FMO DATABASE

FMODB ID: 3JG7L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1130923.599245
FMO2-HF: Nuclear repulsion	1073610.762013
FMO2-HF: Total energy	-57312.837232
FMO2-MP2: Total energy	-57479.735109

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.
-9.534	-5.061	1.172	-2.203	-3.442	0.01

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 : 0.049 / q_NPA : 0.021

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	0.044	0.022	2.813	-4.343	-1.635	0.874	-1.420	-2.162	0.010
4	A	2	SER	0	-0.029	-0.017	2.617	-3.589	-1.990	0.299	-0.716	-1.182	0.000
5	A	3	GLN	0	0.018	0.013	4.447	-0.578	-0.412	-0.001	-0.067	-0.098	0.000
6	A	4	SER	0	-0.017	-0.024	6.432	-0.049	-0.049	0.000	0.000	0.000	0.000
7	A	5	ASN	0	0.044	0.013	7.953	-0.340	-0.340	0.000	0.000	0.000	0.000
8	A	6	ARG	1	0.952	0.983	8.624	-0.223	-0.223	0.000	0.000	0.000	0.000
9	A	7	GLU	-1	-0.866	-0.926	10.368	0.362	0.362	0.000	0.000	0.000	0.000
10	A	8	LEU	0	0.021	0.005	12.006	-0.069	-0.069	0.000	0.000	0.000	0.000
11	A	9	VAL	0	-0.006	0.005	13.351	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	10	VAL	0	0.001	-0.004	14.425	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.861	-0.903	16.273	0.241	0.241	0.000	0.000	0.000	0.000
14	A	12	PHE	0	0.035	0.021	17.900	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	13	LEU	0	0.001	-0.001	18.277	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	14	SER	0	-0.001	-0.010	20.010	-0.029	-0.029	0.000	0.000	0.000	0.000
17	A	15	TYR	0	-0.087	-0.057	22.126	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	16	LYS	1	0.800	0.875	23.645	-0.191	-0.191	0.000	0.000	0.000	0.000
19	A	17	LEU	0	0.014	0.004	23.752	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	18	SER	0	-0.012	-0.013	26.056	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.042	-0.024	27.957	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	20	LYS	1	0.784	0.869	29.404	-0.132	-0.132	0.000	0.000	0.000	0.000
23	A	21	GLY	0	0.020	0.022	31.603	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	22	TYR	0	-0.019	-0.015	28.900	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	23	SER	0	-0.002	-0.008	28.486	0.009	0.009	0.000	0.000	0.000	0.000
26	A	24	TRP	0	-0.012	0.004	25.673	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	81	ILE	0	0.040	0.007	14.815	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	82	PRO	0	-0.007	0.009	15.087	0.079	0.079	0.000	0.000	0.000	0.000
29	A	83	MET	0	0.081	0.015	10.783	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	84	ALA	0	0.000	0.006	15.385	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	85	ALA	0	0.042	0.028	19.027	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	86	VAL	0	-0.013	0.000	14.579	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	87	LYS	1	0.823	0.891	15.271	-0.357	-0.357	0.000	0.000	0.000	0.000
34	A	88	GLN	0	-0.075	-0.038	18.563	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	89	ALA	0	0.051	0.021	20.691	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	90	LEU	0	-0.035	-0.013	16.773	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	91	ARG	1	0.843	0.902	20.652	-0.262	-0.262	0.000	0.000	0.000	0.000
38	A	92	GLU	-1	-0.829	-0.898	23.204	0.220	0.220	0.000	0.000	0.000	0.000
39	A	93	ALA	0	0.004	0.006	23.333	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	94	GLY	0	0.008	-0.009	24.233	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	95	ASP	-1	-0.752	-0.847	25.101	0.169	0.169	0.000	0.000	0.000	0.000
42	A	96	GLU	-1	-0.832	-0.892	28.426	0.175	0.175	0.000	0.000	0.000	0.000
43	A	97	PHE	0	-0.022	-0.020	27.126	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	98	GLU	-1	-0.810	-0.883	28.799	0.132	0.132	0.000	0.000	0.000	0.000
45	A	99	LEU	0	-0.005	-0.007	30.418	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	100	ARG	1	0.774	0.886	31.604	-0.179	-0.179	0.000	0.000	0.000	0.000
47	A	101	TYR	0	-0.005	-0.014	30.104	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	102	ARG	1	0.808	0.901	30.570	-0.110	-0.110	0.000	0.000	0.000	0.000
49	A	103	ARG	1	0.912	0.941	33.465	-0.112	-0.112	0.000	0.000	0.000	0.000
50	A	104	ALA	0	-0.024	0.009	34.813	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	105	PHE	0	-0.046	-0.028	31.459	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	106	SER	0	0.028	0.027	34.974	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	107	ASP	-1	-0.798	-0.882	33.863	0.067	0.067	0.000	0.000	0.000	0.000
54	A	108	LEU	0	-0.011	-0.007	27.874	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	109	THR	0	-0.015	-0.030	30.362	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	110	SER	0	-0.024	-0.034	31.399	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	111	GLN	0	-0.020	-0.013	33.819	0.000	0.000	0.000	0.000	0.000	0.000
58	A	112	LEU	0	-0.043	-0.019	28.085	0.000	0.000	0.000	0.000	0.000	0.000
59	A	113	HIS	0	-0.072	-0.034	32.243	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	114	ILE	0	-0.022	0.010	27.631	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	115	THR	0	0.040	0.025	31.371	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	116	PRO	0	0.027	-0.008	29.629	0.002	0.002	0.000	0.000	0.000	0.000
63	A	117	GLY	0	-0.004	0.011	28.233	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	118	THR	0	-0.003	-0.016	28.253	0.001	0.001	0.000	0.000	0.000	0.000
65	A	119	ALA	0	0.033	0.039	25.951	0.010	0.010	0.000	0.000	0.000	0.000
66	A	120	TYR	0	-0.055	-0.056	17.971	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	121	GLN	0	0.001	-0.010	22.831	0.017	0.017	0.000	0.000	0.000	0.000
68	A	122	SER	0	0.052	0.017	25.094	0.011	0.011	0.000	0.000	0.000	0.000
69	A	123	PHE	0	-0.032	-0.012	18.000	0.013	0.013	0.000	0.000	0.000	0.000
70	A	124	GLU	-1	-0.803	-0.888	18.077	0.189	0.189	0.000	0.000	0.000	0.000
71	A	125	GLN	0	-0.032	-0.010	21.954	0.015	0.015	0.000	0.000	0.000	0.000
72	A	126	VAL	0	0.001	0.010	25.077	0.007	0.007	0.000	0.000	0.000	0.000
73	A	127	VAL	0	-0.022	-0.014	18.587	0.019	0.019	0.000	0.000	0.000	0.000
74	A	128	ASN	0	-0.065	-0.057	19.939	0.036	0.036	0.000	0.000	0.000	0.000
75	A	129	GLU	-1	-0.845	-0.902	22.557	0.148	0.148	0.000	0.000	0.000	0.000
76	A	130	LEU	0	-0.073	-0.029	22.190	0.006	0.006	0.000	0.000	0.000	0.000
77	A	131	PHE	0	-0.027	-0.038	18.623	0.035	0.035	0.000	0.000	0.000	0.000
78	A	132	ARG	1	0.832	0.917	22.672	-0.144	-0.144	0.000	0.000	0.000	0.000
79	A	133	ASP	-1	-0.833	-0.883	25.174	0.186	0.186	0.000	0.000	0.000	0.000
80	A	134	GLY	0	-0.001	0.002	22.391	0.001	0.001	0.000	0.000	0.000	0.000
81	A	135	VAL	0	0.005	0.007	17.139	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	136	ASN	0	0.006	-0.002	20.558	0.000	0.000	0.000	0.000	0.000	0.000
83	A	137	TRP	0	0.086	0.024	15.100	0.002	0.002	0.000	0.000	0.000	0.000
84	A	138	GLY	0	0.034	0.033	21.024	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	139	ARG	1	0.811	0.880	22.086	-0.257	-0.257	0.000	0.000	0.000	0.000
86	A	140	ILE	0	0.010	0.013	16.352	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	141	VAL	0	0.006	-0.001	19.557	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	142	ALA	0	-0.007	0.006	21.966	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	143	PHE	0	0.002	0.001	15.516	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	144	PHE	0	0.001	-0.005	14.231	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	145	SER	0	-0.018	-0.011	20.038	-0.036	-0.036	0.000	0.000	0.000	0.000
92	A	146	PHE	0	-0.013	0.003	22.501	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	147	GLY	0	0.037	0.018	20.686	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	148	GLY	0	-0.005	-0.018	21.761	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	149	ALA	0	-0.012	-0.002	23.331	-0.020	-0.020	0.000	0.000	0.000	0.000
96	A	150	LEU	0	0.033	0.016	24.233	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	151	CYS	0	-0.034	0.003	22.648	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	152	VAL	0	0.004	-0.001	24.725	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	153	GLU	-1	-0.707	-0.826	27.916	0.083	0.083	0.000	0.000	0.000	0.000
100	A	154	SER	0	-0.016	-0.023	26.666	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	155	VAL	0	-0.028	-0.014	26.494	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	156	ASP	-1	-0.826	-0.899	29.226	0.046	0.046	0.000	0.000	0.000	0.000
103	A	157	LYS	1	0.790	0.891	32.256	-0.064	-0.064	0.000	0.000	0.000	0.000
104	A	158	GLU	-1	-0.791	-0.895	30.490	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	159	MET	0	-0.017	0.008	32.764	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	160	GLN	0	-0.039	-0.025	34.343	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	161	VAL	0	-0.013	-0.001	35.382	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	162	LEU	0	-0.046	-0.025	32.396	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	163	VAL	0	0.012	0.007	36.904	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	164	SER	0	-0.020	-0.003	39.828	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	165	ARG	1	0.830	0.894	34.115	0.005	0.005	0.000	0.000	0.000	0.000
112	A	166	ILE	0	0.022	0.011	37.787	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	167	ALA	0	0.027	0.013	42.028	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	168	ALA	0	0.013	0.013	44.667	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	169	TRP	0	-0.039	-0.014	38.761	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	170	MET	0	-0.004	-0.005	45.276	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	171	ALA	0	0.016	0.014	47.834	0.000	0.000	0.000	0.000	0.000	0.000
118	A	172	THR	0	-0.040	-0.027	49.289	0.000	0.000	0.000	0.000	0.000	0.000
119	A	173	TYR	0	-0.012	-0.009	50.038	0.000	0.000	0.000	0.000	0.000	0.000
120	A	174	LEU	0	0.007	0.002	51.893	0.000	0.000	0.000	0.000	0.000	0.000
121	A	175	ASN	0	-0.018	-0.014	53.820	0.001	0.001	0.000	0.000	0.000	0.000
122	A	176	ASP	-1	-0.926	-0.964	54.600	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	177	HIS	0	-0.081	-0.045	54.172	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	178	LEU	0	-0.043	-0.016	53.546	0.000	0.000	0.000	0.000	0.000	0.000
125	A	179	GLU	-1	-0.816	-0.898	57.687	0.002	0.002	0.000	0.000	0.000	0.000
126	A	180	PRO	0	-0.024	-0.014	59.472	0.001	0.001	0.000	0.000	0.000	0.000
127	A	181	TRP	0	0.064	0.042	59.703	0.001	0.001	0.000	0.000	0.000	0.000
128	A	182	ILE	0	0.004	0.005	57.097	0.000	0.000	0.000	0.000	0.000	0.000
129	A	183	GLN	0	-0.067	-0.046	61.754	0.001	0.001	0.000	0.000	0.000	0.000
130	A	184	GLU	-1	-0.993	-0.998	64.915	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	185	ASN	0	-0.100	-0.053	63.933	0.000	0.000	0.000	0.000	0.000	0.000
132	A	186	GLY	0	-0.012	0.008	65.998	0.001	0.001	0.000	0.000	0.000	0.000
133	A	187	GLY	0	0.023	0.015	63.375	0.001	0.001	0.000	0.000	0.000	0.000
134	A	188	TRP	0	-0.020	-0.028	54.345	0.000	0.000	0.000	0.000	0.000	0.000
135	A	189	ASP	-1	-0.912	-0.950	60.826	0.007	0.007	0.000	0.000	0.000	0.000
136	A	190	THR	0	-0.023	-0.024	63.480	0.000	0.000	0.000	0.000	0.000	0.000
137	A	191	PHE	0	-0.015	-0.004	54.794	0.000	0.000	0.000	0.000	0.000	0.000
138	A	192	VAL	0	-0.034	-0.026	58.735	0.000	0.000	0.000	0.000	0.000	0.000
139	A	193	GLU	-1	-0.951	-0.965	60.630	0.006	0.006	0.000	0.000	0.000	0.000
140	A	194	LEU	0	-0.091	-0.044	61.561	0.000	0.000	0.000	0.000	0.000	0.000
141	A	195	TYR	0	-0.095	-0.038	53.159	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	196	GLY	0	-0.007	0.007	58.600	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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