FMO DATABASE

FMODB ID: N1L8Q

Calculation Name: 3E3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E3V

Chain ID: A

ChEMBL ID:

UniProt ID: Q1WV04

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1401184.504102
FMO2-HF: Nuclear repulsion	1339632.80112
FMO2-HF: Total energy	-61551.702982
FMO2-MP2: Total energy	-61734.2291

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:55:LEU)

Summations of interaction energy for fragment #1(A:55:LEU)

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.
-10.857	-8.932	9.797	-5.575	-6.15	-0.025

Interaction energy analysis for fragmet #1(A:55:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.015

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	57	ASP	-1	-0.897	-0.947	1.861	-12.560	-12.398	9.569	-5.022	-4.710	-0.024
4	A	58	ASP	-1	-0.864	-0.940	2.519	-2.519	-1.145	0.230	-0.502	-1.102	-0.001
5	A	59	ILE	0	0.092	0.037	4.354	1.066	1.281	-0.001	-0.034	-0.181	0.000
6	A	60	SER	0	-0.055	-0.014	6.904	0.675	0.675	0.000	0.000	0.000	0.000
7	A	61	LYS	1	0.888	0.931	5.374	2.469	2.469	0.000	0.000	0.000	0.000
8	A	62	GLY	0	0.043	0.013	8.666	0.301	0.301	0.000	0.000	0.000	0.000
9	A	63	TYR	0	-0.052	-0.049	10.533	0.266	0.266	0.000	0.000	0.000	0.000
10	A	64	ASN	0	-0.015	-0.005	12.286	0.200	0.200	0.000	0.000	0.000	0.000
11	A	65	ALA	0	-0.002	0.009	13.293	0.115	0.115	0.000	0.000	0.000	0.000
12	A	66	ALA	0	0.007	0.007	14.820	0.089	0.089	0.000	0.000	0.000	0.000
13	A	67	LEU	0	0.055	0.011	16.763	0.063	0.063	0.000	0.000	0.000	0.000
14	A	68	ASN	0	-0.100	-0.039	17.172	0.085	0.085	0.000	0.000	0.000	0.000
15	A	69	TYR	0	-0.060	-0.050	19.290	0.052	0.052	0.000	0.000	0.000	0.000
16	A	70	LEU	0	-0.004	-0.005	20.136	0.026	0.026	0.000	0.000	0.000	0.000
17	A	71	SER	0	-0.061	-0.006	22.691	0.027	0.027	0.000	0.000	0.000	0.000
18	A	72	TYR	0	-0.044	-0.012	23.204	0.030	0.030	0.000	0.000	0.000	0.000
19	A	73	GLN	0	-0.026	-0.016	26.456	0.007	0.007	0.000	0.000	0.000	0.000
20	A	74	LEU	0	0.072	0.052	26.233	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	75	ARG	1	0.806	0.889	22.895	0.219	0.219	0.000	0.000	0.000	0.000
22	A	76	THR	0	-0.014	-0.015	25.323	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	77	ARG	1	0.945	0.928	20.104	0.250	0.250	0.000	0.000	0.000	0.000
24	A	78	LYS	1	0.851	0.913	21.241	0.163	0.163	0.000	0.000	0.000	0.000
25	A	79	GLU	-1	-0.751	-0.854	21.538	-0.197	-0.197	0.000	0.000	0.000	0.000
26	A	80	VAL	0	0.005	-0.007	17.374	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	81	GLU	-1	-0.791	-0.890	17.464	-0.338	-0.338	0.000	0.000	0.000	0.000
28	A	82	ASP	-1	-0.877	-0.926	17.003	-0.246	-0.246	0.000	0.000	0.000	0.000
29	A	83	LYS	1	0.895	0.977	17.371	0.346	0.346	0.000	0.000	0.000	0.000
30	A	84	LEU	0	0.000	-0.008	12.335	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	85	ARG	1	0.913	0.929	12.455	0.269	0.269	0.000	0.000	0.000	0.000
32	A	86	SER	0	-0.119	-0.050	14.561	0.037	0.037	0.000	0.000	0.000	0.000
33	A	87	LEU	0	-0.088	-0.057	11.476	0.051	0.051	0.000	0.000	0.000	0.000
34	A	88	ASP	-1	-0.981	-0.969	10.271	-0.305	-0.305	0.000	0.000	0.000	0.000
35	A	89	ILE	0	0.008	0.027	7.801	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	90	HIS	0	0.040	0.018	6.606	0.206	0.206	0.000	0.000	0.000	0.000
37	A	91	GLU	-1	-0.760	-0.878	10.056	-0.475	-0.475	0.000	0.000	0.000	0.000
38	A	92	ASP	-1	-0.954	-0.968	9.400	-0.385	-0.385	0.000	0.000	0.000	0.000
39	A	93	TYR	0	-0.010	-0.016	3.849	-0.258	-0.084	-0.001	-0.017	-0.157	0.000
40	A	94	ILE	0	-0.037	-0.003	9.918	0.031	0.031	0.000	0.000	0.000	0.000
41	A	95	SER	0	0.020	0.008	12.724	0.056	0.056	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.884	-0.918	9.433	-0.928	-0.928	0.000	0.000	0.000	0.000
43	A	97	ILE	0	0.009	-0.003	9.853	0.058	0.058	0.000	0.000	0.000	0.000
44	A	98	ILE	0	0.003	-0.010	14.041	0.074	0.074	0.000	0.000	0.000	0.000
45	A	99	ASN	0	-0.035	-0.025	17.157	0.077	0.077	0.000	0.000	0.000	0.000
46	A	100	LYS	1	0.949	1.000	14.954	0.483	0.483	0.000	0.000	0.000	0.000
47	A	101	LEU	0	0.000	-0.017	16.666	0.033	0.033	0.000	0.000	0.000	0.000
48	A	102	ILE	0	-0.023	-0.009	19.732	0.034	0.034	0.000	0.000	0.000	0.000
49	A	103	ASP	-1	-0.963	-0.964	20.500	-0.229	-0.229	0.000	0.000	0.000	0.000
50	A	104	LEU	0	-0.086	-0.048	19.103	0.016	0.016	0.000	0.000	0.000	0.000
51	A	105	ASP	-1	-0.865	-0.917	23.099	-0.169	-0.169	0.000	0.000	0.000	0.000
52	A	106	LEU	0	-0.064	-0.029	20.652	0.003	0.003	0.000	0.000	0.000	0.000
53	A	107	ILE	0	-0.043	-0.014	19.701	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	108	ASN	0	0.004	-0.027	23.930	0.014	0.014	0.000	0.000	0.000	0.000
55	A	109	ASP	-1	-0.759	-0.895	26.281	-0.190	-0.190	0.000	0.000	0.000	0.000
56	A	110	LYS	1	0.921	0.963	28.967	0.118	0.118	0.000	0.000	0.000	0.000
57	A	111	ASN	0	0.008	-0.001	30.259	0.018	0.018	0.000	0.000	0.000	0.000
58	A	112	TYR	0	-0.044	-0.021	28.180	0.014	0.014	0.000	0.000	0.000	0.000
59	A	113	ALA	0	0.018	-0.005	31.181	0.008	0.008	0.000	0.000	0.000	0.000
60	A	114	GLU	-1	-0.774	-0.872	33.922	-0.096	-0.096	0.000	0.000	0.000	0.000
61	A	115	SER	0	-0.028	-0.010	33.520	0.006	0.006	0.000	0.000	0.000	0.000
62	A	116	TYR	0	0.027	0.023	34.112	0.008	0.008	0.000	0.000	0.000	0.000
63	A	117	VAL	0	0.021	0.004	36.063	0.006	0.006	0.000	0.000	0.000	0.000
64	A	118	ARG	1	0.905	0.944	38.278	0.102	0.102	0.000	0.000	0.000	0.000
65	A	119	THR	0	0.001	-0.004	37.533	0.005	0.005	0.000	0.000	0.000	0.000
66	A	120	MET	0	-0.032	0.003	38.900	0.005	0.005	0.000	0.000	0.000	0.000
67	A	121	MET	0	-0.026	0.032	41.508	0.004	0.004	0.000	0.000	0.000	0.000
68	A	122	ASN	0	-0.035	-0.033	43.215	0.007	0.007	0.000	0.000	0.000	0.000
69	A	123	THR	0	-0.070	-0.040	41.793	0.002	0.002	0.000	0.000	0.000	0.000
70	A	124	SER	0	-0.062	-0.040	42.749	0.001	0.001	0.000	0.000	0.000	0.000
71	A	125	ASP	-1	-0.783	-0.874	44.893	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	126	LYS	1	0.849	0.903	42.698	0.068	0.068	0.000	0.000	0.000	0.000
73	A	127	GLY	0	0.077	0.035	45.451	0.000	0.000	0.000	0.000	0.000	0.000
74	A	128	PRO	0	0.043	-0.002	43.550	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	129	LYS	1	0.904	0.968	42.237	0.049	0.049	0.000	0.000	0.000	0.000
76	A	130	VAL	0	0.000	0.001	41.309	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	131	ILE	0	-0.007	0.000	39.077	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	132	LYS	1	0.882	0.940	37.739	0.078	0.078	0.000	0.000	0.000	0.000
79	A	133	LEU	0	0.007	0.018	36.654	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	134	ASN	0	-0.054	-0.040	35.575	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	135	LEU	0	0.017	0.015	33.358	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	136	SER	0	0.040	0.018	31.960	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	137	LYS	1	0.850	0.932	31.283	0.092	0.092	0.000	0.000	0.000	0.000
84	A	138	LYS	1	0.830	0.915	27.986	0.154	0.154	0.000	0.000	0.000	0.000
85	A	139	GLY	0	-0.015	0.002	27.065	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	140	ILE	0	-0.057	-0.009	27.973	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	141	ASP	-1	-0.856	-0.927	29.324	-0.135	-0.135	0.000	0.000	0.000	0.000
88	A	142	ASP	-1	-0.859	-0.929	31.787	-0.089	-0.089	0.000	0.000	0.000	0.000
89	A	143	ASN	0	0.015	0.005	34.640	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	144	ILE	0	0.055	0.029	30.384	0.003	0.003	0.000	0.000	0.000	0.000
91	A	145	ALA	0	-0.035	-0.022	34.559	0.002	0.002	0.000	0.000	0.000	0.000
92	A	146	GLU	-1	-0.926	-0.986	36.338	-0.075	-0.075	0.000	0.000	0.000	0.000
93	A	147	ASP	-1	-0.896	-0.935	37.343	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	148	ALA	0	-0.039	-0.021	36.597	0.003	0.003	0.000	0.000	0.000	0.000
95	A	149	LEU	0	-0.047	-0.047	38.738	0.003	0.003	0.000	0.000	0.000	0.000
96	A	150	ILE	0	0.005	0.026	41.603	0.005	0.005	0.000	0.000	0.000	0.000
97	A	151	LEU	0	-0.057	-0.028	40.028	0.003	0.003	0.000	0.000	0.000	0.000
98	A	152	TYR	0	-0.051	-0.040	44.077	0.003	0.003	0.000	0.000	0.000	0.000
99	A	153	THR	0	0.039	0.013	45.871	0.002	0.002	0.000	0.000	0.000	0.000
100	A	154	ASP	-1	-0.838	-0.921	49.198	-0.052	-0.052	0.000	0.000	0.000	0.000
101	A	155	LYN	0	0.021	-0.004	52.120	0.000	0.000	0.000	0.000	0.000	0.000
102	A	156	LEU	0	0.031	0.020	48.438	0.001	0.001	0.000	0.000	0.000	0.000
103	A	157	GLN	0	-0.055	-0.041	48.442	0.001	0.001	0.000	0.000	0.000	0.000
104	A	158	VAL	0	0.013	0.000	50.942	0.001	0.001	0.000	0.000	0.000	0.000
105	A	159	GLU	-1	-0.884	-0.926	53.730	-0.048	-0.048	0.000	0.000	0.000	0.000
106	A	160	LYS	1	0.822	0.920	47.240	0.063	0.063	0.000	0.000	0.000	0.000
107	A	161	GLY	0	-0.004	-0.027	52.508	0.001	0.001	0.000	0.000	0.000	0.000
108	A	162	VAL	0	0.054	0.020	54.059	0.001	0.001	0.000	0.000	0.000	0.000
109	A	163	THR	0	0.015	0.026	54.364	0.001	0.001	0.000	0.000	0.000	0.000
110	A	164	LEU	0	-0.117	-0.061	50.657	0.001	0.001	0.000	0.000	0.000	0.000
111	A	165	ALA	0	0.011	-0.004	55.147	0.001	0.001	0.000	0.000	0.000	0.000
112	A	166	GLU	-1	-0.822	-0.917	58.153	-0.037	-0.037	0.000	0.000	0.000	0.000
113	A	167	LYS	1	0.891	0.953	53.849	0.048	0.048	0.000	0.000	0.000	0.000
114	A	168	LEU	0	-0.049	-0.033	55.287	0.001	0.001	0.000	0.000	0.000	0.000
115	A	169	ALA	0	0.034	0.029	59.397	0.001	0.001	0.000	0.000	0.000	0.000
116	A	170	ASN	0	-0.009	-0.022	62.566	0.002	0.002	0.000	0.000	0.000	0.000
117	A	171	ARG	1	0.903	0.973	54.943	0.040	0.040	0.000	0.000	0.000	0.000
118	A	172	TYR	0	0.011	-0.014	57.455	0.001	0.001	0.000	0.000	0.000	0.000
119	A	173	SER	0	0.043	0.017	64.142	0.001	0.001	0.000	0.000	0.000	0.000
120	A	174	HIS	0	-0.012	-0.009	67.309	0.001	0.001	0.000	0.000	0.000	0.000
121	A	175	ASP	-1	-0.834	-0.890	65.118	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	176	SER	0	0.014	-0.001	68.327	0.000	0.000	0.000	0.000	0.000	0.000
123	A	177	TYR	0	-0.019	-0.057	67.703	0.000	0.000	0.000	0.000	0.000	0.000
124	A	178	ARG	1	0.959	0.976	66.613	0.025	0.025	0.000	0.000	0.000	0.000
125	A	179	ASN	0	-0.015	-0.009	65.249	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	180	LYS	1	0.835	0.951	63.606	0.028	0.028	0.000	0.000	0.000	0.000
127	A	181	GLN	0	0.060	0.020	62.223	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	182	ASN	0	-0.056	-0.022	60.800	0.000	0.000	0.000	0.000	0.000	0.000
129	A	183	LYS	1	0.867	0.922	58.946	0.029	0.029	0.000	0.000	0.000	0.000
130	A	184	ILE	0	0.011	0.010	57.392	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	185	LYS	1	0.912	0.951	56.298	0.034	0.034	0.000	0.000	0.000	0.000
132	A	186	GLN	0	0.010	0.012	54.669	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	187	SER	0	-0.019	-0.016	52.997	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	188	LEU	0	0.034	0.012	51.458	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	189	LEU	0	-0.005	0.007	50.658	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.104	-0.048	48.647	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	191	LYS	1	0.859	0.926	46.907	0.050	0.050	0.000	0.000	0.000	0.000
138	A	192	GLY	0	0.001	0.011	45.816	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	193	PHE	0	0.039	0.029	46.764	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	194	SER	0	0.020	-0.004	49.729	0.001	0.001	0.000	0.000	0.000	0.000
141	A	195	TYR	0	0.046	0.004	51.304	0.000	0.000	0.000	0.000	0.000	0.000
142	A	196	ASP	-1	-0.834	-0.907	54.394	-0.042	-0.042	0.000	0.000	0.000	0.000
143	A	197	ILE	0	0.004	0.014	51.454	0.001	0.001	0.000	0.000	0.000	0.000
144	A	198	ILE	0	-0.044	-0.029	52.791	0.001	0.001	0.000	0.000	0.000	0.000
145	A	199	ASP	-1	-0.888	-0.944	56.271	-0.035	-0.035	0.000	0.000	0.000	0.000
146	A	200	THR	0	0.004	0.005	57.637	0.001	0.001	0.000	0.000	0.000	0.000
147	A	201	ILE	0	-0.033	-0.004	54.095	0.000	0.000	0.000	0.000	0.000	0.000
148	A	202	ILE	0	-0.081	-0.047	58.749	0.001	0.001	0.000	0.000	0.000	0.000
149	A	203	GLN	0	-0.003	0.009	61.667	0.001	0.001	0.000	0.000	0.000	0.000
150	A	204	GLU	-1	-0.924	-0.971	60.621	-0.036	-0.036	0.000	0.000	0.000	0.000
151	A	205	LEU	0	-0.038	-0.024	61.396	0.001	0.001	0.000	0.000	0.000	0.000
152	A	206	ASP	-1	-0.800	-0.874	63.436	-0.030	-0.030	0.000	0.000	0.000	0.000
153	A	207	LEU	0	-0.054	-0.001	66.212	0.001	0.001	0.000	0.000	0.000	0.000
154	A	208	ILE	0	-0.120	-0.050	62.683	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:55:LEU)