FMO DATABASE

FMODB ID: 1NM7Z

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1313867.672582
FMO2-HF: Nuclear repulsion	1256743.844032
FMO2-HF: Total energy	-57123.82855
FMO2-MP2: Total energy	-57288.798145

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.
-21.863	-15.658	2.438	-3.32	-5.323	-0.015

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 : 0.039 / q_NPA : 0.018

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	0.959	0.961	3.436	-7.560	-5.466	0.019	-0.951	-1.162	0.005
4	A	51	LEU	0	0.027	0.027	2.974	-2.883	-1.745	0.127	-0.374	-0.891	0.001
5	A	52	LEU	0	0.061	0.024	3.942	-1.192	-0.712	0.001	-0.156	-0.325	0.000
6	A	53	ARG	1	0.808	0.907	6.093	-1.073	-1.073	0.000	0.000	0.000	0.000
7	A	54	GLY	0	-0.018	0.001	8.218	-0.208	-0.208	0.000	0.000	0.000	0.000
8	A	55	GLU	-1	-0.787	-0.871	9.398	-0.130	-0.130	0.000	0.000	0.000	0.000
9	A	56	SER	0	-0.016	0.004	10.406	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	57	ASN	0	-0.004	-0.015	12.291	-0.101	-0.101	0.000	0.000	0.000	0.000
11	A	58	LEU	0	0.024	0.027	13.917	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	59	PHE	0	0.096	0.038	14.295	-0.041	-0.041	0.000	0.000	0.000	0.000
13	A	60	TYR	0	0.006	0.012	16.696	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	61	THR	0	-0.094	-0.048	18.644	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	62	LEU	0	-0.007	-0.005	18.560	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	63	ALA	0	0.015	0.011	20.806	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	64	LYS	1	0.831	0.920	22.607	-0.103	-0.103	0.000	0.000	0.000	0.000
18	A	65	TRP	0	0.050	0.012	26.200	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	66	GLU	-1	-0.851	-0.900	28.425	0.034	0.034	0.000	0.000	0.000	0.000
20	A	67	ASN	0	-0.018	-0.019	31.863	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	68	ASN	0	-0.022	-0.007	31.357	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.913	0.953	28.843	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	70	ILE	0	0.004	0.019	22.587	0.015	0.015	0.000	0.000	0.000	0.000
24	A	71	SER	0	-0.038	-0.033	26.073	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	72	VAL	0	-0.017	-0.032	20.571	0.022	0.022	0.000	0.000	0.000	0.000
26	A	73	GLU	-1	-0.897	-0.927	23.949	0.009	0.009	0.000	0.000	0.000	0.000
27	A	74	LEU	0	-0.017	-0.024	20.469	0.015	0.015	0.000	0.000	0.000	0.000
28	A	75	PRO	0	-0.036	-0.021	20.564	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	76	GLU	-1	-0.889	-0.948	23.378	0.034	0.034	0.000	0.000	0.000	0.000
30	A	77	ASN	0	-0.089	-0.053	24.574	0.003	0.003	0.000	0.000	0.000	0.000
31	A	78	LEU	0	-0.007	0.013	17.092	0.009	0.009	0.000	0.000	0.000	0.000
32	A	79	ASP	-1	-0.838	-0.927	17.436	-0.141	-0.141	0.000	0.000	0.000	0.000
33	A	80	MET	0	-0.052	-0.028	17.567	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	81	GLN	0	-0.065	-0.031	17.687	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	82	SER	0	0.001	0.016	12.808	-0.031	-0.031	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.029	0.019	9.479	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	84	THR	0	-0.067	-0.054	8.717	-0.263	-0.263	0.000	0.000	0.000	0.000
38	A	85	MET	0	0.009	0.014	11.305	0.126	0.126	0.000	0.000	0.000	0.000
39	A	86	THR	0	-0.003	-0.001	12.507	-0.074	-0.074	0.000	0.000	0.000	0.000
40	A	87	LEU	0	-0.029	-0.010	14.013	0.022	0.022	0.000	0.000	0.000	0.000
41	A	88	ILE	0	0.008	-0.001	15.916	0.041	0.041	0.000	0.000	0.000	0.000
42	A	89	TYR	0	0.047	0.017	16.522	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	90	ASP	-1	-0.723	-0.834	20.414	0.020	0.020	0.000	0.000	0.000	0.000
44	A	91	GLU	-1	-0.879	-0.926	21.982	0.076	0.076	0.000	0.000	0.000	0.000
45	A	92	THR	0	-0.099	-0.075	23.082	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	93	GLY	0	-0.006	-0.003	21.419	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	94	LYS	1	0.836	0.908	22.453	0.024	0.024	0.000	0.000	0.000	0.000
48	A	95	LEU	0	-0.024	-0.010	19.453	0.017	0.017	0.000	0.000	0.000	0.000
49	A	96	LEU	0	-0.050	-0.031	22.103	0.009	0.009	0.000	0.000	0.000	0.000
50	A	97	TRP	0	0.037	0.009	17.839	0.006	0.006	0.000	0.000	0.000	0.000
51	A	98	THR	0	-0.031	-0.040	18.867	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	99	GLN	0	0.043	0.037	15.122	0.017	0.017	0.000	0.000	0.000	0.000
53	A	100	ARG	1	0.839	0.903	18.957	0.327	0.327	0.000	0.000	0.000	0.000
54	A	101	ASN	0	-0.007	0.003	20.072	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	102	ILE	0	0.061	0.034	18.117	0.007	0.007	0.000	0.000	0.000	0.000
56	A	103	PRO	0	0.033	0.001	20.301	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	104	CYS	0	-0.108	-0.031	18.932	0.016	0.016	0.000	0.000	0.000	0.000
58	A	105	LEU	0	0.100	0.055	14.018	-0.025	-0.025	0.000	0.000	0.000	0.000
59	A	106	ILE	0	0.002	-0.006	17.171	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	107	LYS	1	0.899	0.948	19.062	0.350	0.350	0.000	0.000	0.000	0.000
61	A	108	SER	0	-0.005	-0.001	16.559	0.019	0.019	0.000	0.000	0.000	0.000
62	A	109	ILE	0	-0.064	-0.022	13.389	-0.089	-0.089	0.000	0.000	0.000	0.000
63	A	110	GLN	0	-0.001	-0.016	15.599	0.063	0.063	0.000	0.000	0.000	0.000
64	A	111	PRO	0	0.036	0.015	16.890	0.028	0.028	0.000	0.000	0.000	0.000
65	A	112	GLU	-1	-0.848	-0.914	17.450	-0.264	-0.264	0.000	0.000	0.000	0.000
66	A	113	TRP	0	0.023	-0.007	11.918	0.055	0.055	0.000	0.000	0.000	0.000
67	A	114	LEU	0	0.003	0.009	15.117	0.080	0.080	0.000	0.000	0.000	0.000
68	A	115	LYS	1	0.853	0.933	17.010	0.112	0.112	0.000	0.000	0.000	0.000
69	A	116	THR	0	-0.030	-0.002	14.178	0.025	0.025	0.000	0.000	0.000	0.000
70	A	117	ASN	0	0.015	0.016	11.576	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	118	GLY	0	0.001	-0.007	8.899	0.052	0.052	0.000	0.000	0.000	0.000
72	A	119	PHE	0	0.010	-0.002	2.442	-3.637	-1.268	2.291	-1.816	-2.845	-0.021
73	A	120	HIS	1	0.849	0.926	6.150	0.796	0.796	0.000	0.000	0.000	0.000
74	A	121	GLU	-1	-0.714	-0.846	5.961	-4.727	-4.727	0.000	0.000	0.000	0.000
75	A	122	ILE	0	-0.054	-0.026	9.212	0.306	0.306	0.000	0.000	0.000	0.000
76	A	123	GLU	-1	-0.873	-0.924	12.326	-0.928	-0.928	0.000	0.000	0.000	0.000
77	A	124	THR	0	-0.059	-0.043	15.008	0.110	0.110	0.000	0.000	0.000	0.000
78	A	125	ASN	0	0.072	0.033	17.322	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	126	VAL	0	0.108	0.065	18.854	-0.043	-0.043	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.787	-0.857	20.506	-0.358	-0.358	0.000	0.000	0.000	0.000
81	A	129	THR	0	0.022	-0.001	15.640	-0.057	-0.057	0.000	0.000	0.000	0.000
82	A	130	SER	0	0.008	-0.007	17.679	0.004	0.004	0.000	0.000	0.000	0.000
83	A	131	THR	0	-0.059	-0.040	20.735	0.040	0.040	0.000	0.000	0.000	0.000
84	A	132	LEU	0	-0.071	-0.035	13.476	0.026	0.026	0.000	0.000	0.000	0.000
85	A	133	LEU	0	0.018	0.010	14.550	0.019	0.019	0.000	0.000	0.000	0.000
86	A	134	SER	0	-0.036	-0.021	18.470	0.021	0.021	0.000	0.000	0.000	0.000
87	A	135	GLU	-1	-0.799	-0.872	21.233	-0.257	-0.257	0.000	0.000	0.000	0.000
88	A	136	ASP	-1	-0.810	-0.867	17.397	-0.399	-0.399	0.000	0.000	0.000	0.000
89	A	137	HIS	0	0.030	0.001	20.395	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	138	SER	0	-0.063	-0.057	19.219	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	139	ALA	0	-0.017	-0.015	17.265	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	140	GLN	0	-0.033	-0.029	19.127	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	141	GLU	-1	-0.870	-0.917	22.497	-0.262	-0.262	0.000	0.000	0.000	0.000
94	A	142	LYS	1	0.880	0.939	16.657	0.485	0.485	0.000	0.000	0.000	0.000
95	A	143	LEU	0	0.010	-0.005	17.698	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	144	LYS	1	0.733	0.883	21.419	0.280	0.280	0.000	0.000	0.000	0.000
97	A	145	GLU	-1	-0.909	-0.957	22.737	-0.362	-0.362	0.000	0.000	0.000	0.000
98	A	146	VAL	0	-0.024	-0.029	19.570	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	147	ARG	1	0.791	0.884	22.887	0.372	0.372	0.000	0.000	0.000	0.000
100	A	148	GLU	-1	-0.942	-0.963	25.231	-0.242	-0.242	0.000	0.000	0.000	0.000
101	A	149	ASP	-1	-0.964	-0.971	25.178	-0.308	-0.308	0.000	0.000	0.000	0.000
102	A	150	ASP	-1	-0.919	-0.966	23.161	-0.414	-0.414	0.000	0.000	0.000	0.000
103	A	151	ASP	-1	-0.954	-0.977	24.671	-0.309	-0.309	0.000	0.000	0.000	0.000
104	A	152	ASP	-1	-1.004	-1.008	24.735	-0.384	-0.384	0.000	0.000	0.000	0.000
105	A	153	ALA	0	-0.002	0.009	20.620	-0.039	-0.039	0.000	0.000	0.000	0.000
106	A	154	GLU	-1	-0.951	-0.977	16.430	-0.705	-0.705	0.000	0.000	0.000	0.000
107	A	155	MET	0	-0.071	-0.039	15.086	-0.068	-0.068	0.000	0.000	0.000	0.000
108	A	156	THR	0	-0.024	-0.035	10.300	0.028	0.028	0.000	0.000	0.000	0.000
109	A	157	HIS	1	0.770	0.876	9.406	0.997	0.997	0.000	0.000	0.000	0.000
110	A	158	SER	0	-0.026	-0.029	4.011	-0.253	-0.129	0.000	-0.023	-0.100	0.000
111	A	159	VAL	0	-0.013	0.000	5.992	0.565	0.565	0.000	0.000	0.000	0.000
112	A	160	ALA	0	-0.053	-0.024	5.681	-0.036	-0.036	0.000	0.000	0.000	0.000
113	A	161	VAL	0	0.018	0.017	7.277	0.061	0.061	0.000	0.000	0.000	0.000
114	A	162	ASN	0	-0.006	-0.011	9.012	0.500	0.500	0.000	0.000	0.000	0.000
115	A	163	ILE	0	0.020	0.012	12.737	-0.072	-0.072	0.000	0.000	0.000	0.000
116	A	164	TYR	0	-0.013	-0.033	13.101	0.159	0.159	0.000	0.000	0.000	0.000
117	A	165	PRO	0	0.037	0.022	18.747	-0.047	-0.047	0.000	0.000	0.000	0.000
118	A	166	ALA	0	0.017	0.011	22.241	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	167	THR	0	-0.035	-0.022	24.372	0.016	0.016	0.000	0.000	0.000	0.000
120	A	168	ALA	0	-0.005	-0.012	27.239	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	169	ARG	1	0.833	0.923	22.785	-0.202	-0.202	0.000	0.000	0.000	0.000
122	A	170	MET	0	-0.014	0.008	23.190	-0.022	-0.022	0.000	0.000	0.000	0.000
123	A	171	PRO	0	0.053	0.031	25.623	0.014	0.014	0.000	0.000	0.000	0.000
124	A	172	GLN	0	-0.060	-0.041	22.016	0.049	0.049	0.000	0.000	0.000	0.000
125	A	173	LEU	0	-0.043	-0.022	19.982	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	174	THR	0	-0.023	-0.021	15.510	0.068	0.068	0.000	0.000	0.000	0.000
127	A	175	ILE	0	-0.027	0.002	13.669	-0.049	-0.049	0.000	0.000	0.000	0.000
128	A	176	VAL	0	-0.021	-0.021	11.467	0.049	0.049	0.000	0.000	0.000	0.000
129	A	177	VAL	0	0.008	0.007	8.735	0.031	0.031	0.000	0.000	0.000	0.000
130	A	178	VAL	0	0.007	-0.005	8.400	-0.256	-0.256	0.000	0.000	0.000	0.000
131	A	179	ASP	-1	-0.800	-0.889	6.361	-2.323	-2.323	0.000	0.000	0.000	0.000
132	A	180	THR	0	-0.006	-0.020	8.477	0.065	0.065	0.000	0.000	0.000	0.000
133	A	181	ILE	0	0.017	0.000	9.420	0.117	0.117	0.000	0.000	0.000	0.000
134	A	182	PRO	0	0.006	0.018	9.552	-0.331	-0.331	0.000	0.000	0.000	0.000
135	A	183	ILE	0	-0.001	-0.025	6.205	-0.056	-0.056	0.000	0.000	0.000	0.000
136	A	184	GLU	-1	-0.783	-0.867	9.719	-1.153	-1.153	0.000	0.000	0.000	0.000
137	A	185	LEU	0	0.041	0.013	12.761	0.099	0.099	0.000	0.000	0.000	0.000
138	A	186	LYS	1	0.741	0.896	5.005	3.398	3.398	0.000	0.000	0.000	0.000
139	A	187	ARG	1	0.860	0.930	10.632	1.007	1.007	0.000	0.000	0.000	0.000

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