FMO DATABASE

FMODB ID: YR112

Calculation Name: 2JNS-A-Other547

Preferred Name: Bromodomain-containing protein 4

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JNS

Chain ID: A

ChEMBL ID: CHEMBL3085619

UniProt ID: Q9ESU6

Base Structure: SolutionNMR

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	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-578559.374972
FMO2-HF: Nuclear repulsion	542137.819439
FMO2-HF: Total energy	-36421.555533
FMO2-MP2: Total energy	-36526.748674

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:1:GLY)

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

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.
-48.81	-47.415	6.614	-4.462	-3.547	-0.06

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.903

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].
3	A	3	SER	0	0.018	0.021	2.926	14.890	16.223	0.039	-0.554	-0.818	-0.003
4	A	4	GLY	0	0.012	-0.001	1.874	-43.121	-43.152	6.576	-3.862	-2.683	-0.057
5	A	5	SER	0	-0.011	-0.005	4.259	8.170	8.263	-0.001	-0.046	-0.046	0.000
6	A	6	SER	0	-0.017	-0.014	7.973	-1.775	-1.775	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.022	0.017	10.930	0.628	0.628	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.934	-0.958	14.302	-19.968	-19.968	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.052	-0.066	16.014	0.327	0.327	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.960	-0.974	17.713	-16.598	-16.598	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.979	-1.001	15.278	-19.743	-19.743	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.882	-0.916	18.701	-14.285	-14.285	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.839	-0.897	21.653	-11.075	-11.075	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.889	0.968	18.418	16.974	16.974	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.030	-0.032	23.486	0.339	0.339	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.843	0.918	27.226	11.185	11.185	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.007	-0.002	29.825	0.130	0.130	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.003	0.010	32.405	0.070	0.070	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.029	0.007	35.781	0.034	0.034	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.019	0.011	39.124	0.024	0.024	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.864	-0.939	42.506	-6.925	-6.925	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.905	-0.949	37.703	-8.266	-8.266	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.830	0.909	37.512	8.491	8.491	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.923	0.964	41.519	6.871	6.871	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.009	-0.018	43.222	0.218	0.218	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.018	0.011	38.823	0.083	0.083	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.023	-0.002	42.808	0.124	0.124	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.009	0.005	45.682	0.151	0.151	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.861	-0.929	44.272	-7.018	-7.018	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.014	-0.018	41.697	0.027	0.027	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.046	-0.031	45.826	0.191	0.191	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.881	0.949	48.428	6.330	6.330	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.062	-0.016	44.220	0.028	0.028	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.013	0.022	48.825	0.082	0.082	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.084	0.029	49.408	-0.141	-0.141	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.857	-0.941	49.012	-6.473	-6.473	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.874	0.935	45.424	6.808	6.808	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.049	0.033	44.692	-0.233	-0.233	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.060	0.026	44.865	-0.142	-0.142	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.849	0.930	38.972	7.946	7.946	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.014	-0.001	40.329	-0.255	-0.255	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.072	0.038	39.491	-0.272	-0.272	0.000	0.000	0.000	0.000
43	A	43	HIS	0	0.040	0.017	37.617	-0.264	-0.264	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.044	-0.019	34.371	-0.296	-0.296	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.061	0.034	34.448	-0.314	-0.314	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.026	-0.007	34.824	-0.297	-0.297	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.057	-0.014	31.255	-0.333	-0.333	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.759	0.860	27.777	10.441	10.441	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.772	-0.865	30.870	-9.962	-9.962	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.031	-0.027	30.081	0.245	0.245	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.015	-0.015	32.877	0.076	0.076	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.071	0.035	35.959	0.203	0.203	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.895	0.968	30.926	10.106	10.106	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.035	-0.016	36.681	0.028	0.028	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.001	0.018	39.890	0.219	0.219	0.000	0.000	0.000	0.000
56	A	56	ASN	0	0.040	0.012	42.594	-0.138	-0.138	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.032	-0.038	43.978	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.933	-0.964	45.053	-6.324	-6.324	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.967	-0.967	46.345	-6.384	-6.384	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.110	-0.058	41.002	-0.167	-0.167	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.881	-0.933	44.542	-6.693	-6.693	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.061	-0.039	40.876	-0.248	-0.248	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.766	-0.853	40.853	-7.856	-7.856	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.015	-0.033	39.911	-0.230	-0.230	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.982	-0.980	39.559	-7.427	-7.427	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.063	-0.051	38.235	-0.216	-0.216	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.029	-0.004	36.021	-0.377	-0.377	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.882	0.917	29.816	9.947	9.947	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.002	-0.008	30.150	0.151	0.151	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.060	0.022	28.199	0.252	0.252	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.064	0.024	30.330	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.004	0.012	33.169	0.225	0.225	0.000	0.000	0.000	0.000
73	A	73	ARG	1	1.002	0.995	31.606	9.816	9.816	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.910	-0.940	29.150	-10.694	-10.694	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.014	-0.005	33.669	0.204	0.204	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.861	-0.941	36.496	-8.465	-8.465	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.932	0.964	29.714	10.297	10.297	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.058	-0.028	36.303	0.093	0.093	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.055	0.027	38.496	0.162	0.162	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.016	-0.010	39.039	0.248	0.248	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.125	-0.073	37.773	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.088	-0.026	40.275	0.137	0.137	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.018	0.012	43.471	0.179	0.179	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.904	0.963	41.453	7.632	7.632	0.000	0.000	0.000	0.000
85	A	85	LYS	1	1.023	1.006	41.316	6.847	6.847	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.951	0.971	37.873	8.256	8.256	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.973	0.975	39.774	7.477	7.477	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.936	0.968	42.077	7.595	7.595	0.000	0.000	0.000	0.000
89	A	89	PRO	0	-0.022	-0.005	44.005	-0.141	-0.141	0.000	0.000	0.000	0.000
90	A	90	GLN	-1	-0.882	-0.924	45.215	-6.579	-6.579	0.000	0.000	0.000	0.000

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