FMO DATABASE

FMODB ID: Z6YNN

Calculation Name: 2Z5C-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z5C

Chain ID: E

ChEMBL ID:

UniProt ID: Q07951

Base Structure: X-ray

Registration Date: 2023-06-21

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-926735.334103
FMO2-HF: Nuclear repulsion	881647.44443
FMO2-HF: Total energy	-45087.889673
FMO2-MP2: Total energy	-45218.503713

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(E:2:ILE)

Summations of interaction energy for fragment #1(E:2:ILE)

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.
-9.149	-1.225	3.195	-3.953	-7.167	-0.023

Interaction energy analysis for fragmet #1(E:2:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.016

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	E	4	TYR	0	-0.003	0.001	2.666	-4.589	-0.880	2.507	-2.198	-4.018	-0.013
4	E	5	GLU	-1	-0.925	-0.987	5.704	0.254	0.254	0.000	0.000	0.000	0.000
5	E	6	PHE	0	0.061	0.034	9.516	-0.002	-0.002	0.000	0.000	0.000	0.000
6	E	7	GLN	0	0.026	0.022	12.885	0.038	0.038	0.000	0.000	0.000	0.000
7	E	8	THR	0	-0.018	-0.002	16.527	-0.003	-0.003	0.000	0.000	0.000	0.000
8	E	9	HIS	0	0.000	-0.002	19.744	0.003	0.003	0.000	0.000	0.000	0.000
9	E	25	LYS	1	0.902	0.940	26.909	0.014	0.014	0.000	0.000	0.000	0.000
10	E	26	GLU	-1	-0.937	-0.972	20.535	0.016	0.016	0.000	0.000	0.000	0.000
11	E	27	LEU	0	-0.043	-0.016	18.621	0.006	0.006	0.000	0.000	0.000	0.000
12	E	28	TYR	0	-0.001	-0.001	12.508	-0.012	-0.012	0.000	0.000	0.000	0.000
13	E	29	VAL	0	0.001	-0.005	12.274	-0.008	-0.008	0.000	0.000	0.000	0.000
14	E	30	GLN	0	0.052	0.016	6.745	-0.037	-0.037	0.000	0.000	0.000	0.000
15	E	31	ALA	0	-0.017	-0.007	7.234	0.027	0.027	0.000	0.000	0.000	0.000
16	E	32	THR	0	0.010	0.006	3.583	-0.192	0.201	0.010	-0.128	-0.275	0.000
17	E	33	HIS	0	-0.048	-0.030	2.513	-0.719	0.975	0.534	-0.556	-1.672	0.000
18	E	34	PHE	0	-0.008	0.006	2.949	-3.371	-1.338	0.145	-1.070	-1.109	-0.010
19	E	35	ASN	0	-0.006	-0.021	4.942	-0.138	-0.043	-0.001	-0.001	-0.093	0.000
20	E	36	ASN	0	-0.016	-0.013	7.008	-0.033	-0.033	0.000	0.000	0.000	0.000
21	E	37	THR	0	-0.012	-0.017	8.165	0.129	0.129	0.000	0.000	0.000	0.000
22	E	38	ILE	0	0.007	0.022	7.118	-0.243	-0.243	0.000	0.000	0.000	0.000
23	E	39	LEU	0	-0.005	0.003	7.684	0.229	0.229	0.000	0.000	0.000	0.000
24	E	40	LEU	0	-0.011	-0.003	8.548	-0.035	-0.035	0.000	0.000	0.000	0.000
25	E	41	GLN	0	0.002	-0.009	10.285	0.099	0.099	0.000	0.000	0.000	0.000
26	E	42	ILE	0	-0.007	-0.025	13.463	-0.044	-0.044	0.000	0.000	0.000	0.000
27	E	43	ARG	1	0.892	0.950	15.119	-0.138	-0.138	0.000	0.000	0.000	0.000
28	E	44	LEU	0	-0.002	-0.008	18.821	-0.019	-0.019	0.000	0.000	0.000	0.000
29	E	45	ASN	0	0.050	0.025	22.416	0.007	0.007	0.000	0.000	0.000	0.000
30	E	46	GLY	0	0.034	0.022	20.157	0.011	0.011	0.000	0.000	0.000	0.000
31	E	47	GLU	-1	-0.934	-0.967	20.455	0.052	0.052	0.000	0.000	0.000	0.000
32	E	48	MET	0	-0.014	-0.028	15.285	-0.025	-0.025	0.000	0.000	0.000	0.000
33	E	49	ASP	-1	-0.919	-0.950	20.215	0.015	0.015	0.000	0.000	0.000	0.000
34	E	50	SER	0	0.022	0.019	21.082	0.000	0.000	0.000	0.000	0.000	0.000
35	E	51	THR	0	-0.056	-0.034	16.462	0.000	0.000	0.000	0.000	0.000	0.000
36	E	52	TYR	0	0.009	0.011	18.179	0.009	0.009	0.000	0.000	0.000	0.000
37	E	53	GLU	-1	-0.921	-0.954	16.329	-0.161	-0.161	0.000	0.000	0.000	0.000
38	E	54	VAL	0	-0.011	-0.011	16.731	0.022	0.022	0.000	0.000	0.000	0.000
39	E	55	SER	0	0.025	0.021	16.958	-0.040	-0.040	0.000	0.000	0.000	0.000
40	E	56	SER	0	0.025	0.004	17.783	0.023	0.023	0.000	0.000	0.000	0.000
41	E	57	LYS	1	0.912	0.947	19.564	0.136	0.136	0.000	0.000	0.000	0.000
42	E	58	GLY	0	-0.034	-0.004	19.690	0.013	0.013	0.000	0.000	0.000	0.000
43	E	59	LEU	0	-0.025	-0.028	20.466	-0.021	-0.021	0.000	0.000	0.000	0.000
44	E	60	ASN	0	-0.025	-0.021	23.234	-0.006	-0.006	0.000	0.000	0.000	0.000
45	E	61	HIS	0	-0.043	-0.028	25.774	0.002	0.002	0.000	0.000	0.000	0.000
46	E	62	LEU	0	0.003	0.018	28.446	0.003	0.003	0.000	0.000	0.000	0.000
47	E	63	SER	0	-0.032	-0.036	26.324	0.008	0.008	0.000	0.000	0.000	0.000
48	E	64	ASP	-1	-0.809	-0.883	24.542	-0.152	-0.152	0.000	0.000	0.000	0.000
49	E	95	TYR	0	-0.002	-0.007	18.371	-0.023	-0.023	0.000	0.000	0.000	0.000
50	E	96	GLN	0	-0.007	-0.020	21.505	0.012	0.012	0.000	0.000	0.000	0.000
51	E	97	VAL	0	-0.001	0.013	21.377	-0.003	-0.003	0.000	0.000	0.000	0.000
52	E	98	VAL	0	0.003	0.012	21.328	0.018	0.018	0.000	0.000	0.000	0.000
53	E	99	THR	0	-0.011	-0.018	21.386	-0.008	-0.008	0.000	0.000	0.000	0.000
54	E	100	LYS	1	0.870	0.946	18.570	0.071	0.071	0.000	0.000	0.000	0.000
55	E	101	LEU	0	0.024	0.004	21.885	0.014	0.014	0.000	0.000	0.000	0.000
56	E	102	GLY	0	0.058	0.032	22.838	-0.006	-0.006	0.000	0.000	0.000	0.000
57	E	103	ASP	-1	-0.842	-0.926	25.614	-0.036	-0.036	0.000	0.000	0.000	0.000
58	E	104	SER	0	-0.038	-0.032	27.172	-0.007	-0.007	0.000	0.000	0.000	0.000
59	E	105	ALA	0	-0.045	-0.018	28.150	-0.006	-0.006	0.000	0.000	0.000	0.000
60	E	106	ASP	-1	-0.831	-0.901	28.550	-0.067	-0.067	0.000	0.000	0.000	0.000
61	E	107	PRO	0	-0.027	-0.019	28.995	-0.009	-0.009	0.000	0.000	0.000	0.000
62	E	108	LYS	1	0.883	0.931	28.041	0.058	0.058	0.000	0.000	0.000	0.000
63	E	109	VAL	0	0.020	0.020	23.506	-0.014	-0.014	0.000	0.000	0.000	0.000
64	E	110	PRO	0	-0.012	-0.017	24.090	-0.018	-0.018	0.000	0.000	0.000	0.000
65	E	111	VAL	0	0.032	0.027	24.235	-0.015	-0.015	0.000	0.000	0.000	0.000
66	E	112	VAL	0	0.039	0.002	20.823	-0.019	-0.019	0.000	0.000	0.000	0.000
67	E	113	CYS	0	-0.050	-0.008	19.584	-0.026	-0.026	0.000	0.000	0.000	0.000
68	E	114	VAL	0	0.025	0.011	19.208	-0.035	-0.035	0.000	0.000	0.000	0.000
69	E	115	GLN	0	-0.008	-0.003	20.639	-0.016	-0.016	0.000	0.000	0.000	0.000
70	E	116	ILE	0	-0.012	-0.002	15.114	-0.028	-0.028	0.000	0.000	0.000	0.000
71	E	117	ALA	0	-0.005	-0.013	15.882	-0.059	-0.059	0.000	0.000	0.000	0.000
72	E	118	GLU	-1	-0.841	-0.931	16.470	-0.314	-0.314	0.000	0.000	0.000	0.000
73	E	119	LEU	0	-0.080	-0.023	15.404	-0.016	-0.016	0.000	0.000	0.000	0.000
74	E	120	TYR	0	0.001	-0.012	8.869	0.021	0.021	0.000	0.000	0.000	0.000
75	E	121	ARG	1	0.969	0.960	13.807	0.330	0.330	0.000	0.000	0.000	0.000
76	E	122	ARG	1	0.815	0.928	15.430	0.281	0.281	0.000	0.000	0.000	0.000
77	E	123	VAL	0	-0.026	-0.019	15.666	0.046	0.046	0.000	0.000	0.000	0.000
78	E	124	ILE	0	-0.028	0.001	10.203	0.005	0.005	0.000	0.000	0.000	0.000
79	E	125	LEU	0	-0.046	-0.010	8.792	-0.108	-0.108	0.000	0.000	0.000	0.000
80	E	126	PRO	0	0.011	0.026	8.773	0.108	0.108	0.000	0.000	0.000	0.000
81	E	138	GLN	0	0.002	-0.010	15.026	-0.004	-0.004	0.000	0.000	0.000	0.000
82	E	139	PHE	0	-0.001	-0.003	12.708	-0.048	-0.048	0.000	0.000	0.000	0.000
83	E	140	SER	0	0.020	0.001	12.601	0.091	0.091	0.000	0.000	0.000	0.000
84	E	141	LEU	0	0.009	0.034	11.625	-0.103	-0.103	0.000	0.000	0.000	0.000
85	E	142	LEU	0	0.029	0.008	11.981	0.085	0.085	0.000	0.000	0.000	0.000
86	E	143	ILE	0	-0.010	-0.011	12.618	-0.044	-0.044	0.000	0.000	0.000	0.000
87	E	144	SER	0	0.027	0.009	14.794	0.042	0.042	0.000	0.000	0.000	0.000
88	E	145	MET	0	0.010	-0.006	16.310	-0.020	-0.020	0.000	0.000	0.000	0.000
89	E	146	SER	0	0.051	0.037	19.058	0.016	0.016	0.000	0.000	0.000	0.000
90	E	147	SER	0	-0.010	0.004	22.361	-0.016	-0.016	0.000	0.000	0.000	0.000
91	E	148	LYS	1	0.924	0.948	25.054	-0.019	-0.019	0.000	0.000	0.000	0.000
92	E	149	ILE	0	-0.050	0.002	21.646	0.000	0.000	0.000	0.000	0.000	0.000
93	E	150	TRP	0	-0.029	-0.021	22.419	-0.006	-0.006	0.000	0.000	0.000	0.000
94	E	161	ASN	0	-0.003	-0.007	29.868	-0.002	-0.002	0.000	0.000	0.000	0.000
95	E	162	ASP	-1	-0.872	-0.953	28.761	-0.075	-0.075	0.000	0.000	0.000	0.000
96	E	163	PHE	0	0.040	0.037	27.910	-0.006	-0.006	0.000	0.000	0.000	0.000
97	E	164	GLY	0	0.038	-0.008	26.847	-0.010	-0.010	0.000	0.000	0.000	0.000
98	E	165	LYS	1	0.893	0.955	25.037	0.066	0.066	0.000	0.000	0.000	0.000
99	E	166	LEU	0	0.067	0.043	22.316	-0.008	-0.008	0.000	0.000	0.000	0.000
100	E	167	VAL	0	0.028	0.015	21.888	-0.021	-0.021	0.000	0.000	0.000	0.000
101	E	168	PHE	0	-0.018	-0.002	21.573	-0.020	-0.020	0.000	0.000	0.000	0.000
102	E	169	VAL	0	0.039	0.015	18.060	-0.014	-0.014	0.000	0.000	0.000	0.000
103	E	170	LEU	0	0.005	-0.004	17.322	-0.033	-0.033	0.000	0.000	0.000	0.000
104	E	171	LYS	1	0.875	0.942	16.822	0.155	0.155	0.000	0.000	0.000	0.000
105	E	172	CYS	0	-0.046	-0.009	16.287	-0.007	-0.007	0.000	0.000	0.000	0.000
106	E	173	ILE	0	0.029	0.020	11.967	-0.025	-0.025	0.000	0.000	0.000	0.000
107	E	174	LYS	1	0.940	0.952	11.745	0.270	0.270	0.000	0.000	0.000	0.000
108	E	175	ASP	-1	-0.895	-0.927	12.888	-0.299	-0.299	0.000	0.000	0.000	0.000
109	E	176	MET	0	-0.049	0.005	8.640	0.082	0.082	0.000	0.000	0.000	0.000
110	E	177	TYR	0	-0.082	-0.051	7.994	-0.154	-0.154	0.000	0.000	0.000	0.000
111	E	178	ALA	0	0.045	0.058	6.490	-0.281	-0.281	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(E:2:ILE)