FMO DATABASE

FMODB ID: 3ZLYL

Calculation Name: 5LXY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: bromide ion

Ligand 3-letter code: BR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LXY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y580

Base Structure: X-ray

Registration Date: 2025-10-04

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-515156.385823
FMO2-HF: Nuclear repulsion	484593.451752
FMO2-HF: Total energy	-30562.934071
FMO2-MP2: Total energy	-30654.441902

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:7:GLU)

Summations of interaction energy for fragment #1(A:7:GLU)

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.
1.791	3.238	-0.006	-0.59	-0.852	0

Interaction energy analysis for fragmet #1(A:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.134 / q_NPA : -0.077

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].
3	A	9	ASP	-1	-0.850	-0.918	3.841	-19.646	-18.199	-0.006	-0.590	-0.852
4	A	10	ARG	1	0.855	0.928	5.492	16.977	16.977	0.000	0.000	0.000
5	A	11	THR	0	-0.051	-0.035	8.568	1.541	1.541	0.000	0.000	0.000
6	A	12	LEU	0	0.031	0.037	10.980	0.326	0.326	0.000	0.000	0.000
7	A	13	PHE	0	-0.017	-0.002	14.426	-0.023	-0.023	0.000	0.000	0.000
8	A	14	VAL	0	0.019	0.006	16.788	0.279	0.279	0.000	0.000	0.000
9	A	15	GLY	0	0.062	0.019	20.291	-0.021	-0.021	0.000	0.000	0.000
10	A	16	ASN	0	-0.062	-0.038	23.387	0.119	0.119	0.000	0.000	0.000
11	A	17	LEU	0	0.022	0.027	23.054	0.097	0.097	0.000	0.000	0.000
12	A	18	GLU	-1	-0.812	-0.895	27.356	-0.912	-0.912	0.000	0.000	0.000
13	A	19	THR	0	0.005	-0.018	29.849	-0.073	-0.073	0.000	0.000	0.000
14	A	20	LYS	1	0.837	0.923	31.527	0.884	0.884	0.000	0.000	0.000
15	A	21	VAL	0	-0.049	-0.021	25.906	0.012	0.012	0.000	0.000	0.000
16	A	22	THR	0	0.009	0.000	27.040	-0.030	-0.030	0.000	0.000	0.000
17	A	23	GLU	-1	-0.729	-0.853	22.248	-2.356	-2.356	0.000	0.000	0.000
18	A	24	GLU	-1	-0.821	-0.909	22.992	-1.772	-1.772	0.000	0.000	0.000
19	A	25	LEU	0	0.005	0.016	25.400	0.011	0.011	0.000	0.000	0.000
20	A	26	LEU	0	-0.011	-0.014	21.717	0.022	0.022	0.000	0.000	0.000
21	A	27	PHE	0	-0.015	-0.013	19.259	-0.096	-0.096	0.000	0.000	0.000
22	A	28	GLU	-1	-0.951	-0.974	22.134	-1.196	-1.196	0.000	0.000	0.000
23	A	29	LEU	0	-0.035	-0.017	24.390	0.046	0.046	0.000	0.000	0.000
24	A	30	PHE	0	0.008	-0.024	18.759	0.033	0.033	0.000	0.000	0.000
25	A	31	HIS	0	0.029	0.019	20.219	-0.216	-0.216	0.000	0.000	0.000
26	A	32	GLN	0	-0.014	0.001	21.415	0.056	0.056	0.000	0.000	0.000
27	A	33	ALA	0	-0.035	-0.009	19.601	0.142	0.142	0.000	0.000	0.000
28	A	34	GLY	0	0.013	0.004	17.993	-0.004	-0.004	0.000	0.000	0.000
29	A	35	PRO	0	-0.039	-0.034	16.228	-0.162	-0.162	0.000	0.000	0.000
30	A	36	VAL	0	0.029	0.030	15.460	-0.532	-0.532	0.000	0.000	0.000
31	A	37	ILE	0	-0.078	-0.033	11.365	0.149	0.149	0.000	0.000	0.000
32	A	38	LYS	1	0.939	0.963	11.600	6.338	6.338	0.000	0.000	0.000
33	A	39	VAL	0	0.028	0.018	16.197	-0.262	-0.262	0.000	0.000	0.000
34	A	40	LYS	1	0.792	0.878	17.618	2.550	2.550	0.000	0.000	0.000
35	A	41	ILE	0	0.021	0.016	19.186	-0.118	-0.118	0.000	0.000	0.000
36	A	42	PRO	0	-0.060	-0.020	18.954	0.058	0.058	0.000	0.000	0.000
37	A	43	LYS	0	0.047	0.054	21.610	0.191	0.191	0.000	0.000	0.000
38	A	44	ASP	-1	-0.839	-0.920	24.581	-1.423	-1.423	0.000	0.000	0.000
39	A	45	LYS	1	0.943	0.963	27.243	1.011	1.011	0.000	0.000	0.000
40	A	46	ASP	-1	-0.928	-0.962	29.511	-0.984	-0.984	0.000	0.000	0.000
41	A	47	GLY	0	0.028	-0.001	28.870	0.017	0.017	0.000	0.000	0.000
42	A	48	LYS	1	0.838	0.925	29.254	1.195	1.195	0.000	0.000	0.000
43	A	49	PRO	0	0.014	0.001	26.509	-0.068	-0.068	0.000	0.000	0.000
44	A	50	LYS	1	0.856	0.929	23.545	1.815	1.815	0.000	0.000	0.000
45	A	51	GLN	0	-0.012	-0.013	25.721	-0.008	-0.008	0.000	0.000	0.000
46	A	52	PHE	0	-0.011	-0.026	20.057	0.093	0.093	0.000	0.000	0.000
47	A	53	ALA	0	0.005	0.005	20.055	0.008	0.008	0.000	0.000	0.000
48	A	54	PHE	0	0.006	0.004	14.411	-0.055	-0.055	0.000	0.000	0.000
49	A	55	VAL	0	0.023	0.024	15.884	0.040	0.040	0.000	0.000	0.000
50	A	56	ASN	0	-0.037	-0.029	8.974	-0.254	-0.254	0.000	0.000	0.000
51	A	57	PHE	0	0.070	0.031	12.079	0.430	0.430	0.000	0.000	0.000
52	A	58	LYS	1	0.944	0.973	10.864	1.234	1.234	0.000	0.000	0.000
53	A	59	HIS	0	-0.020	-0.034	10.260	-0.303	-0.303	0.000	0.000	0.000
54	A	60	GLU	-1	-0.811	-0.913	6.086	-6.148	-6.148	0.000	0.000	0.000
55	A	61	VAL	0	0.015	-0.001	10.110	0.341	0.341	0.000	0.000	0.000
56	A	62	SER	0	0.014	0.005	12.920	0.287	0.287	0.000	0.000	0.000
57	A	63	VAL	0	-0.005	0.019	11.280	0.240	0.240	0.000	0.000	0.000
58	A	64	PRO	0	0.019	-0.003	12.711	0.284	0.284	0.000	0.000	0.000
59	A	65	TYR	0	-0.016	0.010	15.805	0.250	0.250	0.000	0.000	0.000
60	A	66	ALA	0	0.039	0.006	17.555	0.142	0.142	0.000	0.000	0.000
61	A	67	MET	0	-0.032	-0.001	18.080	0.194	0.194	0.000	0.000	0.000
62	A	68	ASN	0	-0.029	-0.031	19.798	0.094	0.094	0.000	0.000	0.000
63	A	69	LEU	0	-0.015	0.008	22.011	0.096	0.096	0.000	0.000	0.000
64	A	70	LEU	0	0.010	-0.006	21.169	0.055	0.055	0.000	0.000	0.000
65	A	71	ASN	0	0.018	0.011	22.718	-0.026	-0.026	0.000	0.000	0.000
66	A	72	GLY	0	-0.058	-0.029	24.447	0.124	0.124	0.000	0.000	0.000
67	A	73	ILE	0	0.037	0.031	26.700	0.088	0.088	0.000	0.000	0.000
68	A	74	LYS	1	0.892	0.945	28.834	0.605	0.605	0.000	0.000	0.000
69	A	75	LEU	0	0.058	0.042	26.609	0.019	0.019	0.000	0.000	0.000
70	A	76	TYR	0	0.020	-0.011	30.977	0.046	0.046	0.000	0.000	0.000
71	A	77	GLY	0	0.036	0.023	34.306	0.031	0.031	0.000	0.000	0.000
72	A	78	ARG	1	0.881	0.926	30.924	0.953	0.953	0.000	0.000	0.000
73	A	79	PRO	0	-0.021	0.002	30.135	-0.043	-0.043	0.000	0.000	0.000
74	A	80	ILE	0	0.031	0.024	23.838	-0.012	-0.012	0.000	0.000	0.000
75	A	81	LYS	1	0.877	0.928	24.375	1.104	1.104	0.000	0.000	0.000
76	A	82	ILE	0	-0.008	0.008	18.523	-0.141	-0.141	0.000	0.000	0.000
77	A	83	GLN	0	-0.052	-0.028	18.799	0.156	0.156	0.000	0.000	0.000
78	A	84	PHE	-1	-0.864	-0.926	9.635	-2.108	-2.108	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLU)