FMO DATABASE

FMODB ID: G5761

Calculation Name: 4EJQ-A-Xray372

Preferred Name: Kinesin-like protein KIF1A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4EJQ

Chain ID: A

ChEMBL ID: CHEMBL3308914

UniProt ID: Q12756

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1384233.277062
FMO2-HF: Nuclear repulsion	1322202.256307
FMO2-HF: Total energy	-62031.020755
FMO2-MP2: Total energy	-62208.032596

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:454:GLY)

Summations of interaction energy for fragment #1(A:454:GLY)

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.
1.074	4.352	0.337	-1.512	-2.102	0.001

Interaction energy analysis for fragmet #1(A:454:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.040

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	456	GLU	-1	-0.853	-0.929	3.500	-3.502	-1.567	0.032	-0.939	-1.028	0.001
4	A	457	PHE	0	-0.015	-0.003	2.477	0.470	1.396	0.305	-0.412	-0.819	0.000
5	A	458	THR	0	-0.020	-0.028	3.524	2.068	2.485	0.000	-0.161	-0.255	0.000
6	A	459	GLU	-1	-0.809	-0.888	5.796	-0.498	-0.498	0.000	0.000	0.000	0.000
7	A	460	ALA	0	-0.008	0.011	7.665	0.491	0.491	0.000	0.000	0.000	0.000
8	A	461	ILE	0	0.016	0.005	7.821	0.366	0.366	0.000	0.000	0.000	0.000
9	A	462	ARG	1	0.693	0.811	9.917	1.323	1.323	0.000	0.000	0.000	0.000
10	A	463	MET	0	0.016	-0.005	11.145	0.229	0.229	0.000	0.000	0.000	0.000
11	A	464	GLU	-1	-0.898	-0.934	12.961	-0.414	-0.414	0.000	0.000	0.000	0.000
12	A	465	ARG	1	0.911	0.959	12.016	1.024	1.024	0.000	0.000	0.000	0.000
13	A	466	GLU	-1	-0.896	-0.937	15.862	-0.597	-0.597	0.000	0.000	0.000	0.000
14	A	467	ALA	0	0.021	0.006	17.554	0.070	0.070	0.000	0.000	0.000	0.000
15	A	468	LEU	0	0.019	0.008	18.630	0.057	0.057	0.000	0.000	0.000	0.000
16	A	469	LEU	0	-0.032	-0.027	19.254	0.046	0.046	0.000	0.000	0.000	0.000
17	A	470	ALA	0	-0.012	0.001	21.917	0.039	0.039	0.000	0.000	0.000	0.000
18	A	471	GLU	-1	-0.932	-0.965	23.377	-0.206	-0.206	0.000	0.000	0.000	0.000
19	A	472	MET	0	-0.062	-0.035	24.077	0.032	0.032	0.000	0.000	0.000	0.000
20	A	473	GLY	0	-0.018	0.001	26.235	0.015	0.015	0.000	0.000	0.000	0.000
21	A	474	VAL	0	-0.010	-0.011	24.154	0.018	0.018	0.000	0.000	0.000	0.000
22	A	475	ALA	0	-0.010	0.007	25.160	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	476	MET	0	-0.011	0.000	20.556	0.008	0.008	0.000	0.000	0.000	0.000
24	A	477	ARG	1	0.824	0.890	24.561	0.237	0.237	0.000	0.000	0.000	0.000
25	A	478	GLU	-1	-0.913	-0.960	23.773	-0.257	-0.257	0.000	0.000	0.000	0.000
26	A	479	ASP	-1	-0.857	-0.899	23.267	-0.267	-0.267	0.000	0.000	0.000	0.000
27	A	480	GLY	0	0.009	0.007	20.218	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	481	GLY	0	-0.006	0.005	20.773	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	482	THR	0	0.001	-0.028	23.260	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	483	LEU	0	-0.060	-0.032	25.125	0.017	0.017	0.000	0.000	0.000	0.000
31	A	484	GLY	0	0.012	-0.002	28.221	0.020	0.020	0.000	0.000	0.000	0.000
32	A	485	VAL	0	-0.004	0.003	28.265	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	486	PHE	0	-0.052	-0.029	29.298	0.018	0.018	0.000	0.000	0.000	0.000
34	A	487	SER	0	0.035	0.022	31.971	0.000	0.000	0.000	0.000	0.000	0.000
35	A	488	PRO	0	0.023	0.004	31.921	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	489	LYS	1	0.922	0.964	31.202	0.201	0.201	0.000	0.000	0.000	0.000
37	A	490	LYS	1	0.862	0.923	32.200	0.159	0.159	0.000	0.000	0.000	0.000
38	A	491	THR	0	0.029	0.018	32.888	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	492	PRO	0	0.036	0.026	35.224	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	493	HIS	0	0.015	0.002	35.974	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	494	LEU	0	0.000	0.020	38.077	0.005	0.005	0.000	0.000	0.000	0.000
42	A	495	VAL	0	-0.020	-0.016	38.535	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	496	ASN	0	-0.011	-0.025	40.157	0.010	0.010	0.000	0.000	0.000	0.000
44	A	497	LEU	0	-0.066	-0.043	42.075	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	498	ASN	0	-0.014	-0.007	44.061	0.005	0.005	0.000	0.000	0.000	0.000
46	A	499	GLU	-1	-0.938	-0.973	43.561	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	500	ASP	-1	-0.879	-0.933	44.038	-0.074	-0.074	0.000	0.000	0.000	0.000
48	A	501	PRO	0	-0.050	-0.026	40.081	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	502	LEU	0	-0.060	-0.039	39.294	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	503	MET	0	-0.030	0.020	39.444	0.004	0.004	0.000	0.000	0.000	0.000
51	A	504	SER	0	-0.010	-0.012	39.164	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	505	GLU	-1	-0.817	-0.884	38.367	-0.074	-0.074	0.000	0.000	0.000	0.000
53	A	506	CYS	0	0.018	0.012	35.041	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	507	LEU	0	0.042	0.018	35.882	0.004	0.004	0.000	0.000	0.000	0.000
55	A	508	LEU	0	-0.048	-0.028	33.428	0.002	0.002	0.000	0.000	0.000	0.000
56	A	509	TYR	0	0.047	0.032	35.194	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	510	TYR	0	0.017	-0.007	29.149	0.006	0.006	0.000	0.000	0.000	0.000
58	A	511	ILE	0	-0.033	-0.009	34.863	0.005	0.005	0.000	0.000	0.000	0.000
59	A	512	LYS	1	0.912	0.952	27.938	0.178	0.178	0.000	0.000	0.000	0.000
60	A	513	ASP	-1	-0.824	-0.904	34.633	-0.095	-0.095	0.000	0.000	0.000	0.000
61	A	514	GLY	0	0.019	0.024	35.999	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	515	ILE	0	-0.051	-0.040	38.017	0.006	0.006	0.000	0.000	0.000	0.000
63	A	516	THR	0	-0.043	-0.019	37.404	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	517	ARG	1	0.878	0.943	39.423	0.061	0.061	0.000	0.000	0.000	0.000
65	A	518	VAL	0	0.016	0.004	40.784	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	519	GLY	0	0.055	0.014	43.135	0.004	0.004	0.000	0.000	0.000	0.000
67	A	520	ARG	1	0.787	0.884	43.764	0.046	0.046	0.000	0.000	0.000	0.000
68	A	521	GLU	-1	-0.826	-0.925	37.981	-0.070	-0.070	0.000	0.000	0.000	0.000
69	A	522	ASP	-1	-0.940	-0.979	39.970	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	523	GLY	0	-0.090	-0.014	41.387	0.003	0.003	0.000	0.000	0.000	0.000
71	A	524	GLU	-1	-0.938	-0.978	43.552	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	525	ARG	1	0.771	0.859	42.502	0.046	0.046	0.000	0.000	0.000	0.000
73	A	526	ARG	1	0.889	0.937	35.494	0.073	0.073	0.000	0.000	0.000	0.000
74	A	527	GLN	0	-0.033	-0.025	40.138	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	528	ASP	-1	-0.804	-0.900	36.433	-0.082	-0.082	0.000	0.000	0.000	0.000
76	A	529	ILE	0	-0.053	-0.025	36.532	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	530	VAL	0	0.019	0.021	38.618	0.005	0.005	0.000	0.000	0.000	0.000
78	A	531	LEU	0	-0.067	-0.042	40.421	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	532	SER	0	-0.007	-0.027	43.257	0.005	0.005	0.000	0.000	0.000	0.000
80	A	533	GLY	0	0.030	0.022	45.267	0.004	0.004	0.000	0.000	0.000	0.000
81	A	534	HIS	0	-0.008	-0.011	48.807	0.000	0.000	0.000	0.000	0.000	0.000
82	A	535	PHE	0	-0.026	-0.023	51.812	0.002	0.002	0.000	0.000	0.000	0.000
83	A	536	ILE	0	-0.051	-0.004	46.059	0.000	0.000	0.000	0.000	0.000	0.000
84	A	537	LYS	1	0.927	0.954	49.546	0.042	0.042	0.000	0.000	0.000	0.000
85	A	538	GLU	-1	-0.842	-0.930	47.055	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	539	GLU	-1	-0.730	-0.827	45.307	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	540	HIS	0	-0.063	-0.035	46.907	0.004	0.004	0.000	0.000	0.000	0.000
88	A	541	CYS	0	-0.054	-0.045	46.787	0.000	0.000	0.000	0.000	0.000	0.000
89	A	542	VAL	0	0.010	0.010	43.475	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	543	PHE	0	0.052	0.019	41.529	0.001	0.001	0.000	0.000	0.000	0.000
91	A	544	ARG	1	0.784	0.849	42.128	0.059	0.059	0.000	0.000	0.000	0.000
92	A	545	SER	0	-0.041	-0.039	39.168	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	546	ASP	-1	-0.756	-0.860	40.739	-0.075	-0.075	0.000	0.000	0.000	0.000
94	A	547	SER	0	0.019	0.020	38.701	0.001	0.001	0.000	0.000	0.000	0.000
95	A	548	ARG	1	0.830	0.909	40.836	0.068	0.068	0.000	0.000	0.000	0.000
96	A	549	GLY	0	0.000	-0.011	43.581	0.002	0.002	0.000	0.000	0.000	0.000
97	A	550	GLY	0	-0.020	0.023	41.722	0.000	0.000	0.000	0.000	0.000	0.000
98	A	551	SER	0	-0.044	-0.039	41.282	0.005	0.005	0.000	0.000	0.000	0.000
99	A	552	GLU	-1	-0.855	-0.935	40.186	-0.094	-0.094	0.000	0.000	0.000	0.000
100	A	553	ALA	0	0.026	0.016	38.799	0.004	0.004	0.000	0.000	0.000	0.000
101	A	554	VAL	0	0.006	0.005	40.878	0.001	0.001	0.000	0.000	0.000	0.000
102	A	555	VAL	0	-0.017	-0.009	41.372	0.001	0.001	0.000	0.000	0.000	0.000
103	A	556	THR	0	-0.006	-0.010	44.086	0.003	0.003	0.000	0.000	0.000	0.000
104	A	557	LEU	0	-0.029	-0.016	45.448	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	558	GLU	-1	-0.812	-0.858	47.605	-0.055	-0.055	0.000	0.000	0.000	0.000
106	A	559	PRO	0	-0.004	0.002	49.075	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	560	CYS	0	-0.019	0.008	48.874	0.000	0.000	0.000	0.000	0.000	0.000
108	A	561	GLU	-1	-0.828	-0.921	51.533	-0.035	-0.035	0.000	0.000	0.000	0.000
109	A	562	GLY	0	-0.004	-0.006	54.409	0.000	0.000	0.000	0.000	0.000	0.000
110	A	563	ALA	0	-0.048	0.009	51.789	0.000	0.000	0.000	0.000	0.000	0.000
111	A	564	ASP	-1	-0.836	-0.907	52.953	-0.042	-0.042	0.000	0.000	0.000	0.000
112	A	565	THR	0	0.052	0.034	49.043	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	566	TYR	0	-0.079	-0.047	51.765	0.003	0.003	0.000	0.000	0.000	0.000
114	A	567	VAL	0	0.045	0.017	49.904	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	568	ASN	0	-0.002	-0.011	52.028	0.000	0.000	0.000	0.000	0.000	0.000
116	A	569	GLY	0	0.020	0.024	54.131	0.002	0.002	0.000	0.000	0.000	0.000
117	A	570	LYS	1	0.926	0.979	55.580	0.053	0.053	0.000	0.000	0.000	0.000
118	A	571	LYS	1	0.907	0.946	55.550	0.042	0.042	0.000	0.000	0.000	0.000
119	A	572	VAL	0	-0.039	-0.028	51.218	0.000	0.000	0.000	0.000	0.000	0.000
120	A	573	THR	0	-0.045	-0.045	54.470	0.000	0.000	0.000	0.000	0.000	0.000
121	A	574	GLU	-1	-0.869	-0.910	54.396	-0.043	-0.043	0.000	0.000	0.000	0.000
122	A	575	PRO	0	0.008	-0.019	49.995	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	576	SER	0	-0.037	0.001	51.171	0.001	0.001	0.000	0.000	0.000	0.000
124	A	577	ILE	0	0.004	-0.009	48.288	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	578	LEU	0	-0.051	-0.006	45.081	0.002	0.002	0.000	0.000	0.000	0.000
126	A	579	ARG	1	0.792	0.843	47.389	0.073	0.073	0.000	0.000	0.000	0.000
127	A	580	SER	0	0.008	0.006	43.981	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	581	GLY	0	-0.039	-0.020	45.657	0.002	0.002	0.000	0.000	0.000	0.000
129	A	582	ASN	0	-0.023	-0.016	47.314	0.002	0.002	0.000	0.000	0.000	0.000
130	A	583	ARG	1	0.976	1.002	47.404	0.060	0.060	0.000	0.000	0.000	0.000
131	A	584	ILE	0	-0.017	-0.013	45.851	0.004	0.004	0.000	0.000	0.000	0.000
132	A	585	ILE	0	-0.018	-0.004	48.502	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	586	MET	0	0.015	0.008	44.318	0.001	0.001	0.000	0.000	0.000	0.000
134	A	587	GLY	0	0.054	0.025	49.430	0.000	0.000	0.000	0.000	0.000	0.000
135	A	588	LYS	1	0.816	0.887	51.726	0.044	0.044	0.000	0.000	0.000	0.000
136	A	589	SER	0	0.002	0.000	49.143	0.002	0.002	0.000	0.000	0.000	0.000
137	A	590	HIS	0	0.061	0.064	45.202	0.001	0.001	0.000	0.000	0.000	0.000
138	A	591	VAL	0	-0.006	-0.016	46.725	0.002	0.002	0.000	0.000	0.000	0.000
139	A	592	PHE	0	0.056	0.029	41.225	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	593	ARG	1	0.882	0.931	41.617	0.102	0.102	0.000	0.000	0.000	0.000
141	A	594	PHE	0	0.029	0.017	41.622	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	595	ASN	0	-0.015	0.001	39.062	0.009	0.009	0.000	0.000	0.000	0.000
143	A	596	HIS	0	0.061	0.002	40.151	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	597	PRO	0	-0.004	0.010	36.621	0.004	0.004	0.000	0.000	0.000	0.000
145	A	598	GLU	-1	-0.859	-0.932	36.671	-0.129	-0.129	0.000	0.000	0.000	0.000
146	A	599	GLN	0	0.056	0.052	40.104	0.004	0.004	0.000	0.000	0.000	0.000
147	A	600	ALA	0	-0.020	-0.020	42.708	0.003	0.003	0.000	0.000	0.000	0.000
148	A	601	ARG	1	0.820	0.909	38.229	0.128	0.128	0.000	0.000	0.000	0.000
149	A	602	GLN	0	0.034	-0.002	42.615	0.005	0.005	0.000	0.000	0.000	0.000
150	A	603	GLU	-1	-0.837	-0.877	44.942	-0.073	-0.073	0.000	0.000	0.000	0.000
151	A	604	ARG	1	0.865	0.926	44.878	0.099	0.099	0.000	0.000	0.000	0.000
152	A	605	GLU	-1	-0.824	-0.894	42.157	-0.109	-0.109	0.000	0.000	0.000	0.000
153	A	606	ARG	1	0.884	0.953	47.068	0.074	0.074	0.000	0.000	0.000	0.000
154	A	607	THR	0	-0.013	-0.001	50.431	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:454:GLY)