FMO DATABASE

FMODB ID: YYJV2

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	OptHSide
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	-565252.698368
FMO2-HF: Nuclear repulsion	524508.70616
FMO2-HF: Total energy	-40743.992208
FMO2-MP2: Total energy	-40862.092125

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.
-115.634	-106.26	2.779	-5.534	-6.62	0.001

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 : -0.914 / q_NPA : -0.956

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	0.014	0.018	3.809	0.921	3.721	-0.028	-1.566	-1.206	0.006
4	E	39	TYR	0	-0.023	-0.010	4.306	-4.959	-4.803	-0.001	-0.012	-0.143	0.000
5	E	40	VAL	0	-0.019	-0.012	9.452	-0.633	-0.633	0.000	0.000	0.000	0.000
6	E	41	ALA	0	-0.014	-0.005	13.010	-0.078	-0.078	0.000	0.000	0.000	0.000
7	E	42	PRO	0	0.002	-0.001	15.355	-0.586	-0.586	0.000	0.000	0.000	0.000
8	E	43	GLU	-1	-0.913	-0.949	18.428	12.476	12.476	0.000	0.000	0.000	0.000
9	E	44	LYS	1	0.879	0.933	19.533	-11.682	-11.682	0.000	0.000	0.000	0.000
10	E	45	PHE	0	0.084	0.039	19.449	-0.173	-0.173	0.000	0.000	0.000	0.000
11	E	46	SER	0	0.000	0.005	21.377	-0.262	-0.262	0.000	0.000	0.000	0.000
12	E	47	SER	0	-0.009	-0.009	24.297	-0.308	-0.308	0.000	0.000	0.000	0.000
13	E	48	LYS	1	0.904	0.942	20.871	-12.485	-12.485	0.000	0.000	0.000	0.000
14	E	49	VAL	0	0.049	0.027	16.930	0.117	0.117	0.000	0.000	0.000	0.000
15	E	50	LEU	0	0.024	0.026	14.694	0.162	0.162	0.000	0.000	0.000	0.000
16	E	51	THR	0	0.028	0.003	10.420	0.249	0.249	0.000	0.000	0.000	0.000
17	E	52	TRP	0	-0.006	0.022	5.467	1.556	1.556	0.000	0.000	0.000	0.000
18	E	53	LEU	0	0.022	-0.017	6.981	1.822	1.822	0.000	0.000	0.000	0.000
19	E	54	GLY	0	0.047	0.035	3.430	2.517	3.043	0.063	-0.381	-0.209	0.003
20	E	55	LYS	1	0.907	0.954	2.598	-68.967	-65.729	0.848	-1.624	-2.463	0.014
21	E	56	MET	0	0.053	0.030	2.402	0.696	2.248	1.330	-1.416	-1.465	-0.020
22	E	57	PRO	0	-0.019	0.001	4.986	0.164	0.164	0.000	0.000	0.000	0.000
23	E	58	LEU	0	0.001	-0.009	7.079	-3.131	-3.131	0.000	0.000	0.000	0.000
24	E	59	PHE	0	0.058	0.007	9.588	-0.566	-0.566	0.000	0.000	0.000	0.000
25	E	60	LYS	1	0.972	0.996	12.577	-18.453	-18.453	0.000	0.000	0.000	0.000
26	E	61	ASN	0	-0.016	0.009	11.651	-2.589	-2.589	0.000	0.000	0.000	0.000
27	E	62	THR	0	0.088	0.022	12.745	1.221	1.221	0.000	0.000	0.000	0.000
28	E	63	GLU	-1	-0.793	-0.888	13.754	17.771	17.771	0.000	0.000	0.000	0.000
29	E	64	VAL	0	-0.052	-0.025	8.500	0.606	0.606	0.000	0.000	0.000	0.000
30	E	65	VAL	0	-0.012	-0.007	8.981	2.136	2.136	0.000	0.000	0.000	0.000
31	E	66	GLN	0	-0.050	-0.020	9.585	0.713	0.713	0.000	0.000	0.000	0.000
32	E	67	LYS	1	0.900	0.940	10.053	-19.396	-19.396	0.000	0.000	0.000	0.000
33	E	68	HIS	0	-0.055	-0.015	2.614	-3.176	-2.074	0.567	-0.535	-1.134	-0.002
34	E	69	THR	0	-0.029	-0.042	7.257	0.659	0.659	0.000	0.000	0.000	0.000
35	E	70	GLU	-1	-0.869	-0.928	9.403	18.643	18.643	0.000	0.000	0.000	0.000
36	E	71	ASN	0	-0.084	-0.048	7.568	-1.014	-1.014	0.000	0.000	0.000	0.000
37	E	72	ILE	0	-0.019	0.011	5.787	1.184	1.184	0.000	0.000	0.000	0.000
38	E	73	ARG	1	0.933	0.947	8.205	-22.593	-22.593	0.000	0.000	0.000	0.000
39	E	74	VAL	0	0.005	0.006	10.908	0.019	0.019	0.000	0.000	0.000	0.000
40	E	75	GLN	0	-0.029	-0.012	12.715	-0.511	-0.511	0.000	0.000	0.000	0.000
41	E	76	ASP	-1	-0.844	-0.908	16.456	14.325	14.325	0.000	0.000	0.000	0.000
42	E	77	GLN	0	-0.019	-0.019	12.393	-0.393	-0.393	0.000	0.000	0.000	0.000
43	E	78	LYS	1	0.970	0.980	14.916	-12.896	-12.896	0.000	0.000	0.000	0.000
44	E	79	ILE	0	0.013	0.014	17.401	-0.075	-0.075	0.000	0.000	0.000	0.000
45	E	80	LEU	0	0.001	-0.006	9.505	0.080	0.080	0.000	0.000	0.000	0.000
46	E	81	GLN	0	0.084	0.044	13.111	0.862	0.862	0.000	0.000	0.000	0.000
47	E	82	THR	0	0.030	0.019	13.981	-0.313	-0.313	0.000	0.000	0.000	0.000
48	E	83	PHE	0	-0.003	0.003	13.236	-0.289	-0.289	0.000	0.000	0.000	0.000
49	E	84	LEU	0	0.015	0.000	9.465	0.013	0.013	0.000	0.000	0.000	0.000
50	E	85	HIS	0	0.009	0.013	13.547	0.510	0.510	0.000	0.000	0.000	0.000
51	E	86	ALA	0	0.023	0.014	16.686	-0.405	-0.405	0.000	0.000	0.000	0.000
52	E	87	LEU	0	-0.069	-0.047	13.066	-0.372	-0.372	0.000	0.000	0.000	0.000
53	E	88	THR	0	-0.061	-0.041	14.581	0.333	0.333	0.000	0.000	0.000	0.000
54	E	89	GLU	-1	-0.924	-0.964	16.473	12.551	12.551	0.000	0.000	0.000	0.000
55	E	90	LYS	1	0.863	0.950	17.836	-16.268	-16.268	0.000	0.000	0.000	0.000
56	E	91	TYR	0	-0.038	-0.020	17.797	-0.225	-0.225	0.000	0.000	0.000	0.000
57	E	92	GLY	0	0.045	0.033	21.309	0.253	0.253	0.000	0.000	0.000	0.000
58	E	93	GLU	-1	-0.925	-0.974	22.559	11.458	11.458	0.000	0.000	0.000	0.000
59	E	94	THR	0	0.006	-0.003	25.989	-0.237	-0.237	0.000	0.000	0.000	0.000
60	E	95	ALA	0	0.050	0.040	24.588	-0.316	-0.316	0.000	0.000	0.000	0.000
61	E	96	VAL	0	-0.009	-0.010	24.634	-0.323	-0.323	0.000	0.000	0.000	0.000
62	E	97	ASN	0	-0.041	-0.031	27.310	-0.537	-0.537	0.000	0.000	0.000	0.000
63	E	98	ASP	-1	-0.810	-0.913	30.092	9.496	9.496	0.000	0.000	0.000	0.000
64	E	99	ALA	0	-0.039	-0.015	28.900	-0.295	-0.295	0.000	0.000	0.000	0.000
65	E	100	LEU	0	-0.020	-0.007	31.005	-0.305	-0.305	0.000	0.000	0.000	0.000
66	E	101	LEU	0	0.003	0.016	33.341	-0.385	-0.385	0.000	0.000	0.000	0.000
67	E	102	MET	0	0.021	0.022	33.722	-0.297	-0.297	0.000	0.000	0.000	0.000
68	E	103	SER	0	-0.098	-0.060	34.199	-0.236	-0.236	0.000	0.000	0.000	0.000
69	E	104	ARG	1	0.945	0.976	36.166	-8.542	-8.542	0.000	0.000	0.000	0.000
70	E	105	ILE	0	-0.019	-0.014	38.821	-0.254	-0.254	0.000	0.000	0.000	0.000
71	E	106	ASN	0	-0.049	-0.023	37.097	-0.387	-0.387	0.000	0.000	0.000	0.000
72	E	107	MET	0	-0.004	0.014	40.119	-0.117	-0.117	0.000	0.000	0.000	0.000
73	E	108	ASN	0	0.027	0.016	39.115	0.004	0.004	0.000	0.000	0.000	0.000
74	E	109	LYS	1	0.909	0.942	42.266	-6.674	-6.674	0.000	0.000	0.000	0.000
75	E	110	PRO	0	0.055	0.016	45.042	0.104	0.104	0.000	0.000	0.000	0.000
76	E	111	LEU	0	0.027	0.007	44.704	-0.127	-0.127	0.000	0.000	0.000	0.000
77	E	112	THR	0	0.006	-0.008	47.172	-0.054	-0.054	0.000	0.000	0.000	0.000
78	E	113	GLN	0	-0.007	0.002	50.001	-0.078	-0.078	0.000	0.000	0.000	0.000
79	E	114	ARG	1	0.888	0.966	44.798	-6.978	-6.978	0.000	0.000	0.000	0.000
80	E	115	LEU	0	0.013	0.015	51.616	-0.033	-0.033	0.000	0.000	0.000	0.000
81	E	116	ALA	0	-0.003	-0.007	52.121	0.091	0.091	0.000	0.000	0.000	0.000
82	E	117	VAL	0	0.018	0.000	53.828	-0.106	-0.106	0.000	0.000	0.000	0.000
83	E	118	GLN	0	-0.004	0.010	53.429	0.046	0.046	0.000	0.000	0.000	0.000
84	E	119	ILE	0	-0.019	-0.023	53.941	-0.119	-0.119	0.000	0.000	0.000	0.000
85	E	120	THR	0	0.006	-0.011	55.297	0.061	0.061	0.000	0.000	0.000	0.000
86	E	121	GLU	-1	-0.814	-0.913	57.838	5.118	5.118	0.000	0.000	0.000	0.000
87	E	122	CYS	0	-0.064	-0.029	57.097	-0.075	-0.075	0.000	0.000	0.000	0.000
88	E	123	VAL	0	0.023	0.014	55.300	-0.025	-0.025	0.000	0.000	0.000	0.000
89	E	124	LYS	1	1.010	1.030	58.406	-5.040	-5.040	0.000	0.000	0.000	0.000
90	E	125	ALA	0	0.016	0.007	61.867	-0.074	-0.074	0.000	0.000	0.000	0.000
91	E	126	ALA	0	-0.062	-0.043	59.859	-0.072	-0.072	0.000	0.000	0.000	0.000
92	E	127	ASP	-1	-0.883	-0.941	60.056	5.245	5.245	0.000	0.000	0.000	0.000
93	E	128	GLU	-1	-0.996	-1.004	62.670	4.662	4.662	0.000	0.000	0.000	0.000
94	E	129	GLY	0	-0.004	0.011	65.112	-0.087	-0.087	0.000	0.000	0.000	0.000
95	E	130	PHE	0	0.000	-0.006	65.962	-0.047	-0.047	0.000	0.000	0.000	0.000
96	E	131	ILE	0	-0.001	-0.017	60.737	-0.020	-0.020	0.000	0.000	0.000	0.000
97	E	132	ASN	0	-0.003	0.001	64.650	0.044	0.044	0.000	0.000	0.000	0.000
98	E	133	LEU	0	0.028	0.031	65.986	-0.035	-0.035	0.000	0.000	0.000	0.000
99	E	134	ILE	0	-0.014	-0.014	66.580	-0.044	-0.044	0.000	0.000	0.000	0.000
100	E	135	LYS	1	0.918	0.949	59.465	-5.247	-5.247	0.000	0.000	0.000	0.000
101	E	136	SER	0	-0.016	0.003	66.434	-0.002	-0.002	0.000	0.000	0.000	0.000
102	E	137	LYS	1	0.877	0.958	69.439	-4.556	-4.556	0.000	0.000	0.000	0.000

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