FMO DATABASE

FMODB ID: ZYMNN

Calculation Name: 1LKT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LKT

Chain ID: A

ChEMBL ID:

UniProt ID: P12528

Base Structure: X-ray

Registration Date: 2023-06-21

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-723154.444667
FMO2-HF: Nuclear repulsion	684155.110359
FMO2-HF: Total energy	-38999.334307
FMO2-MP2: Total energy	-39115.264547

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:6:ALA)

Summations of interaction energy for fragment #1(A:6:ALA)

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.
-1.356	0.76	-0.003	-0.978	-1.135	0.001

Interaction energy analysis for fragmet #1(A:6:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.013

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	8	VAL	0	-0.016	0.004	3.348	-1.515	0.497	-0.002	-0.974	-1.037	0.001
4	A	9	VAL	0	0.025	0.018	5.386	-0.415	-0.311	-0.001	-0.004	-0.098	0.000
5	A	10	VAL	0	0.015	0.008	7.511	0.300	0.300	0.000	0.000	0.000	0.000
6	A	11	SER	0	-0.007	-0.005	9.769	-0.022	-0.022	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.034	-0.034	13.307	0.058	0.058	0.000	0.000	0.000	0.000
8	A	13	PRO	0	0.029	0.022	15.671	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	14	ARG	1	0.921	0.953	17.600	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.037	0.034	21.361	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	16	ILE	0	-0.051	-0.034	23.362	0.003	0.003	0.000	0.000	0.000	0.000
12	A	17	PHE	0	0.027	0.020	26.111	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	18	THR	0	0.011	-0.015	28.689	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	19	GLU	-1	-0.884	-0.958	31.283	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	20	SER	0	-0.022	-0.012	33.642	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.906	0.942	34.691	0.034	0.034	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.023	0.001	35.372	0.001	0.001	0.000	0.000	0.000	0.000
18	A	23	PHE	0	0.041	0.020	27.676	0.001	0.001	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.934	0.960	32.963	0.037	0.037	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.045	0.034	31.220	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	26	VAL	0	-0.005	0.012	32.460	0.002	0.002	0.000	0.000	0.000	0.000
22	A	27	ALA	0	-0.006	-0.009	34.792	0.004	0.004	0.000	0.000	0.000	0.000
23	A	28	ASN	0	-0.031	-0.017	36.209	0.001	0.001	0.000	0.000	0.000	0.000
24	A	29	GLY	0	0.044	0.029	36.461	0.002	0.002	0.000	0.000	0.000	0.000
25	A	30	LYS	1	0.760	0.883	36.744	0.008	0.008	0.000	0.000	0.000	0.000
26	A	31	ILE	0	0.014	0.000	31.040	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	32	TYR	0	0.010	0.014	35.103	0.003	0.003	0.000	0.000	0.000	0.000
28	A	33	ILE	0	0.005	-0.012	31.542	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	34	GLY	0	0.054	0.016	35.168	0.002	0.002	0.000	0.000	0.000	0.000
30	A	35	GLN	0	0.025	0.020	35.906	0.002	0.002	0.000	0.000	0.000	0.000
31	A	36	ILE	0	-0.020	0.004	33.197	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	37	ASP	-1	-0.833	-0.902	36.664	0.008	0.008	0.000	0.000	0.000	0.000
33	A	38	THR	0	-0.016	-0.005	38.587	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.783	-0.889	39.506	0.002	0.002	0.000	0.000	0.000	0.000
35	A	40	PRO	0	-0.007	0.016	37.045	0.002	0.002	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.021	-0.001	39.954	0.001	0.001	0.000	0.000	0.000	0.000
37	A	42	ASN	0	-0.002	-0.009	42.351	0.001	0.001	0.000	0.000	0.000	0.000
38	A	43	PRO	0	0.047	0.013	43.527	0.002	0.002	0.000	0.000	0.000	0.000
39	A	44	ALA	0	-0.045	-0.016	43.786	0.002	0.002	0.000	0.000	0.000	0.000
40	A	45	ASN	0	-0.050	-0.017	41.725	0.002	0.002	0.000	0.000	0.000	0.000
41	A	46	GLN	0	-0.062	-0.022	39.261	0.003	0.003	0.000	0.000	0.000	0.000
42	A	47	ILE	0	-0.054	-0.021	33.628	0.002	0.002	0.000	0.000	0.000	0.000
43	A	48	PRO	0	-0.002	-0.003	35.335	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.000	0.015	32.624	0.002	0.002	0.000	0.000	0.000	0.000
45	A	50	TYR	0	-0.007	-0.016	30.136	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	51	ILE	0	0.024	0.012	28.513	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.793	-0.869	22.068	0.133	0.133	0.000	0.000	0.000	0.000
48	A	53	ASN	0	-0.071	-0.044	25.688	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	54	GLU	-1	-0.963	-0.989	21.338	0.114	0.114	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.867	-0.911	22.633	0.130	0.130	0.000	0.000	0.000	0.000
51	A	56	GLY	0	-0.001	0.011	23.797	0.012	0.012	0.000	0.000	0.000	0.000
52	A	57	SER	0	-0.073	-0.044	24.587	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	58	HIS	0	-0.030	-0.037	25.264	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	59	VAL	0	-0.017	-0.010	29.840	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	60	GLN	0	-0.020	-0.008	32.910	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	61	ILE	0	-0.043	-0.016	33.108	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	62	THR	0	0.005	-0.001	36.449	0.000	0.000	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.001	0.015	36.611	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	64	PRO	0	-0.010	-0.013	37.837	0.000	0.000	0.000	0.000	0.000	0.000
60	A	65	LEU	0	0.004	-0.001	31.120	0.002	0.002	0.000	0.000	0.000	0.000
61	A	66	ILE	0	0.014	0.009	34.719	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	67	ILE	0	-0.005	0.014	31.372	0.001	0.001	0.000	0.000	0.000	0.000
63	A	68	ASN	0	0.055	0.015	29.575	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	69	ALA	0	0.048	-0.001	33.247	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	70	ALA	0	-0.043	-0.007	28.842	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	71	GLY	0	0.041	0.017	28.861	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	72	LYS	1	0.867	0.926	22.654	0.044	0.044	0.000	0.000	0.000	0.000
68	A	73	ILE	0	0.041	0.031	27.880	0.001	0.001	0.000	0.000	0.000	0.000
69	A	74	VAL	0	-0.073	-0.036	29.079	0.002	0.002	0.000	0.000	0.000	0.000
70	A	75	TYR	0	0.075	0.028	31.750	0.000	0.000	0.000	0.000	0.000	0.000
71	A	76	ASN	0	0.008	-0.002	33.015	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	77	GLY	0	0.013	0.012	34.587	0.001	0.001	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.030	-0.006	29.458	0.001	0.001	0.000	0.000	0.000	0.000
74	A	79	LEU	0	0.017	-0.001	25.734	0.000	0.000	0.000	0.000	0.000	0.000
75	A	80	VAL	0	0.004	0.014	26.263	0.006	0.006	0.000	0.000	0.000	0.000
76	A	81	LYS	1	0.837	0.910	20.346	-0.127	-0.127	0.000	0.000	0.000	0.000
77	A	82	ILE	0	-0.006	-0.009	25.091	0.003	0.003	0.000	0.000	0.000	0.000
78	A	83	VAL	0	-0.018	-0.006	24.747	0.000	0.000	0.000	0.000	0.000	0.000
79	A	84	THR	0	0.020	-0.001	27.612	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.000	0.006	28.614	0.006	0.006	0.000	0.000	0.000	0.000
81	A	86	GLN	0	0.021	0.014	29.889	0.007	0.007	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.027	0.016	29.664	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.006	-0.016	28.457	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	89	SER	0	-0.001	0.012	32.381	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	90	MET	0	-0.025	-0.020	28.507	0.001	0.001	0.000	0.000	0.000	0.000
86	A	91	ALA	0	0.001	0.008	33.913	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.012	0.004	31.344	0.003	0.003	0.000	0.000	0.000	0.000
88	A	93	TYR	0	0.045	0.024	35.919	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	94	ASP	-1	-0.708	-0.848	37.998	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	95	ALA	0	-0.053	-0.015	39.595	0.003	0.003	0.000	0.000	0.000	0.000
91	A	96	ASN	0	-0.079	-0.068	41.556	0.003	0.003	0.000	0.000	0.000	0.000
92	A	97	GLY	0	0.013	0.016	43.159	0.001	0.001	0.000	0.000	0.000	0.000
93	A	98	SER	0	-0.012	0.003	42.339	0.001	0.001	0.000	0.000	0.000	0.000
94	A	99	GLN	0	-0.044	-0.032	39.221	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.058	-0.024	35.110	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	101	ASP	-1	-0.865	-0.941	32.367	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	102	TYR	0	-0.081	-0.059	35.526	0.004	0.004	0.000	0.000	0.000	0.000
98	A	103	ILE	0	0.003	0.019	30.171	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	104	ALA	0	0.041	0.017	33.581	0.005	0.005	0.000	0.000	0.000	0.000
100	A	105	ASN	0	0.033	-0.007	31.658	0.006	0.006	0.000	0.000	0.000	0.000
101	A	106	VAL	0	0.043	0.020	27.049	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.015	-0.008	26.383	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	108	LYS	1	0.764	0.878	27.738	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	109	TYR	0	-0.066	-0.021	25.399	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:ALA)