FMO DATABASE

FMODB ID: R8K98

Calculation Name: 1LK3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LK3

Chain ID: A

ChEMBL ID:

UniProt ID: P20759

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1350531.566395
FMO2-HF: Nuclear repulsion	1292621.313305
FMO2-HF: Total energy	-57910.25309
FMO2-MP2: Total energy	-58074.190577

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:21:ASN)

Summations of interaction energy for fragment #1(A:21: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.
-4.704	-0.635	2.568	-2.138	-4.499	-0.001

Interaction energy analysis for fragmet #1(A:21:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.002

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	23	LEU	0	0.049	0.008	2.166	-2.174	0.646	2.535	-1.912	-3.443	-0.001
4	A	24	ARG	1	0.939	0.978	3.169	2.672	3.285	0.025	-0.133	-0.506	0.000
5	A	25	ASP	-1	-0.812	-0.891	4.767	-1.092	-0.912	-0.001	-0.012	-0.167	0.000
6	A	26	LEU	0	-0.039	-0.017	7.019	0.446	0.446	0.000	0.000	0.000	0.000
7	A	27	ARG	1	0.813	0.860	4.489	4.709	4.829	-0.001	-0.002	-0.116	0.000
8	A	28	ASP	-1	-0.918	-0.946	8.617	-2.236	-2.236	0.000	0.000	0.000	0.000
9	A	29	ALA	0	-0.039	-0.022	10.595	0.283	0.283	0.000	0.000	0.000	0.000
10	A	30	PHE	0	0.017	0.017	11.874	0.137	0.137	0.000	0.000	0.000	0.000
11	A	31	SER	0	-0.066	-0.044	12.754	0.185	0.185	0.000	0.000	0.000	0.000
12	A	32	ARG	1	0.933	0.961	13.149	1.179	1.179	0.000	0.000	0.000	0.000
13	A	33	VAL	0	0.021	0.013	16.651	0.095	0.095	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.929	0.977	15.855	1.090	1.090	0.000	0.000	0.000	0.000
15	A	35	THR	0	-0.015	-0.030	18.453	0.036	0.036	0.000	0.000	0.000	0.000
16	A	36	PHE	0	0.010	0.014	21.733	0.034	0.034	0.000	0.000	0.000	0.000
17	A	37	PHE	0	0.035	0.007	20.690	0.037	0.037	0.000	0.000	0.000	0.000
18	A	38	GLN	0	-0.028	0.008	20.687	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	39	MET	0	-0.033	-0.012	23.242	0.044	0.044	0.000	0.000	0.000	0.000
20	A	40	LYS	1	0.912	0.937	26.316	0.332	0.332	0.000	0.000	0.000	0.000
21	A	41	ASP	-1	-0.901	-0.956	28.709	-0.269	-0.269	0.000	0.000	0.000	0.000
22	A	42	GLN	0	-0.001	0.020	27.283	0.039	0.039	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.039	0.028	28.994	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	44	ASP	-1	-0.922	-0.994	24.972	-0.353	-0.353	0.000	0.000	0.000	0.000
25	A	45	ASN	0	-0.060	-0.022	25.898	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	46	LEU	0	-0.005	0.013	20.013	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.071	-0.043	21.767	0.044	0.044	0.000	0.000	0.000	0.000
28	A	48	LEU	0	-0.046	-0.021	16.630	0.058	0.058	0.000	0.000	0.000	0.000
29	A	49	LYS	1	0.956	0.984	19.698	0.133	0.133	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-0.868	-0.938	19.968	-0.136	-0.136	0.000	0.000	0.000	0.000
31	A	51	SER	0	0.036	0.025	20.656	0.029	0.029	0.000	0.000	0.000	0.000
32	A	52	LEU	0	0.004	0.013	17.833	0.042	0.042	0.000	0.000	0.000	0.000
33	A	53	LEU	0	-0.031	-0.003	14.110	0.061	0.061	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.937	-0.989	17.418	0.090	0.090	0.000	0.000	0.000	0.000
35	A	55	ASP	-1	-0.837	-0.910	20.065	0.171	0.171	0.000	0.000	0.000	0.000
36	A	56	PHE	0	-0.099	-0.052	13.516	0.063	0.063	0.000	0.000	0.000	0.000
37	A	57	LYS	1	0.935	0.956	14.191	-0.065	-0.065	0.000	0.000	0.000	0.000
38	A	58	GLY	0	0.033	0.041	16.964	0.033	0.033	0.000	0.000	0.000	0.000
39	A	59	TYR	0	-0.007	-0.010	19.761	0.048	0.048	0.000	0.000	0.000	0.000
40	A	60	LEU	0	-0.013	-0.006	21.756	0.032	0.032	0.000	0.000	0.000	0.000
41	A	61	GLY	0	0.062	0.038	17.817	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	62	CYS	0	-0.090	0.001	16.403	-0.045	-0.045	0.000	0.000	0.000	0.000
43	A	63	GLN	0	0.036	-0.003	17.490	0.006	0.006	0.000	0.000	0.000	0.000
44	A	64	ALA	0	0.081	0.057	18.669	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	65	LEU	0	0.006	0.013	11.473	-0.056	-0.056	0.000	0.000	0.000	0.000
46	A	66	SER	0	-0.070	-0.043	15.887	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	67	GLU	-1	-0.905	-0.965	17.280	0.089	0.089	0.000	0.000	0.000	0.000
48	A	68	MET	0	-0.006	0.004	16.514	-0.043	-0.043	0.000	0.000	0.000	0.000
49	A	69	ILE	0	-0.030	-0.016	12.525	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	70	GLN	0	-0.058	-0.027	16.143	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	71	PHE	0	0.040	0.030	19.657	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	72	TYR	0	0.001	-0.027	16.857	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	73	LEU	0	-0.087	-0.063	16.255	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.970	-0.989	19.429	0.017	0.017	0.000	0.000	0.000	0.000
55	A	75	GLU	-1	-0.895	-0.936	22.833	-0.062	-0.062	0.000	0.000	0.000	0.000
56	A	76	VAL	0	-0.069	-0.024	20.572	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	77	MET	0	-0.011	-0.015	16.100	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	78	PRO	0	0.043	0.032	21.477	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	79	GLN	0	-0.017	-0.011	24.694	0.002	0.002	0.000	0.000	0.000	0.000
60	A	80	ALA	0	-0.030	-0.015	22.409	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.919	-0.975	22.717	-0.257	-0.257	0.000	0.000	0.000	0.000
62	A	82	ASN	0	-0.061	-0.027	25.175	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	83	GLN	0	-0.049	-0.021	26.904	0.012	0.012	0.000	0.000	0.000	0.000
64	A	84	ASP	-1	-0.808	-0.908	27.767	-0.283	-0.283	0.000	0.000	0.000	0.000
65	A	85	PRO	0	-0.040	-0.017	27.688	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	86	ASP	-1	-0.911	-0.957	27.515	-0.287	-0.287	0.000	0.000	0.000	0.000
67	A	87	ILE	0	-0.095	-0.031	21.942	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	88	LYS	1	1.002	1.000	22.770	0.165	0.165	0.000	0.000	0.000	0.000
69	A	89	ALA	0	0.014	0.006	22.920	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	90	HIS	0	0.036	0.007	19.092	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	91	VAL	0	-0.006	0.012	18.125	-0.072	-0.072	0.000	0.000	0.000	0.000
72	A	92	ASN	0	-0.024	-0.014	18.519	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	93	SER	0	-0.025	-0.005	16.343	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	94	LEU	0	-0.007	0.001	12.677	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.053	0.010	14.020	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	96	GLU	-1	-0.853	-0.936	15.512	-0.093	-0.093	0.000	0.000	0.000	0.000
77	A	97	ASN	0	-0.026	-0.024	10.768	0.014	0.014	0.000	0.000	0.000	0.000
78	A	98	LEU	0	-0.002	0.012	10.964	0.055	0.055	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.878	0.937	12.332	0.270	0.270	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.012	-0.007	10.522	0.169	0.169	0.000	0.000	0.000	0.000
81	A	101	LEU	0	0.003	0.004	6.050	0.251	0.251	0.000	0.000	0.000	0.000
82	A	102	ARG	1	0.957	0.978	9.488	0.169	0.169	0.000	0.000	0.000	0.000
83	A	103	LEU	0	-0.030	-0.017	12.497	0.180	0.180	0.000	0.000	0.000	0.000
84	A	104	ARG	1	0.926	0.969	6.386	-1.920	-1.920	0.000	0.000	0.000	0.000
85	A	105	LEU	0	-0.025	-0.021	7.961	0.282	0.282	0.000	0.000	0.000	0.000
86	A	106	ARG	1	0.936	0.954	11.616	-0.371	-0.371	0.000	0.000	0.000	0.000
87	A	107	ARG	1	0.934	0.983	14.293	-0.631	-0.631	0.000	0.000	0.000	0.000
88	A	108	CYS	0	0.013	-0.007	12.198	0.096	0.096	0.000	0.000	0.000	0.000
89	A	109	HIS	0	0.035	0.045	10.389	-0.168	-0.168	0.000	0.000	0.000	0.000
90	A	110	ARG	1	0.992	0.988	13.663	-1.411	-1.411	0.000	0.000	0.000	0.000
91	A	111	PHE	0	0.033	-0.028	7.322	-0.259	-0.259	0.000	0.000	0.000	0.000
92	A	112	LEU	0	0.032	0.031	13.108	-0.096	-0.096	0.000	0.000	0.000	0.000
93	A	113	PRO	0	-0.035	-0.013	15.868	-0.061	-0.061	0.000	0.000	0.000	0.000
94	A	115	GLU	-1	-0.933	-0.964	20.199	0.294	0.294	0.000	0.000	0.000	0.000
95	A	117	LYS	1	0.988	0.982	25.744	-0.163	-0.163	0.000	0.000	0.000	0.000
96	A	118	SER	0	-0.004	-0.024	22.677	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	119	LYS	1	1.003	0.997	24.695	-0.049	-0.049	0.000	0.000	0.000	0.000
98	A	120	ALA	0	0.029	0.015	22.537	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.047	0.018	20.582	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	122	GLU	-1	-0.905	-0.953	23.226	0.000	0.000	0.000	0.000	0.000	0.000
101	A	123	GLN	0	-0.062	-0.028	26.234	-0.017	-0.017	0.000	0.000	0.000	0.000
102	A	124	VAL	0	0.014	0.009	21.513	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	125	LYS	1	0.978	0.993	23.780	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	126	ASN	0	-0.019	-0.009	26.339	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	127	ALA	0	-0.041	-0.014	26.876	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	128	PHE	0	-0.001	-0.005	24.712	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	129	ASN	0	0.057	0.012	27.217	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	130	LYS	1	0.884	0.957	30.381	0.102	0.102	0.000	0.000	0.000	0.000
109	A	131	LEU	0	-0.070	-0.024	27.356	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	132	GLN	0	0.020	0.011	30.895	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	133	GLU	-1	-0.832	-0.925	29.464	-0.179	-0.179	0.000	0.000	0.000	0.000
112	A	134	LYS	1	0.916	0.975	28.705	0.208	0.208	0.000	0.000	0.000	0.000
113	A	135	GLY	0	0.005	-0.022	26.906	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	136	ILE	0	0.020	0.025	24.730	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	137	TYR	0	0.010	0.003	23.453	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	138	LYS	1	0.863	0.933	23.017	0.270	0.270	0.000	0.000	0.000	0.000
117	A	139	ALA	0	0.035	0.008	20.865	-0.038	-0.038	0.000	0.000	0.000	0.000
118	A	140	MET	0	-0.005	0.015	18.403	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	141	SER	0	-0.060	-0.029	18.082	-0.079	-0.079	0.000	0.000	0.000	0.000
120	A	142	GLU	-1	-0.731	-0.851	17.819	-0.440	-0.440	0.000	0.000	0.000	0.000
121	A	143	PHE	0	0.037	0.009	11.397	0.008	0.008	0.000	0.000	0.000	0.000
122	A	144	ASP	-1	-0.875	-0.939	12.092	-1.066	-1.066	0.000	0.000	0.000	0.000
123	A	145	ILE	0	-0.009	-0.004	11.848	-0.135	-0.135	0.000	0.000	0.000	0.000
124	A	146	PHE	0	0.010	0.004	13.027	0.094	0.094	0.000	0.000	0.000	0.000
125	A	147	ILE	0	0.005	-0.004	7.051	0.088	0.088	0.000	0.000	0.000	0.000
126	A	148	ASN	0	0.036	0.033	8.264	-0.298	-0.298	0.000	0.000	0.000	0.000
127	A	149	TYR	0	-0.026	-0.025	10.070	0.225	0.225	0.000	0.000	0.000	0.000
128	A	150	ILE	0	0.010	0.006	7.445	0.280	0.280	0.000	0.000	0.000	0.000
129	A	151	GLU	-1	-0.854	-0.936	3.926	-4.494	-4.158	0.010	-0.079	-0.267	0.000
130	A	152	ALA	0	-0.034	-0.005	7.129	0.752	0.752	0.000	0.000	0.000	0.000
131	A	153	TYR	0	-0.079	-0.059	10.201	0.219	0.219	0.000	0.000	0.000	0.000
132	A	154	MET	0	-0.036	-0.018	4.843	0.341	0.341	0.000	0.000	0.000	0.000
133	A	155	THR	0	-0.117	-0.048	6.693	0.627	0.627	0.000	0.000	0.000	0.000
134	A	156	MET	0	-0.006	0.001	7.979	-0.409	-0.409	0.000	0.000	0.000	0.000
135	A	157	LYS	1	0.840	0.948	10.243	-1.449	-1.449	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:21:ASN)