FMO DATABASE

FMODB ID: 1NV6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1017294.052597
FMO2-HF: Nuclear repulsion	962696.709533
FMO2-HF: Total energy	-54597.343064
FMO2-MP2: Total energy	-54755.912815

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.
-11.854	-6.988	0.898	-2.085	-3.678	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 : 0.035 / q_NPA : 0.010

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	0.065	0.028	3.219	-4.222	-1.149	0.124	-1.466	-1.731	0.006
4	B	2	SER	0	-0.009	-0.020	2.476	-5.152	-3.545	0.776	-0.589	-1.793	0.003
5	B	3	GLN	0	0.004	0.007	4.874	-1.331	-1.222	-0.001	-0.021	-0.087	0.000
6	B	4	SER	0	0.058	0.027	6.718	-0.215	-0.215	0.000	0.000	0.000	0.000
7	B	5	ASN	0	-0.004	-0.005	7.941	-0.289	-0.289	0.000	0.000	0.000	0.000
8	B	6	ARG	1	0.899	0.934	4.241	-0.207	-0.130	-0.001	-0.009	-0.067	0.000
9	B	7	GLU	-1	-0.881	-0.935	10.260	0.479	0.479	0.000	0.000	0.000	0.000
10	B	8	LEU	0	-0.024	-0.020	12.333	-0.108	-0.108	0.000	0.000	0.000	0.000
11	B	9	VAL	0	-0.021	-0.012	12.660	-0.092	-0.092	0.000	0.000	0.000	0.000
12	B	10	VAL	0	0.051	0.028	14.354	-0.064	-0.064	0.000	0.000	0.000	0.000
13	B	11	ASP	-1	-0.831	-0.902	16.350	0.338	0.338	0.000	0.000	0.000	0.000
14	B	12	PHE	0	0.000	0.002	17.914	-0.041	-0.041	0.000	0.000	0.000	0.000
15	B	13	LEU	0	0.011	-0.004	17.986	-0.039	-0.039	0.000	0.000	0.000	0.000
16	B	14	SER	0	0.012	0.018	20.479	-0.036	-0.036	0.000	0.000	0.000	0.000
17	B	15	TYR	0	-0.053	-0.032	22.170	-0.024	-0.024	0.000	0.000	0.000	0.000
18	B	16	LYS	1	0.846	0.919	23.607	-0.247	-0.247	0.000	0.000	0.000	0.000
19	B	17	LEU	0	0.031	0.010	23.346	-0.018	-0.018	0.000	0.000	0.000	0.000
20	B	18	SER	0	0.020	0.021	26.239	-0.021	-0.021	0.000	0.000	0.000	0.000
21	B	19	GLN	0	-0.062	-0.007	28.125	-0.011	-0.011	0.000	0.000	0.000	0.000
22	B	20	LYS	1	0.789	0.858	29.317	-0.174	-0.174	0.000	0.000	0.000	0.000
23	B	21	GLY	0	0.001	0.017	31.201	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	22	TYR	0	-0.048	-0.065	28.523	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	23	SER	0	0.038	0.006	28.029	0.005	0.005	0.000	0.000	0.000	0.000
26	B	24	TRP	0	-0.034	-0.015	28.060	0.012	0.012	0.000	0.000	0.000	0.000
27	B	25	SER	0	-0.019	-0.022	23.889	0.001	0.001	0.000	0.000	0.000	0.000
28	B	26	GLN	0	-0.084	-0.048	23.127	0.004	0.004	0.000	0.000	0.000	0.000
29	B	27	PHE	0	-0.035	-0.029	23.057	0.006	0.006	0.000	0.000	0.000	0.000
30	B	28	SER	0	-0.013	0.014	23.179	-0.014	-0.014	0.000	0.000	0.000	0.000
31	B	29	ASP	-1	-0.927	-0.967	17.681	0.025	0.025	0.000	0.000	0.000	0.000
32	B	30	VAL	0	-0.057	-0.030	20.733	-0.019	-0.019	0.000	0.000	0.000	0.000
33	B	31	GLU	-1	-0.953	-0.966	22.684	0.002	0.002	0.000	0.000	0.000	0.000
34	B	32	GLU	-1	-1.017	-0.989	21.317	-0.087	-0.087	0.000	0.000	0.000	0.000
35	B	82	PRO	0	0.059	0.001	17.589	0.012	0.012	0.000	0.000	0.000	0.000
36	B	83	MET	0	0.037	0.025	13.304	0.046	0.046	0.000	0.000	0.000	0.000
37	B	84	ALA	0	0.003	0.009	16.501	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	85	ALA	0	0.033	0.021	19.849	-0.028	-0.028	0.000	0.000	0.000	0.000
39	B	86	VAL	0	-0.005	-0.006	15.027	-0.011	-0.011	0.000	0.000	0.000	0.000
40	B	87	LYS	1	0.896	0.957	16.257	-0.462	-0.462	0.000	0.000	0.000	0.000
41	B	88	GLN	0	0.003	0.008	19.046	-0.015	-0.015	0.000	0.000	0.000	0.000
42	B	89	ALA	0	0.025	0.014	20.631	-0.023	-0.023	0.000	0.000	0.000	0.000
43	B	90	LEU	0	-0.026	-0.016	16.799	-0.017	-0.017	0.000	0.000	0.000	0.000
44	B	91	ARG	1	0.808	0.878	20.759	-0.331	-0.331	0.000	0.000	0.000	0.000
45	B	92	GLU	-1	-0.904	-0.946	23.430	0.249	0.249	0.000	0.000	0.000	0.000
46	B	93	ALA	0	0.015	0.014	22.777	-0.016	-0.016	0.000	0.000	0.000	0.000
47	B	94	GLY	0	-0.002	-0.015	23.948	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	95	ASP	-1	-0.810	-0.900	24.941	0.204	0.204	0.000	0.000	0.000	0.000
49	B	96	GLU	-1	-0.933	-0.964	28.201	0.231	0.231	0.000	0.000	0.000	0.000
50	B	97	PHE	0	-0.061	-0.037	26.464	-0.014	-0.014	0.000	0.000	0.000	0.000
51	B	98	GLU	-1	-0.849	-0.914	28.503	0.164	0.164	0.000	0.000	0.000	0.000
52	B	99	LEU	0	-0.016	-0.001	30.187	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	100	ARG	1	0.878	0.966	31.694	-0.177	-0.177	0.000	0.000	0.000	0.000
54	B	101	TYR	0	-0.074	-0.052	29.539	-0.017	-0.017	0.000	0.000	0.000	0.000
55	B	102	ARG	1	0.976	1.002	32.753	-0.102	-0.102	0.000	0.000	0.000	0.000
56	B	103	ARG	1	0.994	0.984	32.626	-0.099	-0.099	0.000	0.000	0.000	0.000
57	B	104	ALA	0	0.034	0.029	29.653	0.002	0.002	0.000	0.000	0.000	0.000
58	B	105	PHE	0	-0.013	-0.005	31.649	-0.009	-0.009	0.000	0.000	0.000	0.000
59	B	121	GLN	0	0.024	0.003	16.918	0.023	0.023	0.000	0.000	0.000	0.000
60	B	122	SER	0	0.025	0.001	20.753	0.003	0.003	0.000	0.000	0.000	0.000
61	B	123	PHE	0	-0.003	-0.008	17.169	0.002	0.002	0.000	0.000	0.000	0.000
62	B	124	GLU	-1	-0.839	-0.931	16.191	0.242	0.242	0.000	0.000	0.000	0.000
63	B	125	GLN	0	-0.056	-0.018	19.835	0.013	0.013	0.000	0.000	0.000	0.000
64	B	126	VAL	0	0.005	-0.007	22.779	0.008	0.008	0.000	0.000	0.000	0.000
65	B	127	VAL	0	0.014	0.002	18.227	0.013	0.013	0.000	0.000	0.000	0.000
66	B	128	ASN	0	-0.020	-0.014	18.896	0.056	0.056	0.000	0.000	0.000	0.000
67	B	129	GLU	-1	-0.915	-0.936	21.164	0.137	0.137	0.000	0.000	0.000	0.000
68	B	130	LEU	0	-0.074	-0.029	22.094	0.002	0.002	0.000	0.000	0.000	0.000
69	B	131	PHE	0	-0.054	-0.019	18.313	0.036	0.036	0.000	0.000	0.000	0.000
70	B	132	ARG	1	0.940	0.935	21.622	-0.209	-0.209	0.000	0.000	0.000	0.000
71	B	133	ASP	-1	-0.846	-0.876	23.688	0.215	0.215	0.000	0.000	0.000	0.000
72	B	134	GLY	0	-0.048	-0.063	23.532	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	135	VAL	0	0.025	0.049	16.777	0.017	0.017	0.000	0.000	0.000	0.000
74	B	136	ASN	0	0.042	0.016	20.135	0.000	0.000	0.000	0.000	0.000	0.000
75	B	137	TRP	0	0.072	0.020	15.493	0.003	0.003	0.000	0.000	0.000	0.000
76	B	138	GLY	0	0.030	0.017	20.585	0.005	0.005	0.000	0.000	0.000	0.000
77	B	139	ARG	1	0.845	0.915	21.093	-0.293	-0.293	0.000	0.000	0.000	0.000
78	B	140	ILE	0	0.018	0.015	15.266	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	141	VAL	0	0.026	0.016	18.780	0.016	0.016	0.000	0.000	0.000	0.000
80	B	142	ALA	0	0.001	0.002	21.270	-0.022	-0.022	0.000	0.000	0.000	0.000
81	B	143	PHE	0	-0.046	-0.020	15.007	-0.024	-0.024	0.000	0.000	0.000	0.000
82	B	144	PHE	0	0.010	-0.001	14.396	-0.008	-0.008	0.000	0.000	0.000	0.000
83	B	145	SER	0	0.004	-0.004	19.890	-0.036	-0.036	0.000	0.000	0.000	0.000
84	B	146	PHE	0	-0.033	-0.001	21.892	-0.029	-0.029	0.000	0.000	0.000	0.000
85	B	147	GLY	0	0.050	0.033	20.365	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	148	GLY	0	0.028	0.004	21.412	-0.024	-0.024	0.000	0.000	0.000	0.000
87	B	149	ALA	0	-0.008	-0.009	23.298	-0.023	-0.023	0.000	0.000	0.000	0.000
88	B	150	LEU	0	-0.001	0.006	22.120	-0.019	-0.019	0.000	0.000	0.000	0.000
89	B	151	CYS	0	-0.035	-0.013	21.938	-0.020	-0.020	0.000	0.000	0.000	0.000
90	B	152	VAL	0	0.044	0.013	24.721	-0.017	-0.017	0.000	0.000	0.000	0.000
91	B	153	GLU	-1	-0.935	-0.946	27.874	0.103	0.103	0.000	0.000	0.000	0.000
92	B	154	SER	0	-0.093	-0.073	26.752	-0.016	-0.016	0.000	0.000	0.000	0.000
93	B	155	VAL	0	-0.018	-0.021	26.734	-0.012	-0.012	0.000	0.000	0.000	0.000
94	B	156	ASP	-1	-0.825	-0.889	29.351	0.085	0.085	0.000	0.000	0.000	0.000
95	B	157	LYS	1	0.855	0.944	29.423	-0.058	-0.058	0.000	0.000	0.000	0.000
96	B	158	GLU	-1	-0.916	-0.970	31.081	0.022	0.022	0.000	0.000	0.000	0.000
97	B	159	MET	0	0.021	0.040	33.149	-0.006	-0.006	0.000	0.000	0.000	0.000
98	B	160	GLN	0	0.039	0.023	34.605	-0.002	-0.002	0.000	0.000	0.000	0.000
99	B	161	VAL	0	-0.016	0.025	36.171	-0.005	-0.005	0.000	0.000	0.000	0.000
100	B	162	LEU	0	-0.010	-0.015	33.100	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	163	VAL	0	0.029	0.012	37.272	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	164	SER	0	-0.048	-0.066	39.577	-0.003	-0.003	0.000	0.000	0.000	0.000
103	B	165	ARG	1	0.924	0.977	38.920	-0.013	-0.013	0.000	0.000	0.000	0.000
104	B	166	ILE	0	0.034	0.021	39.473	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	167	ALA	0	0.032	0.014	42.906	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	168	ALA	0	-0.010	0.003	45.164	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	169	TRP	0	-0.020	-0.017	41.492	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	170	MET	0	-0.022	-0.011	45.540	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	171	ALA	0	0.021	0.011	48.412	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	172	THR	0	-0.034	-0.026	50.468	0.000	0.000	0.000	0.000	0.000	0.000
111	B	173	TYR	0	0.004	0.004	51.090	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	174	LEU	0	-0.015	-0.019	52.358	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	175	ASN	0	-0.028	-0.025	54.098	0.000	0.000	0.000	0.000	0.000	0.000
114	B	176	ASP	-1	-0.929	-0.948	55.928	0.005	0.005	0.000	0.000	0.000	0.000
115	B	177	HIS	0	-0.108	-0.062	54.897	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	178	LEU	0	-0.047	-0.029	53.748	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	179	GLU	-1	-0.870	-0.933	57.984	0.012	0.012	0.000	0.000	0.000	0.000
118	B	180	PRO	0	-0.029	-0.009	60.002	0.000	0.000	0.000	0.000	0.000	0.000
119	B	181	TRP	0	0.036	0.019	59.616	0.000	0.000	0.000	0.000	0.000	0.000
120	B	182	ILE	0	0.004	0.000	57.189	0.000	0.000	0.000	0.000	0.000	0.000
121	B	183	GLN	0	-0.061	-0.029	61.844	0.000	0.000	0.000	0.000	0.000	0.000
122	B	184	GLU	-1	-0.980	-0.974	64.688	0.003	0.003	0.000	0.000	0.000	0.000
123	B	185	ASN	0	-0.059	-0.023	63.608	0.000	0.000	0.000	0.000	0.000	0.000
124	B	186	GLY	0	-0.034	-0.015	64.684	0.000	0.000	0.000	0.000	0.000	0.000
125	B	187	GLY	0	0.053	0.032	63.025	0.001	0.001	0.000	0.000	0.000	0.000
126	B	188	TRP	0	-0.022	-0.038	54.442	0.000	0.000	0.000	0.000	0.000	0.000
127	B	189	ASP	-1	-0.894	-0.940	60.030	0.016	0.016	0.000	0.000	0.000	0.000
128	B	190	THR	0	0.044	0.016	62.270	0.001	0.001	0.000	0.000	0.000	0.000
129	B	191	PHE	0	-0.039	-0.008	53.724	0.000	0.000	0.000	0.000	0.000	0.000
130	B	192	VAL	0	0.001	-0.016	57.584	0.000	0.000	0.000	0.000	0.000	0.000
131	B	193	GLU	-1	-0.991	-0.992	59.380	0.013	0.013	0.000	0.000	0.000	0.000
132	B	194	LEU	0	-0.103	-0.038	59.905	0.000	0.000	0.000	0.000	0.000	0.000
133	B	195	TYR	0	-0.110	-0.039	54.250	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:-1:SER)