FMO DATABASE

FMODB ID: ZY5KN

Calculation Name: 4UF3-A-Xray372

Preferred Name: Bcl-2-like protein 11

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UF3

Chain ID: A

ChEMBL ID: CHEMBL5777

UniProt ID: O43521

Base Structure: X-ray

Registration Date: 2023-06-19

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1186231.882823
FMO2-HF: Nuclear repulsion	1130986.463703
FMO2-HF: Total energy	-55245.41912
FMO2-MP2: Total energy	-55407.044572

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-3.189	-0.43	0.099	-1.247	-1.611	0.002

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.001

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	5	ILE	0	0.047	0.024	2.921	-0.997	1.684	0.100	-1.239	-1.542	0.002
4	A	6	GLU	-1	-0.916	-0.951	5.221	-2.253	-2.175	-0.001	-0.008	-0.069	0.000
5	A	7	PHE	0	-0.009	-0.017	8.358	0.465	0.465	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.874	-0.942	6.750	-1.366	-1.366	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.856	-0.930	9.812	-0.441	-0.441	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.010	0.001	13.009	0.128	0.128	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.030	0.012	11.815	0.106	0.106	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.873	0.921	11.922	0.662	0.662	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.933	0.970	15.758	0.414	0.414	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.013	-0.004	17.661	0.048	0.048	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.008	0.015	16.482	0.043	0.043	0.000	0.000	0.000	0.000
14	A	16	ASN	0	0.004	0.001	19.683	0.052	0.052	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.011	0.008	22.005	0.025	0.025	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.023	0.014	22.477	0.022	0.022	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.048	0.011	23.075	0.017	0.017	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.050	-0.043	25.404	0.024	0.024	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.933	-0.950	27.546	-0.121	-0.121	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.004	0.002	27.098	0.013	0.013	0.000	0.000	0.000	0.000
21	A	23	CYS	0	-0.059	-0.030	28.831	0.011	0.011	0.000	0.000	0.000	0.000
22	A	24	THR	0	0.054	0.036	31.619	0.008	0.008	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.059	-0.037	32.516	0.008	0.008	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.053	-0.032	33.854	0.006	0.006	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.913	-0.966	34.917	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.916	0.948	37.169	0.093	0.093	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.854	0.934	34.362	0.069	0.069	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.037	-0.014	39.500	0.004	0.004	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.024	0.047	42.004	0.002	0.002	0.000	0.000	0.000	0.000
30	A	32	ASN	0	0.016	0.009	44.446	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.019	-0.029	47.533	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.031	0.028	49.226	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.784	-0.904	46.194	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.892	0.955	42.865	0.052	0.052	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.065	-0.031	46.230	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.066	0.031	48.421	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.005	-0.002	40.798	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.875	-0.928	44.673	-0.070	-0.070	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.950	0.978	45.947	0.049	0.049	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.019	0.036	43.973	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	TYR	0	0.017	0.014	37.923	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.856	0.910	43.805	0.066	0.066	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.020	-0.024	46.565	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	CYS	0	-0.016	-0.013	43.863	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.871	-0.928	40.780	-0.101	-0.101	0.000	0.000	0.000	0.000
46	A	48	TYR	0	-0.053	-0.015	44.569	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	ILE	0	-0.009	-0.012	47.415	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.836	0.909	39.397	0.104	0.104	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.943	0.990	44.970	0.079	0.079	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.085	-0.050	46.216	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	TYR	0	-0.035	0.004	48.228	0.003	0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.911	-0.938	43.043	-0.100	-0.100	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.022	-0.033	44.877	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.866	-0.944	46.787	-0.074	-0.074	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.043	0.003	43.490	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.019	-0.002	41.519	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.020	-0.009	42.939	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	60	MET	0	-0.034	-0.007	45.281	0.002	0.002	0.000	0.000	0.000	0.000
59	A	61	TYR	0	0.004	-0.009	34.948	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	62	ASN	0	0.006	-0.012	40.140	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.063	-0.018	41.280	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.010	0.002	38.941	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.038	-0.018	35.066	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	66	ILE	0	-0.010	0.015	36.235	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.030	-0.050	33.329	0.006	0.006	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.953	-0.968	36.226	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	69	ILE	0	0.012	0.026	38.620	0.004	0.004	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.024	-0.008	37.709	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	71	THR	0	0.035	-0.005	35.253	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.005	-0.016	38.241	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.843	-0.886	41.684	-0.071	-0.071	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.013	0.003	37.549	0.001	0.001	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.885	0.950	40.111	0.075	0.075	0.000	0.000	0.000	0.000
74	A	76	SER	0	-0.019	-0.029	43.206	0.003	0.003	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.986	1.004	45.290	0.070	0.070	0.000	0.000	0.000	0.000
76	A	78	ILE	0	-0.024	-0.013	41.957	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.037	-0.023	46.232	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.894	-0.955	48.299	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.027	-0.010	50.518	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.001	-0.017	48.339	0.002	0.002	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.091	-0.024	51.937	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.015	-0.003	54.230	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.782	-0.859	55.592	-0.045	-0.045	0.000	0.000	0.000	0.000
84	A	86	SER	0	-0.001	-0.002	54.863	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.830	0.876	55.966	0.046	0.046	0.000	0.000	0.000	0.000
86	A	88	PRO	0	0.060	0.030	54.017	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	89	SER	0	0.025	0.009	52.816	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.036	0.029	52.319	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.837	0.947	50.056	0.046	0.046	0.000	0.000	0.000	0.000
90	A	92	LEU	0	0.007	0.012	47.863	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.020	0.019	47.733	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	THR	0	0.019	0.010	45.928	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.010	-0.010	42.705	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	96	SER	0	0.011	-0.023	42.921	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	97	PHE	0	0.002	0.016	42.693	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	98	ILE	0	0.010	-0.001	39.442	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.067	-0.031	38.771	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.041	0.009	37.995	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	101	ILE	0	-0.021	-0.012	36.035	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.042	-0.031	34.319	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.907	-0.958	33.047	-0.130	-0.130	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.911	0.974	33.069	0.125	0.125	0.000	0.000	0.000	0.000
103	A	105	TRP	0	-0.055	-0.027	30.808	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.065	0.028	28.556	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.964	-0.979	23.926	-0.301	-0.301	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.859	0.949	24.725	0.154	0.154	0.000	0.000	0.000	0.000
107	A	109	ASN	0	0.019	0.000	25.409	0.002	0.002	0.000	0.000	0.000	0.000
108	A	110	ARG	1	1.093	1.042	26.837	0.157	0.157	0.000	0.000	0.000	0.000
109	A	111	ALA	0	-0.002	-0.011	28.504	0.011	0.011	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.945	0.970	28.158	0.176	0.176	0.000	0.000	0.000	0.000
111	A	113	ILE	0	0.010	0.028	31.314	0.007	0.007	0.000	0.000	0.000	0.000
112	A	114	MET	0	-0.032	-0.023	32.653	0.006	0.006	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.914	-0.956	33.159	-0.104	-0.104	0.000	0.000	0.000	0.000
114	A	116	ILE	0	-0.022	-0.007	36.104	0.005	0.005	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.005	0.001	38.117	0.005	0.005	0.000	0.000	0.000	0.000
116	A	118	SER	0	0.001	-0.021	37.866	0.006	0.006	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.039	-0.006	40.036	0.003	0.003	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.808	-0.923	42.541	-0.060	-0.060	0.000	0.000	0.000	0.000
119	A	121	ILE	0	-0.024	-0.003	42.914	0.003	0.003	0.000	0.000	0.000	0.000
120	A	122	VAL	0	0.023	0.003	42.590	0.001	0.001	0.000	0.000	0.000	0.000
121	A	123	GLU	-1	-0.910	-0.947	44.904	-0.048	-0.048	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.918	0.976	47.684	0.048	0.048	0.000	0.000	0.000	0.000
123	A	125	ILE	0	-0.034	-0.034	45.628	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.014	0.002	47.121	0.002	0.002	0.000	0.000	0.000	0.000
125	A	127	ASN	0	-0.053	-0.021	49.851	0.002	0.002	0.000	0.000	0.000	0.000
126	A	128	ASN	0	-0.053	-0.036	53.139	0.000	0.000	0.000	0.000	0.000	0.000
127	A	129	GLY	0	0.096	0.047	52.682	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	130	LYS	1	0.957	0.977	53.363	0.032	0.032	0.000	0.000	0.000	0.000
129	A	131	ASP	-1	-0.809	-0.904	56.228	-0.038	-0.038	0.000	0.000	0.000	0.000
130	A	132	PHE	0	-0.080	-0.038	48.619	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.006	-0.016	51.209	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.898	-0.948	53.657	-0.040	-0.040	0.000	0.000	0.000	0.000
133	A	135	PHE	0	-0.082	-0.040	53.742	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	ILE	0	-0.008	0.000	50.290	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	137	ASP	-1	-0.942	-0.977	53.597	-0.047	-0.047	0.000	0.000	0.000	0.000
136	A	138	ARG	1	0.880	0.951	55.046	0.044	0.044	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)