FMO DATABASE

FMODB ID: YV4V2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1410793.66038
FMO2-HF: Nuclear repulsion	1352613.411581
FMO2-HF: Total energy	-58180.248799
FMO2-MP2: Total energy	-58353.633806

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.
-15.627	-10.212	1.425	-2.701	-4.138	-0.016

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 : 0.002 / q_NPA : -0.016

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	-0.855	-0.938	3.754	1.065	2.486	0.001	-0.465	-0.955	0.003
4	A	9	LYS	1	0.852	0.896	3.501	-4.668	-3.470	0.029	-0.358	-0.870	0.002
5	A	10	GLU	-1	-0.885	-0.947	2.627	-14.115	-11.378	1.396	-1.875	-2.259	-0.021
6	A	11	LEU	0	0.008	0.008	5.341	0.495	0.554	-0.001	-0.003	-0.054	0.000
7	A	12	LEU	0	-0.010	-0.002	8.091	0.065	0.065	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.864	-0.911	7.386	1.263	1.263	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.038	-0.034	8.565	0.032	0.032	0.000	0.000	0.000	0.000
10	A	15	PHE	0	-0.004	-0.001	11.369	0.040	0.040	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.896	0.945	13.047	-0.877	-0.877	0.000	0.000	0.000	0.000
12	A	17	LYS	1	0.953	0.991	13.517	0.306	0.306	0.000	0.000	0.000	0.000
13	A	18	ASN	0	0.027	-0.003	15.271	0.013	0.013	0.000	0.000	0.000	0.000
14	A	19	ILE	0	0.050	0.036	17.418	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.054	-0.030	17.892	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	21	GLN	0	-0.027	-0.018	18.006	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	22	TYR	0	0.029	0.015	21.238	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	23	ALA	0	-0.030	-0.020	23.004	0.001	0.001	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.873	0.934	23.977	-0.051	-0.051	0.000	0.000	0.000	0.000
20	A	25	GLN	0	0.025	0.012	25.671	0.000	0.000	0.000	0.000	0.000	0.000
21	A	26	LEU	0	0.012	0.033	27.615	0.000	0.000	0.000	0.000	0.000	0.000
22	A	27	GLU	-1	-0.835	-0.915	28.588	0.070	0.070	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.023	0.007	28.431	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.045	-0.041	31.569	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	30	ILE	0	-0.003	0.001	32.750	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.986	-0.989	33.717	0.031	0.031	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.971	0.978	33.530	0.009	0.009	0.000	0.000	0.000	0.000
28	A	33	VAL	0	0.055	0.034	37.906	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	34	TYR	0	-0.062	-0.052	39.022	0.002	0.002	0.000	0.000	0.000	0.000
30	A	35	ASP	-1	-0.922	-0.950	39.242	0.024	0.024	0.000	0.000	0.000	0.000
31	A	36	GLU	-1	-1.005	-0.991	40.841	0.000	0.000	0.000	0.000	0.000	0.000
32	A	37	LYS	1	0.815	0.877	43.683	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	38	GLY	0	0.006	0.017	44.731	0.001	0.001	0.000	0.000	0.000	0.000
34	A	39	SER	0	0.008	-0.017	43.616	0.000	0.000	0.000	0.000	0.000	0.000
35	A	40	VAL	0	-0.020	-0.015	44.474	0.003	0.003	0.000	0.000	0.000	0.000
36	A	41	ASN	0	0.006	-0.012	46.504	0.003	0.003	0.000	0.000	0.000	0.000
37	A	42	ALA	0	0.086	0.068	41.197	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	43	GLN	0	-0.015	0.004	41.089	0.000	0.000	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.869	0.914	42.186	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.824	-0.875	40.143	0.029	0.029	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.024	-0.011	35.863	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	47	GLN	0	-0.023	-0.018	36.265	0.005	0.005	0.000	0.000	0.000	0.000
43	A	48	ASN	0	-0.021	-0.020	36.520	0.004	0.004	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.046	0.034	33.702	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.034	-0.034	32.048	0.002	0.002	0.000	0.000	0.000	0.000
46	A	51	SER	0	0.009	-0.027	31.610	0.007	0.007	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.881	-0.924	32.457	0.020	0.020	0.000	0.000	0.000	0.000
48	A	53	TYR	0	0.027	-0.001	26.885	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.071	-0.041	27.373	0.004	0.004	0.000	0.000	0.000	0.000
50	A	55	ASN	0	-0.038	-0.006	28.497	0.009	0.009	0.000	0.000	0.000	0.000
51	A	56	MET	0	-0.026	0.016	20.517	0.001	0.001	0.000	0.000	0.000	0.000
52	A	57	GLN	0	0.024	0.012	23.067	0.004	0.004	0.000	0.000	0.000	0.000
53	A	58	GLU	-1	-0.818	-0.906	18.731	0.063	0.063	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.011	0.003	21.725	0.052	0.052	0.000	0.000	0.000	0.000
55	A	60	GLY	0	-0.037	-0.022	24.334	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.802	-0.870	26.236	0.169	0.169	0.000	0.000	0.000	0.000
57	A	62	ILE	0	0.042	0.035	27.434	0.016	0.016	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.747	0.839	29.606	-0.220	-0.220	0.000	0.000	0.000	0.000
59	A	64	PHE	0	0.028	0.018	31.537	0.004	0.004	0.000	0.000	0.000	0.000
60	A	65	ILE	0	-0.012	0.001	32.139	0.000	0.000	0.000	0.000	0.000	0.000
61	A	66	ASP	-1	-0.750	-0.874	35.531	0.111	0.111	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.884	0.927	37.432	-0.095	-0.095	0.000	0.000	0.000	0.000
63	A	68	ASP	-1	-0.910	-0.934	38.796	0.113	0.113	0.000	0.000	0.000	0.000
64	A	69	GLN	0	-0.032	-0.019	36.002	0.013	0.013	0.000	0.000	0.000	0.000
65	A	70	ILE	0	0.003	0.012	37.814	0.009	0.009	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.010	-0.005	35.493	0.000	0.000	0.000	0.000	0.000	0.000
67	A	72	ILE	0	-0.016	0.004	37.695	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	73	ALA	0	0.007	0.001	36.879	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	74	THR	0	-0.002	-0.021	33.843	0.009	0.009	0.000	0.000	0.000	0.000
70	A	75	THR	0	0.030	0.043	30.816	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.852	0.934	29.553	-0.180	-0.180	0.000	0.000	0.000	0.000
72	A	77	GLN	0	0.095	0.053	34.358	0.007	0.007	0.000	0.000	0.000	0.000
73	A	78	SER	0	0.005	-0.013	35.270	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	79	ASN	0	-0.025	-0.017	32.569	0.002	0.002	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.933	0.955	36.980	-0.102	-0.102	0.000	0.000	0.000	0.000
76	A	81	SER	0	-0.017	-0.013	39.872	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.013	-0.002	34.775	0.001	0.001	0.000	0.000	0.000	0.000
78	A	83	ILE	0	-0.017	-0.004	39.111	0.002	0.002	0.000	0.000	0.000	0.000
79	A	84	ASN	0	-0.039	-0.040	40.859	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	85	GLN	0	-0.017	0.009	39.822	0.006	0.006	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.888	0.940	39.367	-0.127	-0.127	0.000	0.000	0.000	0.000
82	A	87	ALA	0	0.002	-0.004	33.903	0.005	0.005	0.000	0.000	0.000	0.000
83	A	88	ASN	0	-0.058	-0.032	34.698	0.007	0.007	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.736	-0.827	29.295	0.301	0.301	0.000	0.000	0.000	0.000
85	A	90	SER	0	0.048	0.002	29.447	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	91	SER	0	-0.069	-0.037	25.700	0.001	0.001	0.000	0.000	0.000	0.000
87	A	92	VAL	0	0.034	0.012	27.677	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	93	GLN	0	0.007	-0.009	30.239	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	94	LYS	1	0.962	1.000	23.749	-0.373	-0.373	0.000	0.000	0.000	0.000
90	A	95	ALA	0	-0.011	-0.006	27.683	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	96	LEU	0	-0.024	-0.011	29.208	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.076	-0.041	32.570	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	98	LEU	0	-0.006	-0.009	27.644	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	99	GLY	0	-0.008	0.006	30.783	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	100	GLN	0	-0.046	-0.027	25.500	0.007	0.007	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.050	0.011	22.903	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.151	-0.073	21.916	0.041	0.041	0.000	0.000	0.000	0.000
98	A	103	ASP	-1	-0.769	-0.873	17.199	0.650	0.650	0.000	0.000	0.000	0.000
99	A	104	HIS	0	-0.018	-0.006	18.927	0.071	0.071	0.000	0.000	0.000	0.000
100	A	105	LEU	0	0.037	0.021	14.324	-0.033	-0.033	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.041	-0.014	19.030	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	107	LEU	0	0.008	0.006	20.105	0.032	0.032	0.000	0.000	0.000	0.000
103	A	108	LYS	1	0.799	0.876	23.031	-0.305	-0.305	0.000	0.000	0.000	0.000
104	A	109	ASP	-1	-0.834	-0.895	25.307	0.301	0.301	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.051	-0.071	24.487	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	111	GLY	0	-0.010	-0.004	29.369	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	112	GLY	0	-0.019	-0.001	27.848	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	113	GLY	0	0.032	0.031	26.858	0.014	0.014	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.880	0.921	24.260	-0.363	-0.363	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.795	-0.866	21.613	0.426	0.426	0.000	0.000	0.000	0.000
111	A	116	ARG	1	0.868	0.924	13.415	-1.042	-1.042	0.000	0.000	0.000	0.000
112	A	117	VAL	0	-0.024	-0.004	19.250	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	118	TRP	0	-0.042	-0.039	17.197	0.035	0.035	0.000	0.000	0.000	0.000
114	A	119	VAL	0	0.016	0.009	19.236	-0.068	-0.068	0.000	0.000	0.000	0.000
115	A	120	TYR	0	0.035	0.019	20.490	0.035	0.035	0.000	0.000	0.000	0.000
116	A	121	ASN	0	0.000	-0.010	22.516	-0.054	-0.054	0.000	0.000	0.000	0.000
117	A	122	ILE	0	0.007	-0.002	24.821	0.012	0.012	0.000	0.000	0.000	0.000
118	A	123	PRO	0	-0.013	-0.002	26.723	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	124	VAL	0	0.021	0.006	30.017	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	125	LYS	1	0.831	0.911	30.720	-0.106	-0.106	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.104	0.057	34.550	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	127	ASP	-1	-0.829	-0.906	37.780	0.043	0.043	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.921	0.951	35.173	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	129	LYS	1	0.831	0.916	36.367	-0.044	-0.044	0.000	0.000	0.000	0.000
125	A	130	VAL	0	0.003	0.017	33.365	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	131	ILE	0	0.011	-0.001	35.940	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	132	GLY	0	0.035	0.014	35.383	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	133	ASN	0	-0.073	-0.058	29.024	0.003	0.003	0.000	0.000	0.000	0.000
129	A	134	ILE	0	0.022	0.034	27.829	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	135	TYR	0	-0.070	-0.052	27.458	0.018	0.018	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.028	0.004	23.698	-0.020	-0.020	0.000	0.000	0.000	0.000
132	A	137	GLU	-1	-0.722	-0.785	23.759	0.302	0.302	0.000	0.000	0.000	0.000
133	A	138	SER	0	0.024	-0.003	20.003	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	139	LYS	1	0.915	0.938	20.378	-0.115	-0.115	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.010	-0.009	13.424	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	141	ASN	0	-0.024	-0.026	15.145	0.147	0.147	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.876	-0.933	16.606	0.300	0.300	0.000	0.000	0.000	0.000
138	A	143	VAL	0	-0.039	-0.021	10.703	-0.031	-0.031	0.000	0.000	0.000	0.000
139	A	144	TYR	0	-0.028	-0.019	10.511	-0.065	-0.065	0.000	0.000	0.000	0.000
140	A	145	ASN	0	-0.010	-0.009	13.183	0.101	0.101	0.000	0.000	0.000	0.000
141	A	146	GLN	0	0.061	0.040	13.164	0.030	0.030	0.000	0.000	0.000	0.000
142	A	147	LEU	0	-0.019	-0.017	7.668	-0.060	-0.060	0.000	0.000	0.000	0.000
143	A	148	ASN	0	-0.024	-0.010	11.405	0.188	0.188	0.000	0.000	0.000	0.000
144	A	149	ASN	0	-0.069	-0.033	13.988	-0.037	-0.037	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.042	-0.004	9.662	-0.092	-0.092	0.000	0.000	0.000	0.000
146	A	151	ASN	0	-0.077	-0.034	11.881	0.048	0.048	0.000	0.000	0.000	0.000
147	A	152	GLN	0	-0.017	-0.004	6.491	0.878	0.878	0.000	0.000	0.000	0.000

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