FMO DATABASE

FMODB ID: VRJQ1

Calculation Name: 1JYO-E-Xray372

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: 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	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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-565906.755792
FMO2-HF: Nuclear repulsion	525162.317657
FMO2-HF: Total energy	-40744.438135
FMO2-MP2: Total energy	-40862.509202

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:36:ASP)

Summations of interaction energy for fragment #1(E:36:ASP)

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.
-198.487	-206.403	44.702	-19.927	-16.859	0.105

Interaction energy analysis for fragmet #1(E:36:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.836 / q_NPA : -0.908

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

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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	38	ALA	0	0.021	0.030	3.862	5.056	6.980	-0.007	-1.054	-0.864	0.003
4	E	39	TYR	0	-0.035	-0.019	3.940	-5.667	-5.445	-0.001	-0.023	-0.198	0.000
5	E	40	VAL	0	-0.023	-0.011	9.303	-0.629	-0.629	0.000	0.000	0.000	0.000
6	E	41	ALA	0	-0.006	0.000	12.875	0.244	0.244	0.000	0.000	0.000	0.000
7	E	42	PRO	0	-0.001	-0.001	15.283	-0.625	-0.625	0.000	0.000	0.000	0.000
8	E	43	GLU	-1	-0.911	-0.950	18.386	13.061	13.061	0.000	0.000	0.000	0.000
9	E	44	LYS	1	0.839	0.912	19.263	-11.729	-11.729	0.000	0.000	0.000	0.000
10	E	45	PHE	0	0.087	0.043	19.367	-0.176	-0.176	0.000	0.000	0.000	0.000
11	E	46	SER	0	0.000	0.000	21.327	-0.270	-0.270	0.000	0.000	0.000	0.000
12	E	47	SER	0	0.004	-0.003	24.192	-0.150	-0.150	0.000	0.000	0.000	0.000
13	E	48	LYS	1	0.927	0.967	20.567	-12.899	-12.899	0.000	0.000	0.000	0.000
14	E	49	VAL	0	0.052	0.021	16.652	0.037	0.037	0.000	0.000	0.000	0.000
15	E	50	LEU	0	0.040	0.036	14.402	0.277	0.277	0.000	0.000	0.000	0.000
16	E	51	THR	0	0.007	-0.019	10.363	0.065	0.065	0.000	0.000	0.000	0.000
17	E	52	TRP	0	-0.003	0.033	4.389	0.588	0.845	-0.001	-0.017	-0.239	0.000
18	E	53	LEU	0	0.040	-0.010	6.777	1.471	1.471	0.000	0.000	0.000	0.000
19	E	54	GLY	0	0.059	0.044	2.958	0.579	1.424	0.745	-0.890	-0.699	0.008
20	E	55	LYS	1	0.796	0.873	1.670	-150.180	-158.583	33.482	-13.972	-11.107	0.139
21	E	56	MET	0	0.045	0.038	1.880	-3.313	-7.407	10.094	-3.494	-2.507	-0.043
22	E	57	PRO	0	-0.025	-0.007	4.688	1.196	1.306	-0.001	-0.008	-0.100	0.000
23	E	58	LEU	0	0.025	0.001	6.982	-2.666	-2.666	0.000	0.000	0.000	0.000
24	E	59	PHE	0	0.057	0.013	9.042	-1.056	-1.056	0.000	0.000	0.000	0.000
25	E	60	LYS	1	0.977	0.996	12.354	-18.457	-18.457	0.000	0.000	0.000	0.000
26	E	61	ASN	0	-0.023	-0.001	11.755	-2.314	-2.314	0.000	0.000	0.000	0.000
27	E	62	THR	0	0.062	0.022	12.447	0.933	0.933	0.000	0.000	0.000	0.000
28	E	63	GLU	-1	-0.793	-0.878	13.477	16.719	16.719	0.000	0.000	0.000	0.000
29	E	64	VAL	0	-0.034	-0.020	8.144	0.374	0.374	0.000	0.000	0.000	0.000
30	E	65	VAL	0	-0.011	-0.001	8.912	1.911	1.911	0.000	0.000	0.000	0.000
31	E	66	GLN	0	-0.026	0.002	9.741	0.574	0.574	0.000	0.000	0.000	0.000
32	E	67	LYS	1	0.886	0.920	10.809	-17.510	-17.510	0.000	0.000	0.000	0.000
33	E	68	HIS	0	-0.070	-0.036	2.796	-2.817	-1.594	0.391	-0.469	-1.145	-0.002
34	E	69	THR	0	-0.029	-0.038	7.329	0.819	0.819	0.000	0.000	0.000	0.000
35	E	70	GLU	-1	-0.863	-0.934	9.485	17.472	17.472	0.000	0.000	0.000	0.000
36	E	71	ASN	0	-0.091	-0.042	8.239	-1.089	-1.089	0.000	0.000	0.000	0.000
37	E	72	ILE	0	-0.031	-0.014	6.488	1.707	1.707	0.000	0.000	0.000	0.000
38	E	73	ARG	1	0.939	0.959	9.002	-21.670	-21.670	0.000	0.000	0.000	0.000
39	E	74	VAL	0	0.008	0.006	11.126	0.382	0.382	0.000	0.000	0.000	0.000
40	E	75	GLN	0	-0.010	-0.009	13.000	-0.571	-0.571	0.000	0.000	0.000	0.000
41	E	76	ASP	-1	-0.842	-0.902	16.414	14.252	14.252	0.000	0.000	0.000	0.000
42	E	77	GLN	0	-0.039	-0.021	12.292	-0.814	-0.814	0.000	0.000	0.000	0.000
43	E	78	LYS	1	1.001	0.989	14.480	-12.577	-12.577	0.000	0.000	0.000	0.000
44	E	79	ILE	0	0.028	0.031	17.179	-0.118	-0.118	0.000	0.000	0.000	0.000
45	E	80	LEU	0	0.020	0.015	9.112	0.029	0.029	0.000	0.000	0.000	0.000
46	E	81	GLN	0	0.038	0.013	13.103	1.024	1.024	0.000	0.000	0.000	0.000
47	E	82	THR	0	-0.019	-0.018	14.018	-0.287	-0.287	0.000	0.000	0.000	0.000
48	E	83	PHE	0	-0.007	-0.005	13.144	-0.239	-0.239	0.000	0.000	0.000	0.000
49	E	84	LEU	0	0.013	0.000	9.271	0.145	0.145	0.000	0.000	0.000	0.000
50	E	85	HIS	0	0.033	0.028	13.286	0.386	0.386	0.000	0.000	0.000	0.000
51	E	86	ALA	0	0.042	0.024	16.451	-0.288	-0.288	0.000	0.000	0.000	0.000
52	E	87	LEU	0	-0.072	-0.050	12.924	-0.323	-0.323	0.000	0.000	0.000	0.000
53	E	88	THR	0	-0.049	-0.041	14.545	0.506	0.506	0.000	0.000	0.000	0.000
54	E	89	GLU	-1	-0.932	-0.970	16.436	12.448	12.448	0.000	0.000	0.000	0.000
55	E	90	LYS	1	0.848	0.938	16.960	-16.979	-16.979	0.000	0.000	0.000	0.000
56	E	91	TYR	0	-0.021	-0.007	17.160	-0.062	-0.062	0.000	0.000	0.000	0.000
57	E	92	GLY	0	0.033	0.028	21.020	0.189	0.189	0.000	0.000	0.000	0.000
58	E	93	GLU	-1	-0.931	-0.979	22.406	11.416	11.416	0.000	0.000	0.000	0.000
59	E	94	THR	0	-0.008	-0.003	25.894	-0.258	-0.258	0.000	0.000	0.000	0.000
60	E	95	ALA	0	0.091	0.059	24.450	-0.321	-0.321	0.000	0.000	0.000	0.000
61	E	96	VAL	0	-0.021	-0.008	24.495	-0.212	-0.212	0.000	0.000	0.000	0.000
62	E	97	ASN	0	-0.021	-0.015	27.171	-0.498	-0.498	0.000	0.000	0.000	0.000
63	E	98	ASP	-1	-0.840	-0.925	29.617	9.738	9.738	0.000	0.000	0.000	0.000
64	E	99	ALA	0	-0.018	-0.005	28.437	-0.302	-0.302	0.000	0.000	0.000	0.000
65	E	100	LEU	0	-0.015	-0.004	30.520	-0.331	-0.331	0.000	0.000	0.000	0.000
66	E	101	LEU	0	-0.027	-0.005	32.807	-0.388	-0.388	0.000	0.000	0.000	0.000
67	E	102	MET	0	0.011	0.003	33.206	-0.303	-0.303	0.000	0.000	0.000	0.000
68	E	103	SER	0	-0.100	-0.072	33.606	-0.236	-0.236	0.000	0.000	0.000	0.000
69	E	104	ARG	1	0.944	0.976	35.576	-8.728	-8.728	0.000	0.000	0.000	0.000
70	E	105	ILE	0	0.005	0.005	38.389	-0.265	-0.265	0.000	0.000	0.000	0.000
71	E	106	ASN	0	-0.029	-0.009	36.595	-0.376	-0.376	0.000	0.000	0.000	0.000
72	E	107	MET	0	-0.005	0.003	39.550	-0.130	-0.130	0.000	0.000	0.000	0.000
73	E	108	ASN	0	0.018	0.022	38.403	-0.015	-0.015	0.000	0.000	0.000	0.000
74	E	109	LYS	1	0.916	0.946	42.049	-6.715	-6.715	0.000	0.000	0.000	0.000
75	E	110	PRO	0	0.088	0.032	45.271	0.060	0.060	0.000	0.000	0.000	0.000
76	E	111	LEU	0	0.026	0.006	44.704	-0.139	-0.139	0.000	0.000	0.000	0.000
77	E	112	THR	0	0.008	-0.014	47.007	-0.056	-0.056	0.000	0.000	0.000	0.000
78	E	113	GLN	0	-0.008	0.018	49.863	-0.059	-0.059	0.000	0.000	0.000	0.000
79	E	114	ARG	1	0.833	0.928	44.174	-7.123	-7.123	0.000	0.000	0.000	0.000
80	E	115	LEU	0	0.015	0.015	51.441	-0.025	-0.025	0.000	0.000	0.000	0.000
81	E	116	ALA	0	0.001	0.000	51.603	0.095	0.095	0.000	0.000	0.000	0.000
82	E	117	VAL	0	0.019	-0.003	53.426	-0.109	-0.109	0.000	0.000	0.000	0.000
83	E	118	GLN	0	-0.013	0.002	53.378	0.038	0.038	0.000	0.000	0.000	0.000
84	E	119	ILE	0	-0.002	-0.009	53.217	-0.123	-0.123	0.000	0.000	0.000	0.000
85	E	120	THR	0	0.012	-0.002	54.683	0.049	0.049	0.000	0.000	0.000	0.000
86	E	121	GLU	-1	-0.828	-0.923	57.224	5.217	5.217	0.000	0.000	0.000	0.000
87	E	122	CYS	0	-0.075	-0.037	56.835	-0.077	-0.077	0.000	0.000	0.000	0.000
88	E	123	VAL	0	0.014	0.017	54.994	-0.014	-0.014	0.000	0.000	0.000	0.000
89	E	124	LYS	1	0.963	0.995	58.000	-5.067	-5.067	0.000	0.000	0.000	0.000
90	E	125	ALA	0	-0.018	-0.010	61.561	-0.081	-0.081	0.000	0.000	0.000	0.000
91	E	126	ALA	0	-0.048	-0.025	59.523	-0.069	-0.069	0.000	0.000	0.000	0.000
92	E	127	ASP	-1	-0.876	-0.934	59.869	5.293	5.293	0.000	0.000	0.000	0.000
93	E	128	GLU	-1	-0.909	-0.953	62.516	4.757	4.757	0.000	0.000	0.000	0.000
94	E	129	GLY	0	-0.001	0.005	64.950	-0.089	-0.089	0.000	0.000	0.000	0.000
95	E	130	PHE	0	0.004	-0.003	65.465	-0.025	-0.025	0.000	0.000	0.000	0.000
96	E	131	ILE	0	0.013	-0.017	60.124	-0.027	-0.027	0.000	0.000	0.000	0.000
97	E	132	ASN	0	-0.015	-0.003	64.151	0.060	0.060	0.000	0.000	0.000	0.000
98	E	133	LEU	0	0.022	0.029	65.496	-0.037	-0.037	0.000	0.000	0.000	0.000
99	E	134	ILE	0	-0.008	-0.012	66.012	-0.047	-0.047	0.000	0.000	0.000	0.000
100	E	135	LYS	1	0.918	0.962	59.249	-5.282	-5.282	0.000	0.000	0.000	0.000
101	E	136	SER	0	-0.010	-0.010	66.188	-0.033	-0.033	0.000	0.000	0.000	0.000
102	E	137	LYS	1	0.847	0.942	69.155	-4.619	-4.619	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:36:ASP)