FMO DATABASE

FMODB ID: 8N6ZY

Calculation Name: 3FXD-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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

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	-230627.33298
FMO2-HF: Nuclear repulsion	211478.641238
FMO2-HF: Total energy	-19148.691742
FMO2-MP2: Total energy	-19206.177921

3D Structure

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.
-0.879	0.579	-0.013	-0.591	-0.854	0.001

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 : 0.193 / q_NPA : 0.043

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

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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	-0.120	0.080	3.588	0.016	0.204	-0.001	0.062	-0.249	0.000
5	A	6	SER	0	0.057	-0.063	3.872	0.844	2.114	-0.012	-0.653	-0.605	0.001
6	A	6	SER	0	-0.027	0.050	7.270	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	7	ASP	0	0.045	-0.125	6.420	0.175	0.175	0.000	0.000	0.000	0.000
8	A	7	ASP	-1	-0.850	-0.769	8.477	1.191	1.191	0.000	0.000	0.000	0.000
9	A	8	GLU	0	0.165	-0.064	9.026	0.022	0.022	0.000	0.000	0.000	0.000
10	A	8	GLU	-1	-0.952	-0.806	10.761	-0.275	-0.275	0.000	0.000	0.000	0.000
11	A	9	GLN	0	0.101	-0.120	8.421	0.043	0.043	0.000	0.000	0.000	0.000
12	A	9	GLN	0	-0.064	0.112	6.309	-0.332	-0.332	0.000	0.000	0.000	0.000
13	A	10	LYS	0	0.060	-0.108	9.006	-0.121	-0.121	0.000	0.000	0.000	0.000
14	A	10	LYS	1	0.737	0.988	5.519	-2.450	-2.450	0.000	0.000	0.000	0.000
15	A	11	GLU	0	0.105	-0.124	10.117	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	11	GLU	-1	-1.009	-0.818	13.353	0.219	0.219	0.000	0.000	0.000	0.000
17	A	12	THR	0	0.029	-0.050	13.250	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	12	THR	0	-0.048	0.053	12.488	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	13	ILE	0	0.065	-0.093	12.243	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	13	ILE	0	-0.081	0.083	9.573	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	14	LEU	0	0.078	-0.115	13.662	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	14	LEU	0	-0.086	0.114	14.189	0.011	0.011	0.000	0.000	0.000	0.000
23	A	15	LYS	0	0.062	-0.103	15.495	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	15	LYS	1	0.855	1.049	18.489	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	16	ALA	0	0.121	-0.100	17.167	0.007	0.007	0.000	0.000	0.000	0.000
26	A	16	ALA	0	-0.088	0.113	16.410	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	17	LEU	0	0.059	-0.100	17.148	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	17	LEU	0	-0.097	0.077	14.419	0.005	0.005	0.000	0.000	0.000	0.000
29	A	18	ASN	0	0.071	-0.088	18.522	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	18	ASN	0	-0.079	0.080	19.203	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	19	ASP	0	0.120	-0.051	21.148	0.005	0.005	0.000	0.000	0.000	0.000
32	A	19	ASP	-1	-0.902	-0.809	21.973	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	20	ALA	0	0.179	-0.070	21.939	0.000	0.000	0.000	0.000	0.000	0.000
34	A	20	ALA	0	-0.098	0.103	21.628	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	21	ILE	0	0.016	-0.120	23.004	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	21	ILE	0	-0.114	0.077	21.229	0.003	0.003	0.000	0.000	0.000	0.000
37	A	22	GLU	0	0.091	-0.103	24.744	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	22	GLU	-1	-1.012	-0.836	25.762	0.029	0.029	0.000	0.000	0.000	0.000
39	A	23	LYS	0	0.029	-0.083	26.856	0.002	0.002	0.000	0.000	0.000	0.000
40	A	23	LYS	1	0.760	0.977	26.017	0.000	0.000	0.000	0.000	0.000	0.000
41	A	24	GLY	0	0.012	-0.093	27.740	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	25	PRO	0	-0.003	-0.024	28.697	0.006	0.006	0.000	0.000	0.000	0.000
43	A	26	TRP	0	0.027	-0.029	29.660	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	26	TRP	0	-0.117	0.078	25.490	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	27	ASP	0	0.073	-0.107	30.923	0.002	0.002	0.000	0.000	0.000	0.000
46	A	27	ASP	-1	-0.826	-0.766	33.898	0.011	0.011	0.000	0.000	0.000	0.000
47	A	28	LYS	0	0.002	-0.111	34.279	0.002	0.002	0.000	0.000	0.000	0.000
48	A	28	LYS	1	0.792	1.011	34.825	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	29	SER	0	0.027	-0.075	35.334	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	29	SER	0	-0.011	0.065	36.103	0.000	0.000	0.000	0.000	0.000	0.000
51	A	30	ASN	0	0.125	-0.053	34.968	0.002	0.002	0.000	0.000	0.000	0.000
52	A	30	ASN	0	-0.046	0.088	37.262	0.003	0.003	0.000	0.000	0.000	0.000
53	A	31	PHE	0	0.105	-0.068	33.803	0.004	0.004	0.000	0.000	0.000	0.000
54	A	31	PHE	0	-0.044	0.101	31.117	0.000	0.000	0.000	0.000	0.000	0.000
55	A	32	LEU	0	0.043	-0.127	31.115	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	32	LEU	0	-0.039	0.133	30.618	0.000	0.000	0.000	0.000	0.000	0.000
57	A	33	ARG	0	0.209	-0.035	29.996	0.000	0.000	0.000	0.000	0.000	0.000
58	A	33	ARG	1	0.814	1.047	32.015	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	34	VAL	0	0.026	-0.143	29.631	0.009	0.009	0.000	0.000	0.000	0.000
60	A	34	VAL	0	-0.071	0.111	28.654	0.000	0.000	0.000	0.000	0.000	0.000
61	A	35	ILE	0	0.024	-0.119	26.618	0.005	0.005	0.000	0.000	0.000	0.000
62	A	35	ILE	0	-0.077	0.122	25.900	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	36	GLY	0	0.110	-0.068	25.285	0.000	0.000	0.000	0.000	0.000	0.000
64	A	37	LYS	0	0.047	-0.005	25.123	0.010	0.010	0.000	0.000	0.000	0.000
65	A	37	LYS	1	0.876	1.068	27.106	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	38	LYS	0	0.081	-0.089	23.515	0.017	0.017	0.000	0.000	0.000	0.000
67	A	38	LYS	1	0.874	1.081	20.579	0.015	0.015	0.000	0.000	0.000	0.000
68	A	39	LEU	0	0.093	-0.115	20.967	0.004	0.004	0.000	0.000	0.000	0.000
69	A	39	LEU	0	-0.060	0.133	19.933	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	40	ILE	0	0.124	-0.080	20.252	0.009	0.009	0.000	0.000	0.000	0.000
71	A	40	ILE	0	-0.109	0.087	23.310	0.000	0.000	0.000	0.000	0.000	0.000
72	A	41	ALA	0	0.160	-0.080	20.508	0.029	0.029	0.000	0.000	0.000	0.000
73	A	41	ALA	0	-0.124	0.084	21.352	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	42	ILE	0	0.037	-0.110	17.199	0.036	0.036	0.000	0.000	0.000	0.000
75	A	42	ILE	0	-0.112	0.085	15.716	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	43	ARG	0	0.108	-0.088	15.929	0.029	0.029	0.000	0.000	0.000	0.000
77	A	43	ARG	1	0.737	0.986	17.841	-0.154	-0.154	0.000	0.000	0.000	0.000
78	A	44	ASP	0	0.094	-0.099	16.466	0.062	0.062	0.000	0.000	0.000	0.000
79	A	44	ASP	-1	-0.894	-0.782	19.720	0.170	0.170	0.000	0.000	0.000	0.000
80	A	45	ARG	0	0.058	-0.112	15.764	0.068	0.068	0.000	0.000	0.000	0.000
81	A	45	ARG	1	0.828	1.051	13.469	-0.277	-0.277	0.000	0.000	0.000	0.000
82	A	46	PHE	0	0.080	-0.094	12.114	0.084	0.084	0.000	0.000	0.000	0.000
83	A	46	PHE	0	-0.079	0.097	9.108	0.013	0.013	0.000	0.000	0.000	0.000
84	A	47	LEU	0	0.090	-0.110	12.198	0.189	0.189	0.000	0.000	0.000	0.000
85	A	47	LEU	0	-0.082	0.111	15.102	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	48	LYS	0	0.139	-0.044	13.670	0.116	0.116	0.000	0.000	0.000	0.000
87	A	48	LYS	1	0.821	1.032	15.279	-0.301	-0.301	0.000	0.000	0.000	0.000
88	A	49	ARG	0	0.015	-0.107	10.129	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	49	ARG	1	0.837	1.025	8.400	-0.482	-0.482	0.000	0.000	0.000	0.000
90	A	50	ILE	0	0.043	-0.087	8.965	0.351	0.351	0.000	0.000	0.000	0.000
91	A	50	ILE	0	-0.064	0.101	8.344	0.004	0.004	0.000	0.000	0.000	0.000
92	A	51	GLY	0	0.018	-0.095	10.002	0.059	0.059	0.000	0.000	0.000	0.000
93	A	52	ALA	0	-0.099	-0.045	10.582	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	52	ALA	0	0.031	0.034	10.341	0.002	0.002	0.000	0.000	0.000	0.000

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