FMO DATABASE

FMODB ID: 59LGZ

Calculation Name: 1JYO-E-Xray314

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JYO

Chain ID: E

ChEMBL ID:

UniProt ID: P0CL16

Base Structure: X-ray

Registration Date: 2021-09-06

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	104
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-570864.353534
FMO2-HF: Nuclear repulsion	529950.351717
FMO2-HF: Total energy	-40914.001817
FMO2-MP2: Total energy	-41032.800899

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(E:35:ACE )

Summations of interaction energy for fragment #1(E:35: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.
39.482	-25.204	60.847	16.17	-12.331	-0.078

Interaction energy analysis for fragmet #1(E:35:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : -0.044

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	E	37	LYS	1	0.985	0.960	1.979	16.151	-8.136	12.356	15.588	-3.658	-0.005
4	E	38	ALA	0	0.036	0.019	2.917	-2.275	-0.691	0.269	-1.003	-0.850	-0.013
5	E	39	TYR	0	-0.028	-0.010	4.672	0.227	0.193	0.000	-0.010	0.044	0.000
6	E	40	VAL	0	-0.009	-0.006	7.906	-0.160	-0.160	0.000	0.000	0.000	0.000
7	E	41	ALA	0	-0.018	-0.007	11.282	0.039	0.039	0.000	0.000	0.000	0.000
8	E	42	PRO	0	-0.002	-0.002	13.713	-0.016	-0.016	0.000	0.000	0.000	0.000
9	E	43	GLU	-1	-0.906	-0.946	16.941	0.047	0.047	0.000	0.000	0.000	0.000
10	E	44	LYS	1	0.885	0.935	17.802	-0.014	-0.014	0.000	0.000	0.000	0.000
11	E	45	PHE	0	0.078	0.036	17.679	0.001	0.001	0.000	0.000	0.000	0.000
12	E	46	SER	0	0.007	0.009	19.559	-0.011	-0.011	0.000	0.000	0.000	0.000
13	E	47	SER	0	-0.012	-0.032	22.533	-0.005	-0.005	0.000	0.000	0.000	0.000
14	E	48	LYS	1	0.912	0.968	19.108	0.076	0.076	0.000	0.000	0.000	0.000
15	E	49	VAL	0	0.047	0.029	14.907	0.007	0.007	0.000	0.000	0.000	0.000
16	E	50	LEU	0	0.032	0.030	12.782	-0.031	-0.031	0.000	0.000	0.000	0.000
17	E	51	THR	0	0.031	0.004	8.457	0.077	0.077	0.000	0.000	0.000	0.000
18	E	52	TRP	0	0.005	0.029	5.550	0.084	0.084	0.000	0.000	0.000	0.000
19	E	53	LEU	0	0.032	-0.009	5.111	0.349	0.381	0.000	-0.024	-0.008	0.000
20	E	54	GLY	0	0.015	0.008	1.798	1.591	-2.520	11.974	-5.584	-2.279	-0.022
21	E	55	LYS	1	0.853	0.967	2.369	8.932	-4.293	12.764	2.912	-2.451	-0.010
22	E	56	MET	0	0.091	0.092	2.109	12.854	-9.359	17.075	7.252	-2.114	-0.021
23	E	57	PRO	0	-0.035	0.006	4.499	0.588	0.649	0.000	-0.025	-0.036	0.000
24	E	58	LEU	0	0.006	-0.011	7.419	0.032	0.032	0.000	0.000	0.000	0.000
25	E	59	PHE	0	0.067	0.011	8.861	0.023	0.023	0.000	0.000	0.000	0.000
26	E	60	LYS	1	0.972	1.001	12.214	0.257	0.257	0.000	0.000	0.000	0.000
27	E	61	ASN	0	-0.015	0.007	12.466	0.079	0.079	0.000	0.000	0.000	0.000
28	E	62	THR	0	0.090	0.023	12.901	-0.054	-0.054	0.000	0.000	0.000	0.000
29	E	63	GLU	-1	-0.872	-0.935	13.490	-0.188	-0.188	0.000	0.000	0.000	0.000
30	E	64	VAL	0	-0.065	-0.028	9.255	0.013	0.013	0.000	0.000	0.000	0.000
31	E	65	VAL	0	-0.019	-0.020	8.641	-0.060	-0.060	0.000	0.000	0.000	0.000
32	E	66	GLN	0	0.012	0.006	8.958	-0.091	-0.091	0.000	0.000	0.000	0.000
33	E	67	LYS	1	0.977	0.993	10.757	0.106	0.106	0.000	0.000	0.000	0.000
34	E	68	HIS	0	-0.082	-0.031	1.904	0.878	-1.651	6.409	-2.923	-0.956	-0.007
35	E	69	THR	0	-0.041	-0.039	6.724	-0.028	-0.028	0.000	0.000	0.000	0.000
36	E	70	GLU	-1	-0.914	-0.958	8.199	-0.080	-0.080	0.000	0.000	0.000	0.000
37	E	71	ASN	0	-0.077	-0.022	7.524	0.076	0.076	0.000	0.000	0.000	0.000
38	E	72	ILE	0	-0.038	-0.006	4.777	0.335	0.371	0.000	-0.013	-0.023	0.000
39	E	73	ARG	1	0.937	0.948	7.144	-0.363	-0.363	0.000	0.000	0.000	0.000
40	E	74	VAL	0	0.009	0.011	9.353	-0.016	-0.016	0.000	0.000	0.000	0.000
41	E	75	GLN	0	0.025	0.015	11.097	0.008	0.008	0.000	0.000	0.000	0.000
42	E	76	ASP	-1	-0.868	-0.927	14.835	-0.154	-0.154	0.000	0.000	0.000	0.000
43	E	77	GLN	0	-0.001	-0.013	11.476	-0.054	-0.054	0.000	0.000	0.000	0.000
44	E	78	LYS	1	0.969	0.976	13.495	0.081	0.081	0.000	0.000	0.000	0.000
45	E	79	ILE	0	0.028	0.018	15.311	-0.017	-0.017	0.000	0.000	0.000	0.000
46	E	80	LEU	0	0.000	-0.008	7.899	-0.023	-0.023	0.000	0.000	0.000	0.000
47	E	81	GLN	0	0.038	0.020	11.294	-0.026	-0.026	0.000	0.000	0.000	0.000
48	E	82	THR	0	0.093	0.054	12.570	0.011	0.011	0.000	0.000	0.000	0.000
49	E	83	PHE	0	-0.011	0.000	11.609	0.005	0.005	0.000	0.000	0.000	0.000
50	E	84	LEU	0	-0.001	-0.011	7.916	-0.016	-0.016	0.000	0.000	0.000	0.000
51	E	85	HIS	0	0.012	0.023	12.077	-0.003	-0.003	0.000	0.000	0.000	0.000
52	E	86	ALA	0	0.020	0.012	15.427	0.025	0.025	0.000	0.000	0.000	0.000
53	E	87	LEU	0	-0.088	-0.053	11.331	0.022	0.022	0.000	0.000	0.000	0.000
54	E	88	THR	0	-0.061	-0.035	13.520	0.001	0.001	0.000	0.000	0.000	0.000
55	E	89	GLU	-1	-0.915	-0.963	15.447	-0.178	-0.178	0.000	0.000	0.000	0.000
56	E	90	LYS	1	0.893	0.964	16.676	0.323	0.323	0.000	0.000	0.000	0.000
57	E	91	TYR	0	-0.059	-0.031	16.902	0.012	0.012	0.000	0.000	0.000	0.000
58	E	92	GLY	0	0.040	0.028	20.433	0.000	0.000	0.000	0.000	0.000	0.000
59	E	93	GLU	-1	-0.927	-0.976	21.804	-0.123	-0.123	0.000	0.000	0.000	0.000
60	E	94	THR	0	0.017	0.004	25.354	0.008	0.008	0.000	0.000	0.000	0.000
61	E	95	ALA	0	0.055	0.043	23.679	0.008	0.008	0.000	0.000	0.000	0.000
62	E	96	VAL	0	-0.022	-0.013	24.046	0.010	0.010	0.000	0.000	0.000	0.000
63	E	97	ASN	0	-0.028	-0.028	26.561	0.013	0.013	0.000	0.000	0.000	0.000
64	E	98	ASP	-1	-0.809	-0.914	29.059	-0.104	-0.104	0.000	0.000	0.000	0.000
65	E	99	ALA	0	-0.034	-0.012	27.957	0.007	0.007	0.000	0.000	0.000	0.000
66	E	100	LEU	0	-0.015	-0.006	30.080	0.008	0.008	0.000	0.000	0.000	0.000
67	E	101	LEU	0	-0.008	0.015	32.589	0.009	0.009	0.000	0.000	0.000	0.000
68	E	102	MET	0	0.021	0.023	32.698	0.005	0.005	0.000	0.000	0.000	0.000
69	E	103	SER	0	-0.101	-0.064	33.373	0.006	0.006	0.000	0.000	0.000	0.000
70	E	104	ARG	1	0.944	0.977	35.288	0.073	0.073	0.000	0.000	0.000	0.000
71	E	105	ILE	0	-0.026	-0.017	37.877	0.005	0.005	0.000	0.000	0.000	0.000
72	E	106	ASN	0	-0.045	-0.025	36.031	0.008	0.008	0.000	0.000	0.000	0.000
73	E	107	MET	0	-0.002	0.018	39.094	0.003	0.003	0.000	0.000	0.000	0.000
74	E	108	ASN	0	0.040	0.018	38.349	-0.001	-0.001	0.000	0.000	0.000	0.000
75	E	109	LYS	1	0.880	0.931	41.313	0.046	0.046	0.000	0.000	0.000	0.000
76	E	110	PRO	0	0.050	0.017	44.004	-0.001	-0.001	0.000	0.000	0.000	0.000
77	E	111	LEU	0	0.034	0.010	43.563	0.001	0.001	0.000	0.000	0.000	0.000
78	E	112	THR	0	0.012	-0.003	46.056	0.001	0.001	0.000	0.000	0.000	0.000
79	E	113	GLN	0	-0.009	0.000	48.949	0.002	0.002	0.000	0.000	0.000	0.000
80	E	114	ARG	1	0.892	0.964	43.739	0.046	0.046	0.000	0.000	0.000	0.000
81	E	115	LEU	0	0.023	0.019	50.453	0.001	0.001	0.000	0.000	0.000	0.000
82	E	116	ALA	0	-0.008	-0.008	50.830	-0.001	-0.001	0.000	0.000	0.000	0.000
83	E	117	VAL	0	0.020	0.003	52.508	0.001	0.001	0.000	0.000	0.000	0.000
84	E	118	GLN	0	-0.005	0.007	51.705	-0.001	-0.001	0.000	0.000	0.000	0.000
85	E	119	ILE	0	-0.017	-0.021	52.334	0.001	0.001	0.000	0.000	0.000	0.000
86	E	120	THR	0	0.020	-0.006	53.695	-0.001	-0.001	0.000	0.000	0.000	0.000
87	E	121	GLU	-1	-0.865	-0.932	56.214	-0.023	-0.023	0.000	0.000	0.000	0.000
88	E	122	CYS	0	-0.062	-0.031	55.408	0.001	0.001	0.000	0.000	0.000	0.000
89	E	123	VAL	0	0.047	0.029	53.549	0.000	0.000	0.000	0.000	0.000	0.000
90	E	124	LYS	1	1.013	1.026	56.653	0.022	0.022	0.000	0.000	0.000	0.000
91	E	125	ALA	0	0.017	0.008	60.105	0.001	0.001	0.000	0.000	0.000	0.000
92	E	126	ALA	0	-0.057	-0.042	58.126	0.000	0.000	0.000	0.000	0.000	0.000
93	E	127	ASP	-1	-0.890	-0.941	58.285	-0.026	-0.026	0.000	0.000	0.000	0.000
94	E	128	GLU	-1	-0.990	-1.001	60.853	-0.020	-0.020	0.000	0.000	0.000	0.000
95	E	129	GLY	0	-0.005	0.010	63.324	0.001	0.001	0.000	0.000	0.000	0.000
96	E	130	PHE	0	0.004	-0.004	64.488	0.000	0.000	0.000	0.000	0.000	0.000
97	E	131	ILE	0	0.007	-0.012	58.828	0.000	0.000	0.000	0.000	0.000	0.000
98	E	132	ASN	0	-0.007	-0.004	62.953	-0.001	-0.001	0.000	0.000	0.000	0.000
99	E	133	LEU	0	0.030	0.029	64.254	0.000	0.000	0.000	0.000	0.000	0.000
100	E	134	ILE	0	-0.025	-0.020	64.854	0.000	0.000	0.000	0.000	0.000	0.000
101	E	135	LYS	1	0.903	0.940	57.863	0.029	0.029	0.000	0.000	0.000	0.000
102	E	136	SER	0	-0.004	0.004	64.792	0.000	0.000	0.000	0.000	0.000	0.000
103	E	137	LYS	1	0.905	0.980	67.770	0.021	0.021	0.000	0.000	0.000	0.000
104	E	138	NME	0	-0.030	-0.010	68.224	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(E:35:ACE )