FMO DATABASE

FMODB ID: 1NV7Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1382143.137979
FMO2-HF: Nuclear repulsion	1320112.812067
FMO2-HF: Total energy	-62030.325913
FMO2-MP2: Total energy	-62207.353172

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.
1.083	4.521	0.139	-1.573	-2.005	0.003

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 : 0.075 / q_NPA : 0.035

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	-0.854	-0.930	3.810	-3.891	-1.742	-0.008	-1.095	-1.046	0.003
4	A	457	PHE	0	-0.031	-0.003	2.808	0.714	1.494	0.139	-0.297	-0.622	0.000
5	A	458	THR	0	-0.013	-0.030	3.054	2.206	2.715	0.008	-0.181	-0.337	0.000
6	A	459	GLU	-1	-0.800	-0.874	5.547	-0.511	-0.511	0.000	0.000	0.000	0.000
7	A	460	ALA	0	-0.004	0.015	7.637	0.554	0.554	0.000	0.000	0.000	0.000
8	A	461	ILE	0	0.003	0.001	8.200	0.384	0.384	0.000	0.000	0.000	0.000
9	A	462	ARG	1	0.709	0.821	9.898	1.389	1.389	0.000	0.000	0.000	0.000
10	A	463	MET	0	0.008	-0.007	11.169	0.240	0.240	0.000	0.000	0.000	0.000
11	A	464	GLU	-1	-0.896	-0.928	13.204	-0.479	-0.479	0.000	0.000	0.000	0.000
12	A	465	ARG	1	0.919	0.955	12.016	0.960	0.960	0.000	0.000	0.000	0.000
13	A	466	GLU	-1	-0.903	-0.941	15.884	-0.588	-0.588	0.000	0.000	0.000	0.000
14	A	467	ALA	0	0.017	0.004	17.768	0.073	0.073	0.000	0.000	0.000	0.000
15	A	468	LEU	0	0.054	0.022	18.889	0.060	0.060	0.000	0.000	0.000	0.000
16	A	469	LEU	0	-0.048	-0.030	19.207	0.050	0.050	0.000	0.000	0.000	0.000
17	A	470	ALA	0	-0.030	-0.018	22.054	0.042	0.042	0.000	0.000	0.000	0.000
18	A	471	GLU	-1	-1.000	-0.985	23.537	-0.267	-0.267	0.000	0.000	0.000	0.000
19	A	472	MET	0	-0.055	-0.025	24.511	0.033	0.033	0.000	0.000	0.000	0.000
20	A	473	GLY	0	-0.035	-0.007	26.569	0.019	0.019	0.000	0.000	0.000	0.000
21	A	474	VAL	0	-0.005	0.000	24.176	0.022	0.022	0.000	0.000	0.000	0.000
22	A	475	ALA	0	-0.024	-0.002	25.034	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	476	MET	0	-0.012	-0.002	20.393	0.012	0.012	0.000	0.000	0.000	0.000
24	A	477	ARG	1	0.825	0.880	24.583	0.195	0.195	0.000	0.000	0.000	0.000
25	A	478	GLU	-1	-0.900	-0.956	23.840	-0.222	-0.222	0.000	0.000	0.000	0.000
26	A	479	ASP	-1	-0.868	-0.903	23.170	-0.221	-0.221	0.000	0.000	0.000	0.000
27	A	480	GLY	0	0.016	0.009	20.396	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	481	GLY	0	-0.005	0.007	20.815	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	482	THR	0	-0.009	-0.023	23.280	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	483	LEU	0	-0.049	-0.027	24.993	0.019	0.019	0.000	0.000	0.000	0.000
31	A	484	GLY	0	0.015	0.001	28.039	0.019	0.019	0.000	0.000	0.000	0.000
32	A	485	VAL	0	-0.006	0.004	28.482	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	486	PHE	0	-0.056	-0.034	28.804	0.017	0.017	0.000	0.000	0.000	0.000
34	A	487	SER	0	0.037	0.026	32.069	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	488	PRO	0	0.022	-0.001	32.483	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	489	LYS	1	0.897	0.951	31.346	0.200	0.200	0.000	0.000	0.000	0.000
37	A	490	LYS	1	0.926	0.953	32.831	0.176	0.176	0.000	0.000	0.000	0.000
38	A	491	THR	0	0.033	0.038	33.284	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	492	PRO	0	0.035	0.027	35.662	0.000	0.000	0.000	0.000	0.000	0.000
40	A	493	HIS	0	0.000	-0.012	36.540	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	494	LEU	0	-0.018	0.007	38.624	0.006	0.006	0.000	0.000	0.000	0.000
42	A	495	VAL	0	-0.018	-0.021	38.945	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	496	ASN	0	0.000	-0.017	40.284	0.010	0.010	0.000	0.000	0.000	0.000
44	A	497	LEU	0	-0.065	-0.050	42.189	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	498	ASN	0	-0.011	-0.007	43.875	0.006	0.006	0.000	0.000	0.000	0.000
46	A	499	GLU	-1	-0.931	-0.969	43.631	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	500	ASP	-1	-0.896	-0.935	44.121	-0.069	-0.069	0.000	0.000	0.000	0.000
48	A	501	PRO	0	-0.044	-0.024	39.784	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	502	LEU	0	-0.065	-0.038	39.112	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	503	MET	0	-0.039	0.009	39.181	0.004	0.004	0.000	0.000	0.000	0.000
51	A	504	SER	0	0.000	-0.005	39.322	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	505	GLU	-1	-0.841	-0.912	38.328	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	506	CYS	0	0.004	0.005	35.154	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	507	LEU	0	0.044	0.023	35.734	0.005	0.005	0.000	0.000	0.000	0.000
55	A	508	LEU	0	-0.034	-0.019	33.675	0.003	0.003	0.000	0.000	0.000	0.000
56	A	509	TYR	0	0.062	0.039	35.194	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	510	TYR	0	0.026	-0.004	29.892	0.005	0.005	0.000	0.000	0.000	0.000
58	A	511	ILE	0	-0.023	-0.006	35.313	0.005	0.005	0.000	0.000	0.000	0.000
59	A	512	LYS	1	0.948	0.963	29.760	0.177	0.177	0.000	0.000	0.000	0.000
60	A	513	ASP	-1	-0.905	-0.948	35.400	-0.115	-0.115	0.000	0.000	0.000	0.000
61	A	514	GLY	0	0.023	0.023	36.425	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	515	ILE	0	-0.045	-0.038	38.776	0.005	0.005	0.000	0.000	0.000	0.000
63	A	516	THR	0	-0.025	-0.011	38.278	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	517	ARG	1	0.919	0.959	40.073	0.079	0.079	0.000	0.000	0.000	0.000
65	A	518	VAL	0	0.014	0.010	41.268	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	519	GLY	0	0.055	0.014	43.462	0.004	0.004	0.000	0.000	0.000	0.000
67	A	520	ARG	1	0.789	0.892	44.311	0.051	0.051	0.000	0.000	0.000	0.000
68	A	521	GLU	-1	-0.861	-0.946	38.610	-0.079	-0.079	0.000	0.000	0.000	0.000
69	A	522	ASP	-1	-0.972	-0.984	40.677	-0.055	-0.055	0.000	0.000	0.000	0.000
70	A	523	GLY	0	-0.082	-0.006	42.175	0.003	0.003	0.000	0.000	0.000	0.000
71	A	524	GLU	-1	-0.872	-0.950	43.847	-0.042	-0.042	0.000	0.000	0.000	0.000
72	A	525	ARG	1	0.734	0.823	42.986	0.059	0.059	0.000	0.000	0.000	0.000
73	A	526	ARG	1	0.979	0.989	36.019	0.090	0.090	0.000	0.000	0.000	0.000
74	A	527	GLN	0	-0.046	-0.030	40.521	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	528	ASP	-1	-0.868	-0.927	37.014	-0.102	-0.102	0.000	0.000	0.000	0.000
76	A	529	ILE	0	-0.055	-0.026	37.154	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	530	VAL	0	0.022	0.019	39.286	0.005	0.005	0.000	0.000	0.000	0.000
78	A	531	LEU	0	-0.069	-0.038	41.054	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	532	SER	0	-0.008	-0.016	43.826	0.004	0.004	0.000	0.000	0.000	0.000
80	A	533	GLY	0	0.050	0.023	45.864	0.004	0.004	0.000	0.000	0.000	0.000
81	A	534	HIS	0	-0.007	-0.003	49.125	0.000	0.000	0.000	0.000	0.000	0.000
82	A	535	PHE	0	-0.048	-0.038	52.326	0.002	0.002	0.000	0.000	0.000	0.000
83	A	536	ILE	0	-0.035	0.001	46.727	0.000	0.000	0.000	0.000	0.000	0.000
84	A	537	LYS	1	0.886	0.925	50.220	0.048	0.048	0.000	0.000	0.000	0.000
85	A	538	GLU	-1	-0.865	-0.938	47.921	-0.049	-0.049	0.000	0.000	0.000	0.000
86	A	539	GLU	-1	-0.741	-0.822	46.445	-0.064	-0.064	0.000	0.000	0.000	0.000
87	A	540	HIS	0	-0.040	-0.028	47.214	0.004	0.004	0.000	0.000	0.000	0.000
88	A	541	CYS	0	-0.052	-0.029	47.143	0.001	0.001	0.000	0.000	0.000	0.000
89	A	542	VAL	0	-0.007	-0.003	44.045	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	543	PHE	0	0.041	0.012	42.153	0.002	0.002	0.000	0.000	0.000	0.000
91	A	544	ARG	1	0.799	0.863	42.719	0.070	0.070	0.000	0.000	0.000	0.000
92	A	545	SER	0	-0.001	-0.002	39.741	0.002	0.002	0.000	0.000	0.000	0.000
93	A	546	ASP	-1	-0.766	-0.867	40.764	-0.093	-0.093	0.000	0.000	0.000	0.000
94	A	547	SER	0	0.059	0.035	39.203	0.001	0.001	0.000	0.000	0.000	0.000
95	A	548	ARG	1	0.804	0.947	41.346	0.081	0.081	0.000	0.000	0.000	0.000
96	A	549	GLY	0	0.018	-0.018	44.415	0.002	0.002	0.000	0.000	0.000	0.000
97	A	550	GLY	0	-0.044	-0.001	41.881	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	551	SER	0	-0.038	-0.046	41.332	0.006	0.006	0.000	0.000	0.000	0.000
99	A	552	GLU	-1	-0.840	-0.950	40.592	-0.104	-0.104	0.000	0.000	0.000	0.000
100	A	553	ALA	0	0.005	0.004	39.571	0.004	0.004	0.000	0.000	0.000	0.000
101	A	554	VAL	0	0.015	0.018	41.603	0.003	0.003	0.000	0.000	0.000	0.000
102	A	555	VAL	0	0.006	-0.011	41.944	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	556	THR	0	-0.003	0.001	44.715	0.003	0.003	0.000	0.000	0.000	0.000
104	A	557	LEU	0	-0.025	-0.013	46.150	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	558	GLU	-1	-0.797	-0.860	48.212	-0.065	-0.065	0.000	0.000	0.000	0.000
106	A	559	PRO	0	-0.013	0.002	49.694	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	560	CYS	0	-0.008	0.008	49.447	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	561	GLU	-1	-0.862	-0.943	52.102	-0.042	-0.042	0.000	0.000	0.000	0.000
109	A	562	GLY	0	0.029	0.017	54.824	0.000	0.000	0.000	0.000	0.000	0.000
110	A	563	ALA	0	-0.045	0.000	52.069	0.001	0.001	0.000	0.000	0.000	0.000
111	A	564	ASP	-1	-0.920	-0.943	54.196	-0.047	-0.047	0.000	0.000	0.000	0.000
112	A	565	THR	0	0.062	0.013	49.761	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	566	TYR	0	-0.047	-0.012	52.415	0.002	0.002	0.000	0.000	0.000	0.000
114	A	567	VAL	0	0.063	0.029	50.572	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	568	ASN	0	-0.018	-0.017	52.529	0.000	0.000	0.000	0.000	0.000	0.000
116	A	569	GLY	0	0.009	0.011	54.643	0.002	0.002	0.000	0.000	0.000	0.000
117	A	570	LYS	1	0.957	0.986	56.646	0.057	0.057	0.000	0.000	0.000	0.000
118	A	571	LYS	1	0.895	0.936	56.200	0.046	0.046	0.000	0.000	0.000	0.000
119	A	572	VAL	0	-0.022	-0.018	52.002	0.001	0.001	0.000	0.000	0.000	0.000
120	A	573	THR	0	-0.023	-0.018	55.227	0.001	0.001	0.000	0.000	0.000	0.000
121	A	574	GLU	-1	-0.921	-0.958	54.975	-0.050	-0.050	0.000	0.000	0.000	0.000
122	A	575	PRO	0	0.015	-0.005	50.449	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	576	SER	0	-0.054	-0.015	51.281	0.002	0.002	0.000	0.000	0.000	0.000
124	A	577	ILE	0	-0.011	-0.014	48.554	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	578	LEU	0	-0.038	-0.002	45.440	0.002	0.002	0.000	0.000	0.000	0.000
126	A	579	ARG	1	0.793	0.856	47.762	0.077	0.077	0.000	0.000	0.000	0.000
127	A	580	SER	0	0.036	0.012	44.531	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	581	GLY	0	-0.069	-0.037	45.983	0.003	0.003	0.000	0.000	0.000	0.000
129	A	582	ASN	0	-0.026	-0.001	47.757	0.003	0.003	0.000	0.000	0.000	0.000
130	A	583	ARG	1	0.985	0.993	47.895	0.061	0.061	0.000	0.000	0.000	0.000
131	A	584	ILE	0	0.009	-0.005	46.157	0.003	0.003	0.000	0.000	0.000	0.000
132	A	585	ILE	0	-0.031	-0.006	48.747	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	586	MET	0	0.017	0.013	44.621	0.001	0.001	0.000	0.000	0.000	0.000
134	A	587	GLY	0	0.054	0.029	49.938	0.000	0.000	0.000	0.000	0.000	0.000
135	A	588	LYS	1	0.892	0.927	52.302	0.044	0.044	0.000	0.000	0.000	0.000
136	A	589	SER	0	0.015	0.007	49.350	0.001	0.001	0.000	0.000	0.000	0.000
137	A	590	HIS	0	0.045	0.053	45.191	0.001	0.001	0.000	0.000	0.000	0.000
138	A	591	VAL	0	0.006	-0.008	47.074	0.002	0.002	0.000	0.000	0.000	0.000
139	A	592	PHE	0	0.060	0.031	41.414	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	593	ARG	1	0.882	0.950	41.729	0.102	0.102	0.000	0.000	0.000	0.000
141	A	594	PHE	0	0.036	0.023	42.240	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	595	ASN	0	-0.023	-0.014	39.799	0.009	0.009	0.000	0.000	0.000	0.000
143	A	596	HIS	0	0.048	-0.004	40.796	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	597	PRO	0	0.005	0.018	37.302	0.005	0.005	0.000	0.000	0.000	0.000
145	A	598	GLU	-1	-0.886	-0.952	36.781	-0.141	-0.141	0.000	0.000	0.000	0.000
146	A	599	GLN	0	0.092	0.069	40.503	0.006	0.006	0.000	0.000	0.000	0.000
147	A	600	ALA	0	-0.044	-0.036	43.402	0.005	0.005	0.000	0.000	0.000	0.000
148	A	601	ARG	1	0.805	0.902	38.327	0.133	0.133	0.000	0.000	0.000	0.000
149	A	602	GLN	0	0.020	0.007	43.005	0.004	0.004	0.000	0.000	0.000	0.000
150	A	603	GLU	-1	-0.842	-0.881	45.300	-0.076	-0.076	0.000	0.000	0.000	0.000
151	A	604	ARG	1	0.875	0.920	44.603	0.102	0.102	0.000	0.000	0.000	0.000
152	A	605	GLU	-1	-0.851	-0.909	42.631	-0.113	-0.113	0.000	0.000	0.000	0.000
153	A	606	ARG	1	0.888	0.955	47.604	0.077	0.077	0.000	0.000	0.000	0.000
154	A	607	THR	0	-0.013	-0.003	50.907	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)