FMO DATABASE

FMODB ID: J4MK9

Calculation Name: 1ZBE-4-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ZBE

Chain ID: 4

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2025-07-11

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157644.967933
FMO2-HF: Nuclear repulsion	138539.505678
FMO2-HF: Total energy	-19105.462255
FMO2-MP2: Total energy	-19159.82881

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15:SER)

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.
-0.59	1.369	0.015	-0.977	-0.998	0.005

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.057

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	4	17	ASN	0	0.006	0.014	3.782	-1.188	0.660	-0.019	-1.017	-0.812	0.005
5	4	17	ASN	0	-0.104	0.069	7.540	0.105	0.105	0.000	0.000	0.000	0.000
6	4	18	THR	0	0.070	-0.097	4.429	0.815	0.930	0.000	-0.012	-0.103	0.000
7	4	18	THR	0	-0.011	0.085	3.415	0.246	0.287	0.036	0.056	-0.133	0.000
8	4	19	GLY	0	0.013	-0.090	5.099	-0.766	-0.811	-0.002	-0.004	0.050	0.000
9	4	20	SER	0	-0.014	-0.004	7.370	0.311	0.311	0.000	0.000	0.000	0.000
10	4	20	SER	0	-0.027	0.087	8.966	-0.074	-0.074	0.000	0.000	0.000	0.000
11	4	21	ILE	0	0.112	-0.065	8.653	0.012	0.012	0.000	0.000	0.000	0.000
12	4	21	ILE	0	-0.083	0.090	10.935	0.007	0.007	0.000	0.000	0.000	0.000
13	4	22	ILE	0	0.037	-0.112	11.206	0.138	0.138	0.000	0.000	0.000	0.000
14	4	22	ILE	0	-0.072	0.106	13.899	-0.002	-0.002	0.000	0.000	0.000	0.000
15	4	23	ASN	0	0.172	-0.052	11.077	-0.084	-0.084	0.000	0.000	0.000	0.000
16	4	23	ASN	0	-0.109	0.067	11.935	0.092	0.092	0.000	0.000	0.000	0.000
17	4	24	ASN	0	0.088	-0.094	11.132	-0.101	-0.101	0.000	0.000	0.000	0.000
18	4	24	ASN	0	-0.085	0.095	9.949	0.049	0.049	0.000	0.000	0.000	0.000
19	4	25	TYR	0	0.114	-0.074	12.113	0.070	0.070	0.000	0.000	0.000	0.000
20	4	25	TYR	0	-0.098	0.083	16.142	-0.008	-0.008	0.000	0.000	0.000	0.000
21	4	26	TYR	0	0.032	-0.104	14.470	0.017	0.017	0.000	0.000	0.000	0.000
22	4	26	TYR	0	-0.072	0.094	14.790	0.002	0.002	0.000	0.000	0.000	0.000
23	4	27	MET	0	0.139	-0.111	14.088	0.036	0.036	0.000	0.000	0.000	0.000
24	4	27	MET	0	-0.094	0.119	16.878	0.003	0.003	0.000	0.000	0.000	0.000
25	4	28	GLN	0	0.171	-0.103	12.307	-0.073	-0.073	0.000	0.000	0.000	0.000
26	4	28	GLN	0	-0.111	0.122	10.623	0.084	0.084	0.000	0.000	0.000	0.000
27	4	29	GLN	0	0.067	-0.104	13.135	0.017	0.017	0.000	0.000	0.000	0.000
28	4	29	GLN	0	-0.101	0.088	16.964	-0.031	-0.031	0.000	0.000	0.000	0.000
29	4	30	TYR	0	0.080	-0.125	15.344	-0.012	-0.012	0.000	0.000	0.000	0.000
30	4	30	TYR	0	-0.094	0.090	16.591	-0.002	-0.002	0.000	0.000	0.000	0.000
31	4	31	GLN	0	0.100	-0.092	11.857	-0.054	-0.054	0.000	0.000	0.000	0.000
32	4	31	GLN	0	-0.102	0.118	10.128	0.015	0.015	0.000	0.000	0.000	0.000
33	4	32	ASN	0	0.006	-0.100	10.630	-0.116	-0.116	0.000	0.000	0.000	0.000
34	4	32	ASN	0	-0.102	0.056	8.314	0.049	0.049	0.000	0.000	0.000	0.000
35	4	33	SER	0	0.112	-0.012	11.969	-0.014	-0.014	0.000	0.000	0.000	0.000
36	4	33	SER	0	-0.023	0.059	13.226	0.014	0.014	0.000	0.000	0.000	0.000
37	4	34	MET	0	0.050	-0.135	12.406	0.113	0.113	0.000	0.000	0.000	0.000
38	4	34	MET	0	-0.079	0.121	14.419	0.001	0.001	0.000	0.000	0.000	0.000
39	4	35	SER	0	-0.001	-0.073	12.909	-0.113	-0.113	0.000	0.000	0.000	0.000
40	4	35	SER	0	-0.003	0.075	11.594	0.018	0.018	0.000	0.000	0.000	0.000
41	4	36	THR	0	0.025	-0.046	14.109	0.038	0.038	0.000	0.000	0.000	0.000
42	4	36	THR	0	-0.027	0.044	18.107	-0.011	-0.011	0.000	0.000	0.000	0.000
43	4	37	GLN	0	0.032	-0.136	17.052	0.013	0.013	0.000	0.000	0.000	0.000
44	4	37	GLN	0	-0.044	0.109	14.881	0.089	0.089	0.000	0.000	0.000	0.000
45	4	38	LEU	0	0.065	-0.082	18.926	-0.013	-0.013	0.000	0.000	0.000	0.000
46	4	38	LEU	0	-0.045	0.130	22.006	-0.005	-0.005	0.000	0.000	0.000	0.000
47	4	39	GLY	0	-0.021	-0.104	21.997	-0.004	-0.004	0.000	0.000	0.000	0.000
48	4	62	THR	0	0.057	0.080	9.342	0.015	0.015	0.000	0.000	0.000	0.000
49	4	62	THR	0	-0.027	0.028	7.828	-0.075	-0.075	0.000	0.000	0.000	0.000
50	4	63	GLN	0	0.078	-0.091	10.889	0.039	0.039	0.000	0.000	0.000	0.000
51	4	63	GLN	0	-0.087	0.073	14.613	0.042	0.042	0.000	0.000	0.000	0.000
52	4	64	ASN	0	0.153	-0.020	12.122	0.026	0.026	0.000	0.000	0.000	0.000
53	4	64	ASN	0	-0.094	0.057	14.275	-0.032	-0.032	0.000	0.000	0.000	0.000
54	4	65	ASN	0	0.023	-0.109	13.605	-0.074	-0.074	0.000	0.000	0.000	0.000
55	4	65	ASN	0	-0.123	0.048	14.658	-0.043	-0.043	0.000	0.000	0.000	0.000
56	4	66	ASP	0	0.137	-0.116	13.668	0.026	0.026	0.000	0.000	0.000	0.000
57	4	66	ASP	-1	-0.930	-0.772	11.807	0.061	0.061	0.000	0.000	0.000	0.000
58	4	67	TRP	0	0.107	-0.142	14.633	-0.013	-0.013	0.000	0.000	0.000	0.000
59	4	67	TRP	0	-0.058	0.110	18.341	0.012	0.012	0.000	0.000	0.000	0.000
60	4	68	PHE	0	0.075	-0.074	17.092	0.007	0.007	0.000	0.000	0.000	0.000
61	4	68	PHE	0	-0.066	0.113	16.466	-0.005	-0.005	0.000	0.000	0.000	0.000
62	4	69	SER	0	0.196	-0.035	15.011	-0.035	-0.035	0.000	0.000	0.000	0.000
63	4	69	SER	0	-0.063	0.073	14.091	-0.001	-0.001	0.000	0.000	0.000	0.000
64	4	70	LYS	0	0.029	-0.088	16.206	-0.014	-0.014	0.000	0.000	0.000	0.000
65	4	70	LYS	1	0.835	1.037	17.737	-0.191	-0.191	0.000	0.000	0.000	0.000
66	4	71	LEU	0	0.154	-0.111	19.116	-0.002	-0.002	0.000	0.000	0.000	0.000
67	4	71	LEU	0	-0.142	0.119	20.699	-0.001	-0.001	0.000	0.000	0.000	0.000
68	4	72	ALA	0	0.124	-0.085	19.686	0.004	0.004	0.000	0.000	0.000	0.000
69	4	72	ALA	0	-0.091	0.125	18.808	-0.007	-0.007	0.000	0.000	0.000	0.000
70	4	73	SER	0	-0.009	-0.124	19.877	-0.016	-0.016	0.000	0.000	0.000	0.000
71	4	73	SER	0	-0.070	0.051	18.609	0.005	0.005	0.000	0.000	0.000	0.000
72	4	74	SER	0	-0.046	-0.078	21.057	0.003	0.003	0.000	0.000	0.000	0.000
73	4	74	SER	0	-0.090	0.033	23.709	0.003	0.003	0.000	0.000	0.000	0.000
74	4	75	ALA	0	0.079	-0.109	24.029	0.007	0.007	0.000	0.000	0.000	0.000
75	4	75	ALA	0	-0.072	0.127	24.832	-0.003	-0.003	0.000	0.000	0.000	0.000
76	4	76	PHE	0	0.065	-0.105	26.030	0.004	0.004	0.000	0.000	0.000	0.000
77	4	76	PHE	0	-0.078	0.093	30.749	0.000	0.000	0.000	0.000	0.000	0.000
78	4	77	THR	0	-0.025	-0.126	28.520	-0.007	-0.007	0.000	0.000	0.000	0.000
79	4	77	THR	0	-0.019	0.092	27.077	-0.002	-0.002	0.000	0.000	0.000	0.000
80	4	78	GLY	0	-0.049	-0.107	29.459	-0.004	-0.004	0.000	0.000	0.000	0.000
81	4	79	LEU	0	0.167	-0.009	32.908	-0.005	-0.005	0.000	0.000	0.000	0.000
82	4	79	LEU	0	-0.072	0.141	36.375	0.000	0.000	0.000	0.000	0.000	0.000
83	4	80	PHE	0	0.074	-0.090	36.280	0.004	0.004	0.000	0.000	0.000	0.000
84	4	80	PHE	0	-0.094	0.085	37.382	0.000	0.000	0.000	0.000	0.000	0.000
85	4	81	GLY	0	-0.033	-0.106	38.544	-0.003	-0.003	0.000	0.000	0.000	0.000
86	4	82	ALA	0	0.117	0.001	41.653	0.002	0.002	0.000	0.000	0.000	0.000
87	4	82	ALA	0	-0.071	0.113	45.547	0.000	0.000	0.000	0.000	0.000	0.000
88	4	83	LEU	0	0.060	-0.122	42.056	-0.002	-0.002	0.000	0.000	0.000	0.000
89	4	83	LEU	0	-0.093	0.123	40.281	0.000	0.000	0.000	0.000	0.000	0.000
90	4	84	LEU	0	0.042	-0.137	43.373	0.003	0.003	0.000	0.000	0.000	0.000
91	4	84	LEU	0	-0.100	0.116	46.864	0.000	0.000	0.000	0.000	0.000	0.000
92	4	85	ALA	0	-0.039	-0.124	43.169	-0.001	-0.001	0.000	0.000	0.000	0.000
93	4	85	ALA	0	0.072	0.045	42.329	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)