FMO DATABASE

FMODB ID: VQ951

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	OptHSide
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	-1313455.96386
FMO2-HF: Nuclear repulsion	1256332.618593
FMO2-HF: Total energy	-57123.345267
FMO2-MP2: Total energy	-57288.338996

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.
-20.947	-14.744	3.364	-3.477	-6.088	-0.011

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 : 0.040 / q_NPA : 0.013

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	3.316	-6.643	-4.533	0.020	-0.900	-1.231	0.005
4	A	51	LEU	0	0.017	0.015	2.795	-4.041	-2.279	0.742	-0.754	-1.750	0.004
5	A	52	LEU	0	0.054	0.031	3.739	-2.112	-1.483	0.007	-0.228	-0.407	0.000
6	A	53	ARG	1	0.856	0.928	5.929	-1.484	-1.484	0.000	0.000	0.000	0.000
7	A	54	GLY	0	-0.017	-0.006	8.333	-0.319	-0.319	0.000	0.000	0.000	0.000
8	A	55	GLU	-1	-0.762	-0.865	9.292	0.033	0.033	0.000	0.000	0.000	0.000
9	A	56	SER	0	-0.011	0.003	10.255	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	57	ASN	0	-0.021	-0.020	12.167	-0.146	-0.146	0.000	0.000	0.000	0.000
11	A	58	LEU	0	0.023	0.027	13.822	-0.078	-0.078	0.000	0.000	0.000	0.000
12	A	59	PHE	0	0.073	0.019	14.078	-0.060	-0.060	0.000	0.000	0.000	0.000
13	A	60	TYR	0	-0.017	-0.001	16.386	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	61	THR	0	-0.118	-0.067	18.270	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	62	LEU	0	-0.015	-0.006	18.468	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	63	ALA	0	-0.003	0.018	21.046	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	64	LYS	1	0.873	0.938	22.730	-0.159	-0.159	0.000	0.000	0.000	0.000
18	A	65	TRP	0	0.049	0.025	26.364	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	66	GLU	-1	-0.836	-0.902	28.242	0.073	0.073	0.000	0.000	0.000	0.000
20	A	67	ASN	0	-0.031	-0.020	31.718	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	68	ASN	0	-0.047	-0.027	31.648	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.935	0.977	29.006	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	70	ILE	0	0.021	0.022	22.751	0.013	0.013	0.000	0.000	0.000	0.000
24	A	71	SER	0	-0.046	-0.043	26.260	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	72	VAL	0	-0.009	-0.025	20.384	0.023	0.023	0.000	0.000	0.000	0.000
26	A	73	GLU	-1	-0.937	-0.946	23.735	0.055	0.055	0.000	0.000	0.000	0.000
27	A	74	LEU	0	-0.014	-0.025	20.353	0.022	0.022	0.000	0.000	0.000	0.000
28	A	75	PRO	0	-0.011	-0.010	20.259	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	76	GLU	-1	-0.900	-0.956	23.266	0.078	0.078	0.000	0.000	0.000	0.000
30	A	77	ASN	0	-0.094	-0.050	24.465	0.002	0.002	0.000	0.000	0.000	0.000
31	A	78	LEU	0	-0.002	0.017	17.291	0.013	0.013	0.000	0.000	0.000	0.000
32	A	79	ASP	-1	-0.861	-0.939	16.922	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	80	MET	0	-0.045	-0.024	17.551	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	81	GLN	0	-0.061	-0.030	17.413	-0.052	-0.052	0.000	0.000	0.000	0.000
35	A	82	SER	0	0.018	0.029	12.434	-0.041	-0.041	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.036	0.015	9.461	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	84	THR	0	-0.062	-0.052	8.469	-0.233	-0.233	0.000	0.000	0.000	0.000
38	A	85	MET	0	-0.012	0.008	11.059	0.094	0.094	0.000	0.000	0.000	0.000
39	A	86	THR	0	0.003	-0.009	12.805	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	87	LEU	0	-0.045	-0.012	14.363	0.008	0.008	0.000	0.000	0.000	0.000
41	A	88	ILE	0	0.016	0.004	16.134	0.041	0.041	0.000	0.000	0.000	0.000
42	A	89	TYR	0	0.043	0.019	16.393	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	90	ASP	-1	-0.741	-0.854	20.483	0.052	0.052	0.000	0.000	0.000	0.000
44	A	91	GLU	-1	-0.877	-0.939	21.902	0.099	0.099	0.000	0.000	0.000	0.000
45	A	92	THR	0	-0.109	-0.063	23.189	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	93	GLY	0	-0.013	-0.003	21.217	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	94	LYS	1	0.875	0.928	22.218	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	95	LEU	0	-0.020	-0.004	19.660	0.016	0.016	0.000	0.000	0.000	0.000
49	A	96	LEU	0	-0.059	-0.038	22.107	0.005	0.005	0.000	0.000	0.000	0.000
50	A	97	TRP	0	0.022	-0.001	17.752	0.003	0.003	0.000	0.000	0.000	0.000
51	A	98	THR	0	-0.006	-0.019	19.274	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	99	GLN	0	0.057	0.046	15.354	0.008	0.008	0.000	0.000	0.000	0.000
53	A	100	ARG	1	0.851	0.907	18.407	0.235	0.235	0.000	0.000	0.000	0.000
54	A	101	ASN	0	-0.011	-0.002	20.389	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	102	ILE	0	0.044	0.030	18.526	0.005	0.005	0.000	0.000	0.000	0.000
56	A	103	PRO	0	0.038	0.000	20.575	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	104	CYS	0	-0.109	-0.029	19.173	0.022	0.022	0.000	0.000	0.000	0.000
58	A	105	LEU	0	0.095	0.051	14.345	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	106	ILE	0	-0.008	-0.008	17.186	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	107	LYS	1	0.907	0.956	19.162	0.287	0.287	0.000	0.000	0.000	0.000
61	A	108	SER	0	-0.009	-0.017	16.542	0.000	0.000	0.000	0.000	0.000	0.000
62	A	109	ILE	0	-0.065	-0.012	13.502	-0.066	-0.066	0.000	0.000	0.000	0.000
63	A	110	GLN	0	0.003	-0.002	15.517	0.046	0.046	0.000	0.000	0.000	0.000
64	A	111	PRO	0	0.072	0.017	16.708	0.026	0.026	0.000	0.000	0.000	0.000
65	A	112	GLU	-1	-0.876	-0.934	17.814	-0.217	-0.217	0.000	0.000	0.000	0.000
66	A	113	TRP	0	0.004	-0.019	12.204	0.057	0.057	0.000	0.000	0.000	0.000
67	A	114	LEU	0	-0.011	0.007	14.710	0.067	0.067	0.000	0.000	0.000	0.000
68	A	115	LYS	1	0.894	0.949	16.652	0.084	0.084	0.000	0.000	0.000	0.000
69	A	116	THR	0	-0.030	0.004	14.466	0.028	0.028	0.000	0.000	0.000	0.000
70	A	117	ASN	0	0.026	0.009	11.490	0.034	0.034	0.000	0.000	0.000	0.000
71	A	118	GLY	0	-0.014	-0.009	9.696	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	119	PHE	0	0.013	0.005	2.708	-2.102	-0.522	2.597	-1.579	-2.597	-0.020
73	A	120	HIS	1	0.851	0.921	6.688	0.521	0.521	0.000	0.000	0.000	0.000
74	A	121	GLU	-1	-0.762	-0.885	7.039	-3.209	-3.209	0.000	0.000	0.000	0.000
75	A	122	ILE	0	-0.051	-0.015	9.552	0.235	0.235	0.000	0.000	0.000	0.000
76	A	123	GLU	-1	-0.879	-0.922	12.506	-0.864	-0.864	0.000	0.000	0.000	0.000
77	A	124	THR	0	-0.050	-0.046	15.207	0.106	0.106	0.000	0.000	0.000	0.000
78	A	125	ASN	0	0.116	0.051	17.475	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	126	VAL	0	0.105	0.051	19.282	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.806	-0.879	20.319	-0.297	-0.297	0.000	0.000	0.000	0.000
81	A	129	THR	0	0.037	0.011	15.376	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	130	SER	0	0.023	0.011	17.774	0.006	0.006	0.000	0.000	0.000	0.000
83	A	131	THR	0	-0.067	-0.037	20.681	0.039	0.039	0.000	0.000	0.000	0.000
84	A	132	LEU	0	-0.085	-0.038	14.102	0.021	0.021	0.000	0.000	0.000	0.000
85	A	133	LEU	0	-0.004	-0.013	14.451	0.023	0.023	0.000	0.000	0.000	0.000
86	A	134	SER	0	-0.034	-0.006	18.469	0.015	0.015	0.000	0.000	0.000	0.000
87	A	135	GLU	-1	-0.817	-0.894	21.053	-0.190	-0.190	0.000	0.000	0.000	0.000
88	A	136	ASP	-1	-0.847	-0.907	17.178	-0.336	-0.336	0.000	0.000	0.000	0.000
89	A	137	HIS	0	0.069	0.020	20.446	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	138	SER	0	-0.029	-0.022	19.346	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	139	ALA	0	-0.036	-0.018	17.194	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	140	GLN	0	-0.013	-0.023	18.966	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	141	GLU	-1	-0.909	-0.942	22.198	-0.234	-0.234	0.000	0.000	0.000	0.000
94	A	142	LYS	1	0.900	0.943	17.037	0.418	0.418	0.000	0.000	0.000	0.000
95	A	143	LEU	0	-0.008	-0.007	17.846	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	144	LYS	1	0.771	0.900	21.286	0.245	0.245	0.000	0.000	0.000	0.000
97	A	145	GLU	-1	-0.915	-0.955	22.972	-0.330	-0.330	0.000	0.000	0.000	0.000
98	A	146	VAL	0	-0.025	-0.021	19.456	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	147	ARG	1	0.833	0.908	22.727	0.323	0.323	0.000	0.000	0.000	0.000
100	A	148	GLU	-1	-0.960	-0.985	24.967	-0.219	-0.219	0.000	0.000	0.000	0.000
101	A	149	ASP	-1	-0.972	-0.975	24.877	-0.298	-0.298	0.000	0.000	0.000	0.000
102	A	150	ASP	-1	-0.945	-0.985	23.562	-0.382	-0.382	0.000	0.000	0.000	0.000
103	A	151	ASP	-1	-0.949	-0.972	24.612	-0.283	-0.283	0.000	0.000	0.000	0.000
104	A	152	ASP	-1	-1.030	-1.015	24.400	-0.342	-0.342	0.000	0.000	0.000	0.000
105	A	153	ALA	0	0.014	0.036	20.604	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	154	GLU	-1	-0.969	-0.990	16.492	-0.638	-0.638	0.000	0.000	0.000	0.000
107	A	155	MET	0	-0.091	-0.052	15.018	-0.067	-0.067	0.000	0.000	0.000	0.000
108	A	156	THR	0	0.022	-0.014	10.186	0.045	0.045	0.000	0.000	0.000	0.000
109	A	157	HIS	1	0.744	0.861	9.673	0.838	0.838	0.000	0.000	0.000	0.000
110	A	158	SER	0	-0.005	-0.004	4.346	-0.394	-0.308	-0.001	-0.014	-0.071	0.000
111	A	159	VAL	0	-0.003	0.001	6.372	0.396	0.396	0.000	0.000	0.000	0.000
112	A	160	ALA	0	-0.053	-0.020	5.663	0.015	0.015	0.000	0.000	0.000	0.000
113	A	161	VAL	0	0.006	0.002	7.340	0.073	0.073	0.000	0.000	0.000	0.000
114	A	162	ASN	0	-0.017	-0.013	9.349	0.491	0.491	0.000	0.000	0.000	0.000
115	A	163	ILE	0	0.013	0.011	12.669	-0.076	-0.076	0.000	0.000	0.000	0.000
116	A	164	TYR	0	-0.039	-0.034	13.131	0.123	0.123	0.000	0.000	0.000	0.000
117	A	165	PRO	0	0.038	0.022	18.710	-0.047	-0.047	0.000	0.000	0.000	0.000
118	A	166	ALA	0	0.006	0.004	22.087	0.006	0.006	0.000	0.000	0.000	0.000
119	A	167	THR	0	-0.047	-0.034	24.020	0.009	0.009	0.000	0.000	0.000	0.000
120	A	168	ALA	0	0.003	-0.007	26.827	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	169	ARG	1	0.858	0.932	23.216	-0.240	-0.240	0.000	0.000	0.000	0.000
122	A	170	MET	0	-0.023	0.006	23.033	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	171	PRO	0	0.061	0.046	25.630	0.013	0.013	0.000	0.000	0.000	0.000
124	A	172	GLN	0	-0.041	-0.041	21.706	0.046	0.046	0.000	0.000	0.000	0.000
125	A	173	LEU	0	-0.028	-0.012	19.824	-0.026	-0.026	0.000	0.000	0.000	0.000
126	A	174	THR	0	-0.029	-0.012	15.358	0.061	0.061	0.000	0.000	0.000	0.000
127	A	175	ILE	0	-0.036	-0.012	13.622	-0.042	-0.042	0.000	0.000	0.000	0.000
128	A	176	VAL	0	-0.011	-0.013	11.578	0.063	0.063	0.000	0.000	0.000	0.000
129	A	177	VAL	0	0.010	0.008	8.495	0.017	0.017	0.000	0.000	0.000	0.000
130	A	178	VAL	0	0.005	-0.005	8.534	-0.264	-0.264	0.000	0.000	0.000	0.000
131	A	179	ASP	-1	-0.791	-0.873	6.158	-2.142	-2.142	0.000	0.000	0.000	0.000
132	A	180	THR	0	-0.020	-0.029	8.495	0.021	0.021	0.000	0.000	0.000	0.000
133	A	181	ILE	0	0.030	0.006	9.548	0.112	0.112	0.000	0.000	0.000	0.000
134	A	182	PRO	0	-0.009	0.011	9.162	-0.304	-0.304	0.000	0.000	0.000	0.000
135	A	183	ILE	0	0.035	-0.006	6.222	-0.076	-0.076	0.000	0.000	0.000	0.000
136	A	184	GLU	-1	-0.773	-0.869	9.612	-1.085	-1.085	0.000	0.000	0.000	0.000
137	A	185	LEU	0	0.030	-0.002	12.328	0.108	0.108	0.000	0.000	0.000	0.000
138	A	186	LYS	1	0.756	0.900	4.764	3.098	3.134	-0.001	-0.002	-0.032	0.000
139	A	187	ARG	1	0.855	0.943	10.813	1.030	1.030	0.000	0.000	0.000	0.000

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