FMO DATABASE

FMODB ID: G57Y1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1017356.701447
FMO2-HF: Nuclear repulsion	962758.718186
FMO2-HF: Total energy	-54597.983261
FMO2-MP2: Total energy	-54756.531185

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.
-11.459	-6.422	0.557	-2.275	-3.319	0.01

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 : 0.026 / q_NPA : 0.006

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	0.060	0.023	3.169	-3.691	-0.740	0.106	-1.385	-1.673	0.005
4	B	2	SER	0	-0.015	-0.016	2.550	-4.893	-2.983	0.453	-0.864	-1.499	0.005
5	B	3	GLN	0	0.014	0.010	4.852	-1.557	-1.447	-0.001	-0.021	-0.088	0.000
6	B	4	SER	0	0.050	0.019	6.715	-0.177	-0.177	0.000	0.000	0.000	0.000
7	B	5	ASN	0	-0.004	-0.007	7.947	-0.366	-0.366	0.000	0.000	0.000	0.000
8	B	6	ARG	1	0.916	0.946	4.408	-0.348	-0.282	-0.001	-0.005	-0.059	0.000
9	B	7	GLU	-1	-0.818	-0.894	10.249	0.428	0.428	0.000	0.000	0.000	0.000
10	B	8	LEU	0	-0.012	-0.009	12.316	-0.107	-0.107	0.000	0.000	0.000	0.000
11	B	9	VAL	0	-0.019	-0.014	12.912	-0.090	-0.090	0.000	0.000	0.000	0.000
12	B	10	VAL	0	0.052	0.028	14.245	-0.065	-0.065	0.000	0.000	0.000	0.000
13	B	11	ASP	-1	-0.834	-0.894	16.339	0.317	0.317	0.000	0.000	0.000	0.000
14	B	12	PHE	0	0.012	0.005	17.897	-0.039	-0.039	0.000	0.000	0.000	0.000
15	B	13	LEU	0	0.011	0.000	17.778	-0.039	-0.039	0.000	0.000	0.000	0.000
16	B	14	SER	0	0.024	0.014	20.241	-0.031	-0.031	0.000	0.000	0.000	0.000
17	B	15	TYR	0	-0.068	-0.046	22.152	-0.029	-0.029	0.000	0.000	0.000	0.000
18	B	16	LYS	1	0.797	0.853	23.592	-0.249	-0.249	0.000	0.000	0.000	0.000
19	B	17	LEU	0	0.025	0.011	23.365	-0.019	-0.019	0.000	0.000	0.000	0.000
20	B	18	SER	0	0.006	-0.001	26.063	-0.021	-0.021	0.000	0.000	0.000	0.000
21	B	19	GLN	0	-0.052	0.000	28.114	-0.012	-0.012	0.000	0.000	0.000	0.000
22	B	20	LYS	1	0.773	0.843	29.334	-0.178	-0.178	0.000	0.000	0.000	0.000
23	B	21	GLY	0	-0.001	0.014	31.187	-0.009	-0.009	0.000	0.000	0.000	0.000
24	B	22	TYR	0	-0.054	-0.070	28.531	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	23	SER	0	0.024	0.001	28.023	0.006	0.006	0.000	0.000	0.000	0.000
26	B	24	TRP	0	-0.036	-0.025	28.065	0.010	0.010	0.000	0.000	0.000	0.000
27	B	25	SER	0	-0.018	-0.021	23.863	0.002	0.002	0.000	0.000	0.000	0.000
28	B	26	GLN	0	-0.081	-0.043	23.125	0.003	0.003	0.000	0.000	0.000	0.000
29	B	27	PHE	0	-0.035	-0.028	23.058	0.005	0.005	0.000	0.000	0.000	0.000
30	B	28	SER	0	-0.003	0.015	23.412	-0.011	-0.011	0.000	0.000	0.000	0.000
31	B	29	ASP	-1	-0.945	-0.972	17.719	0.037	0.037	0.000	0.000	0.000	0.000
32	B	30	VAL	0	-0.049	-0.030	20.742	-0.020	-0.020	0.000	0.000	0.000	0.000
33	B	31	GLU	-1	-0.939	-0.951	22.694	0.008	0.008	0.000	0.000	0.000	0.000
34	B	32	GLU	-1	-1.015	-0.988	21.469	-0.083	-0.083	0.000	0.000	0.000	0.000
35	B	82	PRO	0	0.028	-0.010	17.682	0.020	0.020	0.000	0.000	0.000	0.000
36	B	83	MET	0	0.040	0.025	12.742	0.051	0.051	0.000	0.000	0.000	0.000
37	B	84	ALA	0	0.013	0.013	16.497	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	85	ALA	0	0.028	0.018	19.827	-0.024	-0.024	0.000	0.000	0.000	0.000
39	B	86	VAL	0	-0.005	-0.006	14.984	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	87	LYS	1	0.828	0.910	15.977	-0.455	-0.455	0.000	0.000	0.000	0.000
41	B	88	GLN	0	-0.052	-0.030	19.046	-0.017	-0.017	0.000	0.000	0.000	0.000
42	B	89	ALA	0	0.022	0.014	20.646	-0.021	-0.021	0.000	0.000	0.000	0.000
43	B	90	LEU	0	-0.029	-0.020	16.808	-0.015	-0.015	0.000	0.000	0.000	0.000
44	B	91	ARG	1	0.824	0.889	20.759	-0.325	-0.325	0.000	0.000	0.000	0.000
45	B	92	GLU	-1	-0.848	-0.911	23.430	0.251	0.251	0.000	0.000	0.000	0.000
46	B	93	ALA	0	0.011	0.013	22.764	-0.015	-0.015	0.000	0.000	0.000	0.000
47	B	94	GLY	0	0.003	-0.010	23.946	-0.016	-0.016	0.000	0.000	0.000	0.000
48	B	95	ASP	-1	-0.780	-0.843	24.941	0.208	0.208	0.000	0.000	0.000	0.000
49	B	96	GLU	-1	-0.923	-0.956	28.184	0.226	0.226	0.000	0.000	0.000	0.000
50	B	97	PHE	0	-0.059	-0.039	26.463	-0.014	-0.014	0.000	0.000	0.000	0.000
51	B	98	GLU	-1	-0.837	-0.891	28.503	0.171	0.171	0.000	0.000	0.000	0.000
52	B	99	LEU	0	-0.006	0.006	30.187	-0.016	-0.016	0.000	0.000	0.000	0.000
53	B	100	ARG	1	0.864	0.962	31.634	-0.178	-0.178	0.000	0.000	0.000	0.000
54	B	101	TYR	0	-0.065	-0.049	29.526	-0.018	-0.018	0.000	0.000	0.000	0.000
55	B	102	ARG	1	0.989	1.005	32.753	-0.106	-0.106	0.000	0.000	0.000	0.000
56	B	103	ARG	1	0.941	0.950	32.552	-0.110	-0.110	0.000	0.000	0.000	0.000
57	B	104	ALA	0	0.015	0.021	29.719	0.002	0.002	0.000	0.000	0.000	0.000
58	B	105	PHE	0	-0.011	0.005	31.673	-0.008	-0.008	0.000	0.000	0.000	0.000
59	B	121	GLN	0	0.016	-0.002	16.543	0.001	0.001	0.000	0.000	0.000	0.000
60	B	122	SER	0	0.033	0.007	20.740	0.003	0.003	0.000	0.000	0.000	0.000
61	B	123	PHE	0	-0.017	-0.012	17.322	0.002	0.002	0.000	0.000	0.000	0.000
62	B	124	GLU	-1	-0.832	-0.939	16.402	0.272	0.272	0.000	0.000	0.000	0.000
63	B	125	GLN	0	-0.053	-0.014	19.854	0.016	0.016	0.000	0.000	0.000	0.000
64	B	126	VAL	0	0.002	-0.005	22.875	0.007	0.007	0.000	0.000	0.000	0.000
65	B	127	VAL	0	0.022	0.004	18.088	0.012	0.012	0.000	0.000	0.000	0.000
66	B	128	ASN	0	-0.045	-0.031	19.056	0.058	0.058	0.000	0.000	0.000	0.000
67	B	129	GLU	-1	-0.888	-0.913	21.255	0.150	0.150	0.000	0.000	0.000	0.000
68	B	130	LEU	0	-0.070	-0.021	22.156	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	131	PHE	0	-0.034	-0.015	18.018	0.033	0.033	0.000	0.000	0.000	0.000
70	B	132	ARG	1	0.907	0.925	21.707	-0.223	-0.223	0.000	0.000	0.000	0.000
71	B	133	ASP	-1	-0.835	-0.883	23.492	0.222	0.222	0.000	0.000	0.000	0.000
72	B	134	GLY	0	-0.057	-0.054	23.367	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	135	VAL	0	0.015	0.035	16.911	0.020	0.020	0.000	0.000	0.000	0.000
74	B	136	ASN	0	0.037	0.008	20.198	0.008	0.008	0.000	0.000	0.000	0.000
75	B	137	TRP	0	0.076	0.021	15.153	0.006	0.006	0.000	0.000	0.000	0.000
76	B	138	GLY	0	0.025	0.021	20.585	0.005	0.005	0.000	0.000	0.000	0.000
77	B	139	ARG	1	0.860	0.921	21.316	-0.298	-0.298	0.000	0.000	0.000	0.000
78	B	140	ILE	0	0.016	0.014	15.658	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	141	VAL	0	0.028	0.019	18.830	0.017	0.017	0.000	0.000	0.000	0.000
80	B	142	ALA	0	0.000	0.012	21.270	-0.023	-0.023	0.000	0.000	0.000	0.000
81	B	143	PHE	0	-0.042	-0.021	14.952	-0.020	-0.020	0.000	0.000	0.000	0.000
82	B	144	PHE	0	0.010	0.001	14.319	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	145	SER	0	0.003	-0.015	19.878	-0.036	-0.036	0.000	0.000	0.000	0.000
84	B	146	PHE	0	-0.036	-0.006	22.039	-0.030	-0.030	0.000	0.000	0.000	0.000
85	B	147	GLY	0	0.053	0.036	20.345	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	148	GLY	0	0.035	0.009	21.391	-0.025	-0.025	0.000	0.000	0.000	0.000
87	B	149	ALA	0	-0.017	-0.012	23.279	-0.024	-0.024	0.000	0.000	0.000	0.000
88	B	150	LEU	0	-0.014	-0.001	22.341	-0.020	-0.020	0.000	0.000	0.000	0.000
89	B	151	CYS	0	-0.037	-0.021	21.986	-0.019	-0.019	0.000	0.000	0.000	0.000
90	B	152	VAL	0	0.048	0.017	24.707	-0.017	-0.017	0.000	0.000	0.000	0.000
91	B	153	GLU	-1	-0.878	-0.925	27.860	0.108	0.108	0.000	0.000	0.000	0.000
92	B	154	SER	0	-0.074	-0.048	26.714	-0.017	-0.017	0.000	0.000	0.000	0.000
93	B	155	VAL	0	-0.018	-0.021	26.638	-0.012	-0.012	0.000	0.000	0.000	0.000
94	B	156	ASP	-1	-0.828	-0.882	29.342	0.091	0.091	0.000	0.000	0.000	0.000
95	B	157	LYS	1	0.785	0.883	29.566	-0.066	-0.066	0.000	0.000	0.000	0.000
96	B	158	GLU	-1	-0.847	-0.915	30.997	0.034	0.034	0.000	0.000	0.000	0.000
97	B	159	MET	0	0.033	0.041	33.141	-0.006	-0.006	0.000	0.000	0.000	0.000
98	B	160	GLN	0	0.020	0.014	34.599	-0.003	-0.003	0.000	0.000	0.000	0.000
99	B	161	VAL	0	-0.002	0.009	36.187	-0.006	-0.006	0.000	0.000	0.000	0.000
100	B	162	LEU	0	-0.020	-0.018	33.032	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	163	VAL	0	0.028	0.007	37.241	-0.004	-0.004	0.000	0.000	0.000	0.000
102	B	164	SER	0	-0.043	-0.037	39.574	-0.004	-0.004	0.000	0.000	0.000	0.000
103	B	165	ARG	1	0.928	0.977	38.930	-0.020	-0.020	0.000	0.000	0.000	0.000
104	B	166	ILE	0	0.029	0.020	39.877	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	167	ALA	0	0.032	0.015	42.905	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	168	ALA	0	0.000	0.007	45.162	-0.001	-0.001	0.000	0.000	0.000	0.000
107	B	169	TRP	0	-0.021	-0.009	41.425	-0.002	-0.002	0.000	0.000	0.000	0.000
108	B	170	MET	0	-0.014	-0.005	45.409	-0.001	-0.001	0.000	0.000	0.000	0.000
109	B	171	ALA	0	0.022	0.015	48.413	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	172	THR	0	-0.027	-0.028	50.384	0.000	0.000	0.000	0.000	0.000	0.000
111	B	173	TYR	0	0.006	0.007	51.111	-0.001	-0.001	0.000	0.000	0.000	0.000
112	B	174	LEU	0	-0.006	-0.014	52.278	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	175	ASN	0	-0.061	-0.053	54.100	0.000	0.000	0.000	0.000	0.000	0.000
114	B	176	ASP	-1	-0.920	-0.944	55.826	0.007	0.007	0.000	0.000	0.000	0.000
115	B	177	HIS	0	-0.115	-0.062	55.435	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	178	LEU	0	-0.036	-0.024	53.762	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	179	GLU	-1	-0.815	-0.888	57.987	0.013	0.013	0.000	0.000	0.000	0.000
118	B	180	PRO	0	-0.030	-0.015	60.003	0.000	0.000	0.000	0.000	0.000	0.000
119	B	181	TRP	0	0.007	0.012	59.165	0.000	0.000	0.000	0.000	0.000	0.000
120	B	182	ILE	0	0.033	0.017	57.205	0.000	0.000	0.000	0.000	0.000	0.000
121	B	183	GLN	0	-0.101	-0.063	61.847	0.000	0.000	0.000	0.000	0.000	0.000
122	B	184	GLU	-1	-0.949	-0.955	64.689	0.004	0.004	0.000	0.000	0.000	0.000
123	B	185	ASN	0	-0.131	-0.077	63.781	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	186	GLY	0	-0.008	-0.005	64.687	0.000	0.000	0.000	0.000	0.000	0.000
125	B	187	GLY	0	0.043	0.030	63.021	0.001	0.001	0.000	0.000	0.000	0.000
126	B	188	TRP	0	-0.023	-0.037	54.342	0.000	0.000	0.000	0.000	0.000	0.000
127	B	189	ASP	-1	-0.909	-0.947	60.031	0.017	0.017	0.000	0.000	0.000	0.000
128	B	190	THR	0	0.038	0.018	62.271	0.001	0.001	0.000	0.000	0.000	0.000
129	B	191	PHE	0	-0.047	-0.014	53.701	0.000	0.000	0.000	0.000	0.000	0.000
130	B	192	VAL	0	0.006	-0.012	57.373	0.000	0.000	0.000	0.000	0.000	0.000
131	B	193	GLU	-1	-0.971	-0.983	59.382	0.013	0.013	0.000	0.000	0.000	0.000
132	B	194	LEU	0	-0.101	-0.038	60.091	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	195	TYR	0	-0.104	-0.036	53.970	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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