FMO DATABASE

FMODB ID: 982Y2

Calculation Name: 1JYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JYH

Chain ID: A

ChEMBL ID:

UniProt ID: P33012

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1537033.941487
FMO2-HF: Nuclear repulsion	1474102.116376
FMO2-HF: Total energy	-62931.825111
FMO2-MP2: Total energy	-63113.755663

3D Structure Molmil

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:1:MET)

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

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.
-21.096	-34.3	53.837	-23.622	-17.006	-0.033

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.078 / q_NPA : 0.014

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	3	TYR	0	-0.025	-0.042	3.014	-3.695	0.124	0.175	-1.813	-2.181	-0.006
4	A	4	GLU	-1	-0.955	-0.962	5.305	0.401	0.431	-0.001	-0.003	-0.025	0.000
5	A	5	ILE	0	-0.020	-0.005	9.074	-0.028	-0.028	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.954	0.982	11.829	-0.077	-0.077	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.025	-0.015	14.350	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.834	-0.914	15.483	0.014	0.014	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.951	-0.976	18.408	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.826	0.904	20.750	0.032	0.032	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.790	0.873	16.015	0.058	0.058	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.015	0.018	22.367	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.005	-0.008	20.706	0.001	0.001	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.024	0.004	23.990	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.034	-0.005	24.483	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.001	0.008	24.235	0.010	0.010	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.006	0.007	23.664	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.083	-0.045	22.678	0.011	0.011	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.005	-0.003	23.471	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.015	-0.002	23.886	0.012	0.012	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.000	-0.006	21.503	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.089	0.024	14.128	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.919	-0.951	18.317	-0.376	-0.376	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.077	-0.041	19.805	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.016	-0.013	21.281	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.102	0.063	15.935	0.022	0.022	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.982	0.989	19.331	0.242	0.242	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.936	0.975	20.628	0.169	0.169	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.005	-0.003	22.675	0.016	0.016	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.050	-0.001	16.441	0.019	0.019	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.932	-0.956	21.702	-0.159	-0.159	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.012	-0.015	24.727	0.006	0.006	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.039	-0.003	21.330	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.004	-0.007	22.052	0.012	0.012	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.002	0.016	25.501	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.016	-0.011	27.124	0.009	0.009	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.006	-0.004	24.829	0.008	0.008	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.884	-0.937	28.183	-0.087	-0.087	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.131	-0.065	30.159	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.801	0.900	31.759	0.070	0.070	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.053	-0.014	31.713	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.017	-0.003	27.053	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.011	-0.007	26.501	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.039	-0.009	22.236	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.911	0.953	21.837	0.039	0.039	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.777	-0.860	17.002	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.070	0.037	17.081	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.007	-0.014	15.112	-0.012	-0.012	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.034	0.031	13.924	0.014	0.014	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.038	-0.018	14.578	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.052	-0.048	12.231	0.021	0.021	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.088	-0.095	16.131	0.011	0.011	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.817	-0.891	17.738	-0.193	-0.193	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.069	0.041	15.388	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.015	-0.029	14.270	0.042	0.042	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.942	-0.961	15.753	-0.339	-0.339	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.990	-0.985	17.663	-0.202	-0.202	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.069	-0.032	20.048	0.039	0.039	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.003	-0.012	21.611	-0.014	-0.014	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.100	0.032	22.218	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.983	-0.995	23.221	-0.144	-0.144	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.876	0.924	25.133	0.146	0.146	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.005	0.039	18.851	0.007	0.007	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.839	0.907	21.075	0.195	0.195	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.032	-0.014	18.097	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.784	-0.847	19.222	-0.143	-0.143	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.015	0.006	18.748	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.040	-0.020	19.658	0.021	0.021	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.033	0.025	19.965	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.027	-0.032	19.080	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.011	-0.004	22.015	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.033	-0.032	25.559	0.003	0.003	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.053	0.027	27.781	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.034	-0.020	29.193	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.014	-0.011	29.592	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.004	0.003	31.697	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.006	-0.005	31.548	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.019	0.013	32.841	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.889	-0.932	35.790	-0.045	-0.045	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.060	-0.037	37.533	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.037	0.004	33.089	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.945	-0.972	34.051	-0.074	-0.074	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.014	-0.019	32.651	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.034	0.006	28.586	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.039	-0.008	24.938	0.008	0.008	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.006	-0.015	27.929	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.017	-0.008	24.773	0.008	0.008	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.867	-0.941	24.753	-0.050	-0.050	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.031	0.050	18.048	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.030	-0.028	20.691	0.014	0.014	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.100	0.058	19.907	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.088	-0.053	19.446	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.007	0.002	15.488	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.017	-0.023	12.280	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.009	0.018	7.766	0.048	0.048	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.004	-0.013	8.248	-0.056	-0.056	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.030	0.014	2.949	-0.476	-0.556	1.916	-0.691	-1.144	0.001
98	A	98	VAL	0	0.011	0.009	4.482	-0.708	-0.456	0.005	-0.062	-0.195	0.000
99	A	99	ALA	0	-0.038	-0.018	2.191	-0.083	0.768	1.321	-0.711	-1.461	-0.005
100	A	100	ARG	1	0.831	0.903	4.263	0.153	0.266	0.000	-0.037	-0.075	0.000
101	A	101	VAL	0	-0.022	-0.006	6.724	-0.252	-0.252	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.004	-0.008	8.414	0.170	0.170	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.027	-0.012	11.637	-0.031	-0.031	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.897	-0.958	13.357	-0.396	-0.396	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.909	-0.962	10.005	-1.064	-1.064	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.036	-0.003	8.710	-0.238	-0.238	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.025	0.024	8.210	-0.139	-0.139	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.910	0.964	5.567	1.164	1.164	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.020	0.007	2.830	-1.422	-0.784	0.333	-0.227	-0.745	0.000
110	A	110	TRP	0	0.073	0.018	2.759	-3.392	-1.973	0.461	-0.750	-1.130	-0.013
111	A	111	TYR	0	-0.022	-0.009	5.495	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	112	GLN	0	-0.043	-0.031	2.468	-2.853	-1.186	1.640	-0.853	-2.454	-0.007
113	A	113	PHE	0	-0.013	-0.001	2.615	-3.826	-0.531	0.523	-1.389	-2.429	-0.009
114	A	114	PHE	0	0.049	0.000	3.391	1.342	1.377	0.021	0.202	-0.257	0.000
115	A	115	ASN	0	-0.038	-0.019	5.226	0.250	0.250	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.027	-0.065	1.572	-3.276	-29.233	47.106	-17.093	-4.055	0.007
117	A	117	LEU	0	0.009	0.010	4.376	-0.138	0.028	0.000	-0.073	-0.093	0.000
118	A	118	LEU	0	-0.042	-0.010	7.142	0.083	0.083	0.000	0.000	0.000	0.000
119	A	119	GLN	0	-0.013	-0.021	7.776	-0.060	-0.060	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.810	-0.837	9.568	0.424	0.424	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.056	-0.043	10.740	-0.112	-0.112	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.028	-0.019	13.743	-0.056	-0.056	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.041	-0.025	12.447	-0.066	-0.066	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.903	-0.955	13.395	0.082	0.082	0.000	0.000	0.000	0.000
125	A	125	MET	0	0.005	-0.002	10.466	-0.065	-0.065	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.020	0.001	14.313	0.020	0.020	0.000	0.000	0.000	0.000
127	A	127	PRO	0	-0.010	0.006	16.763	-0.035	-0.035	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.857	0.919	17.621	0.107	0.107	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.013	0.022	16.655	-0.024	-0.024	0.000	0.000	0.000	0.000
130	A	130	CYS	0	-0.004	0.019	11.518	0.007	0.007	0.000	0.000	0.000	0.000
131	A	131	PHE	0	-0.011	-0.019	12.462	0.002	0.002	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.821	-0.903	9.451	-0.686	-0.686	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.017	0.013	11.140	0.003	0.003	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.034	-0.028	11.233	0.011	0.011	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.020	-0.016	10.255	0.031	0.031	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.044	-0.023	13.211	0.003	0.003	0.000	0.000	0.000	0.000
137	A	137	ASN	0	0.051	0.023	15.401	-0.045	-0.045	0.000	0.000	0.000	0.000
138	A	138	GLY	0	0.100	0.021	15.235	0.011	0.011	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.114	-0.053	16.127	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-1.008	-0.997	19.401	-0.100	-0.100	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.859	-0.913	16.618	-0.115	-0.115	0.000	0.000	0.000	0.000
142	A	142	GLY	0	-0.068	-0.028	17.317	0.007	0.007	0.000	0.000	0.000	0.000
143	A	143	TYR	0	-0.102	-0.055	12.075	-0.029	-0.029	0.000	0.000	0.000	0.000
144	A	144	TRP	0	0.031	0.034	10.861	0.057	0.057	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.784	-0.866	8.754	-0.279	-0.279	0.000	0.000	0.000	0.000
146	A	146	ILE	0	-0.020	-0.019	5.235	0.004	0.004	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.868	-0.939	6.966	0.258	0.258	0.000	0.000	0.000	0.000
148	A	148	MET	0	-0.048	-0.006	2.866	-0.925	-0.377	0.337	-0.122	-0.762	-0.001
149	A	149	TYR	0	-0.010	-0.009	8.189	0.158	0.158	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.029	0.002	8.701	-0.068	-0.068	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.011	0.006	11.154	0.055	0.055	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.015	-0.007	11.333	-0.019	-0.019	0.000	0.000	0.000	0.000
153	A	153	GLN	0	-0.030	-0.020	14.574	0.000	0.000	0.000	0.000	0.000	0.000
154	A	154	PRO	0	-0.026	-0.014	16.732	0.009	0.009	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.881	0.964	14.402	-0.255	-0.255	0.000	0.000	0.000	0.000

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