FMO DATABASE

FMODB ID: 229ZR

Calculation Name: 3LYS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYS

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CGT4

Base Structure: X-ray

Registration Date: 2023-06-19

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-874120.528611
FMO2-HF: Nuclear repulsion	830949.365221
FMO2-HF: Total energy	-43171.163389
FMO2-MP2: Total energy	-43297.216915

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:55:PRO)

Summations of interaction energy for fragment #1(A:55:PRO)

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.
0.108	3.629	0.07	-1.498	-2.093	-0.001

Interaction energy analysis for fragmet #1(A:55:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.011

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	57	LYS	1	0.929	0.956	3.722	-0.255	1.791	-0.015	-1.000	-1.030	0.000
4	A	58	GLN	0	0.098	0.033	5.508	0.026	0.026	0.000	0.000	0.000	0.000
5	A	59	GLU	-1	-0.837	-0.914	9.139	-0.112	-0.112	0.000	0.000	0.000	0.000
6	A	60	ILE	0	-0.022	-0.017	12.600	-0.047	-0.047	0.000	0.000	0.000	0.000
7	A	61	SER	0	-0.012	-0.018	13.863	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	62	GLU	-1	-0.942	-0.969	13.750	-0.507	-0.507	0.000	0.000	0.000	0.000
9	A	63	TYR	0	0.048	0.006	10.382	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	64	PHE	0	-0.069	-0.025	13.524	0.027	0.027	0.000	0.000	0.000	0.000
11	A	65	LYS	1	0.880	0.925	16.277	0.300	0.300	0.000	0.000	0.000	0.000
12	A	66	ASP	-1	-0.910	-0.944	13.573	-0.676	-0.676	0.000	0.000	0.000	0.000
13	A	67	TRP	0	0.066	0.023	13.774	0.065	0.065	0.000	0.000	0.000	0.000
14	A	68	MET	0	-0.064	-0.022	15.462	0.041	0.041	0.000	0.000	0.000	0.000
15	A	69	GLU	-1	-0.913	-0.972	18.930	-0.244	-0.244	0.000	0.000	0.000	0.000
16	A	70	LEU	0	0.019	0.021	14.359	0.015	0.015	0.000	0.000	0.000	0.000
17	A	71	TYR	0	-0.031	-0.018	12.756	0.061	0.061	0.000	0.000	0.000	0.000
18	A	72	LYS	1	0.871	0.931	19.294	0.139	0.139	0.000	0.000	0.000	0.000
19	A	73	LYS	1	0.954	0.976	22.182	0.185	0.185	0.000	0.000	0.000	0.000
20	A	74	ASN	0	-0.046	-0.022	24.136	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	75	ALA	0	0.008	0.029	24.272	0.009	0.009	0.000	0.000	0.000	0.000
22	A	76	ILE	0	-0.092	-0.039	25.758	0.016	0.016	0.000	0.000	0.000	0.000
23	A	77	ASP	-1	-0.801	-0.912	27.580	-0.067	-0.067	0.000	0.000	0.000	0.000
24	A	78	GLU	-1	-0.883	-0.952	29.731	-0.106	-0.106	0.000	0.000	0.000	0.000
25	A	79	MET	0	0.008	-0.007	31.185	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	80	THR	0	-0.046	-0.026	27.765	0.006	0.006	0.000	0.000	0.000	0.000
27	A	81	TYR	0	0.038	0.028	23.243	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	82	LYS	1	0.966	0.989	26.918	0.071	0.071	0.000	0.000	0.000	0.000
29	A	83	GLY	0	-0.026	-0.007	28.000	0.000	0.000	0.000	0.000	0.000	0.000
30	A	84	TYR	0	0.013	-0.008	21.280	0.007	0.007	0.000	0.000	0.000	0.000
31	A	85	GLU	-1	-0.822	-0.917	23.632	-0.135	-0.135	0.000	0.000	0.000	0.000
32	A	86	GLN	0	-0.060	-0.020	25.672	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	87	THR	0	0.004	0.000	21.628	0.007	0.007	0.000	0.000	0.000	0.000
34	A	88	LEU	0	0.057	0.042	20.135	0.003	0.003	0.000	0.000	0.000	0.000
35	A	89	LYS	1	0.934	0.969	22.372	0.073	0.073	0.000	0.000	0.000	0.000
36	A	90	TYR	0	-0.017	-0.030	24.507	0.006	0.006	0.000	0.000	0.000	0.000
37	A	91	LEU	0	0.011	0.002	17.394	0.011	0.011	0.000	0.000	0.000	0.000
38	A	92	LYS	1	0.951	0.973	20.823	0.183	0.183	0.000	0.000	0.000	0.000
39	A	93	THR	0	-0.064	-0.008	21.910	0.005	0.005	0.000	0.000	0.000	0.000
40	A	94	TYR	0	-0.032	-0.025	23.275	0.004	0.004	0.000	0.000	0.000	0.000
41	A	95	MET	0	-0.076	-0.042	16.483	0.022	0.022	0.000	0.000	0.000	0.000
42	A	96	PRO	0	0.073	0.051	19.095	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	97	ASN	0	-0.008	0.011	16.503	0.009	0.009	0.000	0.000	0.000	0.000
44	A	98	VAL	0	-0.041	-0.013	14.590	0.013	0.013	0.000	0.000	0.000	0.000
45	A	99	LEU	0	0.086	0.046	8.847	-0.071	-0.071	0.000	0.000	0.000	0.000
46	A	100	ILE	0	-0.010	-0.006	7.326	0.138	0.138	0.000	0.000	0.000	0.000
47	A	101	SER	0	-0.023	-0.022	6.244	0.099	0.099	0.000	0.000	0.000	0.000
48	A	102	GLU	-1	-0.961	-0.985	8.035	0.227	0.227	0.000	0.000	0.000	0.000
49	A	103	ILE	0	-0.067	-0.004	11.624	0.003	0.003	0.000	0.000	0.000	0.000
50	A	104	THR	0	0.040	0.012	12.363	0.071	0.071	0.000	0.000	0.000	0.000
51	A	105	ALA	0	0.047	-0.003	14.973	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	106	SER	0	-0.035	-0.013	17.604	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	107	SER	0	-0.024	0.002	16.668	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	108	TYR	0	0.064	-0.068	17.023	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	109	GLN	0	0.018	0.014	18.958	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	110	ARG	1	0.989	0.993	21.364	-0.139	-0.139	0.000	0.000	0.000	0.000
57	A	111	ALA	0	-0.005	0.000	20.857	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	112	LEU	0	-0.018	-0.029	21.525	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	113	ASN	0	-0.053	-0.031	24.285	0.002	0.002	0.000	0.000	0.000	0.000
60	A	114	LYS	1	0.893	0.947	26.217	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	115	PHE	0	-0.034	-0.007	25.984	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	116	ALA	0	-0.019	-0.034	28.008	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	117	GLU	-1	-0.855	-0.892	30.413	0.027	0.027	0.000	0.000	0.000	0.000
64	A	118	THR	0	0.018	0.008	31.768	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	119	HIS	1	0.820	0.918	30.144	0.007	0.007	0.000	0.000	0.000	0.000
66	A	120	ALA	0	0.152	0.079	33.066	0.006	0.006	0.000	0.000	0.000	0.000
67	A	121	LYS	1	0.838	0.921	32.156	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	122	ALA	0	0.027	0.006	31.191	0.000	0.000	0.000	0.000	0.000	0.000
69	A	123	SER	0	-0.022	-0.012	30.675	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	124	THR	0	0.048	0.018	27.847	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	125	LYS	1	0.929	0.960	26.506	-0.034	-0.034	0.000	0.000	0.000	0.000
72	A	126	GLY	0	-0.004	-0.021	26.047	0.002	0.002	0.000	0.000	0.000	0.000
73	A	127	PHE	0	0.002	0.004	21.167	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	128	HIS	0	0.092	0.139	20.491	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	129	THR	0	-0.100	-0.013	21.130	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	130	ARG	1	0.950	0.957	21.246	0.052	0.052	0.000	0.000	0.000	0.000
77	A	131	VAL	0	0.048	0.033	16.929	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.875	0.948	16.825	-0.164	-0.164	0.000	0.000	0.000	0.000
79	A	133	ALA	0	-0.014	-0.012	16.617	0.012	0.012	0.000	0.000	0.000	0.000
80	A	134	SER	0	-0.042	-0.042	15.031	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	135	ILE	0	0.004	0.003	11.836	-0.060	-0.060	0.000	0.000	0.000	0.000
82	A	136	GLN	0	-0.003	-0.002	11.968	0.071	0.071	0.000	0.000	0.000	0.000
83	A	137	CYS	0	-0.026	-0.016	11.830	0.089	0.089	0.000	0.000	0.000	0.000
84	A	138	LEU	0	0.025	0.015	7.412	-0.045	-0.045	0.000	0.000	0.000	0.000
85	A	139	ILE	0	-0.074	-0.046	7.814	0.171	0.171	0.000	0.000	0.000	0.000
86	A	140	GLU	-1	-0.974	-0.982	9.466	0.304	0.304	0.000	0.000	0.000	0.000
87	A	141	GLU	-1	-0.801	-0.880	7.475	-0.803	-0.803	0.000	0.000	0.000	0.000
88	A	142	GLY	0	-0.044	-0.010	6.844	-0.097	-0.097	0.000	0.000	0.000	0.000
89	A	143	ARG	1	0.862	0.926	2.942	2.355	3.358	0.065	-0.288	-0.781	0.000
90	A	144	LEU	0	-0.061	-0.025	3.639	0.135	0.607	0.020	-0.210	-0.282	-0.001
91	A	145	GLN	0	0.044	0.016	5.959	0.228	0.228	0.000	0.000	0.000	0.000
92	A	146	LYS	1	0.954	0.970	7.816	-1.001	-1.001	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.664	-0.783	11.144	0.181	0.181	0.000	0.000	0.000	0.000
94	A	148	PHE	0	0.011	0.006	11.151	-0.042	-0.042	0.000	0.000	0.000	0.000
95	A	149	THR	0	-0.079	-0.080	14.787	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	150	THR	0	-0.029	-0.010	16.819	-0.047	-0.047	0.000	0.000	0.000	0.000
97	A	151	ARG	1	0.980	0.976	18.519	-0.204	-0.204	0.000	0.000	0.000	0.000
98	A	152	ALA	0	-0.025	0.008	20.239	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	153	VAL	0	-0.027	-0.018	21.938	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	154	VAL	0	-0.031	-0.010	24.374	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.068	0.051	25.963	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	156	GLY	0	-0.018	-0.017	27.845	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	157	LEU	0	-0.021	-0.060	30.536	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.794	-0.876	33.665	0.016	0.016	0.000	0.000	0.000	0.000
105	A	159	HIS	0	-0.046	-0.011	36.446	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:55:PRO)