FMO DATABASE

FMODB ID: 5J4NZ

Calculation Name: 4YWZ-A-Xray372

Preferred Name: Sensor protein kinase WalK

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4YWZ

Chain ID: A

ChEMBL ID: CHEMBL4295968

UniProt ID: Q9RDT3

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1409413.251698
FMO2-HF: Nuclear repulsion	1351234.087875
FMO2-HF: Total energy	-58179.163823
FMO2-MP2: Total energy	-58352.611597

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:6:ASN)

Summations of interaction energy for fragment #1(A:6:ASN)

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.
-13.121	-8.156	0.263	-1.775	-3.451	0.006

Interaction energy analysis for fragmet #1(A:6:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.017

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	8	GLU	-1	-0.870	-0.941	3.754	0.604	2.055	-0.001	-0.476	-0.973	0.003
4	A	9	LYS	1	0.896	0.942	2.995	-8.371	-6.387	0.173	-0.719	-1.437	0.007
5	A	10	GLU	-1	-0.910	-0.954	2.971	-7.072	-5.602	0.092	-0.577	-0.985	-0.004
6	A	11	LEU	0	0.004	0.000	5.250	0.351	0.411	-0.001	-0.003	-0.056	0.000
7	A	12	LEU	0	-0.030	-0.009	8.051	0.072	0.072	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.897	-0.955	7.632	2.398	2.398	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.009	-0.006	8.947	-0.062	-0.062	0.000	0.000	0.000	0.000
10	A	15	PHE	0	-0.012	-0.008	11.281	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.970	0.983	12.054	-1.240	-1.240	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.951	0.990	13.442	-0.233	-0.233	0.000	0.000	0.000	0.000
13	A	18	ASN	0	-0.001	-0.014	15.221	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	19	ILE	0	0.054	0.043	17.339	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.056	-0.032	17.416	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	21	GLN	0	-0.022	-0.015	18.119	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	22	TYR	0	0.040	0.016	21.178	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	23	ALA	0	-0.027	-0.017	22.956	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.873	0.945	23.926	-0.203	-0.203	0.000	0.000	0.000	0.000
20	A	25	GLN	0	0.011	0.008	25.632	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.017	0.033	27.559	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	27	GLU	-1	-0.834	-0.935	28.549	0.164	0.164	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.041	0.019	28.525	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.033	-0.029	31.549	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.012	-0.006	32.780	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.979	-0.986	33.611	0.124	0.124	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.975	0.981	34.045	-0.088	-0.088	0.000	0.000	0.000	0.000
28	A	33	VAL	0	0.039	0.027	37.862	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	34	TYR	0	-0.056	-0.050	38.728	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.910	-0.948	38.981	0.091	0.091	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-1.010	-0.995	41.159	0.058	0.058	0.000	0.000	0.000	0.000
32	A	37	LYS	1	0.813	0.889	43.746	-0.071	-0.071	0.000	0.000	0.000	0.000
33	A	38	GLY	0	0.006	0.018	44.690	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	39	SER	0	0.005	-0.018	43.602	0.000	0.000	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.018	-0.010	44.451	0.002	0.002	0.000	0.000	0.000	0.000
36	A	41	ASN	0	0.019	-0.020	46.473	0.001	0.001	0.000	0.000	0.000	0.000
37	A	42	ALA	0	0.101	0.071	41.128	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	43	GLN	0	-0.039	-0.014	40.805	0.008	0.008	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.857	0.920	42.151	-0.070	-0.070	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.795	-0.868	40.178	0.072	0.072	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.047	-0.022	35.822	0.001	0.001	0.000	0.000	0.000	0.000
42	A	47	GLN	0	-0.021	-0.013	36.214	0.006	0.006	0.000	0.000	0.000	0.000
43	A	48	ASN	0	-0.009	-0.014	36.458	0.001	0.001	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.056	0.038	33.635	0.001	0.001	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.033	-0.034	32.009	0.006	0.006	0.000	0.000	0.000	0.000
46	A	51	SER	0	-0.021	-0.037	31.546	0.006	0.006	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.894	-0.931	32.368	0.076	0.076	0.000	0.000	0.000	0.000
48	A	53	TYR	0	0.014	-0.005	26.906	0.001	0.001	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.066	-0.041	27.293	0.008	0.008	0.000	0.000	0.000	0.000
50	A	55	ASN	0	-0.010	0.012	28.417	0.006	0.006	0.000	0.000	0.000	0.000
51	A	56	MET	0	-0.056	-0.002	20.402	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	57	GLN	0	0.022	0.003	22.912	0.003	0.003	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.865	-0.938	18.583	0.136	0.136	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.023	-0.006	21.642	0.049	0.049	0.000	0.000	0.000	0.000
55	A	60	GLY	0	-0.047	-0.023	24.269	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.823	-0.895	26.234	0.174	0.174	0.000	0.000	0.000	0.000
57	A	62	ILE	0	0.038	0.031	27.404	0.021	0.021	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.803	0.880	29.572	-0.230	-0.230	0.000	0.000	0.000	0.000
59	A	64	PHE	0	0.018	0.017	31.522	0.011	0.011	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.007	0.006	32.061	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	66	ASP	-1	-0.747	-0.873	35.465	0.146	0.146	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.920	0.946	37.189	-0.143	-0.143	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.918	-0.933	38.540	0.140	0.140	0.000	0.000	0.000	0.000
64	A	69	GLN	0	-0.022	-0.026	35.720	0.009	0.009	0.000	0.000	0.000	0.000
65	A	70	ILE	0	0.014	0.022	37.631	0.005	0.005	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.007	-0.008	35.556	0.004	0.004	0.000	0.000	0.000	0.000
67	A	72	ILE	0	-0.015	0.014	37.697	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	73	ALA	0	0.005	-0.003	36.785	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	74	THR	0	-0.006	-0.027	33.780	0.011	0.011	0.000	0.000	0.000	0.000
70	A	75	THR	0	0.036	0.036	30.871	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.912	0.977	29.583	-0.183	-0.183	0.000	0.000	0.000	0.000
72	A	77	GLN	0	0.049	0.023	34.354	0.002	0.002	0.000	0.000	0.000	0.000
73	A	78	SER	0	-0.002	-0.019	35.133	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	79	ASN	0	-0.010	-0.006	32.694	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.958	0.978	36.977	-0.101	-0.101	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.043	-0.032	40.082	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	82	LEU	0	0.032	0.023	34.731	0.001	0.001	0.000	0.000	0.000	0.000
78	A	83	ILE	0	-0.028	-0.003	39.103	0.003	0.003	0.000	0.000	0.000	0.000
79	A	84	ASN	0	-0.023	-0.035	40.847	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	85	GLN	0	-0.032	0.002	39.831	0.003	0.003	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.876	0.941	39.266	-0.144	-0.144	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.010	-0.005	33.768	0.002	0.002	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.060	-0.032	34.683	0.007	0.007	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.754	-0.844	29.232	0.313	0.313	0.000	0.000	0.000	0.000
85	A	90	SER	0	0.057	0.016	29.410	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	91	SER	0	-0.088	-0.050	25.571	0.009	0.009	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.036	0.010	27.555	0.001	0.001	0.000	0.000	0.000	0.000
88	A	93	GLN	0	-0.012	-0.021	30.063	0.001	0.001	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.967	0.988	23.820	-0.438	-0.438	0.000	0.000	0.000	0.000
90	A	95	ALA	0	-0.016	-0.001	27.470	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	96	LEU	0	-0.022	-0.014	28.938	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.065	-0.019	32.344	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	98	LEU	0	-0.016	-0.022	27.391	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	99	GLY	0	-0.012	0.006	30.422	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	100	GLN	0	-0.064	-0.045	25.112	0.019	0.019	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.064	0.025	22.745	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.153	-0.075	21.628	0.034	0.034	0.000	0.000	0.000	0.000
98	A	103	ASP	-1	-0.813	-0.906	17.019	0.767	0.767	0.000	0.000	0.000	0.000
99	A	104	HIS	0	-0.026	-0.010	18.863	0.059	0.059	0.000	0.000	0.000	0.000
100	A	105	LEU	0	0.027	0.014	14.417	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.026	-0.003	19.020	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.004	-0.003	19.971	0.023	0.023	0.000	0.000	0.000	0.000
103	A	108	LYS	1	0.828	0.895	23.037	-0.282	-0.282	0.000	0.000	0.000	0.000
104	A	109	ASP	-1	-0.857	-0.907	25.319	0.225	0.225	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.068	-0.084	24.557	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	111	GLY	0	-0.013	-0.005	29.381	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	112	GLY	0	-0.017	0.000	27.871	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.028	0.031	26.890	0.004	0.004	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.882	0.922	24.279	-0.284	-0.284	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.827	-0.888	21.645	0.305	0.305	0.000	0.000	0.000	0.000
111	A	116	ARG	1	0.891	0.918	13.979	-0.739	-0.739	0.000	0.000	0.000	0.000
112	A	117	VAL	0	-0.018	0.007	19.260	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	118	TRP	0	-0.050	-0.038	16.928	0.032	0.032	0.000	0.000	0.000	0.000
114	A	119	VAL	0	0.021	0.012	19.226	-0.057	-0.057	0.000	0.000	0.000	0.000
115	A	120	TYR	0	0.012	-0.002	20.295	0.029	0.029	0.000	0.000	0.000	0.000
116	A	121	ASN	0	0.012	0.003	22.479	-0.067	-0.067	0.000	0.000	0.000	0.000
117	A	122	ILE	0	-0.015	-0.013	24.637	0.027	0.027	0.000	0.000	0.000	0.000
118	A	123	PRO	0	-0.018	0.003	26.691	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	124	VAL	0	0.019	0.001	30.006	0.000	0.000	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.856	0.926	30.532	-0.209	-0.209	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.111	0.064	34.532	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	127	ASP	-1	-0.906	-0.949	37.776	0.103	0.103	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.913	0.953	35.147	-0.121	-0.121	0.000	0.000	0.000	0.000
124	A	129	LYS	1	0.923	0.960	36.067	-0.111	-0.111	0.000	0.000	0.000	0.000
125	A	130	VAL	0	-0.015	0.010	33.107	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.019	-0.020	35.692	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	132	GLY	0	0.036	0.019	35.262	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	133	ASN	0	-0.072	-0.060	28.814	0.017	0.017	0.000	0.000	0.000	0.000
129	A	134	ILE	0	0.017	0.035	27.470	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	135	TYR	0	-0.066	-0.062	27.478	0.025	0.025	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.023	-0.002	23.534	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	137	GLU	-1	-0.772	-0.799	23.742	0.303	0.303	0.000	0.000	0.000	0.000
133	A	138	SER	0	0.016	-0.003	19.890	-0.022	-0.022	0.000	0.000	0.000	0.000
134	A	139	LYS	1	1.000	0.986	20.380	-0.142	-0.142	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.010	-0.006	13.430	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	141	ASN	0	0.022	0.006	15.154	0.093	0.093	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.891	-0.938	16.626	0.227	0.227	0.000	0.000	0.000	0.000
138	A	143	VAL	0	-0.032	-0.015	10.807	-0.038	-0.038	0.000	0.000	0.000	0.000
139	A	144	TYR	0	-0.030	-0.020	10.809	-0.050	-0.050	0.000	0.000	0.000	0.000
140	A	145	ASN	0	0.000	-0.006	13.208	0.036	0.036	0.000	0.000	0.000	0.000
141	A	146	GLN	0	0.042	0.028	13.375	0.003	0.003	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.014	-0.016	7.766	-0.058	-0.058	0.000	0.000	0.000	0.000
143	A	148	ASN	0	-0.005	-0.001	11.445	0.082	0.082	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.053	-0.018	14.034	-0.037	-0.037	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.062	-0.012	9.560	-0.072	-0.072	0.000	0.000	0.000	0.000
146	A	151	ASN	0	-0.078	-0.040	11.895	0.011	0.011	0.000	0.000	0.000	0.000
147	A	152	GLN	0	-0.005	0.003	6.707	0.836	0.836	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ASN)