FMO DATABASE

FMODB ID: V5GJ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1262356.288524
FMO2-HF: Nuclear repulsion	1206827.940482
FMO2-HF: Total energy	-55528.348042
FMO2-MP2: Total energy	-55689.603529

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.
-24.122	-27.297	13.36	-5.58	-4.604	0.047

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 : -0.022 / q_NPA : -0.008

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	-0.017	-0.026	3.840	-0.620	0.634	0.001	-0.620	-0.635	0.001
4	A	334	LEU	0	0.029	0.034	6.497	-0.062	-0.062	0.000	0.000	0.000	0.000
5	A	335	SER	0	-0.010	-0.005	10.130	0.072	0.072	0.000	0.000	0.000	0.000
6	A	336	ARG	1	0.800	0.878	13.338	-0.130	-0.130	0.000	0.000	0.000	0.000
7	A	337	GLU	-1	-0.889	-0.944	15.259	0.005	0.005	0.000	0.000	0.000	0.000
8	A	338	LEU	0	-0.024	-0.011	18.295	0.009	0.009	0.000	0.000	0.000	0.000
9	A	339	HIS	0	0.016	0.010	21.531	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	340	PRO	0	-0.022	-0.018	25.118	0.003	0.003	0.000	0.000	0.000	0.000
11	A	341	VAL	0	0.042	0.023	27.925	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	342	ALA	0	0.024	0.016	30.148	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	343	PRO	0	0.012	-0.010	31.707	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	344	LEU	0	0.012	0.019	28.438	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	345	LEU	0	0.020	0.005	33.159	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	346	ASP	-1	-0.902	-0.945	35.561	0.010	0.010	0.000	0.000	0.000	0.000
17	A	347	ASN	0	-0.052	-0.026	36.386	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	348	LEU	0	0.007	0.011	34.515	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	349	ILE	0	0.031	0.021	38.666	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	350	SER	0	-0.031	-0.018	41.371	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	351	ALA	0	-0.088	-0.042	41.344	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	352	LEU	0	0.028	0.000	40.457	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	353	ASN	0	0.052	0.026	44.229	0.000	0.000	0.000	0.000	0.000	0.000
24	A	354	LYS	1	0.902	0.950	45.635	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	355	VAL	0	-0.028	0.005	45.473	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	356	TYR	0	-0.014	-0.033	45.290	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	357	GLN	0	-0.022	-0.011	49.921	0.000	0.000	0.000	0.000	0.000	0.000
28	A	358	ARG	1	0.872	0.923	52.268	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	359	LYS	1	0.749	0.878	49.888	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	360	GLY	0	-0.016	0.002	53.895	0.000	0.000	0.000	0.000	0.000	0.000
31	A	361	VAL	0	-0.031	-0.017	47.467	0.000	0.000	0.000	0.000	0.000	0.000
32	A	362	ASN	0	-0.045	-0.014	49.210	0.000	0.000	0.000	0.000	0.000	0.000
33	A	363	ILE	0	-0.033	-0.024	42.827	0.001	0.001	0.000	0.000	0.000	0.000
34	A	364	SER	0	-0.086	-0.068	43.907	0.000	0.000	0.000	0.000	0.000	0.000
35	A	365	MET	0	-0.028	-0.034	37.071	0.001	0.001	0.000	0.000	0.000	0.000
36	A	366	ASP	-1	-0.960	-0.957	39.026	0.024	0.024	0.000	0.000	0.000	0.000
37	A	367	ILE	0	-0.022	-0.025	32.696	0.002	0.002	0.000	0.000	0.000	0.000
38	A	368	SER	0	-0.030	-0.039	32.428	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	369	PRO	0	0.000	-0.020	31.821	0.001	0.001	0.000	0.000	0.000	0.000
40	A	370	GLU	-1	-0.917	-0.912	27.864	0.042	0.042	0.000	0.000	0.000	0.000
41	A	371	ILE	0	-0.007	0.012	27.063	0.004	0.004	0.000	0.000	0.000	0.000
42	A	372	SER	0	-0.031	-0.031	24.342	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	373	PHE	0	0.021	0.016	23.823	0.007	0.007	0.000	0.000	0.000	0.000
44	A	374	VAL	0	-0.041	-0.017	17.433	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	375	GLY	0	0.017	-0.010	19.883	0.005	0.005	0.000	0.000	0.000	0.000
46	A	376	GLU	-1	-0.856	-0.892	20.824	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	377	GLN	0	-0.010	-0.025	23.060	0.001	0.001	0.000	0.000	0.000	0.000
48	A	378	ASN	0	-0.071	-0.066	26.053	0.002	0.002	0.000	0.000	0.000	0.000
49	A	379	ASP	-1	-0.765	-0.861	24.471	0.009	0.009	0.000	0.000	0.000	0.000
50	A	380	PHE	0	-0.008	-0.006	26.836	0.001	0.001	0.000	0.000	0.000	0.000
51	A	381	VAL	0	-0.002	-0.011	28.590	0.000	0.000	0.000	0.000	0.000	0.000
52	A	382	GLU	-1	-0.914	-0.955	31.183	0.003	0.003	0.000	0.000	0.000	0.000
53	A	383	VAL	0	-0.011	-0.003	29.320	0.000	0.000	0.000	0.000	0.000	0.000
54	A	384	MET	0	0.012	0.006	31.560	0.001	0.001	0.000	0.000	0.000	0.000
55	A	385	GLY	0	0.011	0.005	34.128	0.000	0.000	0.000	0.000	0.000	0.000
56	A	386	ASN	0	-0.059	-0.042	35.835	0.000	0.000	0.000	0.000	0.000	0.000
57	A	387	VAL	0	0.044	0.002	34.788	0.000	0.000	0.000	0.000	0.000	0.000
58	A	388	LEU	0	0.006	0.008	37.362	0.000	0.000	0.000	0.000	0.000	0.000
59	A	389	ASP	-1	-0.756	-0.846	39.891	0.008	0.008	0.000	0.000	0.000	0.000
60	A	390	ASN	0	-0.034	-0.026	40.920	0.000	0.000	0.000	0.000	0.000	0.000
61	A	391	ALA	0	0.084	0.048	41.982	0.000	0.000	0.000	0.000	0.000	0.000
62	A	392	CYS	0	-0.012	-0.014	43.507	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	393	LYS	1	0.751	0.859	44.602	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	394	TYR	-1	-0.921	-0.984	46.510	0.010	0.010	0.000	0.000	0.000	0.000
65	A	395	CYS	0	-0.086	0.001	47.471	0.000	0.000	0.000	0.000	0.000	0.000
66	A	396	LEU	0	-0.036	-0.002	49.145	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	397	GLU	-1	-0.978	-1.010	52.010	0.010	0.010	0.000	0.000	0.000	0.000
68	A	398	PHE	0	-0.019	-0.007	48.377	0.000	0.000	0.000	0.000	0.000	0.000
69	A	399	VAL	0	0.004	-0.006	42.568	0.000	0.000	0.000	0.000	0.000	0.000
70	A	400	GLU	-1	-0.865	-0.892	43.046	0.018	0.018	0.000	0.000	0.000	0.000
71	A	401	ILE	0	-0.006	-0.006	36.807	0.001	0.001	0.000	0.000	0.000	0.000
72	A	402	SER	0	0.041	0.019	36.786	0.001	0.001	0.000	0.000	0.000	0.000
73	A	403	ALA	0	0.008	-0.002	31.337	0.000	0.000	0.000	0.000	0.000	0.000
74	A	404	ARG	1	0.913	0.955	30.756	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	405	GLN	0	0.012	0.012	24.714	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	406	THR	0	-0.058	-0.029	24.723	0.001	0.001	0.000	0.000	0.000	0.000
77	A	407	ASP	-1	-0.928	-0.968	19.630	0.146	0.146	0.000	0.000	0.000	0.000
78	A	408	ASP	-1	-0.835	-0.924	17.992	0.154	0.154	0.000	0.000	0.000	0.000
79	A	409	HIS	0	0.014	0.017	20.335	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	410	LEU	0	-0.020	0.003	23.903	0.000	0.000	0.000	0.000	0.000	0.000
81	A	411	HIS	0	-0.081	-0.041	26.300	0.002	0.002	0.000	0.000	0.000	0.000
82	A	412	ILE	0	0.021	-0.003	29.659	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	413	PHE	0	-0.037	-0.024	32.454	0.001	0.001	0.000	0.000	0.000	0.000
84	A	414	VAL	0	0.014	0.006	36.111	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	415	GLU	-1	-0.835	-0.890	38.989	0.026	0.026	0.000	0.000	0.000	0.000
86	A	416	ASP	-1	-0.740	-0.895	42.453	0.015	0.015	0.000	0.000	0.000	0.000
87	A	417	ASP	-1	-0.724	-0.851	46.001	0.013	0.013	0.000	0.000	0.000	0.000
88	A	418	GLY	0	0.024	0.020	48.611	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	419	PRO	0	-0.076	-0.041	50.114	0.000	0.000	0.000	0.000	0.000	0.000
90	A	420	GLY	0	0.076	0.047	49.234	0.001	0.001	0.000	0.000	0.000	0.000
91	A	421	ILE	0	0.035	0.023	43.711	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	422	PRO	0	-0.043	-0.024	45.607	0.000	0.000	0.000	0.000	0.000	0.000
93	A	423	HIS	0	-0.042	-0.013	47.644	0.001	0.001	0.000	0.000	0.000	0.000
94	A	438	THR	0	-0.048	-0.039	53.862	0.000	0.000	0.000	0.000	0.000	0.000
95	A	439	LEU	0	-0.037	-0.006	51.031	0.000	0.000	0.000	0.000	0.000	0.000
96	A	440	ARG	0	-0.038	-0.009	43.273	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	441	PRO	0	-0.026	-0.014	44.793	0.001	0.001	0.000	0.000	0.000	0.000
98	A	442	GLY	0	0.076	0.031	42.217	0.000	0.000	0.000	0.000	0.000	0.000
99	A	443	GLN	0	-0.025	-0.018	41.014	0.000	0.000	0.000	0.000	0.000	0.000
100	A	444	GLY	0	0.033	0.026	39.728	0.000	0.000	0.000	0.000	0.000	0.000
101	A	445	VAL	0	-0.057	-0.030	40.071	0.000	0.000	0.000	0.000	0.000	0.000
102	A	446	GLY	0	0.066	0.038	41.421	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	447	LEU	0	-0.020	0.014	36.963	0.000	0.000	0.000	0.000	0.000	0.000
104	A	448	ALA	0	-0.059	-0.020	36.060	0.001	0.001	0.000	0.000	0.000	0.000
105	A	449	VAL	0	0.102	0.051	33.338	0.001	0.001	0.000	0.000	0.000	0.000
106	A	450	ALA	0	0.017	0.011	32.304	0.001	0.001	0.000	0.000	0.000	0.000
107	A	451	ARG	1	0.884	0.940	31.360	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	452	GLU	-1	-0.930	-0.965	30.308	0.008	0.008	0.000	0.000	0.000	0.000
109	A	453	ILE	0	0.002	0.000	27.056	0.000	0.000	0.000	0.000	0.000	0.000
110	A	454	THR	0	-0.039	-0.031	26.502	0.002	0.002	0.000	0.000	0.000	0.000
111	A	455	GLU	-1	-0.924	-0.954	25.848	0.032	0.032	0.000	0.000	0.000	0.000
112	A	456	GLN	0	-0.049	-0.019	23.364	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	457	TYR	0	-0.125	-0.086	20.829	0.002	0.002	0.000	0.000	0.000	0.000
114	A	458	ALA	0	-0.101	-0.054	21.491	0.012	0.012	0.000	0.000	0.000	0.000
115	A	459	GLY	0	0.022	0.021	23.343	0.009	0.009	0.000	0.000	0.000	0.000
116	A	460	GLN	0	-0.051	-0.026	26.248	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	461	ILE	0	0.003	-0.007	30.061	0.001	0.001	0.000	0.000	0.000	0.000
118	A	462	ILE	0	-0.054	-0.015	32.446	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	463	ALA	0	0.001	0.000	36.041	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	464	SER	0	-0.042	-0.037	39.801	0.002	0.002	0.000	0.000	0.000	0.000
121	A	465	ASP	-1	-0.861	-0.941	41.843	0.020	0.020	0.000	0.000	0.000	0.000
122	A	466	SER	0	-0.001	-0.024	43.907	0.001	0.001	0.000	0.000	0.000	0.000
123	A	467	LEU	0	-0.066	-0.045	45.432	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	468	LEU	0	-0.025	-0.005	45.385	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	469	GLY	0	-0.054	-0.024	48.918	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	470	GLY	0	-0.008	0.015	48.317	0.000	0.000	0.000	0.000	0.000	0.000
127	A	471	ALA	0	-0.048	-0.033	43.367	0.001	0.001	0.000	0.000	0.000	0.000
128	A	472	ARG	1	0.810	0.911	36.423	-0.032	-0.032	0.000	0.000	0.000	0.000
129	A	473	MET	0	-0.037	-0.006	38.104	0.001	0.001	0.000	0.000	0.000	0.000
130	A	474	GLU	-1	-0.809	-0.892	32.882	0.043	0.043	0.000	0.000	0.000	0.000
131	A	475	VAL	0	-0.017	-0.017	30.477	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	476	VAL	0	-0.008	0.004	26.834	0.002	0.002	0.000	0.000	0.000	0.000
133	A	477	PHE	0	0.031	0.010	24.616	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	478	GLY	0	0.109	0.048	22.685	0.006	0.006	0.000	0.000	0.000	0.000
135	A	479	ARG	1	0.899	0.951	17.560	-0.052	-0.052	0.000	0.000	0.000	0.000
136	A	480	GLN	0	0.000	0.005	18.187	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	481	HIS	0	0.044	0.027	11.972	-0.046	-0.046	0.000	0.000	0.000	0.000
138	A	482	PRO	0	0.023	0.018	15.294	0.002	0.002	0.000	0.000	0.000	0.000
139	A	483	THR	0	-0.085	-0.038	10.680	0.018	0.018	0.000	0.000	0.000	0.000
140	A	484	GLN	0	0.003	-0.008	9.032	0.038	0.038	0.000	0.000	0.000	0.000
141	A	485	LYS	1	0.863	0.916	1.938	-23.521	-27.950	13.359	-4.960	-3.969	0.046
142	A	486	GLU	-1	-0.890	-0.921	4.990	-0.586	-0.586	0.000	0.000	0.000	0.000
143	A	487	GLU	-1	-1.009	-1.016	6.423	0.300	0.300	0.000	0.000	0.000	0.000

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