FMO DATABASE

FMODB ID: GY4K1

Calculation Name: 3FXD-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3FXD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZYC9

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	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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-229927.272744
FMO2-HF: Nuclear repulsion	210778.761386
FMO2-HF: Total energy	-19148.511358
FMO2-MP2: Total energy	-19206.019695

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:4:GLN)

Summations of interaction energy for fragment #1(A:4:GLN)

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.
-0.62	1.095	-0.013	-0.855	-0.847	0.003

Interaction energy analysis for fragmet #1(A:4:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.192 / q_NPA : 0.056

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	5	LEU	0	-0.122	0.070	3.808	-0.072	0.197	-0.001	-0.055	-0.213	0.000
5	A	6	SER	0	0.029	-0.067	3.811	0.859	2.305	-0.012	-0.800	-0.634	0.003
6	A	6	SER	0	0.027	0.079	6.356	-0.015	-0.015	0.000	0.000	0.000	0.000
7	A	7	ASP	0	0.120	-0.134	6.037	0.086	0.086	0.000	0.000	0.000	0.000
8	A	7	ASP	-1	-0.896	-0.760	8.298	0.989	0.989	0.000	0.000	0.000	0.000
9	A	8	GLU	0	0.146	-0.100	9.152	0.028	0.028	0.000	0.000	0.000	0.000
10	A	8	GLU	-1	-1.032	-0.845	10.502	-0.264	-0.264	0.000	0.000	0.000	0.000
11	A	9	GLN	0	0.068	-0.120	8.545	0.045	0.045	0.000	0.000	0.000	0.000
12	A	9	GLN	0	-0.053	0.113	6.180	-0.332	-0.332	0.000	0.000	0.000	0.000
13	A	10	LYS	0	0.045	-0.119	9.116	-0.093	-0.093	0.000	0.000	0.000	0.000
14	A	10	LYS	1	0.780	1.008	5.764	-2.077	-2.077	0.000	0.000	0.000	0.000
15	A	11	GLU	0	0.043	-0.143	10.278	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	11	GLU	-1	-0.966	-0.805	13.264	0.151	0.151	0.000	0.000	0.000	0.000
17	A	12	THR	0	0.001	-0.053	12.870	0.005	0.005	0.000	0.000	0.000	0.000
18	A	12	THR	0	-0.042	0.059	12.500	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	13	ILE	0	0.072	-0.101	12.558	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	13	ILE	0	-0.097	0.082	9.884	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	14	LEU	0	0.074	-0.115	13.967	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	14	LEU	0	-0.072	0.119	14.633	0.009	0.009	0.000	0.000	0.000	0.000
23	A	15	LYS	0	0.060	-0.109	15.805	0.003	0.003	0.000	0.000	0.000	0.000
24	A	15	LYS	1	0.907	1.078	18.434	0.008	0.008	0.000	0.000	0.000	0.000
25	A	16	ALA	0	0.131	-0.080	17.608	0.013	0.013	0.000	0.000	0.000	0.000
26	A	16	ALA	0	-0.067	0.123	17.056	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	17	LEU	0	0.061	-0.096	17.756	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	17	LEU	0	-0.088	0.081	15.145	0.004	0.004	0.000	0.000	0.000	0.000
29	A	18	ASN	0	0.063	-0.097	19.163	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	18	ASN	0	-0.064	0.080	19.943	0.003	0.003	0.000	0.000	0.000	0.000
31	A	19	ASP	0	0.153	-0.028	21.627	0.007	0.007	0.000	0.000	0.000	0.000
32	A	19	ASP	-1	-0.946	-0.836	22.367	-0.034	-0.034	0.000	0.000	0.000	0.000
33	A	20	ALA	0	0.153	-0.082	22.446	0.004	0.004	0.000	0.000	0.000	0.000
34	A	20	ALA	0	-0.089	0.104	22.180	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	21	ILE	0	0.030	-0.117	23.399	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	21	ILE	0	-0.121	0.075	21.447	0.003	0.003	0.000	0.000	0.000	0.000
37	A	22	GLU	0	0.069	-0.114	25.064	0.002	0.002	0.000	0.000	0.000	0.000
38	A	22	GLU	-1	-1.018	-0.853	26.306	0.002	0.002	0.000	0.000	0.000	0.000
39	A	23	LYS	0	0.040	-0.073	27.142	0.003	0.003	0.000	0.000	0.000	0.000
40	A	23	LYS	1	0.751	0.996	26.161	0.025	0.025	0.000	0.000	0.000	0.000
41	A	24	GLY	0	-0.007	-0.108	27.870	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	25	PRO	0	-0.011	-0.027	29.114	0.006	0.006	0.000	0.000	0.000	0.000
43	A	26	TRP	0	0.016	-0.033	30.086	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	26	TRP	0	-0.107	0.090	25.915	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	27	ASP	0	0.137	-0.100	31.377	0.002	0.002	0.000	0.000	0.000	0.000
46	A	27	ASP	-1	-0.910	-0.788	34.382	0.000	0.000	0.000	0.000	0.000	0.000
47	A	28	LYS	0	-0.002	-0.129	34.796	0.003	0.003	0.000	0.000	0.000	0.000
48	A	28	LYS	1	0.819	1.048	34.956	0.009	0.009	0.000	0.000	0.000	0.000
49	A	29	SER	0	0.060	-0.077	35.838	0.000	0.000	0.000	0.000	0.000	0.000
50	A	29	SER	0	-0.009	0.062	36.413	0.000	0.000	0.000	0.000	0.000	0.000
51	A	30	ASN	0	0.120	-0.046	35.404	0.001	0.001	0.000	0.000	0.000	0.000
52	A	30	ASN	0	-0.047	0.086	37.334	0.002	0.002	0.000	0.000	0.000	0.000
53	A	31	PHE	0	0.101	-0.071	34.293	0.003	0.003	0.000	0.000	0.000	0.000
54	A	31	PHE	0	-0.038	0.106	31.647	0.001	0.001	0.000	0.000	0.000	0.000
55	A	32	LEU	0	0.026	-0.141	31.614	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	32	LEU	0	-0.020	0.136	30.972	0.000	0.000	0.000	0.000	0.000	0.000
57	A	33	ARG	0	0.238	-0.023	30.552	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	33	ARG	1	0.799	1.039	32.094	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	34	VAL	0	0.018	-0.141	29.900	0.005	0.005	0.000	0.000	0.000	0.000
60	A	34	VAL	0	-0.083	0.110	29.251	0.000	0.000	0.000	0.000	0.000	0.000
61	A	35	ILE	0	0.017	-0.130	27.200	0.003	0.003	0.000	0.000	0.000	0.000
62	A	35	ILE	0	-0.070	0.125	26.412	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	36	GLY	0	0.098	-0.069	25.760	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	37	LYS	0	0.044	-0.007	25.505	0.006	0.006	0.000	0.000	0.000	0.000
65	A	37	LYS	1	0.875	1.066	27.310	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	38	LYS	0	0.085	-0.083	23.758	0.014	0.014	0.000	0.000	0.000	0.000
67	A	38	LYS	1	0.891	1.087	20.709	0.037	0.037	0.000	0.000	0.000	0.000
68	A	39	LEU	0	0.094	-0.105	21.323	0.001	0.001	0.000	0.000	0.000	0.000
69	A	39	LEU	0	-0.040	0.135	20.501	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	40	ILE	0	0.125	-0.085	20.623	0.003	0.003	0.000	0.000	0.000	0.000
71	A	40	ILE	0	-0.080	0.102	23.448	0.001	0.001	0.000	0.000	0.000	0.000
72	A	41	ALA	0	0.155	-0.072	20.969	0.023	0.023	0.000	0.000	0.000	0.000
73	A	41	ALA	0	-0.126	0.079	21.562	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	42	ILE	0	0.015	-0.124	17.604	0.028	0.028	0.000	0.000	0.000	0.000
75	A	42	ILE	0	-0.113	0.084	16.160	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	43	ARG	0	0.094	-0.100	16.287	0.010	0.010	0.000	0.000	0.000	0.000
77	A	43	ARG	1	0.738	0.997	18.122	-0.095	-0.095	0.000	0.000	0.000	0.000
78	A	44	ASP	0	0.065	-0.130	16.855	0.042	0.042	0.000	0.000	0.000	0.000
79	A	44	ASP	-1	-0.899	-0.778	20.063	0.110	0.110	0.000	0.000	0.000	0.000
80	A	45	ARG	0	0.061	-0.107	16.118	0.058	0.058	0.000	0.000	0.000	0.000
81	A	45	ARG	1	0.828	1.049	13.489	-0.178	-0.178	0.000	0.000	0.000	0.000
82	A	46	PHE	0	0.067	-0.107	12.405	0.071	0.071	0.000	0.000	0.000	0.000
83	A	46	PHE	0	-0.066	0.105	9.238	0.012	0.012	0.000	0.000	0.000	0.000
84	A	47	LEU	0	0.088	-0.115	12.446	0.136	0.136	0.000	0.000	0.000	0.000
85	A	47	LEU	0	-0.065	0.119	15.539	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	48	LYS	0	0.175	-0.029	14.239	0.092	0.092	0.000	0.000	0.000	0.000
87	A	48	LYS	1	0.812	1.031	15.344	-0.244	-0.244	0.000	0.000	0.000	0.000
88	A	49	ARG	0	0.002	-0.096	10.585	0.032	0.032	0.000	0.000	0.000	0.000
89	A	49	ARG	1	0.838	1.017	8.881	-0.347	-0.347	0.000	0.000	0.000	0.000
90	A	50	ILE	0	0.046	-0.076	9.373	0.262	0.262	0.000	0.000	0.000	0.000
91	A	50	ILE	0	-0.054	0.099	8.744	0.001	0.001	0.000	0.000	0.000	0.000
92	A	51	GLY	0	0.000	-0.095	10.395	0.053	0.053	0.000	0.000	0.000	0.000
93	A	52	ALA	0	-0.061	-0.028	11.302	0.006	0.006	0.000	0.000	0.000	0.000
94	A	52	ALA	0	-0.003	0.017	11.187	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLN)