FMO DATABASE

FMODB ID: KGZ93

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1352858.485268
FMO2-HF: Nuclear repulsion	1294946.668155
FMO2-HF: Total energy	-57911.817113
FMO2-MP2: Total energy	-58075.544506

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.
-24.761	-23.181	10.736	-5.832	-6.483	-0.05

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 : -0.007 / q_NPA : -0.021

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	0.021	0.008	2.698	-2.348	0.836	0.291	-1.310	-2.165	0.002
4	A	24	ARG	1	0.792	0.881	3.531	1.160	1.915	0.008	-0.302	-0.461	0.000
5	A	25	ASP	-1	-0.800	-0.877	5.225	0.044	0.152	-0.001	-0.009	-0.098	0.000
6	A	26	LEU	0	0.017	0.006	7.167	0.312	0.312	0.000	0.000	0.000	0.000
7	A	27	ARG	1	0.834	0.877	3.437	9.328	9.617	-0.001	-0.085	-0.203	0.000
8	A	28	ASP	-1	-0.851	-0.921	9.059	-1.174	-1.174	0.000	0.000	0.000	0.000
9	A	29	ALA	0	-0.051	-0.022	11.118	0.246	0.246	0.000	0.000	0.000	0.000
10	A	30	PHE	0	0.013	0.009	11.970	0.121	0.121	0.000	0.000	0.000	0.000
11	A	31	SER	0	-0.066	-0.049	13.128	0.198	0.198	0.000	0.000	0.000	0.000
12	A	32	ARG	1	0.924	0.970	13.460	0.924	0.924	0.000	0.000	0.000	0.000
13	A	33	VAL	0	0.019	0.005	16.726	0.088	0.088	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.845	0.929	15.697	1.374	1.374	0.000	0.000	0.000	0.000
15	A	35	THR	0	-0.010	-0.032	18.521	0.020	0.020	0.000	0.000	0.000	0.000
16	A	36	PHE	0	0.012	0.019	21.847	0.041	0.041	0.000	0.000	0.000	0.000
17	A	37	PHE	0	0.031	0.008	20.504	0.033	0.033	0.000	0.000	0.000	0.000
18	A	38	GLN	0	-0.039	-0.013	20.283	-0.079	-0.079	0.000	0.000	0.000	0.000
19	A	39	MET	0	-0.045	-0.011	22.976	0.066	0.066	0.000	0.000	0.000	0.000
20	A	40	LYS	1	0.936	0.958	25.614	0.413	0.413	0.000	0.000	0.000	0.000
21	A	41	ASP	-1	-0.903	-0.957	28.229	-0.415	-0.415	0.000	0.000	0.000	0.000
22	A	42	GLN	0	0.045	0.020	26.524	0.045	0.045	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.029	0.027	28.588	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	44	ASP	-1	-0.902	-0.969	23.974	-0.625	-0.625	0.000	0.000	0.000	0.000
25	A	45	ASN	0	-0.069	-0.031	24.723	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	46	LEU	0	-0.039	0.011	18.252	0.011	0.011	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.017	-0.017	21.514	0.066	0.066	0.000	0.000	0.000	0.000
28	A	48	LEU	0	-0.028	-0.015	15.646	0.039	0.039	0.000	0.000	0.000	0.000
29	A	49	LYS	1	0.922	0.968	18.091	0.454	0.454	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-0.825	-0.916	18.508	-0.711	-0.711	0.000	0.000	0.000	0.000
31	A	51	SER	0	0.014	0.008	19.067	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	52	LEU	0	-0.006	-0.007	16.884	0.036	0.036	0.000	0.000	0.000	0.000
33	A	53	LEU	0	-0.034	-0.009	12.566	-0.039	-0.039	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.920	-0.969	16.090	-0.526	-0.526	0.000	0.000	0.000	0.000
35	A	55	ASP	-1	-0.844	-0.907	18.891	-0.370	-0.370	0.000	0.000	0.000	0.000
36	A	56	PHE	0	-0.031	-0.029	12.722	0.046	0.046	0.000	0.000	0.000	0.000
37	A	57	LYS	1	0.832	0.902	11.199	1.175	1.175	0.000	0.000	0.000	0.000
38	A	58	GLY	0	0.017	0.033	16.293	0.079	0.079	0.000	0.000	0.000	0.000
39	A	59	TYR	0	-0.022	-0.021	19.225	0.002	0.002	0.000	0.000	0.000	0.000
40	A	60	LEU	0	0.019	0.011	21.249	0.033	0.033	0.000	0.000	0.000	0.000
41	A	61	GLY	0	0.060	0.043	17.321	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	62	CYS	0	-0.081	-0.024	16.710	-0.084	-0.084	0.000	0.000	0.000	0.000
43	A	63	GLN	0	0.022	0.017	17.756	0.018	0.018	0.000	0.000	0.000	0.000
44	A	64	ALA	0	0.028	0.023	18.056	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	65	LEU	0	0.011	0.012	12.128	-0.060	-0.060	0.000	0.000	0.000	0.000
46	A	66	SER	0	-0.042	-0.045	15.875	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	67	GLU	-1	-0.828	-0.925	17.751	-0.297	-0.297	0.000	0.000	0.000	0.000
48	A	68	MET	0	-0.009	0.011	16.592	0.021	0.021	0.000	0.000	0.000	0.000
49	A	69	ILE	0	-0.029	-0.025	12.791	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	70	GLN	0	-0.082	-0.043	16.352	0.017	0.017	0.000	0.000	0.000	0.000
51	A	71	PHE	0	0.030	0.010	20.019	0.008	0.008	0.000	0.000	0.000	0.000
52	A	72	TYR	0	-0.008	-0.037	16.725	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	73	LEU	0	-0.037	-0.035	16.232	0.037	0.037	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.817	-0.888	19.541	-0.198	-0.198	0.000	0.000	0.000	0.000
55	A	75	GLU	-1	-0.903	-0.933	22.808	-0.265	-0.265	0.000	0.000	0.000	0.000
56	A	76	VAL	0	-0.053	-0.019	20.789	0.006	0.006	0.000	0.000	0.000	0.000
57	A	77	MET	0	0.006	-0.006	16.477	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	78	PRO	0	0.011	0.016	21.570	0.014	0.014	0.000	0.000	0.000	0.000
59	A	79	GLN	0	-0.001	-0.003	24.889	0.030	0.030	0.000	0.000	0.000	0.000
60	A	80	ALA	0	0.000	-0.010	22.325	0.009	0.009	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.901	-0.958	22.940	-0.301	-0.301	0.000	0.000	0.000	0.000
62	A	82	ASN	0	-0.072	-0.039	25.046	0.043	0.043	0.000	0.000	0.000	0.000
63	A	83	GLN	0	-0.002	0.017	26.731	0.017	0.017	0.000	0.000	0.000	0.000
64	A	84	ASP	-1	-0.812	-0.914	27.716	-0.321	-0.321	0.000	0.000	0.000	0.000
65	A	85	PRO	0	-0.027	-0.012	27.947	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	86	ASP	-1	-0.902	-0.943	27.642	-0.262	-0.262	0.000	0.000	0.000	0.000
67	A	87	ILE	0	-0.100	-0.045	22.114	-0.032	-0.032	0.000	0.000	0.000	0.000
68	A	88	LYS	1	0.906	0.961	22.798	0.213	0.213	0.000	0.000	0.000	0.000
69	A	89	ALA	0	0.032	0.010	22.933	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	90	HIS	0	0.023	0.007	18.993	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	91	VAL	0	-0.002	0.001	18.149	-0.082	-0.082	0.000	0.000	0.000	0.000
72	A	92	ASN	0	-0.024	-0.013	18.740	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	93	SER	0	-0.019	-0.004	16.974	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	94	LEU	0	-0.003	0.004	12.759	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.050	0.022	14.288	-0.080	-0.080	0.000	0.000	0.000	0.000
76	A	96	GLU	-1	-0.780	-0.880	16.005	-0.168	-0.168	0.000	0.000	0.000	0.000
77	A	97	ASN	0	-0.057	-0.024	11.046	0.071	0.071	0.000	0.000	0.000	0.000
78	A	98	LEU	0	0.016	0.014	11.588	0.012	0.012	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.823	0.887	12.824	0.285	0.285	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.034	-0.028	10.838	0.171	0.171	0.000	0.000	0.000	0.000
81	A	101	LEU	0	-0.007	-0.003	6.898	0.292	0.292	0.000	0.000	0.000	0.000
82	A	102	ARG	1	0.811	0.900	10.022	0.453	0.453	0.000	0.000	0.000	0.000
83	A	103	LEU	0	-0.027	-0.025	13.199	0.120	0.120	0.000	0.000	0.000	0.000
84	A	104	ARG	1	0.923	0.967	7.637	-2.491	-2.491	0.000	0.000	0.000	0.000
85	A	105	LEU	0	-0.014	-0.010	7.830	0.320	0.320	0.000	0.000	0.000	0.000
86	A	106	ARG	1	0.962	0.982	11.519	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	107	ARG	1	0.944	0.977	14.414	-0.564	-0.564	0.000	0.000	0.000	0.000
88	A	108	CYS	0	-0.056	-0.015	12.016	0.227	0.227	0.000	0.000	0.000	0.000
89	A	109	HIS	0	0.102	0.042	11.721	-0.100	-0.100	0.000	0.000	0.000	0.000
90	A	110	ARG	1	0.984	1.000	13.873	-0.931	-0.931	0.000	0.000	0.000	0.000
91	A	111	PHE	0	0.004	-0.022	7.601	-0.120	-0.120	0.000	0.000	0.000	0.000
92	A	112	LEU	0	0.024	0.012	12.831	-0.212	-0.212	0.000	0.000	0.000	0.000
93	A	113	PRO	0	-0.029	-0.009	15.693	0.025	0.025	0.000	0.000	0.000	0.000
94	A	115	GLU	-1	-0.936	-0.957	20.379	0.015	0.015	0.000	0.000	0.000	0.000
95	A	117	LYS	1	0.973	0.972	25.526	0.151	0.151	0.000	0.000	0.000	0.000
96	A	118	SER	0	-0.049	-0.035	21.687	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	119	LYS	1	1.005	0.996	23.909	0.278	0.278	0.000	0.000	0.000	0.000
98	A	120	ALA	0	0.020	0.014	21.418	0.003	0.003	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.025	0.008	20.223	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	122	GLU	-1	-0.843	-0.912	22.741	-0.297	-0.297	0.000	0.000	0.000	0.000
101	A	123	GLN	0	-0.037	-0.005	25.048	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	124	VAL	0	0.007	0.003	20.676	0.004	0.004	0.000	0.000	0.000	0.000
103	A	125	LYS	1	0.854	0.918	24.006	0.331	0.331	0.000	0.000	0.000	0.000
104	A	126	ASN	0	-0.032	-0.030	26.093	0.029	0.029	0.000	0.000	0.000	0.000
105	A	127	ALA	0	-0.018	-0.002	26.175	0.016	0.016	0.000	0.000	0.000	0.000
106	A	128	PHE	0	0.007	-0.001	24.672	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	129	ASN	0	0.042	0.014	27.019	0.007	0.007	0.000	0.000	0.000	0.000
108	A	130	LYS	1	0.892	0.954	30.465	0.295	0.295	0.000	0.000	0.000	0.000
109	A	131	LEU	0	-0.048	-0.021	26.709	0.011	0.011	0.000	0.000	0.000	0.000
110	A	132	GLN	0	-0.004	0.003	30.384	0.008	0.008	0.000	0.000	0.000	0.000
111	A	133	GLU	-1	-0.857	-0.932	29.272	-0.315	-0.315	0.000	0.000	0.000	0.000
112	A	134	LYS	1	0.896	0.951	28.480	0.389	0.389	0.000	0.000	0.000	0.000
113	A	135	GLY	0	0.015	-0.004	26.489	-0.043	-0.043	0.000	0.000	0.000	0.000
114	A	136	ILE	0	0.008	0.021	24.428	-0.059	-0.059	0.000	0.000	0.000	0.000
115	A	137	TYR	0	0.003	-0.004	23.187	-0.071	-0.071	0.000	0.000	0.000	0.000
116	A	138	LYS	1	0.824	0.899	22.622	0.619	0.619	0.000	0.000	0.000	0.000
117	A	139	ALA	0	0.052	0.025	20.538	-0.082	-0.082	0.000	0.000	0.000	0.000
118	A	140	MET	0	-0.017	0.013	18.530	-0.120	-0.120	0.000	0.000	0.000	0.000
119	A	141	SER	0	-0.077	-0.049	18.031	-0.104	-0.104	0.000	0.000	0.000	0.000
120	A	142	GLU	-1	-0.740	-0.852	16.936	-0.917	-0.917	0.000	0.000	0.000	0.000
121	A	143	PHE	0	0.052	0.016	11.688	-0.144	-0.144	0.000	0.000	0.000	0.000
122	A	144	ASP	-1	-0.801	-0.897	11.278	-1.892	-1.892	0.000	0.000	0.000	0.000
123	A	145	ILE	0	0.001	0.008	10.606	-0.472	-0.472	0.000	0.000	0.000	0.000
124	A	146	PHE	0	0.022	0.014	11.858	-0.149	-0.149	0.000	0.000	0.000	0.000
125	A	147	ILE	0	0.000	-0.005	6.620	-0.191	-0.191	0.000	0.000	0.000	0.000
126	A	148	ASN	0	0.020	0.008	7.318	-1.474	-1.474	0.000	0.000	0.000	0.000
127	A	149	TYR	0	-0.019	-0.022	8.368	-0.171	-0.171	0.000	0.000	0.000	0.000
128	A	150	ILE	0	0.008	0.007	7.850	0.266	0.266	0.000	0.000	0.000	0.000
129	A	151	GLU	-1	-0.799	-0.875	1.818	-28.930	-31.763	10.440	-4.127	-3.479	-0.052
130	A	152	ALA	0	-0.003	0.015	5.641	0.578	0.578	0.000	0.000	0.000	0.000
131	A	153	TYR	0	-0.030	-0.033	8.672	0.583	0.583	0.000	0.000	0.000	0.000
132	A	154	MET	0	-0.046	-0.023	4.943	0.946	0.946	0.000	0.000	0.000	0.000
133	A	155	THR	0	-0.057	-0.035	5.081	0.376	0.453	-0.001	0.001	-0.077	0.000
134	A	156	MET	0	-0.006	0.005	7.006	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	157	LYS	1	0.859	0.969	9.742	0.301	0.301	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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