FMO DATABASE

FMODB ID: KGQQ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1151900.031297
FMO2-HF: Nuclear repulsion	1094889.858126
FMO2-HF: Total energy	-57010.173171
FMO2-MP2: Total energy	-57177.283639

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.
-15.896	-8.551	4.396	-4.536	-7.206	-0.025

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 : 0.005 / q_NPA : 0.009

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	-0.898	-0.956	3.102	-5.305	-1.823	0.094	-1.901	-1.675	0.001
4	B	25	GLU	-1	-0.927	-0.970	5.997	-1.339	-1.339	0.000	0.000	0.000	0.000
5	B	26	GLN	0	-0.029	-0.034	2.343	-0.939	0.551	0.856	-0.586	-1.760	0.000
6	B	27	VAL	0	0.058	0.043	2.881	-1.421	-0.167	0.161	-0.303	-1.113	-0.002
7	B	28	ALA	0	0.010	0.025	4.545	0.505	0.603	-0.001	-0.008	-0.090	0.000
8	B	29	GLN	0	-0.035	-0.022	5.996	0.168	0.168	0.000	0.000	0.000	0.000
9	B	30	ASP	-1	-0.827	-0.922	2.479	-8.962	-8.343	3.173	-1.657	-2.135	-0.023
10	B	31	THR	0	-0.060	-0.058	5.966	0.718	0.718	0.000	0.000	0.000	0.000
11	B	32	GLU	-1	-0.850	-0.898	8.925	-0.492	-0.492	0.000	0.000	0.000	0.000
12	B	33	GLU	-1	-0.884	-0.960	8.703	-0.703	-0.703	0.000	0.000	0.000	0.000
13	B	34	VAL	0	-0.011	-0.008	7.766	0.190	0.190	0.000	0.000	0.000	0.000
14	B	35	PHE	0	-0.013	-0.009	10.527	0.136	0.136	0.000	0.000	0.000	0.000
15	B	36	ARG	1	0.844	0.903	13.853	0.619	0.619	0.000	0.000	0.000	0.000
16	B	37	SER	0	-0.058	-0.034	13.425	0.059	0.059	0.000	0.000	0.000	0.000
17	B	38	TYR	0	-0.014	-0.004	14.656	0.041	0.041	0.000	0.000	0.000	0.000
18	B	39	VAL	0	-0.022	-0.019	16.304	0.034	0.034	0.000	0.000	0.000	0.000
19	B	40	PHE	0	-0.035	-0.009	18.673	0.026	0.026	0.000	0.000	0.000	0.000
20	B	41	TYR	0	0.003	-0.028	16.905	0.032	0.032	0.000	0.000	0.000	0.000
21	B	42	ARG	1	0.850	0.930	20.359	0.027	0.027	0.000	0.000	0.000	0.000
22	B	43	HIS	0	-0.004	0.009	22.065	0.004	0.004	0.000	0.000	0.000	0.000
23	B	44	GLN	0	-0.082	-0.050	22.715	0.023	0.023	0.000	0.000	0.000	0.000
24	B	45	GLN	0	-0.064	-0.019	23.155	0.000	0.000	0.000	0.000	0.000	0.000
25	B	46	GLU	-1	-0.752	-0.832	25.734	-0.038	-0.038	0.000	0.000	0.000	0.000
26	B	47	GLN	0	-0.077	-0.024	28.160	-0.008	-0.008	0.000	0.000	0.000	0.000
27	B	48	GLU	-1	-0.972	-0.975	30.292	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	69	SER	0	0.049	0.012	10.542	0.030	0.030	0.000	0.000	0.000	0.000
29	B	70	THR	0	-0.046	-0.025	6.111	0.155	0.155	0.000	0.000	0.000	0.000
30	B	71	MET	0	0.052	0.032	2.764	0.436	0.838	0.113	-0.081	-0.433	-0.001
31	B	72	GLY	0	0.074	0.041	7.804	0.131	0.131	0.000	0.000	0.000	0.000
32	B	73	GLN	0	-0.007	0.011	11.184	0.033	0.033	0.000	0.000	0.000	0.000
33	B	74	VAL	0	0.015	0.023	7.244	0.078	0.078	0.000	0.000	0.000	0.000
34	B	75	GLY	0	0.045	0.016	10.546	0.047	0.047	0.000	0.000	0.000	0.000
35	B	76	ARG	1	0.874	0.941	12.832	-0.025	-0.025	0.000	0.000	0.000	0.000
36	B	77	GLN	0	-0.037	-0.029	13.818	-0.021	-0.021	0.000	0.000	0.000	0.000
37	B	78	LEU	0	-0.022	-0.016	11.711	0.015	0.015	0.000	0.000	0.000	0.000
38	B	79	ALA	0	-0.009	0.003	15.777	-0.010	-0.010	0.000	0.000	0.000	0.000
39	B	80	ILE	0	0.019	0.010	18.620	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	81	ILE	0	0.014	0.014	16.734	0.008	0.008	0.000	0.000	0.000	0.000
41	B	82	GLY	0	-0.051	-0.021	20.530	0.000	0.000	0.000	0.000	0.000	0.000
42	B	83	ASP	-1	-0.814	-0.905	22.323	0.037	0.037	0.000	0.000	0.000	0.000
43	B	84	ASP	-1	-0.991	-0.990	24.995	0.101	0.101	0.000	0.000	0.000	0.000
44	B	85	ILE	0	0.044	0.019	22.136	-0.010	-0.010	0.000	0.000	0.000	0.000
45	B	86	ASN	0	-0.015	-0.007	21.312	-0.009	-0.009	0.000	0.000	0.000	0.000
46	B	87	ARG	1	0.932	0.964	23.577	-0.070	-0.070	0.000	0.000	0.000	0.000
47	B	88	ARG	1	0.835	0.885	27.205	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	89	TYR	0	0.027	0.007	21.901	-0.016	-0.016	0.000	0.000	0.000	0.000
49	B	90	ASP	-1	-0.791	-0.862	24.990	-0.048	-0.048	0.000	0.000	0.000	0.000
50	B	91	SER	0	0.048	0.026	26.391	-0.008	-0.008	0.000	0.000	0.000	0.000
51	B	92	GLU	-1	-0.852	-0.885	28.625	-0.019	-0.019	0.000	0.000	0.000	0.000
52	B	93	PHE	0	-0.013	-0.023	22.737	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	94	GLN	0	-0.002	-0.007	28.133	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	95	THR	0	-0.031	-0.016	30.411	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	96	MET	0	-0.009	-0.014	30.664	-0.005	-0.005	0.000	0.000	0.000	0.000
56	B	97	LEU	0	0.005	0.005	26.990	-0.007	-0.007	0.000	0.000	0.000	0.000
57	B	98	GLN	0	-0.031	-0.003	31.715	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	99	HIS	0	-0.046	-0.027	35.040	0.003	0.003	0.000	0.000	0.000	0.000
59	B	100	LEU	0	-0.021	0.012	31.824	0.000	0.000	0.000	0.000	0.000	0.000
60	B	101	GLN	0	-0.027	-0.020	33.260	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	102	PRO	0	0.000	0.013	29.638	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	103	THR	0	0.043	0.021	31.999	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	104	ALA	0	0.008	-0.016	28.837	-0.008	-0.008	0.000	0.000	0.000	0.000
64	B	105	GLU	-1	-0.964	-0.971	29.006	-0.152	-0.152	0.000	0.000	0.000	0.000
65	B	106	ASN	0	-0.012	0.001	31.170	0.002	0.002	0.000	0.000	0.000	0.000
66	B	107	ALA	0	-0.010	-0.006	26.224	-0.002	-0.002	0.000	0.000	0.000	0.000
67	B	108	TYR	0	0.030	0.022	22.888	0.002	0.002	0.000	0.000	0.000	0.000
68	B	109	GLU	-1	-0.783	-0.884	25.708	-0.150	-0.150	0.000	0.000	0.000	0.000
69	B	110	TYR	0	-0.013	-0.039	27.999	0.005	0.005	0.000	0.000	0.000	0.000
70	B	111	PHE	0	0.041	0.019	18.483	0.007	0.007	0.000	0.000	0.000	0.000
71	B	112	THR	0	0.023	-0.004	23.337	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	113	LYS	1	0.836	0.937	24.398	0.131	0.131	0.000	0.000	0.000	0.000
73	B	114	ILE	0	-0.005	0.020	24.711	0.012	0.012	0.000	0.000	0.000	0.000
74	B	115	ALA	0	0.021	0.007	20.491	0.011	0.011	0.000	0.000	0.000	0.000
75	B	116	THR	0	-0.047	-0.056	21.701	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	117	SER	0	0.006	-0.010	23.070	0.008	0.008	0.000	0.000	0.000	0.000
77	B	118	LEU	0	-0.066	-0.012	20.474	0.019	0.019	0.000	0.000	0.000	0.000
78	B	119	PHE	0	-0.038	-0.044	16.074	0.021	0.021	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.920	-0.934	20.393	-0.125	-0.125	0.000	0.000	0.000	0.000
80	B	121	SER	0	-0.031	-0.016	23.280	0.005	0.005	0.000	0.000	0.000	0.000
81	B	122	GLY	0	-0.004	0.008	19.318	0.020	0.020	0.000	0.000	0.000	0.000
82	B	123	ILE	0	0.013	0.007	13.030	0.014	0.014	0.000	0.000	0.000	0.000
83	B	124	ASN	0	0.000	-0.004	15.431	0.044	0.044	0.000	0.000	0.000	0.000
84	B	125	TRP	0	0.087	0.016	8.464	-0.098	-0.098	0.000	0.000	0.000	0.000
85	B	126	GLY	0	0.007	0.011	14.881	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	127	ARG	1	0.899	0.940	17.796	0.031	0.031	0.000	0.000	0.000	0.000
87	B	128	VAL	0	0.019	0.014	11.765	-0.041	-0.041	0.000	0.000	0.000	0.000
88	B	129	VAL	0	0.009	0.004	14.546	-0.043	-0.043	0.000	0.000	0.000	0.000
89	B	130	ALA	0	0.004	0.015	16.268	-0.036	-0.036	0.000	0.000	0.000	0.000
90	B	131	LEU	0	0.010	0.008	15.485	-0.017	-0.017	0.000	0.000	0.000	0.000
91	B	132	LEU	0	-0.014	0.002	12.838	-0.036	-0.036	0.000	0.000	0.000	0.000
92	B	133	GLY	0	0.021	0.009	17.061	-0.011	-0.011	0.000	0.000	0.000	0.000
93	B	134	PHE	0	-0.038	-0.016	20.519	-0.005	-0.005	0.000	0.000	0.000	0.000
94	B	135	GLY	0	0.039	0.014	19.482	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	136	TYR	0	-0.055	-0.065	20.359	-0.014	-0.014	0.000	0.000	0.000	0.000
96	B	137	ARG	1	0.772	0.839	21.738	0.051	0.051	0.000	0.000	0.000	0.000
97	B	138	LEU	0	-0.004	0.001	23.403	0.004	0.004	0.000	0.000	0.000	0.000
98	B	139	ALA	0	-0.010	-0.007	22.441	-0.002	-0.002	0.000	0.000	0.000	0.000
99	B	140	LEU	0	0.011	0.002	24.592	0.002	0.002	0.000	0.000	0.000	0.000
100	B	141	HIS	0	0.011	0.008	27.394	0.003	0.003	0.000	0.000	0.000	0.000
101	B	142	VAL	0	-0.037	-0.018	26.077	0.003	0.003	0.000	0.000	0.000	0.000
102	B	143	TYR	0	-0.017	0.007	27.672	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	144	GLN	0	0.000	-0.005	29.549	0.006	0.006	0.000	0.000	0.000	0.000
104	B	145	HIS	0	0.015	0.012	32.711	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	146	GLY	0	0.022	0.007	31.609	0.002	0.002	0.000	0.000	0.000	0.000
106	B	147	LEU	0	-0.042	-0.016	32.682	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	148	THR	0	-0.046	-0.042	34.092	0.002	0.002	0.000	0.000	0.000	0.000
108	B	149	GLY	0	0.035	0.034	36.434	0.005	0.005	0.000	0.000	0.000	0.000
109	B	150	PHE	0	-0.019	-0.006	32.656	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	151	LEU	0	0.048	0.016	36.328	-0.002	-0.002	0.000	0.000	0.000	0.000
111	B	152	GLY	0	0.052	0.045	39.688	0.002	0.002	0.000	0.000	0.000	0.000
112	B	153	GLN	0	0.004	0.001	34.582	0.004	0.004	0.000	0.000	0.000	0.000
113	B	154	VAL	0	0.004	-0.003	36.969	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	155	THR	0	-0.036	-0.038	39.200	0.004	0.004	0.000	0.000	0.000	0.000
115	B	156	ARG	1	0.939	0.964	37.253	0.129	0.129	0.000	0.000	0.000	0.000
116	B	157	PHE	0	-0.012	0.009	34.899	0.000	0.000	0.000	0.000	0.000	0.000
117	B	158	VAL	0	0.005	0.008	40.796	0.001	0.001	0.000	0.000	0.000	0.000
118	B	159	VAL	0	0.010	0.000	43.731	0.002	0.002	0.000	0.000	0.000	0.000
119	B	160	ASP	-1	-0.865	-0.927	42.664	-0.105	-0.105	0.000	0.000	0.000	0.000
120	B	161	PHE	0	-0.011	0.002	41.853	0.002	0.002	0.000	0.000	0.000	0.000
121	B	162	MET	0	-0.012	-0.028	44.536	0.003	0.003	0.000	0.000	0.000	0.000
122	B	163	LEU	0	-0.005	0.006	48.046	0.004	0.004	0.000	0.000	0.000	0.000
123	B	164	HIS	0	0.008	-0.014	44.612	0.000	0.000	0.000	0.000	0.000	0.000
124	B	165	HIS	1	0.881	0.950	43.362	0.108	0.108	0.000	0.000	0.000	0.000
125	B	166	SER	0	-0.011	-0.007	48.505	0.003	0.003	0.000	0.000	0.000	0.000
126	B	167	ILE	0	0.026	0.031	48.455	0.003	0.003	0.000	0.000	0.000	0.000
127	B	168	ALA	0	0.040	0.017	51.730	0.003	0.003	0.000	0.000	0.000	0.000
128	B	169	ARG	1	0.932	0.958	53.386	0.075	0.075	0.000	0.000	0.000	0.000
129	B	170	TRP	0	0.023	0.015	54.783	0.003	0.003	0.000	0.000	0.000	0.000
130	B	171	ILE	0	0.036	0.012	52.684	0.003	0.003	0.000	0.000	0.000	0.000
131	B	172	ALA	0	0.002	0.002	56.920	0.003	0.003	0.000	0.000	0.000	0.000
132	B	173	GLN	0	-0.020	-0.002	59.327	0.002	0.002	0.000	0.000	0.000	0.000
133	B	174	ARG	1	0.840	0.921	58.365	0.061	0.061	0.000	0.000	0.000	0.000
134	B	175	GLY	0	0.043	0.040	61.612	0.002	0.002	0.000	0.000	0.000	0.000
135	B	176	GLY	0	-0.024	-0.013	58.716	0.001	0.001	0.000	0.000	0.000	0.000
136	B	177	TRP	0	0.035	-0.024	50.334	0.001	0.001	0.000	0.000	0.000	0.000
137	B	178	VAL	0	0.017	0.014	57.200	0.000	0.000	0.000	0.000	0.000	0.000
138	B	179	ALA	0	0.009	0.011	59.939	0.001	0.001	0.000	0.000	0.000	0.000
139	B	180	ALA	0	-0.066	-0.030	55.752	0.000	0.000	0.000	0.000	0.000	0.000
140	B	181	LEU	0	-0.026	-0.006	57.829	0.000	0.000	0.000	0.000	0.000	0.000
141	B	182	ASN	0	-0.013	0.012	59.886	0.001	0.001	0.000	0.000	0.000	0.000

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