FMO DATABASE

FMODB ID: 6N79Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1377338.305599
FMO2-HF: Nuclear repulsion	1319765.654069
FMO2-HF: Total energy	-57572.65153
FMO2-MP2: Total energy	-57742.132666

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.
-3.511	-1.851	-0.026	-0.794	-0.84	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 : -0.059 / 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	-0.814	-0.901	3.811	-4.852	-3.192	-0.026	-0.794	-0.840	0.002
4	A	27	PRO	0	-0.034	-0.019	6.857	0.574	0.574	0.000	0.000	0.000	0.000
5	A	28	ASN	0	-0.088	-0.046	8.728	0.446	0.446	0.000	0.000	0.000	0.000
6	A	29	TYR	0	-0.010	-0.005	11.633	0.116	0.116	0.000	0.000	0.000	0.000
7	A	30	THR	0	0.022	-0.008	14.679	0.008	0.008	0.000	0.000	0.000	0.000
8	A	31	GLU	-1	-0.857	-0.928	17.718	-0.248	-0.248	0.000	0.000	0.000	0.000
9	A	32	MET	0	-0.002	0.017	21.047	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	33	GLU	-1	-0.841	-0.931	15.783	-0.450	-0.450	0.000	0.000	0.000	0.000
11	A	34	GLY	0	-0.034	-0.028	18.935	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	35	LYS	1	0.847	0.915	19.681	0.228	0.228	0.000	0.000	0.000	0.000
13	A	36	VAL	0	0.036	0.016	21.740	0.016	0.016	0.000	0.000	0.000	0.000
14	A	37	ARG	1	0.871	0.963	13.957	0.662	0.662	0.000	0.000	0.000	0.000
15	A	38	GLU	-1	-0.862	-0.929	20.587	-0.280	-0.280	0.000	0.000	0.000	0.000
16	A	39	ALA	0	-0.049	-0.029	23.193	0.020	0.020	0.000	0.000	0.000	0.000
17	A	40	THR	0	-0.075	-0.053	22.867	0.015	0.015	0.000	0.000	0.000	0.000
18	A	41	ASN	0	0.067	0.045	22.473	0.009	0.009	0.000	0.000	0.000	0.000
19	A	42	ASN	0	-0.002	-0.016	23.308	0.030	0.030	0.000	0.000	0.000	0.000
20	A	43	GLU	-1	-0.861	-0.905	25.037	-0.209	-0.209	0.000	0.000	0.000	0.000
21	A	44	PRO	0	-0.049	-0.045	27.834	0.005	0.005	0.000	0.000	0.000	0.000
22	A	45	TRP	0	0.014	-0.006	29.995	0.010	0.010	0.000	0.000	0.000	0.000
23	A	46	GLY	0	-0.019	0.007	31.144	0.008	0.008	0.000	0.000	0.000	0.000
24	A	47	ALA	0	0.009	0.014	28.945	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	48	SER	0	0.041	0.014	30.579	0.011	0.011	0.000	0.000	0.000	0.000
26	A	49	SER	0	0.039	0.005	32.740	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	50	THR	0	0.052	0.017	33.347	0.001	0.001	0.000	0.000	0.000	0.000
28	A	51	LEU	0	-0.010	0.017	26.386	0.000	0.000	0.000	0.000	0.000	0.000
29	A	52	MET	0	0.003	-0.010	29.960	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	53	ASP	-1	-0.886	-0.929	31.536	-0.113	-0.113	0.000	0.000	0.000	0.000
31	A	54	GLN	0	0.073	0.048	29.297	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	55	ILE	0	0.000	-0.005	26.403	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	56	SER	0	-0.069	-0.058	28.773	0.007	0.007	0.000	0.000	0.000	0.000
34	A	57	GLN	0	-0.022	-0.008	31.441	0.006	0.006	0.000	0.000	0.000	0.000
35	A	58	GLY	0	0.088	0.051	27.592	0.007	0.007	0.000	0.000	0.000	0.000
36	A	59	THR	0	-0.067	-0.054	28.051	0.008	0.008	0.000	0.000	0.000	0.000
37	A	60	TYR	0	-0.064	-0.023	29.727	0.014	0.014	0.000	0.000	0.000	0.000
38	A	61	ASN	0	-0.076	-0.047	26.582	0.009	0.009	0.000	0.000	0.000	0.000
39	A	62	PHE	0	-0.007	-0.012	23.168	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	63	ARG	1	1.015	1.005	21.703	0.058	0.058	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.752	-0.858	22.571	-0.175	-0.175	0.000	0.000	0.000	0.000
42	A	65	ARG	1	0.866	0.948	23.907	0.071	0.071	0.000	0.000	0.000	0.000
43	A	66	GLU	-1	-0.943	-0.965	20.925	-0.094	-0.094	0.000	0.000	0.000	0.000
44	A	67	GLU	-1	-0.821	-0.899	18.520	-0.248	-0.248	0.000	0.000	0.000	0.000
45	A	68	ILE	0	-0.024	-0.019	20.704	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	69	LEU	0	-0.028	-0.014	23.455	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	70	SER	0	0.002	0.002	18.561	0.004	0.004	0.000	0.000	0.000	0.000
48	A	71	MET	0	-0.025	-0.010	17.071	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	72	ILE	0	0.000	-0.003	20.019	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	73	PHE	0	0.005	-0.012	22.788	0.001	0.001	0.000	0.000	0.000	0.000
51	A	74	ARG	1	0.892	0.938	15.779	0.330	0.330	0.000	0.000	0.000	0.000
52	A	75	ARG	1	0.820	0.904	16.605	0.387	0.387	0.000	0.000	0.000	0.000
53	A	76	PHE	0	-0.003	-0.017	21.598	0.007	0.007	0.000	0.000	0.000	0.000
54	A	77	THR	0	-0.018	-0.003	19.591	0.016	0.016	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.815	-0.869	15.519	-0.457	-0.457	0.000	0.000	0.000	0.000
56	A	79	LYS	1	0.770	0.880	18.371	0.313	0.313	0.000	0.000	0.000	0.000
57	A	80	ALA	0	0.040	0.016	21.903	0.024	0.024	0.000	0.000	0.000	0.000
58	A	81	GLY	0	0.026	0.016	24.943	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	82	SER	0	0.030	-0.002	25.499	0.006	0.006	0.000	0.000	0.000	0.000
60	A	83	GLU	-1	-0.831	-0.891	20.578	-0.291	-0.291	0.000	0.000	0.000	0.000
61	A	84	TRP	0	0.030	0.008	25.178	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	85	ARG	1	0.875	0.961	27.986	0.152	0.152	0.000	0.000	0.000	0.000
63	A	86	GLN	0	0.012	-0.004	20.657	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	87	ILE	0	0.008	0.011	25.236	0.000	0.000	0.000	0.000	0.000	0.000
65	A	88	TYR	0	-0.004	-0.014	26.970	0.009	0.009	0.000	0.000	0.000	0.000
66	A	89	LYS	1	0.796	0.898	26.786	0.224	0.224	0.000	0.000	0.000	0.000
67	A	90	ALA	0	0.019	0.012	25.321	0.004	0.004	0.000	0.000	0.000	0.000
68	A	91	LEU	0	-0.035	-0.014	27.368	0.010	0.010	0.000	0.000	0.000	0.000
69	A	92	GLN	0	-0.050	-0.027	30.779	0.003	0.003	0.000	0.000	0.000	0.000
70	A	93	LEU	0	0.013	0.015	26.432	0.008	0.008	0.000	0.000	0.000	0.000
71	A	94	LEU	0	0.032	0.014	28.917	0.008	0.008	0.000	0.000	0.000	0.000
72	A	95	ASP	-1	-0.788	-0.881	31.103	-0.088	-0.088	0.000	0.000	0.000	0.000
73	A	96	TYR	0	0.030	0.012	33.222	0.007	0.007	0.000	0.000	0.000	0.000
74	A	97	LEU	0	0.021	0.016	28.698	0.007	0.007	0.000	0.000	0.000	0.000
75	A	98	ILE	0	-0.031	-0.001	33.284	0.007	0.007	0.000	0.000	0.000	0.000
76	A	99	LYS	1	0.791	0.869	35.782	0.093	0.093	0.000	0.000	0.000	0.000
77	A	100	HIS	0	-0.032	-0.021	35.660	0.008	0.008	0.000	0.000	0.000	0.000
78	A	101	GLY	0	0.026	0.023	33.509	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	102	SER	0	-0.043	-0.037	32.103	0.009	0.009	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.787	-0.898	34.604	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	104	ARG	1	0.817	0.908	31.170	0.054	0.054	0.000	0.000	0.000	0.000
82	A	105	PHE	0	0.058	0.026	27.584	0.000	0.000	0.000	0.000	0.000	0.000
83	A	106	ILE	0	0.017	0.016	31.416	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	107	ASP	-1	-0.846	-0.909	34.139	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	108	ASP	-1	-0.864	-0.949	28.460	-0.074	-0.074	0.000	0.000	0.000	0.000
86	A	109	THR	0	-0.033	-0.027	29.808	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.783	0.863	30.856	0.055	0.055	0.000	0.000	0.000	0.000
88	A	111	ASN	0	-0.029	-0.006	30.519	0.005	0.005	0.000	0.000	0.000	0.000
89	A	112	SER	0	-0.002	0.020	27.586	0.002	0.002	0.000	0.000	0.000	0.000
90	A	113	ILE	0	0.018	0.002	29.556	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.010	-0.003	28.324	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	115	LEU	0	0.012	0.000	24.496	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	116	ILE	0	0.000	0.006	28.280	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	117	ARG	1	0.877	0.923	30.640	0.063	0.063	0.000	0.000	0.000	0.000
95	A	118	ILE	0	-0.006	0.015	27.644	0.003	0.003	0.000	0.000	0.000	0.000
96	A	119	LEU	0	-0.012	-0.008	27.277	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	120	GLU	-1	-0.817	-0.915	31.279	-0.069	-0.069	0.000	0.000	0.000	0.000
98	A	121	THR	0	-0.044	-0.015	33.854	0.003	0.003	0.000	0.000	0.000	0.000
99	A	122	PHE	0	0.005	0.024	27.462	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	123	HIS	0	-0.016	-0.035	31.774	0.008	0.008	0.000	0.000	0.000	0.000
101	A	124	TYR	0	0.018	-0.002	30.595	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	125	ILE	0	0.024	0.029	32.885	0.003	0.003	0.000	0.000	0.000	0.000
103	A	126	ASP	-1	-0.771	-0.872	33.402	-0.108	-0.108	0.000	0.000	0.000	0.000
104	A	127	SER	0	0.016	-0.006	33.478	0.003	0.003	0.000	0.000	0.000	0.000
105	A	128	GLN	0	-0.063	-0.039	35.384	0.000	0.000	0.000	0.000	0.000	0.000
106	A	129	GLY	0	0.017	0.019	38.211	0.005	0.005	0.000	0.000	0.000	0.000
107	A	130	ARG	1	0.872	0.942	36.685	0.102	0.102	0.000	0.000	0.000	0.000
108	A	131	ASP	-1	-0.762	-0.877	37.286	-0.094	-0.094	0.000	0.000	0.000	0.000
109	A	132	GLN	0	-0.031	-0.033	33.601	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	133	GLY	0	-0.003	-0.005	33.336	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	134	ILE	0	0.015	0.003	34.338	0.000	0.000	0.000	0.000	0.000	0.000
112	A	135	ASN	0	-0.039	-0.010	34.634	0.006	0.006	0.000	0.000	0.000	0.000
113	A	136	VAL	0	0.006	-0.003	30.621	0.000	0.000	0.000	0.000	0.000	0.000
114	A	137	ARG	1	0.846	0.927	33.542	0.089	0.089	0.000	0.000	0.000	0.000
115	A	138	THR	0	-0.007	-0.008	36.159	0.003	0.003	0.000	0.000	0.000	0.000
116	A	139	ARG	1	0.868	0.942	33.899	0.111	0.111	0.000	0.000	0.000	0.000
117	A	140	VAL	0	0.018	0.002	32.497	0.002	0.002	0.000	0.000	0.000	0.000
118	A	141	LYS	1	0.793	0.909	35.257	0.070	0.070	0.000	0.000	0.000	0.000
119	A	142	ALA	0	0.014	0.001	38.892	0.004	0.004	0.000	0.000	0.000	0.000
120	A	143	LEU	0	-0.006	0.001	32.485	0.003	0.003	0.000	0.000	0.000	0.000
121	A	144	ILE	0	-0.018	-0.012	35.070	0.003	0.003	0.000	0.000	0.000	0.000
122	A	145	GLU	-1	-0.799	-0.912	37.799	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	146	LEU	0	-0.065	-0.022	38.777	0.004	0.004	0.000	0.000	0.000	0.000
124	A	147	LEU	0	0.053	0.018	34.123	0.003	0.003	0.000	0.000	0.000	0.000
125	A	148	SER	0	-0.076	-0.022	38.620	0.004	0.004	0.000	0.000	0.000	0.000
126	A	149	ASP	-1	-0.802	-0.908	41.302	-0.044	-0.044	0.000	0.000	0.000	0.000
127	A	150	ASP	-1	-0.772	-0.876	42.143	-0.050	-0.050	0.000	0.000	0.000	0.000
128	A	151	ASN	0	-0.087	-0.048	44.048	0.000	0.000	0.000	0.000	0.000	0.000
129	A	152	LYS	1	0.898	0.965	43.585	0.058	0.058	0.000	0.000	0.000	0.000
130	A	153	ILE	0	0.012	0.012	39.340	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	154	ARG	1	0.935	0.966	42.639	0.041	0.041	0.000	0.000	0.000	0.000
132	A	155	ALA	0	-0.013	-0.009	45.049	0.000	0.000	0.000	0.000	0.000	0.000
133	A	156	GLU	-1	-0.823	-0.904	42.313	-0.070	-0.070	0.000	0.000	0.000	0.000
134	A	157	ARG	1	0.789	0.878	37.853	0.067	0.067	0.000	0.000	0.000	0.000
135	A	158	LYS	1	0.804	0.896	42.894	0.047	0.047	0.000	0.000	0.000	0.000
136	A	159	LYS	1	0.880	0.926	44.864	0.066	0.066	0.000	0.000	0.000	0.000
137	A	160	ALA	0	-0.016	-0.007	41.157	0.000	0.000	0.000	0.000	0.000	0.000
138	A	161	ARG	1	0.904	0.960	40.774	0.061	0.061	0.000	0.000	0.000	0.000
139	A	162	GLU	-1	-0.891	-0.916	44.702	-0.052	-0.052	0.000	0.000	0.000	0.000
140	A	163	THR	0	-0.030	-0.010	44.251	0.000	0.000	0.000	0.000	0.000	0.000

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