FMO DATABASE

FMODB ID: GNJ21

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	OptH
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	-1366895.547825
FMO2-HF: Nuclear repulsion	1310835.383531
FMO2-HF: Total energy	-56060.164294
FMO2-MP2: Total energy	-56226.506225

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.
-14.706	-8.538	1.442	-2.653	-4.956	0.006

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 : 0.011 / q_NPA : -0.013

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	0.046	0.030	3.344	-2.809	0.014	-0.017	-1.305	-1.501	0.000
4	A	51	ARG	1	0.915	0.956	2.899	-5.444	-4.381	0.150	-0.328	-0.886	-0.001
5	A	52	LEU	0	0.013	0.001	6.514	-0.251	-0.251	0.000	0.000	0.000	0.000
6	A	53	LEU	0	0.018	0.013	9.868	0.237	0.237	0.000	0.000	0.000	0.000
7	A	54	ARG	1	0.878	0.931	13.052	-0.772	-0.772	0.000	0.000	0.000	0.000
8	A	55	ASP	-1	-0.749	-0.870	16.188	0.502	0.502	0.000	0.000	0.000	0.000
9	A	56	GLU	-1	-0.876	-0.966	19.268	0.450	0.450	0.000	0.000	0.000	0.000
10	A	57	SER	0	-0.064	-0.028	22.054	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	58	ALA	0	-0.010	-0.002	22.958	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	59	GLN	0	-0.040	-0.032	24.103	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	60	LEU	0	-0.061	-0.004	18.447	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	61	ARG	1	0.967	0.975	22.404	-0.267	-0.267	0.000	0.000	0.000	0.000
15	A	62	ILE	0	-0.004	-0.006	18.259	0.027	0.027	0.000	0.000	0.000	0.000
16	A	63	ALA	0	0.018	0.002	19.761	0.022	0.022	0.000	0.000	0.000	0.000
17	A	64	ASP	-1	-0.804	-0.897	21.059	0.358	0.358	0.000	0.000	0.000	0.000
18	A	65	VAL	0	0.013	-0.002	15.301	0.045	0.045	0.000	0.000	0.000	0.000
19	A	66	LEU	0	-0.049	-0.023	15.923	0.064	0.064	0.000	0.000	0.000	0.000
20	A	67	GLN	0	-0.039	-0.020	16.880	0.002	0.002	0.000	0.000	0.000	0.000
21	A	68	ARG	1	0.939	0.983	15.772	-0.499	-0.499	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.948	0.974	11.534	-0.326	-0.326	0.000	0.000	0.000	0.000
23	A	70	GLU	-1	-0.878	-0.936	10.349	1.056	1.056	0.000	0.000	0.000	0.000
24	A	71	GLN	0	-0.024	-0.022	10.770	0.332	0.332	0.000	0.000	0.000	0.000
25	A	72	PHE	0	-0.014	0.015	8.430	0.034	0.034	0.000	0.000	0.000	0.000
26	A	73	ARG	1	0.865	0.922	6.739	-1.840	-1.840	0.000	0.000	0.000	0.000
27	A	74	PRO	0	0.000	-0.004	2.533	-3.562	-1.550	1.311	-1.005	-2.318	0.007
28	A	75	LEU	0	-0.010	0.007	4.461	-0.363	-0.205	-0.001	-0.013	-0.143	0.000
29	A	76	ALA	0	0.002	0.000	4.950	-0.124	-0.012	-0.001	-0.002	-0.108	0.000
30	A	77	LYS	1	0.944	0.971	7.506	-0.722	-0.722	0.000	0.000	0.000	0.000
31	A	78	ARG	1	0.892	0.949	5.910	-1.404	-1.404	0.000	0.000	0.000	0.000
32	A	79	SER	0	0.004	-0.001	9.946	-0.139	-0.139	0.000	0.000	0.000	0.000
33	A	80	PHE	0	-0.030	-0.022	12.094	0.088	0.088	0.000	0.000	0.000	0.000
34	A	81	ILE	0	0.027	0.002	14.585	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	82	PHE	0	-0.026	-0.008	14.205	0.036	0.036	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.033	0.005	19.920	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	84	ALA	0	-0.005	0.003	23.332	0.020	0.020	0.000	0.000	0.000	0.000
38	A	85	SER	0	0.004	0.000	23.089	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	86	PRO	0	0.030	0.012	25.079	0.001	0.001	0.000	0.000	0.000	0.000
40	A	87	GLN	0	0.035	0.064	18.980	0.050	0.050	0.000	0.000	0.000	0.000
41	A	88	ALA	0	-0.022	-0.020	20.498	-0.025	-0.025	0.000	0.000	0.000	0.000
42	A	89	VAL	0	-0.036	-0.010	14.548	0.057	0.057	0.000	0.000	0.000	0.000
43	A	90	TRP	0	0.003	-0.008	14.675	-0.066	-0.066	0.000	0.000	0.000	0.000
44	A	91	LEU	0	-0.022	-0.005	9.455	0.121	0.121	0.000	0.000	0.000	0.000
45	A	92	GLN	0	-0.017	-0.024	8.609	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	93	VAL	0	0.007	0.007	8.070	0.084	0.084	0.000	0.000	0.000	0.000
47	A	94	GLN	0	-0.040	-0.008	6.887	-0.180	-0.180	0.000	0.000	0.000	0.000
48	A	95	LEU	0	0.019	0.009	7.600	0.096	0.096	0.000	0.000	0.000	0.000
49	A	96	PRO	0	0.033	0.025	9.079	-0.045	-0.045	0.000	0.000	0.000	0.000
50	A	97	ALA	0	0.040	0.032	11.897	0.069	0.069	0.000	0.000	0.000	0.000
51	A	98	GLN	0	-0.015	-0.009	12.481	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	99	LYS	1	0.972	0.968	16.642	0.200	0.200	0.000	0.000	0.000	0.000
53	A	100	VAL	0	0.018	0.017	18.375	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	101	PRO	0	0.009	0.003	19.420	0.017	0.017	0.000	0.000	0.000	0.000
55	A	102	SER	0	0.044	0.033	16.700	0.014	0.014	0.000	0.000	0.000	0.000
56	A	103	TRP	0	0.007	0.001	17.976	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	104	LEU	0	-0.030	-0.001	13.237	0.032	0.032	0.000	0.000	0.000	0.000
58	A	105	TRP	0	0.050	0.009	16.010	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	106	ILE	0	-0.008	-0.019	16.008	0.060	0.060	0.000	0.000	0.000	0.000
60	A	107	PHE	0	0.023	0.033	18.113	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	108	ALA	0	0.023	-0.013	19.362	0.030	0.030	0.000	0.000	0.000	0.000
62	A	109	PRO	0	0.007	0.013	20.964	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	110	ARG	1	0.983	0.989	24.033	-0.189	-0.189	0.000	0.000	0.000	0.000
64	A	111	VAL	0	-0.019	0.025	20.680	0.008	0.008	0.000	0.000	0.000	0.000
65	A	112	GLN	0	-0.050	-0.041	24.141	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	113	TYR	0	-0.015	-0.007	24.993	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	114	LEU	0	0.027	0.006	19.433	0.029	0.029	0.000	0.000	0.000	0.000
68	A	115	ASP	-1	-0.846	-0.899	20.983	0.264	0.264	0.000	0.000	0.000	0.000
69	A	116	TYR	0	0.035	0.017	16.765	0.029	0.029	0.000	0.000	0.000	0.000
70	A	117	TYR	0	0.019	0.000	18.316	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	118	LEU	0	0.000	0.006	16.605	0.035	0.035	0.000	0.000	0.000	0.000
72	A	119	VAL	0	-0.023	-0.014	16.450	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	120	GLN	0	-0.006	-0.057	16.917	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	121	ASP	-1	-0.811	-0.898	18.710	0.029	0.029	0.000	0.000	0.000	0.000
75	A	122	GLY	0	-0.045	-0.019	18.909	0.003	0.003	0.000	0.000	0.000	0.000
76	A	123	GLN	0	-0.019	-0.007	20.199	0.005	0.005	0.000	0.000	0.000	0.000
77	A	124	LEU	0	-0.046	-0.027	20.798	0.009	0.009	0.000	0.000	0.000	0.000
78	A	125	VAL	0	0.011	0.006	21.501	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	126	ARG	1	0.948	0.961	21.770	-0.150	-0.150	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.832	-0.906	21.970	0.255	0.255	0.000	0.000	0.000	0.000
81	A	128	GLN	0	0.003	0.004	23.158	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	129	HIS	1	0.760	0.852	23.682	-0.221	-0.221	0.000	0.000	0.000	0.000
83	A	130	THR	0	0.056	0.013	23.955	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	131	GLY	0	0.034	0.020	25.384	0.015	0.015	0.000	0.000	0.000	0.000
85	A	132	GLU	-1	-0.886	-0.953	26.173	0.189	0.189	0.000	0.000	0.000	0.000
86	A	133	SER	0	-0.040	-0.021	28.838	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	134	ARG	1	0.763	0.885	25.743	-0.235	-0.235	0.000	0.000	0.000	0.000
88	A	135	PRO	0	0.009	0.012	31.016	0.000	0.000	0.000	0.000	0.000	0.000
89	A	136	PHE	0	-0.012	-0.023	33.480	0.000	0.000	0.000	0.000	0.000	0.000
90	A	137	GLN	0	0.018	0.037	29.016	0.004	0.004	0.000	0.000	0.000	0.000
91	A	138	GLU	-1	-0.939	-0.963	32.152	0.112	0.112	0.000	0.000	0.000	0.000
92	A	139	ARG	1	0.868	0.922	25.909	-0.189	-0.189	0.000	0.000	0.000	0.000
93	A	140	PRO	0	0.023	0.016	27.894	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	141	LEU	0	0.019	0.013	24.505	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	142	PRO	0	0.103	0.057	28.652	0.010	0.010	0.000	0.000	0.000	0.000
96	A	143	SER	0	-0.066	-0.030	25.607	0.008	0.008	0.000	0.000	0.000	0.000
97	A	144	ARG	1	0.903	0.946	26.731	-0.138	-0.138	0.000	0.000	0.000	0.000
98	A	145	SER	0	-0.004	-0.011	22.026	0.023	0.023	0.000	0.000	0.000	0.000
99	A	146	TYR	0	-0.065	-0.033	20.716	-0.022	-0.022	0.000	0.000	0.000	0.000
100	A	147	LEU	0	0.034	0.016	20.704	0.019	0.019	0.000	0.000	0.000	0.000
101	A	148	PHE	0	-0.030	-0.014	18.666	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	149	SER	0	-0.007	0.009	19.232	0.009	0.009	0.000	0.000	0.000	0.000
103	A	150	LEU	0	-0.013	-0.028	14.564	0.014	0.014	0.000	0.000	0.000	0.000
104	A	151	PRO	0	-0.053	-0.011	18.456	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	152	VAL	0	0.011	0.011	18.980	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	153	ASP	-1	-0.814	-0.898	20.330	0.041	0.041	0.000	0.000	0.000	0.000
107	A	154	GLY	0	-0.031	-0.009	20.529	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	155	LYS	1	0.876	0.940	18.457	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	156	PRO	0	-0.018	0.001	13.404	0.006	0.006	0.000	0.000	0.000	0.000
110	A	157	MET	0	0.031	0.024	13.218	0.051	0.051	0.000	0.000	0.000	0.000
111	A	158	THR	0	-0.092	-0.054	11.028	0.010	0.010	0.000	0.000	0.000	0.000
112	A	159	LEU	0	0.014	0.014	12.331	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	160	TYR	0	0.005	-0.002	12.713	0.102	0.102	0.000	0.000	0.000	0.000
114	A	161	VAL	0	0.008	0.002	14.599	-0.058	-0.058	0.000	0.000	0.000	0.000
115	A	162	ARG	1	0.912	0.985	15.857	-0.301	-0.301	0.000	0.000	0.000	0.000
116	A	163	MET	0	-0.008	-0.004	14.769	-0.049	-0.049	0.000	0.000	0.000	0.000
117	A	164	THR	0	0.014	0.007	19.862	0.015	0.015	0.000	0.000	0.000	0.000
118	A	165	SER	0	0.000	-0.048	22.873	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	166	ASN	0	0.051	0.060	25.323	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	167	HIS	0	0.016	0.010	26.627	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	168	PRO	0	-0.009	-0.022	23.931	0.018	0.018	0.000	0.000	0.000	0.000
122	A	169	LEU	0	0.003	0.018	19.154	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	170	MET	0	-0.026	-0.014	18.544	0.028	0.028	0.000	0.000	0.000	0.000
124	A	171	ALA	0	0.007	0.000	16.104	-0.023	-0.023	0.000	0.000	0.000	0.000
125	A	172	TRP	0	-0.001	0.007	14.996	0.048	0.048	0.000	0.000	0.000	0.000
126	A	173	PHE	0	-0.024	-0.019	9.590	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	174	ASP	-1	-0.801	-0.903	11.586	0.683	0.683	0.000	0.000	0.000	0.000
128	A	175	GLN	0	-0.101	-0.048	11.944	0.031	0.031	0.000	0.000	0.000	0.000
129	A	176	ILE	0	-0.033	-0.001	13.739	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	177	ASP	-1	-0.819	-0.933	16.907	0.034	0.034	0.000	0.000	0.000	0.000
131	A	178	GLU	-1	-0.940	-0.989	19.235	0.028	0.028	0.000	0.000	0.000	0.000
132	A	179	ALA	0	0.077	0.039	21.567	0.005	0.005	0.000	0.000	0.000	0.000
133	A	180	GLY	0	-0.030	-0.011	20.145	0.002	0.002	0.000	0.000	0.000	0.000
134	A	181	LEU	0	-0.059	-0.037	21.178	0.010	0.010	0.000	0.000	0.000	0.000
135	A	182	VAL	0	0.001	-0.008	23.347	0.005	0.005	0.000	0.000	0.000	0.000
136	A	183	GLY	0	-0.007	0.016	24.916	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	184	LEU	0	-0.098	-0.040	21.120	0.013	0.013	0.000	0.000	0.000	0.000
138	A	185	GLU	-1	-0.885	-0.928	25.217	0.088	0.088	0.000	0.000	0.000	0.000

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