FMO DATABASE

FMODB ID: QV55Y

Calculation Name: 4U2U-B-Xray372

Preferred Name: Bcl-2 homologous antagonist/killer

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4U2U

Chain ID: B

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1150555.989222
FMO2-HF: Nuclear repulsion	1093546.711271
FMO2-HF: Total energy	-57009.277951
FMO2-MP2: Total energy	-57176.352307

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(B:22:MET)

Summations of interaction energy for fragment #1(B:22:MET)

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.
-6.911	-0.812	0.716	-2.275	-4.54	-0.009

Interaction energy analysis for fragmet #1(B:22:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.012

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	B	24	GLU	-1	-0.905	-0.959	3.296	-3.160	-0.747	0.036	-1.171	-1.279	-0.001
4	B	25	GLU	-1	-0.934	-0.971	6.181	-0.150	-0.150	0.000	0.000	0.000	0.000
5	B	26	GLN	0	-0.023	-0.024	2.689	-1.501	-0.354	0.271	-0.259	-1.158	-0.002
6	B	27	VAL	0	0.067	0.048	3.482	-0.284	0.732	0.224	-0.230	-1.011	-0.001
7	B	28	ALA	0	0.001	0.028	5.231	-0.137	-0.091	0.000	-0.012	-0.034	0.000
8	B	29	GLN	0	-0.027	-0.018	7.752	0.002	0.002	0.000	0.000	0.000	0.000
9	B	30	ASP	-1	-0.818	-0.911	3.648	-1.765	-0.570	0.171	-0.565	-0.801	-0.005
10	B	31	THR	0	-0.061	-0.069	7.299	-0.041	-0.041	0.000	0.000	0.000	0.000
11	B	32	GLU	-1	-0.959	-0.970	9.926	-0.244	-0.244	0.000	0.000	0.000	0.000
12	B	33	GLU	-1	-0.948	-0.982	9.320	-0.502	-0.502	0.000	0.000	0.000	0.000
13	B	34	VAL	0	-0.028	-0.016	8.346	0.019	0.019	0.000	0.000	0.000	0.000
14	B	35	PHE	0	-0.020	-0.006	11.210	0.021	0.021	0.000	0.000	0.000	0.000
15	B	36	ARG	1	0.943	0.973	14.662	0.216	0.216	0.000	0.000	0.000	0.000
16	B	37	SER	0	0.003	0.012	13.720	0.016	0.016	0.000	0.000	0.000	0.000
17	B	38	TYR	0	-0.055	-0.008	15.231	0.017	0.017	0.000	0.000	0.000	0.000
18	B	39	VAL	0	-0.007	-0.014	16.818	0.013	0.013	0.000	0.000	0.000	0.000
19	B	40	PHE	0	-0.030	-0.007	19.355	0.010	0.010	0.000	0.000	0.000	0.000
20	B	41	TYR	0	-0.005	-0.033	17.377	0.013	0.013	0.000	0.000	0.000	0.000
21	B	42	ARG	1	0.888	0.973	20.824	0.088	0.088	0.000	0.000	0.000	0.000
22	B	43	HIS	0	0.014	0.017	22.477	0.004	0.004	0.000	0.000	0.000	0.000
23	B	44	GLN	0	-0.094	-0.054	23.264	0.009	0.009	0.000	0.000	0.000	0.000
24	B	45	GLN	0	-0.031	-0.001	23.482	0.000	0.000	0.000	0.000	0.000	0.000
25	B	46	GLU	-1	-0.847	-0.916	26.018	-0.069	-0.069	0.000	0.000	0.000	0.000
26	B	47	GLN	0	-0.097	-0.032	28.524	0.003	0.003	0.000	0.000	0.000	0.000
27	B	48	GLU	-1	-0.974	-0.977	30.684	-0.047	-0.047	0.000	0.000	0.000	0.000
28	B	69	SER	0	0.084	0.026	11.105	0.005	0.005	0.000	0.000	0.000	0.000
29	B	70	THR	0	-0.047	-0.026	6.563	0.098	0.098	0.000	0.000	0.000	0.000
30	B	71	MET	0	0.073	0.035	3.468	-0.043	0.239	0.014	-0.038	-0.257	0.000
31	B	72	GLY	0	0.049	0.027	8.231	0.103	0.103	0.000	0.000	0.000	0.000
32	B	73	GLN	0	-0.034	-0.029	11.123	0.058	0.058	0.000	0.000	0.000	0.000
33	B	74	VAL	0	0.010	0.017	7.148	0.056	0.056	0.000	0.000	0.000	0.000
34	B	75	GLY	0	0.050	0.021	10.581	0.048	0.048	0.000	0.000	0.000	0.000
35	B	76	ARG	1	0.893	0.955	13.165	0.146	0.146	0.000	0.000	0.000	0.000
36	B	77	GLN	0	-0.039	-0.031	13.715	0.018	0.018	0.000	0.000	0.000	0.000
37	B	78	LEU	0	-0.011	-0.009	11.680	0.018	0.018	0.000	0.000	0.000	0.000
38	B	79	ALA	0	-0.013	-0.006	15.831	0.008	0.008	0.000	0.000	0.000	0.000
39	B	80	ILE	0	0.020	0.014	18.833	0.006	0.006	0.000	0.000	0.000	0.000
40	B	81	ILE	0	0.012	0.013	16.461	0.008	0.008	0.000	0.000	0.000	0.000
41	B	82	GLY	0	-0.071	-0.043	20.450	0.005	0.005	0.000	0.000	0.000	0.000
42	B	83	ASP	-1	-0.820	-0.918	22.407	-0.059	-0.059	0.000	0.000	0.000	0.000
43	B	84	ASP	-1	-0.988	-0.992	24.926	-0.031	-0.031	0.000	0.000	0.000	0.000
44	B	85	ILE	0	0.022	0.007	21.863	0.000	0.000	0.000	0.000	0.000	0.000
45	B	86	ASN	0	-0.038	-0.012	21.549	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	87	ARG	1	0.957	0.984	23.658	0.042	0.042	0.000	0.000	0.000	0.000
47	B	88	ARG	1	0.934	0.968	27.309	0.056	0.056	0.000	0.000	0.000	0.000
48	B	89	TYR	0	0.042	0.013	22.329	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	90	ASP	-1	-0.813	-0.894	25.310	-0.073	-0.073	0.000	0.000	0.000	0.000
50	B	91	SER	0	0.025	0.017	26.723	0.000	0.000	0.000	0.000	0.000	0.000
51	B	92	GLU	-1	-0.935	-0.964	28.528	-0.060	-0.060	0.000	0.000	0.000	0.000
52	B	93	PHE	0	-0.021	-0.025	22.803	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	94	GLN	0	0.003	-0.013	28.294	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	95	THR	0	-0.049	-0.019	30.813	0.003	0.003	0.000	0.000	0.000	0.000
55	B	96	MET	0	-0.006	-0.010	30.861	0.000	0.000	0.000	0.000	0.000	0.000
56	B	97	LEU	0	-0.007	-0.002	27.411	0.000	0.000	0.000	0.000	0.000	0.000
57	B	98	GLN	0	-0.033	0.001	32.127	0.003	0.003	0.000	0.000	0.000	0.000
58	B	99	HIS	0	-0.064	-0.038	35.460	0.002	0.002	0.000	0.000	0.000	0.000
59	B	100	LEU	0	-0.041	0.003	32.267	0.002	0.002	0.000	0.000	0.000	0.000
60	B	101	GLN	0	0.014	-0.002	33.782	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	102	PRO	0	-0.001	0.014	30.469	0.000	0.000	0.000	0.000	0.000	0.000
62	B	103	THR	0	0.054	0.025	32.760	0.000	0.000	0.000	0.000	0.000	0.000
63	B	104	ALA	0	0.015	-0.015	29.932	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	105	GLU	-1	-0.977	-0.980	30.112	-0.071	-0.071	0.000	0.000	0.000	0.000
65	B	106	ASN	0	-0.002	-0.002	32.097	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	107	ALA	0	-0.029	-0.016	27.167	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	108	TYR	0	0.017	0.019	23.274	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	109	GLU	-1	-0.889	-0.946	26.325	-0.084	-0.084	0.000	0.000	0.000	0.000
69	B	110	TYR	0	0.009	-0.010	28.435	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	111	PHE	0	0.021	0.002	18.983	0.000	0.000	0.000	0.000	0.000	0.000
71	B	112	THR	0	0.041	0.009	23.588	-0.007	-0.007	0.000	0.000	0.000	0.000
72	B	113	LYS	1	0.967	0.996	24.465	0.072	0.072	0.000	0.000	0.000	0.000
73	B	114	ILE	0	-0.027	0.000	24.913	0.003	0.003	0.000	0.000	0.000	0.000
74	B	115	ALA	0	0.022	0.008	20.491	0.000	0.000	0.000	0.000	0.000	0.000
75	B	116	THR	0	-0.039	-0.050	21.632	-0.008	-0.008	0.000	0.000	0.000	0.000
76	B	117	SER	0	-0.003	-0.001	23.017	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	118	LEU	0	-0.050	-0.007	20.032	0.005	0.005	0.000	0.000	0.000	0.000
78	B	119	PHE	0	-0.044	-0.046	15.972	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.914	-0.936	20.378	-0.105	-0.105	0.000	0.000	0.000	0.000
80	B	121	SER	0	-0.092	-0.042	23.305	0.003	0.003	0.000	0.000	0.000	0.000
81	B	122	GLY	0	0.012	0.015	19.364	0.007	0.007	0.000	0.000	0.000	0.000
82	B	123	ILE	0	0.015	0.010	13.127	0.012	0.012	0.000	0.000	0.000	0.000
83	B	124	ASN	0	-0.003	-0.009	15.535	0.010	0.010	0.000	0.000	0.000	0.000
84	B	125	TRP	0	0.078	0.015	8.709	-0.029	-0.029	0.000	0.000	0.000	0.000
85	B	126	GLY	0	0.011	0.013	14.981	0.003	0.003	0.000	0.000	0.000	0.000
86	B	127	ARG	1	0.934	0.957	17.978	0.110	0.110	0.000	0.000	0.000	0.000
87	B	128	VAL	0	0.025	0.018	11.779	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	129	VAL	0	0.010	0.003	14.591	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	130	ALA	0	0.005	0.019	16.302	-0.003	-0.003	0.000	0.000	0.000	0.000
90	B	131	LEU	0	0.011	0.008	15.751	0.002	0.002	0.000	0.000	0.000	0.000
91	B	132	LEU	0	-0.009	0.004	13.279	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	133	GLY	0	0.025	0.009	17.470	0.001	0.001	0.000	0.000	0.000	0.000
93	B	134	PHE	0	-0.031	-0.008	20.988	0.004	0.004	0.000	0.000	0.000	0.000
94	B	135	GLY	0	0.033	0.007	20.107	0.003	0.003	0.000	0.000	0.000	0.000
95	B	136	TYR	0	-0.051	-0.062	21.037	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	137	ARG	1	0.894	0.937	22.424	0.075	0.075	0.000	0.000	0.000	0.000
97	B	138	LEU	0	0.002	0.001	23.905	0.004	0.004	0.000	0.000	0.000	0.000
98	B	139	ALA	0	-0.018	-0.008	23.405	0.003	0.003	0.000	0.000	0.000	0.000
99	B	140	LEU	0	-0.001	-0.002	25.521	0.003	0.003	0.000	0.000	0.000	0.000
100	B	141	HIS	0	0.009	0.008	28.172	0.003	0.003	0.000	0.000	0.000	0.000
101	B	142	VAL	0	-0.038	-0.018	27.304	0.003	0.003	0.000	0.000	0.000	0.000
102	B	143	TYR	0	-0.014	0.007	28.641	0.001	0.001	0.000	0.000	0.000	0.000
103	B	144	GLN	0	0.010	-0.003	30.540	0.002	0.002	0.000	0.000	0.000	0.000
104	B	145	HIS	0	0.010	0.009	33.676	0.000	0.000	0.000	0.000	0.000	0.000
105	B	146	GLY	0	0.022	0.010	32.826	0.002	0.002	0.000	0.000	0.000	0.000
106	B	147	LEU	0	-0.050	-0.021	33.624	0.001	0.001	0.000	0.000	0.000	0.000
107	B	148	THR	0	-0.034	-0.039	35.150	0.002	0.002	0.000	0.000	0.000	0.000
108	B	149	GLY	0	0.036	0.037	37.643	0.003	0.003	0.000	0.000	0.000	0.000
109	B	150	PHE	0	-0.010	-0.006	34.408	0.001	0.001	0.000	0.000	0.000	0.000
110	B	151	LEU	0	0.047	0.016	37.690	0.000	0.000	0.000	0.000	0.000	0.000
111	B	152	GLY	0	0.050	0.041	41.036	0.002	0.002	0.000	0.000	0.000	0.000
112	B	153	GLN	0	-0.016	-0.003	35.689	0.004	0.004	0.000	0.000	0.000	0.000
113	B	154	VAL	0	0.005	-0.007	38.409	0.001	0.001	0.000	0.000	0.000	0.000
114	B	155	THR	0	-0.022	-0.027	40.758	0.002	0.002	0.000	0.000	0.000	0.000
115	B	156	ARG	1	0.995	0.994	38.247	0.059	0.059	0.000	0.000	0.000	0.000
116	B	157	PHE	0	-0.041	-0.007	36.262	0.001	0.001	0.000	0.000	0.000	0.000
117	B	158	VAL	0	0.001	0.006	42.379	0.001	0.001	0.000	0.000	0.000	0.000
118	B	159	VAL	0	0.007	0.000	45.369	0.002	0.002	0.000	0.000	0.000	0.000
119	B	160	ASP	-1	-0.874	-0.939	44.682	-0.045	-0.045	0.000	0.000	0.000	0.000
120	B	161	PHE	0	-0.001	0.009	43.727	0.001	0.001	0.000	0.000	0.000	0.000
121	B	162	MET	0	0.004	-0.029	46.125	0.002	0.002	0.000	0.000	0.000	0.000
122	B	163	LEU	0	-0.014	0.007	49.664	0.002	0.002	0.000	0.000	0.000	0.000
123	B	164	HIS	0	-0.008	-0.016	46.563	0.001	0.001	0.000	0.000	0.000	0.000
124	B	165	HIS	1	0.866	0.941	44.894	0.044	0.044	0.000	0.000	0.000	0.000
125	B	166	SER	0	-0.034	-0.018	49.941	0.001	0.001	0.000	0.000	0.000	0.000
126	B	167	ILE	0	0.028	0.029	50.043	0.001	0.001	0.000	0.000	0.000	0.000
127	B	168	ALA	0	0.040	0.015	53.351	0.001	0.001	0.000	0.000	0.000	0.000
128	B	169	ARG	1	0.964	0.981	55.046	0.031	0.031	0.000	0.000	0.000	0.000
129	B	170	TRP	0	0.011	0.004	56.469	0.001	0.001	0.000	0.000	0.000	0.000
130	B	171	ILE	0	0.037	0.012	54.367	0.001	0.001	0.000	0.000	0.000	0.000
131	B	172	ALA	0	-0.002	-0.001	58.637	0.001	0.001	0.000	0.000	0.000	0.000
132	B	173	GLN	0	-0.042	-0.022	60.994	0.001	0.001	0.000	0.000	0.000	0.000
133	B	174	ARG	1	0.861	0.949	60.503	0.027	0.027	0.000	0.000	0.000	0.000
134	B	175	GLY	0	0.049	0.042	63.328	0.001	0.001	0.000	0.000	0.000	0.000
135	B	176	GLY	0	-0.025	-0.013	60.377	0.000	0.000	0.000	0.000	0.000	0.000
136	B	177	TRP	0	0.032	-0.025	52.166	0.000	0.000	0.000	0.000	0.000	0.000
137	B	178	VAL	0	0.013	0.011	58.799	0.000	0.000	0.000	0.000	0.000	0.000
138	B	179	ALA	0	0.023	0.016	61.606	0.000	0.000	0.000	0.000	0.000	0.000
139	B	180	ALA	0	-0.067	-0.029	57.282	0.000	0.000	0.000	0.000	0.000	0.000
140	B	181	LEU	0	-0.034	-0.011	59.350	0.000	0.000	0.000	0.000	0.000	0.000
141	B	182	ASN	0	-0.010	0.013	61.284	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:22:MET)