FMO DATABASE

FMODB ID: 76ZJK

Calculation Name: 1JYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1538723.46984
FMO2-HF: Nuclear repulsion	1475790.905529
FMO2-HF: Total energy	-62932.564311
FMO2-MP2: Total energy	-63114.507331

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(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.
-19.19	-9.256	18.388	-8.782	-19.541	-0.063

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 : -0.050 / 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	-0.057	-0.050	2.789	-3.665	0.081	0.404	-1.998	-2.152	-0.006
4	A	4	GLU	-1	-0.886	-0.923	5.038	-0.240	-0.198	-0.001	-0.005	-0.036	0.000
5	A	5	ILE	0	-0.029	-0.013	8.849	0.061	0.061	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.884	0.947	11.505	0.277	0.277	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.019	-0.020	14.134	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.835	-0.901	15.320	-0.062	-0.062	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.939	-0.978	18.286	-0.063	-0.063	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.774	0.863	20.420	0.035	0.035	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.805	0.860	15.224	-0.044	-0.044	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.025	-0.025	21.656	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.008	-0.005	20.484	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.020	0.007	23.858	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.040	0.002	24.107	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.014	-0.003	23.834	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.001	0.003	23.225	0.003	0.003	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.074	-0.041	22.736	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.005	0.000	23.220	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.008	0.000	23.803	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.021	0.012	21.188	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.092	0.043	13.892	0.010	0.010	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.889	-0.951	17.627	0.142	0.142	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.105	-0.057	19.132	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.045	-0.028	21.176	0.006	0.006	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.099	0.052	15.428	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.850	0.911	18.883	-0.133	-0.133	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.904	0.942	20.232	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.024	0.005	22.084	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.069	0.012	15.828	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.836	-0.895	21.199	0.126	0.126	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.024	-0.002	24.261	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.040	-0.001	20.908	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.004	0.000	22.011	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.028	0.020	25.070	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.024	-0.015	26.829	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.025	0.008	24.619	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.877	-0.933	27.914	0.094	0.094	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.136	-0.078	29.891	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.776	0.875	31.416	-0.050	-0.050	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.063	-0.028	31.368	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.016	0.004	26.717	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.003	-0.001	26.738	0.007	0.007	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.045	-0.006	22.160	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.850	0.918	21.650	-0.032	-0.032	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.786	-0.844	16.311	0.125	0.125	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.074	0.021	17.003	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.009	-0.003	15.213	0.037	0.037	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.021	0.020	13.745	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.025	-0.012	14.422	0.015	0.015	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.041	-0.045	11.813	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.082	-0.078	16.655	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.794	-0.864	17.719	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.045	0.009	15.249	0.032	0.032	0.000	0.000	0.000	0.000
55	A	55	PRO	0	-0.018	-0.019	14.422	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.954	-0.966	15.728	0.023	0.023	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.949	-0.951	17.769	-0.138	-0.138	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.078	-0.055	20.273	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.004	-0.009	21.765	0.013	0.013	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.084	0.035	22.429	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.890	-0.941	23.453	0.021	0.021	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.802	0.873	25.169	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.004	0.038	18.824	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.829	0.891	21.310	0.035	0.035	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.049	-0.021	18.259	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.793	-0.864	19.029	0.022	0.022	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.010	0.003	18.324	0.016	0.016	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.025	-0.014	19.357	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.038	0.025	19.701	0.020	0.020	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.031	-0.036	18.976	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.000	0.006	21.917	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.020	-0.006	25.225	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.028	0.016	27.667	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.024	-0.014	29.030	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.017	-0.017	29.495	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.008	0.001	31.534	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.009	0.005	31.101	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.021	0.015	32.421	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.899	-0.932	35.378	0.023	0.023	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.042	-0.019	37.120	0.002	0.002	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.042	0.010	32.825	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.933	-0.959	33.740	0.033	0.033	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.021	-0.023	32.303	0.004	0.004	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.037	-0.001	28.410	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.038	-0.010	24.423	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.003	-0.016	27.793	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.014	-0.004	24.410	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.769	-0.865	24.191	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.034	0.042	17.579	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.024	-0.019	20.831	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.096	0.060	19.842	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.085	-0.047	19.661	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.039	0.008	15.726	0.018	0.018	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.020	-0.028	12.318	0.018	0.018	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.015	0.029	8.068	-0.038	-0.038	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.018	-0.017	8.078	0.178	0.178	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.031	0.017	3.038	-1.181	-0.823	1.058	-0.458	-0.958	-0.001
98	A	98	VAL	0	0.014	0.010	4.484	-0.060	0.247	0.008	-0.083	-0.232	0.000
99	A	99	ALA	0	-0.036	-0.016	2.317	0.378	1.126	1.329	-0.584	-1.493	-0.004
100	A	100	ARG	1	0.820	0.879	4.352	-1.038	-0.920	0.000	-0.038	-0.081	0.000
101	A	101	VAL	0	-0.035	-0.003	6.368	0.013	0.013	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.011	-0.018	8.110	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.001	0.002	11.374	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.884	-0.949	12.324	0.290	0.290	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.894	-0.937	9.645	0.505	0.505	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.070	0.009	7.861	0.051	0.051	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.004	0.016	7.413	0.006	0.006	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.858	0.922	5.733	-0.779	-0.779	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.032	0.014	2.302	-0.335	-0.634	3.112	-1.015	-1.798	-0.001
110	A	110	TRP	0	0.077	0.002	2.600	-0.068	-0.521	0.925	1.055	-1.527	-0.019
111	A	111	TYR	0	-0.010	-0.001	5.368	-0.438	-0.374	-0.001	-0.004	-0.058	0.000
112	A	112	GLN	0	-0.029	-0.019	2.175	-3.563	-1.587	1.875	-1.151	-2.700	0.005
113	A	113	PHE	0	0.002	0.010	2.534	-8.914	-4.475	2.308	-2.531	-4.216	-0.017
114	A	114	PHE	0	0.066	0.007	3.091	-0.155	-0.537	0.082	0.645	-0.345	0.000
115	A	115	ASN	0	-0.027	-0.013	5.099	-0.165	-0.165	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.051	-0.041	2.252	-2.488	-3.085	5.052	-2.194	-2.261	-0.019
117	A	117	LEU	0	0.009	0.004	4.614	0.483	0.635	-0.001	-0.044	-0.108	0.000
118	A	118	LEU	0	-0.031	-0.006	7.285	0.466	0.466	0.000	0.000	0.000	0.000
119	A	119	GLN	0	-0.047	-0.037	7.547	0.397	0.397	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.787	-0.832	9.767	-1.325	-1.325	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.031	-0.023	10.781	0.202	0.202	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.038	-0.021	13.958	0.138	0.138	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.016	0.002	12.787	0.154	0.154	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.852	-0.927	13.683	-0.545	-0.545	0.000	0.000	0.000	0.000
125	A	125	MET	0	-0.003	0.007	10.507	0.044	0.044	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.010	-0.001	14.384	0.058	0.058	0.000	0.000	0.000	0.000
127	A	127	PRO	0	-0.007	0.004	16.956	0.008	0.008	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.829	0.914	17.710	0.212	0.212	0.000	0.000	0.000	0.000
129	A	129	PRO	0	0.010	0.017	16.958	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	130	CYS	0	-0.050	0.000	11.766	-0.039	-0.039	0.000	0.000	0.000	0.000
131	A	131	PHE	0	0.005	-0.010	12.371	0.012	0.012	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.792	-0.845	9.522	0.450	0.450	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.003	-0.003	10.806	-0.091	-0.091	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.055	-0.053	11.155	0.084	0.084	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.028	-0.019	10.204	-0.051	-0.051	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.055	-0.040	13.274	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	137	ASN	0	0.024	-0.010	15.432	0.009	0.009	0.000	0.000	0.000	0.000
138	A	138	GLY	0	0.064	0.019	14.900	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.104	-0.045	15.824	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.957	-0.964	19.060	0.156	0.156	0.000	0.000	0.000	0.000
141	A	141	ASP	-1	-0.824	-0.894	16.072	0.292	0.292	0.000	0.000	0.000	0.000
142	A	142	GLY	0	-0.055	-0.015	17.121	0.011	0.011	0.000	0.000	0.000	0.000
143	A	143	TYR	0	-0.142	-0.093	11.687	0.029	0.029	0.000	0.000	0.000	0.000
144	A	144	TRP	0	0.041	0.038	10.602	-0.029	-0.029	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.769	-0.837	8.753	0.708	0.708	0.000	0.000	0.000	0.000
146	A	146	ILE	0	-0.020	-0.013	5.287	-0.117	-0.117	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.857	-0.903	6.944	0.696	0.696	0.000	0.000	0.000	0.000
148	A	148	MET	0	-0.045	-0.010	2.748	-0.703	-0.988	2.238	-0.377	-1.576	-0.001
149	A	149	TYR	0	-0.029	-0.049	7.721	-0.163	-0.163	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.035	0.003	8.993	0.029	0.029	0.000	0.000	0.000	0.000
151	A	151	ALA	0	-0.003	0.006	11.326	-0.090	-0.090	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.033	-0.020	11.713	-0.056	-0.056	0.000	0.000	0.000	0.000
153	A	153	GLN	0	-0.057	-0.037	14.908	0.102	0.102	0.000	0.000	0.000	0.000
154	A	154	PRO	0	0.005	-0.009	16.702	-0.072	-0.072	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.810	0.917	13.719	0.892	0.892	0.000	0.000	0.000	0.000

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