FMO DATABASE

FMODB ID: VQZ51

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1382142.020835
FMO2-HF: Nuclear repulsion	1320112.365679
FMO2-HF: Total energy	-62029.655156
FMO2-MP2: Total energy	-62206.725646

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.
1.107	3.783	0.069	-0.98	-1.765	-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 : 0.038 / q_NPA : 0.003

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	-0.873	-0.934	3.810	-0.547	0.858	-0.005	-0.618	-0.783	-0.001
4	A	457	PHE	0	-0.022	0.006	2.993	-0.174	0.481	0.066	-0.212	-0.509	0.000
5	A	458	THR	0	-0.009	-0.022	2.976	0.864	1.339	0.009	-0.144	-0.340	0.000
6	A	459	GLU	-1	-0.798	-0.864	5.322	-0.495	-0.354	-0.001	-0.006	-0.133	0.000
7	A	460	ALA	0	0.009	0.023	7.643	0.283	0.283	0.000	0.000	0.000	0.000
8	A	461	ILE	0	-0.002	-0.001	7.877	0.106	0.106	0.000	0.000	0.000	0.000
9	A	462	ARG	1	0.719	0.829	9.662	0.770	0.770	0.000	0.000	0.000	0.000
10	A	463	MET	0	0.004	-0.012	11.450	0.120	0.120	0.000	0.000	0.000	0.000
11	A	464	GLU	-1	-0.877	-0.919	12.987	-0.073	-0.073	0.000	0.000	0.000	0.000
12	A	465	ARG	1	0.924	0.965	11.898	0.585	0.585	0.000	0.000	0.000	0.000
13	A	466	GLU	-1	-0.935	-0.973	15.656	-0.290	-0.290	0.000	0.000	0.000	0.000
14	A	467	ALA	0	0.019	0.004	17.505	0.032	0.032	0.000	0.000	0.000	0.000
15	A	468	LEU	0	0.060	0.023	17.989	0.021	0.021	0.000	0.000	0.000	0.000
16	A	469	LEU	0	-0.063	-0.035	19.054	0.017	0.017	0.000	0.000	0.000	0.000
17	A	470	ALA	0	-0.033	-0.019	21.833	0.018	0.018	0.000	0.000	0.000	0.000
18	A	471	GLU	-1	-0.972	-0.983	23.278	-0.070	-0.070	0.000	0.000	0.000	0.000
19	A	472	MET	0	-0.064	-0.020	24.048	0.016	0.016	0.000	0.000	0.000	0.000
20	A	473	GLY	0	-0.040	-0.011	26.330	0.004	0.004	0.000	0.000	0.000	0.000
21	A	474	VAL	0	0.004	0.007	24.018	0.006	0.006	0.000	0.000	0.000	0.000
22	A	475	ALA	0	-0.026	-0.010	24.853	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	476	MET	0	-0.016	-0.002	20.183	0.008	0.008	0.000	0.000	0.000	0.000
24	A	477	ARG	1	0.879	0.932	24.467	0.164	0.164	0.000	0.000	0.000	0.000
25	A	478	GLU	-1	-0.908	-0.961	23.774	-0.184	-0.184	0.000	0.000	0.000	0.000
26	A	479	ASP	-1	-0.911	-0.951	23.148	-0.206	-0.206	0.000	0.000	0.000	0.000
27	A	480	GLY	0	0.013	0.010	20.367	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	481	GLY	0	-0.005	0.007	20.759	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	482	THR	0	-0.013	-0.021	23.062	0.001	0.001	0.000	0.000	0.000	0.000
30	A	483	LEU	0	-0.049	-0.027	24.901	0.010	0.010	0.000	0.000	0.000	0.000
31	A	484	GLY	0	0.011	-0.002	27.916	0.011	0.011	0.000	0.000	0.000	0.000
32	A	485	VAL	0	-0.007	0.006	28.300	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	486	PHE	0	-0.078	-0.043	28.573	0.009	0.009	0.000	0.000	0.000	0.000
34	A	487	SER	0	0.030	0.023	31.858	0.002	0.002	0.000	0.000	0.000	0.000
35	A	488	PRO	0	0.032	0.006	32.228	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	489	LYS	1	0.895	0.942	31.306	0.096	0.096	0.000	0.000	0.000	0.000
37	A	490	LYS	1	0.930	0.946	32.844	0.065	0.065	0.000	0.000	0.000	0.000
38	A	491	THR	0	0.032	0.047	33.177	0.002	0.002	0.000	0.000	0.000	0.000
39	A	492	PRO	0	0.022	0.025	35.483	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	493	HIS	0	-0.007	-0.028	36.301	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	494	LEU	0	-0.014	0.010	38.369	0.001	0.001	0.000	0.000	0.000	0.000
42	A	495	VAL	0	-0.017	-0.019	38.798	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	496	ASN	0	0.011	-0.008	40.085	0.005	0.005	0.000	0.000	0.000	0.000
44	A	497	LEU	0	-0.065	-0.051	41.993	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	498	ASN	0	-0.022	-0.007	43.780	0.001	0.001	0.000	0.000	0.000	0.000
46	A	499	GLU	-1	-0.925	-0.966	43.474	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	500	ASP	-1	-0.901	-0.940	44.028	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	501	PRO	0	-0.042	-0.021	39.781	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	502	LEU	0	-0.058	-0.035	38.999	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	503	MET	0	-0.045	-0.001	38.995	0.004	0.004	0.000	0.000	0.000	0.000
51	A	504	SER	0	-0.003	-0.010	39.180	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	505	GLU	-1	-0.842	-0.921	38.160	-0.031	-0.031	0.000	0.000	0.000	0.000
53	A	506	CYS	0	-0.010	-0.004	34.815	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	507	LEU	0	0.045	0.024	35.304	0.002	0.002	0.000	0.000	0.000	0.000
55	A	508	LEU	0	-0.034	-0.018	33.623	0.002	0.002	0.000	0.000	0.000	0.000
56	A	509	TYR	0	0.071	0.048	34.976	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	510	TYR	0	0.020	-0.009	29.961	0.001	0.001	0.000	0.000	0.000	0.000
58	A	511	ILE	0	-0.022	-0.002	35.063	0.003	0.003	0.000	0.000	0.000	0.000
59	A	512	LYS	1	0.958	0.965	30.056	0.035	0.035	0.000	0.000	0.000	0.000
60	A	513	ASP	-1	-0.904	-0.950	35.455	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	514	GLY	0	0.025	0.027	36.554	0.001	0.001	0.000	0.000	0.000	0.000
62	A	515	ILE	0	-0.050	-0.044	38.922	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	516	THR	0	-0.012	-0.001	38.491	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	517	ARG	1	0.904	0.947	40.048	0.006	0.006	0.000	0.000	0.000	0.000
65	A	518	VAL	0	0.017	0.016	41.157	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	519	GLY	0	0.055	0.012	43.275	0.002	0.002	0.000	0.000	0.000	0.000
67	A	520	ARG	1	0.794	0.900	44.086	0.013	0.013	0.000	0.000	0.000	0.000
68	A	521	GLU	-1	-0.866	-0.935	38.335	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	522	ASP	-1	-0.966	-0.988	40.594	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	523	GLY	0	-0.109	-0.023	42.057	0.002	0.002	0.000	0.000	0.000	0.000
71	A	524	GLU	-1	-0.835	-0.929	43.832	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	525	ARG	1	0.790	0.887	42.953	0.004	0.004	0.000	0.000	0.000	0.000
73	A	526	ARG	1	0.968	0.979	35.879	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	527	GLN	0	-0.014	-0.010	40.433	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	528	ASP	-1	-0.859	-0.921	36.911	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	529	ILE	0	-0.056	-0.028	36.971	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	530	VAL	0	0.036	0.022	39.070	0.002	0.002	0.000	0.000	0.000	0.000
78	A	531	LEU	0	-0.071	-0.038	40.847	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	532	SER	0	-0.005	-0.007	43.621	0.002	0.002	0.000	0.000	0.000	0.000
80	A	533	GLY	0	0.032	0.014	45.678	0.001	0.001	0.000	0.000	0.000	0.000
81	A	534	HIS	0	-0.005	-0.010	48.935	0.001	0.001	0.000	0.000	0.000	0.000
82	A	535	PHE	0	-0.057	-0.044	52.138	0.001	0.001	0.000	0.000	0.000	0.000
83	A	536	ILE	0	-0.026	0.006	46.536	0.000	0.000	0.000	0.000	0.000	0.000
84	A	537	LYS	1	0.933	0.960	50.002	0.012	0.012	0.000	0.000	0.000	0.000
85	A	538	GLU	-1	-0.868	-0.939	47.776	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	539	GLU	-1	-0.830	-0.901	46.491	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	540	HIS	0	-0.050	-0.035	47.091	0.001	0.001	0.000	0.000	0.000	0.000
88	A	541	CYS	0	-0.036	-0.024	47.008	0.000	0.000	0.000	0.000	0.000	0.000
89	A	542	VAL	0	-0.016	-0.004	44.125	0.000	0.000	0.000	0.000	0.000	0.000
90	A	543	PHE	0	0.020	0.004	42.053	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	544	ARG	1	0.783	0.853	42.763	0.010	0.010	0.000	0.000	0.000	0.000
92	A	545	SER	0	0.002	0.000	39.765	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	546	ASP	-1	-0.814	-0.911	40.905	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	547	SER	0	0.046	0.030	39.427	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	548	ARG	1	0.855	0.986	41.529	0.010	0.010	0.000	0.000	0.000	0.000
96	A	549	GLY	0	0.015	-0.016	44.721	0.000	0.000	0.000	0.000	0.000	0.000
97	A	550	GLY	0	-0.037	0.005	42.076	0.000	0.000	0.000	0.000	0.000	0.000
98	A	551	SER	0	-0.038	-0.047	41.416	0.002	0.002	0.000	0.000	0.000	0.000
99	A	552	GLU	-1	-0.851	-0.949	40.710	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	553	ALA	0	-0.006	-0.003	39.634	0.002	0.002	0.000	0.000	0.000	0.000
101	A	554	VAL	0	0.022	0.021	41.645	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	555	VAL	0	0.003	-0.010	41.927	0.001	0.001	0.000	0.000	0.000	0.000
103	A	556	THR	0	-0.004	-0.001	44.683	0.000	0.000	0.000	0.000	0.000	0.000
104	A	557	LEU	0	-0.026	-0.014	46.107	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	558	GLU	-1	-0.796	-0.864	48.123	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	559	PRO	0	-0.014	0.000	49.617	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	560	CYS	0	0.000	0.010	49.336	0.001	0.001	0.000	0.000	0.000	0.000
108	A	561	GLU	-1	-0.882	-0.951	52.062	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	562	GLY	0	0.003	0.004	54.743	0.000	0.000	0.000	0.000	0.000	0.000
110	A	563	ALA	0	-0.032	-0.009	51.893	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	564	ASP	-1	-0.917	-0.947	54.018	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	565	THR	0	0.064	0.016	49.624	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	566	TYR	0	-0.052	-0.013	52.181	0.001	0.001	0.000	0.000	0.000	0.000
114	A	567	VAL	0	0.066	0.027	50.434	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	568	ASN	0	-0.024	-0.018	52.499	0.000	0.000	0.000	0.000	0.000	0.000
116	A	569	GLY	0	0.002	0.006	54.401	0.001	0.001	0.000	0.000	0.000	0.000
117	A	570	LYS	1	0.955	0.985	56.406	0.017	0.017	0.000	0.000	0.000	0.000
118	A	571	LYS	1	0.899	0.945	55.945	0.012	0.012	0.000	0.000	0.000	0.000
119	A	572	VAL	0	-0.014	-0.010	51.830	0.000	0.000	0.000	0.000	0.000	0.000
120	A	573	THR	0	-0.012	-0.017	55.065	0.000	0.000	0.000	0.000	0.000	0.000
121	A	574	GLU	-1	-0.930	-0.962	54.962	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	575	PRO	0	0.018	0.004	50.540	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	576	SER	0	-0.045	-0.018	51.237	0.000	0.000	0.000	0.000	0.000	0.000
124	A	577	ILE	0	-0.006	-0.007	48.644	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	578	LEU	0	-0.037	-0.003	45.270	0.000	0.000	0.000	0.000	0.000	0.000
126	A	579	ARG	1	0.867	0.911	47.608	0.026	0.026	0.000	0.000	0.000	0.000
127	A	580	SER	0	0.024	0.006	44.071	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	581	GLY	0	-0.023	-0.014	45.718	0.001	0.001	0.000	0.000	0.000	0.000
129	A	582	ASN	0	-0.048	-0.012	47.517	0.002	0.002	0.000	0.000	0.000	0.000
130	A	583	ARG	1	0.998	1.003	47.657	0.027	0.027	0.000	0.000	0.000	0.000
131	A	584	ILE	0	0.015	-0.003	45.690	0.002	0.002	0.000	0.000	0.000	0.000
132	A	585	ILE	0	-0.038	-0.010	48.522	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	586	MET	0	0.020	0.013	44.459	0.001	0.001	0.000	0.000	0.000	0.000
134	A	587	GLY	0	0.052	0.028	49.709	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	588	LYS	1	0.889	0.928	52.082	0.015	0.015	0.000	0.000	0.000	0.000
136	A	589	SER	0	0.021	0.004	49.012	0.000	0.000	0.000	0.000	0.000	0.000
137	A	590	HIS	0	0.034	0.056	45.269	0.000	0.000	0.000	0.000	0.000	0.000
138	A	591	VAL	0	0.022	0.002	46.872	0.001	0.001	0.000	0.000	0.000	0.000
139	A	592	PHE	0	0.053	0.028	41.471	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	593	ARG	1	0.922	0.971	41.679	0.047	0.047	0.000	0.000	0.000	0.000
141	A	594	PHE	0	0.030	0.020	42.065	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	595	ASN	0	-0.030	-0.014	39.993	0.002	0.002	0.000	0.000	0.000	0.000
143	A	596	HIS	0	0.006	-0.018	40.781	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	597	PRO	0	0.010	0.007	37.205	0.001	0.001	0.000	0.000	0.000	0.000
145	A	598	GLU	-1	-0.885	-0.948	36.245	-0.043	-0.043	0.000	0.000	0.000	0.000
146	A	599	GLN	0	0.084	0.059	40.334	0.000	0.000	0.000	0.000	0.000	0.000
147	A	600	ALA	0	-0.044	-0.037	43.177	0.001	0.001	0.000	0.000	0.000	0.000
148	A	601	ARG	1	0.873	0.941	37.698	0.054	0.054	0.000	0.000	0.000	0.000
149	A	602	GLN	0	0.036	0.027	42.138	0.002	0.002	0.000	0.000	0.000	0.000
150	A	603	GLU	-1	-0.879	-0.916	45.150	-0.028	-0.028	0.000	0.000	0.000	0.000
151	A	604	ARG	1	0.877	0.908	44.116	0.044	0.044	0.000	0.000	0.000	0.000
152	A	605	GLU	-1	-0.944	-0.960	42.563	-0.042	-0.042	0.000	0.000	0.000	0.000
153	A	606	ARG	1	0.893	0.966	47.384	0.031	0.031	0.000	0.000	0.000	0.000
154	A	607	THR	0	-0.017	-0.007	50.673	0.001	0.001	0.000	0.000	0.000	0.000

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