FMO DATABASE

FMODB ID: YV7R2

Calculation Name: 4U2U-A-Xray372

Preferred Name: Bcl-2 homologous antagonist/killer

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4U2U

Chain ID: A

ChEMBL ID: CHEMBL5609

UniProt ID: Q16611

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1217777.68015
FMO2-HF: Nuclear repulsion	1159085.563675
FMO2-HF: Total energy	-58692.116476
FMO2-MP2: Total energy	-58864.154394

3D Structure

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:21:SER)

Summations of interaction energy for fragment #1(A:21:SER)

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.
-2.44	-0.395	-0.014	-0.972	-1.06	0.005

Interaction energy analysis for fragmet #1(A:21:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.005

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	23	SER	0	-0.004	-0.001	3.854	-0.202	1.843	-0.014	-0.972	-1.060	0.005
4	A	24	GLU	-1	-0.915	-0.969	6.083	-0.477	-0.477	0.000	0.000	0.000	0.000
5	A	25	GLU	-1	-0.913	-0.963	9.132	-0.995	-0.995	0.000	0.000	0.000	0.000
6	A	26	GLN	0	-0.067	-0.046	5.637	-0.383	-0.383	0.000	0.000	0.000	0.000
7	A	27	VAL	0	0.058	0.027	8.361	0.312	0.312	0.000	0.000	0.000	0.000
8	A	28	ALA	0	0.001	0.026	10.862	0.195	0.195	0.000	0.000	0.000	0.000
9	A	29	GLN	0	-0.025	-0.014	10.582	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	30	ASP	-1	-0.820	-0.909	9.355	-1.140	-1.140	0.000	0.000	0.000	0.000
11	A	31	THR	0	-0.046	-0.053	12.645	0.171	0.171	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.840	-0.894	15.881	-0.331	-0.331	0.000	0.000	0.000	0.000
13	A	33	GLU	-1	-0.849	-0.905	13.723	-0.430	-0.430	0.000	0.000	0.000	0.000
14	A	34	VAL	0	-0.045	-0.022	14.989	0.068	0.068	0.000	0.000	0.000	0.000
15	A	35	PHE	0	0.000	-0.003	17.729	0.052	0.052	0.000	0.000	0.000	0.000
16	A	36	ARG	1	0.848	0.906	20.394	0.354	0.354	0.000	0.000	0.000	0.000
17	A	37	SER	0	-0.056	-0.035	20.429	0.030	0.030	0.000	0.000	0.000	0.000
18	A	38	TYR	0	-0.009	-0.002	21.840	0.023	0.023	0.000	0.000	0.000	0.000
19	A	39	VAL	0	-0.011	-0.013	23.514	0.020	0.020	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.022	-0.003	25.720	0.013	0.013	0.000	0.000	0.000	0.000
21	A	41	TYR	0	0.014	-0.017	23.741	0.019	0.019	0.000	0.000	0.000	0.000
22	A	42	ARG	1	0.807	0.902	26.809	0.082	0.082	0.000	0.000	0.000	0.000
23	A	43	HIS	0	-0.042	-0.007	29.195	0.008	0.008	0.000	0.000	0.000	0.000
24	A	44	GLN	0	-0.033	-0.024	30.045	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	45	GLN	0	-0.020	-0.019	29.613	0.000	0.000	0.000	0.000	0.000	0.000
26	A	46	GLU	-1	-0.734	-0.817	32.691	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	47	GLN	0	-0.047	-0.006	34.804	0.001	0.001	0.000	0.000	0.000	0.000
28	A	48	GLU	-1	-0.916	-0.951	34.017	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	49	ALA	0	-0.052	-0.016	36.288	0.005	0.005	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-1.018	-1.001	37.980	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	67	PRO	0	-0.006	-0.030	21.787	0.005	0.005	0.000	0.000	0.000	0.000
32	A	68	SER	0	-0.015	0.011	20.360	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	69	SER	0	0.000	-0.028	15.013	0.028	0.028	0.000	0.000	0.000	0.000
34	A	70	THR	0	0.029	0.000	11.312	0.053	0.053	0.000	0.000	0.000	0.000
35	A	71	MET	0	0.028	0.024	9.789	0.119	0.119	0.000	0.000	0.000	0.000
36	A	72	GLY	0	0.054	0.028	14.518	0.024	0.024	0.000	0.000	0.000	0.000
37	A	73	GLN	0	-0.004	0.000	17.216	0.017	0.017	0.000	0.000	0.000	0.000
38	A	74	VAL	0	-0.008	0.015	13.960	0.030	0.030	0.000	0.000	0.000	0.000
39	A	75	GLY	0	0.047	0.020	17.373	0.022	0.022	0.000	0.000	0.000	0.000
40	A	76	ARG	1	0.922	0.974	19.835	0.070	0.070	0.000	0.000	0.000	0.000
41	A	77	GLN	0	-0.010	-0.016	20.549	0.010	0.010	0.000	0.000	0.000	0.000
42	A	78	LEU	0	-0.028	-0.020	18.412	0.014	0.014	0.000	0.000	0.000	0.000
43	A	79	ALA	0	0.013	0.021	22.507	0.006	0.006	0.000	0.000	0.000	0.000
44	A	80	ILE	0	-0.052	-0.011	25.116	0.009	0.009	0.000	0.000	0.000	0.000
45	A	81	ILE	0	-0.070	-0.035	22.494	0.010	0.010	0.000	0.000	0.000	0.000
46	A	82	GLY	0	0.090	0.057	26.637	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	83	ASP	-1	-0.860	-0.930	27.911	0.008	0.008	0.000	0.000	0.000	0.000
48	A	84	ASP	-1	-0.833	-0.913	30.367	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	85	ILE	0	0.005	0.001	27.466	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	86	ASN	0	-0.003	-0.021	25.424	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	87	ARG	1	0.905	0.958	29.477	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	88	ARG	1	0.839	0.904	33.021	0.004	0.004	0.000	0.000	0.000	0.000
53	A	89	TYR	0	0.004	0.009	27.744	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	90	ASP	-1	-0.791	-0.864	31.736	-0.069	-0.069	0.000	0.000	0.000	0.000
55	A	91	SER	0	0.028	-0.001	33.052	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	92	GLU	-1	-0.909	-0.942	34.504	-0.052	-0.052	0.000	0.000	0.000	0.000
57	A	93	PHE	0	-0.016	-0.030	29.118	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	94	GLN	0	-0.050	-0.029	34.697	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	95	THR	0	-0.002	-0.003	37.480	0.000	0.000	0.000	0.000	0.000	0.000
60	A	96	MET	0	-0.053	-0.022	33.883	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	97	LEU	0	-0.035	-0.016	33.890	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	98	GLN	0	0.008	0.013	38.418	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	99	HIS	0	-0.036	-0.008	41.688	0.003	0.003	0.000	0.000	0.000	0.000
64	A	100	LEU	0	-0.072	-0.055	38.127	0.000	0.000	0.000	0.000	0.000	0.000
65	A	101	GLN	0	-0.053	-0.017	41.416	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	102	PRO	0	-0.041	0.002	36.742	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	103	THR	0	0.000	-0.012	39.232	0.001	0.001	0.000	0.000	0.000	0.000
68	A	104	ALA	0	0.023	-0.009	36.486	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	105	GLU	-1	-0.854	-0.904	36.197	-0.103	-0.103	0.000	0.000	0.000	0.000
70	A	106	ASN	0	0.052	0.026	37.337	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	107	ALA	0	0.063	0.039	33.469	0.000	0.000	0.000	0.000	0.000	0.000
72	A	108	TYR	0	-0.002	0.010	28.236	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.833	-0.934	31.770	-0.144	-0.144	0.000	0.000	0.000	0.000
74	A	110	TYR	0	-0.045	-0.027	34.165	0.005	0.005	0.000	0.000	0.000	0.000
75	A	111	PHE	0	0.023	0.007	24.941	0.004	0.004	0.000	0.000	0.000	0.000
76	A	112	THR	0	0.027	0.002	28.996	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	113	LYS	1	0.942	0.995	30.031	0.093	0.093	0.000	0.000	0.000	0.000
78	A	114	ILE	0	-0.011	0.022	30.931	0.007	0.007	0.000	0.000	0.000	0.000
79	A	115	ALA	0	0.035	0.016	26.266	0.005	0.005	0.000	0.000	0.000	0.000
80	A	116	THR	0	-0.051	-0.058	27.410	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	117	SER	0	-0.007	-0.026	28.372	0.006	0.006	0.000	0.000	0.000	0.000
82	A	118	LEU	0	-0.052	-0.003	26.764	0.011	0.011	0.000	0.000	0.000	0.000
83	A	119	PHE	0	-0.042	-0.047	22.054	0.009	0.009	0.000	0.000	0.000	0.000
84	A	120	GLU	-1	-0.918	-0.934	25.699	-0.084	-0.084	0.000	0.000	0.000	0.000
85	A	121	SER	0	-0.031	-0.016	28.252	0.005	0.005	0.000	0.000	0.000	0.000
86	A	122	GLY	0	-0.008	0.007	24.237	0.014	0.014	0.000	0.000	0.000	0.000
87	A	123	ILE	0	0.015	0.007	18.591	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	124	ASN	0	-0.002	-0.006	20.963	0.021	0.021	0.000	0.000	0.000	0.000
89	A	125	TRP	0	0.078	0.012	14.069	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	126	GLY	0	0.013	0.013	20.519	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	127	ARG	1	0.904	0.942	23.770	0.056	0.056	0.000	0.000	0.000	0.000
92	A	128	VAL	0	0.011	0.013	17.690	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	129	VAL	0	0.013	0.007	20.722	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	130	ALA	0	0.003	0.015	22.459	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	131	LEU	0	0.007	0.007	21.654	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	132	LEU	0	-0.014	0.000	19.755	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	133	GLY	0	0.038	0.013	23.959	0.001	0.001	0.000	0.000	0.000	0.000
98	A	134	PHE	0	-0.046	-0.017	27.471	0.003	0.003	0.000	0.000	0.000	0.000
99	A	135	GLY	0	0.035	0.013	26.434	0.001	0.001	0.000	0.000	0.000	0.000
100	A	136	TYR	0	-0.043	-0.057	27.497	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	137	ARG	1	0.784	0.852	28.829	0.072	0.072	0.000	0.000	0.000	0.000
102	A	138	LEU	0	0.001	0.006	30.189	0.005	0.005	0.000	0.000	0.000	0.000
103	A	139	ALA	0	-0.027	-0.004	29.686	0.001	0.001	0.000	0.000	0.000	0.000
104	A	140	LEU	0	0.000	-0.012	31.803	0.005	0.005	0.000	0.000	0.000	0.000
105	A	141	HIS	0	0.009	0.010	34.184	0.007	0.007	0.000	0.000	0.000	0.000
106	A	142	VAL	0	0.013	0.003	35.389	0.005	0.005	0.000	0.000	0.000	0.000
107	A	143	TYR	0	-0.052	-0.029	32.188	0.000	0.000	0.000	0.000	0.000	0.000
108	A	144	GLN	0	-0.013	-0.008	36.994	0.003	0.003	0.000	0.000	0.000	0.000
109	A	145	HIS	0	-0.016	0.006	39.713	0.008	0.008	0.000	0.000	0.000	0.000
110	A	146	GLY	0	0.019	0.026	40.795	0.004	0.004	0.000	0.000	0.000	0.000
111	A	147	LEU	0	0.018	-0.016	41.883	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	148	THR	0	-0.005	-0.001	44.142	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	149	GLY	0	0.011	0.022	40.592	0.000	0.000	0.000	0.000	0.000	0.000
114	A	150	PHE	0	0.017	-0.006	36.739	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	151	LEU	0	-0.006	0.002	42.090	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	152	GLY	0	0.040	0.045	44.908	0.003	0.003	0.000	0.000	0.000	0.000
117	A	153	GLN	0	0.025	0.021	40.701	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	154	VAL	0	0.007	-0.007	44.612	0.002	0.002	0.000	0.000	0.000	0.000
119	A	155	THR	0	-0.040	-0.040	47.304	0.004	0.004	0.000	0.000	0.000	0.000
120	A	156	ARG	1	0.836	0.872	43.498	0.092	0.092	0.000	0.000	0.000	0.000
121	A	157	PHE	0	0.007	0.022	43.578	0.001	0.001	0.000	0.000	0.000	0.000
122	A	158	VAL	0	-0.009	-0.001	49.636	0.002	0.002	0.000	0.000	0.000	0.000
123	A	159	VAL	0	-0.001	-0.006	52.945	0.002	0.002	0.000	0.000	0.000	0.000
124	A	160	ASP	-1	-0.841	-0.915	50.329	-0.071	-0.071	0.000	0.000	0.000	0.000
125	A	161	PHE	0	-0.048	-0.017	53.167	0.002	0.002	0.000	0.000	0.000	0.000
126	A	162	MET	0	-0.009	-0.028	54.696	0.002	0.002	0.000	0.000	0.000	0.000
127	A	163	LEU	0	-0.001	0.010	56.263	0.003	0.003	0.000	0.000	0.000	0.000
128	A	164	HIS	0	-0.019	-0.025	53.641	0.001	0.001	0.000	0.000	0.000	0.000
129	A	165	HIS	1	0.895	0.958	54.844	0.064	0.064	0.000	0.000	0.000	0.000
130	A	166	SER	0	-0.025	-0.015	59.559	0.002	0.002	0.000	0.000	0.000	0.000
131	A	167	ILE	0	0.038	0.035	59.905	0.002	0.002	0.000	0.000	0.000	0.000
132	A	168	ALA	0	0.050	0.022	60.579	0.002	0.002	0.000	0.000	0.000	0.000
133	A	169	ARG	1	0.921	0.954	62.618	0.048	0.048	0.000	0.000	0.000	0.000
134	A	170	TRP	0	0.016	0.011	65.626	0.002	0.002	0.000	0.000	0.000	0.000
135	A	171	ILE	0	0.048	0.017	62.835	0.002	0.002	0.000	0.000	0.000	0.000
136	A	172	ALA	0	0.005	0.004	66.456	0.001	0.001	0.000	0.000	0.000	0.000
137	A	173	GLN	0	-0.037	-0.016	68.093	0.001	0.001	0.000	0.000	0.000	0.000
138	A	174	ARG	1	0.837	0.924	69.923	0.040	0.040	0.000	0.000	0.000	0.000
139	A	175	GLY	0	0.048	0.041	70.867	0.001	0.001	0.000	0.000	0.000	0.000
140	A	176	GLY	0	-0.019	-0.009	67.102	0.000	0.000	0.000	0.000	0.000	0.000
141	A	177	TRP	0	0.043	-0.022	59.701	0.001	0.001	0.000	0.000	0.000	0.000
142	A	178	VAL	0	0.008	0.010	65.859	0.000	0.000	0.000	0.000	0.000	0.000
143	A	179	ALA	0	-0.014	0.000	68.910	0.001	0.001	0.000	0.000	0.000	0.000
144	A	180	ALA	0	-0.054	-0.019	66.331	0.000	0.000	0.000	0.000	0.000	0.000
145	A	181	LEU	0	-0.029	-0.002	67.013	0.000	0.000	0.000	0.000	0.000	0.000
146	A	182	ASN	0	0.004	0.010	70.035	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:SER)