FMO DATABASE

FMODB ID: 82RVY

Calculation Name: 3JYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JYB

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1368515.127348
FMO2-HF: Nuclear repulsion	1312454.369074
FMO2-HF: Total energy	-56060.758274
FMO2-MP2: Total energy	-56227.095913

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:48:GLN)

Summations of interaction energy for fragment #1(A:48:GLN)

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.
-17.264	-10.652	2.177	-3.134	-5.655	0.008

Interaction energy analysis for fragmet #1(A:48:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.007

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	50	TRP	0	0.056	0.037	3.354	-3.055	-0.231	-0.016	-1.313	-1.495	0.000
4	A	51	ARG	1	0.901	0.950	2.307	-8.957	-7.469	0.872	-0.785	-1.575	0.002
5	A	52	LEU	0	0.008	0.002	6.530	-0.239	-0.239	0.000	0.000	0.000	0.000
6	A	53	LEU	0	0.015	0.011	9.884	0.208	0.208	0.000	0.000	0.000	0.000
7	A	54	ARG	1	0.851	0.919	13.073	-0.604	-0.604	0.000	0.000	0.000	0.000
8	A	55	ASP	-1	-0.744	-0.860	16.207	0.500	0.500	0.000	0.000	0.000	0.000
9	A	56	GLU	-1	-0.820	-0.919	19.278	0.391	0.391	0.000	0.000	0.000	0.000
10	A	57	SER	0	-0.055	-0.035	22.073	-0.045	-0.045	0.000	0.000	0.000	0.000
11	A	58	ALA	0	-0.002	0.006	22.975	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	59	GLN	0	-0.042	-0.033	24.121	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	60	LEU	0	-0.039	0.002	18.507	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	61	ARG	1	1.003	0.996	22.383	-0.333	-0.333	0.000	0.000	0.000	0.000
15	A	62	ILE	0	0.016	0.002	18.326	0.033	0.033	0.000	0.000	0.000	0.000
16	A	63	ALA	0	0.029	0.010	19.722	0.038	0.038	0.000	0.000	0.000	0.000
17	A	64	ASP	-1	-0.796	-0.889	21.020	0.449	0.449	0.000	0.000	0.000	0.000
18	A	65	VAL	0	0.011	0.007	15.377	0.051	0.051	0.000	0.000	0.000	0.000
19	A	66	LEU	0	-0.024	-0.006	15.888	0.092	0.092	0.000	0.000	0.000	0.000
20	A	67	GLN	0	-0.059	-0.023	16.836	0.035	0.035	0.000	0.000	0.000	0.000
21	A	68	ARG	1	0.842	0.921	15.772	-0.560	-0.560	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.911	0.951	11.498	-0.663	-0.663	0.000	0.000	0.000	0.000
23	A	70	GLU	-1	-0.812	-0.900	10.319	1.371	1.371	0.000	0.000	0.000	0.000
24	A	71	GLN	0	-0.049	-0.037	10.570	0.276	0.276	0.000	0.000	0.000	0.000
25	A	72	PHE	0	-0.011	0.011	8.416	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	73	ARG	1	0.837	0.900	6.774	-1.661	-1.661	0.000	0.000	0.000	0.000
27	A	74	PRO	0	-0.007	-0.010	2.507	-3.066	-1.032	1.323	-1.020	-2.337	0.006
28	A	75	LEU	0	-0.009	0.010	4.482	-0.543	-0.381	-0.001	-0.014	-0.147	0.000
29	A	76	ALA	0	-0.002	-0.004	4.945	-0.271	-0.167	-0.001	-0.002	-0.101	0.000
30	A	77	LYS	1	0.937	0.969	7.500	-0.402	-0.402	0.000	0.000	0.000	0.000
31	A	78	ARG	1	0.870	0.932	6.251	-1.364	-1.364	0.000	0.000	0.000	0.000
32	A	79	SER	0	0.024	0.003	9.933	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	80	PHE	0	-0.044	-0.026	12.091	0.037	0.037	0.000	0.000	0.000	0.000
34	A	81	ILE	0	0.019	-0.003	14.585	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	82	PHE	0	-0.014	0.000	14.092	0.015	0.015	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.032	0.005	19.926	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	84	ALA	0	-0.006	0.004	23.341	0.022	0.022	0.000	0.000	0.000	0.000
38	A	85	SER	0	0.003	-0.001	23.272	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	86	PRO	0	0.034	0.015	25.090	0.004	0.004	0.000	0.000	0.000	0.000
40	A	87	GLN	0	-0.014	0.019	18.869	0.054	0.054	0.000	0.000	0.000	0.000
41	A	88	ALA	0	-0.004	-0.014	20.540	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	89	VAL	0	-0.025	-0.005	14.615	0.054	0.054	0.000	0.000	0.000	0.000
43	A	90	TRP	0	-0.004	-0.014	14.693	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	91	LEU	0	-0.021	-0.005	9.500	0.104	0.104	0.000	0.000	0.000	0.000
45	A	92	GLN	0	-0.008	-0.016	8.487	0.128	0.128	0.000	0.000	0.000	0.000
46	A	93	VAL	0	0.005	0.003	8.071	0.124	0.124	0.000	0.000	0.000	0.000
47	A	94	GLN	0	-0.032	-0.002	6.537	-0.062	-0.062	0.000	0.000	0.000	0.000
48	A	95	LEU	0	0.021	0.015	7.594	0.166	0.166	0.000	0.000	0.000	0.000
49	A	96	PRO	0	0.031	0.021	9.103	-0.051	-0.051	0.000	0.000	0.000	0.000
50	A	97	ALA	0	0.035	0.029	11.892	0.038	0.038	0.000	0.000	0.000	0.000
51	A	98	GLN	0	-0.014	-0.006	12.467	-0.038	-0.038	0.000	0.000	0.000	0.000
52	A	99	LYS	1	0.968	0.962	16.637	0.020	0.020	0.000	0.000	0.000	0.000
53	A	100	VAL	0	0.022	0.020	18.370	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	101	PRO	0	0.012	0.004	19.415	0.027	0.027	0.000	0.000	0.000	0.000
55	A	102	SER	0	0.035	0.028	16.658	0.016	0.016	0.000	0.000	0.000	0.000
56	A	103	TRP	0	-0.001	-0.002	17.983	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	104	LEU	0	-0.022	0.001	13.230	0.037	0.037	0.000	0.000	0.000	0.000
58	A	105	TRP	0	0.040	0.006	16.048	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	106	ILE	0	-0.010	-0.023	16.057	0.057	0.057	0.000	0.000	0.000	0.000
60	A	107	PHE	0	0.038	0.041	18.104	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	108	ALA	0	0.026	-0.012	19.354	0.018	0.018	0.000	0.000	0.000	0.000
62	A	109	PRO	0	0.004	0.013	20.960	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	110	ARG	1	0.970	0.983	24.031	-0.155	-0.155	0.000	0.000	0.000	0.000
64	A	111	VAL	0	-0.025	0.023	20.715	0.007	0.007	0.000	0.000	0.000	0.000
65	A	112	GLN	0	0.013	-0.004	24.142	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	113	TYR	0	-0.031	-0.013	25.021	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	114	LEU	0	0.031	0.009	19.636	0.026	0.026	0.000	0.000	0.000	0.000
68	A	115	ASP	-1	-0.842	-0.902	20.983	0.304	0.304	0.000	0.000	0.000	0.000
69	A	116	TYR	0	0.041	0.026	16.860	0.036	0.036	0.000	0.000	0.000	0.000
70	A	117	TYR	0	0.012	-0.006	18.321	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	118	LEU	0	0.001	0.015	16.874	0.052	0.052	0.000	0.000	0.000	0.000
72	A	119	VAL	0	-0.015	-0.013	16.477	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	120	GLN	0	0.024	-0.028	16.914	0.036	0.036	0.000	0.000	0.000	0.000
74	A	121	ASP	-1	-0.799	-0.880	18.715	0.214	0.214	0.000	0.000	0.000	0.000
75	A	122	GLY	0	-0.031	-0.016	18.953	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	123	GLN	0	-0.029	-0.008	20.174	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	124	LEU	0	-0.048	-0.027	21.026	0.020	0.020	0.000	0.000	0.000	0.000
78	A	125	VAL	0	0.009	0.006	21.482	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	126	ARG	1	0.934	0.958	21.862	-0.278	-0.278	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.810	-0.899	21.970	0.346	0.346	0.000	0.000	0.000	0.000
81	A	128	GLN	0	-0.007	0.005	23.163	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	129	HIS	1	0.775	0.860	23.687	-0.276	-0.276	0.000	0.000	0.000	0.000
83	A	130	THR	0	0.063	0.009	23.860	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	131	GLY	0	0.037	0.033	25.412	0.014	0.014	0.000	0.000	0.000	0.000
85	A	132	GLU	-1	-0.864	-0.942	26.174	0.177	0.177	0.000	0.000	0.000	0.000
86	A	133	SER	0	-0.047	-0.026	28.841	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	134	ARG	1	0.741	0.861	25.574	-0.262	-0.262	0.000	0.000	0.000	0.000
88	A	135	PRO	0	0.011	0.012	31.016	0.001	0.001	0.000	0.000	0.000	0.000
89	A	136	PHE	0	-0.015	-0.026	33.480	0.002	0.002	0.000	0.000	0.000	0.000
90	A	137	GLN	0	0.015	0.042	28.890	0.006	0.006	0.000	0.000	0.000	0.000
91	A	138	GLU	-1	-0.912	-0.949	32.147	0.136	0.136	0.000	0.000	0.000	0.000
92	A	139	ARG	1	0.851	0.912	25.819	-0.200	-0.200	0.000	0.000	0.000	0.000
93	A	140	PRO	0	0.013	0.008	27.901	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	141	LEU	0	0.018	0.015	24.485	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	142	PRO	0	0.066	0.036	28.639	0.009	0.009	0.000	0.000	0.000	0.000
96	A	143	SER	0	-0.036	-0.023	25.649	0.008	0.008	0.000	0.000	0.000	0.000
97	A	144	ARG	1	0.878	0.928	26.721	-0.142	-0.142	0.000	0.000	0.000	0.000
98	A	145	SER	0	0.005	0.002	22.022	0.022	0.022	0.000	0.000	0.000	0.000
99	A	146	TYR	0	-0.069	-0.039	20.731	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	147	LEU	0	0.033	0.019	20.512	0.020	0.020	0.000	0.000	0.000	0.000
101	A	148	PHE	0	-0.033	-0.018	18.799	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	149	SER	0	-0.004	0.010	19.232	0.018	0.018	0.000	0.000	0.000	0.000
103	A	150	LEU	0	-0.019	-0.028	14.579	0.023	0.023	0.000	0.000	0.000	0.000
104	A	151	PRO	0	-0.045	-0.006	18.399	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	152	VAL	0	0.004	0.006	18.974	0.012	0.012	0.000	0.000	0.000	0.000
106	A	153	ASP	-1	-0.819	-0.917	20.435	0.193	0.193	0.000	0.000	0.000	0.000
107	A	154	GLY	0	-0.020	-0.004	20.525	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	155	LYS	1	0.849	0.917	18.488	-0.191	-0.191	0.000	0.000	0.000	0.000
109	A	156	PRO	0	-0.031	-0.007	13.251	0.007	0.007	0.000	0.000	0.000	0.000
110	A	157	MET	0	0.018	0.017	13.203	0.018	0.018	0.000	0.000	0.000	0.000
111	A	158	THR	0	-0.101	-0.060	11.000	0.095	0.095	0.000	0.000	0.000	0.000
112	A	159	LEU	0	0.007	0.019	12.333	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	160	TYR	0	0.014	-0.008	12.713	0.141	0.141	0.000	0.000	0.000	0.000
114	A	161	VAL	0	0.006	-0.002	14.606	-0.072	-0.072	0.000	0.000	0.000	0.000
115	A	162	ARG	1	0.888	0.980	15.866	-0.330	-0.330	0.000	0.000	0.000	0.000
116	A	163	MET	0	-0.007	-0.003	14.743	-0.053	-0.053	0.000	0.000	0.000	0.000
117	A	164	THR	0	0.004	0.001	19.877	0.008	0.008	0.000	0.000	0.000	0.000
118	A	165	SER	0	-0.003	-0.037	22.882	-0.020	-0.020	0.000	0.000	0.000	0.000
119	A	166	ASN	0	0.020	0.035	25.330	0.004	0.004	0.000	0.000	0.000	0.000
120	A	167	HIS	0	0.013	0.007	26.632	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	168	PRO	0	-0.019	-0.028	23.931	0.017	0.017	0.000	0.000	0.000	0.000
122	A	169	LEU	0	0.005	0.025	19.282	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	170	MET	0	-0.028	-0.017	18.522	0.008	0.008	0.000	0.000	0.000	0.000
124	A	171	ALA	0	0.005	0.001	16.096	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	172	TRP	0	-0.010	0.000	14.985	0.027	0.027	0.000	0.000	0.000	0.000
126	A	173	PHE	0	-0.010	-0.014	9.666	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	174	ASP	-1	-0.781	-0.881	11.301	0.769	0.769	0.000	0.000	0.000	0.000
128	A	175	GLN	0	-0.082	-0.046	11.981	0.036	0.036	0.000	0.000	0.000	0.000
129	A	176	ILE	0	-0.028	-0.003	13.739	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	177	ASP	-1	-0.819	-0.929	16.907	0.119	0.119	0.000	0.000	0.000	0.000
131	A	178	GLU	-1	-0.943	-0.989	19.235	0.064	0.064	0.000	0.000	0.000	0.000
132	A	179	ALA	0	0.073	0.037	21.548	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	180	GLY	0	-0.023	-0.009	20.146	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	181	LEU	0	-0.068	-0.038	21.178	0.003	0.003	0.000	0.000	0.000	0.000
135	A	182	VAL	0	0.011	-0.002	23.347	0.000	0.000	0.000	0.000	0.000	0.000
136	A	183	GLY	0	-0.014	0.011	24.916	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	184	LEU	0	-0.086	-0.036	21.142	0.006	0.006	0.000	0.000	0.000	0.000
138	A	185	GLU	-1	-0.853	-0.904	25.217	0.105	0.105	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:48:GLN)