FMO DATABASE

FMODB ID: QV4YY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1351245.396002
FMO2-HF: Nuclear repulsion	1293334.08054
FMO2-HF: Total energy	-57911.315462
FMO2-MP2: Total energy	-58075.148018

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.
-19.941	-15.471	6.066	-4.08	-6.457	-0.026

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 : -0.003 / q_NPA : -0.009

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	0.031	0.003	2.065	-2.223	0.944	2.139	-1.942	-3.365	0.005
4	A	24	ARG	1	0.839	0.911	3.385	1.598	2.126	0.014	-0.062	-0.480	0.000
5	A	25	ASP	-1	-0.766	-0.852	4.925	-0.839	-0.708	-0.001	-0.010	-0.119	0.000
6	A	26	LEU	0	0.007	0.005	6.965	0.353	0.353	0.000	0.000	0.000	0.000
7	A	27	ARG	1	0.823	0.858	3.482	8.404	8.628	-0.001	-0.047	-0.176	0.000
8	A	28	ASP	-1	-0.922	-0.950	8.795	-1.445	-1.445	0.000	0.000	0.000	0.000
9	A	29	ALA	0	-0.039	-0.022	10.750	0.248	0.248	0.000	0.000	0.000	0.000
10	A	30	PHE	0	0.019	0.015	12.054	0.125	0.125	0.000	0.000	0.000	0.000
11	A	31	SER	0	-0.065	-0.041	12.908	0.197	0.197	0.000	0.000	0.000	0.000
12	A	32	ARG	1	0.931	0.961	12.983	1.053	1.053	0.000	0.000	0.000	0.000
13	A	33	VAL	0	0.010	0.005	16.824	0.093	0.093	0.000	0.000	0.000	0.000
14	A	34	LYS	1	0.842	0.932	15.501	1.301	1.301	0.000	0.000	0.000	0.000
15	A	35	THR	0	-0.007	-0.029	18.589	0.022	0.022	0.000	0.000	0.000	0.000
16	A	36	PHE	0	0.001	0.011	21.858	0.029	0.029	0.000	0.000	0.000	0.000
17	A	37	PHE	0	0.037	0.010	20.633	0.032	0.032	0.000	0.000	0.000	0.000
18	A	38	GLN	0	-0.025	0.004	19.946	-0.057	-0.057	0.000	0.000	0.000	0.000
19	A	39	MET	0	-0.040	-0.016	22.892	0.066	0.066	0.000	0.000	0.000	0.000
20	A	40	LYS	1	0.917	0.938	25.684	0.397	0.397	0.000	0.000	0.000	0.000
21	A	41	ASP	-1	-0.882	-0.943	28.004	-0.383	-0.383	0.000	0.000	0.000	0.000
22	A	42	GLN	0	-0.005	0.024	25.819	0.050	0.050	0.000	0.000	0.000	0.000
23	A	43	LEU	0	0.018	0.018	28.112	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	44	ASP	-1	-0.929	-0.996	24.019	-0.568	-0.568	0.000	0.000	0.000	0.000
25	A	45	ASN	0	-0.049	-0.021	24.719	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	46	LEU	0	-0.021	0.013	18.606	0.001	0.001	0.000	0.000	0.000	0.000
27	A	47	LEU	0	-0.036	-0.023	21.579	0.058	0.058	0.000	0.000	0.000	0.000
28	A	48	LEU	0	-0.023	-0.011	15.969	0.039	0.039	0.000	0.000	0.000	0.000
29	A	49	LYS	1	0.951	0.984	18.459	0.398	0.398	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-0.810	-0.914	18.552	-0.597	-0.597	0.000	0.000	0.000	0.000
31	A	51	SER	0	0.030	0.024	19.272	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	52	LEU	0	-0.009	0.003	17.233	0.034	0.034	0.000	0.000	0.000	0.000
33	A	53	LEU	0	-0.022	0.001	12.931	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	54	GLU	-1	-0.944	-0.992	16.259	-0.394	-0.394	0.000	0.000	0.000	0.000
35	A	55	ASP	-1	-0.859	-0.907	18.983	-0.258	-0.258	0.000	0.000	0.000	0.000
36	A	56	PHE	0	-0.076	-0.044	12.846	0.049	0.049	0.000	0.000	0.000	0.000
37	A	57	LYS	1	0.924	0.957	12.544	0.884	0.884	0.000	0.000	0.000	0.000
38	A	58	GLY	0	0.027	0.038	16.214	0.076	0.076	0.000	0.000	0.000	0.000
39	A	59	TYR	0	-0.011	-0.012	19.384	0.019	0.019	0.000	0.000	0.000	0.000
40	A	60	LEU	0	-0.009	-0.002	21.622	0.036	0.036	0.000	0.000	0.000	0.000
41	A	61	GLY	0	0.064	0.038	17.541	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	62	CYS	0	-0.125	-0.024	16.482	-0.070	-0.070	0.000	0.000	0.000	0.000
43	A	63	GLN	0	0.046	0.004	17.569	0.001	0.001	0.000	0.000	0.000	0.000
44	A	64	ALA	0	0.064	0.045	18.569	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	65	LEU	0	0.008	0.015	11.712	-0.057	-0.057	0.000	0.000	0.000	0.000
46	A	66	SER	0	-0.070	-0.040	15.916	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	67	GLU	-1	-0.850	-0.939	17.300	-0.250	-0.250	0.000	0.000	0.000	0.000
48	A	68	MET	0	-0.009	0.005	16.523	0.007	0.007	0.000	0.000	0.000	0.000
49	A	69	ILE	0	-0.030	-0.021	12.365	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	70	GLN	0	-0.091	-0.045	16.109	0.000	0.000	0.000	0.000	0.000	0.000
51	A	71	PHE	0	0.029	0.026	19.621	0.005	0.005	0.000	0.000	0.000	0.000
52	A	72	TYR	0	-0.006	-0.035	16.842	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	73	LEU	0	-0.058	-0.047	15.975	0.019	0.019	0.000	0.000	0.000	0.000
54	A	74	GLU	-1	-0.857	-0.946	19.350	-0.195	-0.195	0.000	0.000	0.000	0.000
55	A	75	GLU	-1	-0.894	-0.929	22.750	-0.244	-0.244	0.000	0.000	0.000	0.000
56	A	76	VAL	0	-0.067	-0.022	20.494	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	77	MET	0	0.002	-0.012	16.221	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	78	PRO	0	0.035	0.034	21.364	0.006	0.006	0.000	0.000	0.000	0.000
59	A	79	GLN	0	-0.014	-0.019	24.580	0.031	0.031	0.000	0.000	0.000	0.000
60	A	80	ALA	0	-0.017	-0.015	22.264	0.009	0.009	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.882	-0.944	22.893	-0.330	-0.330	0.000	0.000	0.000	0.000
62	A	82	ASN	0	-0.077	-0.038	25.035	0.032	0.032	0.000	0.000	0.000	0.000
63	A	83	GLN	0	-0.036	-0.004	26.862	0.020	0.020	0.000	0.000	0.000	0.000
64	A	84	ASP	-1	-0.800	-0.908	27.824	-0.314	-0.314	0.000	0.000	0.000	0.000
65	A	85	PRO	0	-0.029	-0.015	27.698	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	86	ASP	-1	-0.899	-0.944	27.637	-0.288	-0.288	0.000	0.000	0.000	0.000
67	A	87	ILE	0	-0.109	-0.042	22.072	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	88	LYS	1	0.908	0.955	22.797	0.221	0.221	0.000	0.000	0.000	0.000
69	A	89	ALA	0	0.036	0.013	22.785	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	90	HIS	0	0.047	0.013	19.233	-0.043	-0.043	0.000	0.000	0.000	0.000
71	A	91	VAL	0	-0.009	0.005	18.116	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	92	ASN	0	-0.036	-0.025	18.376	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	93	SER	0	-0.023	-0.005	16.588	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	94	LEU	0	-0.007	0.003	12.456	-0.044	-0.044	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.055	0.020	13.889	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	96	GLU	-1	-0.795	-0.887	15.406	-0.223	-0.223	0.000	0.000	0.000	0.000
77	A	97	ASN	0	-0.048	-0.033	10.638	0.026	0.026	0.000	0.000	0.000	0.000
78	A	98	LEU	0	0.009	0.012	10.864	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	99	LYS	1	0.830	0.896	12.238	0.343	0.343	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.040	-0.026	10.801	0.171	0.171	0.000	0.000	0.000	0.000
81	A	101	LEU	0	-0.001	0.006	6.057	0.245	0.245	0.000	0.000	0.000	0.000
82	A	102	ARG	1	0.898	0.960	9.446	0.477	0.477	0.000	0.000	0.000	0.000
83	A	103	LEU	0	-0.018	-0.010	12.485	0.158	0.158	0.000	0.000	0.000	0.000
84	A	104	ARG	1	0.932	0.973	6.917	-2.055	-2.055	0.000	0.000	0.000	0.000
85	A	105	LEU	0	-0.024	-0.021	7.936	0.279	0.279	0.000	0.000	0.000	0.000
86	A	106	ARG	1	0.925	0.955	11.628	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	107	ARG	1	0.943	0.983	14.298	-0.507	-0.507	0.000	0.000	0.000	0.000
88	A	108	CYS	0	-0.016	-0.015	12.193	0.196	0.196	0.000	0.000	0.000	0.000
89	A	109	HIS	0	0.065	0.047	11.073	-0.142	-0.142	0.000	0.000	0.000	0.000
90	A	110	ARG	1	0.974	0.986	13.669	-0.997	-0.997	0.000	0.000	0.000	0.000
91	A	111	PHE	0	0.026	-0.020	7.473	-0.206	-0.206	0.000	0.000	0.000	0.000
92	A	112	LEU	0	0.027	0.012	13.140	-0.179	-0.179	0.000	0.000	0.000	0.000
93	A	113	PRO	0	-0.025	-0.003	15.958	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	115	GLU	-1	-0.925	-0.960	20.268	0.064	0.064	0.000	0.000	0.000	0.000
95	A	117	LYS	1	0.978	0.980	25.791	0.097	0.097	0.000	0.000	0.000	0.000
96	A	118	SER	0	-0.015	-0.038	22.340	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	119	LYS	1	1.000	0.994	24.587	0.216	0.216	0.000	0.000	0.000	0.000
98	A	120	ALA	0	0.038	0.016	22.004	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.046	0.013	20.486	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	122	GLU	-1	-0.843	-0.907	23.033	-0.252	-0.252	0.000	0.000	0.000	0.000
101	A	123	GLN	0	-0.045	-0.012	25.693	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	124	VAL	0	0.012	0.008	21.054	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	125	LYS	1	0.867	0.928	23.775	0.274	0.274	0.000	0.000	0.000	0.000
104	A	126	ASN	0	-0.047	-0.035	26.292	0.021	0.021	0.000	0.000	0.000	0.000
105	A	127	ALA	0	-0.031	-0.009	26.354	0.011	0.011	0.000	0.000	0.000	0.000
106	A	128	PHE	0	0.009	-0.001	24.255	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	129	ASN	0	0.042	0.006	26.987	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	130	LYS	1	0.888	0.959	30.316	0.257	0.257	0.000	0.000	0.000	0.000
109	A	131	LEU	0	-0.061	-0.025	26.891	0.009	0.009	0.000	0.000	0.000	0.000
110	A	132	GLN	0	0.016	0.008	30.516	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	133	GLU	-1	-0.845	-0.928	29.367	-0.297	-0.297	0.000	0.000	0.000	0.000
112	A	134	LYS	1	0.925	0.975	28.591	0.346	0.346	0.000	0.000	0.000	0.000
113	A	135	GLY	0	0.020	-0.008	26.554	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	136	ILE	0	0.014	0.023	24.645	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	137	TYR	0	0.021	0.004	23.339	-0.063	-0.063	0.000	0.000	0.000	0.000
116	A	138	LYS	1	0.816	0.899	22.650	0.552	0.552	0.000	0.000	0.000	0.000
117	A	139	ALA	0	0.032	0.009	20.563	-0.072	-0.072	0.000	0.000	0.000	0.000
118	A	140	MET	0	-0.008	0.019	18.384	-0.103	-0.103	0.000	0.000	0.000	0.000
119	A	141	SER	0	-0.062	-0.029	17.852	-0.102	-0.102	0.000	0.000	0.000	0.000
120	A	142	GLU	-1	-0.750	-0.861	16.904	-0.822	-0.822	0.000	0.000	0.000	0.000
121	A	143	PHE	0	0.049	0.014	11.380	-0.107	-0.107	0.000	0.000	0.000	0.000
122	A	144	ASP	-1	-0.817	-0.907	11.404	-1.701	-1.701	0.000	0.000	0.000	0.000
123	A	145	ILE	0	-0.005	0.002	10.760	-0.392	-0.392	0.000	0.000	0.000	0.000
124	A	146	PHE	0	0.017	0.009	11.912	-0.114	-0.114	0.000	0.000	0.000	0.000
125	A	147	ILE	0	0.014	0.000	6.446	-0.114	-0.114	0.000	0.000	0.000	0.000
126	A	148	ASN	0	0.027	0.024	7.484	-1.217	-1.217	0.000	0.000	0.000	0.000
127	A	149	TYR	0	-0.023	-0.024	8.622	-0.083	-0.083	0.000	0.000	0.000	0.000
128	A	150	ILE	0	0.009	0.008	7.492	0.234	0.234	0.000	0.000	0.000	0.000
129	A	151	GLU	-1	-0.827	-0.899	2.083	-22.882	-22.538	3.916	-2.015	-2.246	-0.031
130	A	152	ALA	0	-0.034	-0.004	6.088	0.662	0.662	0.000	0.000	0.000	0.000
131	A	153	TYR	0	-0.053	-0.045	8.995	0.488	0.488	0.000	0.000	0.000	0.000
132	A	154	MET	0	-0.010	-0.011	4.542	0.660	0.736	-0.001	-0.004	-0.071	0.000
133	A	155	THR	0	-0.117	-0.054	5.516	0.414	0.414	0.000	0.000	0.000	0.000
134	A	156	MET	0	-0.009	-0.007	7.317	0.034	0.034	0.000	0.000	0.000	0.000
135	A	157	LYS	1	0.863	0.958	10.226	-0.149	-0.149	0.000	0.000	0.000	0.000

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