FMO DATABASE

FMODB ID: 538NZ

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	OptH
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	-565334.30576
FMO2-HF: Nuclear repulsion	524591.002982
FMO2-HF: Total energy	-40743.302778
FMO2-MP2: Total energy	-40861.496506

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.
-106.985	-98.347	2.938	-5.245	-6.329	-0.003

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 : -0.911 / q_NPA : -0.952

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	0.018	0.016	3.809	0.485	3.352	-0.030	-1.608	-1.230	0.007
4	E	39	TYR	0	-0.027	-0.010	4.734	-4.448	-4.337	-0.001	-0.007	-0.103	0.000
5	E	40	VAL	0	-0.019	-0.011	9.452	-0.614	-0.614	0.000	0.000	0.000	0.000
6	E	41	ALA	0	-0.016	-0.007	13.010	-0.074	-0.074	0.000	0.000	0.000	0.000
7	E	42	PRO	0	-0.003	-0.003	15.355	-0.589	-0.589	0.000	0.000	0.000	0.000
8	E	43	GLU	-1	-0.909	-0.948	18.466	12.249	12.249	0.000	0.000	0.000	0.000
9	E	44	LYS	1	0.886	0.936	19.533	-11.684	-11.684	0.000	0.000	0.000	0.000
10	E	45	PHE	0	0.079	0.037	19.478	-0.183	-0.183	0.000	0.000	0.000	0.000
11	E	46	SER	0	0.005	0.008	21.390	-0.253	-0.253	0.000	0.000	0.000	0.000
12	E	47	SER	0	-0.016	-0.035	24.310	-0.324	-0.324	0.000	0.000	0.000	0.000
13	E	48	LYS	1	0.912	0.968	20.953	-12.472	-12.472	0.000	0.000	0.000	0.000
14	E	49	VAL	0	0.047	0.029	16.870	0.107	0.107	0.000	0.000	0.000	0.000
15	E	50	LEU	0	0.027	0.026	14.619	0.155	0.155	0.000	0.000	0.000	0.000
16	E	51	THR	0	0.028	0.002	10.369	0.231	0.231	0.000	0.000	0.000	0.000
17	E	52	TRP	0	-0.008	0.024	5.909	1.254	1.254	0.000	0.000	0.000	0.000
18	E	53	LEU	0	0.020	-0.020	6.994	1.792	1.792	0.000	0.000	0.000	0.000
19	E	54	GLY	0	0.047	0.033	3.442	2.607	3.119	0.063	-0.378	-0.196	0.003
20	E	55	LYS	1	0.907	0.953	2.697	-58.768	-56.467	0.711	-1.093	-1.918	0.009
21	E	56	MET	0	0.063	0.029	2.402	0.592	2.220	1.339	-1.438	-1.528	-0.021
22	E	57	PRO	0	-0.032	0.006	5.110	0.164	0.262	-0.001	-0.002	-0.095	0.000
23	E	58	LEU	0	0.002	-0.013	7.071	-3.153	-3.153	0.000	0.000	0.000	0.000
24	E	59	PHE	0	0.067	0.011	9.917	-0.442	-0.442	0.000	0.000	0.000	0.000
25	E	60	LYS	1	0.965	0.998	12.572	-18.648	-18.648	0.000	0.000	0.000	0.000
26	E	61	ASN	0	-0.016	0.007	11.707	-2.640	-2.640	0.000	0.000	0.000	0.000
27	E	62	THR	0	0.088	0.022	12.748	1.687	1.687	0.000	0.000	0.000	0.000
28	E	63	GLU	-1	-0.879	-0.938	13.749	17.361	17.361	0.000	0.000	0.000	0.000
29	E	64	VAL	0	-0.060	-0.026	8.501	0.748	0.748	0.000	0.000	0.000	0.000
30	E	65	VAL	0	-0.016	-0.018	8.989	2.297	2.297	0.000	0.000	0.000	0.000
31	E	66	GLN	0	0.010	0.005	9.572	1.229	1.229	0.000	0.000	0.000	0.000
32	E	67	LYS	1	0.968	0.989	10.127	-20.553	-20.553	0.000	0.000	0.000	0.000
33	E	68	HIS	0	-0.056	-0.028	2.504	-3.017	-1.896	0.857	-0.719	-1.259	-0.001
34	E	69	THR	0	-0.035	-0.036	7.238	0.597	0.597	0.000	0.000	0.000	0.000
35	E	70	GLU	-1	-0.924	-0.964	9.379	18.422	18.422	0.000	0.000	0.000	0.000
36	E	71	ASN	0	-0.079	-0.024	7.236	-2.239	-2.239	0.000	0.000	0.000	0.000
37	E	72	ILE	0	-0.025	0.002	5.669	1.374	1.374	0.000	0.000	0.000	0.000
38	E	73	ARG	1	0.931	0.946	8.171	-22.684	-22.684	0.000	0.000	0.000	0.000
39	E	74	VAL	0	0.010	0.012	10.954	-0.048	-0.048	0.000	0.000	0.000	0.000
40	E	75	GLN	0	0.021	0.013	12.725	-0.067	-0.067	0.000	0.000	0.000	0.000
41	E	76	ASP	-1	-0.874	-0.930	16.466	14.386	14.386	0.000	0.000	0.000	0.000
42	E	77	GLN	0	0.002	-0.011	13.003	0.134	0.134	0.000	0.000	0.000	0.000
43	E	78	LYS	1	0.967	0.975	14.922	-12.831	-12.831	0.000	0.000	0.000	0.000
44	E	79	ILE	0	0.023	0.015	17.215	-0.073	-0.073	0.000	0.000	0.000	0.000
45	E	80	LEU	0	0.008	-0.006	9.538	-0.006	-0.006	0.000	0.000	0.000	0.000
46	E	81	GLN	0	0.039	0.023	12.217	0.432	0.432	0.000	0.000	0.000	0.000
47	E	82	THR	0	0.086	0.051	13.985	-0.309	-0.309	0.000	0.000	0.000	0.000
48	E	83	PHE	0	-0.012	-0.001	13.546	-0.275	-0.275	0.000	0.000	0.000	0.000
49	E	84	LEU	0	0.002	-0.009	9.384	-0.003	-0.003	0.000	0.000	0.000	0.000
50	E	85	HIS	0	0.012	0.022	13.550	0.266	0.266	0.000	0.000	0.000	0.000
51	E	86	ALA	0	0.015	0.009	16.687	-0.405	-0.405	0.000	0.000	0.000	0.000
52	E	87	LEU	0	-0.086	-0.053	12.961	-0.385	-0.385	0.000	0.000	0.000	0.000
53	E	88	THR	0	-0.055	-0.033	14.592	0.334	0.334	0.000	0.000	0.000	0.000
54	E	89	GLU	-1	-0.919	-0.964	16.472	12.456	12.456	0.000	0.000	0.000	0.000
55	E	90	LYS	1	0.891	0.963	18.080	-15.841	-15.841	0.000	0.000	0.000	0.000
56	E	91	TYR	0	-0.059	-0.031	17.980	-0.242	-0.242	0.000	0.000	0.000	0.000
57	E	92	GLY	0	0.041	0.029	21.307	0.255	0.255	0.000	0.000	0.000	0.000
58	E	93	GLU	-1	-0.929	-0.977	22.557	11.386	11.386	0.000	0.000	0.000	0.000
59	E	94	THR	0	0.017	0.004	25.985	-0.248	-0.248	0.000	0.000	0.000	0.000
60	E	95	ALA	0	0.054	0.043	24.614	-0.304	-0.304	0.000	0.000	0.000	0.000
61	E	96	VAL	0	-0.018	-0.011	24.753	-0.324	-0.324	0.000	0.000	0.000	0.000
62	E	97	ASN	0	-0.031	-0.029	27.307	-0.496	-0.496	0.000	0.000	0.000	0.000
63	E	98	ASP	-1	-0.808	-0.914	30.100	9.494	9.494	0.000	0.000	0.000	0.000
64	E	99	ALA	0	-0.035	-0.012	28.895	-0.296	-0.296	0.000	0.000	0.000	0.000
65	E	100	LEU	0	-0.015	-0.006	31.003	-0.300	-0.300	0.000	0.000	0.000	0.000
66	E	101	LEU	0	-0.010	0.014	33.338	-0.393	-0.393	0.000	0.000	0.000	0.000
67	E	102	MET	0	0.023	0.023	33.717	-0.283	-0.283	0.000	0.000	0.000	0.000
68	E	103	SER	0	-0.101	-0.065	34.206	-0.238	-0.238	0.000	0.000	0.000	0.000
69	E	104	ARG	1	0.943	0.976	36.165	-8.475	-8.475	0.000	0.000	0.000	0.000
70	E	105	ILE	0	-0.025	-0.017	38.820	-0.257	-0.257	0.000	0.000	0.000	0.000
71	E	106	ASN	0	-0.044	-0.024	37.093	-0.445	-0.445	0.000	0.000	0.000	0.000
72	E	107	MET	0	-0.003	0.018	40.119	-0.125	-0.125	0.000	0.000	0.000	0.000
73	E	108	ASN	0	0.040	0.017	39.275	0.006	0.006	0.000	0.000	0.000	0.000
74	E	109	LYS	1	0.880	0.932	42.266	-6.686	-6.686	0.000	0.000	0.000	0.000
75	E	110	PRO	0	0.051	0.017	45.043	0.106	0.106	0.000	0.000	0.000	0.000
76	E	111	LEU	0	0.034	0.010	44.785	-0.124	-0.124	0.000	0.000	0.000	0.000
77	E	112	THR	0	0.014	-0.003	47.174	-0.056	-0.056	0.000	0.000	0.000	0.000
78	E	113	GLN	0	-0.012	-0.002	50.003	-0.094	-0.094	0.000	0.000	0.000	0.000
79	E	114	ARG	1	0.894	0.965	44.900	-6.898	-6.898	0.000	0.000	0.000	0.000
80	E	115	LEU	0	0.022	0.018	51.618	-0.033	-0.033	0.000	0.000	0.000	0.000
81	E	116	ALA	0	-0.009	-0.009	52.121	0.091	0.091	0.000	0.000	0.000	0.000
82	E	117	VAL	0	0.019	0.004	53.832	-0.104	-0.104	0.000	0.000	0.000	0.000
83	E	118	GLN	0	-0.004	0.008	53.219	0.023	0.023	0.000	0.000	0.000	0.000
84	E	119	ILE	0	-0.017	-0.021	53.885	-0.119	-0.119	0.000	0.000	0.000	0.000
85	E	120	THR	0	0.025	-0.004	55.303	0.067	0.067	0.000	0.000	0.000	0.000
86	E	121	GLU	-1	-0.871	-0.934	57.844	5.112	5.112	0.000	0.000	0.000	0.000
87	E	122	CYS	0	-0.060	-0.030	57.082	-0.074	-0.074	0.000	0.000	0.000	0.000
88	E	123	VAL	0	0.047	0.029	55.327	-0.026	-0.026	0.000	0.000	0.000	0.000
89	E	124	LYS	1	1.013	1.026	58.413	-5.002	-5.002	0.000	0.000	0.000	0.000
90	E	125	ALA	0	0.017	0.007	61.874	-0.073	-0.073	0.000	0.000	0.000	0.000
91	E	126	ALA	0	-0.058	-0.043	59.907	-0.071	-0.071	0.000	0.000	0.000	0.000
92	E	127	ASP	-1	-0.889	-0.941	60.127	5.230	5.230	0.000	0.000	0.000	0.000
93	E	128	GLU	-1	-0.990	-1.001	62.677	4.657	4.657	0.000	0.000	0.000	0.000
94	E	129	GLY	0	-0.007	0.010	65.121	-0.086	-0.086	0.000	0.000	0.000	0.000
95	E	130	PHE	0	0.005	-0.003	66.203	-0.047	-0.047	0.000	0.000	0.000	0.000
96	E	131	ILE	0	0.008	-0.011	60.515	-0.019	-0.019	0.000	0.000	0.000	0.000
97	E	132	ASN	0	-0.007	-0.005	64.655	0.035	0.035	0.000	0.000	0.000	0.000
98	E	133	LEU	0	0.026	0.027	65.991	-0.033	-0.033	0.000	0.000	0.000	0.000
99	E	134	ILE	0	-0.024	-0.020	66.497	-0.044	-0.044	0.000	0.000	0.000	0.000
100	E	135	LYS	1	0.905	0.946	59.543	-5.225	-5.225	0.000	0.000	0.000	0.000
101	E	136	SER	0	0.002	0.019	66.439	-0.002	-0.002	0.000	0.000	0.000	0.000
102	E	137	LYS	1	0.872	0.953	69.444	-4.536	-4.536	0.000	0.000	0.000	0.000

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