FMO DATABASE

FMODB ID: 9LNY2

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	OptAll
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	-331372.730421
FMO2-HF: Nuclear repulsion	304313.902049
FMO2-HF: Total energy	-27058.828372
FMO2-MP2: Total energy	-27136.995527

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.
-0.38	1.794	-0.015	-1.243	-0.916	0.003

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 : 0.038 / q_NPA : 0.030

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	-0.092	0.063	4.179	-0.019	0.393	0.001	-0.202	-0.211	0.000
5	C	12	GLU	0	0.065	-0.095	3.869	-0.858	0.904	-0.016	-1.041	-0.705	0.003
6	C	12	GLU	-1	-0.906	-0.790	6.526	1.407	1.407	0.000	0.000	0.000	0.000
7	C	13	GLY	0	0.029	-0.100	6.987	-0.674	-0.674	0.000	0.000	0.000	0.000
8	C	14	PRO	0	-0.006	-0.020	8.762	0.071	0.071	0.000	0.000	0.000	0.000
9	C	15	LEU	0	0.124	0.020	9.916	0.057	0.057	0.000	0.000	0.000	0.000
10	C	15	LEU	0	-0.069	0.103	13.703	-0.003	-0.003	0.000	0.000	0.000	0.000
11	C	16	ASP	0	0.092	-0.083	11.757	0.014	0.014	0.000	0.000	0.000	0.000
12	C	16	ASP	-1	-0.857	-0.811	9.722	0.083	0.083	0.000	0.000	0.000	0.000
13	C	17	LEU	0	0.091	-0.100	7.805	0.232	0.232	0.000	0.000	0.000	0.000
14	C	17	LEU	0	-0.078	0.113	4.823	-0.083	-0.083	0.000	0.000	0.000	0.000
15	C	18	LEU	0	0.106	-0.064	9.082	0.107	0.107	0.000	0.000	0.000	0.000
16	C	18	LEU	0	-0.084	0.093	11.992	-0.018	-0.018	0.000	0.000	0.000	0.000
17	C	19	LEU	0	0.042	-0.126	12.045	0.022	0.022	0.000	0.000	0.000	0.000
18	C	19	LEU	0	-0.058	0.101	13.977	0.005	0.005	0.000	0.000	0.000	0.000
19	C	20	HIS	0	0.000	-0.111	10.797	0.015	0.015	0.000	0.000	0.000	0.000
20	C	20	HIS	1	0.684	0.912	8.747	-0.702	-0.702	0.000	0.000	0.000	0.000
21	C	21	LEU	0	0.146	-0.049	11.993	0.096	0.096	0.000	0.000	0.000	0.000
22	C	21	LEU	0	-0.123	0.090	11.371	-0.016	-0.016	0.000	0.000	0.000	0.000
23	C	22	ILE	0	0.069	-0.101	13.060	0.023	0.023	0.000	0.000	0.000	0.000
24	C	22	ILE	0	-0.077	0.103	15.740	-0.007	-0.007	0.000	0.000	0.000	0.000
25	C	23	ASN	0	0.147	-0.062	16.559	-0.012	-0.012	0.000	0.000	0.000	0.000
26	C	23	ASN	0	-0.131	0.056	16.964	0.040	0.040	0.000	0.000	0.000	0.000
27	C	24	ARG	0	0.112	-0.078	15.840	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	24	ARG	1	0.706	0.957	14.137	-0.197	-0.197	0.000	0.000	0.000	0.000
29	C	25	LEU	0	0.043	-0.116	17.180	0.017	0.017	0.000	0.000	0.000	0.000
30	C	25	LEU	0	-0.099	0.080	15.650	-0.008	-0.008	0.000	0.000	0.000	0.000
31	C	26	GLU	0	0.158	-0.078	18.747	-0.014	-0.014	0.000	0.000	0.000	0.000
32	C	26	GLU	-1	-0.943	-0.781	20.594	0.057	0.057	0.000	0.000	0.000	0.000
33	C	27	ILE	0	0.121	-0.071	20.851	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	27	ILE	0	-0.098	0.080	19.801	0.007	0.007	0.000	0.000	0.000	0.000
35	C	28	ASP	0	0.079	-0.132	20.863	0.002	0.002	0.000	0.000	0.000	0.000
36	C	28	ASP	-1	-0.937	-0.794	19.164	0.144	0.144	0.000	0.000	0.000	0.000
37	C	29	ILE	0	0.034	-0.082	22.219	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	29	ILE	0	-0.125	0.078	22.007	-0.006	-0.006	0.000	0.000	0.000	0.000
39	C	30	TYR	0	-0.015	-0.146	24.837	-0.006	-0.006	0.000	0.000	0.000	0.000
40	C	30	TYR	0	-0.055	0.090	24.291	-0.008	-0.008	0.000	0.000	0.000	0.000
41	C	31	ASP	0	0.066	-0.064	25.539	-0.007	-0.007	0.000	0.000	0.000	0.000
42	C	31	ASP	-1	-0.900	-0.815	24.876	0.082	0.082	0.000	0.000	0.000	0.000
43	C	32	ILE	0	0.128	-0.095	26.554	0.019	0.019	0.000	0.000	0.000	0.000
44	C	32	ILE	0	-0.128	0.090	24.852	0.001	0.001	0.000	0.000	0.000	0.000
45	C	33	PRO	0	-0.044	-0.138	27.179	-0.008	-0.008	0.000	0.000	0.000	0.000
46	C	34	VAL	0	0.094	0.091	30.311	-0.008	-0.008	0.000	0.000	0.000	0.000
47	C	34	VAL	0	-0.139	0.026	32.722	-0.002	-0.002	0.000	0.000	0.000	0.000
48	C	35	ALA	0	0.093	-0.129	29.803	0.008	0.008	0.000	0.000	0.000	0.000
49	C	35	ALA	0	-0.076	0.132	29.324	0.001	0.001	0.000	0.000	0.000	0.000
50	C	36	LYS	0	0.102	-0.086	30.428	-0.003	-0.003	0.000	0.000	0.000	0.000
51	C	36	LYS	1	0.839	1.051	31.914	-0.045	-0.045	0.000	0.000	0.000	0.000
52	C	37	ILE	0	0.089	-0.085	31.760	-0.004	-0.004	0.000	0.000	0.000	0.000
53	C	37	ILE	0	-0.068	0.097	32.691	0.000	0.000	0.000	0.000	0.000	0.000
54	C	38	THR	0	-0.049	-0.109	32.857	0.001	0.001	0.000	0.000	0.000	0.000
55	C	38	THR	0	-0.008	0.049	32.417	0.000	0.000	0.000	0.000	0.000	0.000
56	C	39	GLU	0	0.154	-0.085	33.605	0.002	0.002	0.000	0.000	0.000	0.000
57	C	39	GLU	-1	-0.996	-0.846	35.945	-0.015	-0.015	0.000	0.000	0.000	0.000
58	C	40	GLN	0	0.014	-0.111	31.301	-0.003	-0.003	0.000	0.000	0.000	0.000
59	C	40	GLN	0	0.015	0.123	30.644	0.005	0.005	0.000	0.000	0.000	0.000
60	C	41	TYR	0	0.122	-0.062	28.907	-0.010	-0.010	0.000	0.000	0.000	0.000
61	C	41	TYR	0	-0.113	0.060	26.489	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	42	LEU	0	0.061	-0.090	29.531	0.000	0.000	0.000	0.000	0.000	0.000
63	C	42	LEU	0	-0.092	0.092	32.744	0.000	0.000	0.000	0.000	0.000	0.000
64	C	43	LEU	0	0.165	-0.073	31.665	0.000	0.000	0.000	0.000	0.000	0.000
65	C	43	LEU	0	-0.135	0.092	30.186	-0.001	-0.001	0.000	0.000	0.000	0.000
66	C	44	TYR	0	0.096	-0.084	27.154	-0.010	-0.010	0.000	0.000	0.000	0.000
67	C	44	TYR	0	-0.142	0.037	22.016	-0.011	-0.011	0.000	0.000	0.000	0.000
68	C	45	VAL	0	0.089	-0.092	26.998	-0.009	-0.009	0.000	0.000	0.000	0.000
69	C	45	VAL	0	-0.079	0.098	26.975	0.002	0.002	0.000	0.000	0.000	0.000
70	C	46	HIS	0	0.076	-0.072	28.084	0.000	0.000	0.000	0.000	0.000	0.000
71	C	46	HIS	0	-0.090	0.065	31.892	0.004	0.004	0.000	0.000	0.000	0.000
72	C	47	THR	0	0.004	-0.104	28.537	0.001	0.001	0.000	0.000	0.000	0.000
73	C	47	THR	0	-0.095	0.039	27.919	-0.004	-0.004	0.000	0.000	0.000	0.000
74	C	48	MET	0	0.165	-0.076	24.875	-0.015	-0.015	0.000	0.000	0.000	0.000
75	C	48	MET	0	-0.113	0.108	21.124	-0.006	-0.006	0.000	0.000	0.000	0.000
76	C	49	ARG	0	0.080	-0.082	25.679	-0.007	-0.007	0.000	0.000	0.000	0.000
77	C	49	ARG	1	0.794	1.039	27.204	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	50	VAL	0	0.039	-0.116	27.894	0.009	0.009	0.000	0.000	0.000	0.000
79	C	50	VAL	0	-0.098	0.096	30.320	0.000	0.000	0.000	0.000	0.000	0.000
80	C	51	LEU	0	0.161	-0.063	25.896	0.002	0.002	0.000	0.000	0.000	0.000
81	C	51	LEU	0	-0.082	0.100	23.078	-0.004	-0.004	0.000	0.000	0.000	0.000
82	C	52	GLU	0	0.042	-0.137	25.214	-0.016	-0.016	0.000	0.000	0.000	0.000
83	C	52	GLU	-1	-0.955	-0.850	23.813	0.008	0.008	0.000	0.000	0.000	0.000
84	C	53	LEU	0	0.100	-0.082	26.109	0.000	0.000	0.000	0.000	0.000	0.000
85	C	53	LEU	0	-0.134	0.086	30.836	0.002	0.002	0.000	0.000	0.000	0.000
86	C	54	ASP	0	0.101	-0.111	29.440	0.004	0.004	0.000	0.000	0.000	0.000
87	C	54	ASP	-1	-0.978	-0.839	28.497	-0.077	-0.077	0.000	0.000	0.000	0.000
88	C	55	ILE	0	0.138	-0.070	25.251	-0.004	-0.004	0.000	0.000	0.000	0.000
89	C	55	ILE	0	-0.104	0.094	22.574	-0.004	-0.004	0.000	0.000	0.000	0.000
90	C	56	ALA	0	0.081	-0.110	26.713	-0.008	-0.008	0.000	0.000	0.000	0.000
91	C	56	ALA	0	-0.080	0.103	27.939	0.003	0.003	0.000	0.000	0.000	0.000
92	C	57	SER	0	-0.043	-0.111	28.445	0.005	0.005	0.000	0.000	0.000	0.000
93	C	57	SER	0	-0.063	0.051	31.147	0.000	0.000	0.000	0.000	0.000	0.000
94	C	58	GLU	0	0.124	-0.094	28.898	0.008	0.008	0.000	0.000	0.000	0.000
95	C	58	GLU	-1	-1.019	-0.852	27.954	-0.118	-0.118	0.000	0.000	0.000	0.000
96	C	59	TYR	0	0.078	-0.108	27.709	-0.004	-0.004	0.000	0.000	0.000	0.000
97	C	59	TYR	0	-0.131	0.082	22.090	0.001	0.001	0.000	0.000	0.000	0.000
98	C	60	LEU	0	0.125	-0.094	28.813	0.003	0.003	0.000	0.000	0.000	0.000
99	C	60	LEU	0	-0.116	0.102	32.346	0.002	0.002	0.000	0.000	0.000	0.000
100	C	61	VAL	0	0.066	-0.125	32.338	0.007	0.007	0.000	0.000	0.000	0.000
101	C	61	VAL	0	-0.055	0.134	33.058	0.000	0.000	0.000	0.000	0.000	0.000
102	C	62	MET	0	0.114	-0.086	30.444	0.004	0.004	0.000	0.000	0.000	0.000
103	C	62	MET	0	-0.098	0.109	29.143	0.002	0.002	0.000	0.000	0.000	0.000
104	C	63	ALA	0	0.106	-0.101	31.728	-0.002	-0.002	0.000	0.000	0.000	0.000
105	C	63	ALA	0	-0.065	0.106	31.272	0.002	0.002	0.000	0.000	0.000	0.000
106	C	64	ALA	0	0.067	-0.120	32.764	0.004	0.004	0.000	0.000	0.000	0.000
107	C	64	ALA	0	-0.058	0.122	36.625	0.000	0.000	0.000	0.000	0.000	0.000
108	C	65	THR	0	-0.001	-0.106	35.429	0.006	0.006	0.000	0.000	0.000	0.000
109	C	65	THR	0	-0.069	0.060	34.613	-0.002	-0.002	0.000	0.000	0.000	0.000
110	C	66	LEU	0	0.085	-0.118	33.768	0.001	0.001	0.000	0.000	0.000	0.000
111	C	66	LEU	0	-0.082	0.117	30.528	0.000	0.000	0.000	0.000	0.000	0.000
112	C	67	LEU	0	0.106	-0.089	35.177	0.002	0.002	0.000	0.000	0.000	0.000
113	C	67	LEU	0	-0.111	0.106	36.867	0.001	0.001	0.000	0.000	0.000	0.000
114	C	68	SER	0	0.051	-0.078	37.762	0.004	0.004	0.000	0.000	0.000	0.000
115	C	68	SER	0	-0.023	0.081	40.029	-0.001	-0.001	0.000	0.000	0.000	0.000
116	C	69	ILE	0	0.037	-0.092	38.130	0.004	0.004	0.000	0.000	0.000	0.000
117	C	69	ILE	0	-0.056	0.104	36.021	-0.001	-0.001	0.000	0.000	0.000	0.000
118	C	70	LYS	0	0.096	-0.098	38.361	0.000	0.000	0.000	0.000	0.000	0.000
119	C	70	LYS	1	0.864	1.074	37.383	0.032	0.032	0.000	0.000	0.000	0.000
120	C	71	SER	0	-0.005	-0.114	39.389	0.003	0.003	0.000	0.000	0.000	0.000
121	C	71	SER	0	-0.067	0.052	42.457	0.001	0.001	0.000	0.000	0.000	0.000
122	C	72	ARG	0	0.097	-0.075	42.474	0.004	0.004	0.000	0.000	0.000	0.000
123	C	72	ARG	1	0.818	1.046	42.813	0.047	0.047	0.000	0.000	0.000	0.000
124	C	73	MET	0	0.091	-0.091	41.952	-0.001	-0.001	0.000	0.000	0.000	0.000
125	C	73	MET	0	-0.138	0.055	38.741	0.000	0.000	0.000	0.000	0.000	0.000
126	C	74	LEU	0	0.019	-0.085	43.254	0.001	0.001	0.000	0.000	0.000	0.000
127	C	74	LEU	0	-0.094	0.082	43.326	0.001	0.001	0.000	0.000	0.000	0.000
128	C	75	LEU	0	0.040	-0.078	46.228	-0.001	-0.001	0.000	0.000	0.000	0.000
129	C	75	LEU	0	-0.028	0.099	49.499	0.000	0.000	0.000	0.000	0.000	0.000
130	C	76	PRO	0	-0.023	-0.114	48.212	-0.005	-0.005	0.000	0.000	0.000	0.000

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