FMO DATABASE

FMODB ID: R5G68

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1186215.491319
FMO2-HF: Nuclear repulsion	1130969.17462
FMO2-HF: Total energy	-55246.3167
FMO2-MP2: Total energy	-55407.907087

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.
-3.199	-0.512	0.159	-1.209	-1.637	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 : -0.002 / q_NPA : -0.006

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	0.056	0.028	2.746	-0.901	1.721	0.160	-1.200	-1.582	0.002
4	A	6	GLU	-1	-0.906	-0.952	5.304	-2.433	-2.368	-0.001	-0.009	-0.055	0.000
5	A	7	PHE	0	-0.008	-0.015	8.457	0.473	0.473	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.883	-0.943	6.880	-1.220	-1.220	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.857	-0.928	9.895	-0.465	-0.465	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.015	-0.003	13.104	0.125	0.125	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.033	0.016	12.078	0.100	0.100	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.869	0.919	11.327	0.682	0.682	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.874	0.937	15.832	0.407	0.407	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.024	0.003	17.532	0.045	0.045	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.007	0.013	16.188	0.041	0.041	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.050	-0.032	19.196	0.053	0.053	0.000	0.000	0.000	0.000
15	A	17	ILE	0	0.013	0.014	22.079	0.024	0.024	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.015	0.012	22.422	0.021	0.021	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.038	0.005	22.930	0.017	0.017	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.033	-0.028	25.440	0.023	0.023	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.917	-0.940	27.611	-0.114	-0.114	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.017	-0.006	27.142	0.012	0.012	0.000	0.000	0.000	0.000
21	A	23	CYS	0	-0.063	-0.025	28.913	0.011	0.011	0.000	0.000	0.000	0.000
22	A	24	THR	0	0.040	0.017	31.661	0.007	0.007	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.060	-0.032	32.644	0.008	0.008	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.049	-0.029	33.867	0.006	0.006	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.906	-0.966	34.444	-0.074	-0.074	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.934	0.955	36.683	0.090	0.090	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.889	0.950	34.411	0.064	0.064	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.029	-0.014	39.078	0.004	0.004	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.012	0.046	42.016	0.002	0.002	0.000	0.000	0.000	0.000
30	A	32	ASN	0	-0.009	-0.027	44.460	0.001	0.001	0.000	0.000	0.000	0.000
31	A	33	ASN	0	0.021	-0.019	47.552	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.042	0.034	49.249	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.765	-0.871	46.319	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.833	0.924	43.041	0.047	0.047	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.052	-0.028	46.253	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.045	0.019	48.392	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.010	0.001	40.927	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.849	-0.916	44.758	-0.067	-0.067	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.846	0.915	45.998	0.046	0.046	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.012	0.019	44.118	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	43	TYR	0	0.016	0.013	37.832	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.841	0.902	43.891	0.063	0.063	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.020	-0.016	46.655	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	CYS	0	-0.019	-0.012	43.837	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.851	-0.912	40.845	-0.097	-0.097	0.000	0.000	0.000	0.000
46	A	48	TYR	0	-0.045	-0.012	44.656	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.000	-0.003	47.658	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.805	0.879	39.457	0.101	0.101	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.925	0.979	45.050	0.077	0.077	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.094	-0.063	46.301	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	TYR	0	-0.024	0.004	48.303	0.003	0.003	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.913	-0.938	42.669	-0.099	-0.099	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.014	-0.025	44.950	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	56	ASP	-1	-0.881	-0.950	46.854	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.042	0.002	43.631	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	ASN	0	-0.010	0.002	41.013	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.022	-0.013	42.999	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	60	MET	0	-0.022	-0.001	45.337	0.001	0.001	0.000	0.000	0.000	0.000
59	A	61	TYR	0	-0.023	-0.024	35.088	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.002	-0.018	40.193	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	63	GLN	0	-0.051	-0.013	41.325	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.005	0.000	39.147	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.020	-0.001	34.943	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	66	ILE	0	-0.021	0.007	36.275	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.024	-0.043	32.952	0.005	0.005	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.948	-0.961	36.229	-0.083	-0.083	0.000	0.000	0.000	0.000
67	A	69	ILE	0	0.002	0.020	38.488	0.004	0.004	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.030	-0.045	37.732	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	71	THR	0	0.022	-0.011	35.086	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.031	0.003	38.269	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.856	-0.870	41.683	-0.068	-0.068	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.015	0.010	37.555	0.001	0.001	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.823	0.916	40.031	0.071	0.071	0.000	0.000	0.000	0.000
74	A	76	SER	0	-0.029	-0.035	43.245	0.003	0.003	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.873	0.924	45.254	0.065	0.065	0.000	0.000	0.000	0.000
76	A	78	ILE	0	-0.015	-0.008	41.946	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.030	-0.018	46.280	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.808	-0.896	48.344	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.020	-0.006	50.569	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.011	-0.006	48.269	0.002	0.002	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.087	-0.030	51.982	0.003	0.003	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.020	-0.008	54.275	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.797	-0.867	55.825	-0.043	-0.043	0.000	0.000	0.000	0.000
84	A	86	SER	0	0.000	-0.002	54.918	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.854	0.894	56.026	0.045	0.045	0.000	0.000	0.000	0.000
86	A	88	PRO	0	0.045	0.019	54.076	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	89	SER	0	0.032	0.014	52.885	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.034	0.026	52.427	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.841	0.953	50.045	0.044	0.044	0.000	0.000	0.000	0.000
90	A	92	LEU	0	0.001	0.010	47.985	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.011	0.021	47.805	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	THR	0	0.016	-0.012	46.019	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.013	-0.009	42.861	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	96	SER	0	0.025	-0.020	42.990	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	97	PHE	0	-0.006	0.012	42.765	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	98	ILE	0	0.007	-0.004	39.504	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	99	SER	0	-0.071	-0.030	38.837	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.054	0.015	38.068	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	101	ILE	0	-0.024	-0.018	36.225	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.043	-0.026	34.365	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	103	GLU	-1	-0.900	-0.932	33.118	-0.123	-0.123	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.936	0.981	33.146	0.115	0.115	0.000	0.000	0.000	0.000
103	A	105	TRP	0	-0.031	-0.021	30.888	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.066	0.029	28.628	0.000	0.000	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.888	-0.931	23.590	-0.318	-0.318	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.825	0.940	24.782	0.139	0.139	0.000	0.000	0.000	0.000
107	A	109	ASN	0	0.015	0.001	24.761	0.006	0.006	0.000	0.000	0.000	0.000
108	A	110	ARG	1	1.072	1.030	26.887	0.144	0.144	0.000	0.000	0.000	0.000
109	A	111	ALA	0	0.013	-0.003	28.553	0.010	0.010	0.000	0.000	0.000	0.000
110	A	112	LYS	1	0.960	0.976	28.495	0.156	0.156	0.000	0.000	0.000	0.000
111	A	113	ILE	0	0.003	0.022	31.222	0.007	0.007	0.000	0.000	0.000	0.000
112	A	114	MET	0	-0.027	-0.022	32.920	0.006	0.006	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.923	-0.961	33.129	-0.097	-0.097	0.000	0.000	0.000	0.000
114	A	116	ILE	0	-0.028	-0.011	36.144	0.005	0.005	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.004	-0.003	38.164	0.005	0.005	0.000	0.000	0.000	0.000
116	A	118	SER	0	0.009	-0.017	37.407	0.005	0.005	0.000	0.000	0.000	0.000
117	A	119	ASN	0	-0.040	-0.027	40.084	0.002	0.002	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.748	-0.865	42.582	-0.059	-0.059	0.000	0.000	0.000	0.000
119	A	121	ILE	0	-0.003	0.005	43.132	0.003	0.003	0.000	0.000	0.000	0.000
120	A	122	VAL	0	0.029	0.009	42.399	0.001	0.001	0.000	0.000	0.000	0.000
121	A	123	GLU	-1	-0.902	-0.933	44.957	-0.044	-0.044	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.894	0.966	47.733	0.046	0.046	0.000	0.000	0.000	0.000
123	A	125	ILE	0	-0.019	-0.023	45.706	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	SER	0	0.003	-0.009	47.249	0.001	0.001	0.000	0.000	0.000	0.000
125	A	127	ASN	0	-0.050	-0.018	49.909	0.003	0.003	0.000	0.000	0.000	0.000
126	A	128	ASN	0	-0.049	-0.040	53.193	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	129	GLY	0	0.090	0.045	52.747	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	130	LYS	1	0.850	0.906	53.427	0.032	0.032	0.000	0.000	0.000	0.000
129	A	131	ASP	-1	-0.790	-0.885	56.296	-0.036	-0.036	0.000	0.000	0.000	0.000
130	A	132	PHE	0	-0.081	-0.042	48.620	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	133	ILE	0	0.014	-0.005	51.191	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.820	-0.888	53.732	-0.037	-0.037	0.000	0.000	0.000	0.000
133	A	135	PHE	0	-0.057	-0.030	53.495	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	ILE	0	0.008	0.007	50.344	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	137	ASP	-1	-0.878	-0.923	53.677	-0.045	-0.045	0.000	0.000	0.000	0.000
136	A	138	ARG	1	0.885	0.950	55.129	0.042	0.042	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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