FMO DATABASE

FMODB ID: 66KJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-873315.252233
FMO2-HF: Nuclear repulsion	830142.907844
FMO2-HF: Total energy	-43172.344389
FMO2-MP2: Total energy	-43298.26664

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.
0.605	3.679	0.024	-1.305	-1.791	-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 : 0.027 / q_NPA : -0.003

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	0.921	0.958	3.868	-0.075	1.746	-0.017	-0.879	-0.924	-0.001
4	A	58	GLN	0	0.039	0.002	5.526	-0.226	-0.226	0.000	0.000	0.000	0.000
5	A	59	GLU	-1	-0.817	-0.897	9.142	-0.041	-0.041	0.000	0.000	0.000	0.000
6	A	60	ILE	0	-0.024	-0.021	12.622	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	61	SER	0	-0.002	-0.013	13.882	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	62	GLU	-1	-0.867	-0.925	13.166	-0.482	-0.482	0.000	0.000	0.000	0.000
9	A	63	TYR	0	0.024	0.000	10.879	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	64	PHE	0	-0.041	-0.014	13.546	0.027	0.027	0.000	0.000	0.000	0.000
11	A	65	LYS	1	0.835	0.883	16.389	0.246	0.246	0.000	0.000	0.000	0.000
12	A	66	ASP	-1	-0.921	-0.952	13.295	-0.537	-0.537	0.000	0.000	0.000	0.000
13	A	67	TRP	0	0.080	0.029	13.718	0.052	0.052	0.000	0.000	0.000	0.000
14	A	68	MET	0	-0.065	-0.019	15.595	0.033	0.033	0.000	0.000	0.000	0.000
15	A	69	GLU	-1	-0.870	-0.930	19.036	-0.189	-0.189	0.000	0.000	0.000	0.000
16	A	70	LEU	0	0.004	0.019	14.569	0.012	0.012	0.000	0.000	0.000	0.000
17	A	71	TYR	0	-0.028	-0.017	12.760	0.032	0.032	0.000	0.000	0.000	0.000
18	A	72	LYS	1	0.875	0.933	19.446	0.058	0.058	0.000	0.000	0.000	0.000
19	A	73	LYS	1	0.914	0.964	22.310	0.117	0.117	0.000	0.000	0.000	0.000
20	A	74	ASN	0	-0.026	-0.017	24.256	0.002	0.002	0.000	0.000	0.000	0.000
21	A	75	ALA	0	0.002	0.028	24.400	0.007	0.007	0.000	0.000	0.000	0.000
22	A	76	ILE	0	-0.084	-0.037	25.860	0.013	0.013	0.000	0.000	0.000	0.000
23	A	77	ASP	-1	-0.740	-0.871	27.756	-0.035	-0.035	0.000	0.000	0.000	0.000
24	A	78	GLU	-1	-0.842	-0.914	29.898	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	79	MET	0	-0.012	-0.013	31.339	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	80	THR	0	-0.063	-0.056	27.977	0.005	0.005	0.000	0.000	0.000	0.000
27	A	81	TYR	0	0.023	0.018	23.430	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	82	LYS	1	0.895	0.953	27.076	0.053	0.053	0.000	0.000	0.000	0.000
29	A	83	GLY	0	-0.026	-0.006	28.188	0.000	0.000	0.000	0.000	0.000	0.000
30	A	84	TYR	0	0.002	-0.019	21.641	0.009	0.009	0.000	0.000	0.000	0.000
31	A	85	GLU	-1	-0.785	-0.904	23.779	-0.089	-0.089	0.000	0.000	0.000	0.000
32	A	86	GLN	0	-0.051	-0.020	25.690	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	87	THR	0	-0.005	-0.003	21.455	0.005	0.005	0.000	0.000	0.000	0.000
34	A	88	LEU	0	0.042	0.032	19.796	0.004	0.004	0.000	0.000	0.000	0.000
35	A	89	LYS	1	0.958	0.979	22.386	0.045	0.045	0.000	0.000	0.000	0.000
36	A	90	TYR	0	-0.030	-0.035	24.523	0.003	0.003	0.000	0.000	0.000	0.000
37	A	91	LEU	0	0.008	0.004	17.191	0.008	0.008	0.000	0.000	0.000	0.000
38	A	92	LYS	1	0.959	0.977	20.681	0.146	0.146	0.000	0.000	0.000	0.000
39	A	93	THR	0	-0.076	-0.018	21.936	0.001	0.001	0.000	0.000	0.000	0.000
40	A	94	TYR	0	-0.014	-0.014	23.362	0.002	0.002	0.000	0.000	0.000	0.000
41	A	95	MET	0	-0.087	-0.043	16.704	0.021	0.021	0.000	0.000	0.000	0.000
42	A	96	PRO	0	0.070	0.048	19.020	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	97	ASN	0	-0.038	-0.011	16.569	0.009	0.009	0.000	0.000	0.000	0.000
44	A	98	VAL	0	-0.045	-0.026	14.564	0.010	0.010	0.000	0.000	0.000	0.000
45	A	99	LEU	0	0.075	0.043	8.910	-0.057	-0.057	0.000	0.000	0.000	0.000
46	A	100	ILE	0	-0.009	0.003	7.386	0.138	0.138	0.000	0.000	0.000	0.000
47	A	101	SER	0	-0.015	-0.018	6.269	0.093	0.093	0.000	0.000	0.000	0.000
48	A	102	GLU	-1	-0.967	-0.988	8.062	0.213	0.213	0.000	0.000	0.000	0.000
49	A	103	ILE	0	-0.061	-0.013	11.652	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	104	THR	0	0.019	0.001	12.380	0.074	0.074	0.000	0.000	0.000	0.000
51	A	105	ALA	0	0.032	-0.008	14.988	-0.039	-0.039	0.000	0.000	0.000	0.000
52	A	106	SER	0	-0.019	-0.002	17.613	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	107	SER	0	-0.020	0.002	16.734	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	108	TYR	0	0.083	0.013	16.997	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	109	GLN	0	0.010	0.008	18.972	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	110	ARG	1	0.983	0.988	21.619	-0.142	-0.142	0.000	0.000	0.000	0.000
57	A	111	ALA	0	-0.002	0.003	20.891	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	112	LEU	0	-0.019	-0.023	21.237	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	113	ASN	0	-0.069	-0.038	24.298	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	114	LYS	1	0.850	0.905	26.294	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	115	PHE	0	-0.029	-0.018	25.923	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	116	ALA	0	-0.026	-0.030	28.024	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	117	GLU	-1	-0.817	-0.864	30.426	0.037	0.037	0.000	0.000	0.000	0.000
64	A	118	THR	0	0.018	0.005	31.652	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	119	HIS	1	0.832	0.925	30.261	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	120	ALA	0	0.109	0.065	33.078	0.005	0.005	0.000	0.000	0.000	0.000
67	A	121	LYS	1	0.904	0.964	31.918	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	122	ALA	0	0.007	-0.003	31.195	0.002	0.002	0.000	0.000	0.000	0.000
69	A	123	SER	0	0.006	0.001	30.224	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	124	THR	0	0.020	0.012	27.799	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	125	LYS	1	0.919	0.957	26.511	-0.062	-0.062	0.000	0.000	0.000	0.000
72	A	126	GLY	0	0.003	-0.003	26.047	0.005	0.005	0.000	0.000	0.000	0.000
73	A	127	PHE	0	-0.022	-0.006	21.467	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	128	HIS	0	0.072	0.056	20.475	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	129	THR	0	-0.046	-0.012	21.130	0.007	0.007	0.000	0.000	0.000	0.000
76	A	130	ARG	1	0.942	0.964	21.241	0.014	0.014	0.000	0.000	0.000	0.000
77	A	131	VAL	0	0.025	0.021	16.914	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.851	0.909	16.824	-0.222	-0.222	0.000	0.000	0.000	0.000
79	A	133	ALA	0	-0.017	-0.011	16.609	0.023	0.023	0.000	0.000	0.000	0.000
80	A	134	SER	0	-0.029	-0.023	15.430	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	135	ILE	0	0.005	0.007	11.898	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	136	GLN	0	-0.003	-0.005	11.980	0.095	0.095	0.000	0.000	0.000	0.000
83	A	137	CYS	0	-0.020	-0.002	12.072	0.086	0.086	0.000	0.000	0.000	0.000
84	A	138	LEU	0	0.021	0.016	7.649	0.014	0.014	0.000	0.000	0.000	0.000
85	A	139	ILE	0	-0.070	-0.042	8.118	0.276	0.276	0.000	0.000	0.000	0.000
86	A	140	GLU	-1	-0.958	-0.977	9.776	0.478	0.478	0.000	0.000	0.000	0.000
87	A	141	GLU	-1	-0.779	-0.870	7.634	-0.431	-0.431	0.000	0.000	0.000	0.000
88	A	142	GLY	0	-0.038	-0.009	7.111	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	143	ARG	1	0.833	0.905	3.522	2.198	2.993	0.020	-0.219	-0.595	0.001
90	A	144	LEU	0	-0.041	-0.023	3.625	-0.087	0.371	0.021	-0.207	-0.272	-0.001
91	A	145	GLN	0	0.013	0.005	5.666	0.251	0.251	0.000	0.000	0.000	0.000
92	A	146	LYS	1	0.967	0.977	7.801	-0.937	-0.937	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.654	-0.800	11.135	0.263	0.263	0.000	0.000	0.000	0.000
94	A	148	PHE	0	0.019	0.005	10.821	-0.063	-0.063	0.000	0.000	0.000	0.000
95	A	149	THR	0	-0.060	-0.037	14.790	-0.059	-0.059	0.000	0.000	0.000	0.000
96	A	150	THR	0	-0.037	-0.018	16.862	-0.051	-0.051	0.000	0.000	0.000	0.000
97	A	151	ARG	1	0.990	0.989	18.512	-0.211	-0.211	0.000	0.000	0.000	0.000
98	A	152	ALA	0	-0.015	0.008	20.202	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	153	VAL	0	-0.033	-0.027	21.941	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	154	VAL	0	-0.015	0.004	24.372	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.059	0.050	25.968	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	156	GLY	0	-0.008	-0.012	27.849	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	157	LEU	0	-0.025	-0.060	30.544	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.791	-0.888	33.673	0.028	0.028	0.000	0.000	0.000	0.000
105	A	159	HIS	0	-0.050	-0.009	36.455	-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:55:PRO)