FMO DATABASE

FMODB ID: Q171Y

Calculation Name: 3LYS-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-879906.671353
FMO2-HF: Nuclear repulsion	836564.405262
FMO2-HF: Total energy	-43342.266091
FMO2-MP2: Total energy	-43468.834238

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:54:ACE )

Summations of interaction energy for fragment #1(A:54:ACE )

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.
-0.915	0.83	2.155	-2.033	-1.867	-0.016

Interaction energy analysis for fragmet #1(A:54:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.020

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	56	ILE	0	0.011	0.010	3.881	0.749	1.259	-0.001	-0.298	-0.211	0.001
4	A	57	LYS	1	0.921	0.951	6.835	0.864	0.864	0.000	0.000	0.000	0.000
5	A	58	GLN	0	0.095	0.031	10.078	0.142	0.142	0.000	0.000	0.000	0.000
6	A	59	GLU	-1	-0.836	-0.914	12.808	-0.250	-0.250	0.000	0.000	0.000	0.000
7	A	60	ILE	0	-0.023	-0.017	15.523	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	61	SER	0	-0.015	-0.019	16.497	0.013	0.013	0.000	0.000	0.000	0.000
9	A	62	GLU	-1	-0.939	-0.968	16.453	-0.194	-0.194	0.000	0.000	0.000	0.000
10	A	63	TYR	0	0.047	0.005	11.195	0.001	0.001	0.000	0.000	0.000	0.000
11	A	64	PHE	0	-0.067	-0.024	14.986	0.034	0.034	0.000	0.000	0.000	0.000
12	A	65	LYS	1	0.880	0.925	17.525	0.121	0.121	0.000	0.000	0.000	0.000
13	A	66	ASP	-1	-0.907	-0.942	14.562	-0.148	-0.148	0.000	0.000	0.000	0.000
14	A	67	TRP	0	0.064	0.023	14.101	0.030	0.030	0.000	0.000	0.000	0.000
15	A	68	MET	0	-0.074	-0.025	16.105	0.027	0.027	0.000	0.000	0.000	0.000
16	A	69	GLU	-1	-0.902	-0.967	19.609	-0.064	-0.064	0.000	0.000	0.000	0.000
17	A	70	LEU	0	0.019	0.021	14.614	0.017	0.017	0.000	0.000	0.000	0.000
18	A	71	TYR	0	-0.034	-0.018	12.462	0.027	0.027	0.000	0.000	0.000	0.000
19	A	72	LYS	1	0.864	0.927	19.225	0.099	0.099	0.000	0.000	0.000	0.000
20	A	73	LYS	1	0.963	0.979	22.410	0.059	0.059	0.000	0.000	0.000	0.000
21	A	74	ASN	0	-0.055	-0.025	24.429	0.001	0.001	0.000	0.000	0.000	0.000
22	A	75	ALA	0	0.013	0.031	24.100	0.005	0.005	0.000	0.000	0.000	0.000
23	A	76	ILE	0	-0.092	-0.039	25.939	0.001	0.001	0.000	0.000	0.000	0.000
24	A	77	ASP	-1	-0.803	-0.913	27.622	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	78	GLU	-1	-0.880	-0.951	30.058	-0.051	-0.051	0.000	0.000	0.000	0.000
26	A	79	MET	0	0.008	-0.006	31.747	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	80	THR	0	-0.045	-0.027	28.170	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	81	TYR	0	0.037	0.027	23.794	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	82	LYS	1	0.965	0.989	27.702	0.042	0.042	0.000	0.000	0.000	0.000
30	A	83	GLY	0	-0.022	-0.006	28.824	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	84	TYR	0	0.012	-0.008	21.807	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	85	GLU	-1	-0.837	-0.922	24.733	-0.080	-0.080	0.000	0.000	0.000	0.000
33	A	86	GLN	0	-0.047	-0.016	26.779	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	87	THR	0	0.003	-0.001	23.188	0.002	0.002	0.000	0.000	0.000	0.000
35	A	88	LEU	0	0.055	0.042	21.578	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	89	LYS	1	0.937	0.970	23.912	0.070	0.070	0.000	0.000	0.000	0.000
37	A	90	TYR	0	-0.016	-0.029	26.571	0.000	0.000	0.000	0.000	0.000	0.000
38	A	91	LEU	0	0.005	-0.001	19.474	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	92	LYS	1	0.955	0.974	23.422	0.112	0.112	0.000	0.000	0.000	0.000
40	A	93	THR	0	-0.064	-0.008	24.715	0.006	0.006	0.000	0.000	0.000	0.000
41	A	94	TYR	0	-0.035	-0.025	26.165	0.000	0.000	0.000	0.000	0.000	0.000
42	A	95	MET	0	-0.075	-0.043	19.433	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	96	PRO	0	0.073	0.052	22.390	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	97	ASN	0	-0.008	0.011	21.005	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	98	VAL	0	-0.042	-0.013	18.137	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	99	LEU	0	0.086	0.045	13.865	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	100	ILE	0	-0.010	-0.004	10.468	0.003	0.003	0.000	0.000	0.000	0.000
48	A	101	SER	0	-0.020	-0.020	10.194	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	102	GLU	-1	-0.962	-0.986	11.861	-0.296	-0.296	0.000	0.000	0.000	0.000
50	A	103	ILE	0	-0.070	-0.004	15.266	0.067	0.067	0.000	0.000	0.000	0.000
51	A	104	THR	0	0.044	0.012	15.563	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	105	ALA	0	0.047	-0.004	17.990	0.018	0.018	0.000	0.000	0.000	0.000
53	A	106	SER	0	-0.038	-0.013	19.942	0.021	0.021	0.000	0.000	0.000	0.000
54	A	107	SER	0	-0.023	0.002	20.086	0.022	0.022	0.000	0.000	0.000	0.000
55	A	108	TYR	0	0.064	-0.068	19.595	0.017	0.017	0.000	0.000	0.000	0.000
56	A	109	GLN	0	0.017	0.015	21.679	0.013	0.013	0.000	0.000	0.000	0.000
57	A	110	ARG	1	0.988	0.993	24.725	0.166	0.166	0.000	0.000	0.000	0.000
58	A	111	ALA	0	-0.002	0.001	23.809	0.012	0.012	0.000	0.000	0.000	0.000
59	A	112	LEU	0	-0.017	-0.028	23.731	0.012	0.012	0.000	0.000	0.000	0.000
60	A	113	ASN	0	-0.059	-0.034	26.751	0.005	0.005	0.000	0.000	0.000	0.000
61	A	114	LYS	1	0.893	0.947	29.333	0.103	0.103	0.000	0.000	0.000	0.000
62	A	115	PHE	0	-0.033	-0.006	28.613	0.008	0.008	0.000	0.000	0.000	0.000
63	A	116	ALA	0	-0.023	-0.036	30.655	0.006	0.006	0.000	0.000	0.000	0.000
64	A	117	GLU	-1	-0.851	-0.889	32.762	-0.082	-0.082	0.000	0.000	0.000	0.000
65	A	118	THR	0	0.017	0.008	34.542	0.002	0.002	0.000	0.000	0.000	0.000
66	A	119	HIS	1	0.814	0.915	32.641	0.089	0.089	0.000	0.000	0.000	0.000
67	A	120	ALA	0	0.115	0.050	35.232	0.000	0.000	0.000	0.000	0.000	0.000
68	A	121	LYS	1	0.886	0.954	33.441	0.071	0.071	0.000	0.000	0.000	0.000
69	A	122	ALA	0	0.017	0.002	32.516	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	123	SER	0	-0.023	-0.007	31.930	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	124	THR	0	0.046	0.018	29.728	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	125	LYS	1	0.927	0.960	28.015	0.078	0.078	0.000	0.000	0.000	0.000
73	A	126	GLY	0	0.001	-0.020	26.989	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	127	PHE	0	0.003	0.005	23.554	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	128	HIS	0	0.092	0.139	21.607	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	129	THR	0	-0.100	-0.012	22.111	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	130	ARG	1	0.942	0.955	21.606	0.095	0.095	0.000	0.000	0.000	0.000
78	A	131	VAL	0	0.047	0.033	18.480	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	132	ARG	1	0.876	0.949	17.523	0.174	0.174	0.000	0.000	0.000	0.000
80	A	133	ALA	0	-0.009	-0.011	16.768	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	134	SER	0	-0.042	-0.042	15.909	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	135	ILE	0	0.006	0.003	12.490	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	136	GLN	0	-0.009	-0.004	11.821	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	137	CYS	0	-0.025	-0.017	11.407	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	138	LEU	0	0.026	0.017	8.092	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	139	ILE	0	-0.072	-0.044	7.292	-0.255	-0.255	0.000	0.000	0.000	0.000
87	A	140	GLU	-1	-0.977	-0.983	7.716	-0.062	-0.062	0.000	0.000	0.000	0.000
88	A	141	GLU	-1	-0.800	-0.880	6.591	-0.170	-0.170	0.000	0.000	0.000	0.000
89	A	142	GLY	0	-0.047	-0.014	4.421	0.279	0.443	0.000	-0.029	-0.134	0.000
90	A	143	ARG	1	0.853	0.913	2.398	-3.013	-1.828	2.155	-1.712	-1.629	-0.017
91	A	144	LEU	0	-0.048	-0.016	4.050	-0.027	-0.141	0.001	0.006	0.107	0.000
92	A	145	GLN	0	0.042	0.015	6.216	0.044	0.044	0.000	0.000	0.000	0.000
93	A	146	LYS	1	0.953	0.968	8.344	0.573	0.573	0.000	0.000	0.000	0.000
94	A	147	ASP	-1	-0.666	-0.784	11.983	-0.313	-0.313	0.000	0.000	0.000	0.000
95	A	148	PHE	0	0.016	0.008	13.627	0.086	0.086	0.000	0.000	0.000	0.000
96	A	149	THR	0	-0.082	-0.081	16.521	0.049	0.049	0.000	0.000	0.000	0.000
97	A	150	THR	0	-0.030	-0.010	17.250	0.046	0.046	0.000	0.000	0.000	0.000
98	A	151	ARG	1	0.983	0.976	19.126	0.144	0.144	0.000	0.000	0.000	0.000
99	A	152	ALA	0	-0.026	0.008	21.634	0.014	0.014	0.000	0.000	0.000	0.000
100	A	153	VAL	0	-0.029	-0.017	23.435	0.006	0.006	0.000	0.000	0.000	0.000
101	A	154	VAL	0	-0.028	-0.010	25.353	0.012	0.012	0.000	0.000	0.000	0.000
102	A	155	LYN	0	0.060	0.050	27.666	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	156	GLY	0	-0.010	-0.015	29.389	0.008	0.008	0.000	0.000	0.000	0.000
104	A	157	LEU	0	-0.024	-0.061	32.442	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	158	GLU	-1	-0.810	-0.907	35.400	-0.069	-0.069	0.000	0.000	0.000	0.000
106	A	159	HIS	0	-0.104	-0.057	38.354	0.000	0.000	0.000	0.000	0.000	0.000
107	A	160	NME	0	0.083	0.070	41.835	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:54:ACE )