FMO DATABASE

FMODB ID: G59N1

Calculation Name: 3O48-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O48

Chain ID: A

ChEMBL ID:

UniProt ID: P40515

Base Structure: X-ray

Registration Date: 2023-09-24

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1193751.681221
FMO2-HF: Nuclear repulsion	1140418.818241
FMO2-HF: Total energy	-53332.86298
FMO2-MP2: Total energy	-53488.879767

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
-6.163	-2.302	0.47	-1.473	-2.858	0.004

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.949 / q_NPA : -0.973

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	7	TRP	0	0.035	0.007	2.800	-7.497	-3.825	0.471	-1.456	-2.688	0.004
4	A	8	PRO	0	0.023	0.026	5.630	-2.391	-2.391	0.000	0.000	0.000	0.000
5	A	9	THR	0	-0.007	0.015	9.360	-0.352	-0.352	0.000	0.000	0.000	0.000
6	A	10	LEU	0	0.047	0.009	12.173	-0.236	-0.236	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.915	0.952	14.958	-15.497	-15.497	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.766	-0.884	12.419	20.004	20.004	0.000	0.000	0.000	0.000
9	A	13	ALA	0	-0.029	-0.011	14.343	-0.281	-0.281	0.000	0.000	0.000	0.000
10	A	14	TYR	0	-0.048	-0.018	15.699	-0.871	-0.871	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.931	-0.956	17.797	14.967	14.967	0.000	0.000	0.000	0.000
12	A	16	PRO	0	-0.010	0.006	18.629	0.624	0.624	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.034	-0.012	17.449	0.184	0.184	0.000	0.000	0.000	0.000
14	A	18	TYR	0	-0.003	-0.010	21.202	-0.559	-0.559	0.000	0.000	0.000	0.000
15	A	19	PRO	0	0.070	0.025	24.089	0.348	0.348	0.000	0.000	0.000	0.000
16	A	20	GLN	0	0.055	0.013	26.066	0.351	0.351	0.000	0.000	0.000	0.000
17	A	21	GLN	0	0.007	0.007	21.378	0.081	0.081	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.034	0.026	20.789	0.512	0.512	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.758	-0.864	22.623	11.313	11.313	0.000	0.000	0.000	0.000
20	A	24	ILE	0	-0.024	-0.014	22.415	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.032	-0.014	17.736	0.271	0.271	0.000	0.000	0.000	0.000
22	A	26	ARG	1	0.841	0.906	21.090	-10.996	-10.996	0.000	0.000	0.000	0.000
23	A	27	GLN	0	-0.013	-0.021	23.460	0.004	0.004	0.000	0.000	0.000	0.000
24	A	28	GLN	0	-0.035	-0.004	19.795	-0.564	-0.564	0.000	0.000	0.000	0.000
25	A	29	VAL	0	0.000	0.015	19.424	0.058	0.058	0.000	0.000	0.000	0.000
26	A	30	VAL	0	-0.018	-0.016	21.907	-0.214	-0.214	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.089	-0.047	23.893	-0.272	-0.272	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.746	-0.830	19.264	16.456	16.456	0.000	0.000	0.000	0.000
29	A	33	GLY	0	0.053	0.032	23.504	0.126	0.126	0.000	0.000	0.000	0.000
30	A	34	GLY	0	-0.013	-0.022	23.581	-0.216	-0.216	0.000	0.000	0.000	0.000
31	A	35	PRO	0	-0.026	-0.019	21.959	0.696	0.696	0.000	0.000	0.000	0.000
32	A	36	THR	0	-0.053	-0.021	21.770	0.294	0.294	0.000	0.000	0.000	0.000
33	A	37	ALA	0	0.008	0.032	19.977	0.168	0.168	0.000	0.000	0.000	0.000
34	A	38	THR	0	-0.014	-0.039	15.553	1.132	1.132	0.000	0.000	0.000	0.000
35	A	39	ILE	0	0.016	-0.002	11.546	0.093	0.093	0.000	0.000	0.000	0.000
36	A	40	GLN	0	-0.040	-0.028	9.542	2.098	2.098	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.016	-0.034	12.753	0.435	0.435	0.000	0.000	0.000	0.000
38	A	42	ARG	1	0.830	0.917	16.229	-17.211	-17.211	0.000	0.000	0.000	0.000
39	A	43	PHE	0	0.007	-0.001	8.579	-0.810	-0.810	0.000	0.000	0.000	0.000
40	A	44	ASN	0	0.020	0.004	12.639	1.208	1.208	0.000	0.000	0.000	0.000
41	A	45	TYR	0	0.006	0.011	14.508	-0.703	-0.703	0.000	0.000	0.000	0.000
42	A	46	ALA	0	0.030	0.015	15.390	-0.603	-0.603	0.000	0.000	0.000	0.000
43	A	47	TRP	0	0.048	0.009	11.867	-0.571	-0.571	0.000	0.000	0.000	0.000
44	A	48	GLY	0	-0.013	-0.019	14.753	-0.467	-0.467	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.048	-0.021	17.665	-0.600	-0.600	0.000	0.000	0.000	0.000
46	A	50	ILE	0	-0.009	0.005	15.194	-0.447	-0.447	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.909	0.969	14.292	-19.006	-19.006	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.066	-0.014	18.422	-0.626	-0.626	0.000	0.000	0.000	0.000
49	A	53	THR	0	0.026	0.003	22.133	0.109	0.109	0.000	0.000	0.000	0.000
50	A	54	ASP	-1	-0.869	-0.921	24.764	10.338	10.338	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.095	0.029	25.032	0.333	0.333	0.000	0.000	0.000	0.000
52	A	56	ASN	0	-0.059	-0.030	25.469	0.297	0.297	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.876	-0.938	23.385	12.099	12.099	0.000	0.000	0.000	0.000
54	A	58	GLU	-1	-0.897	-0.955	21.083	13.681	13.681	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.917	0.957	21.064	-10.852	-10.852	0.000	0.000	0.000	0.000
56	A	60	LEU	0	-0.039	-0.015	22.764	0.273	0.273	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.046	0.010	19.252	0.368	0.368	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.042	0.024	17.980	0.997	0.997	0.000	0.000	0.000	0.000
59	A	63	LYS	1	0.933	0.987	19.057	-11.241	-11.241	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.019	0.013	17.821	0.211	0.211	0.000	0.000	0.000	0.000
61	A	65	LEU	0	0.011	-0.001	12.368	0.585	0.585	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.058	-0.049	15.590	0.982	0.982	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.946	-0.968	17.956	14.202	14.202	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.029	-0.013	13.561	0.342	0.342	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.020	-0.011	12.011	0.393	0.393	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.860	0.914	14.238	-14.146	-14.146	0.000	0.000	0.000	0.000
67	A	71	GLU	-1	-0.823	-0.897	16.352	15.867	15.867	0.000	0.000	0.000	0.000
68	A	72	ALA	0	-0.014	0.005	10.652	0.456	0.456	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.937	-0.970	11.121	21.984	21.984	0.000	0.000	0.000	0.000
70	A	74	SER	0	-0.016	-0.021	8.092	0.825	0.825	0.000	0.000	0.000	0.000
71	A	75	ARG	1	0.966	0.991	6.090	-26.756	-26.756	0.000	0.000	0.000	0.000
72	A	76	ARG	1	0.911	0.966	7.309	-21.512	-21.512	0.000	0.000	0.000	0.000
73	A	77	ARG	1	0.975	0.982	5.873	-34.597	-34.597	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.873	-0.926	4.493	43.801	43.990	-0.001	-0.017	-0.170	0.000
75	A	79	CYS	0	-0.010	-0.015	6.318	-4.989	-4.989	0.000	0.000	0.000	0.000
76	A	80	LEU	0	0.004	0.015	9.770	-2.336	-2.336	0.000	0.000	0.000	0.000
77	A	81	TYR	0	-0.047	-0.021	7.501	-2.546	-2.546	0.000	0.000	0.000	0.000
78	A	82	TYR	0	0.025	-0.004	6.360	-3.606	-3.606	0.000	0.000	0.000	0.000
79	A	83	LEU	0	0.006	-0.003	11.011	-1.806	-1.806	0.000	0.000	0.000	0.000
80	A	84	THR	0	-0.058	-0.023	12.792	-1.824	-1.824	0.000	0.000	0.000	0.000
81	A	85	ILE	0	-0.024	-0.009	11.282	-1.412	-1.412	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.034	0.011	14.803	-1.076	-1.076	0.000	0.000	0.000	0.000
83	A	87	CYS	0	-0.036	-0.022	17.057	-0.698	-0.698	0.000	0.000	0.000	0.000
84	A	88	TYR	0	-0.038	-0.023	17.737	-0.998	-0.998	0.000	0.000	0.000	0.000
85	A	89	LYS	1	0.754	0.865	17.882	-15.271	-15.271	0.000	0.000	0.000	0.000
86	A	90	LEU	0	-0.012	0.010	20.742	-0.666	-0.666	0.000	0.000	0.000	0.000
87	A	91	GLY	0	-0.013	0.002	22.843	-0.573	-0.573	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.918	-0.956	22.105	12.603	12.603	0.000	0.000	0.000	0.000
89	A	93	TYR	0	0.047	0.002	21.703	0.505	0.505	0.000	0.000	0.000	0.000
90	A	94	SER	0	0.036	0.019	21.719	0.546	0.546	0.000	0.000	0.000	0.000
91	A	95	MET	0	-0.022	-0.013	20.167	0.075	0.075	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.036	0.017	17.607	0.752	0.752	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.926	0.963	17.000	-12.448	-12.448	0.000	0.000	0.000	0.000
94	A	98	ARG	1	0.945	0.970	18.083	-12.396	-12.396	0.000	0.000	0.000	0.000
95	A	99	TYR	0	0.013	0.001	14.314	0.418	0.418	0.000	0.000	0.000	0.000
96	A	100	VAL	0	0.039	0.017	12.646	1.350	1.350	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.837	-0.920	13.614	16.126	16.126	0.000	0.000	0.000	0.000
98	A	102	THR	0	-0.061	-0.031	13.610	0.119	0.119	0.000	0.000	0.000	0.000
99	A	103	LEU	0	-0.056	-0.026	7.130	0.731	0.731	0.000	0.000	0.000	0.000
100	A	104	PHE	0	0.010	-0.008	10.463	1.293	1.293	0.000	0.000	0.000	0.000
101	A	105	GLU	-1	-0.947	-0.967	12.549	16.944	16.944	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.100	-0.060	9.782	0.474	0.474	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.892	-0.955	5.517	41.692	41.692	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.952	0.987	9.118	-18.630	-18.630	0.000	0.000	0.000	0.000
105	A	109	ASN	0	-0.012	-0.005	10.612	-1.590	-1.590	0.000	0.000	0.000	0.000
106	A	110	ASN	0	0.022	0.031	4.802	-2.302	-2.302	0.000	0.000	0.000	0.000
107	A	111	LYS	1	0.995	0.984	8.551	-20.014	-20.014	0.000	0.000	0.000	0.000
108	A	112	GLN	0	-0.007	-0.009	6.585	0.967	0.967	0.000	0.000	0.000	0.000
109	A	113	VAL	0	0.052	0.026	7.578	-1.482	-1.482	0.000	0.000	0.000	0.000
110	A	114	GLY	0	0.011	0.012	10.299	-1.573	-1.573	0.000	0.000	0.000	0.000
111	A	115	ALA	0	-0.031	-0.020	12.927	-1.284	-1.284	0.000	0.000	0.000	0.000
112	A	116	LEU	0	-0.005	0.000	11.645	-1.160	-1.160	0.000	0.000	0.000	0.000
113	A	117	LYS	1	0.906	0.947	14.165	-16.615	-16.615	0.000	0.000	0.000	0.000
114	A	118	SER	0	0.032	0.019	15.984	-0.922	-0.922	0.000	0.000	0.000	0.000
115	A	119	MET	0	-0.022	0.003	17.676	-0.797	-0.797	0.000	0.000	0.000	0.000
116	A	120	VAL	0	-0.028	-0.023	16.925	-0.724	-0.724	0.000	0.000	0.000	0.000
117	A	121	GLU	-1	-0.896	-0.954	19.728	13.498	13.498	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.887	-0.936	22.016	12.139	12.139	0.000	0.000	0.000	0.000
119	A	123	LYS	1	0.844	0.921	23.235	-12.258	-12.258	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.013	-0.002	23.049	-0.381	-0.381	0.000	0.000	0.000	0.000
121	A	125	GLN	0	0.011	0.007	25.724	-0.232	-0.232	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.890	0.933	27.721	-10.791	-10.791	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.881	-0.911	29.063	9.794	9.794	0.000	0.000	0.000	0.000
124	A	128	GLU	-1	-0.881	-0.942	30.007	9.034	9.034	0.000	0.000	0.000	0.000
125	A	129	ASN	0	-0.014	-0.012	31.734	-0.247	-0.247	0.000	0.000	0.000	0.000
126	A	130	LEU	0	-0.042	-0.019	33.831	-0.324	-0.324	0.000	0.000	0.000	0.000
127	A	131	TYR	0	-0.115	-0.075	32.392	-0.399	-0.399	0.000	0.000	0.000	0.000
128	A	132	PHE	0	-0.042	-0.010	34.835	-0.229	-0.229	0.000	0.000	0.000	0.000
129	A	133	GLN	0	-0.081	-0.023	37.495	-0.078	-0.078	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)