FMO DATABASE

FMODB ID: NN62Q

Calculation Name: 4HNJ-A-Xray372

Preferred Name: Apoptosis regulator Bcl-X

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4HNJ

Chain ID: A

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1124588.284594
FMO2-HF: Nuclear repulsion	1067276.32547
FMO2-HF: Total energy	-57311.959125
FMO2-MP2: Total energy	-57478.877635

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:-1:SER)

Summations of interaction energy for fragment #1(A:-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.
-10.904	-5.827	1.286	-2.577	-3.786	0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.017

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	1	MET	0	0.045	0.014	3.086	-5.415	-2.343	0.333	-1.472	-1.932	0.010
4	A	2	SER	0	-0.053	-0.038	2.442	-4.242	-2.391	0.954	-1.036	-1.769	-0.003
5	A	3	GLN	0	0.023	0.012	4.352	-0.571	-0.417	-0.001	-0.069	-0.085	0.000
6	A	4	SER	0	0.003	-0.010	6.195	-0.037	-0.037	0.000	0.000	0.000	0.000
7	A	5	ASN	0	0.057	0.017	7.718	-0.210	-0.210	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.950	0.982	8.702	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.935	-0.976	10.461	0.317	0.317	0.000	0.000	0.000	0.000
10	A	8	LEU	0	-0.024	-0.005	12.254	-0.061	-0.061	0.000	0.000	0.000	0.000
11	A	9	VAL	0	0.022	0.014	13.444	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	10	VAL	0	0.011	0.009	14.405	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.859	-0.902	16.279	0.212	0.212	0.000	0.000	0.000	0.000
14	A	12	PHE	0	0.014	0.008	17.927	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	13	LEU	0	0.000	-0.011	18.509	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	14	SER	0	-0.024	-0.042	19.925	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	15	TYR	0	-0.127	-0.093	22.146	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	16	LYS	1	0.835	0.898	23.736	-0.159	-0.159	0.000	0.000	0.000	0.000
19	A	17	LEU	0	0.017	0.016	23.977	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	18	SER	0	-0.014	0.000	26.704	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.015	0.007	28.197	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	20	LYS	1	0.818	0.908	29.623	-0.103	-0.103	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.006	0.012	31.732	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	22	TYR	0	-0.008	-0.009	29.085	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	23	SER	0	-0.031	-0.022	28.860	0.005	0.005	0.000	0.000	0.000	0.000
26	A	24	TRP	0	0.001	0.011	25.751	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	81	ILE	0	0.004	-0.005	15.567	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	82	PRO	0	0.020	0.015	15.542	0.087	0.087	0.000	0.000	0.000	0.000
29	A	83	MET	0	0.089	0.020	12.152	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	84	ALA	0	0.002	-0.001	15.853	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	85	ALA	0	0.027	0.027	19.386	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	86	VAL	0	0.016	0.008	14.971	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	87	LYS	1	0.922	0.965	15.912	-0.329	-0.329	0.000	0.000	0.000	0.000
34	A	88	GLN	0	-0.023	0.004	19.016	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	89	ALA	0	0.044	0.026	20.700	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	90	LEU	0	-0.024	-0.013	16.933	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	91	ARG	1	0.833	0.908	20.961	-0.233	-0.233	0.000	0.000	0.000	0.000
38	A	92	GLU	-1	-0.870	-0.929	23.432	0.216	0.216	0.000	0.000	0.000	0.000
39	A	93	ALA	0	0.006	0.009	23.385	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	94	GLY	0	0.000	-0.011	24.361	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	95	ASP	-1	-0.756	-0.864	25.263	0.147	0.147	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.942	-0.963	28.557	0.179	0.179	0.000	0.000	0.000	0.000
43	A	97	PHE	0	-0.021	-0.022	27.101	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	98	GLU	-1	-0.861	-0.944	28.977	0.107	0.107	0.000	0.000	0.000	0.000
45	A	99	LEU	0	-0.008	-0.015	30.522	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	100	ARG	1	0.857	0.950	32.232	-0.154	-0.154	0.000	0.000	0.000	0.000
47	A	101	TYR	0	-0.037	-0.032	30.469	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	102	ARG	1	0.899	0.969	31.689	-0.088	-0.088	0.000	0.000	0.000	0.000
49	A	103	ARG	1	0.961	0.960	33.660	-0.093	-0.093	0.000	0.000	0.000	0.000
50	A	104	ALA	0	-0.024	0.009	35.212	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	105	PHE	0	-0.041	-0.010	31.030	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	106	SER	0	-0.017	0.001	35.156	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	107	ASP	-1	-0.776	-0.885	34.280	0.043	0.043	0.000	0.000	0.000	0.000
54	A	108	LEU	0	0.021	-0.002	28.031	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	109	THR	0	0.006	-0.012	30.547	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	110	SER	0	-0.061	-0.052	31.730	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	111	GLN	0	-0.022	-0.025	33.914	0.000	0.000	0.000	0.000	0.000	0.000
58	A	112	LEU	0	-0.034	-0.008	28.213	0.001	0.001	0.000	0.000	0.000	0.000
59	A	113	HIS	0	-0.087	-0.027	32.342	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	114	ILE	0	-0.008	0.006	27.789	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	115	THR	0	0.029	0.024	31.503	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	116	PRO	0	0.045	0.000	30.022	0.000	0.000	0.000	0.000	0.000	0.000
63	A	117	GLY	0	-0.027	-0.011	28.441	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	118	THR	0	-0.046	-0.029	28.043	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	119	ALA	0	0.062	0.038	25.629	0.009	0.009	0.000	0.000	0.000	0.000
66	A	120	TYR	0	-0.001	-0.006	17.669	0.005	0.005	0.000	0.000	0.000	0.000
67	A	121	GLN	0	0.036	0.012	22.751	0.020	0.020	0.000	0.000	0.000	0.000
68	A	122	SER	0	0.071	0.044	24.999	0.014	0.014	0.000	0.000	0.000	0.000
69	A	123	PHE	0	-0.045	-0.017	18.029	0.016	0.016	0.000	0.000	0.000	0.000
70	A	124	GLU	-1	-0.896	-0.961	18.168	0.095	0.095	0.000	0.000	0.000	0.000
71	A	125	GLN	0	-0.046	-0.027	21.851	0.015	0.015	0.000	0.000	0.000	0.000
72	A	126	VAL	0	0.004	0.017	24.771	0.011	0.011	0.000	0.000	0.000	0.000
73	A	127	VAL	0	-0.015	-0.016	18.786	0.020	0.020	0.000	0.000	0.000	0.000
74	A	128	ASN	0	-0.017	-0.025	20.740	0.042	0.042	0.000	0.000	0.000	0.000
75	A	129	GLU	-1	-0.941	-0.956	22.693	0.117	0.117	0.000	0.000	0.000	0.000
76	A	130	LEU	0	-0.089	-0.031	22.214	0.008	0.008	0.000	0.000	0.000	0.000
77	A	131	PHE	0	-0.069	-0.056	18.889	0.031	0.031	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.989	1.018	22.707	-0.119	-0.119	0.000	0.000	0.000	0.000
79	A	133	ASP	-1	-0.904	-0.938	25.079	0.181	0.181	0.000	0.000	0.000	0.000
80	A	134	GLY	0	0.003	0.004	22.148	0.006	0.006	0.000	0.000	0.000	0.000
81	A	135	VAL	0	0.009	-0.003	17.676	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	136	ASN	0	0.010	0.009	20.874	0.006	0.006	0.000	0.000	0.000	0.000
83	A	137	TRP	0	0.090	0.017	15.591	0.002	0.002	0.000	0.000	0.000	0.000
84	A	138	GLY	0	0.036	0.030	21.398	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	139	ARG	1	0.831	0.902	22.195	-0.236	-0.236	0.000	0.000	0.000	0.000
86	A	140	ILE	0	0.028	0.014	16.153	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	141	VAL	0	0.006	0.013	19.680	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	142	ALA	0	0.017	0.007	21.996	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	143	PHE	0	-0.017	0.001	15.409	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	144	PHE	0	-0.002	-0.010	14.521	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	145	SER	0	-0.036	-0.017	20.023	-0.036	-0.036	0.000	0.000	0.000	0.000
92	A	146	PHE	0	-0.004	-0.001	22.335	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	147	GLY	0	0.031	0.016	20.836	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	148	GLY	0	-0.004	-0.011	21.903	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	149	ALA	0	-0.014	0.001	23.570	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	150	LEU	0	0.063	0.032	23.572	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	151	CYS	0	-0.061	-0.003	22.643	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	152	VAL	0	0.035	0.010	24.895	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	153	GLU	-1	-0.802	-0.896	27.953	0.051	0.051	0.000	0.000	0.000	0.000
100	A	154	SER	0	-0.044	-0.039	26.894	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	155	VAL	0	-0.008	-0.008	26.651	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	156	ASP	-1	-0.890	-0.936	29.344	0.024	0.024	0.000	0.000	0.000	0.000
103	A	157	LYS	1	0.865	0.934	32.368	-0.035	-0.035	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.899	-0.959	30.442	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	159	MET	0	-0.015	0.007	32.824	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	160	GLN	0	-0.035	-0.020	34.523	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	161	VAL	0	-0.012	0.009	35.031	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	162	LEU	0	-0.038	-0.028	32.517	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	163	VAL	0	-0.006	-0.003	36.930	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	164	SER	0	-0.013	-0.009	39.850	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	165	ARG	1	0.947	0.968	35.242	0.040	0.040	0.000	0.000	0.000	0.000
112	A	166	ILE	0	0.003	0.008	38.089	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	167	ALA	0	0.048	0.028	42.234	0.000	0.000	0.000	0.000	0.000	0.000
114	A	168	ALA	0	0.022	0.016	44.682	0.000	0.000	0.000	0.000	0.000	0.000
115	A	169	TRP	0	-0.053	-0.032	39.255	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	170	MET	0	-0.009	-0.007	45.429	0.000	0.000	0.000	0.000	0.000	0.000
117	A	171	ALA	0	0.022	0.013	47.997	0.000	0.000	0.000	0.000	0.000	0.000
118	A	172	THR	0	-0.034	-0.011	49.659	0.001	0.001	0.000	0.000	0.000	0.000
119	A	173	TYR	0	-0.010	0.000	50.219	0.000	0.000	0.000	0.000	0.000	0.000
120	A	174	LEU	0	0.014	-0.008	51.761	0.000	0.000	0.000	0.000	0.000	0.000
121	A	175	ASN	0	0.015	0.006	54.031	0.001	0.001	0.000	0.000	0.000	0.000
122	A	176	ASP	-1	-0.924	-0.956	54.742	-0.020	-0.020	0.000	0.000	0.000	0.000
123	A	177	HIS	0	-0.093	-0.057	54.466	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	178	LEU	0	-0.068	-0.032	53.580	0.000	0.000	0.000	0.000	0.000	0.000
125	A	179	GLU	-1	-0.892	-0.946	57.613	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	180	PRO	0	-0.022	-0.010	59.623	0.001	0.001	0.000	0.000	0.000	0.000
127	A	181	TRP	0	0.042	0.023	59.815	0.001	0.001	0.000	0.000	0.000	0.000
128	A	182	ILE	0	0.014	0.006	57.190	0.001	0.001	0.000	0.000	0.000	0.000
129	A	183	GLN	0	-0.019	-0.010	61.792	0.001	0.001	0.000	0.000	0.000	0.000
130	A	184	GLU	-1	-1.026	-1.000	64.918	-0.013	-0.013	0.000	0.000	0.000	0.000
131	A	185	ASN	0	-0.110	-0.049	64.158	0.000	0.000	0.000	0.000	0.000	0.000
132	A	186	GLY	0	0.021	0.021	65.556	0.000	0.000	0.000	0.000	0.000	0.000
133	A	187	GLY	0	0.047	0.030	63.129	0.001	0.001	0.000	0.000	0.000	0.000
134	A	188	TRP	0	-0.001	-0.022	54.752	0.000	0.000	0.000	0.000	0.000	0.000
135	A	189	ASP	-1	-0.897	-0.943	60.921	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.056	-0.046	63.599	0.000	0.000	0.000	0.000	0.000	0.000
137	A	191	PHE	0	-0.027	-0.003	54.984	0.000	0.000	0.000	0.000	0.000	0.000
138	A	192	VAL	0	-0.030	-0.035	58.797	0.000	0.000	0.000	0.000	0.000	0.000
139	A	193	GLU	-1	-0.983	-0.969	60.751	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	194	LEU	0	-0.053	-0.034	61.314	0.000	0.000	0.000	0.000	0.000	0.000
141	A	195	TYR	0	-0.099	-0.031	53.663	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	196	GLY	0	0.002	0.006	59.301	0.001	0.001	0.000	0.000	0.000	0.000

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