FMO DATABASE

FMODB ID: 5JGGZ

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	OptH
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	-1216824.586988
FMO2-HF: Nuclear repulsion	1158133.208473
FMO2-HF: Total energy	-58691.378515
FMO2-MP2: Total energy	-58863.390917

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.
-0.99	0.438	-0.008	-0.588	-0.831	0.002

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 : -0.019 / q_NPA : -0.029

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	-0.013	-0.006	3.854	-0.435	0.993	-0.008	-0.588	-0.831	0.002
4	A	24	GLU	-1	-0.927	-0.972	6.208	-0.070	-0.070	0.000	0.000	0.000	0.000
5	A	25	GLU	-1	-0.921	-0.964	9.185	-0.653	-0.653	0.000	0.000	0.000	0.000
6	A	26	GLN	0	-0.025	-0.012	5.548	-0.310	-0.310	0.000	0.000	0.000	0.000
7	A	27	VAL	0	0.058	0.023	8.184	0.316	0.316	0.000	0.000	0.000	0.000
8	A	28	ALA	0	0.005	0.035	10.852	0.129	0.129	0.000	0.000	0.000	0.000
9	A	29	GLN	0	-0.021	-0.014	10.221	-0.084	-0.084	0.000	0.000	0.000	0.000
10	A	30	ASP	-1	-0.828	-0.922	9.671	0.292	0.292	0.000	0.000	0.000	0.000
11	A	31	THR	0	-0.052	-0.064	12.826	0.076	0.076	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.949	-0.966	16.013	-0.083	-0.083	0.000	0.000	0.000	0.000
13	A	33	GLU	-1	-0.864	-0.916	13.996	0.143	0.143	0.000	0.000	0.000	0.000
14	A	34	VAL	0	-0.033	-0.016	15.493	0.026	0.026	0.000	0.000	0.000	0.000
15	A	35	PHE	0	-0.010	-0.001	18.208	0.008	0.008	0.000	0.000	0.000	0.000
16	A	36	ARG	1	0.942	0.973	21.049	0.047	0.047	0.000	0.000	0.000	0.000
17	A	37	SER	0	0.006	0.013	20.715	0.006	0.006	0.000	0.000	0.000	0.000
18	A	38	TYR	0	-0.034	0.001	22.373	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	39	VAL	0	-0.003	-0.014	24.097	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.023	-0.002	26.270	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	41	TYR	0	0.016	-0.018	24.428	0.005	0.005	0.000	0.000	0.000	0.000
22	A	42	ARG	1	0.884	0.951	27.358	-0.088	-0.088	0.000	0.000	0.000	0.000
23	A	43	HIS	0	-0.039	-0.003	29.763	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	44	GLN	0	0.019	0.018	31.020	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	45	GLN	0	-0.044	-0.030	30.541	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	46	GLU	-1	-0.837	-0.936	33.278	0.064	0.064	0.000	0.000	0.000	0.000
27	A	47	GLN	0	-0.056	-0.017	35.675	0.000	0.000	0.000	0.000	0.000	0.000
28	A	48	GLU	-1	-0.990	-1.001	35.105	0.091	0.091	0.000	0.000	0.000	0.000
29	A	49	ALA	0	-0.078	-0.032	36.770	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-0.990	-0.981	38.494	0.061	0.061	0.000	0.000	0.000	0.000
31	A	67	PRO	0	-0.002	-0.031	22.625	0.007	0.007	0.000	0.000	0.000	0.000
32	A	68	SER	0	-0.017	0.014	21.041	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	69	SER	0	0.006	-0.020	15.581	0.059	0.059	0.000	0.000	0.000	0.000
34	A	70	THR	0	0.034	0.002	12.111	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	71	MET	0	0.018	0.012	10.916	0.031	0.031	0.000	0.000	0.000	0.000
36	A	72	GLY	0	0.028	0.018	15.259	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	73	GLN	0	-0.029	-0.029	18.033	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	74	VAL	0	-0.013	0.010	14.417	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	75	GLY	0	0.051	0.023	17.899	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	76	ARG	1	0.941	0.975	20.434	-0.198	-0.198	0.000	0.000	0.000	0.000
41	A	77	GLN	0	-0.023	-0.023	20.829	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	78	LEU	0	-0.027	-0.019	18.458	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	79	ALA	0	-0.003	0.010	22.641	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	80	ILE	0	-0.059	-0.015	25.444	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	81	ILE	0	-0.078	-0.040	22.437	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	82	GLY	0	0.064	0.042	26.616	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	83	ASP	-1	-0.888	-0.943	27.733	0.168	0.168	0.000	0.000	0.000	0.000
48	A	84	ASP	-1	-0.916	-0.981	30.346	0.093	0.093	0.000	0.000	0.000	0.000
49	A	85	ILE	0	-0.003	-0.003	27.686	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	86	ASN	0	0.031	-0.002	25.332	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	87	ARG	1	0.943	0.981	29.453	-0.124	-0.124	0.000	0.000	0.000	0.000
52	A	88	ARG	1	0.909	0.953	33.008	-0.091	-0.091	0.000	0.000	0.000	0.000
53	A	89	TYR	0	0.011	0.012	28.074	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	90	ASP	-1	-0.783	-0.871	31.770	0.060	0.060	0.000	0.000	0.000	0.000
55	A	91	SER	0	0.039	0.011	33.027	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	92	GLU	-1	-0.926	-0.943	34.458	0.031	0.031	0.000	0.000	0.000	0.000
57	A	93	PHE	0	-0.021	-0.031	29.064	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	94	GLN	0	-0.052	-0.029	34.671	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	95	THR	0	-0.001	-0.006	37.470	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	96	MET	0	-0.043	-0.012	33.588	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	97	LEU	0	-0.031	-0.021	33.983	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	98	GLN	0	0.013	0.012	38.418	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	99	HIS	0	-0.029	-0.004	41.692	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	100	LEU	0	-0.071	-0.057	38.042	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	101	GLN	0	-0.046	-0.009	41.472	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	102	PRO	0	-0.042	-0.001	36.792	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	103	THR	0	-0.050	-0.031	39.167	0.003	0.003	0.000	0.000	0.000	0.000
68	A	104	ALA	0	0.011	-0.020	36.300	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	105	GLU	-1	-0.917	-0.973	36.018	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	106	ASN	0	0.075	0.052	37.171	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	107	ALA	0	0.060	0.033	33.301	0.002	0.002	0.000	0.000	0.000	0.000
72	A	108	TYR	0	0.010	0.015	27.973	0.004	0.004	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.864	-0.953	31.736	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	110	TYR	0	-0.042	-0.025	34.165	0.004	0.004	0.000	0.000	0.000	0.000
75	A	111	PHE	0	0.014	-0.001	24.921	0.006	0.006	0.000	0.000	0.000	0.000
76	A	112	THR	0	0.032	0.009	28.900	0.003	0.003	0.000	0.000	0.000	0.000
77	A	113	LYS	1	0.968	1.000	29.931	0.016	0.016	0.000	0.000	0.000	0.000
78	A	114	ILE	0	-0.016	0.022	30.927	0.004	0.004	0.000	0.000	0.000	0.000
79	A	115	ALA	0	0.032	0.015	26.251	0.007	0.007	0.000	0.000	0.000	0.000
80	A	116	THR	0	-0.049	-0.054	27.309	0.002	0.002	0.000	0.000	0.000	0.000
81	A	117	SER	0	-0.005	-0.028	28.286	0.006	0.006	0.000	0.000	0.000	0.000
82	A	118	LEU	0	-0.049	-0.003	26.447	0.009	0.009	0.000	0.000	0.000	0.000
83	A	119	PHE	0	-0.052	-0.050	21.894	0.017	0.017	0.000	0.000	0.000	0.000
84	A	120	GLU	-1	-0.915	-0.936	25.630	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	121	SER	0	-0.087	-0.041	28.190	0.001	0.001	0.000	0.000	0.000	0.000
86	A	122	GLY	0	0.006	0.013	24.198	0.010	0.010	0.000	0.000	0.000	0.000
87	A	123	ILE	0	0.015	0.009	18.629	0.004	0.004	0.000	0.000	0.000	0.000
88	A	124	ASN	0	-0.007	-0.012	20.942	0.022	0.022	0.000	0.000	0.000	0.000
89	A	125	TRP	0	0.071	0.011	14.060	-0.037	-0.037	0.000	0.000	0.000	0.000
90	A	126	GLY	0	0.022	0.018	20.493	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	127	ARG	1	0.941	0.958	23.782	-0.077	-0.077	0.000	0.000	0.000	0.000
92	A	128	VAL	0	0.013	0.014	17.678	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	129	VAL	0	0.017	0.010	20.693	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	130	ALA	0	0.007	0.017	22.434	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	131	LEU	0	0.006	0.005	21.806	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	132	LEU	0	-0.008	0.003	19.878	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	133	GLY	0	0.039	0.014	24.062	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	134	PHE	0	-0.036	-0.009	27.528	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	135	GLY	0	0.030	0.007	26.595	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	136	TYR	0	-0.042	-0.030	27.664	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	137	ARG	1	0.871	0.932	29.137	-0.061	-0.061	0.000	0.000	0.000	0.000
102	A	138	LEU	0	0.000	0.007	29.986	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	139	ALA	0	-0.024	-0.001	29.821	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	140	LEU	0	-0.003	-0.013	31.925	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	141	HIS	0	-0.010	0.002	34.437	0.002	0.002	0.000	0.000	0.000	0.000
106	A	142	VAL	0	0.002	-0.012	35.443	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	143	TYR	0	-0.065	-0.032	31.999	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	144	GLN	0	-0.017	-0.014	37.127	0.002	0.002	0.000	0.000	0.000	0.000
109	A	145	HIS	0	-0.019	0.009	39.938	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	146	GLY	0	0.028	0.029	40.885	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	147	LEU	0	0.021	-0.016	41.862	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	148	THR	0	-0.009	0.001	44.311	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	149	GLY	0	0.039	0.042	40.519	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	150	PHE	0	0.016	-0.014	36.510	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	151	LEU	0	-0.018	0.000	41.898	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	152	GLY	0	0.037	0.029	44.732	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	153	GLN	0	0.024	0.022	41.348	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	154	VAL	0	0.019	-0.004	44.441	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	155	THR	0	-0.030	-0.024	47.131	0.001	0.001	0.000	0.000	0.000	0.000
120	A	156	ARG	1	0.932	0.949	43.598	0.034	0.034	0.000	0.000	0.000	0.000
121	A	157	PHE	0	-0.004	0.023	43.525	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	158	VAL	0	-0.014	-0.004	49.479	0.000	0.000	0.000	0.000	0.000	0.000
123	A	159	VAL	0	-0.004	-0.007	52.778	0.000	0.000	0.000	0.000	0.000	0.000
124	A	160	ASP	-1	-0.846	-0.916	50.859	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	161	PHE	0	-0.043	-0.007	53.056	0.000	0.000	0.000	0.000	0.000	0.000
126	A	162	MET	0	0.010	-0.027	54.551	0.000	0.000	0.000	0.000	0.000	0.000
127	A	163	LEU	0	-0.013	0.007	56.357	0.001	0.001	0.000	0.000	0.000	0.000
128	A	164	HIS	0	-0.008	-0.025	53.725	0.001	0.001	0.000	0.000	0.000	0.000
129	A	165	HIS	1	0.884	0.953	54.966	0.035	0.035	0.000	0.000	0.000	0.000
130	A	166	SER	0	-0.048	-0.024	59.425	0.001	0.001	0.000	0.000	0.000	0.000
131	A	167	ILE	0	0.036	0.033	59.538	0.001	0.001	0.000	0.000	0.000	0.000
132	A	168	ALA	0	0.048	0.018	60.455	0.001	0.001	0.000	0.000	0.000	0.000
133	A	169	ARG	1	0.950	0.974	62.464	0.026	0.026	0.000	0.000	0.000	0.000
134	A	170	TRP	0	0.024	0.013	65.485	0.001	0.001	0.000	0.000	0.000	0.000
135	A	171	ILE	0	0.027	0.005	62.736	0.001	0.001	0.000	0.000	0.000	0.000
136	A	172	ALA	0	0.003	0.002	66.330	0.001	0.001	0.000	0.000	0.000	0.000
137	A	173	GLN	0	-0.035	-0.023	67.934	0.000	0.000	0.000	0.000	0.000	0.000
138	A	174	ARG	1	0.847	0.943	69.652	0.018	0.018	0.000	0.000	0.000	0.000
139	A	175	GLY	0	0.050	0.041	70.710	0.001	0.001	0.000	0.000	0.000	0.000
140	A	176	GLY	0	-0.019	-0.008	66.933	0.001	0.001	0.000	0.000	0.000	0.000
141	A	177	TRP	0	0.041	-0.023	59.860	0.000	0.000	0.000	0.000	0.000	0.000
142	A	178	VAL	0	0.006	0.009	65.680	0.000	0.000	0.000	0.000	0.000	0.000
143	A	179	ALA	0	-0.004	0.003	68.725	0.000	0.000	0.000	0.000	0.000	0.000
144	A	180	ALA	0	-0.053	-0.018	66.181	0.000	0.000	0.000	0.000	0.000	0.000
145	A	181	LEU	0	-0.036	-0.005	66.826	0.000	0.000	0.000	0.000	0.000	0.000
146	A	182	ASN	0	0.003	0.010	69.846	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)