FMO DATABASE

FMODB ID: YV4Z2

Calculation Name: 4UEY-A-Xray372

Preferred Name: Virulence sensor histidine kinase phoQ

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UEY

Chain ID: A

ChEMBL ID: CHEMBL6096

UniProt ID: P0DM80

Base Structure: X-ray

Registration Date: 2023-09-23

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1311830.277657
FMO2-HF: Nuclear repulsion	1254707.967479
FMO2-HF: Total energy	-57122.310178
FMO2-MP2: Total energy	-57287.323241

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:48:THR)

Summations of interaction energy for fragment #1(A:48:THR)

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.
-12.552	-6.533	3.57	-3.213	-6.375	-0.019

Interaction energy analysis for fragmet #1(A:48:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.005

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	50	ARG	1	0.947	0.952	3.666	-6.696	-4.713	0.028	-0.857	-1.154	0.004
4	A	51	LEU	0	0.007	0.007	2.269	-2.699	-1.411	1.624	-0.810	-2.102	-0.005
5	A	52	LEU	0	0.062	0.034	3.660	0.314	1.082	0.012	-0.252	-0.527	0.000
6	A	53	ARG	1	0.871	0.943	5.944	0.569	0.569	0.000	0.000	0.000	0.000
7	A	54	GLY	0	-0.026	-0.009	7.642	0.232	0.232	0.000	0.000	0.000	0.000
8	A	55	GLU	-1	-0.795	-0.901	9.143	-0.840	-0.840	0.000	0.000	0.000	0.000
9	A	56	SER	0	-0.008	-0.053	10.267	0.211	0.211	0.000	0.000	0.000	0.000
10	A	57	ASN	0	-0.033	-0.018	11.990	0.159	0.159	0.000	0.000	0.000	0.000
11	A	58	LEU	0	0.028	0.033	13.526	0.089	0.089	0.000	0.000	0.000	0.000
12	A	59	PHE	0	0.052	0.005	14.348	0.098	0.098	0.000	0.000	0.000	0.000
13	A	60	TYR	0	-0.031	-0.006	16.395	0.070	0.070	0.000	0.000	0.000	0.000
14	A	61	THR	0	-0.145	-0.077	18.044	0.043	0.043	0.000	0.000	0.000	0.000
15	A	62	LEU	0	-0.019	-0.005	18.500	0.025	0.025	0.000	0.000	0.000	0.000
16	A	63	ALA	0	0.008	0.031	21.066	0.020	0.020	0.000	0.000	0.000	0.000
17	A	64	LYS	1	0.887	0.935	22.739	0.168	0.168	0.000	0.000	0.000	0.000
18	A	65	TRP	0	0.062	0.026	26.372	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	66	GLU	-1	-0.839	-0.901	28.246	-0.120	-0.120	0.000	0.000	0.000	0.000
20	A	67	ASN	0	-0.030	-0.018	31.720	0.003	0.003	0.000	0.000	0.000	0.000
21	A	68	ASN	0	-0.056	-0.031	31.578	0.001	0.001	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.945	0.981	29.056	0.114	0.114	0.000	0.000	0.000	0.000
23	A	70	ILE	0	0.021	0.020	22.809	0.005	0.005	0.000	0.000	0.000	0.000
24	A	71	SER	0	-0.056	-0.049	26.258	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	72	VAL	0	0.008	-0.013	20.503	0.001	0.001	0.000	0.000	0.000	0.000
26	A	73	GLU	-1	-0.959	-0.961	23.741	-0.208	-0.208	0.000	0.000	0.000	0.000
27	A	74	LEU	0	-0.018	-0.028	20.453	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	75	PRO	0	-0.008	-0.006	20.124	0.022	0.022	0.000	0.000	0.000	0.000
29	A	76	GLU	-1	-0.899	-0.951	23.286	-0.234	-0.234	0.000	0.000	0.000	0.000
30	A	77	ASN	0	-0.087	-0.047	24.476	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	78	LEU	0	-0.008	0.008	18.061	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	79	ASP	-1	-0.860	-0.932	16.862	-0.607	-0.607	0.000	0.000	0.000	0.000
33	A	80	MET	0	-0.029	-0.018	17.566	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	81	GLN	0	-0.062	-0.033	17.421	0.025	0.025	0.000	0.000	0.000	0.000
35	A	82	SER	0	0.002	0.021	12.431	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.047	0.021	9.530	0.041	0.041	0.000	0.000	0.000	0.000
37	A	84	THR	0	-0.056	-0.025	8.376	-0.271	-0.271	0.000	0.000	0.000	0.000
38	A	85	MET	0	0.012	0.029	11.053	0.209	0.209	0.000	0.000	0.000	0.000
39	A	86	THR	0	-0.020	-0.015	12.789	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	87	LEU	0	-0.043	-0.013	14.353	0.087	0.087	0.000	0.000	0.000	0.000
41	A	88	ILE	0	0.023	0.010	16.106	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	89	TYR	0	0.042	0.023	16.371	0.025	0.025	0.000	0.000	0.000	0.000
43	A	90	ASP	-1	-0.727	-0.810	20.389	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	91	GLU	-1	-0.900	-0.968	21.740	0.050	0.050	0.000	0.000	0.000	0.000
45	A	92	THR	0	-0.163	-0.130	22.985	0.018	0.018	0.000	0.000	0.000	0.000
46	A	93	GLY	0	-0.005	-0.003	21.084	0.009	0.009	0.000	0.000	0.000	0.000
47	A	94	LYS	1	0.908	0.954	22.087	0.008	0.008	0.000	0.000	0.000	0.000
48	A	95	LEU	0	-0.015	-0.006	19.727	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	96	LEU	0	-0.077	-0.045	22.073	0.010	0.010	0.000	0.000	0.000	0.000
50	A	97	TRP	0	0.022	0.001	17.918	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	98	THR	0	-0.016	-0.030	19.258	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	99	GLN	0	0.066	0.050	15.484	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	100	ARG	1	0.954	0.969	18.450	0.453	0.453	0.000	0.000	0.000	0.000
54	A	101	ASN	0	0.002	0.007	20.369	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	102	ILE	0	0.040	0.031	18.021	0.019	0.019	0.000	0.000	0.000	0.000
56	A	103	PRO	0	0.043	0.001	20.579	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	104	CYS	0	-0.120	-0.058	18.598	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	105	LEU	0	0.108	0.042	13.809	0.016	0.016	0.000	0.000	0.000	0.000
59	A	106	ILE	0	-0.011	-0.014	17.310	0.006	0.006	0.000	0.000	0.000	0.000
60	A	107	LYS	1	0.896	0.965	19.266	0.186	0.186	0.000	0.000	0.000	0.000
61	A	108	SER	0	0.002	0.003	16.566	0.033	0.033	0.000	0.000	0.000	0.000
62	A	109	ILE	0	-0.061	-0.008	13.498	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	110	GLN	0	0.004	0.002	15.506	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	111	PRO	0	0.046	0.008	16.612	0.014	0.014	0.000	0.000	0.000	0.000
65	A	112	GLU	-1	-0.905	-0.956	17.655	0.113	0.113	0.000	0.000	0.000	0.000
66	A	113	TRP	0	-0.012	-0.022	12.570	0.048	0.048	0.000	0.000	0.000	0.000
67	A	114	LEU	0	0.001	0.009	14.490	0.035	0.035	0.000	0.000	0.000	0.000
68	A	115	LYS	1	0.967	0.986	16.467	-0.130	-0.130	0.000	0.000	0.000	0.000
69	A	116	THR	0	-0.048	-0.004	14.290	0.042	0.042	0.000	0.000	0.000	0.000
70	A	117	ASN	0	0.033	0.009	11.235	-0.133	-0.133	0.000	0.000	0.000	0.000
71	A	118	GLY	0	-0.013	-0.010	9.444	0.130	0.130	0.000	0.000	0.000	0.000
72	A	119	PHE	0	-0.002	-0.003	2.788	-2.464	-0.637	1.908	-1.276	-2.459	-0.018
73	A	120	HIS	1	0.874	0.931	6.435	-0.135	-0.135	0.000	0.000	0.000	0.000
74	A	121	GLU	-1	-0.861	-0.939	7.325	-0.357	-0.357	0.000	0.000	0.000	0.000
75	A	122	ILE	0	-0.063	-0.021	9.629	0.096	0.096	0.000	0.000	0.000	0.000
76	A	123	GLU	-1	-0.865	-0.913	12.521	-0.071	-0.071	0.000	0.000	0.000	0.000
77	A	124	THR	0	-0.052	-0.032	14.934	0.004	0.004	0.000	0.000	0.000	0.000
78	A	125	ASN	0	0.104	0.035	17.143	0.000	0.000	0.000	0.000	0.000	0.000
79	A	126	VAL	0	0.100	0.041	18.657	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.839	-0.900	19.776	-0.232	-0.232	0.000	0.000	0.000	0.000
81	A	129	THR	0	0.047	0.016	14.823	-0.067	-0.067	0.000	0.000	0.000	0.000
82	A	130	SER	0	0.007	0.007	17.167	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	131	THR	0	-0.052	-0.023	20.139	0.008	0.008	0.000	0.000	0.000	0.000
84	A	132	LEU	0	-0.097	-0.043	13.445	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	133	LEU	0	-0.023	-0.021	14.072	-0.034	-0.034	0.000	0.000	0.000	0.000
86	A	134	SER	0	-0.069	-0.073	17.969	0.019	0.019	0.000	0.000	0.000	0.000
87	A	135	GLU	-1	-0.868	-0.897	21.059	-0.372	-0.372	0.000	0.000	0.000	0.000
88	A	136	ASP	-1	-0.886	-0.927	16.829	-0.602	-0.602	0.000	0.000	0.000	0.000
89	A	137	HIS	0	0.060	0.021	20.128	0.006	0.006	0.000	0.000	0.000	0.000
90	A	138	SER	0	-0.028	-0.023	19.642	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	139	ALA	0	-0.001	0.007	16.983	0.022	0.022	0.000	0.000	0.000	0.000
92	A	140	GLN	0	-0.002	-0.016	18.727	0.043	0.043	0.000	0.000	0.000	0.000
93	A	141	GLU	-1	-0.965	-0.965	21.880	-0.227	-0.227	0.000	0.000	0.000	0.000
94	A	142	LYS	1	0.912	0.947	17.954	0.486	0.486	0.000	0.000	0.000	0.000
95	A	143	LEU	0	-0.013	-0.008	17.308	0.016	0.016	0.000	0.000	0.000	0.000
96	A	144	LYS	1	0.910	0.951	20.952	0.232	0.232	0.000	0.000	0.000	0.000
97	A	145	GLU	-1	-0.909	-0.944	22.934	-0.229	-0.229	0.000	0.000	0.000	0.000
98	A	146	VAL	0	-0.029	-0.020	19.101	0.010	0.010	0.000	0.000	0.000	0.000
99	A	147	ARG	1	0.848	0.915	22.443	0.279	0.279	0.000	0.000	0.000	0.000
100	A	148	GLU	-1	-1.033	-1.012	24.580	-0.158	-0.158	0.000	0.000	0.000	0.000
101	A	149	ASP	-1	-0.985	-0.981	24.584	-0.153	-0.153	0.000	0.000	0.000	0.000
102	A	150	ASP	-1	-0.943	-0.983	23.459	-0.115	-0.115	0.000	0.000	0.000	0.000
103	A	151	ASP	-1	-0.963	-0.976	24.207	-0.146	-0.146	0.000	0.000	0.000	0.000
104	A	152	ASP	-1	-0.993	-0.990	23.916	-0.124	-0.124	0.000	0.000	0.000	0.000
105	A	153	ALA	0	-0.003	0.013	20.407	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	154	GLU	-1	-0.954	-0.979	16.267	-0.126	-0.126	0.000	0.000	0.000	0.000
107	A	155	MET	0	-0.092	-0.053	14.465	-0.075	-0.075	0.000	0.000	0.000	0.000
108	A	156	THR	0	0.044	-0.006	9.931	0.022	0.022	0.000	0.000	0.000	0.000
109	A	157	HIS	1	0.741	0.859	9.012	0.657	0.657	0.000	0.000	0.000	0.000
110	A	158	SER	0	0.011	0.009	4.448	-0.185	-0.089	-0.001	-0.012	-0.083	0.000
111	A	159	VAL	0	0.031	0.019	6.415	-0.155	-0.155	0.000	0.000	0.000	0.000
112	A	160	ALA	0	-0.057	-0.022	5.535	0.324	0.324	0.000	0.000	0.000	0.000
113	A	161	VAL	0	0.003	0.007	7.220	-0.050	-0.050	0.000	0.000	0.000	0.000
114	A	162	ASN	0	-0.001	-0.014	9.418	0.397	0.397	0.000	0.000	0.000	0.000
115	A	163	ILE	0	0.015	0.014	12.431	-0.049	-0.049	0.000	0.000	0.000	0.000
116	A	164	TYR	0	-0.031	0.013	13.672	0.009	0.009	0.000	0.000	0.000	0.000
117	A	165	PRO	0	0.034	0.018	18.710	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	166	ALA	0	0.010	0.004	22.005	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	167	THR	0	-0.041	-0.022	24.025	0.010	0.010	0.000	0.000	0.000	0.000
120	A	168	ALA	0	0.011	-0.007	26.814	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	169	ARG	1	0.876	0.943	23.568	0.118	0.118	0.000	0.000	0.000	0.000
122	A	170	MET	0	-0.027	-0.002	23.088	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	171	PRO	0	0.072	0.049	25.702	0.019	0.019	0.000	0.000	0.000	0.000
124	A	172	GLN	0	-0.045	-0.023	21.520	0.017	0.017	0.000	0.000	0.000	0.000
125	A	173	LEU	0	-0.032	-0.014	19.792	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	174	THR	0	-0.013	-0.005	15.155	0.037	0.037	0.000	0.000	0.000	0.000
127	A	175	ILE	0	-0.025	-0.005	13.531	-0.031	-0.031	0.000	0.000	0.000	0.000
128	A	176	VAL	0	-0.006	-0.008	11.495	0.015	0.015	0.000	0.000	0.000	0.000
129	A	177	VAL	0	0.005	0.007	8.466	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	178	VAL	0	-0.002	-0.009	8.614	-0.245	-0.245	0.000	0.000	0.000	0.000
131	A	179	ASP	-1	-0.846	-0.923	5.620	-2.739	-2.739	0.000	0.000	0.000	0.000
132	A	180	THR	0	-0.016	-0.028	8.108	0.298	0.298	0.000	0.000	0.000	0.000
133	A	181	ILE	0	0.031	0.010	9.241	0.203	0.203	0.000	0.000	0.000	0.000
134	A	182	PRO	0	-0.020	0.006	8.715	-0.232	-0.232	0.000	0.000	0.000	0.000
135	A	183	ILE	0	0.046	-0.003	5.921	-0.145	-0.145	0.000	0.000	0.000	0.000
136	A	184	GLU	-1	-0.759	-0.860	9.336	-0.401	-0.401	0.000	0.000	0.000	0.000
137	A	185	LEU	0	0.033	-0.001	12.108	0.052	0.052	0.000	0.000	0.000	0.000
138	A	186	LYS	1	0.815	0.946	4.295	2.362	2.419	-0.001	-0.006	-0.050	0.000
139	A	187	ARG	1	0.843	0.938	10.860	0.393	0.393	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:48:THR)