FMO DATABASE

FMODB ID: MN2MZ

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	OptHSide
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	-1537597.662629
FMO2-HF: Nuclear repulsion	1474665.155521
FMO2-HF: Total energy	-62932.507108
FMO2-MP2: Total energy	-63114.429563

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.
-12.143	-8.308	26.844	-13.85	-16.827	-0.041

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 : -0.041 / q_NPA : 0.000

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	-0.033	-0.039	3.201	-2.786	1.193	0.069	-1.958	-2.090	0.000
4	A	4	GLU	-1	-0.889	-0.921	5.456	-0.366	-0.366	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.028	-0.014	9.215	0.106	0.106	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.893	0.949	11.930	0.277	0.277	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.026	-0.016	14.457	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.827	-0.902	15.481	-0.105	-0.105	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.950	-0.974	18.482	-0.091	-0.091	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.785	0.858	20.714	0.069	0.069	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.793	0.858	15.876	0.064	0.064	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.010	0.014	22.287	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.001	-0.007	20.800	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.019	0.005	24.140	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.036	-0.004	24.550	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.018	0.000	24.297	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.019	-0.006	23.696	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.068	-0.039	22.828	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.007	-0.002	23.410	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.010	0.001	23.767	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.011	-0.003	21.310	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.080	0.023	13.602	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.917	-0.952	17.895	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.083	-0.046	19.600	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.015	-0.012	21.361	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.097	0.061	15.825	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.897	0.931	19.277	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.917	0.955	20.569	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.013	-0.005	22.646	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.059	0.004	16.420	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.856	-0.899	21.721	0.017	0.017	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.016	-0.002	24.732	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.040	-0.002	21.475	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	MET	0	0.005	0.001	22.398	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.005	0.016	25.570	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.016	-0.011	27.172	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.013	-0.004	25.003	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.884	-0.934	28.219	0.015	0.015	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.136	-0.068	30.267	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.781	0.877	31.841	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.066	-0.024	31.803	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.012	0.003	27.146	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.007	-0.007	26.781	0.003	0.003	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.038	-0.006	22.378	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.905	0.955	21.955	0.036	0.036	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.787	-0.848	16.875	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.076	0.036	17.201	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.007	-0.016	15.378	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.038	0.033	13.992	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.038	-0.019	14.649	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.052	-0.052	11.904	0.007	0.007	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.073	-0.078	16.131	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.822	-0.880	17.675	-0.083	-0.083	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.032	0.000	15.018	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.018	-0.021	14.138	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.947	-0.961	15.389	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.948	-0.952	17.421	-0.110	-0.110	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.068	-0.034	19.879	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.005	-0.006	21.414	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.097	0.033	22.015	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.928	-0.966	23.016	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.811	0.884	24.970	0.031	0.031	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.004	0.046	18.654	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.840	0.890	20.962	0.086	0.086	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.041	-0.012	18.169	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.782	-0.858	19.254	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.019	0.006	18.805	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.026	-0.021	19.743	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.036	0.024	20.082	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.041	-0.045	19.320	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.016	-0.006	22.199	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.016	-0.023	25.646	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.053	0.029	27.765	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.038	-0.024	29.152	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.011	-0.010	29.771	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.015	-0.002	31.821	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.002	-0.001	31.655	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.027	0.016	33.022	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.895	-0.929	35.929	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.041	-0.027	37.645	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.036	0.010	33.139	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.942	-0.968	34.130	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.009	-0.016	32.687	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.039	-0.001	28.652	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.032	-0.004	25.026	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.009	-0.012	28.133	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.020	-0.012	24.950	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.818	-0.896	24.568	-0.065	-0.065	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.042	0.052	17.969	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.036	-0.028	20.658	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.104	0.067	19.917	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.085	-0.051	19.474	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.017	0.007	15.500	0.013	0.013	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.023	-0.038	12.379	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.008	0.019	7.847	-0.020	-0.020	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.003	-0.013	8.330	0.112	0.112	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.029	0.015	3.023	-0.808	-0.576	1.234	-0.509	-0.956	-0.001
98	A	98	VAL	0	0.009	0.007	4.748	-0.333	-0.138	0.001	-0.043	-0.154	0.000
99	A	99	ALA	0	-0.038	-0.018	2.409	0.141	1.042	0.692	-0.430	-1.163	-0.003
100	A	100	ARG	1	0.812	0.874	4.458	-0.469	-0.389	-0.001	-0.022	-0.057	0.000
101	A	101	VAL	0	-0.033	-0.010	6.575	-0.072	-0.072	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.001	-0.008	8.348	0.040	0.040	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.022	-0.006	11.537	0.015	0.015	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.895	-0.957	13.227	0.046	0.046	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.886	-0.942	9.931	0.027	0.027	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.057	0.008	8.519	-0.068	-0.068	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.018	0.020	8.063	-0.076	-0.076	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.859	0.928	5.539	-0.257	-0.257	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.036	0.013	2.538	-0.924	-0.346	0.943	-0.451	-1.069	-0.001
110	A	110	TRP	0	0.071	0.002	2.599	-2.453	-1.287	0.860	-0.577	-1.450	-0.019
111	A	111	TYR	0	-0.018	-0.007	5.352	-0.149	-0.094	-0.001	-0.004	-0.049	0.000
112	A	112	GLN	0	-0.039	-0.025	2.117	-2.067	-1.099	2.638	-0.986	-2.620	-0.003
113	A	113	PHE	0	-0.006	-0.003	2.605	-3.636	-0.284	0.827	-1.354	-2.825	-0.008
114	A	114	PHE	0	0.051	0.003	3.350	-0.324	-0.352	0.027	0.278	-0.277	0.000
115	A	115	ASN	0	-0.036	-0.015	4.957	-0.369	-0.369	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.020	-0.037	1.640	2.734	-5.669	18.973	-7.529	-3.040	-0.005
117	A	117	LEU	0	0.018	0.018	4.235	-0.084	0.149	0.000	-0.099	-0.134	0.000
118	A	118	LEU	0	-0.042	-0.010	6.950	0.304	0.304	0.000	0.000	0.000	0.000
119	A	119	GLN	0	-0.036	-0.026	7.192	0.188	0.188	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.805	-0.839	9.198	-1.134	-1.134	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.031	-0.017	10.315	0.159	0.159	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.040	-0.023	13.278	0.107	0.107	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.025	-0.013	12.470	0.125	0.125	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.874	-0.947	13.155	-0.399	-0.399	0.000	0.000	0.000	0.000
125	A	125	MET	0	-0.008	-0.004	10.417	0.009	0.009	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.011	0.005	14.243	0.053	0.053	0.000	0.000	0.000	0.000
127	A	127	PRO	0	-0.017	-0.001	16.698	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.851	0.921	17.562	0.223	0.223	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.013	0.020	16.743	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	130	CYS	0	-0.036	0.009	11.537	-0.018	-0.018	0.000	0.000	0.000	0.000
131	A	131	PHE	0	0.006	-0.009	12.592	0.015	0.015	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.795	-0.871	9.766	-0.048	-0.048	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.007	0.007	11.322	-0.031	-0.031	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.046	-0.031	11.408	0.046	0.046	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.021	-0.018	10.604	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.037	-0.025	13.491	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	137	ASN	0	0.011	-0.006	15.514	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	138	GLY	0	0.094	0.018	15.274	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.106	-0.049	16.167	0.002	0.002	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.954	-0.967	19.395	0.050	0.050	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.834	-0.887	16.738	0.114	0.114	0.000	0.000	0.000	0.000
142	A	142	GLY	0	-0.065	-0.027	17.308	0.010	0.010	0.000	0.000	0.000	0.000
143	A	143	TYR	0	-0.157	-0.093	11.985	0.019	0.019	0.000	0.000	0.000	0.000
144	A	144	TRP	0	0.039	0.042	10.903	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.761	-0.831	8.876	0.261	0.261	0.000	0.000	0.000	0.000
146	A	146	ILE	0	-0.016	-0.018	5.567	-0.049	-0.049	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.852	-0.907	7.193	0.352	0.352	0.000	0.000	0.000	0.000
148	A	148	MET	0	-0.055	-0.006	2.936	-0.907	-0.380	0.582	-0.166	-0.943	-0.001
149	A	149	TYR	0	-0.024	-0.043	8.055	-0.034	-0.034	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.029	0.002	8.783	0.010	0.010	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.012	0.006	11.113	-0.066	-0.066	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.019	-0.009	11.331	-0.042	-0.042	0.000	0.000	0.000	0.000
153	A	153	GLN	0	-0.023	-0.011	14.560	0.075	0.075	0.000	0.000	0.000	0.000
154	A	154	PRO	0	-0.008	-0.009	16.728	-0.043	-0.043	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.822	0.919	13.701	0.597	0.597	0.000	0.000	0.000	0.000

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