FMO DATABASE

FMODB ID: 17LMZ

Calculation Name: 3EGN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EGN

Chain ID: A

ChEMBL ID:

UniProt ID: Q96LT9

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptAll
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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1053394.438857
FMO2-HF: Nuclear repulsion	1003889.511785
FMO2-HF: Total energy	-49504.927072
FMO2-MP2: Total energy	-49646.545995

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:387:GLU)

Summations of interaction energy for fragment #1(A:387:GLU)

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.
-147.536	-142.947	0.227	-2.274	-2.543	0.016

Interaction energy analysis for fragmet #1(A:387:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.881 / q_NPA : -0.956

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	389	ILE	0	-0.011	0.036	3.881	3.973	6.025	-0.018	-1.032	-1.002	0.002
4	A	390	SER	0	0.045	0.020	6.807	-4.291	-4.291	0.000	0.000	0.000	0.000
5	A	391	ARG	1	0.840	0.871	8.088	-21.295	-21.295	0.000	0.000	0.000	0.000
6	A	392	ARG	1	0.977	0.985	11.422	-22.326	-22.326	0.000	0.000	0.000	0.000
7	A	393	GLU	-1	-0.787	-0.862	8.576	30.126	30.126	0.000	0.000	0.000	0.000
8	A	394	LEU	0	0.039	0.018	11.202	-1.686	-1.686	0.000	0.000	0.000	0.000
9	A	395	GLU	-1	-0.834	-0.894	12.830	15.863	15.863	0.000	0.000	0.000	0.000
10	A	396	LYS	1	0.916	0.946	14.677	-17.508	-17.508	0.000	0.000	0.000	0.000
11	A	397	GLY	0	0.055	0.044	14.940	-0.701	-0.701	0.000	0.000	0.000	0.000
12	A	398	ARG	1	0.796	0.905	15.922	-17.622	-17.622	0.000	0.000	0.000	0.000
13	A	399	ILE	0	-0.019	0.009	18.587	-0.225	-0.225	0.000	0.000	0.000	0.000
14	A	400	SER	0	-0.034	-0.041	22.102	0.219	0.219	0.000	0.000	0.000	0.000
15	A	401	ARG	1	0.865	0.896	24.993	-10.050	-10.050	0.000	0.000	0.000	0.000
16	A	402	GLU	-1	-0.792	-0.880	27.543	10.808	10.808	0.000	0.000	0.000	0.000
17	A	403	GLU	-1	-0.873	-0.933	25.221	11.232	11.232	0.000	0.000	0.000	0.000
18	A	404	MET	0	-0.048	-0.024	23.129	-0.265	-0.265	0.000	0.000	0.000	0.000
19	A	405	GLU	-1	-0.847	-0.897	27.350	9.654	9.654	0.000	0.000	0.000	0.000
20	A	406	THR	0	-0.039	-0.011	30.200	-0.371	-0.371	0.000	0.000	0.000	0.000
21	A	407	LEU	0	0.000	0.009	25.376	-0.162	-0.162	0.000	0.000	0.000	0.000
22	A	408	SER	0	-0.002	-0.027	29.516	-0.107	-0.107	0.000	0.000	0.000	0.000
23	A	409	VAL	0	-0.098	-0.044	25.383	-0.176	-0.176	0.000	0.000	0.000	0.000
24	A	410	PHE	0	0.016	0.000	22.315	0.280	0.280	0.000	0.000	0.000	0.000
25	A	411	ARG	1	0.877	0.941	28.365	-9.312	-9.312	0.000	0.000	0.000	0.000
26	A	412	SER	0	-0.013	-0.010	31.855	0.037	0.037	0.000	0.000	0.000	0.000
27	A	413	TYR	0	-0.052	-0.031	23.662	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	414	GLU	-1	-0.880	-0.933	29.208	9.164	9.164	0.000	0.000	0.000	0.000
29	A	415	PRO	0	-0.027	-0.017	25.944	0.297	0.297	0.000	0.000	0.000	0.000
30	A	416	GLY	0	0.034	0.030	26.137	0.362	0.362	0.000	0.000	0.000	0.000
31	A	417	GLU	-1	-0.936	-0.971	28.615	9.776	9.776	0.000	0.000	0.000	0.000
32	A	418	PRO	0	-0.023	-0.026	25.481	0.372	0.372	0.000	0.000	0.000	0.000
33	A	419	ASN	0	0.033	0.016	23.915	0.075	0.075	0.000	0.000	0.000	0.000
34	A	420	CYS	0	0.002	-0.005	19.933	0.337	0.337	0.000	0.000	0.000	0.000
35	A	421	ARG	1	0.858	0.947	18.986	-11.623	-11.623	0.000	0.000	0.000	0.000
36	A	422	ILE	0	0.018	0.005	15.851	-0.449	-0.449	0.000	0.000	0.000	0.000
37	A	423	TYR	0	-0.061	-0.054	20.304	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	424	VAL	0	0.020	0.016	16.831	0.143	0.143	0.000	0.000	0.000	0.000
39	A	425	LYS	1	0.908	0.953	20.154	-11.720	-11.720	0.000	0.000	0.000	0.000
40	A	426	ASN	0	-0.004	-0.012	21.234	-0.106	-0.106	0.000	0.000	0.000	0.000
41	A	427	LEU	0	0.011	0.027	16.501	0.380	0.380	0.000	0.000	0.000	0.000
42	A	428	ALA	0	0.033	0.011	18.236	-0.845	-0.845	0.000	0.000	0.000	0.000
43	A	429	LYS	1	0.934	0.957	19.064	-12.565	-12.565	0.000	0.000	0.000	0.000
44	A	430	HIS	0	0.014	0.003	16.774	-0.857	-0.857	0.000	0.000	0.000	0.000
45	A	431	VAL	0	-0.007	0.013	13.814	0.783	0.783	0.000	0.000	0.000	0.000
46	A	432	GLN	0	-0.029	-0.020	12.511	-0.150	-0.150	0.000	0.000	0.000	0.000
47	A	433	GLU	-1	-0.876	-0.954	10.738	24.506	24.506	0.000	0.000	0.000	0.000
48	A	434	LYS	1	0.923	0.949	7.417	-23.323	-23.323	0.000	0.000	0.000	0.000
49	A	435	ASP	-1	-0.779	-0.885	7.449	27.351	27.351	0.000	0.000	0.000	0.000
50	A	436	LEU	0	0.001	-0.006	9.231	0.849	0.849	0.000	0.000	0.000	0.000
51	A	437	LYS	1	0.946	0.988	2.996	-56.095	-54.222	0.217	-1.057	-1.034	0.013
52	A	438	TYR	0	-0.043	-0.025	3.184	1.711	2.375	0.028	-0.185	-0.507	0.001
53	A	439	ILE	0	0.008	0.001	6.016	1.513	1.513	0.000	0.000	0.000	0.000
54	A	440	PHE	0	-0.003	-0.031	9.181	-0.485	-0.485	0.000	0.000	0.000	0.000
55	A	441	GLY	0	0.059	0.017	6.810	-1.536	-1.536	0.000	0.000	0.000	0.000
56	A	442	ARG	1	0.760	0.866	7.394	-27.168	-27.168	0.000	0.000	0.000	0.000
57	A	443	TYR	0	-0.104	-0.075	8.374	-1.071	-1.071	0.000	0.000	0.000	0.000
58	A	444	VAL	0	0.007	0.001	8.460	-2.415	-2.415	0.000	0.000	0.000	0.000
59	A	445	ASP	-1	-0.830	-0.880	8.199	24.399	24.399	0.000	0.000	0.000	0.000
60	A	446	PHE	0	-0.012	-0.027	5.344	-0.901	-0.901	0.000	0.000	0.000	0.000
61	A	447	SER	0	-0.030	-0.023	8.217	-0.941	-0.941	0.000	0.000	0.000	0.000
62	A	448	SER	0	0.017	0.011	10.801	-1.505	-1.505	0.000	0.000	0.000	0.000
63	A	449	GLU	-1	-0.786	-0.886	13.208	16.650	16.650	0.000	0.000	0.000	0.000
64	A	450	THR	0	-0.012	-0.012	15.495	0.092	0.092	0.000	0.000	0.000	0.000
65	A	451	GLN	0	0.011	-0.001	12.796	0.597	0.597	0.000	0.000	0.000	0.000
66	A	452	ARG	1	0.808	0.889	9.692	-19.133	-19.133	0.000	0.000	0.000	0.000
67	A	453	ILE	0	-0.001	0.006	12.617	-0.039	-0.039	0.000	0.000	0.000	0.000
68	A	454	MET	0	-0.073	-0.026	15.686	-0.838	-0.838	0.000	0.000	0.000	0.000
69	A	455	PHE	0	-0.044	-0.008	9.341	0.432	0.432	0.000	0.000	0.000	0.000
70	A	456	ASP	-1	-0.800	-0.861	13.698	15.252	15.252	0.000	0.000	0.000	0.000
71	A	457	ILE	0	0.016	0.006	11.109	0.011	0.011	0.000	0.000	0.000	0.000
72	A	458	ARG	1	0.786	0.861	15.611	-14.737	-14.737	0.000	0.000	0.000	0.000
73	A	459	LEU	0	0.060	0.028	14.990	-0.294	-0.294	0.000	0.000	0.000	0.000
74	A	460	MET	0	-0.037	-0.011	19.032	-0.826	-0.826	0.000	0.000	0.000	0.000
75	A	461	LYS	1	0.932	0.972	22.455	-10.063	-10.063	0.000	0.000	0.000	0.000
76	A	462	GLU	-1	-0.758	-0.857	24.971	11.641	11.641	0.000	0.000	0.000	0.000
77	A	463	GLY	0	-0.006	-0.005	26.748	-0.399	-0.399	0.000	0.000	0.000	0.000
78	A	464	ARG	1	0.933	0.951	29.170	-9.204	-9.204	0.000	0.000	0.000	0.000
79	A	465	MET	0	0.056	0.007	27.056	0.230	0.230	0.000	0.000	0.000	0.000
80	A	466	LYS	1	0.853	0.941	23.853	-11.036	-11.036	0.000	0.000	0.000	0.000
81	A	467	GLY	0	-0.027	-0.011	21.314	-0.322	-0.322	0.000	0.000	0.000	0.000
82	A	468	GLN	0	-0.009	-0.012	21.631	-0.134	-0.134	0.000	0.000	0.000	0.000
83	A	469	ALA	0	0.013	-0.003	17.910	0.320	0.320	0.000	0.000	0.000	0.000
84	A	470	PHE	0	-0.025	-0.010	19.908	-0.531	-0.531	0.000	0.000	0.000	0.000
85	A	471	ILE	0	-0.003	-0.002	13.745	0.508	0.508	0.000	0.000	0.000	0.000
86	A	472	GLY	0	-0.026	0.009	16.402	-0.836	-0.836	0.000	0.000	0.000	0.000
87	A	473	LEU	0	0.040	0.005	13.109	1.318	1.318	0.000	0.000	0.000	0.000
88	A	474	PRO	0	0.029	0.008	13.370	-1.113	-1.113	0.000	0.000	0.000	0.000
89	A	475	ASN	0	-0.010	-0.008	16.397	-0.796	-0.796	0.000	0.000	0.000	0.000
90	A	476	GLU	-1	-0.839	-0.917	18.983	12.198	12.198	0.000	0.000	0.000	0.000
91	A	477	LYS	1	0.947	0.981	20.341	-14.048	-14.048	0.000	0.000	0.000	0.000
92	A	478	ALA	0	-0.019	-0.008	15.161	0.375	0.375	0.000	0.000	0.000	0.000
93	A	479	ALA	0	0.043	0.023	16.769	0.703	0.703	0.000	0.000	0.000	0.000
94	A	480	ALA	0	0.020	0.003	18.497	0.102	0.102	0.000	0.000	0.000	0.000
95	A	481	LYS	1	0.832	0.934	13.823	-20.728	-20.728	0.000	0.000	0.000	0.000
96	A	482	ALA	0	0.048	0.020	15.315	0.376	0.376	0.000	0.000	0.000	0.000
97	A	483	LEU	0	-0.017	-0.005	16.358	0.213	0.213	0.000	0.000	0.000	0.000
98	A	484	LYS	1	0.919	0.963	19.741	-13.466	-13.466	0.000	0.000	0.000	0.000
99	A	485	GLU	-1	-0.801	-0.873	13.952	21.689	21.689	0.000	0.000	0.000	0.000
100	A	486	ALA	0	0.050	0.026	14.592	0.514	0.514	0.000	0.000	0.000	0.000
101	A	487	ASN	0	0.030	0.024	16.359	-0.056	-0.056	0.000	0.000	0.000	0.000
102	A	488	GLY	0	0.045	0.017	19.848	-0.299	-0.299	0.000	0.000	0.000	0.000
103	A	489	TYR	0	-0.067	-0.051	10.896	-0.473	-0.473	0.000	0.000	0.000	0.000
104	A	490	VAL	0	-0.005	-0.007	16.767	-0.364	-0.364	0.000	0.000	0.000	0.000
105	A	491	LEU	0	0.019	0.019	11.897	0.724	0.724	0.000	0.000	0.000	0.000
106	A	492	PHE	0	-0.073	-0.049	11.557	-1.396	-1.396	0.000	0.000	0.000	0.000
107	A	493	GLY	0	0.053	0.032	16.360	-0.846	-0.846	0.000	0.000	0.000	0.000
108	A	494	LYS	1	0.894	0.938	18.703	-13.809	-13.809	0.000	0.000	0.000	0.000
109	A	495	PRO	0	0.036	0.041	18.713	0.770	0.770	0.000	0.000	0.000	0.000
110	A	496	MET	0	-0.037	-0.002	14.090	-0.541	-0.541	0.000	0.000	0.000	0.000
111	A	497	VAL	0	0.006	0.005	19.466	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	498	VAL	0	-0.010	-0.016	17.637	0.182	0.182	0.000	0.000	0.000	0.000
113	A	499	GLN	0	0.007	0.012	20.850	-0.340	-0.340	0.000	0.000	0.000	0.000
114	A	500	PHE	0	0.061	0.028	21.926	0.752	0.752	0.000	0.000	0.000	0.000
115	A	501	ALA	0	-0.046	-0.022	23.135	-0.301	-0.301	0.000	0.000	0.000	0.000
116	A	502	ARG	1	1.000	1.010	24.774	-10.179	-10.179	0.000	0.000	0.000	0.000
117	A	503	SER	0	0.073	0.020	25.490	0.437	0.437	0.000	0.000	0.000	0.000
118	A	504	ALA	0	-0.024	-0.012	23.045	-0.190	-0.190	0.000	0.000	0.000	0.000
119	A	505	ARG	1	0.954	0.980	25.212	-10.676	-10.676	0.000	0.000	0.000	0.000
120	A	506	PRO	0	0.053	0.039	28.490	0.089	0.089	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:387:GLU)