FMO DATABASE

FMODB ID: 9RLY2

Calculation Name: 2DWW-A-Xray547

Preferred Name: Bromodomain-containing protein 4

Target Type: SINGLE PROTEIN

Ligand Name: chloride ion

Ligand 3-letter code: CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DWW

Chain ID: A

ChEMBL ID: CHEMBL3085619

UniProt ID: Q9ESU6

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-960522.998395
FMO2-HF: Nuclear repulsion	912012.582575
FMO2-HF: Total energy	-48510.415821
FMO2-MP2: Total energy	-48644.959912

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:LYS)

Summations of interaction energy for fragment #1(A:1: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.
-0.071999999999903	3.805	-0.003	-1.585	-2.291	-0.006

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.884 / q_NPA : 1.926

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	3	SER	0	-0.004	0.009	3.502	2.810	5.691	-0.017	-1.343	-1.522	-0.005
4	A	4	LYS	1	0.863	0.925	3.411	68.778	69.428	0.014	-0.197	-0.468	-0.001
5	A	5	ILE	0	0.047	0.040	3.877	5.480	5.826	0.000	-0.045	-0.301	0.000
6	A	6	SER	0	-0.023	-0.006	6.990	8.401	8.401	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.831	-0.910	8.341	-39.555	-39.555	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.049	0.006	8.602	3.347	3.347	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.043	0.020	10.791	3.985	3.985	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.817	0.902	12.100	45.674	45.674	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.039	-0.023	13.256	2.911	2.911	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.024	-0.006	14.313	2.210	2.210	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.008	0.011	16.987	2.614	2.614	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.015	-0.007	18.612	1.787	1.787	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.019	-0.011	17.576	1.648	1.648	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.054	0.021	21.217	1.352	1.352	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.940	0.974	22.956	25.138	25.138	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.810	-0.876	24.242	-22.469	-22.469	0.000	0.000	0.000	0.000
19	A	19	MET	0	-0.018	-0.006	24.294	0.579	0.579	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.031	0.011	26.583	0.844	0.844	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.023	0.009	29.024	0.798	0.798	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.972	0.970	30.780	16.742	16.742	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.860	0.935	29.373	20.498	20.498	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.036	0.016	28.433	0.739	0.739	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.009	0.014	32.683	0.216	0.216	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.022	-0.017	34.757	0.222	0.222	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.014	-0.037	31.594	0.647	0.647	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.026	0.010	30.912	-0.249	-0.249	0.000	0.000	0.000	0.000
29	A	29	TRP	0	-0.004	0.000	32.547	-0.356	-0.356	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.015	-0.004	34.449	0.020	0.020	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.029	0.012	29.690	-0.169	-0.169	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.004	-0.010	30.047	-0.694	-0.694	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.894	0.962	30.924	18.370	18.370	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.011	0.018	31.228	0.033	0.033	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	0.003	32.862	0.395	0.395	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.878	-0.942	35.432	-15.240	-15.240	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.017	-0.027	37.102	0.107	0.107	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.926	-0.952	39.931	-14.463	-14.463	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.053	-0.009	42.447	0.435	0.435	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.017	-0.025	44.245	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.034	-0.023	45.394	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.019	0.005	38.557	-0.256	-0.256	0.000	0.000	0.000	0.000
43	A	43	HIS	0	0.017	0.012	40.814	-0.257	-0.257	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.806	-0.885	41.330	-14.917	-14.917	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.006	-0.002	32.758	-0.685	-0.685	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.026	-0.031	35.551	-0.592	-0.592	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.904	-0.929	35.657	-15.693	-15.693	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.046	-0.014	34.853	-0.318	-0.318	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.080	-0.032	30.485	-0.751	-0.751	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.932	0.955	27.857	21.053	21.053	0.000	0.000	0.000	0.000
51	A	51	HIS	0	-0.002	0.004	26.035	-0.375	-0.375	0.000	0.000	0.000	0.000
52	A	52	PRO	0	0.090	0.058	27.628	-0.528	-0.528	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.021	-0.010	23.271	-0.656	-0.656	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.737	-0.852	26.860	-20.818	-20.818	0.000	0.000	0.000	0.000
55	A	55	MET	0	0.016	0.007	25.851	-0.722	-0.722	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.044	-0.044	26.045	-0.443	-0.443	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.034	-0.026	24.854	-0.422	-0.422	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.025	0.007	20.792	-0.784	-0.784	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.834	0.899	21.566	22.262	22.262	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.002	-0.012	22.598	-0.575	-0.575	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.852	0.937	19.591	28.663	28.663	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.047	-0.016	16.665	-1.647	-1.647	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.925	-0.946	18.420	-25.885	-25.885	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.035	-0.027	20.776	0.072	0.072	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.869	0.934	13.968	36.728	36.728	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.902	-0.950	16.061	-29.297	-29.297	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.069	-0.067	14.211	0.369	0.369	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.822	0.887	9.916	45.181	45.181	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.885	-0.947	8.199	-58.637	-58.637	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.061	0.011	10.198	4.340	4.340	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.017	-0.014	9.381	1.805	1.805	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.782	-0.869	12.202	-39.411	-39.411	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.025	0.011	14.375	2.383	2.383	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.006	-0.013	15.550	2.086	2.086	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.035	-0.010	16.679	1.716	1.716	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.707	-0.825	18.375	-27.108	-27.108	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.015	-0.008	20.266	1.596	1.596	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.802	0.872	17.129	32.254	32.254	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.033	0.017	22.491	1.089	1.089	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.023	0.008	24.340	1.046	1.046	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.011	-0.011	24.584	0.823	0.823	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.018	-0.031	25.482	0.842	0.842	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.040	-0.030	27.856	0.836	0.836	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.048	-0.002	30.276	0.724	0.724	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.078	-0.075	28.129	0.804	0.804	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.846	0.930	31.317	19.138	19.138	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.038	-0.031	33.512	0.282	0.282	0.000	0.000	0.000	0.000
88	A	88	ASN	0	0.003	0.001	36.018	0.117	0.117	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.049	0.026	37.803	-0.200	-0.200	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.005	-0.011	37.742	-0.193	-0.193	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.928	-0.969	38.752	-14.788	-14.788	0.000	0.000	0.000	0.000
92	A	92	HIS	0	0.055	0.033	39.477	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.904	-0.958	39.220	-15.234	-15.234	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.012	-0.006	35.504	-0.433	-0.433	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.048	0.024	34.496	-0.720	-0.720	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.047	-0.024	34.420	-0.525	-0.525	0.000	0.000	0.000	0.000
97	A	97	MET	0	-0.091	-0.039	35.076	-0.471	-0.471	0.000	0.000	0.000	0.000
98	A	98	ALA	0	0.029	0.014	30.919	-0.535	-0.535	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.941	0.980	30.121	17.226	17.226	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.970	0.998	30.160	16.385	16.385	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.022	-0.005	27.786	-0.368	-0.368	0.000	0.000	0.000	0.000
102	A	102	GLN	0	0.005	0.006	24.119	-0.196	-0.196	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.895	-0.947	25.578	-21.703	-21.703	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.084	-0.044	25.352	-0.757	-0.757	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.015	0.002	18.974	-1.106	-1.106	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.719	-0.830	21.034	-29.959	-29.959	0.000	0.000	0.000	0.000
107	A	107	MET	0	-0.007	0.026	20.854	-1.018	-1.018	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.819	0.874	20.345	25.065	25.065	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.017	-0.005	14.266	-1.662	-1.662	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.004	-0.002	16.184	-2.164	-2.164	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.844	0.906	17.386	27.475	27.475	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.037	0.008	12.302	-0.091	-0.091	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.017	0.005	11.349	-1.697	-1.697	0.000	0.000	0.000	0.000
114	A	114	ASP	-2	-1.802	-1.876	7.077	-121.321	-121.321	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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