FMO DATABASE

FMODB ID: 89KNY

Calculation Name: 4HNJ-B-Xray372

Preferred Name: Apoptosis regulator Bcl-X

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4HNJ

Chain ID: B

ChEMBL ID: CHEMBL4625

UniProt ID: Q07817

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:

Apendix: None

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1020213.918053
FMO2-HF: Nuclear repulsion	965615.523723
FMO2-HF: Total energy	-54598.39433
FMO2-MP2: Total energy	-54756.876179

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:-1:SER)

Summations of interaction energy for fragment #1(B:-1: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.
-8.415	-4.304	0.48	-1.77	-2.82	0.009

Interaction energy analysis for fragmet #1(B:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.016

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	1	MET	0	0.051	0.014	2.847	-3.195	-0.787	0.350	-1.089	-1.669	0.006
4	B	2	SER	0	-0.006	-0.020	2.888	-3.129	-1.532	0.131	-0.668	-1.059	0.003
5	B	3	GLN	0	0.016	0.024	4.856	-1.135	-1.029	-0.001	-0.013	-0.092	0.000
6	B	4	SER	0	0.054	0.018	7.210	-0.061	-0.061	0.000	0.000	0.000	0.000
7	B	5	ASN	0	0.000	-0.009	7.431	-0.425	-0.425	0.000	0.000	0.000	0.000
8	B	6	ARG	1	0.904	0.937	5.096	-0.232	-0.232	0.000	0.000	0.000	0.000
9	B	7	GLU	-1	-0.865	-0.939	10.572	0.430	0.430	0.000	0.000	0.000	0.000
10	B	8	LEU	0	-0.007	-0.013	12.672	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	9	VAL	0	-0.021	-0.002	13.233	-0.078	-0.078	0.000	0.000	0.000	0.000
12	B	10	VAL	0	0.065	0.031	14.417	-0.055	-0.055	0.000	0.000	0.000	0.000
13	B	11	ASP	-1	-0.826	-0.880	16.632	0.301	0.301	0.000	0.000	0.000	0.000
14	B	12	PHE	0	0.018	0.004	18.152	-0.036	-0.036	0.000	0.000	0.000	0.000
15	B	13	LEU	0	-0.004	-0.004	18.010	-0.033	-0.033	0.000	0.000	0.000	0.000
16	B	14	SER	0	0.026	0.001	20.450	-0.027	-0.027	0.000	0.000	0.000	0.000
17	B	15	TYR	0	-0.072	-0.048	22.340	-0.027	-0.027	0.000	0.000	0.000	0.000
18	B	16	LYS	1	0.803	0.864	23.820	-0.240	-0.240	0.000	0.000	0.000	0.000
19	B	17	LEU	0	0.021	0.010	23.648	-0.017	-0.017	0.000	0.000	0.000	0.000
20	B	18	SER	0	-0.008	-0.024	26.097	-0.019	-0.019	0.000	0.000	0.000	0.000
21	B	19	GLN	0	-0.061	-0.021	28.194	-0.011	-0.011	0.000	0.000	0.000	0.000
22	B	20	LYS	1	0.787	0.859	29.650	-0.168	-0.168	0.000	0.000	0.000	0.000
23	B	21	GLY	0	0.019	0.024	31.631	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	22	TYR	0	-0.052	-0.052	28.718	-0.010	-0.010	0.000	0.000	0.000	0.000
25	B	23	SER	0	0.023	0.009	28.227	0.006	0.006	0.000	0.000	0.000	0.000
26	B	24	TRP	0	-0.033	-0.029	28.011	0.010	0.010	0.000	0.000	0.000	0.000
27	B	25	SER	0	-0.001	-0.007	24.090	0.003	0.003	0.000	0.000	0.000	0.000
28	B	26	GLN	0	-0.079	-0.048	23.454	0.001	0.001	0.000	0.000	0.000	0.000
29	B	27	PHE	0	-0.052	-0.035	23.727	0.004	0.004	0.000	0.000	0.000	0.000
30	B	28	SER	0	-0.020	-0.002	23.994	-0.008	-0.008	0.000	0.000	0.000	0.000
31	B	29	ASP	-1	-0.952	-0.967	18.332	0.062	0.062	0.000	0.000	0.000	0.000
32	B	30	VAL	0	-0.046	-0.035	21.421	-0.018	-0.018	0.000	0.000	0.000	0.000
33	B	31	GLU	-1	-0.915	-0.936	23.022	0.023	0.023	0.000	0.000	0.000	0.000
34	B	32	GLU	-1	-1.020	-0.990	21.918	-0.059	-0.059	0.000	0.000	0.000	0.000
35	B	82	PRO	0	0.031	-0.011	17.236	0.024	0.024	0.000	0.000	0.000	0.000
36	B	83	MET	0	0.014	0.019	12.652	0.041	0.041	0.000	0.000	0.000	0.000
37	B	84	ALA	0	0.024	0.019	16.308	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	85	ALA	0	0.042	0.027	19.942	-0.018	-0.018	0.000	0.000	0.000	0.000
39	B	86	VAL	0	-0.023	-0.012	14.862	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	87	LYS	1	0.838	0.930	15.961	-0.429	-0.429	0.000	0.000	0.000	0.000
41	B	88	GLN	0	-0.071	-0.034	19.157	-0.014	-0.014	0.000	0.000	0.000	0.000
42	B	89	ALA	0	0.046	0.019	20.907	-0.016	-0.016	0.000	0.000	0.000	0.000
43	B	90	LEU	0	-0.037	-0.016	16.672	-0.011	-0.011	0.000	0.000	0.000	0.000
44	B	91	ARG	1	0.837	0.900	20.666	-0.310	-0.310	0.000	0.000	0.000	0.000
45	B	92	GLU	-1	-0.832	-0.901	23.294	0.240	0.240	0.000	0.000	0.000	0.000
46	B	93	ALA	0	0.034	0.018	22.967	-0.017	-0.017	0.000	0.000	0.000	0.000
47	B	94	GLY	0	0.003	-0.007	24.108	-0.012	-0.012	0.000	0.000	0.000	0.000
48	B	95	ASP	-1	-0.786	-0.849	24.961	0.200	0.200	0.000	0.000	0.000	0.000
49	B	96	GLU	-1	-0.948	-0.973	28.299	0.210	0.210	0.000	0.000	0.000	0.000
50	B	97	PHE	0	-0.040	-0.031	26.449	-0.013	-0.013	0.000	0.000	0.000	0.000
51	B	98	GLU	-1	-0.842	-0.896	28.453	0.163	0.163	0.000	0.000	0.000	0.000
52	B	99	LEU	0	-0.014	-0.007	30.123	-0.015	-0.015	0.000	0.000	0.000	0.000
53	B	100	ARG	1	0.865	0.955	31.402	-0.165	-0.165	0.000	0.000	0.000	0.000
54	B	101	TYR	0	-0.078	-0.045	29.484	-0.016	-0.016	0.000	0.000	0.000	0.000
55	B	102	ARG	1	0.986	0.998	32.113	-0.099	-0.099	0.000	0.000	0.000	0.000
56	B	103	ARG	1	0.883	0.912	32.300	-0.110	-0.110	0.000	0.000	0.000	0.000
57	B	104	ALA	0	0.003	0.014	29.677	0.001	0.001	0.000	0.000	0.000	0.000
58	B	105	PHE	0	-0.003	0.012	31.591	-0.007	-0.007	0.000	0.000	0.000	0.000
59	B	121	GLN	0	0.009	-0.003	16.193	-0.014	-0.014	0.000	0.000	0.000	0.000
60	B	122	SER	0	0.012	-0.006	20.799	0.006	0.006	0.000	0.000	0.000	0.000
61	B	123	PHE	0	-0.004	0.003	17.549	0.004	0.004	0.000	0.000	0.000	0.000
62	B	124	GLU	-1	-0.805	-0.923	16.787	0.235	0.235	0.000	0.000	0.000	0.000
63	B	125	GLN	0	-0.028	-0.002	19.714	0.017	0.017	0.000	0.000	0.000	0.000
64	B	126	VAL	0	0.002	-0.003	22.864	0.006	0.006	0.000	0.000	0.000	0.000
65	B	127	VAL	0	-0.007	-0.006	17.784	0.015	0.015	0.000	0.000	0.000	0.000
66	B	128	ASN	0	-0.025	-0.027	19.133	0.052	0.052	0.000	0.000	0.000	0.000
67	B	129	GLU	-1	-0.891	-0.920	21.319	0.143	0.143	0.000	0.000	0.000	0.000
68	B	130	LEU	0	-0.062	-0.019	21.967	-0.006	-0.006	0.000	0.000	0.000	0.000
69	B	131	PHE	0	-0.072	-0.044	17.779	0.030	0.030	0.000	0.000	0.000	0.000
70	B	132	ARG	1	0.899	0.936	21.347	-0.190	-0.190	0.000	0.000	0.000	0.000
71	B	133	ASP	-1	-0.820	-0.891	23.668	0.204	0.204	0.000	0.000	0.000	0.000
72	B	134	GLY	0	-0.022	-0.021	23.261	0.002	0.002	0.000	0.000	0.000	0.000
73	B	135	VAL	0	-0.053	-0.007	17.048	0.022	0.022	0.000	0.000	0.000	0.000
74	B	136	ASN	0	0.082	0.040	18.946	0.036	0.036	0.000	0.000	0.000	0.000
75	B	137	TRP	0	0.068	0.013	14.685	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	138	GLY	0	0.011	0.017	20.333	0.001	0.001	0.000	0.000	0.000	0.000
77	B	139	ARG	1	0.857	0.919	21.330	-0.275	-0.275	0.000	0.000	0.000	0.000
78	B	140	ILE	0	0.012	0.012	15.587	0.000	0.000	0.000	0.000	0.000	0.000
79	B	141	VAL	0	0.028	0.015	18.875	0.008	0.008	0.000	0.000	0.000	0.000
80	B	142	ALA	0	-0.002	0.015	21.392	-0.021	-0.021	0.000	0.000	0.000	0.000
81	B	143	PHE	0	-0.015	-0.005	15.199	-0.019	-0.019	0.000	0.000	0.000	0.000
82	B	144	PHE	0	0.010	0.002	14.263	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	145	SER	0	0.011	-0.011	19.886	-0.033	-0.033	0.000	0.000	0.000	0.000
84	B	146	PHE	0	-0.049	-0.015	22.301	-0.027	-0.027	0.000	0.000	0.000	0.000
85	B	147	GLY	0	0.038	0.020	20.475	-0.023	-0.023	0.000	0.000	0.000	0.000
86	B	148	GLY	0	0.030	0.006	21.523	-0.022	-0.022	0.000	0.000	0.000	0.000
87	B	149	ALA	0	0.001	-0.004	23.491	-0.021	-0.021	0.000	0.000	0.000	0.000
88	B	150	LEU	0	-0.008	0.005	22.725	-0.018	-0.018	0.000	0.000	0.000	0.000
89	B	151	CYS	0	-0.036	-0.012	22.192	-0.017	-0.017	0.000	0.000	0.000	0.000
90	B	152	VAL	0	0.025	0.013	24.922	-0.015	-0.015	0.000	0.000	0.000	0.000
91	B	153	GLU	-1	-0.830	-0.896	28.251	0.105	0.105	0.000	0.000	0.000	0.000
92	B	154	SER	0	-0.064	-0.050	26.837	-0.015	-0.015	0.000	0.000	0.000	0.000
93	B	155	VAL	0	0.003	0.002	27.061	-0.012	-0.012	0.000	0.000	0.000	0.000
94	B	156	ASP	-1	-0.838	-0.890	29.757	0.091	0.091	0.000	0.000	0.000	0.000
95	B	157	LYS	1	0.774	0.882	30.756	-0.065	-0.065	0.000	0.000	0.000	0.000
96	B	158	GLU	-1	-0.809	-0.893	30.967	0.039	0.039	0.000	0.000	0.000	0.000
97	B	159	MET	0	0.027	0.013	33.389	-0.005	-0.005	0.000	0.000	0.000	0.000
98	B	160	GLN	0	-0.001	0.007	34.970	-0.003	-0.003	0.000	0.000	0.000	0.000
99	B	161	VAL	0	0.000	0.007	36.416	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	162	LEU	0	-0.016	-0.007	33.342	-0.006	-0.006	0.000	0.000	0.000	0.000
101	B	163	VAL	0	0.026	0.001	37.462	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	164	SER	0	-0.039	-0.036	39.919	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	165	ARG	1	0.896	0.963	39.230	-0.024	-0.024	0.000	0.000	0.000	0.000
104	B	166	ILE	0	0.022	0.018	40.121	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	167	ALA	0	0.041	0.019	43.264	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	168	ALA	0	0.006	0.007	45.718	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	169	TRP	0	-0.020	-0.008	41.882	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	170	MET	0	0.001	0.001	45.794	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	171	ALA	0	0.022	0.015	48.898	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	172	THR	0	-0.035	-0.019	51.030	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	173	TYR	0	0.000	0.000	51.673	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	174	LEU	0	0.011	0.002	52.966	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	175	ASN	0	-0.060	-0.047	54.705	0.000	0.000	0.000	0.000	0.000	0.000
114	B	176	ASP	-1	-0.910	-0.954	56.208	0.009	0.009	0.000	0.000	0.000	0.000
115	B	177	HIS	0	-0.107	-0.053	55.827	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	178	LEU	0	-0.039	-0.018	54.467	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	179	GLU	-1	-0.782	-0.874	58.655	0.015	0.015	0.000	0.000	0.000	0.000
118	B	180	PRO	0	-0.011	-0.005	60.220	0.000	0.000	0.000	0.000	0.000	0.000
119	B	181	TRP	0	0.015	0.014	59.478	0.000	0.000	0.000	0.000	0.000	0.000
120	B	182	ILE	0	0.021	0.010	57.483	0.000	0.000	0.000	0.000	0.000	0.000
121	B	183	GLN	0	-0.100	-0.068	62.111	0.000	0.000	0.000	0.000	0.000	0.000
122	B	184	GLU	-1	-0.951	-0.962	65.113	0.006	0.006	0.000	0.000	0.000	0.000
123	B	185	ASN	0	-0.133	-0.079	64.318	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	186	GLY	0	0.009	0.012	65.718	0.000	0.000	0.000	0.000	0.000	0.000
125	B	187	GLY	0	0.021	0.018	63.641	0.001	0.001	0.000	0.000	0.000	0.000
126	B	188	TRP	0	-0.053	-0.045	54.649	0.000	0.000	0.000	0.000	0.000	0.000
127	B	189	ASP	-1	-0.914	-0.954	60.357	0.019	0.019	0.000	0.000	0.000	0.000
128	B	190	THR	0	0.013	-0.001	62.834	0.001	0.001	0.000	0.000	0.000	0.000
129	B	191	PHE	0	-0.042	-0.015	54.128	0.000	0.000	0.000	0.000	0.000	0.000
130	B	192	VAL	0	-0.005	-0.009	57.929	0.000	0.000	0.000	0.000	0.000	0.000
131	B	193	GLU	-1	-0.943	-0.971	59.846	0.015	0.015	0.000	0.000	0.000	0.000
132	B	194	LEU	0	-0.075	-0.037	60.653	0.000	0.000	0.000	0.000	0.000	0.000
133	B	195	TYR	0	-0.136	-0.048	54.319	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:-1:SER)