	A	354	LYS	1	0.893	0.940	46.547	0.019	0.019	0.000	0.000	0.000	0.000
25	A	355	VAL	0	-0.023	-0.005	45.386	0.001	0.001	0.000	0.000	0.000	0.000
26	A	356	TYR	0	-0.054	-0.042	45.458	0.002	0.002	0.000	0.000	0.000	0.000
27	A	357	GLN	0	-0.008	0.003	50.078	0.000	0.000	0.000	0.000	0.000	0.000
28	A	358	ARG	1	0.871	0.924	52.318	0.009	0.009	0.000	0.000	0.000	0.000
29	A	359	LYS	1	0.781	0.897	50.036	0.009	0.009	0.000	0.000	0.000	0.000
30	A	360	GLY	0	-0.012	0.006	53.386	0.000	0.000	0.000	0.000	0.000	0.000
31	A	361	VAL	0	-0.019	-0.011	47.157	0.000	0.000	0.000	0.000	0.000	0.000
32	A	362	ASN	0	-0.063	-0.024	49.025	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	363	ILE	0	0.001	-0.009	42.309	0.000	0.000	0.000	0.000	0.000	0.000
34	A	364	SER	0	-0.042	-0.008	43.646	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	365	MET	0	-0.004	-0.014	36.713	0.000	0.000	0.000	0.000	0.000	0.000
36	A	366	ASP	-1	-0.956	-0.954	38.767	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	367	ILE	0	-0.018	-0.024	32.395	0.000	0.000	0.000	0.000	0.000	0.000
38	A	368	SER	0	0.008	0.009	32.158	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	369	PRO	0	-0.024	-0.026	31.662	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	370	GLU	-1	-0.985	-0.995	27.790	-0.063	-0.063	0.000	0.000	0.000	0.000
41	A	371	ILE	0	0.000	0.012	26.753	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	372	SER	0	-0.049	-0.032	23.611	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	373	PHE	0	0.021	0.004	23.919	0.004	0.004	0.000	0.000	0.000	0.000
44	A	374	VAL	0	-0.031	-0.012	17.318	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	375	GLY	0	0.017	-0.003	19.779	0.010	0.010	0.000	0.000	0.000	0.000
46	A	376	GLU	-1	-0.919	-0.955	20.714	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	377	GLN	0	-0.016	-0.011	23.261	0.008	0.008	0.000	0.000	0.000	0.000
48	A	378	ASN	0	0.013	-0.011	26.092	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.747	-0.811	24.841	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	380	PHE	0	-0.009	0.002	26.862	0.002	0.002	0.000	0.000	0.000	0.000
51	A	381	VAL	0	0.000	-0.017	28.557	0.002	0.002	0.000	0.000	0.000	0.000
52	A	382	GLU	-1	-0.938	-0.961	31.042	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	383	VAL	0	-0.024	-0.013	29.409	0.002	0.002	0.000	0.000	0.000	0.000
54	A	384	MET	0	-0.005	-0.008	31.541	0.002	0.002	0.000	0.000	0.000	0.000
55	A	385	GLY	0	0.011	0.011	34.139	0.001	0.001	0.000	0.000	0.000	0.000
56	A	386	ASN	0	-0.036	-0.031	36.001	0.002	0.002	0.000	0.000	0.000	0.000
57	A	387	VAL	0	0.048	0.001	34.939	0.001	0.001	0.000	0.000	0.000	0.000
58	A	388	LEU	0	-0.001	0.006	37.098	0.001	0.001	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.852	-0.918	39.787	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	390	ASN	0	-0.098	-0.081	41.135	0.001	0.001	0.000	0.000	0.000	0.000
61	A	391	ALA	0	0.085	0.044	41.760	0.001	0.001	0.000	0.000	0.000	0.000
62	A	392	CYS	0	-0.017	0.003	43.579	0.000	0.000	0.000	0.000	0.000	0.000
63	A	393	LYS	1	0.875	0.949	45.169	0.007	0.007	0.000	0.000	0.000	0.000
64	A	394	TYR	-1	-0.838	-0.912	45.483	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	395	CYS	0	-0.061	0.014	47.114	0.000	0.000	0.000	0.000	0.000	0.000
66	A	396	LEU	0	-0.069	-0.031	48.933	0.001	0.001	0.000	0.000	0.000	0.000
67	A	397	GLU	-1	-0.962	-1.018	51.494	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	398	PHE	0	-0.057	-0.006	48.235	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	399	VAL	0	0.035	0.008	42.428	0.001	0.001	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.937	-0.970	42.430	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	401	ILE	0	-0.010	-0.009	36.256	0.001	0.001	0.000	0.000	0.000	0.000
72	A	402	SER	0	0.037	0.020	36.559	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	403	ALA	0	0.008	-0.006	31.095	0.001	0.001	0.000	0.000	0.000	0.000
74	A	404	ARG	1	0.910	0.956	30.618	0.024	0.024	0.000	0.000	0.000	0.000
75	A	405	GLN	0	0.063	0.041	24.310	0.001	0.001	0.000	0.000	0.000	0.000
76	A	406	THR	0	-0.050	-0.016	24.787	0.003	0.003	0.000	0.000	0.000	0.000
77	A	407	ASP	-1	-0.929	-0.977	19.509	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	408	ASP	-1	-0.865	-0.940	18.479	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	409	HIS	0	-0.010	0.003	20.311	0.001	0.001	0.000	0.000	0.000	0.000
80	A	410	LEU	0	-0.026	0.000	23.664	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	411	HIS	0	-0.071	-0.054	26.080	0.003	0.003	0.000	0.000	0.000	0.000
82	A	412	ILE	0	0.015	0.001	29.740	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	413	PHE	0	-0.044	-0.032	32.430	0.003	0.003	0.000	0.000	0.000	0.000
84	A	414	VAL	0	0.008	0.001	36.038	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	415	GLU	-1	-0.872	-0.919	38.915	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	416	ASP	-1	-0.719	-0.841	42.341	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	417	ASP	-1	-0.695	-0.850	45.748	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	418	GLY	0	0.002	0.011	48.456	0.000	0.000	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.113	-0.053	49.924	0.000	0.000	0.000	0.000	0.000	0.000
90	A	420	GLY	0	0.079	0.036	49.131	0.000	0.000	0.000	0.000	0.000	0.000
91	A	421	ILE	0	0.038	0.017	43.863	0.000	0.000	0.000	0.000	0.000	0.000
92	A	422	PRO	0	-0.083	-0.058	46.119	0.000	0.000	0.000	0.000	0.000	0.000
93	A	423	HIS	0	-0.004	0.028	47.716	0.001	0.001	0.000	0.000	0.000	0.000
94	A	438	THR	0	-0.039	-0.023	53.236	0.000	0.000	0.000	0.000	0.000	0.000
95	A	439	LEU	0	-0.050	-0.035	51.202	0.000	0.000	0.000	0.000	0.000	0.000
96	A	440	ARG	0	-0.031	-0.033	44.245	0.000	0.000	0.000	0.000	0.000	0.000
97	A	441	PRO	0	-0.032	0.022	45.178	0.001	0.001	0.000	0.000	0.000	0.000
98	A	442	GLY	0	0.063	0.016	42.308	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	443	GLN	0	-0.056	-0.049	41.250	0.000	0.000	0.000	0.000	0.000	0.000
100	A	444	GLY	0	0.072	-0.010	39.742	0.000	0.000	0.000	0.000	0.000	0.000
101	A	445	VAL	0	-0.052	-0.032	40.301	0.001	0.001	0.000	0.000	0.000	0.000
102	A	446	GLY	0	0.040	0.014	41.742	0.000	0.000	0.000	0.000	0.000	0.000
103	A	447	LEU	0	0.006	0.028	37.251	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	448	ALA	0	-0.032	-0.033	36.303	0.000	0.000	0.000	0.000	0.000	0.000
105	A	449	VAL	0	0.085	0.048	33.669	0.001	0.001	0.000	0.000	0.000	0.000
106	A	450	ALA	0	0.037	0.024	32.716	0.000	0.000	0.000	0.000	0.000	0.000
107	A	451	ARG	1	0.838	0.960	31.512	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	452	GLU	-1	-0.957	-0.962	30.781	0.004	0.004	0.000	0.000	0.000	0.000
109	A	453	ILE	0	0.047	0.018	27.328	0.001	0.001	0.000	0.000	0.000	0.000
110	A	454	THR	0	-0.062	-0.039	26.684	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	455	GLU	-1	-0.906	-0.952	26.236	0.010	0.010	0.000	0.000	0.000	0.000
112	A	456	GLN	0	-0.049	-0.014	23.722	0.000	0.000	0.000	0.000	0.000	0.000
113	A	457	TYR	0	-0.174	-0.137	21.405	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	458	ALA	0	-0.079	-0.031	21.355	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	459	GLY	0	0.037	0.019	23.396	0.000	0.000	0.000	0.000	0.000	0.000
116	A	460	GLN	0	-0.041	-0.020	26.393	0.003	0.003	0.000	0.000	0.000	0.000
117	A	461	ILE	0	0.001	0.000	30.154	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	462	ILE	0	-0.043	-0.011	32.575	0.002	0.002	0.000	0.000	0.000	0.000
119	A	463	ALA	0	0.014	0.009	36.034	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	464	SER	0	-0.065	-0.030	39.690	0.001	0.001	0.000	0.000	0.000	0.000
121	A	465	ASP	-1	-0.854	-0.935	41.727	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	466	SER	0	-0.020	-0.025	43.870	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	467	LEU	0	-0.050	-0.037	45.031	0.001	0.001	0.000	0.000	0.000	0.000
124	A	468	LEU	0	-0.051	-0.017	45.673	0.000	0.000	0.000	0.000	0.000	0.000
125	A	469	GLY	0	-0.042	-0.019	48.473	0.000	0.000	0.000	0.000	0.000	0.000
126	A	470	GLY	0	-0.008	0.018	47.777	0.001	0.001	0.000	0.000	0.000	0.000
127	A	471	ALA	0	-0.024	-0.017	43.214	0.000	0.000	0.000	0.000	0.000	0.000
128	A	472	ARG	1	0.893	0.964	36.589	0.011	0.011	0.000	0.000	0.000	0.000
129	A	473	MET	0	-0.037	-0.030	37.605	0.002	0.002	0.000	0.000	0.000	0.000
130	A	474	GLU	-1	-0.869	-0.935	32.215	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	475	VAL	0	-0.029	-0.019	30.264	0.002	0.002	0.000	0.000	0.000	0.000
132	A	476	VAL	0	0.004	0.002	26.696	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	477	PHE	0	-0.006	-0.007	24.389	0.003	0.003	0.000	0.000	0.000	0.000
134	A	478	GLY	0	0.114	0.053	22.448	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	479	ARG	1	0.890	0.935	17.708	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	480	GLN	0	0.002	0.005	18.495	-0.016	-0.016	0.000	0.000	0.000	0.000
137	A	481	HIS	0	0.008	0.022	12.179	-0.011	-0.011	0.000	0.000	0.000	0.000
138	A	482	PRO	0	0.058	0.023	15.185	-0.010	-0.010	0.000	0.000	0.000	0.000
139	A	483	THR	0	-0.069	-0.029	10.232	-0.041	-0.041	0.000	0.000	0.000	0.000
140	A	484	GLN	0	-0.009	-0.021	9.026	0.081	0.081	0.000	0.000	0.000	0.000
141	A	485	LYS	1	0.928	0.959	2.790	-3.381	-2.721	0.125	-0.206	-0.579	0.001
142	A	486	GLU	-1	-0.873	-0.914	5.647	0.273	0.273	0.000	0.000	0.000	0.000
143	A	487	GLU	-1	-0.990	-1.016	6.822	-0.232	-0.232	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:331:SER)