FMO DATABASE

FMODB ID: GYN41

Calculation Name: 3ILC-A-Xray372

Preferred Name: Bcl-2-like protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ILC

Chain ID: A

ChEMBL ID: CHEMBL3309112

UniProt ID: Q64373

Base Structure: X-ray

Registration Date: 2023-09-26

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1416885.302229
FMO2-HF: Nuclear repulsion	1358955.011654
FMO2-HF: Total energy	-57930.290575
FMO2-MP2: Total energy	-58099.447374

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-21.669	-19.252	16.731	-6.528	-12.622	0.025

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : 0.040

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	2	SER	0	0.000	-0.016	2.014	-16.181	-15.390	12.594	-4.729	-8.657	0.026
4	A	3	GLN	0	-0.039	-0.018	1.875	-4.587	-3.660	4.118	-1.652	-3.393	-0.001
5	A	4	SER	0	0.003	-0.010	3.478	-0.946	-0.247	0.019	-0.147	-0.572	0.000
6	A	5	ASN	0	0.010	-0.017	5.735	-0.391	-0.391	0.000	0.000	0.000	0.000
7	A	6	ARG	1	0.899	0.959	6.567	-0.393	-0.393	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.821	-0.917	7.372	0.063	0.063	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.012	0.020	9.694	-0.081	-0.081	0.000	0.000	0.000	0.000
10	A	9	VAL	0	-0.033	-0.012	11.283	-0.077	-0.077	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.026	-0.009	12.298	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.837	-0.875	13.711	0.176	0.176	0.000	0.000	0.000	0.000
13	A	12	PHE	0	0.035	0.017	15.472	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	13	LEU	0	0.008	-0.025	16.482	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	14	SER	0	-0.015	-0.028	17.397	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	15	TYR	0	-0.077	-0.049	19.654	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.805	0.883	21.443	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	17	LEU	0	-0.002	-0.011	21.446	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.042	-0.011	23.938	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	19	GLN	0	-0.025	-0.009	25.499	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.779	0.881	27.366	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.023	0.034	29.124	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	22	TYR	0	-0.089	-0.071	26.811	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	23	SER	0	0.009	0.008	26.154	0.012	0.012	0.000	0.000	0.000	0.000
25	A	24	TRP	0	0.052	0.011	20.874	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	25	SER	0	0.005	-0.006	20.873	0.008	0.008	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.069	-0.031	19.952	0.013	0.013	0.000	0.000	0.000	0.000
28	A	27	PHE	0	-0.045	-0.022	16.073	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	28	SER	0	0.014	0.018	14.777	0.016	0.016	0.000	0.000	0.000	0.000
30	A	82	PRO	0	0.106	0.035	11.686	0.018	0.018	0.000	0.000	0.000	0.000
31	A	83	MET	0	-0.022	-0.007	8.973	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	84	ALA	0	-0.008	-0.004	11.559	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	85	ALA	0	0.049	0.024	14.974	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	86	VAL	0	0.023	0.020	12.543	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	87	LYS	1	0.818	0.898	10.842	-0.312	-0.312	0.000	0.000	0.000	0.000
36	A	88	GLN	0	-0.053	-0.033	15.726	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	89	ALA	0	0.070	0.034	18.633	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	90	LEU	0	-0.030	-0.011	15.532	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	91	ARG	1	0.794	0.871	17.592	-0.200	-0.200	0.000	0.000	0.000	0.000
40	A	92	GLU	-1	-0.834	-0.893	21.013	0.131	0.131	0.000	0.000	0.000	0.000
41	A	93	ALA	0	-0.003	0.004	21.798	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	94	GLY	0	0.003	-0.009	22.652	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	95	ASP	-1	-0.768	-0.858	23.720	0.061	0.061	0.000	0.000	0.000	0.000
44	A	96	GLU	-1	-0.777	-0.836	26.797	0.045	0.045	0.000	0.000	0.000	0.000
45	A	97	PHE	0	0.021	0.001	25.934	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	98	GLU	-1	-0.831	-0.900	25.478	0.020	0.020	0.000	0.000	0.000	0.000
47	A	99	LEU	0	-0.041	-0.022	29.188	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	100	ARG	1	0.758	0.836	28.726	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	101	ALA	0	-0.027	-0.018	30.477	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	102	ARG	1	0.890	0.961	32.290	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	103	ARG	1	0.857	0.932	29.437	0.043	0.043	0.000	0.000	0.000	0.000
52	A	104	ALA	0	0.058	0.019	30.652	0.002	0.002	0.000	0.000	0.000	0.000
53	A	105	PHE	0	0.003	-0.011	25.620	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	106	SER	0	0.061	0.031	29.928	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	107	ASP	-1	-0.862	-0.904	31.089	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	108	LEU	0	0.071	0.037	25.007	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	109	THR	0	-0.002	-0.003	27.779	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	110	SER	0	-0.065	-0.025	29.596	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	111	GLN	0	-0.036	-0.028	29.137	0.002	0.002	0.000	0.000	0.000	0.000
60	A	112	LEU	0	-0.042	-0.023	23.560	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	113	HIS	1	0.790	0.891	27.957	0.140	0.140	0.000	0.000	0.000	0.000
62	A	114	ILE	0	0.003	0.014	23.594	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	115	THR	0	0.106	0.045	27.585	0.013	0.013	0.000	0.000	0.000	0.000
64	A	116	PRO	0	0.032	-0.001	26.091	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	117	GLY	0	0.022	0.021	26.141	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	118	THR	0	-0.042	-0.003	23.624	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	119	ALA	0	0.056	0.023	21.705	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	120	TYR	0	0.067	0.021	14.377	0.048	0.048	0.000	0.000	0.000	0.000
69	A	121	GLN	0	0.039	0.013	19.047	0.019	0.019	0.000	0.000	0.000	0.000
70	A	122	SER	0	0.006	0.001	20.393	0.013	0.013	0.000	0.000	0.000	0.000
71	A	123	PHE	0	0.012	0.003	16.908	0.024	0.024	0.000	0.000	0.000	0.000
72	A	124	GLU	-1	-0.847	-0.910	16.839	-0.542	-0.542	0.000	0.000	0.000	0.000
73	A	125	GLN	0	-0.022	-0.018	19.438	0.026	0.026	0.000	0.000	0.000	0.000
74	A	126	VAL	0	-0.005	0.002	22.786	0.021	0.021	0.000	0.000	0.000	0.000
75	A	127	VAL	0	0.041	0.028	18.395	0.025	0.025	0.000	0.000	0.000	0.000
76	A	128	ASN	0	0.001	0.011	18.985	0.015	0.015	0.000	0.000	0.000	0.000
77	A	129	GLU	-1	-0.858	-0.908	21.309	-0.136	-0.136	0.000	0.000	0.000	0.000
78	A	130	LEU	0	-0.080	-0.042	21.289	0.021	0.021	0.000	0.000	0.000	0.000
79	A	131	PHE	0	-0.010	-0.017	18.183	0.025	0.025	0.000	0.000	0.000	0.000
80	A	132	ARG	1	0.910	0.975	21.753	0.105	0.105	0.000	0.000	0.000	0.000
81	A	133	ASP	-1	-0.893	-0.931	24.565	-0.094	-0.094	0.000	0.000	0.000	0.000
82	A	134	GLY	0	0.007	0.007	20.542	0.012	0.012	0.000	0.000	0.000	0.000
83	A	135	VAL	0	-0.033	-0.017	15.782	0.015	0.015	0.000	0.000	0.000	0.000
84	A	136	ASN	0	0.020	0.016	19.009	0.019	0.019	0.000	0.000	0.000	0.000
85	A	137	TRP	0	0.114	0.041	15.109	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	138	GLY	0	0.040	0.034	20.134	0.004	0.004	0.000	0.000	0.000	0.000
87	A	139	ARG	1	0.792	0.882	20.897	0.064	0.064	0.000	0.000	0.000	0.000
88	A	140	ILE	0	0.040	0.027	15.531	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	141	VAL	0	0.005	0.008	18.491	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	142	ALA	0	-0.040	-0.017	20.960	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	143	PHE	0	0.002	0.001	14.836	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	144	PHE	0	0.004	-0.005	13.258	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	145	SER	0	-0.005	-0.009	19.127	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	146	PHE	0	-0.004	0.002	21.788	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	147	GLY	0	0.040	0.002	19.839	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	148	GLY	0	0.018	-0.008	20.920	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	149	ALA	0	0.011	0.003	22.358	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	150	LEU	0	-0.004	0.008	22.279	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	151	CYS	0	-0.082	-0.031	21.042	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	152	VAL	0	0.028	0.011	23.754	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	153	GLU	-1	-0.838	-0.925	27.063	-0.081	-0.081	0.000	0.000	0.000	0.000
102	A	154	SER	0	-0.084	-0.058	25.535	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	155	VAL	0	-0.053	-0.033	26.243	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	156	ASP	-1	-0.800	-0.871	28.785	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	157	LYS	1	0.767	0.885	29.488	0.102	0.102	0.000	0.000	0.000	0.000
106	A	158	GLU	-1	-0.911	-0.946	31.850	-0.052	-0.052	0.000	0.000	0.000	0.000
107	A	159	MET	0	-0.086	-0.031	28.270	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	160	GLN	0	0.099	0.038	26.285	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	161	VAL	0	-0.032	-0.022	24.430	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	162	LEU	0	-0.015	-0.003	22.697	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	163	VAL	0	0.036	0.031	20.280	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	164	SER	0	0.024	0.005	17.681	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	165	ARG	1	0.865	0.927	16.791	0.214	0.214	0.000	0.000	0.000	0.000
114	A	166	ILE	0	0.026	0.020	17.451	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	167	ALA	0	0.049	0.025	14.506	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	168	SER	0	-0.098	-0.051	12.816	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	169	TRP	0	0.025	0.006	13.128	-0.066	-0.066	0.000	0.000	0.000	0.000
118	A	170	MET	0	0.018	0.037	14.432	-0.062	-0.062	0.000	0.000	0.000	0.000
119	A	171	ALA	0	0.017	0.011	9.200	0.030	0.030	0.000	0.000	0.000	0.000
120	A	172	THR	0	-0.044	-0.020	9.707	-0.091	-0.091	0.000	0.000	0.000	0.000
121	A	173	TYR	0	-0.009	-0.028	10.571	-0.147	-0.147	0.000	0.000	0.000	0.000
122	A	174	LEU	0	-0.012	0.001	9.844	-0.053	-0.053	0.000	0.000	0.000	0.000
123	A	175	ASN	0	-0.018	-0.029	6.150	0.805	0.805	0.000	0.000	0.000	0.000
124	A	176	ASP	-1	-0.920	-0.930	7.532	-1.456	-1.456	0.000	0.000	0.000	0.000
125	A	177	HIS	1	0.752	0.834	9.729	0.765	0.765	0.000	0.000	0.000	0.000
126	A	178	LEU	0	-0.024	0.006	11.405	0.071	0.071	0.000	0.000	0.000	0.000
127	A	179	GLU	-1	-0.757	-0.872	6.020	1.368	1.368	0.000	0.000	0.000	0.000
128	A	180	PRO	0	0.003	0.008	9.353	0.151	0.151	0.000	0.000	0.000	0.000
129	A	181	TRP	0	0.051	0.024	10.671	0.103	0.103	0.000	0.000	0.000	0.000
130	A	182	ILE	0	0.006	0.004	11.072	0.038	0.038	0.000	0.000	0.000	0.000
131	A	183	GLN	0	-0.075	-0.060	7.902	0.039	0.039	0.000	0.000	0.000	0.000
132	A	184	GLU	-1	-0.945	-0.948	11.281	0.023	0.023	0.000	0.000	0.000	0.000
133	A	185	ASN	0	-0.146	-0.088	14.310	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	186	GLY	0	0.045	0.034	15.081	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	187	GLY	0	0.006	0.005	12.289	0.088	0.088	0.000	0.000	0.000	0.000
136	A	188	TRP	0	-0.036	-0.061	10.035	-0.233	-0.233	0.000	0.000	0.000	0.000
137	A	189	ASP	-1	-0.902	-0.935	13.569	0.587	0.587	0.000	0.000	0.000	0.000
138	A	190	THR	0	0.048	0.021	15.658	-0.062	-0.062	0.000	0.000	0.000	0.000
139	A	191	PHE	0	-0.053	-0.022	16.531	-0.048	-0.048	0.000	0.000	0.000	0.000
140	A	192	VAL	0	0.001	-0.020	16.483	-0.038	-0.038	0.000	0.000	0.000	0.000
141	A	193	ASP	-1	-0.898	-0.938	19.137	0.267	0.267	0.000	0.000	0.000	0.000
142	A	194	LEU	0	-0.133	-0.063	21.485	-0.032	-0.032	0.000	0.000	0.000	0.000
143	A	195	TYR	0	-0.077	-0.046	21.542	-0.030	-0.030	0.000	0.000	0.000	0.000
144	A	196	GLY	0	-0.019	0.014	21.513	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)