FMO DATABASE

FMODB ID: 74Z9K

Calculation Name: 4D2M-C-Xray547

Preferred Name: Bcl-2-like protein 11

Target Type: SINGLE PROTEIN

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine | (4r)-2-methylpentane-2,4-diol | chloride ion

Ligand 3-letter code: CME | MRD | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4D2M

Chain ID: C

ChEMBL ID: CHEMBL5777

UniProt ID: O43521

Base Structure: X-ray

Registration Date: 2025-10-06

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	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1216540.874272
FMO2-HF: Nuclear repulsion	1157858.698967
FMO2-HF: Total energy	-58682.175305
FMO2-MP2: Total energy	-58844.390988

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(C:51:ILE)

Summations of interaction energy for fragment #1(C:51:ILE)

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.
-103.126	-98.793	19.086	-10.837	-12.582	-0.113

Interaction energy analysis for fragmet #1(C:51:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.888

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	C	53	ASP	-1	-0.795	-0.880	1.742	-108.843	-106.538	12.314	-8.504	-6.116	-0.105
4	C	54	TYR	0	-0.043	-0.026	2.184	8.786	10.431	1.493	-1.182	-1.956	-0.002
5	C	55	LEU	0	-0.088	-0.042	2.518	4.349	5.274	0.874	-0.297	-1.501	-0.002
14	C	64	MET	0	-0.012	0.001	2.444	0.846	1.269	0.504	-0.117	-0.810	0.000
107	C	157	MET	0	0.011	0.006	2.800	-3.810	-4.775	3.901	-0.737	-2.199	-0.004
6	C	56	SER	0	0.039	0.026	5.646	2.285	2.285	0.000	0.000	0.000	0.000
7	C	57	THR	0	-0.034	-0.042	9.216	3.269	3.269	0.000	0.000	0.000	0.000
8	C	58	GLU	-1	-0.847	-0.933	9.925	-22.618	-22.618	0.000	0.000	0.000	0.000
9	C	59	ARG	1	0.945	0.977	11.714	18.677	18.677	0.000	0.000	0.000	0.000
10	C	60	ASP	-1	-0.847	-0.903	7.560	-26.675	-26.675	0.000	0.000	0.000	0.000
11	C	61	HIS	0	0.056	0.026	6.316	-1.768	-1.768	0.000	0.000	0.000	0.000
12	C	62	VAL	0	0.012	0.010	8.278	0.487	0.487	0.000	0.000	0.000	0.000
13	C	63	MET	0	-0.063	-0.029	9.387	1.339	1.339	0.000	0.000	0.000	0.000
15	C	65	ALA	0	0.029	0.016	6.936	0.759	0.759	0.000	0.000	0.000	0.000
16	C	66	VAL	0	0.009	0.004	9.752	1.175	1.175	0.000	0.000	0.000	0.000
17	C	67	ARG	1	0.936	0.954	7.925	25.164	25.164	0.000	0.000	0.000	0.000
18	C	68	TYR	0	0.017	0.027	7.887	1.202	1.202	0.000	0.000	0.000	0.000
19	C	69	TYR	0	0.031	0.014	9.715	1.083	1.083	0.000	0.000	0.000	0.000
20	C	70	MET	0	-0.017	-0.014	13.362	0.717	0.717	0.000	0.000	0.000	0.000
21	C	71	SER	0	-0.042	-0.035	11.290	0.848	0.848	0.000	0.000	0.000	0.000
22	C	72	LYS	1	0.830	0.912	13.010	16.781	16.781	0.000	0.000	0.000	0.000
23	C	73	GLN	0	0.026	0.009	14.625	1.212	1.212	0.000	0.000	0.000	0.000
24	C	74	ARG	1	0.939	0.977	16.691	14.357	14.357	0.000	0.000	0.000	0.000
25	C	75	LEU	0	0.007	-0.005	14.592	0.540	0.540	0.000	0.000	0.000	0.000
26	C	76	ASP	-1	-0.799	-0.879	18.248	-14.375	-14.375	0.000	0.000	0.000	0.000
27	C	77	ASP	-1	-0.818	-0.881	20.304	-10.349	-10.349	0.000	0.000	0.000	0.000
28	C	78	LEU	0	0.008	0.010	20.642	0.469	0.469	0.000	0.000	0.000	0.000
29	C	79	TYR	0	0.038	0.002	21.948	0.558	0.558	0.000	0.000	0.000	0.000
30	C	80	ARG	1	0.810	0.883	23.827	10.761	10.761	0.000	0.000	0.000	0.000
31	C	81	GLN	0	-0.088	-0.059	25.772	0.597	0.597	0.000	0.000	0.000	0.000
32	C	82	LEU	0	-0.027	0.005	24.158	0.372	0.372	0.000	0.000	0.000	0.000
33	C	83	PRO	0	0.027	0.018	28.087	0.087	0.087	0.000	0.000	0.000	0.000
34	C	84	THR	0	0.049	0.002	30.242	-0.277	-0.277	0.000	0.000	0.000	0.000
35	C	85	LYS	1	0.975	1.020	31.279	8.192	8.192	0.000	0.000	0.000	0.000
36	C	86	THR	0	0.054	0.019	26.413	-0.001	-0.001	0.000	0.000	0.000	0.000
37	C	87	ARG	1	0.853	0.937	26.408	9.830	9.830	0.000	0.000	0.000	0.000
38	C	88	SER	0	0.029	0.007	26.888	-0.250	-0.250	0.000	0.000	0.000	0.000
39	C	89	TYR	0	0.042	0.014	28.017	-0.092	-0.092	0.000	0.000	0.000	0.000
40	C	90	ILE	0	-0.016	-0.008	21.851	-0.306	-0.306	0.000	0.000	0.000	0.000
41	C	91	ASP	-1	-0.928	-0.948	23.699	-11.569	-11.569	0.000	0.000	0.000	0.000
42	C	92	ILE	0	0.042	0.023	25.385	-0.311	-0.311	0.000	0.000	0.000	0.000
43	C	93	ILE	0	0.010	-0.006	21.762	-0.190	-0.190	0.000	0.000	0.000	0.000
44	C	94	ASN	0	-0.037	-0.026	19.787	-0.912	-0.912	0.000	0.000	0.000	0.000
45	C	95	ILE	0	0.022	0.018	22.184	-0.264	-0.264	0.000	0.000	0.000	0.000
46	C	96	TYR	0	-0.047	-0.029	25.115	0.130	0.130	0.000	0.000	0.000	0.000
47	C	97	CYS	0	-0.027	-0.014	20.504	0.024	0.024	0.000	0.000	0.000	0.000
48	C	98	ASP	-1	-0.877	-0.923	19.010	-15.981	-15.981	0.000	0.000	0.000	0.000
49	C	99	LYS	1	0.884	0.961	20.628	10.604	10.604	0.000	0.000	0.000	0.000
50	C	100	VAL	0	0.022	0.014	22.545	-0.127	-0.127	0.000	0.000	0.000	0.000
51	C	101	SER	0	-0.030	-0.038	17.415	-0.547	-0.547	0.000	0.000	0.000	0.000
52	C	102	ASN	0	-0.090	-0.047	18.718	-1.156	-1.156	0.000	0.000	0.000	0.000
53	C	103	ASP	-1	-0.925	-0.962	20.425	-12.340	-12.340	0.000	0.000	0.000	0.000
54	C	104	TYR	0	-0.030	-0.014	22.435	0.262	0.262	0.000	0.000	0.000	0.000
55	C	105	ASN	0	0.034	0.034	16.355	-1.356	-1.356	0.000	0.000	0.000	0.000
56	C	106	ARG	1	0.909	0.939	17.579	12.793	12.793	0.000	0.000	0.000	0.000
57	C	107	ASP	-1	-0.835	-0.916	18.937	-13.967	-13.967	0.000	0.000	0.000	0.000
58	C	108	MET	0	-0.020	-0.010	16.835	-0.374	-0.374	0.000	0.000	0.000	0.000
59	C	109	ASN	0	-0.041	-0.009	14.039	-2.166	-2.166	0.000	0.000	0.000	0.000
60	C	110	ILE	0	0.038	0.024	15.186	-0.694	-0.694	0.000	0.000	0.000	0.000
61	C	111	MET	0	0.002	-0.004	17.752	0.365	0.365	0.000	0.000	0.000	0.000
62	C	112	TYR	0	0.003	0.000	9.239	-0.863	-0.863	0.000	0.000	0.000	0.000
63	C	113	ASP	-1	-0.889	-0.947	13.245	-22.266	-22.266	0.000	0.000	0.000	0.000
64	C	114	MET	0	-0.033	-0.004	15.019	0.177	0.177	0.000	0.000	0.000	0.000
65	C	115	ALA	0	-0.007	0.007	16.035	0.498	0.498	0.000	0.000	0.000	0.000
66	C	116	SER	0	-0.095	-0.047	12.696	-0.483	-0.483	0.000	0.000	0.000	0.000
67	C	117	THR	0	-0.037	-0.025	14.513	0.159	0.159	0.000	0.000	0.000	0.000
68	C	118	LYS	1	0.948	0.955	17.796	14.386	14.386	0.000	0.000	0.000	0.000
69	C	119	SER	0	-0.020	-0.012	19.384	0.049	0.049	0.000	0.000	0.000	0.000
70	C	120	PHE	0	0.020	0.039	17.631	0.640	0.640	0.000	0.000	0.000	0.000
71	C	121	THR	0	-0.042	-0.047	19.744	-0.612	-0.612	0.000	0.000	0.000	0.000
72	C	122	VAL	0	0.021	-0.004	16.886	0.196	0.196	0.000	0.000	0.000	0.000
73	C	123	TYR	0	-0.034	-0.019	20.141	0.171	0.171	0.000	0.000	0.000	0.000
74	C	124	ASP	-1	-0.810	-0.881	23.674	-11.583	-11.583	0.000	0.000	0.000	0.000
75	C	125	PHE	0	0.029	0.010	20.959	0.200	0.200	0.000	0.000	0.000	0.000
76	C	126	ASN	0	0.040	0.036	23.088	0.003	0.003	0.000	0.000	0.000	0.000
77	C	127	ASN	0	0.008	0.002	24.572	0.435	0.435	0.000	0.000	0.000	0.000
78	C	128	GLU	-1	-0.900	-0.941	26.515	-10.196	-10.196	0.000	0.000	0.000	0.000
79	C	129	VAL	0	-0.016	-0.007	23.531	0.280	0.280	0.000	0.000	0.000	0.000
80	C	130	ASN	0	-0.021	-0.018	26.956	0.317	0.317	0.000	0.000	0.000	0.000
81	C	131	THR	0	-0.011	-0.007	29.618	0.409	0.409	0.000	0.000	0.000	0.000
82	C	132	ILE	0	0.003	0.003	29.287	0.263	0.263	0.000	0.000	0.000	0.000
83	C	133	MET	0	-0.027	-0.006	28.419	0.186	0.186	0.000	0.000	0.000	0.000
84	C	134	LEU	0	-0.033	0.001	31.450	0.260	0.260	0.000	0.000	0.000	0.000
85	C	135	ASP	-1	-0.884	-0.936	34.845	-8.304	-8.304	0.000	0.000	0.000	0.000
86	C	136	ASN	0	-0.102	-0.047	32.955	0.282	0.282	0.000	0.000	0.000	0.000
87	C	137	LYS	1	0.878	0.932	33.411	8.522	8.522	0.000	0.000	0.000	0.000
88	C	138	GLY	0	0.048	0.042	33.831	0.115	0.115	0.000	0.000	0.000	0.000
89	C	139	LEU	0	0.055	0.030	29.322	-0.276	-0.276	0.000	0.000	0.000	0.000
90	C	140	GLY	0	-0.001	-0.005	28.803	-0.351	-0.351	0.000	0.000	0.000	0.000
91	C	141	VAL	0	0.042	0.017	27.112	-0.466	-0.466	0.000	0.000	0.000	0.000
92	C	142	ARG	1	0.802	0.889	25.952	9.294	9.294	0.000	0.000	0.000	0.000
93	C	143	LEU	0	0.040	0.014	24.290	-0.530	-0.530	0.000	0.000	0.000	0.000
94	C	144	ALA	0	0.002	0.014	22.600	-0.712	-0.712	0.000	0.000	0.000	0.000
95	C	145	THR	0	0.000	-0.013	21.424	-0.772	-0.772	0.000	0.000	0.000	0.000
96	C	146	ILE	0	0.025	0.011	19.681	-0.803	-0.803	0.000	0.000	0.000	0.000
97	C	147	SER	0	-0.023	-0.008	18.160	-0.956	-0.956	0.000	0.000	0.000	0.000
98	C	148	PHE	0	0.034	0.005	16.704	-1.191	-1.191	0.000	0.000	0.000	0.000
99	C	149	ILE	0	0.005	-0.005	15.842	-1.310	-1.310	0.000	0.000	0.000	0.000
100	C	150	THR	0	-0.021	-0.028	13.466	-1.185	-1.185	0.000	0.000	0.000	0.000
101	C	151	GLU	-1	-0.803	-0.870	12.057	-26.495	-26.495	0.000	0.000	0.000	0.000
102	C	152	LEU	0	-0.005	-0.006	11.145	-2.448	-2.448	0.000	0.000	0.000	0.000
103	C	153	GLY	0	-0.050	-0.042	10.604	-1.645	-1.645	0.000	0.000	0.000	0.000
104	C	154	ARG	1	0.840	0.904	7.968	19.684	19.684	0.000	0.000	0.000	0.000
105	C	155	ARG	1	0.815	0.897	6.314	21.621	21.621	0.000	0.000	0.000	0.000
106	C	156	CYS	0	-0.063	-0.005	7.187	-2.593	-2.593	0.000	0.000	0.000	0.000
108	C	158	ASN	0	-0.045	-0.029	5.652	2.712	2.712	0.000	0.000	0.000	0.000
109	C	159	PRO	0	0.089	0.035	7.669	1.497	1.497	0.000	0.000	0.000	0.000
110	C	160	VAL	0	0.010	0.000	10.115	1.401	1.401	0.000	0.000	0.000	0.000
111	C	161	LYS	1	0.929	0.960	12.319	20.828	20.828	0.000	0.000	0.000	0.000
112	C	162	THR	0	0.076	0.054	9.203	1.151	1.151	0.000	0.000	0.000	0.000
113	C	163	ILE	0	0.014	0.008	12.430	0.965	0.965	0.000	0.000	0.000	0.000
114	C	164	LYS	1	0.933	0.981	15.096	15.833	15.833	0.000	0.000	0.000	0.000
115	C	165	MET	0	0.022	0.029	13.019	0.863	0.863	0.000	0.000	0.000	0.000
116	C	166	PHE	0	0.014	0.000	12.281	0.509	0.509	0.000	0.000	0.000	0.000
117	C	167	THR	0	-0.025	-0.013	17.521	0.800	0.800	0.000	0.000	0.000	0.000
118	C	168	LEU	0	-0.038	-0.005	20.369	0.542	0.542	0.000	0.000	0.000	0.000
119	C	169	LEU	0	0.033	0.003	19.646	0.397	0.397	0.000	0.000	0.000	0.000
120	C	170	SER	0	-0.039	-0.022	21.262	0.535	0.535	0.000	0.000	0.000	0.000
121	C	171	HIS	0	-0.038	-0.033	22.802	0.709	0.709	0.000	0.000	0.000	0.000
122	C	172	THR	0	-0.042	-0.043	25.140	0.439	0.439	0.000	0.000	0.000	0.000
123	C	173	ILE	0	-0.005	-0.006	21.775	0.164	0.164	0.000	0.000	0.000	0.000
124	C	174	CYS	0	-0.100	-0.041	25.674	0.210	0.210	0.000	0.000	0.000	0.000
125	C	175	ASP	-1	-0.715	-0.844	28.391	-9.219	-9.219	0.000	0.000	0.000	0.000
126	C	176	ASP	-1	-0.891	-0.952	31.662	-8.513	-8.513	0.000	0.000	0.000	0.000
127	C	177	CYS	0	-0.033	0.014	33.915	-0.025	-0.025	0.000	0.000	0.000	0.000
128	C	178	PHE	0	0.019	-0.017	25.929	-0.137	-0.137	0.000	0.000	0.000	0.000
129	C	179	VAL	0	-0.022	-0.010	31.222	-0.115	-0.115	0.000	0.000	0.000	0.000
130	C	180	ASP	-1	-0.868	-0.918	32.731	-8.109	-8.109	0.000	0.000	0.000	0.000
131	C	181	TYR	0	-0.018	-0.043	32.090	0.005	0.005	0.000	0.000	0.000	0.000
132	C	182	ILE	0	-0.064	-0.039	28.005	-0.080	-0.080	0.000	0.000	0.000	0.000
133	C	183	THR	0	-0.123	-0.081	31.717	0.089	0.089	0.000	0.000	0.000	0.000
134	C	184	ASP	-1	-0.895	-0.931	35.058	-7.793	-7.793	0.000	0.000	0.000	0.000
135	C	185	ILE	0	-0.155	-0.082	31.585	0.044	0.044	0.000	0.000	0.000	0.000
136	C	186	SER	-1	-0.978	-0.975	33.815	-8.537	-8.537	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:51:ILE)