FMO DATABASE

FMODB ID: VQ9Q1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1413933.044847
FMO2-HF: Nuclear repulsion	1355752.173278
FMO2-HF: Total energy	-58180.87157
FMO2-MP2: Total energy	-58354.156193

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.
-18.213	-11.971	3.036	-3.917	-5.36	-0.04

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 : -0.012 / q_NPA : -0.020

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	-0.846	-0.932	3.883	0.898	2.426	-0.003	-0.613	-0.912	0.000
4	A	9	LYS	1	0.865	0.904	2.906	-2.783	-1.740	0.069	-0.239	-0.873	0.001
5	A	10	GLU	-1	-0.885	-0.949	2.421	-18.991	-15.400	2.971	-3.061	-3.501	-0.041
6	A	11	LEU	0	0.018	0.010	5.085	0.716	0.796	-0.001	-0.004	-0.074	0.000
7	A	12	LEU	0	0.000	0.002	7.777	0.192	0.192	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.851	-0.901	6.672	0.430	0.430	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.067	-0.054	8.577	0.223	0.223	0.000	0.000	0.000	0.000
10	A	15	PHE	0	0.009	0.009	11.156	0.089	0.089	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.841	0.905	12.429	-0.525	-0.525	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.959	0.989	13.165	0.665	0.665	0.000	0.000	0.000	0.000
13	A	18	ASN	0	0.000	0.001	14.865	0.028	0.028	0.000	0.000	0.000	0.000
14	A	19	ILE	0	0.050	0.025	17.091	0.021	0.021	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.064	-0.042	17.589	0.009	0.009	0.000	0.000	0.000	0.000
16	A	21	GLN	0	-0.031	-0.021	17.736	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	22	TYR	0	0.022	0.017	20.973	0.015	0.015	0.000	0.000	0.000	0.000
18	A	23	ALA	0	-0.001	0.002	22.576	0.013	0.013	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.875	0.931	23.542	0.053	0.053	0.000	0.000	0.000	0.000
20	A	25	GLN	0	0.018	0.008	25.347	0.012	0.012	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.023	0.035	27.085	0.006	0.006	0.000	0.000	0.000	0.000
22	A	27	GLU	-1	-0.826	-0.916	28.093	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	28	ILE	0	-0.015	-0.013	28.087	0.001	0.001	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.037	-0.034	31.105	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.029	-0.010	32.545	0.004	0.004	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.973	-0.992	32.945	-0.040	-0.040	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.976	0.988	33.127	0.079	0.079	0.000	0.000	0.000	0.000
28	A	33	VAL	0	0.070	0.044	37.534	0.002	0.002	0.000	0.000	0.000	0.000
29	A	34	TYR	0	-0.047	-0.057	38.498	0.006	0.006	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.934	-0.959	39.061	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-0.992	-0.989	40.105	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	37	LYS	1	0.801	0.884	42.816	0.018	0.018	0.000	0.000	0.000	0.000
33	A	38	GLY	0	0.052	0.037	44.510	0.003	0.003	0.000	0.000	0.000	0.000
34	A	39	SER	0	0.015	-0.006	42.824	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	40	VAL	0	0.008	0.003	43.849	0.001	0.001	0.000	0.000	0.000	0.000
36	A	41	ASN	0	-0.036	-0.014	45.839	0.003	0.003	0.000	0.000	0.000	0.000
37	A	42	ALA	0	0.081	0.047	40.495	0.001	0.001	0.000	0.000	0.000	0.000
38	A	43	GLN	0	-0.002	0.002	40.213	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.814	0.901	41.207	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.800	-0.881	39.356	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.010	0.000	35.051	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	47	GLN	0	-0.021	-0.021	35.515	0.004	0.004	0.000	0.000	0.000	0.000
43	A	48	ASN	0	-0.054	-0.012	36.081	0.005	0.005	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.050	0.030	33.118	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.019	-0.024	31.411	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.010	-0.023	31.001	0.005	0.005	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.873	-0.930	31.988	-0.038	-0.038	0.000	0.000	0.000	0.000
48	A	53	TYR	0	0.007	-0.007	26.493	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.040	-0.035	26.938	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	55	ASN	0	-0.056	-0.014	27.983	0.011	0.011	0.000	0.000	0.000	0.000
51	A	56	MET	0	-0.034	0.016	20.049	0.000	0.000	0.000	0.000	0.000	0.000
52	A	57	GLN	0	0.037	0.020	22.679	0.009	0.009	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.813	-0.905	18.187	-0.082	-0.082	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.017	-0.007	20.951	0.049	0.049	0.000	0.000	0.000	0.000
55	A	60	GLY	0	-0.015	-0.005	23.564	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.812	-0.879	25.693	0.126	0.126	0.000	0.000	0.000	0.000
57	A	62	ILE	0	0.018	0.028	26.668	0.009	0.009	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.767	0.847	28.833	-0.153	-0.153	0.000	0.000	0.000	0.000
59	A	64	PHE	0	0.034	0.018	30.712	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.022	-0.002	31.414	0.004	0.004	0.000	0.000	0.000	0.000
61	A	66	ASP	-1	-0.747	-0.872	34.739	0.066	0.066	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.863	0.915	36.475	-0.051	-0.051	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.867	-0.918	38.012	0.081	0.081	0.000	0.000	0.000	0.000
64	A	69	GLN	0	-0.023	-0.002	35.242	0.016	0.016	0.000	0.000	0.000	0.000
65	A	70	ILE	0	0.013	0.019	37.060	0.008	0.008	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.006	-0.010	34.838	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	72	ILE	0	-0.020	-0.004	37.018	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	73	ALA	0	0.022	0.014	35.939	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	74	THR	0	-0.014	-0.034	33.081	0.007	0.007	0.000	0.000	0.000	0.000
70	A	75	THR	0	0.034	0.044	30.149	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.842	0.934	29.102	-0.123	-0.123	0.000	0.000	0.000	0.000
72	A	77	GLN	0	0.090	0.051	33.692	0.009	0.009	0.000	0.000	0.000	0.000
73	A	78	SER	0	0.023	-0.007	35.341	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	79	ASN	0	-0.037	-0.022	32.492	0.003	0.003	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.914	0.947	36.795	-0.070	-0.070	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.001	0.003	39.737	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	82	LEU	0	0.016	0.007	34.832	0.001	0.001	0.000	0.000	0.000	0.000
78	A	83	ILE	0	-0.012	0.007	38.542	0.001	0.001	0.000	0.000	0.000	0.000
79	A	84	ASN	0	-0.031	-0.028	40.158	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	85	GLN	0	-0.044	-0.016	39.308	0.006	0.006	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.831	0.908	38.973	-0.091	-0.091	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.011	-0.010	33.392	0.006	0.006	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.057	-0.024	34.080	0.006	0.006	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.741	-0.819	28.624	0.237	0.237	0.000	0.000	0.000	0.000
85	A	90	SER	0	0.047	-0.007	29.526	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	91	SER	0	-0.073	-0.047	25.097	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.029	0.015	27.121	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	93	GLN	0	0.015	0.000	29.601	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.957	0.997	23.489	-0.278	-0.278	0.000	0.000	0.000	0.000
90	A	95	ALA	0	-0.008	0.000	27.252	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	96	LEU	0	-0.046	-0.027	28.780	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.053	-0.030	32.135	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	98	LEU	0	-0.037	-0.017	27.753	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	99	GLY	0	0.009	0.014	30.435	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	100	GLN	0	-0.041	-0.014	25.157	0.002	0.002	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.052	0.009	22.393	0.008	0.008	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.130	-0.060	21.434	0.039	0.039	0.000	0.000	0.000	0.000
98	A	103	ASP	-1	-0.769	-0.865	16.725	0.451	0.451	0.000	0.000	0.000	0.000
99	A	104	HIS	0	0.011	0.007	18.922	0.067	0.067	0.000	0.000	0.000	0.000
100	A	105	LEU	0	0.016	0.010	14.490	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.002	0.011	19.177	0.001	0.001	0.000	0.000	0.000	0.000
102	A	107	LEU	0	0.032	0.015	19.847	0.013	0.013	0.000	0.000	0.000	0.000
103	A	108	LYS	1	0.801	0.891	23.062	-0.235	-0.235	0.000	0.000	0.000	0.000
104	A	109	ASP	-1	-0.767	-0.890	25.176	0.260	0.260	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.068	-0.068	24.740	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	111	GLY	0	-0.034	-0.014	29.660	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	112	GLY	0	-0.040	-0.017	28.637	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.013	0.020	26.329	0.012	0.012	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.842	0.907	24.149	-0.339	-0.339	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.793	-0.863	21.389	0.376	0.376	0.000	0.000	0.000	0.000
111	A	116	ARG	1	0.852	0.921	13.411	-0.888	-0.888	0.000	0.000	0.000	0.000
112	A	117	VAL	0	-0.026	-0.007	18.998	-0.030	-0.030	0.000	0.000	0.000	0.000
113	A	118	TRP	0	-0.062	-0.047	16.847	0.023	0.023	0.000	0.000	0.000	0.000
114	A	119	VAL	0	0.010	0.004	18.947	-0.061	-0.061	0.000	0.000	0.000	0.000
115	A	120	TYR	0	0.033	0.008	19.657	0.024	0.024	0.000	0.000	0.000	0.000
116	A	121	ASN	0	0.005	-0.005	21.867	-0.038	-0.038	0.000	0.000	0.000	0.000
117	A	122	ILE	0	0.020	0.004	24.020	0.002	0.002	0.000	0.000	0.000	0.000
118	A	123	PRO	0	-0.016	0.000	26.216	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	124	VAL	0	0.009	0.001	29.723	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.816	0.895	29.843	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.095	0.047	34.046	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	127	ASP	-1	-0.784	-0.870	37.430	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.908	0.946	34.597	0.039	0.039	0.000	0.000	0.000	0.000
124	A	129	LYS	1	0.806	0.898	35.290	0.001	0.001	0.000	0.000	0.000	0.000
125	A	130	VAL	0	0.019	0.010	32.603	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	131	ILE	0	0.018	0.010	35.210	0.006	0.006	0.000	0.000	0.000	0.000
127	A	132	GLY	0	0.018	0.000	34.750	0.002	0.002	0.000	0.000	0.000	0.000
128	A	133	ASN	0	-0.060	-0.050	28.189	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	134	ILE	0	0.007	0.026	27.221	0.000	0.000	0.000	0.000	0.000	0.000
130	A	135	TYR	0	-0.044	-0.038	26.729	0.011	0.011	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.021	-0.003	22.971	-0.018	-0.018	0.000	0.000	0.000	0.000
132	A	137	GLU	-1	-0.720	-0.784	23.312	0.227	0.227	0.000	0.000	0.000	0.000
133	A	138	SER	0	0.021	-0.004	19.496	-0.031	-0.031	0.000	0.000	0.000	0.000
134	A	139	LYS	1	0.900	0.940	20.021	-0.026	-0.026	0.000	0.000	0.000	0.000
135	A	140	ILE	0	0.007	0.005	12.941	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	141	ASN	0	-0.012	-0.030	15.040	0.132	0.132	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.868	-0.927	16.452	0.194	0.194	0.000	0.000	0.000	0.000
138	A	143	VAL	0	-0.034	-0.016	10.917	-0.025	-0.025	0.000	0.000	0.000	0.000
139	A	144	TYR	0	-0.004	-0.012	10.339	-0.095	-0.095	0.000	0.000	0.000	0.000
140	A	145	ASN	0	-0.008	0.006	13.017	0.116	0.116	0.000	0.000	0.000	0.000
141	A	146	GLN	0	0.059	0.033	13.292	0.058	0.058	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.041	-0.016	7.744	-0.042	-0.042	0.000	0.000	0.000	0.000
143	A	148	ASN	0	-0.007	-0.008	11.395	0.214	0.214	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.058	-0.019	13.942	0.009	0.009	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.052	-0.025	9.632	-0.047	-0.047	0.000	0.000	0.000	0.000
146	A	151	ASN	0	-0.062	-0.017	12.306	0.069	0.069	0.000	0.000	0.000	0.000
147	A	152	GLN	0	-0.052	-0.027	7.217	0.766	0.766	0.000	0.000	0.000	0.000

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