FMO DATABASE

FMODB ID: 4JGGN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1157167.335918
FMO2-HF: Nuclear repulsion	1100156.701891
FMO2-HF: Total energy	-57010.634027
FMO2-MP2: Total energy	-57177.729693

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.
-16.039	-8.528	5.383	-4.72	-8.174	-0.03

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 : 0.004 / q_NPA : 0.011

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	-0.885	-0.955	3.098	-5.120	-1.957	0.102	-1.710	-1.555	-0.001
4	B	25	GLU	-1	-0.911	-0.957	5.713	-1.551	-1.551	0.000	0.000	0.000	0.000
5	B	26	GLN	0	-0.033	-0.021	2.524	-1.370	0.529	0.888	-0.768	-2.019	-0.003
6	B	27	VAL	0	0.055	0.027	2.558	-1.616	-0.025	0.855	-0.502	-1.943	-0.003
7	B	28	ALA	0	0.002	0.020	3.872	0.717	0.860	0.003	-0.010	-0.136	0.000
8	B	29	GLN	0	-0.022	-0.015	6.038	0.211	0.211	0.000	0.000	0.000	0.000
9	B	30	ASP	-1	-0.841	-0.934	2.503	-9.077	-8.727	3.414	-1.662	-2.102	-0.023
10	B	31	THR	0	-0.049	-0.049	5.798	0.828	0.828	0.000	0.000	0.000	0.000
11	B	32	GLU	-1	-0.827	-0.881	8.404	-0.511	-0.511	0.000	0.000	0.000	0.000
12	B	33	GLU	-1	-0.838	-0.919	8.681	-0.664	-0.664	0.000	0.000	0.000	0.000
13	B	34	VAL	0	-0.017	-0.015	7.479	0.213	0.213	0.000	0.000	0.000	0.000
14	B	35	PHE	0	-0.010	-0.002	10.322	0.154	0.154	0.000	0.000	0.000	0.000
15	B	36	ARG	1	0.820	0.882	13.500	0.707	0.707	0.000	0.000	0.000	0.000
16	B	37	SER	0	-0.049	-0.036	13.123	0.080	0.080	0.000	0.000	0.000	0.000
17	B	38	TYR	0	-0.005	0.000	14.369	0.050	0.050	0.000	0.000	0.000	0.000
18	B	39	VAL	0	-0.003	-0.002	16.013	0.042	0.042	0.000	0.000	0.000	0.000
19	B	40	PHE	0	-0.021	-0.002	18.258	0.030	0.030	0.000	0.000	0.000	0.000
20	B	41	TYR	0	-0.017	-0.024	16.488	0.041	0.041	0.000	0.000	0.000	0.000
21	B	42	ARG	1	0.840	0.914	19.787	0.049	0.049	0.000	0.000	0.000	0.000
22	B	43	HIS	0	-0.011	0.001	21.613	0.004	0.004	0.000	0.000	0.000	0.000
23	B	44	GLN	0	-0.112	-0.070	21.856	0.027	0.027	0.000	0.000	0.000	0.000
24	B	45	GLN	0	-0.049	-0.027	22.251	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	46	GLU	-1	-0.744	-0.815	25.292	-0.052	-0.052	0.000	0.000	0.000	0.000
26	B	47	GLN	0	-0.068	-0.018	27.870	-0.009	-0.009	0.000	0.000	0.000	0.000
27	B	48	GLU	-1	-0.977	-0.981	30.121	-0.018	-0.018	0.000	0.000	0.000	0.000
28	B	69	SER	0	0.021	-0.002	10.377	0.039	0.039	0.000	0.000	0.000	0.000
29	B	70	THR	0	-0.045	-0.017	6.246	0.185	0.185	0.000	0.000	0.000	0.000
30	B	71	MET	0	0.049	0.024	2.804	0.362	0.727	0.121	-0.068	-0.419	0.000
31	B	72	GLY	0	0.042	0.014	7.910	0.151	0.151	0.000	0.000	0.000	0.000
32	B	73	GLN	0	-0.001	0.019	11.348	0.042	0.042	0.000	0.000	0.000	0.000
33	B	74	VAL	0	0.013	0.015	7.169	0.086	0.086	0.000	0.000	0.000	0.000
34	B	75	GLY	0	0.042	0.013	10.432	0.056	0.056	0.000	0.000	0.000	0.000
35	B	76	ARG	1	0.886	0.949	12.574	0.040	0.040	0.000	0.000	0.000	0.000
36	B	77	GLN	0	-0.029	-0.023	13.683	-0.011	-0.011	0.000	0.000	0.000	0.000
37	B	78	LEU	0	-0.023	-0.019	11.190	0.018	0.018	0.000	0.000	0.000	0.000
38	B	79	ALA	0	0.011	0.018	15.295	-0.004	-0.004	0.000	0.000	0.000	0.000
39	B	80	ILE	0	0.009	0.008	18.215	0.007	0.007	0.000	0.000	0.000	0.000
40	B	81	ILE	0	-0.027	-0.018	16.136	0.013	0.013	0.000	0.000	0.000	0.000
41	B	82	GLY	0	-0.028	-0.019	19.913	0.002	0.002	0.000	0.000	0.000	0.000
42	B	83	ASP	-1	-0.794	-0.876	21.414	0.013	0.013	0.000	0.000	0.000	0.000
43	B	84	ASP	-1	-0.989	-0.985	24.179	0.091	0.091	0.000	0.000	0.000	0.000
44	B	85	ILE	0	0.042	0.016	21.441	-0.011	-0.011	0.000	0.000	0.000	0.000
45	B	86	ASN	0	-0.006	-0.004	20.775	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	87	ARG	1	0.915	0.957	22.858	-0.060	-0.060	0.000	0.000	0.000	0.000
47	B	88	ARG	1	0.806	0.867	26.485	-0.013	-0.013	0.000	0.000	0.000	0.000
48	B	89	TYR	0	0.050	0.017	21.910	-0.014	-0.014	0.000	0.000	0.000	0.000
49	B	90	ASP	-1	-0.807	-0.863	24.188	-0.065	-0.065	0.000	0.000	0.000	0.000
50	B	91	SER	0	0.066	0.032	25.527	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	92	GLU	-1	-0.838	-0.872	27.880	-0.025	-0.025	0.000	0.000	0.000	0.000
52	B	93	PHE	0	0.007	-0.006	22.254	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	94	GLN	0	0.004	0.000	27.485	-0.013	-0.013	0.000	0.000	0.000	0.000
54	B	95	THR	0	-0.038	-0.030	29.554	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	96	MET	0	-0.010	-0.011	30.016	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	97	LEU	0	-0.002	-0.004	26.393	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	98	GLN	0	-0.031	-0.007	31.103	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	99	HIS	0	-0.046	-0.022	34.402	0.005	0.005	0.000	0.000	0.000	0.000
59	B	100	LEU	0	-0.037	-0.006	31.264	0.000	0.000	0.000	0.000	0.000	0.000
60	B	101	GLN	0	-0.027	-0.020	32.377	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	102	PRO	0	-0.012	-0.001	28.935	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	103	THR	0	-0.028	-0.035	31.250	0.005	0.005	0.000	0.000	0.000	0.000
63	B	104	ALA	0	-0.004	-0.013	29.032	-0.010	-0.010	0.000	0.000	0.000	0.000
64	B	105	GLU	-1	-0.862	-0.894	28.786	-0.170	-0.170	0.000	0.000	0.000	0.000
65	B	106	ASN	0	-0.025	-0.017	30.197	-0.004	-0.004	0.000	0.000	0.000	0.000
66	B	107	ALA	0	0.008	0.011	25.956	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	108	TYR	0	0.030	0.021	22.616	0.000	0.000	0.000	0.000	0.000	0.000
68	B	109	GLU	-1	-0.791	-0.869	25.285	-0.163	-0.163	0.000	0.000	0.000	0.000
69	B	110	TYR	0	0.007	-0.031	27.357	0.005	0.005	0.000	0.000	0.000	0.000
70	B	111	PHE	0	0.020	0.009	18.025	0.008	0.008	0.000	0.000	0.000	0.000
71	B	112	THR	0	0.013	-0.005	23.024	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	113	LYS	1	0.811	0.906	24.086	0.143	0.143	0.000	0.000	0.000	0.000
73	B	114	ILE	0	0.002	0.016	24.153	0.013	0.013	0.000	0.000	0.000	0.000
74	B	115	ALA	0	0.010	0.004	19.892	0.011	0.011	0.000	0.000	0.000	0.000
75	B	116	THR	0	-0.037	-0.034	21.279	-0.005	-0.005	0.000	0.000	0.000	0.000
76	B	117	SER	0	0.015	-0.006	23.197	0.012	0.012	0.000	0.000	0.000	0.000
77	B	118	LEU	0	-0.081	-0.021	20.021	0.020	0.020	0.000	0.000	0.000	0.000
78	B	119	PHE	0	-0.019	-0.040	16.448	0.027	0.027	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.949	-0.953	20.771	-0.112	-0.112	0.000	0.000	0.000	0.000
80	B	121	SER	0	-0.003	0.008	23.423	0.010	0.010	0.000	0.000	0.000	0.000
81	B	122	GLY	0	-0.015	-0.006	19.671	0.024	0.024	0.000	0.000	0.000	0.000
82	B	123	ILE	0	0.020	0.014	13.561	0.006	0.006	0.000	0.000	0.000	0.000
83	B	124	ASN	0	-0.001	-0.006	15.402	0.049	0.049	0.000	0.000	0.000	0.000
84	B	125	TRP	0	0.096	0.029	8.008	-0.114	-0.114	0.000	0.000	0.000	0.000
85	B	126	GLY	0	0.019	0.020	14.888	-0.030	-0.030	0.000	0.000	0.000	0.000
86	B	127	ARG	1	0.883	0.931	18.123	0.012	0.012	0.000	0.000	0.000	0.000
87	B	128	VAL	0	0.013	0.010	11.596	-0.044	-0.044	0.000	0.000	0.000	0.000
88	B	129	VAL	0	-0.005	-0.008	14.335	-0.053	-0.053	0.000	0.000	0.000	0.000
89	B	130	ALA	0	0.010	0.014	15.977	-0.037	-0.037	0.000	0.000	0.000	0.000
90	B	131	LEU	0	-0.003	0.001	14.869	-0.020	-0.020	0.000	0.000	0.000	0.000
91	B	132	LEU	0	-0.016	0.005	12.504	-0.037	-0.037	0.000	0.000	0.000	0.000
92	B	133	GLY	0	0.033	0.018	16.725	-0.011	-0.011	0.000	0.000	0.000	0.000
93	B	134	PHE	0	-0.034	-0.012	20.270	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	135	GLY	0	0.030	0.008	19.099	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	136	TYR	0	-0.053	-0.063	19.941	-0.017	-0.017	0.000	0.000	0.000	0.000
96	B	137	ARG	1	0.758	0.825	21.363	0.072	0.072	0.000	0.000	0.000	0.000
97	B	138	LEU	0	0.005	0.002	22.865	0.005	0.005	0.000	0.000	0.000	0.000
98	B	139	ALA	0	-0.008	-0.006	21.915	0.000	0.000	0.000	0.000	0.000	0.000
99	B	140	LEU	0	0.011	0.010	24.062	0.003	0.003	0.000	0.000	0.000	0.000
100	B	141	HIS	0	0.017	0.013	26.914	0.002	0.002	0.000	0.000	0.000	0.000
101	B	142	VAL	0	-0.021	-0.021	25.534	0.004	0.004	0.000	0.000	0.000	0.000
102	B	143	TYR	0	-0.009	0.010	27.186	0.002	0.002	0.000	0.000	0.000	0.000
103	B	144	GLN	0	-0.011	-0.008	28.987	0.006	0.006	0.000	0.000	0.000	0.000
104	B	145	HIS	0	0.035	0.024	32.058	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	146	GLY	0	0.025	0.007	31.206	0.003	0.003	0.000	0.000	0.000	0.000
106	B	147	LEU	0	-0.053	-0.031	32.251	0.003	0.003	0.000	0.000	0.000	0.000
107	B	148	THR	0	-0.049	-0.038	33.835	0.005	0.005	0.000	0.000	0.000	0.000
108	B	149	GLY	0	0.029	0.030	35.858	0.006	0.006	0.000	0.000	0.000	0.000
109	B	150	PHE	0	-0.030	-0.019	32.631	0.000	0.000	0.000	0.000	0.000	0.000
110	B	151	LEU	0	0.052	0.019	35.871	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	152	GLY	0	0.045	0.039	39.348	0.004	0.004	0.000	0.000	0.000	0.000
112	B	153	GLN	0	0.021	0.009	34.998	0.004	0.004	0.000	0.000	0.000	0.000
113	B	154	VAL	0	0.016	0.005	36.799	0.001	0.001	0.000	0.000	0.000	0.000
114	B	155	THR	0	-0.027	-0.031	39.128	0.004	0.004	0.000	0.000	0.000	0.000
115	B	156	ARG	1	0.885	0.931	37.155	0.139	0.139	0.000	0.000	0.000	0.000
116	B	157	PHE	0	-0.004	0.005	34.900	0.000	0.000	0.000	0.000	0.000	0.000
117	B	158	VAL	0	0.007	0.011	40.845	0.001	0.001	0.000	0.000	0.000	0.000
118	B	159	VAL	0	0.011	0.004	43.857	0.003	0.003	0.000	0.000	0.000	0.000
119	B	160	ASP	-1	-0.853	-0.918	42.227	-0.114	-0.114	0.000	0.000	0.000	0.000
120	B	161	PHE	0	-0.010	0.000	41.570	0.002	0.002	0.000	0.000	0.000	0.000
121	B	162	MET	0	-0.021	-0.031	44.421	0.003	0.003	0.000	0.000	0.000	0.000
122	B	163	LEU	0	0.001	0.013	47.940	0.004	0.004	0.000	0.000	0.000	0.000
123	B	164	HIS	0	0.008	-0.002	43.943	0.000	0.000	0.000	0.000	0.000	0.000
124	B	165	HIS	1	0.868	0.943	43.002	0.116	0.116	0.000	0.000	0.000	0.000
125	B	166	SER	0	0.005	0.000	48.293	0.004	0.004	0.000	0.000	0.000	0.000
126	B	167	ILE	0	0.035	0.028	48.573	0.004	0.004	0.000	0.000	0.000	0.000
127	B	168	ALA	0	0.041	0.019	51.520	0.004	0.004	0.000	0.000	0.000	0.000
128	B	169	ARG	1	0.925	0.957	53.178	0.080	0.080	0.000	0.000	0.000	0.000
129	B	170	TRP	0	0.016	0.006	54.724	0.003	0.003	0.000	0.000	0.000	0.000
130	B	171	ILE	0	0.035	0.009	52.721	0.003	0.003	0.000	0.000	0.000	0.000
131	B	172	ALA	0	-0.004	0.004	56.822	0.003	0.003	0.000	0.000	0.000	0.000
132	B	173	GLN	0	-0.021	-0.012	59.223	0.002	0.002	0.000	0.000	0.000	0.000
133	B	174	ARG	1	0.835	0.923	58.446	0.065	0.065	0.000	0.000	0.000	0.000
134	B	175	GLY	0	0.042	0.036	61.820	0.002	0.002	0.000	0.000	0.000	0.000
135	B	176	GLY	0	-0.013	-0.006	58.708	0.001	0.001	0.000	0.000	0.000	0.000
136	B	177	TRP	0	0.029	-0.024	50.038	0.001	0.001	0.000	0.000	0.000	0.000
137	B	178	VAL	0	0.018	0.015	57.154	0.000	0.000	0.000	0.000	0.000	0.000
138	B	179	ALA	0	0.040	0.028	59.894	0.001	0.001	0.000	0.000	0.000	0.000
139	B	180	ALA	0	-0.045	-0.023	55.705	0.000	0.000	0.000	0.000	0.000	0.000
140	B	181	LEU	0	-0.033	-0.004	57.785	0.000	0.000	0.000	0.000	0.000	0.000
141	B	182	ASN	0	-0.056	-0.016	60.055	0.003	0.003	0.000	0.000	0.000	0.000

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