FMO DATABASE

FMODB ID: LQML9

Calculation Name: 3ZGX-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ZGX

Chain ID: C

ChEMBL ID:

UniProt ID: P35154

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	OptHSide
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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-332071.343202
FMO2-HF: Nuclear repulsion	305012.816559
FMO2-HF: Total energy	-27058.526644
FMO2-MP2: Total energy	-27136.800903

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(C:10:THR)

Summations of interaction energy for fragment #1(C:10:THR)

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.
-1.886	1.583	-0.025	-2.047	-1.397	0.001

Interaction energy analysis for fragmet #1(C:10:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.021

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	C	11	PHE	0	-0.085	0.049	3.949	-0.153	0.445	0.005	-0.317	-0.286	0.000
5	C	12	GLU	0	0.086	-0.075	3.817	-2.131	0.697	-0.029	-1.723	-1.076	0.001
6	C	12	GLU	-1	-0.915	-0.826	6.426	1.446	1.446	0.000	0.000	0.000	0.000
7	C	13	GLY	0	0.043	-0.076	7.180	-0.617	-0.617	0.000	0.000	0.000	0.000
8	C	14	PRO	0	0.001	-0.015	7.931	-0.060	-0.060	0.000	0.000	0.000	0.000
9	C	15	LEU	0	0.115	0.020	9.816	0.056	0.056	0.000	0.000	0.000	0.000
10	C	15	LEU	0	-0.067	0.095	13.263	-0.002	-0.002	0.000	0.000	0.000	0.000
11	C	16	ASP	0	0.131	-0.073	11.521	-0.005	-0.005	0.000	0.000	0.000	0.000
12	C	16	ASP	-1	-0.855	-0.811	9.601	0.268	0.268	0.000	0.000	0.000	0.000
13	C	17	LEU	0	0.040	-0.145	7.608	0.213	0.213	0.000	0.000	0.000	0.000
14	C	17	LEU	0	-0.048	0.132	4.388	-0.106	-0.063	-0.001	-0.007	-0.035	0.000
15	C	18	LEU	0	0.110	-0.063	8.897	0.090	0.090	0.000	0.000	0.000	0.000
16	C	18	LEU	0	-0.088	0.098	11.684	-0.023	-0.023	0.000	0.000	0.000	0.000
17	C	19	LEU	0	0.041	-0.127	11.853	-0.001	-0.001	0.000	0.000	0.000	0.000
18	C	19	LEU	0	-0.074	0.102	13.654	0.008	0.008	0.000	0.000	0.000	0.000
19	C	20	HIS	0	-0.022	-0.081	10.940	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	20	HIS	1	0.730	0.936	8.427	-0.819	-0.819	0.000	0.000	0.000	0.000
21	C	21	LEU	0	0.192	-0.053	11.655	0.061	0.061	0.000	0.000	0.000	0.000
22	C	21	LEU	0	-0.133	0.089	11.200	-0.019	-0.019	0.000	0.000	0.000	0.000
23	C	22	ILE	0	0.076	-0.106	12.926	0.027	0.027	0.000	0.000	0.000	0.000
24	C	22	ILE	0	-0.065	0.106	15.511	-0.009	-0.009	0.000	0.000	0.000	0.000
25	C	23	ASN	0	0.139	-0.054	16.061	-0.018	-0.018	0.000	0.000	0.000	0.000
26	C	23	ASN	0	-0.113	0.075	16.314	0.039	0.039	0.000	0.000	0.000	0.000
27	C	24	ARG	0	0.107	-0.092	15.471	-0.008	-0.008	0.000	0.000	0.000	0.000
28	C	24	ARG	1	0.707	0.957	13.723	-0.204	-0.204	0.000	0.000	0.000	0.000
29	C	25	LEU	0	0.020	-0.114	16.789	0.015	0.015	0.000	0.000	0.000	0.000
30	C	25	LEU	0	-0.111	0.076	15.691	-0.009	-0.009	0.000	0.000	0.000	0.000
31	C	26	GLU	0	0.151	-0.088	18.734	-0.010	-0.010	0.000	0.000	0.000	0.000
32	C	26	GLU	-1	-0.974	-0.795	20.859	0.062	0.062	0.000	0.000	0.000	0.000
33	C	27	ILE	0	0.115	-0.079	20.881	-0.020	-0.020	0.000	0.000	0.000	0.000
34	C	27	ILE	0	-0.084	0.087	19.612	0.007	0.007	0.000	0.000	0.000	0.000
35	C	28	ASP	0	0.081	-0.116	20.898	0.002	0.002	0.000	0.000	0.000	0.000
36	C	28	ASP	-1	-0.949	-0.816	19.051	0.155	0.155	0.000	0.000	0.000	0.000
37	C	29	ILE	0	0.034	-0.072	22.119	-0.005	-0.005	0.000	0.000	0.000	0.000
38	C	29	ILE	0	-0.147	0.052	22.010	-0.006	-0.006	0.000	0.000	0.000	0.000
39	C	30	TYR	0	0.028	-0.095	24.773	-0.003	-0.003	0.000	0.000	0.000	0.000
40	C	30	TYR	0	-0.080	0.065	24.326	-0.007	-0.007	0.000	0.000	0.000	0.000
41	C	31	ASP	0	0.028	-0.085	25.546	-0.006	-0.006	0.000	0.000	0.000	0.000
42	C	31	ASP	-1	-0.906	-0.828	24.637	0.091	0.091	0.000	0.000	0.000	0.000
43	C	32	ILE	0	0.157	-0.090	26.204	0.020	0.020	0.000	0.000	0.000	0.000
44	C	32	ILE	0	-0.123	0.084	24.802	0.001	0.001	0.000	0.000	0.000	0.000
45	C	33	PRO	0	-0.049	-0.135	26.876	-0.006	-0.006	0.000	0.000	0.000	0.000
46	C	34	VAL	0	0.136	0.111	29.947	-0.009	-0.009	0.000	0.000	0.000	0.000
47	C	34	VAL	0	-0.141	0.019	32.386	-0.003	-0.003	0.000	0.000	0.000	0.000
48	C	35	ALA	0	0.043	-0.135	29.698	0.007	0.007	0.000	0.000	0.000	0.000
49	C	35	ALA	0	-0.062	0.147	28.995	0.001	0.001	0.000	0.000	0.000	0.000
50	C	36	LYS	0	0.110	-0.115	30.412	-0.002	-0.002	0.000	0.000	0.000	0.000
51	C	36	LYS	1	0.830	1.050	32.537	-0.044	-0.044	0.000	0.000	0.000	0.000
52	C	37	ILE	0	0.111	-0.079	31.615	-0.002	-0.002	0.000	0.000	0.000	0.000
53	C	37	ILE	0	-0.084	0.105	32.438	0.000	0.000	0.000	0.000	0.000	0.000
54	C	38	THR	0	-0.022	-0.105	32.581	0.000	0.000	0.000	0.000	0.000	0.000
55	C	38	THR	0	-0.031	0.046	31.964	0.000	0.000	0.000	0.000	0.000	0.000
56	C	39	GLU	0	0.141	-0.097	33.332	0.001	0.001	0.000	0.000	0.000	0.000
57	C	39	GLU	-1	-0.979	-0.837	35.994	-0.012	-0.012	0.000	0.000	0.000	0.000
58	C	40	GLN	0	0.016	-0.102	31.748	-0.002	-0.002	0.000	0.000	0.000	0.000
59	C	40	GLN	0	-0.008	0.120	30.767	0.005	0.005	0.000	0.000	0.000	0.000
60	C	41	TYR	0	0.138	-0.073	29.001	-0.009	-0.009	0.000	0.000	0.000	0.000
61	C	41	TYR	0	-0.100	0.071	26.445	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	42	LEU	0	0.037	-0.090	29.402	0.000	0.000	0.000	0.000	0.000	0.000
63	C	42	LEU	0	-0.082	0.089	32.743	0.000	0.000	0.000	0.000	0.000	0.000
64	C	43	LEU	0	0.160	-0.080	31.180	0.001	0.001	0.000	0.000	0.000	0.000
65	C	43	LEU	0	-0.138	0.095	29.849	-0.001	-0.001	0.000	0.000	0.000	0.000
66	C	44	TYR	0	0.087	-0.092	26.997	-0.009	-0.009	0.000	0.000	0.000	0.000
67	C	44	TYR	0	-0.123	0.047	21.833	-0.012	-0.012	0.000	0.000	0.000	0.000
68	C	45	VAL	0	0.101	-0.097	26.677	-0.007	-0.007	0.000	0.000	0.000	0.000
69	C	45	VAL	0	-0.088	0.099	27.066	0.001	0.001	0.000	0.000	0.000	0.000
70	C	46	HIS	0	0.093	-0.044	27.975	0.000	0.000	0.000	0.000	0.000	0.000
71	C	46	HIS	0	-0.089	0.065	31.594	0.004	0.004	0.000	0.000	0.000	0.000
72	C	47	THR	0	0.000	-0.096	28.116	0.001	0.001	0.000	0.000	0.000	0.000
73	C	47	THR	0	-0.078	0.048	27.375	-0.003	-0.003	0.000	0.000	0.000	0.000
74	C	48	MET	0	0.151	-0.097	24.715	-0.016	-0.016	0.000	0.000	0.000	0.000
75	C	48	MET	0	-0.109	0.117	21.231	-0.006	-0.006	0.000	0.000	0.000	0.000
76	C	49	ARG	0	0.091	-0.064	25.491	-0.005	-0.005	0.000	0.000	0.000	0.000
77	C	49	ARG	1	0.814	1.029	27.162	-0.017	-0.017	0.000	0.000	0.000	0.000
78	C	50	VAL	0	0.025	-0.140	27.713	0.007	0.007	0.000	0.000	0.000	0.000
79	C	50	VAL	0	-0.099	0.092	30.110	0.001	0.001	0.000	0.000	0.000	0.000
80	C	51	LEU	0	0.169	-0.046	25.604	0.001	0.001	0.000	0.000	0.000	0.000
81	C	51	LEU	0	-0.087	0.097	22.614	-0.004	-0.004	0.000	0.000	0.000	0.000
82	C	52	GLU	0	0.044	-0.134	24.940	-0.013	-0.013	0.000	0.000	0.000	0.000
83	C	52	GLU	-1	-0.940	-0.849	23.470	0.019	0.019	0.000	0.000	0.000	0.000
84	C	53	LEU	0	0.096	-0.066	25.788	0.001	0.001	0.000	0.000	0.000	0.000
85	C	53	LEU	0	-0.125	0.091	30.537	0.003	0.003	0.000	0.000	0.000	0.000
86	C	54	ASP	0	0.102	-0.113	28.994	0.005	0.005	0.000	0.000	0.000	0.000
87	C	54	ASP	-1	-0.982	-0.840	28.504	-0.066	-0.066	0.000	0.000	0.000	0.000
88	C	55	ILE	0	0.130	-0.078	24.956	-0.005	-0.005	0.000	0.000	0.000	0.000
89	C	55	ILE	0	-0.122	0.077	22.257	-0.003	-0.003	0.000	0.000	0.000	0.000
90	C	56	ALA	0	0.074	-0.103	26.410	-0.007	-0.007	0.000	0.000	0.000	0.000
91	C	56	ALA	0	-0.085	0.102	27.535	0.003	0.003	0.000	0.000	0.000	0.000
92	C	57	SER	0	-0.040	-0.125	28.056	0.004	0.004	0.000	0.000	0.000	0.000
93	C	57	SER	0	-0.048	0.059	30.852	0.000	0.000	0.000	0.000	0.000	0.000
94	C	58	GLU	0	0.086	-0.105	28.527	0.007	0.007	0.000	0.000	0.000	0.000
95	C	58	GLU	-1	-1.006	-0.850	27.575	-0.106	-0.106	0.000	0.000	0.000	0.000
96	C	59	TYR	0	0.061	-0.130	27.532	-0.006	-0.006	0.000	0.000	0.000	0.000
97	C	59	TYR	0	-0.119	0.087	21.968	0.002	0.002	0.000	0.000	0.000	0.000
98	C	60	LEU	0	0.091	-0.096	28.651	0.005	0.005	0.000	0.000	0.000	0.000
99	C	60	LEU	0	-0.106	0.106	32.066	0.001	0.001	0.000	0.000	0.000	0.000
100	C	61	VAL	0	0.072	-0.131	32.128	0.007	0.007	0.000	0.000	0.000	0.000
101	C	61	VAL	0	-0.054	0.139	32.914	0.000	0.000	0.000	0.000	0.000	0.000
102	C	62	MET	0	0.083	-0.094	30.483	0.004	0.004	0.000	0.000	0.000	0.000
103	C	62	MET	0	-0.082	0.112	29.360	0.001	0.001	0.000	0.000	0.000	0.000
104	C	63	ALA	0	0.099	-0.100	31.960	-0.003	-0.003	0.000	0.000	0.000	0.000
105	C	63	ALA	0	-0.060	0.110	31.312	0.002	0.002	0.000	0.000	0.000	0.000
106	C	64	ALA	0	0.073	-0.122	32.723	0.004	0.004	0.000	0.000	0.000	0.000
107	C	64	ALA	0	-0.049	0.128	36.726	0.000	0.000	0.000	0.000	0.000	0.000
108	C	65	THR	0	-0.039	-0.109	35.295	0.006	0.006	0.000	0.000	0.000	0.000
109	C	65	THR	0	-0.067	0.053	34.390	-0.002	-0.002	0.000	0.000	0.000	0.000
110	C	66	LEU	0	0.137	-0.107	34.007	0.000	0.000	0.000	0.000	0.000	0.000
111	C	66	LEU	0	-0.068	0.129	30.695	0.000	0.000	0.000	0.000	0.000	0.000
112	C	67	LEU	0	0.078	-0.089	35.366	0.002	0.002	0.000	0.000	0.000	0.000
113	C	67	LEU	0	-0.092	0.119	37.054	0.001	0.001	0.000	0.000	0.000	0.000
114	C	68	SER	0	0.079	-0.056	37.925	0.004	0.004	0.000	0.000	0.000	0.000
115	C	68	SER	0	-0.009	0.083	40.265	-0.001	-0.001	0.000	0.000	0.000	0.000
116	C	69	ILE	0	0.030	-0.083	38.216	0.003	0.003	0.000	0.000	0.000	0.000
117	C	69	ILE	0	-0.047	0.106	36.092	-0.001	-0.001	0.000	0.000	0.000	0.000
118	C	70	LYS	0	0.105	-0.108	38.460	0.000	0.000	0.000	0.000	0.000	0.000
119	C	70	LYS	1	0.867	1.074	37.489	0.022	0.022	0.000	0.000	0.000	0.000
120	C	71	SER	0	-0.049	-0.131	39.506	0.003	0.003	0.000	0.000	0.000	0.000
121	C	71	SER	0	-0.073	0.042	42.246	0.001	0.001	0.000	0.000	0.000	0.000
122	C	72	ARG	0	0.097	-0.072	42.318	0.003	0.003	0.000	0.000	0.000	0.000
123	C	72	ARG	1	0.795	1.028	42.826	0.040	0.040	0.000	0.000	0.000	0.000
124	C	73	MET	0	0.107	-0.090	42.057	0.000	0.000	0.000	0.000	0.000	0.000
125	C	73	MET	0	-0.133	0.046	38.748	0.000	0.000	0.000	0.000	0.000	0.000
126	C	74	LEU	0	0.024	-0.067	43.337	0.000	0.000	0.000	0.000	0.000	0.000
127	C	74	LEU	0	-0.107	0.079	42.828	0.001	0.001	0.000	0.000	0.000	0.000
128	C	75	LEU	0	0.029	-0.076	45.743	0.000	0.000	0.000	0.000	0.000	0.000
129	C	75	LEU	0	-0.048	0.077	48.976	0.000	0.000	0.000	0.000	0.000	0.000
130	C	76	PRO	0	0.008	-0.090	47.703	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:10:THR)