FMO DATABASE

FMODB ID: JV1Z9

Calculation Name: 5GXQ-E-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5GXQ

Chain ID: E

ChEMBL ID:

UniProt ID: P04908

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-641337.70758
FMO2-HF: Nuclear repulsion	601877.021194
FMO2-HF: Total energy	-39460.686386
FMO2-MP2: Total energy	-39577.278364

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:37:LYS)

Summations of interaction energy for fragment #1(A:37:LYS)

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.
174.612	173.726	10.713	-0.837	-8.99	-0.08

Interaction energy analysis for fragmet #1(A:37:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.762 / q_NPA : 1.897

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].
3	A	39	HIS	0	0.056	0.009	2.090	-43.345	-43.283	10.658	-2.226	-8.494	-0.078
4	A	40	ARG	1	0.991	0.991	3.147	75.548	74.530	0.056	1.389	-0.427	-0.002
5	A	41	TYR	0	0.029	0.016	5.134	-3.806	-3.736	-0.001	0.000	-0.069	0.000
6	A	42	ARG	1	1.018	1.008	7.979	46.147	46.147	0.000	0.000	0.000	0.000
7	A	43	PRO	0	0.068	0.037	10.080	1.352	1.352	0.000	0.000	0.000	0.000
8	A	44	GLY	0	0.074	0.041	13.426	0.540	0.540	0.000	0.000	0.000	0.000
9	A	45	THR	0	-0.059	-0.048	10.770	0.793	0.793	0.000	0.000	0.000	0.000
10	A	46	VAL	0	-0.021	-0.014	12.288	0.036	0.036	0.000	0.000	0.000	0.000
11	A	47	ALA	0	0.099	0.059	14.710	1.273	1.273	0.000	0.000	0.000	0.000
12	A	48	LEU	0	0.036	0.016	16.649	1.204	1.204	0.000	0.000	0.000	0.000
13	A	49	ARG	1	0.872	0.947	10.911	42.726	42.726	0.000	0.000	0.000	0.000
14	A	50	GLU	-1	-0.927	-0.970	17.498	-30.483	-30.483	0.000	0.000	0.000	0.000
15	A	51	ILE	0	0.042	0.028	20.208	0.971	0.971	0.000	0.000	0.000	0.000
16	A	52	ARG	1	0.956	0.967	17.962	29.677	29.677	0.000	0.000	0.000	0.000
17	A	53	ARG	1	0.860	0.961	21.063	26.379	26.379	0.000	0.000	0.000	0.000
18	A	54	TYR	0	0.051	-0.002	22.457	0.483	0.483	0.000	0.000	0.000	0.000
19	A	55	GLN	0	0.035	0.032	25.689	0.190	0.190	0.000	0.000	0.000	0.000
20	A	56	LYS	1	0.821	0.911	21.902	25.734	25.734	0.000	0.000	0.000	0.000
21	A	57	SER	0	-0.112	-0.078	26.976	0.190	0.190	0.000	0.000	0.000	0.000
22	A	58	THR	0	0.037	0.004	28.649	0.310	0.310	0.000	0.000	0.000	0.000
23	A	59	GLU	-1	-0.866	-0.897	27.338	-21.593	-21.593	0.000	0.000	0.000	0.000
24	A	60	LEU	0	-0.023	-0.005	31.326	-0.299	-0.299	0.000	0.000	0.000	0.000
25	A	61	LEU	0	-0.027	-0.021	27.655	-0.530	-0.530	0.000	0.000	0.000	0.000
26	A	62	VAL	0	-0.043	-0.009	30.196	-0.493	-0.493	0.000	0.000	0.000	0.000
27	A	63	ARG	1	0.937	0.959	30.015	20.432	20.432	0.000	0.000	0.000	0.000
28	A	64	LYS	1	1.017	1.006	33.592	17.458	17.458	0.000	0.000	0.000	0.000
29	A	65	LEU	0	0.006	0.010	37.132	0.373	0.373	0.000	0.000	0.000	0.000
30	A	66	PRO	0	-0.038	-0.042	34.505	0.317	0.317	0.000	0.000	0.000	0.000
31	A	67	PHE	0	0.086	0.063	37.343	0.196	0.196	0.000	0.000	0.000	0.000
32	A	68	GLN	0	0.032	0.015	38.946	0.682	0.682	0.000	0.000	0.000	0.000
33	A	69	ARG	1	0.897	0.947	37.730	16.596	16.596	0.000	0.000	0.000	0.000
34	A	70	LEU	0	0.080	0.051	39.097	0.270	0.270	0.000	0.000	0.000	0.000
35	A	71	VAL	0	0.006	0.006	42.340	0.299	0.299	0.000	0.000	0.000	0.000
36	A	72	ARG	1	0.871	0.921	44.823	13.864	13.864	0.000	0.000	0.000	0.000
37	A	73	GLU	-1	-0.942	-0.957	43.689	-14.367	-14.367	0.000	0.000	0.000	0.000
38	A	74	ILE	0	0.042	0.012	43.554	0.266	0.266	0.000	0.000	0.000	0.000
39	A	75	ALA	0	-0.040	-0.017	47.707	0.276	0.276	0.000	0.000	0.000	0.000
40	A	76	GLN	0	-0.048	-0.022	49.992	0.358	0.358	0.000	0.000	0.000	0.000
41	A	77	ASP	-1	-0.904	-0.952	49.521	-12.565	-12.565	0.000	0.000	0.000	0.000
42	A	78	PHE	0	-0.084	-0.023	52.278	0.189	0.189	0.000	0.000	0.000	0.000
43	A	79	LYS	1	0.895	0.938	54.209	11.017	11.017	0.000	0.000	0.000	0.000
44	A	80	THR	0	0.064	0.033	55.003	-0.163	-0.163	0.000	0.000	0.000	0.000
45	A	81	ASP	-1	-0.929	-0.980	56.195	-10.946	-10.946	0.000	0.000	0.000	0.000
46	A	82	LEU	0	-0.029	0.010	53.448	0.090	0.090	0.000	0.000	0.000	0.000
47	A	83	ARG	1	0.918	0.954	53.008	11.233	11.233	0.000	0.000	0.000	0.000
48	A	84	PHE	0	0.037	0.014	48.754	0.026	0.026	0.000	0.000	0.000	0.000
49	A	85	GLN	0	0.008	0.005	50.273	-0.202	-0.202	0.000	0.000	0.000	0.000
50	A	86	SER	0	0.024	0.000	45.535	-0.093	-0.093	0.000	0.000	0.000	0.000
51	A	87	ALA	0	0.056	0.022	45.332	-0.302	-0.302	0.000	0.000	0.000	0.000
52	A	88	ALA	0	0.023	0.020	46.254	-0.127	-0.127	0.000	0.000	0.000	0.000
53	A	89	ILE	0	-0.021	-0.009	42.343	-0.149	-0.149	0.000	0.000	0.000	0.000
54	A	90	GLY	0	0.010	0.001	41.751	-0.314	-0.314	0.000	0.000	0.000	0.000
55	A	91	ALA	0	0.037	0.016	41.887	-0.285	-0.285	0.000	0.000	0.000	0.000
56	A	92	LEU	0	0.028	0.013	43.580	-0.092	-0.092	0.000	0.000	0.000	0.000
57	A	93	GLN	0	-0.088	-0.044	35.559	0.124	0.124	0.000	0.000	0.000	0.000
58	A	94	GLU	-1	-0.883	-0.959	38.517	-16.639	-16.639	0.000	0.000	0.000	0.000
59	A	95	ALA	0	-0.012	-0.001	39.270	-0.208	-0.208	0.000	0.000	0.000	0.000
60	A	96	SER	0	-0.020	-0.024	38.942	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	97	GLU	-1	-0.752	-0.877	33.440	-18.834	-18.834	0.000	0.000	0.000	0.000
62	A	98	ALA	0	0.010	0.012	35.479	-0.378	-0.378	0.000	0.000	0.000	0.000
63	A	99	TYR	0	-0.085	-0.064	37.351	-0.269	-0.269	0.000	0.000	0.000	0.000
64	A	100	LEU	0	-0.011	-0.013	34.139	-0.184	-0.184	0.000	0.000	0.000	0.000
65	A	101	VAL	0	-0.026	-0.011	31.466	-0.415	-0.415	0.000	0.000	0.000	0.000
66	A	102	GLY	0	0.086	0.046	33.401	-0.279	-0.279	0.000	0.000	0.000	0.000
67	A	103	LEU	0	0.001	0.006	36.029	0.028	0.028	0.000	0.000	0.000	0.000
68	A	104	PHE	0	-0.057	-0.028	30.541	-0.225	-0.225	0.000	0.000	0.000	0.000
69	A	105	GLU	-1	-0.936	-0.963	31.732	-18.692	-18.692	0.000	0.000	0.000	0.000
70	A	106	ASP	-1	-0.767	-0.872	32.881	-16.352	-16.352	0.000	0.000	0.000	0.000
71	A	107	THR	0	-0.031	-0.042	32.000	0.056	0.056	0.000	0.000	0.000	0.000
72	A	108	ASN	0	-0.039	-0.034	27.399	-0.553	-0.553	0.000	0.000	0.000	0.000
73	A	109	LEU	0	0.007	0.015	30.873	-0.278	-0.278	0.000	0.000	0.000	0.000
74	A	110	CYS	0	-0.028	-0.009	33.405	0.248	0.248	0.000	0.000	0.000	0.000
75	A	111	ALA	0	-0.030	-0.013	29.641	0.077	0.077	0.000	0.000	0.000	0.000
76	A	112	ILE	0	-0.006	-0.002	27.922	-0.214	-0.214	0.000	0.000	0.000	0.000
77	A	113	HIS	0	-0.004	0.010	30.758	-0.127	-0.127	0.000	0.000	0.000	0.000
78	A	114	ALA	0	-0.060	-0.027	33.128	0.227	0.227	0.000	0.000	0.000	0.000
79	A	115	LYS	1	0.910	0.950	30.444	17.681	17.681	0.000	0.000	0.000	0.000
80	A	116	ARG	1	0.783	0.890	27.540	18.874	18.874	0.000	0.000	0.000	0.000
81	A	117	VAL	0	0.015	0.005	22.106	0.084	0.084	0.000	0.000	0.000	0.000
82	A	118	THR	0	-0.044	-0.026	23.860	-0.761	-0.761	0.000	0.000	0.000	0.000
83	A	119	ILE	0	0.058	0.039	26.146	0.660	0.660	0.000	0.000	0.000	0.000
84	A	120	MET	0	-0.055	-0.040	28.668	-0.193	-0.193	0.000	0.000	0.000	0.000
85	A	121	PRO	0	0.035	0.005	31.447	0.304	0.304	0.000	0.000	0.000	0.000
86	A	122	LYS	1	0.975	0.993	33.249	18.368	18.368	0.000	0.000	0.000	0.000
87	A	123	ASP	-1	-0.738	-0.857	32.043	-18.503	-18.503	0.000	0.000	0.000	0.000
88	A	124	ILE	0	0.024	0.020	32.810	0.250	0.250	0.000	0.000	0.000	0.000
89	A	125	GLN	0	-0.018	-0.014	36.427	0.302	0.302	0.000	0.000	0.000	0.000
90	A	126	LEU	0	0.007	0.012	38.033	0.361	0.361	0.000	0.000	0.000	0.000
91	A	127	ALA	0	0.048	0.017	37.493	0.335	0.335	0.000	0.000	0.000	0.000
92	A	128	HIS	0	-0.025	-0.021	39.581	0.420	0.420	0.000	0.000	0.000	0.000
93	A	129	SER	0	0.011	0.010	42.005	0.336	0.336	0.000	0.000	0.000	0.000
94	A	130	ILE	0	-0.022	-0.023	41.288	0.289	0.289	0.000	0.000	0.000	0.000
95	A	131	ARG	1	0.717	0.838	38.787	15.735	15.735	0.000	0.000	0.000	0.000
96	A	132	GLY	0	0.000	0.014	44.641	0.226	0.226	0.000	0.000	0.000	0.000
97	A	133	GLU	-1	-0.840	-0.876	42.905	-14.554	-14.554	0.000	0.000	0.000	0.000
98	A	134	ARG	1	0.875	0.915	45.959	12.978	12.978	0.000	0.000	0.000	0.000
99	A	135	ALA	-1	-0.924	-0.926	46.297	-12.999	-12.999	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:LYS)