FMO DATABASE

FMODB ID: 2JR6R

Calculation Name: 3ONL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ONL

Chain ID: A

ChEMBL ID:

UniProt ID: P47160

Base Structure: X-ray

Registration Date: 2023-06-22

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1375268.449
FMO2-HF: Nuclear repulsion	1317696.640224
FMO2-HF: Total energy	-57571.808776
FMO2-MP2: Total energy	-57741.220619

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:24:SER)

Summations of interaction energy for fragment #1(A:24:SER)

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.
-3.793	-2.146	-0.026	-0.793	-0.829	0.002

Interaction energy analysis for fragmet #1(A:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.060 / q_NPA : -0.044

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	26	ASP	-1	-0.819	-0.904	3.811	-4.989	-3.342	-0.026	-0.793	-0.829	0.002
4	A	27	PRO	0	-0.054	-0.031	6.846	0.577	0.577	0.000	0.000	0.000	0.000
5	A	28	ASN	0	-0.040	-0.016	9.052	0.260	0.260	0.000	0.000	0.000	0.000
6	A	29	TYR	0	-0.044	-0.024	11.635	0.106	0.106	0.000	0.000	0.000	0.000
7	A	30	THR	0	0.036	-0.001	14.674	0.004	0.004	0.000	0.000	0.000	0.000
8	A	31	GLU	-1	-0.913	-0.959	17.721	-0.250	-0.250	0.000	0.000	0.000	0.000
9	A	32	MET	0	0.000	0.012	21.045	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	33	GLU	-1	-0.814	-0.916	15.852	-0.444	-0.444	0.000	0.000	0.000	0.000
11	A	34	GLY	0	-0.027	-0.025	18.946	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	35	LYS	1	0.898	0.943	19.690	0.231	0.231	0.000	0.000	0.000	0.000
13	A	36	VAL	0	0.043	0.021	21.762	0.016	0.016	0.000	0.000	0.000	0.000
14	A	37	ARG	1	0.870	0.951	14.454	0.687	0.687	0.000	0.000	0.000	0.000
15	A	38	GLU	-1	-0.937	-0.960	20.614	-0.285	-0.285	0.000	0.000	0.000	0.000
16	A	39	ALA	0	-0.034	-0.025	23.207	0.019	0.019	0.000	0.000	0.000	0.000
17	A	40	THR	0	-0.072	-0.043	22.896	0.014	0.014	0.000	0.000	0.000	0.000
18	A	41	ASN	0	0.100	0.048	22.505	0.008	0.008	0.000	0.000	0.000	0.000
19	A	42	ASN	0	0.014	-0.010	23.325	0.031	0.031	0.000	0.000	0.000	0.000
20	A	43	GLU	-1	-0.894	-0.921	25.063	-0.220	-0.220	0.000	0.000	0.000	0.000
21	A	44	PRO	0	-0.027	-0.046	27.850	0.004	0.004	0.000	0.000	0.000	0.000
22	A	45	TRP	0	0.007	-0.002	30.085	0.009	0.009	0.000	0.000	0.000	0.000
23	A	46	GLY	0	-0.023	0.006	31.163	0.008	0.008	0.000	0.000	0.000	0.000
24	A	47	ALA	0	0.010	0.015	28.950	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	48	SER	0	0.041	0.015	30.598	0.013	0.013	0.000	0.000	0.000	0.000
26	A	49	SER	0	0.038	0.002	32.756	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	50	THR	0	0.065	0.029	32.790	0.002	0.002	0.000	0.000	0.000	0.000
28	A	51	LEU	0	-0.016	0.013	26.432	0.000	0.000	0.000	0.000	0.000	0.000
29	A	52	MET	0	-0.012	-0.020	29.977	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	53	ASP	-1	-0.877	-0.926	31.560	-0.114	-0.114	0.000	0.000	0.000	0.000
31	A	54	GLN	0	0.060	0.053	29.445	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	55	ILE	0	0.000	-0.003	26.322	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	56	SER	0	-0.070	-0.077	28.766	0.007	0.007	0.000	0.000	0.000	0.000
34	A	57	GLN	0	0.008	0.014	31.354	0.007	0.007	0.000	0.000	0.000	0.000
35	A	58	GLY	0	0.082	0.051	27.591	0.007	0.007	0.000	0.000	0.000	0.000
36	A	59	THR	0	-0.053	-0.040	28.057	0.009	0.009	0.000	0.000	0.000	0.000
37	A	60	TYR	0	-0.049	-0.008	29.730	0.015	0.015	0.000	0.000	0.000	0.000
38	A	61	ASN	0	-0.077	-0.044	26.533	0.009	0.009	0.000	0.000	0.000	0.000
39	A	62	PHE	0	-0.013	-0.014	23.511	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	63	ARG	1	1.029	1.010	21.681	0.058	0.058	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.760	-0.861	22.582	-0.176	-0.176	0.000	0.000	0.000	0.000
42	A	65	ARG	1	0.885	0.944	23.911	0.074	0.074	0.000	0.000	0.000	0.000
43	A	66	GLU	-1	-0.957	-0.974	21.030	-0.109	-0.109	0.000	0.000	0.000	0.000
44	A	67	GLU	-1	-0.834	-0.905	18.383	-0.253	-0.253	0.000	0.000	0.000	0.000
45	A	68	ILE	0	-0.043	-0.029	20.706	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	69	LEU	0	-0.017	-0.009	23.445	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	70	SER	0	0.022	0.014	18.562	0.002	0.002	0.000	0.000	0.000	0.000
48	A	71	MET	0	-0.038	-0.015	16.782	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	72	ILE	0	-0.010	-0.006	20.004	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	73	PHE	0	0.005	-0.016	22.731	0.000	0.000	0.000	0.000	0.000	0.000
51	A	74	ARG	1	0.873	0.921	15.639	0.329	0.329	0.000	0.000	0.000	0.000
52	A	75	ARG	1	0.898	0.959	17.197	0.393	0.393	0.000	0.000	0.000	0.000
53	A	76	PHE	0	-0.017	-0.015	21.666	0.006	0.006	0.000	0.000	0.000	0.000
54	A	77	THR	0	-0.010	-0.002	19.509	0.019	0.019	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.905	-0.927	15.508	-0.487	-0.487	0.000	0.000	0.000	0.000
56	A	79	LYS	1	0.871	0.958	17.724	0.380	0.380	0.000	0.000	0.000	0.000
57	A	80	ALA	0	0.049	0.015	21.972	0.024	0.024	0.000	0.000	0.000	0.000
58	A	81	GLY	0	0.030	0.020	25.005	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	82	SER	0	0.019	-0.006	25.568	0.006	0.006	0.000	0.000	0.000	0.000
60	A	83	GLU	-1	-0.915	-0.950	20.854	-0.291	-0.291	0.000	0.000	0.000	0.000
61	A	84	TRP	0	0.002	0.001	25.227	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	85	ARG	1	0.942	0.995	28.042	0.160	0.160	0.000	0.000	0.000	0.000
63	A	86	GLN	0	0.030	0.016	20.471	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	87	ILE	0	0.009	0.018	25.349	0.000	0.000	0.000	0.000	0.000	0.000
65	A	88	TYR	0	-0.005	-0.017	27.030	0.012	0.012	0.000	0.000	0.000	0.000
66	A	89	LYS	1	0.778	0.878	26.831	0.231	0.231	0.000	0.000	0.000	0.000
67	A	90	ALA	0	0.025	0.018	25.411	0.004	0.004	0.000	0.000	0.000	0.000
68	A	91	LEU	0	-0.027	-0.014	27.422	0.010	0.010	0.000	0.000	0.000	0.000
69	A	92	GLN	0	-0.072	-0.036	30.838	0.003	0.003	0.000	0.000	0.000	0.000
70	A	93	LEU	0	0.018	0.021	26.472	0.008	0.008	0.000	0.000	0.000	0.000
71	A	94	LEU	0	0.023	0.008	28.794	0.008	0.008	0.000	0.000	0.000	0.000
72	A	95	ASP	-1	-0.859	-0.943	31.086	-0.090	-0.090	0.000	0.000	0.000	0.000
73	A	96	TYR	0	0.017	0.006	33.256	0.006	0.006	0.000	0.000	0.000	0.000
74	A	97	LEU	0	0.023	0.012	28.739	0.007	0.007	0.000	0.000	0.000	0.000
75	A	98	ILE	0	-0.039	-0.003	33.274	0.007	0.007	0.000	0.000	0.000	0.000
76	A	99	LYS	1	0.829	0.913	35.772	0.096	0.096	0.000	0.000	0.000	0.000
77	A	100	HIS	0	-0.015	-0.004	35.668	0.008	0.008	0.000	0.000	0.000	0.000
78	A	101	GLY	0	0.023	0.021	33.506	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	102	SER	0	-0.068	-0.055	32.049	0.009	0.009	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.898	-0.969	34.606	-0.055	-0.055	0.000	0.000	0.000	0.000
81	A	104	ARG	1	0.957	0.984	31.136	0.052	0.052	0.000	0.000	0.000	0.000
82	A	105	PHE	0	0.052	0.019	27.439	0.000	0.000	0.000	0.000	0.000	0.000
83	A	106	ILE	0	0.016	0.018	31.415	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	107	ASP	-1	-0.928	-0.964	34.135	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	108	ASP	-1	-0.925	-0.968	28.460	-0.077	-0.077	0.000	0.000	0.000	0.000
86	A	109	THR	0	-0.058	-0.046	29.806	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.853	0.903	30.850	0.057	0.057	0.000	0.000	0.000	0.000
88	A	111	ASN	0	-0.026	-0.003	30.369	0.004	0.004	0.000	0.000	0.000	0.000
89	A	112	SER	0	0.000	0.018	27.475	0.001	0.001	0.000	0.000	0.000	0.000
90	A	113	ILE	0	0.005	0.002	29.548	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	114	ASN	0	0.003	0.000	28.647	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	115	LEU	0	-0.004	-0.010	24.535	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	116	ILE	0	0.019	0.017	28.263	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	117	ARG	1	0.941	0.962	30.620	0.065	0.065	0.000	0.000	0.000	0.000
95	A	118	ILE	0	0.000	0.015	27.748	0.003	0.003	0.000	0.000	0.000	0.000
96	A	119	LEU	0	-0.014	-0.011	27.336	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.855	-0.930	31.363	-0.071	-0.071	0.000	0.000	0.000	0.000
98	A	121	THR	0	-0.056	-0.020	33.940	0.003	0.003	0.000	0.000	0.000	0.000
99	A	122	PHE	0	0.015	0.017	27.280	0.000	0.000	0.000	0.000	0.000	0.000
100	A	123	HIS	0	-0.013	-0.016	31.853	0.008	0.008	0.000	0.000	0.000	0.000
101	A	124	TYR	0	0.018	-0.002	30.223	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	125	ILE	0	0.026	0.035	32.950	0.003	0.003	0.000	0.000	0.000	0.000
103	A	126	ASP	-1	-0.787	-0.889	33.444	-0.113	-0.113	0.000	0.000	0.000	0.000
104	A	127	SER	0	0.014	-0.010	33.522	0.003	0.003	0.000	0.000	0.000	0.000
105	A	128	GLN	0	-0.080	-0.053	35.424	0.000	0.000	0.000	0.000	0.000	0.000
106	A	129	GLY	0	0.024	0.026	38.249	0.005	0.005	0.000	0.000	0.000	0.000
107	A	130	ARG	1	0.899	0.962	37.248	0.107	0.107	0.000	0.000	0.000	0.000
108	A	131	ASP	-1	-0.808	-0.917	37.424	-0.097	-0.097	0.000	0.000	0.000	0.000
109	A	132	GLN	0	-0.024	-0.029	33.638	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	133	GLY	0	-0.017	-0.008	33.398	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	134	ILE	0	0.015	0.006	34.403	0.000	0.000	0.000	0.000	0.000	0.000
112	A	135	ASN	0	-0.025	-0.011	34.702	0.008	0.008	0.000	0.000	0.000	0.000
113	A	136	VAL	0	-0.017	-0.006	30.680	0.000	0.000	0.000	0.000	0.000	0.000
114	A	137	ARG	1	0.890	0.944	33.608	0.093	0.093	0.000	0.000	0.000	0.000
115	A	138	THR	0	-0.007	0.002	36.231	0.003	0.003	0.000	0.000	0.000	0.000
116	A	139	ARG	1	0.940	0.982	33.755	0.117	0.117	0.000	0.000	0.000	0.000
117	A	140	VAL	0	0.021	0.004	32.640	0.002	0.002	0.000	0.000	0.000	0.000
118	A	141	LYS	1	0.826	0.922	35.331	0.072	0.072	0.000	0.000	0.000	0.000
119	A	142	ALA	0	0.022	0.002	38.968	0.004	0.004	0.000	0.000	0.000	0.000
120	A	143	LEU	0	0.002	0.006	32.567	0.003	0.003	0.000	0.000	0.000	0.000
121	A	144	ILE	0	-0.023	-0.019	35.264	0.003	0.003	0.000	0.000	0.000	0.000
122	A	145	GLU	-1	-0.880	-0.951	37.781	-0.060	-0.060	0.000	0.000	0.000	0.000
123	A	146	LEU	0	-0.070	-0.038	38.440	0.004	0.004	0.000	0.000	0.000	0.000
124	A	147	LEU	0	0.038	0.007	34.123	0.003	0.003	0.000	0.000	0.000	0.000
125	A	148	SER	0	-0.093	-0.025	38.609	0.004	0.004	0.000	0.000	0.000	0.000
126	A	149	ASP	-1	-0.819	-0.923	41.292	-0.045	-0.045	0.000	0.000	0.000	0.000
127	A	150	ASP	-1	-0.803	-0.890	42.106	-0.051	-0.051	0.000	0.000	0.000	0.000
128	A	151	ASN	0	-0.080	-0.044	44.042	0.000	0.000	0.000	0.000	0.000	0.000
129	A	152	LYS	1	0.928	0.989	44.040	0.059	0.059	0.000	0.000	0.000	0.000
130	A	153	ILE	0	0.027	0.017	39.226	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	154	ARG	1	0.934	0.967	42.630	0.042	0.042	0.000	0.000	0.000	0.000
132	A	155	ALA	0	-0.029	-0.021	45.044	0.000	0.000	0.000	0.000	0.000	0.000
133	A	156	GLU	-1	-0.830	-0.911	42.311	-0.073	-0.073	0.000	0.000	0.000	0.000
134	A	157	ARG	1	0.886	0.944	37.912	0.068	0.068	0.000	0.000	0.000	0.000
135	A	158	LYS	1	0.882	0.943	42.887	0.045	0.045	0.000	0.000	0.000	0.000
136	A	159	LYS	1	0.909	0.954	45.108	0.067	0.067	0.000	0.000	0.000	0.000
137	A	160	ALA	0	-0.032	-0.026	41.158	0.000	0.000	0.000	0.000	0.000	0.000
138	A	161	ARG	1	0.895	0.955	41.230	0.062	0.062	0.000	0.000	0.000	0.000
139	A	162	GLU	-1	-0.947	-0.958	44.695	-0.055	-0.055	0.000	0.000	0.000	0.000
140	A	163	THR	0	-0.038	-0.012	44.407	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:24:SER)