FMO DATABASE

FMODB ID: RYLZ8

Calculation Name: 2ZI0-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ZI0

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UYT3

Base Structure: X-ray

Registration Date: 2025-07-08

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-291806.514696
FMO2-HF: Nuclear repulsion	266426.95499
FMO2-HF: Total energy	-25379.559706
FMO2-MP2: Total energy	-25454.318502

3D Structure Molmil

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:GLU)

Summations of interaction energy for fragment #1(A:5: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.
0.044	1.477	0.019	-0.722	-0.729	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.146 / q_NPA : -0.012

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].
4	A	6	ILE	0	-0.098	0.102	3.512	-0.208	0.287	0.025	-0.219	-0.301	0.001
5	A	7	PRO	0	0.046	-0.062	3.828	-1.792	-0.854	-0.006	-0.503	-0.428	0.002
6	A	8	LEU	0	0.171	-0.005	6.425	0.648	0.648	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.046	0.135	8.943	0.003	0.003	0.000	0.000	0.000	0.000
8	A	9	HIS	0	0.093	-0.077	9.156	0.259	0.259	0.000	0.000	0.000	0.000
9	A	9	HIS	0	-0.059	0.081	10.423	-0.084	-0.084	0.000	0.000	0.000	0.000
10	A	10	GLU	0	0.015	-0.132	9.642	0.176	0.176	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.952	-0.827	8.654	-0.093	-0.093	0.000	0.000	0.000	0.000
12	A	11	ILE	0	0.084	-0.120	9.790	0.308	0.308	0.000	0.000	0.000	0.000
13	A	11	ILE	0	-0.043	0.125	7.632	0.047	0.047	0.000	0.000	0.000	0.000
14	A	12	ILE	0	0.018	-0.122	11.226	0.154	0.154	0.000	0.000	0.000	0.000
15	A	12	ILE	0	-0.046	0.128	13.419	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	13	ARG	0	0.153	-0.085	13.961	0.075	0.075	0.000	0.000	0.000	0.000
17	A	13	ARG	1	0.888	1.088	14.296	0.279	0.279	0.000	0.000	0.000	0.000
18	A	14	LYS	0	0.036	-0.119	13.960	0.093	0.093	0.000	0.000	0.000	0.000
19	A	14	LYS	1	0.891	1.097	13.031	-0.107	-0.107	0.000	0.000	0.000	0.000
20	A	15	LEU	0	0.040	-0.144	15.182	0.086	0.086	0.000	0.000	0.000	0.000
21	A	15	LEU	0	-0.019	0.145	15.178	0.008	0.008	0.000	0.000	0.000	0.000
22	A	16	GLU	0	0.076	-0.130	17.247	0.039	0.039	0.000	0.000	0.000	0.000
23	A	16	GLU	-1	-0.985	-0.805	18.456	-0.276	-0.276	0.000	0.000	0.000	0.000
24	A	17	ARG	0	0.127	-0.084	18.552	0.023	0.023	0.000	0.000	0.000	0.000
25	A	17	ARG	1	0.836	1.052	15.303	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	18	MET	0	0.050	-0.132	19.170	0.037	0.037	0.000	0.000	0.000	0.000
27	A	18	MET	0	-0.111	0.105	17.568	0.000	0.000	0.000	0.000	0.000	0.000
28	A	19	ASN	0	0.091	-0.109	20.705	0.024	0.024	0.000	0.000	0.000	0.000
29	A	19	ASN	0	-0.066	0.115	22.235	0.001	0.001	0.000	0.000	0.000	0.000
30	A	20	GLN	0	0.114	-0.125	23.099	0.006	0.006	0.000	0.000	0.000	0.000
31	A	20	GLN	0	-0.057	0.129	23.198	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	21	LYS	0	0.013	-0.128	23.857	0.010	0.010	0.000	0.000	0.000	0.000
33	A	21	LYS	1	0.914	1.102	23.033	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	22	LYS	0	0.065	-0.109	25.148	0.016	0.016	0.000	0.000	0.000	0.000
35	A	22	LYS	1	0.921	1.102	23.331	0.106	0.106	0.000	0.000	0.000	0.000
36	A	23	GLN	0	0.052	-0.142	27.000	0.007	0.007	0.000	0.000	0.000	0.000
37	A	23	GLN	0	-0.051	0.143	27.543	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	24	ALA	0	0.143	-0.084	28.593	0.000	0.000	0.000	0.000	0.000	0.000
39	A	24	ALA	0	-0.113	0.107	28.863	0.003	0.003	0.000	0.000	0.000	0.000
40	A	25	GLN	0	0.018	-0.156	29.525	0.007	0.007	0.000	0.000	0.000	0.000
41	A	25	GLN	0	-0.077	0.118	27.611	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	26	ARG	0	0.130	-0.064	31.148	0.007	0.007	0.000	0.000	0.000	0.000
43	A	26	ARG	1	0.882	1.085	29.771	0.085	0.085	0.000	0.000	0.000	0.000
44	A	27	LYS	0	0.086	-0.105	33.013	0.000	0.000	0.000	0.000	0.000	0.000
45	A	27	LYS	1	0.882	1.092	33.855	0.022	0.022	0.000	0.000	0.000	0.000
46	A	28	ARG	0	0.052	-0.118	34.181	0.000	0.000	0.000	0.000	0.000	0.000
47	A	28	ARG	1	0.889	1.086	29.533	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	29	HIS	0	0.141	-0.056	35.445	0.004	0.004	0.000	0.000	0.000	0.000
49	A	29	HIS	0	-0.090	0.091	35.545	0.002	0.002	0.000	0.000	0.000	0.000
50	A	30	LYS	0	0.143	-0.095	37.045	0.002	0.002	0.000	0.000	0.000	0.000
51	A	30	LYS	1	0.824	1.056	37.575	0.044	0.044	0.000	0.000	0.000	0.000
52	A	31	LEU	0	-0.047	-0.153	38.876	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	31	LEU	0	-0.029	0.109	38.792	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	32	ASN	0	0.249	-0.001	40.012	0.001	0.001	0.000	0.000	0.000	0.000
55	A	32	ASN	0	-0.134	0.046	38.567	0.001	0.001	0.000	0.000	0.000	0.000
56	A	33	ARG	0	0.039	-0.083	41.439	0.003	0.003	0.000	0.000	0.000	0.000
57	A	33	ARG	1	0.763	1.003	39.665	0.031	0.031	0.000	0.000	0.000	0.000
58	A	34	LYS	0	0.166	-0.052	43.226	0.001	0.001	0.000	0.000	0.000	0.000
59	A	34	LYS	1	0.818	1.040	43.607	0.026	0.026	0.000	0.000	0.000	0.000
60	A	35	GLU	0	0.049	-0.132	44.789	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	35	GLU	-1	-1.032	-0.832	44.506	0.002	0.002	0.000	0.000	0.000	0.000
62	A	36	ARG	0	0.076	-0.108	46.122	0.002	0.002	0.000	0.000	0.000	0.000
63	A	36	ARG	1	0.852	1.061	42.101	0.007	0.007	0.000	0.000	0.000	0.000
64	A	37	GLY	0	0.013	-0.069	47.812	0.000	0.000	0.000	0.000	0.000	0.000
65	A	38	HIS	0	0.099	0.013	46.242	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	38	HIS	0	-0.125	0.063	44.465	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	39	LYS	0	0.032	-0.114	45.377	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	39	LYS	1	0.917	1.089	46.183	0.033	0.033	0.000	0.000	0.000	0.000
69	A	40	SER	0	0.018	-0.057	43.817	0.003	0.003	0.000	0.000	0.000	0.000
70	A	40	SER	0	-0.049	0.039	43.087	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	41	PRO	0	0.141	-0.053	45.240	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	42	SER	0	0.041	0.050	44.282	0.000	0.000	0.000	0.000	0.000	0.000
73	A	42	SER	0	-0.038	0.048	42.475	0.000	0.000	0.000	0.000	0.000	0.000
74	A	43	GLU	0	0.050	-0.140	44.585	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	43	GLU	-1	-0.930	-0.796	41.989	-0.042	-0.042	0.000	0.000	0.000	0.000
76	A	44	GLN	0	0.110	-0.091	45.128	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	44	GLN	0	-0.098	0.124	49.006	0.000	0.000	0.000	0.000	0.000	0.000
78	A	45	ARG	0	0.204	-0.060	48.877	0.001	0.001	0.000	0.000	0.000	0.000
79	A	45	ARG	1	0.854	1.076	45.856	0.054	0.054	0.000	0.000	0.000	0.000
80	A	46	ARG	0	0.075	-0.057	46.195	0.000	0.000	0.000	0.000	0.000	0.000
81	A	46	ARG	1	0.820	1.037	41.534	0.064	0.064	0.000	0.000	0.000	0.000
82	A	47	SER	0	0.019	-0.078	47.715	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	47	SER	0	-0.065	0.037	48.457	0.001	0.001	0.000	0.000	0.000	0.000
84	A	48	GLU	0	0.081	-0.138	49.389	0.000	0.000	0.000	0.000	0.000	0.000
85	A	48	GLU	-1	-0.954	-0.798	52.541	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	49	LEU	0	0.179	-0.065	51.295	0.002	0.002	0.000	0.000	0.000	0.000
87	A	49	LEU	0	-0.108	0.085	50.122	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	50	TRP	0	0.080	-0.090	50.205	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	50	TRP	0	-0.136	0.062	48.787	0.000	0.000	0.000	0.000	0.000	0.000
90	A	51	HIS	0	0.100	-0.091	51.405	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	51	HIS	0	-0.136	0.055	51.616	0.001	0.001	0.000	0.000	0.000	0.000
92	A	52	ALA	0	0.124	-0.090	54.435	0.002	0.002	0.000	0.000	0.000	0.000
93	A	52	ALA	0	-0.069	0.122	55.646	0.000	0.000	0.000	0.000	0.000	0.000
94	A	53	ARG	0	0.146	-0.050	53.952	0.001	0.001	0.000	0.000	0.000	0.000
95	A	53	ARG	1	0.844	1.047	48.941	0.063	0.063	0.000	0.000	0.000	0.000
96	A	54	GLN	0	0.023	-0.113	54.899	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	54	GLN	0	-0.084	0.073	51.694	0.001	0.001	0.000	0.000	0.000	0.000
98	A	55	VAL	0	0.051	-0.073	55.892	0.000	0.000	0.000	0.000	0.000	0.000
99	A	55	VAL	0	-0.071	0.088	58.720	0.000	0.000	0.000	0.000	0.000	0.000
100	A	56	GLU	0	0.144	-0.104	58.738	0.002	0.002	0.000	0.000	0.000	0.000
101	A	56	GLU	-1	-1.035	-0.849	58.196	-0.047	-0.047	0.000	0.000	0.000	0.000
102	A	57	LEU	0	0.038	-0.107	57.025	0.001	0.001	0.000	0.000	0.000	0.000
103	A	57	LEU	0	-0.098	0.074	53.752	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	58	SER	0	0.041	-0.077	58.459	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	58	SER	0	-0.059	0.059	58.970	0.000	0.000	0.000	0.000	0.000	0.000
106	A	59	ALA	0	0.079	-0.092	60.918	0.002	0.002	0.000	0.000	0.000	0.000
107	A	59	ALA	0	-0.065	0.102	63.085	0.000	0.000	0.000	0.000	0.000	0.000
108	A	60	ILE	0	0.084	-0.084	61.540	0.001	0.001	0.000	0.000	0.000	0.000
109	A	60	ILE	0	-0.091	0.084	59.032	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	61	ASN	0	0.070	-0.070	61.806	0.000	0.000	0.000	0.000	0.000	0.000
111	A	61	ASN	0	-0.170	0.034	58.720	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	62	SER	0	0.078	-0.054	62.798	0.001	0.001	0.000	0.000	0.000	0.000
113	A	62	SER	0	-0.025	0.064	66.359	0.000	0.000	0.000	0.000	0.000	0.000
114	A	63	ASP	0	-0.041	-0.119	65.702	0.002	0.002	0.000	0.000	0.000	0.000
115	A	63	ASP	-1	-0.991	-0.852	65.655	-0.039	-0.039	0.000	0.000	0.000	0.000
116	A	64	ASN	0	-0.040	-0.107	66.122	0.000	0.000	0.000	0.000	0.000	0.000
117	A	64	ASN	0	-0.056	-0.034	62.810	-0.001	-0.001	0.000	0.000	0.000	0.000

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