FMO DATABASE

FMODB ID: VQZY1

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	OptAll
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	-1221920.27649
FMO2-HF: Nuclear repulsion	1163227.794203
FMO2-HF: Total energy	-58692.482287
FMO2-MP2: Total energy	-58864.491803

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.
-8.687	-5.001	0.237	-2.046	-1.875	-0.007

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 : 0.033 / q_NPA : 0.015

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	-0.014	-0.020	2.712	-6.333	-2.735	0.238	-2.043	-1.792	-0.007
4	A	24	GLU	-1	-0.919	-0.962	5.215	-0.702	-0.614	-0.001	-0.003	-0.083	0.000
5	A	25	GLU	-1	-0.883	-0.947	8.892	-1.341	-1.341	0.000	0.000	0.000	0.000
6	A	26	GLN	0	-0.076	-0.041	6.042	-0.199	-0.199	0.000	0.000	0.000	0.000
7	A	27	VAL	0	0.043	0.013	8.493	0.539	0.539	0.000	0.000	0.000	0.000
8	A	28	ALA	0	-0.004	0.023	10.875	0.365	0.365	0.000	0.000	0.000	0.000
9	A	29	GLN	0	-0.017	-0.012	10.628	0.028	0.028	0.000	0.000	0.000	0.000
10	A	30	ASP	-1	-0.809	-0.914	9.754	-1.696	-1.696	0.000	0.000	0.000	0.000
11	A	31	THR	0	-0.039	-0.048	12.930	0.253	0.253	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.821	-0.876	16.151	-0.508	-0.508	0.000	0.000	0.000	0.000
13	A	33	GLU	-1	-0.844	-0.904	14.616	-0.586	-0.586	0.000	0.000	0.000	0.000
14	A	34	VAL	0	-0.029	-0.017	15.700	0.101	0.101	0.000	0.000	0.000	0.000
15	A	35	PHE	0	0.006	0.004	18.342	0.078	0.078	0.000	0.000	0.000	0.000
16	A	36	ARG	1	0.817	0.883	19.952	0.571	0.571	0.000	0.000	0.000	0.000
17	A	37	SER	0	-0.048	-0.040	20.943	0.055	0.055	0.000	0.000	0.000	0.000
18	A	38	TYR	0	0.007	0.005	22.332	0.041	0.041	0.000	0.000	0.000	0.000
19	A	39	VAL	0	-0.001	-0.007	24.048	0.034	0.034	0.000	0.000	0.000	0.000
20	A	40	PHE	0	-0.031	-0.003	26.131	0.024	0.024	0.000	0.000	0.000	0.000
21	A	41	TYR	0	0.008	-0.013	24.160	0.030	0.030	0.000	0.000	0.000	0.000
22	A	42	ARG	1	0.793	0.889	27.190	0.204	0.204	0.000	0.000	0.000	0.000
23	A	43	HIS	0	-0.026	-0.002	29.658	0.018	0.018	0.000	0.000	0.000	0.000
24	A	44	GLN	0	-0.047	-0.041	30.425	0.000	0.000	0.000	0.000	0.000	0.000
25	A	45	GLN	0	-0.003	-0.008	29.863	0.005	0.005	0.000	0.000	0.000	0.000
26	A	46	GLU	-1	-0.739	-0.812	33.115	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	47	GLN	0	-0.057	-0.017	35.316	0.006	0.006	0.000	0.000	0.000	0.000
28	A	48	GLU	-1	-0.920	-0.948	34.323	-0.105	-0.105	0.000	0.000	0.000	0.000
29	A	49	ALA	0	-0.058	-0.017	36.916	0.009	0.009	0.000	0.000	0.000	0.000
30	A	50	GLU	-1	-1.017	-1.002	38.694	-0.080	-0.080	0.000	0.000	0.000	0.000
31	A	67	PRO	0	-0.011	-0.034	22.250	0.005	0.005	0.000	0.000	0.000	0.000
32	A	68	SER	0	-0.034	-0.003	20.327	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	69	SER	0	0.008	-0.009	14.968	0.034	0.034	0.000	0.000	0.000	0.000
34	A	70	THR	0	0.014	-0.006	12.329	0.060	0.060	0.000	0.000	0.000	0.000
35	A	71	MET	0	0.014	0.022	10.005	0.134	0.134	0.000	0.000	0.000	0.000
36	A	72	GLY	0	0.068	0.032	14.932	0.035	0.035	0.000	0.000	0.000	0.000
37	A	73	GLN	0	0.015	0.010	17.967	0.035	0.035	0.000	0.000	0.000	0.000
38	A	74	VAL	0	0.005	0.014	14.457	0.043	0.043	0.000	0.000	0.000	0.000
39	A	75	GLY	0	0.035	0.015	17.844	0.028	0.028	0.000	0.000	0.000	0.000
40	A	76	ARG	1	0.907	0.970	20.180	0.198	0.198	0.000	0.000	0.000	0.000
41	A	77	GLN	0	-0.013	-0.012	20.826	0.021	0.021	0.000	0.000	0.000	0.000
42	A	78	LEU	0	-0.032	-0.028	18.386	0.023	0.023	0.000	0.000	0.000	0.000
43	A	79	ALA	0	0.010	0.014	22.605	0.012	0.012	0.000	0.000	0.000	0.000
44	A	80	ILE	0	-0.030	0.000	25.479	0.020	0.020	0.000	0.000	0.000	0.000
45	A	81	ILE	0	-0.040	-0.010	22.682	0.020	0.020	0.000	0.000	0.000	0.000
46	A	82	GLY	0	0.061	0.037	26.826	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	83	ASP	-1	-0.811	-0.907	28.259	-0.106	-0.106	0.000	0.000	0.000	0.000
48	A	84	ASP	-1	-0.801	-0.890	30.254	-0.087	-0.087	0.000	0.000	0.000	0.000
49	A	85	ILE	0	-0.025	-0.019	27.494	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	86	ASN	0	-0.013	-0.025	25.522	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	87	ARG	1	0.847	0.928	29.478	0.081	0.081	0.000	0.000	0.000	0.000
52	A	88	ARG	1	0.837	0.920	33.054	0.084	0.084	0.000	0.000	0.000	0.000
53	A	89	TYR	0	0.018	0.001	27.141	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	90	ASP	-1	-0.781	-0.856	31.430	-0.173	-0.173	0.000	0.000	0.000	0.000
55	A	91	SER	0	0.020	-0.010	32.702	0.003	0.003	0.000	0.000	0.000	0.000
56	A	92	GLU	-1	-0.911	-0.942	33.952	-0.133	-0.133	0.000	0.000	0.000	0.000
57	A	93	PHE	0	0.000	-0.018	28.677	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	94	GLN	0	-0.044	-0.030	34.240	0.004	0.004	0.000	0.000	0.000	0.000
59	A	95	THR	0	-0.019	-0.011	37.283	0.006	0.006	0.000	0.000	0.000	0.000
60	A	96	MET	0	-0.056	-0.027	33.355	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	97	LEU	0	-0.036	-0.011	33.721	0.001	0.001	0.000	0.000	0.000	0.000
62	A	98	GLN	0	0.010	0.008	38.037	0.003	0.003	0.000	0.000	0.000	0.000
63	A	99	HIS	0	-0.033	-0.006	41.191	0.008	0.008	0.000	0.000	0.000	0.000
64	A	100	LEU	0	-0.060	-0.044	37.391	0.002	0.002	0.000	0.000	0.000	0.000
65	A	101	GLN	0	-0.037	-0.014	40.924	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	102	PRO	0	-0.018	0.011	36.444	0.000	0.000	0.000	0.000	0.000	0.000
67	A	103	THR	0	0.026	0.004	38.670	0.004	0.004	0.000	0.000	0.000	0.000
68	A	104	ALA	0	0.025	-0.001	36.313	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	105	GLU	-1	-0.858	-0.913	36.371	-0.164	-0.164	0.000	0.000	0.000	0.000
70	A	106	ASN	0	0.024	0.014	36.642	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	107	ALA	0	0.050	0.029	33.172	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	108	TYR	0	0.011	0.020	27.220	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	109	GLU	-1	-0.832	-0.922	30.722	-0.249	-0.249	0.000	0.000	0.000	0.000
74	A	110	TYR	0	-0.061	-0.044	32.795	0.002	0.002	0.000	0.000	0.000	0.000
75	A	111	PHE	0	0.016	0.003	24.426	0.001	0.001	0.000	0.000	0.000	0.000
76	A	112	THR	0	0.023	0.000	27.690	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	113	LYS	1	0.919	0.978	28.702	0.176	0.176	0.000	0.000	0.000	0.000
78	A	114	ILE	0	-0.001	0.014	30.015	0.009	0.009	0.000	0.000	0.000	0.000
79	A	115	ALA	0	0.026	0.013	25.073	0.002	0.002	0.000	0.000	0.000	0.000
80	A	116	THR	0	-0.045	-0.040	25.851	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	117	SER	0	0.014	-0.008	27.087	0.003	0.003	0.000	0.000	0.000	0.000
82	A	118	LEU	0	-0.079	-0.020	25.507	0.014	0.014	0.000	0.000	0.000	0.000
83	A	119	PHE	0	-0.020	-0.040	21.156	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	120	GLU	-1	-0.954	-0.954	24.530	-0.189	-0.189	0.000	0.000	0.000	0.000
85	A	121	SER	0	0.001	0.009	27.137	0.010	0.010	0.000	0.000	0.000	0.000
86	A	122	GLY	0	-0.018	-0.006	23.253	0.020	0.020	0.000	0.000	0.000	0.000
87	A	123	ILE	0	0.022	0.014	17.712	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	124	ASN	0	-0.008	-0.010	19.770	0.023	0.023	0.000	0.000	0.000	0.000
89	A	125	TRP	0	0.093	0.026	13.650	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	126	GLY	0	0.017	0.019	19.931	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	127	ARG	1	0.880	0.929	22.709	0.207	0.207	0.000	0.000	0.000	0.000
92	A	128	VAL	0	0.009	0.010	17.267	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	129	VAL	0	-0.009	-0.006	20.586	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	130	ALA	0	0.013	0.014	22.639	0.004	0.004	0.000	0.000	0.000	0.000
95	A	131	LEU	0	0.003	0.008	20.993	0.010	0.010	0.000	0.000	0.000	0.000
96	A	132	LEU	0	-0.013	0.002	20.233	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	133	GLY	0	0.035	0.016	24.236	0.014	0.014	0.000	0.000	0.000	0.000
98	A	134	PHE	0	-0.023	-0.004	27.463	0.014	0.014	0.000	0.000	0.000	0.000
99	A	135	GLY	0	0.027	0.008	26.694	0.008	0.008	0.000	0.000	0.000	0.000
100	A	136	TYR	0	-0.049	-0.060	27.725	0.002	0.002	0.000	0.000	0.000	0.000
101	A	137	ARG	1	0.771	0.836	29.329	0.179	0.179	0.000	0.000	0.000	0.000
102	A	138	LEU	0	0.003	-0.001	30.156	0.013	0.013	0.000	0.000	0.000	0.000
103	A	139	ALA	0	-0.014	-0.008	29.965	0.009	0.009	0.000	0.000	0.000	0.000
104	A	140	LEU	0	0.006	0.006	32.090	0.011	0.011	0.000	0.000	0.000	0.000
105	A	141	HIS	0	0.010	0.004	34.553	0.013	0.013	0.000	0.000	0.000	0.000
106	A	142	VAL	0	-0.011	-0.009	35.461	0.011	0.011	0.000	0.000	0.000	0.000
107	A	143	TYR	0	-0.040	-0.024	32.561	0.004	0.004	0.000	0.000	0.000	0.000
108	A	144	GLN	0	-0.014	-0.011	37.396	0.005	0.005	0.000	0.000	0.000	0.000
109	A	145	HIS	0	-0.006	0.014	40.204	0.016	0.016	0.000	0.000	0.000	0.000
110	A	146	GLY	0	0.034	0.033	40.803	0.007	0.007	0.000	0.000	0.000	0.000
111	A	147	LEU	0	0.003	-0.016	41.902	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	148	THR	0	0.000	-0.015	44.189	0.001	0.001	0.000	0.000	0.000	0.000
113	A	149	GLY	0	-0.003	0.016	40.628	0.000	0.000	0.000	0.000	0.000	0.000
114	A	150	PHE	0	-0.003	-0.013	37.004	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	151	LEU	0	-0.007	-0.001	42.152	0.001	0.001	0.000	0.000	0.000	0.000
116	A	152	GLY	0	0.037	0.038	44.994	0.006	0.006	0.000	0.000	0.000	0.000
117	A	153	GLN	0	0.018	0.020	40.591	0.002	0.002	0.000	0.000	0.000	0.000
118	A	154	VAL	0	0.002	-0.006	44.886	0.004	0.004	0.000	0.000	0.000	0.000
119	A	155	THR	0	-0.012	-0.018	47.562	0.007	0.007	0.000	0.000	0.000	0.000
120	A	156	ARG	1	0.843	0.897	43.382	0.150	0.150	0.000	0.000	0.000	0.000
121	A	157	PHE	0	-0.002	0.002	43.472	0.004	0.004	0.000	0.000	0.000	0.000
122	A	158	VAL	0	-0.010	-0.001	49.585	0.004	0.004	0.000	0.000	0.000	0.000
123	A	159	VAL	0	0.005	-0.002	52.906	0.005	0.005	0.000	0.000	0.000	0.000
124	A	160	ASP	-1	-0.838	-0.923	49.823	-0.112	-0.112	0.000	0.000	0.000	0.000
125	A	161	PHE	0	-0.031	-0.012	52.924	0.004	0.004	0.000	0.000	0.000	0.000
126	A	162	MET	0	-0.028	-0.032	54.523	0.004	0.004	0.000	0.000	0.000	0.000
127	A	163	LEU	0	-0.001	0.011	55.670	0.005	0.005	0.000	0.000	0.000	0.000
128	A	164	HIS	0	0.002	-0.001	53.375	0.001	0.001	0.000	0.000	0.000	0.000
129	A	165	HIS	1	0.859	0.939	54.686	0.096	0.096	0.000	0.000	0.000	0.000
130	A	166	SER	0	-0.004	-0.005	59.384	0.004	0.004	0.000	0.000	0.000	0.000
131	A	167	ILE	0	0.044	0.030	60.136	0.003	0.003	0.000	0.000	0.000	0.000
132	A	168	ALA	0	0.049	0.025	60.382	0.002	0.002	0.000	0.000	0.000	0.000
133	A	169	ARG	1	0.918	0.954	62.471	0.073	0.073	0.000	0.000	0.000	0.000
134	A	170	TRP	0	0.002	0.003	65.439	0.003	0.003	0.000	0.000	0.000	0.000
135	A	171	ILE	0	0.057	0.019	62.884	0.002	0.002	0.000	0.000	0.000	0.000
136	A	172	ALA	0	-0.001	0.004	66.157	0.002	0.002	0.000	0.000	0.000	0.000
137	A	173	GLN	0	-0.032	-0.023	67.906	0.001	0.001	0.000	0.000	0.000	0.000
138	A	174	ARG	1	0.830	0.924	70.042	0.061	0.061	0.000	0.000	0.000	0.000
139	A	175	GLY	0	0.044	0.034	71.032	0.001	0.001	0.000	0.000	0.000	0.000
140	A	176	GLY	0	-0.010	-0.002	67.026	0.000	0.000	0.000	0.000	0.000	0.000
141	A	177	TRP	0	0.040	-0.018	59.681	0.001	0.001	0.000	0.000	0.000	0.000
142	A	178	VAL	0	0.013	0.011	65.937	0.000	0.000	0.000	0.000	0.000	0.000
143	A	179	ALA	0	-0.013	-0.001	69.091	0.001	0.001	0.000	0.000	0.000	0.000
144	A	180	ALA	0	-0.048	-0.019	66.380	0.000	0.000	0.000	0.000	0.000	0.000
145	A	181	LEU	0	-0.039	-0.003	67.468	0.000	0.000	0.000	0.000	0.000	0.000
146	A	182	ASN	0	-0.001	0.004	70.206	0.001	0.001	0.000	0.000	0.000	0.000

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