FMO DATABASE

FMODB ID: JQK29

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1126073.226158
FMO2-HF: Nuclear repulsion	1068760.653142
FMO2-HF: Total energy	-57312.573017
FMO2-MP2: Total energy	-57479.522174

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.
-10.404	-5.377	1.013	-2.5	-3.543	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 : 0.038 / q_NPA : 0.015

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	0.047	0.014	3.127	-5.015	-1.984	0.285	-1.437	-1.879	0.010
4	A	2	SER	0	-0.042	-0.025	2.456	-3.882	-2.059	0.729	-0.995	-1.558	-0.003
5	A	3	GLN	0	0.022	0.010	4.355	-0.663	-0.490	-0.001	-0.068	-0.106	0.000
6	A	4	SER	0	-0.019	-0.016	6.204	-0.052	-0.052	0.000	0.000	0.000	0.000
7	A	5	ASN	0	0.047	0.015	7.846	-0.240	-0.240	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.955	0.986	8.695	-0.082	-0.082	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.856	-0.924	10.467	0.328	0.328	0.000	0.000	0.000	0.000
10	A	8	LEU	0	0.010	0.006	12.121	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	9	VAL	0	0.010	0.012	13.374	-0.061	-0.061	0.000	0.000	0.000	0.000
12	A	10	VAL	0	0.008	0.003	14.453	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.854	-0.897	16.282	0.214	0.214	0.000	0.000	0.000	0.000
14	A	12	PHE	0	0.025	0.011	17.923	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	13	LEU	0	0.005	-0.006	18.234	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	14	SER	0	-0.016	-0.016	20.035	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	15	TYR	0	-0.104	-0.081	22.148	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	16	LYS	1	0.803	0.868	23.735	-0.164	-0.164	0.000	0.000	0.000	0.000
19	A	17	LEU	0	0.022	0.013	23.918	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	18	SER	0	-0.013	-0.004	26.382	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.033	-0.006	28.194	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	20	LYS	1	0.804	0.883	29.821	-0.111	-0.111	0.000	0.000	0.000	0.000
23	A	21	GLY	0	-0.013	0.007	31.732	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	22	TYR	0	-0.012	-0.012	29.197	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	23	SER	0	-0.023	-0.018	28.867	0.006	0.006	0.000	0.000	0.000	0.000
26	A	24	TRP	0	-0.002	0.010	25.928	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	81	ILE	0	0.023	-0.004	15.319	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	82	PRO	0	0.003	0.016	15.440	0.085	0.085	0.000	0.000	0.000	0.000
29	A	83	MET	0	0.089	0.016	11.373	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	84	ALA	0	0.004	0.005	15.853	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	85	ALA	0	0.020	0.021	19.362	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	86	VAL	0	0.010	0.007	14.993	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	87	LYS	1	0.826	0.901	15.587	-0.335	-0.335	0.000	0.000	0.000	0.000
34	A	88	GLN	0	-0.044	-0.018	19.016	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	89	ALA	0	0.037	0.022	20.721	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	90	LEU	0	-0.035	-0.018	16.947	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	91	ARG	1	0.837	0.892	20.947	-0.238	-0.238	0.000	0.000	0.000	0.000
38	A	92	GLU	-1	-0.841	-0.903	23.422	0.210	0.210	0.000	0.000	0.000	0.000
39	A	93	ALA	0	-0.010	0.002	23.352	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	94	GLY	0	0.007	-0.008	24.340	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	95	ASP	-1	-0.748	-0.845	25.249	0.149	0.149	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.839	-0.896	28.541	0.171	0.171	0.000	0.000	0.000	0.000
43	A	97	PHE	0	-0.019	-0.020	27.093	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	98	GLU	-1	-0.829	-0.901	28.905	0.112	0.112	0.000	0.000	0.000	0.000
45	A	99	LEU	0	-0.006	-0.014	30.509	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	100	ARG	1	0.772	0.895	31.877	-0.167	-0.167	0.000	0.000	0.000	0.000
47	A	101	TYR	0	-0.039	-0.041	30.272	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	102	ARG	1	0.852	0.925	30.660	-0.095	-0.095	0.000	0.000	0.000	0.000
49	A	103	ARG	1	0.943	0.963	33.647	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	104	ALA	0	-0.022	0.008	35.157	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	105	PHE	0	-0.044	-0.015	31.028	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	106	SER	0	0.018	0.010	35.144	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	107	ASP	-1	-0.788	-0.855	34.239	0.049	0.049	0.000	0.000	0.000	0.000
54	A	108	LEU	0	0.011	-0.004	28.114	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	109	THR	0	-0.008	-0.025	30.723	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	110	SER	0	-0.037	-0.048	31.725	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	111	GLN	0	-0.029	-0.016	33.874	0.001	0.001	0.000	0.000	0.000	0.000
58	A	112	LEU	0	-0.034	-0.012	28.191	0.001	0.001	0.000	0.000	0.000	0.000
59	A	113	HIS	0	-0.081	-0.025	32.333	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	114	ILE	0	-0.011	0.003	27.645	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	115	THR	0	0.025	0.025	31.500	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	116	PRO	0	0.062	0.008	30.012	0.001	0.001	0.000	0.000	0.000	0.000
63	A	117	GLY	0	-0.017	0.001	28.445	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	118	THR	0	-0.053	-0.038	28.072	0.000	0.000	0.000	0.000	0.000	0.000
65	A	119	ALA	0	0.057	0.043	25.674	0.010	0.010	0.000	0.000	0.000	0.000
66	A	120	TYR	0	-0.063	-0.056	17.927	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	121	GLN	0	0.019	0.010	22.745	0.016	0.016	0.000	0.000	0.000	0.000
68	A	122	SER	0	0.078	0.033	24.989	0.013	0.013	0.000	0.000	0.000	0.000
69	A	123	PHE	0	-0.038	-0.020	17.956	0.016	0.016	0.000	0.000	0.000	0.000
70	A	124	GLU	-1	-0.824	-0.901	18.006	0.122	0.122	0.000	0.000	0.000	0.000
71	A	125	GLN	0	-0.031	-0.012	21.839	0.015	0.015	0.000	0.000	0.000	0.000
72	A	126	VAL	0	0.001	0.012	25.012	0.010	0.010	0.000	0.000	0.000	0.000
73	A	127	VAL	0	-0.016	-0.014	18.708	0.019	0.019	0.000	0.000	0.000	0.000
74	A	128	ASN	0	-0.057	-0.055	20.054	0.037	0.037	0.000	0.000	0.000	0.000
75	A	129	GLU	-1	-0.889	-0.935	22.673	0.130	0.130	0.000	0.000	0.000	0.000
76	A	130	LEU	0	-0.076	-0.026	22.124	0.007	0.007	0.000	0.000	0.000	0.000
77	A	131	PHE	0	-0.066	-0.055	18.671	0.031	0.031	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.887	0.965	22.682	-0.131	-0.131	0.000	0.000	0.000	0.000
79	A	133	ASP	-1	-0.819	-0.886	25.170	0.179	0.179	0.000	0.000	0.000	0.000
80	A	134	GLY	0	0.006	0.004	22.236	0.005	0.005	0.000	0.000	0.000	0.000
81	A	135	VAL	0	0.000	-0.001	17.656	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	136	ASN	0	0.016	0.010	20.964	0.005	0.005	0.000	0.000	0.000	0.000
83	A	137	TRP	0	0.091	0.018	15.361	0.004	0.004	0.000	0.000	0.000	0.000
84	A	138	GLY	0	0.032	0.029	21.398	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	139	ARG	1	0.801	0.882	22.295	-0.242	-0.242	0.000	0.000	0.000	0.000
86	A	140	ILE	0	0.032	0.014	16.528	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	141	VAL	0	0.001	0.009	19.661	0.000	0.000	0.000	0.000	0.000	0.000
88	A	142	ALA	0	0.013	0.009	21.977	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	143	PHE	0	-0.016	0.002	15.457	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	144	PHE	0	-0.001	-0.008	14.290	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	145	SER	0	-0.027	-0.014	20.010	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	146	PHE	0	-0.012	-0.005	22.459	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	147	GLY	0	0.031	0.014	20.828	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	148	GLY	0	0.004	-0.007	21.895	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	149	ALA	0	-0.023	-0.005	23.565	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	150	LEU	0	0.038	0.022	23.889	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	151	CYS	0	-0.022	0.002	22.811	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	152	VAL	0	0.010	0.000	24.896	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	153	GLU	-1	-0.738	-0.849	27.954	0.060	0.060	0.000	0.000	0.000	0.000
100	A	154	SER	0	-0.046	-0.031	26.872	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	155	VAL	0	-0.008	-0.013	26.615	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	156	ASP	-1	-0.885	-0.920	29.350	0.029	0.029	0.000	0.000	0.000	0.000
103	A	157	LYS	1	0.867	0.911	32.400	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.870	-0.953	30.504	-0.023	-0.023	0.000	0.000	0.000	0.000
105	A	159	MET	0	-0.016	0.009	32.832	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	160	GLN	0	-0.040	-0.027	34.532	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	161	VAL	0	-0.007	0.008	35.141	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	162	LEU	0	-0.049	-0.031	32.403	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	163	VAL	0	-0.002	-0.005	36.943	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	164	SER	0	-0.020	-0.009	39.862	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	165	ARG	1	0.899	0.956	34.474	0.028	0.028	0.000	0.000	0.000	0.000
112	A	166	ILE	0	0.022	0.014	38.001	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	167	ALA	0	0.039	0.025	42.249	0.000	0.000	0.000	0.000	0.000	0.000
114	A	168	ALA	0	0.028	0.021	44.695	0.000	0.000	0.000	0.000	0.000	0.000
115	A	169	TRP	0	-0.050	-0.022	38.972	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	170	MET	0	0.001	-0.001	45.453	0.000	0.000	0.000	0.000	0.000	0.000
117	A	171	ALA	0	0.015	0.011	48.013	0.000	0.000	0.000	0.000	0.000	0.000
118	A	172	THR	0	-0.033	-0.029	49.446	0.001	0.001	0.000	0.000	0.000	0.000
119	A	173	TYR	0	-0.019	-0.004	50.271	0.000	0.000	0.000	0.000	0.000	0.000
120	A	174	LEU	0	0.014	-0.004	52.128	0.000	0.000	0.000	0.000	0.000	0.000
121	A	175	ASN	0	0.012	0.003	54.047	0.001	0.001	0.000	0.000	0.000	0.000
122	A	176	ASP	-1	-0.930	-0.961	54.809	-0.017	-0.017	0.000	0.000	0.000	0.000
123	A	177	HIS	0	-0.090	-0.054	54.442	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	178	LEU	0	-0.057	-0.027	53.513	0.000	0.000	0.000	0.000	0.000	0.000
125	A	179	GLU	-1	-0.850	-0.912	57.631	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	180	PRO	0	-0.029	-0.015	59.639	0.001	0.001	0.000	0.000	0.000	0.000
127	A	181	TRP	0	0.046	0.030	59.887	0.001	0.001	0.000	0.000	0.000	0.000
128	A	182	ILE	0	0.014	0.007	57.146	0.001	0.001	0.000	0.000	0.000	0.000
129	A	183	GLN	0	-0.064	-0.045	61.809	0.001	0.001	0.000	0.000	0.000	0.000
130	A	184	GLU	-1	-1.011	-0.991	64.934	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	185	ASN	0	-0.119	-0.063	64.161	0.000	0.000	0.000	0.000	0.000	0.000
132	A	186	GLY	0	0.016	0.018	65.573	0.000	0.000	0.000	0.000	0.000	0.000
133	A	187	GLY	0	0.033	0.026	63.135	0.001	0.001	0.000	0.000	0.000	0.000
134	A	188	TRP	0	0.001	-0.023	54.658	0.000	0.000	0.000	0.000	0.000	0.000
135	A	189	ASP	-1	-0.901	-0.945	60.936	0.001	0.001	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.030	-0.031	63.613	0.000	0.000	0.000	0.000	0.000	0.000
137	A	191	PHE	0	-0.034	-0.010	54.993	0.000	0.000	0.000	0.000	0.000	0.000
138	A	192	VAL	0	-0.025	-0.032	58.748	0.000	0.000	0.000	0.000	0.000	0.000
139	A	193	GLU	-1	-0.973	-0.967	60.766	0.001	0.001	0.000	0.000	0.000	0.000
140	A	194	LEU	0	-0.076	-0.038	61.519	0.000	0.000	0.000	0.000	0.000	0.000
141	A	195	TYR	0	-0.099	-0.035	53.439	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	196	GLY	0	0.010	0.011	59.316	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)