FMO DATABASE

FMODB ID: 2277R

Calculation Name: 3JYB-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1372195.839632
FMO2-HF: Nuclear repulsion	1315984.425793
FMO2-HF: Total energy	-56211.413839
FMO2-MP2: Total energy	-56378.172351

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:47:ACE )

Summations of interaction energy for fragment #1(A:47:ACE )

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.
1.121	2.829	0.03	-0.766	-0.97	-0.001

Interaction energy analysis for fragmet #1(A:47:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	49	ASN	0	-0.007	-0.005	3.458	0.051	1.617	0.030	-0.752	-0.844	-0.001
4	A	50	TRP	0	0.047	0.035	4.655	0.201	0.324	0.000	-0.009	-0.113	0.000
5	A	51	ARG	1	0.922	0.959	7.156	0.580	0.580	0.000	0.000	0.000	0.000
6	A	52	LEU	0	0.012	0.002	9.964	0.132	0.132	0.000	0.000	0.000	0.000
7	A	53	LEU	0	0.021	0.013	13.452	-0.027	-0.027	0.000	0.000	0.000	0.000
8	A	54	ARG	1	0.875	0.930	16.928	0.203	0.203	0.000	0.000	0.000	0.000
9	A	55	ASP	-1	-0.752	-0.871	20.011	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	56	GLU	-1	-0.874	-0.964	23.077	-0.119	-0.119	0.000	0.000	0.000	0.000
11	A	57	SER	0	-0.068	-0.030	25.933	0.012	0.012	0.000	0.000	0.000	0.000
12	A	58	ALA	0	-0.007	0.000	26.601	0.009	0.009	0.000	0.000	0.000	0.000
13	A	59	GLN	0	-0.041	-0.032	27.612	0.010	0.010	0.000	0.000	0.000	0.000
14	A	60	LEU	0	-0.064	-0.006	22.498	0.004	0.004	0.000	0.000	0.000	0.000
15	A	61	ARG	1	0.971	0.976	25.719	0.051	0.051	0.000	0.000	0.000	0.000
16	A	62	ILE	0	0.001	-0.003	20.507	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	63	ALA	0	0.013	0.001	22.963	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	64	ASP	-1	-0.803	-0.898	24.873	-0.079	-0.079	0.000	0.000	0.000	0.000
19	A	65	VAL	0	0.010	-0.002	18.930	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	66	LEU	0	-0.046	-0.021	19.087	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	67	GLN	0	-0.040	-0.020	20.961	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	68	ARG	1	0.938	0.982	20.684	0.111	0.111	0.000	0.000	0.000	0.000
23	A	69	LYS	1	0.947	0.974	15.954	0.083	0.083	0.000	0.000	0.000	0.000
24	A	70	GLU	-1	-0.876	-0.935	15.316	-0.223	-0.223	0.000	0.000	0.000	0.000
25	A	71	GLN	0	-0.025	-0.023	16.276	-0.037	-0.037	0.000	0.000	0.000	0.000
26	A	72	PHE	0	-0.012	0.016	12.761	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	73	ARG	1	0.860	0.919	11.839	0.344	0.344	0.000	0.000	0.000	0.000
28	A	74	PRO	0	0.006	-0.001	6.603	0.059	0.059	0.000	0.000	0.000	0.000
29	A	75	LEU	0	-0.017	0.004	8.013	0.174	0.174	0.000	0.000	0.000	0.000
30	A	76	ALA	0	0.006	0.002	7.377	-0.312	-0.312	0.000	0.000	0.000	0.000
31	A	77	LYS	1	0.947	0.971	8.886	0.301	0.301	0.000	0.000	0.000	0.000
32	A	78	ARG	1	0.883	0.944	4.265	-0.438	-0.419	0.000	-0.005	-0.013	0.000
33	A	79	SER	0	0.010	0.003	10.419	0.072	0.072	0.000	0.000	0.000	0.000
34	A	80	PHE	0	-0.034	-0.023	13.879	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	81	ILE	0	0.028	0.003	16.599	0.028	0.028	0.000	0.000	0.000	0.000
36	A	82	PHE	0	-0.027	-0.010	17.455	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	83	PRO	0	0.033	0.004	22.676	0.012	0.012	0.000	0.000	0.000	0.000
38	A	84	ALA	0	-0.003	0.004	26.289	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	85	SER	0	0.002	-0.001	26.523	0.001	0.001	0.000	0.000	0.000	0.000
40	A	86	PRO	0	0.028	0.010	28.140	0.001	0.001	0.000	0.000	0.000	0.000
41	A	87	GLN	0	0.035	0.064	22.381	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	88	ALA	0	-0.019	-0.020	23.587	0.007	0.007	0.000	0.000	0.000	0.000
43	A	89	VAL	0	-0.037	-0.009	17.652	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	90	TRP	0	0.003	-0.009	17.737	0.022	0.022	0.000	0.000	0.000	0.000
45	A	91	LEU	0	-0.024	-0.005	11.135	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	92	GLN	0	-0.014	-0.023	12.119	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	93	VAL	0	0.006	0.007	8.413	-0.100	-0.100	0.000	0.000	0.000	0.000
48	A	94	GLN	0	-0.041	-0.009	8.754	-0.047	-0.047	0.000	0.000	0.000	0.000
49	A	95	LEU	0	0.018	0.008	8.169	0.106	0.106	0.000	0.000	0.000	0.000
50	A	96	PRO	0	0.033	0.024	9.056	-0.061	-0.061	0.000	0.000	0.000	0.000
51	A	97	ALA	0	0.041	0.033	12.101	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	98	GLN	0	-0.019	-0.010	11.733	0.047	0.047	0.000	0.000	0.000	0.000
53	A	99	LYS	1	0.972	0.967	16.010	-0.274	-0.274	0.000	0.000	0.000	0.000
54	A	100	VAL	0	0.020	0.017	16.898	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	101	PRO	0	0.007	0.003	18.235	0.006	0.006	0.000	0.000	0.000	0.000
56	A	102	SER	0	0.045	0.033	15.299	0.019	0.019	0.000	0.000	0.000	0.000
57	A	103	TRP	0	0.011	0.003	16.656	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	104	LEU	0	-0.037	-0.006	13.014	0.018	0.018	0.000	0.000	0.000	0.000
59	A	105	TRP	0	0.058	0.014	15.144	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	106	ILE	0	-0.015	-0.024	15.876	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	107	PHE	0	0.042	0.045	18.173	0.005	0.005	0.000	0.000	0.000	0.000
62	A	108	ALA	0	0.015	-0.018	19.935	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	109	PRO	0	0.017	0.019	21.900	0.003	0.003	0.000	0.000	0.000	0.000
64	A	110	ARG	1	0.977	0.985	25.294	0.037	0.037	0.000	0.000	0.000	0.000
65	A	111	VAL	0	-0.011	0.028	22.386	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	112	GLN	0	-0.055	-0.043	25.839	0.009	0.009	0.000	0.000	0.000	0.000
67	A	113	TYR	0	-0.021	-0.008	27.065	0.007	0.007	0.000	0.000	0.000	0.000
68	A	114	LEU	0	0.025	0.006	20.519	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	115	ASP	-1	-0.843	-0.898	22.883	-0.043	-0.043	0.000	0.000	0.000	0.000
70	A	116	TYR	0	0.040	0.020	17.128	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	117	TYR	0	0.015	-0.003	19.672	0.008	0.008	0.000	0.000	0.000	0.000
72	A	118	LEU	0	0.002	0.007	17.190	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	119	VAL	0	-0.024	-0.015	18.034	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	120	GLN	0	-0.006	-0.057	17.888	0.021	0.021	0.000	0.000	0.000	0.000
75	A	121	ASP	-1	-0.811	-0.898	19.894	0.037	0.037	0.000	0.000	0.000	0.000
76	A	122	GLY	0	-0.046	-0.019	20.563	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	123	GLN	0	-0.021	-0.008	22.148	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	124	LEU	0	-0.044	-0.026	22.357	0.002	0.002	0.000	0.000	0.000	0.000
79	A	125	VAL	0	0.011	0.007	22.187	0.003	0.003	0.000	0.000	0.000	0.000
80	A	126	ARG	1	0.947	0.961	22.182	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	127	ASP	-1	-0.833	-0.906	23.085	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	128	GLN	0	0.005	0.004	24.150	0.006	0.006	0.000	0.000	0.000	0.000
83	A	129	HIS	1	0.757	0.850	24.957	0.029	0.029	0.000	0.000	0.000	0.000
84	A	130	THR	0	0.057	0.014	24.950	0.004	0.004	0.000	0.000	0.000	0.000
85	A	131	GLY	0	0.037	0.021	26.646	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	132	GLU	-1	-0.883	-0.950	27.480	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	133	SER	0	-0.043	-0.023	30.284	0.001	0.001	0.000	0.000	0.000	0.000
88	A	134	ARG	1	0.759	0.882	27.584	0.037	0.037	0.000	0.000	0.000	0.000
89	A	135	PRO	0	0.012	0.013	32.026	0.002	0.002	0.000	0.000	0.000	0.000
90	A	136	PHE	0	-0.017	-0.026	34.457	0.000	0.000	0.000	0.000	0.000	0.000
91	A	137	GLN	0	0.014	0.035	29.745	0.001	0.001	0.000	0.000	0.000	0.000
92	A	138	GLU	-1	-0.943	-0.966	32.410	0.006	0.006	0.000	0.000	0.000	0.000
93	A	139	ARG	1	0.861	0.918	26.010	0.012	0.012	0.000	0.000	0.000	0.000
94	A	140	PRO	0	0.006	0.007	26.943	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	141	LEU	0	0.009	0.011	23.390	0.000	0.000	0.000	0.000	0.000	0.000
96	A	142	PRO	0	0.075	0.050	27.786	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	143	SER	0	-0.078	-0.052	25.060	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	144	ARG	1	0.863	0.920	26.684	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	145	SER	0	-0.008	-0.016	21.567	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	146	TYR	0	-0.075	-0.039	20.933	0.003	0.003	0.000	0.000	0.000	0.000
101	A	147	LEU	0	0.041	0.021	19.766	0.004	0.004	0.000	0.000	0.000	0.000
102	A	148	PHE	0	-0.039	-0.020	18.569	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	149	SER	0	-0.004	0.009	18.600	0.011	0.011	0.000	0.000	0.000	0.000
104	A	150	LEU	0	-0.020	-0.031	13.916	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	151	PRO	0	-0.052	-0.011	18.091	0.009	0.009	0.000	0.000	0.000	0.000
106	A	152	VAL	0	0.012	0.013	18.653	0.015	0.015	0.000	0.000	0.000	0.000
107	A	153	ASP	-1	-0.814	-0.899	20.303	0.074	0.074	0.000	0.000	0.000	0.000
108	A	154	GLY	0	-0.030	-0.010	20.549	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	155	LYS	1	0.872	0.938	19.036	-0.052	-0.052	0.000	0.000	0.000	0.000
110	A	156	PRO	0	-0.017	0.001	14.315	0.015	0.015	0.000	0.000	0.000	0.000
111	A	157	MET	0	0.027	0.022	13.881	-0.029	-0.029	0.000	0.000	0.000	0.000
112	A	158	THR	0	-0.092	-0.054	12.844	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	159	LEU	0	0.014	0.015	12.935	0.003	0.003	0.000	0.000	0.000	0.000
114	A	160	TYR	0	0.006	-0.003	14.322	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	161	VAL	0	0.009	0.003	16.214	0.023	0.023	0.000	0.000	0.000	0.000
116	A	162	ARG	1	0.909	0.983	18.212	0.056	0.056	0.000	0.000	0.000	0.000
117	A	163	MET	0	-0.004	-0.002	16.816	0.018	0.018	0.000	0.000	0.000	0.000
118	A	164	THR	0	0.011	0.005	22.205	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	165	SER	0	0.004	-0.046	25.455	0.008	0.008	0.000	0.000	0.000	0.000
120	A	166	ASN	0	0.046	0.057	27.732	0.000	0.000	0.000	0.000	0.000	0.000
121	A	167	HIS	0	0.017	0.010	28.622	0.000	0.000	0.000	0.000	0.000	0.000
122	A	168	PRO	0	-0.012	-0.022	26.148	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	169	LEU	0	0.002	0.018	21.812	0.004	0.004	0.000	0.000	0.000	0.000
124	A	170	MET	0	-0.023	-0.013	20.404	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	171	ALA	0	0.007	0.001	17.580	0.013	0.013	0.000	0.000	0.000	0.000
126	A	172	TRP	0	-0.005	0.006	15.495	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	173	PHE	0	-0.020	-0.016	10.738	0.001	0.001	0.000	0.000	0.000	0.000
128	A	174	ASP	-1	-0.800	-0.904	10.086	0.188	0.188	0.000	0.000	0.000	0.000
129	A	175	GLN	0	-0.108	-0.051	10.588	0.048	0.048	0.000	0.000	0.000	0.000
130	A	176	ILE	0	-0.027	0.003	12.429	0.032	0.032	0.000	0.000	0.000	0.000
131	A	177	ASP	-1	-0.826	-0.938	15.238	0.207	0.207	0.000	0.000	0.000	0.000
132	A	178	GLU	-1	-0.940	-0.990	17.393	0.091	0.091	0.000	0.000	0.000	0.000
133	A	179	ALA	0	0.071	0.037	19.338	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	180	GLY	0	-0.033	-0.013	18.237	-0.009	-0.009	0.000	0.000	0.000	0.000
135	A	181	LEU	0	-0.055	-0.035	19.233	-0.017	-0.017	0.000	0.000	0.000	0.000
136	A	182	VAL	0	-0.010	-0.013	21.659	-0.012	-0.012	0.000	0.000	0.000	0.000
137	A	183	GLY	0	-0.016	0.008	23.039	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	184	LEU	0	-0.114	-0.053	19.611	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	185	GLU	-2	-1.681	-1.802	23.653	0.046	0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:47:ACE )