FMO DATABASE

FMODB ID: 5N2VZ

Calculation Name: 5IBK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IBK

Chain ID: A

ChEMBL ID:

UniProt ID: Q969H0

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1201888.840711
FMO2-HF: Nuclear repulsion	1145124.289391
FMO2-HF: Total energy	-56764.55132
FMO2-MP2: Total energy	-56928.453376

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:GLY)

Summations of interaction energy for fragment #1(A:-1:GLY)

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.
-2.574	-1.633	-0.001	-0.434	-0.507	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / 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].
3	A	1	MET	0	-0.011	-0.001	3.733	-0.845	0.096	-0.001	-0.434	-0.507
4	A	2	PRO	0	-0.005	-0.006	6.149	0.550	0.550	0.000	0.000	0.000
5	A	3	SER	0	-0.047	-0.035	9.310	-0.100	-0.100	0.000	0.000	0.000
6	A	4	ILE	0	-0.019	0.006	12.424	0.027	0.027	0.000	0.000	0.000
7	A	5	LYS	1	0.879	0.918	15.932	0.166	0.166	0.000	0.000	0.000
8	A	6	LEU	0	0.002	0.008	19.387	-0.002	-0.002	0.000	0.000	0.000
9	A	7	GLN	0	-0.059	-0.036	22.231	0.009	0.009	0.000	0.000	0.000
10	A	8	SER	0	0.012	-0.010	25.833	-0.004	-0.004	0.000	0.000	0.000
11	A	9	SER	0	-0.022	-0.012	28.273	0.005	0.005	0.000	0.000	0.000
12	A	10	ASP	-1	-0.856	-0.904	30.263	-0.085	-0.085	0.000	0.000	0.000
13	A	11	GLY	0	0.032	0.011	30.465	0.007	0.007	0.000	0.000	0.000
14	A	12	GLU	-1	-0.822	-0.888	26.221	-0.090	-0.090	0.000	0.000	0.000
15	A	13	ILE	0	-0.021	-0.006	22.306	-0.010	-0.010	0.000	0.000	0.000
16	A	14	PHE	0	-0.029	-0.016	20.309	0.007	0.007	0.000	0.000	0.000
17	A	15	GLU	-1	-0.861	-0.911	14.882	-0.191	-0.191	0.000	0.000	0.000
18	A	16	VAL	0	-0.024	-0.015	14.619	0.012	0.012	0.000	0.000	0.000
19	A	17	ASP	-1	-0.840	-0.916	8.694	-1.079	-1.079	0.000	0.000	0.000
20	A	18	VAL	0	0.007	-0.018	9.863	0.083	0.083	0.000	0.000	0.000
21	A	19	GLU	-1	-0.878	-0.939	7.368	-1.526	-1.526	0.000	0.000	0.000
22	A	20	ILE	0	-0.035	-0.021	11.274	0.117	0.117	0.000	0.000	0.000
23	A	21	ALA	0	-0.005	-0.003	13.596	0.082	0.082	0.000	0.000	0.000
24	A	22	LYS	1	0.817	0.899	14.454	0.523	0.523	0.000	0.000	0.000
25	A	23	GLN	0	0.004	-0.004	14.339	0.067	0.067	0.000	0.000	0.000
26	A	24	SER	0	-0.084	-0.046	17.847	0.039	0.039	0.000	0.000	0.000
27	A	25	VAL	0	0.032	0.006	20.330	-0.022	-0.022	0.000	0.000	0.000
28	A	26	THR	0	-0.024	-0.025	22.303	-0.002	-0.002	0.000	0.000	0.000
29	A	27	ILE	0	0.037	0.005	18.895	0.005	0.005	0.000	0.000	0.000
30	A	28	LYS	1	0.847	0.913	17.680	0.304	0.304	0.000	0.000	0.000
31	A	29	THR	0	-0.064	-0.053	19.934	0.004	0.004	0.000	0.000	0.000
32	A	30	MET	0	-0.018	-0.020	23.267	0.009	0.009	0.000	0.000	0.000
33	A	31	LEU	0	0.001	0.001	17.197	0.001	0.001	0.000	0.000	0.000
34	A	32	GLU	-1	-0.863	-0.893	17.317	-0.367	-0.367	0.000	0.000	0.000
35	A	33	ASP	-1	-0.877	-0.911	21.038	-0.187	-0.187	0.000	0.000	0.000
36	A	34	LEU	0	-0.065	-0.035	24.519	0.019	0.019	0.000	0.000	0.000
37	A	35	GLY	0	-0.017	0.010	22.347	0.012	0.012	0.000	0.000	0.000
38	A	36	MET	0	-0.077	-0.043	23.406	0.013	0.013	0.000	0.000	0.000
39	A	37	ASP	-1	-0.793	-0.904	18.145	-0.275	-0.275	0.000	0.000	0.000
40	A	44	PRO	0	-0.038	-0.036	21.764	0.016	0.016	0.000	0.000	0.000
41	A	45	VAL	0	0.002	0.009	21.342	0.011	0.011	0.000	0.000	0.000
42	A	46	PRO	0	-0.042	-0.005	24.020	0.004	0.004	0.000	0.000	0.000
43	A	47	LEU	0	0.011	-0.008	23.877	-0.003	-0.003	0.000	0.000	0.000
44	A	48	PRO	0	0.015	-0.008	28.342	0.006	0.006	0.000	0.000	0.000
45	A	49	ASN	0	-0.040	-0.031	30.877	0.004	0.004	0.000	0.000	0.000
46	A	50	VAL	0	0.000	0.006	27.152	0.000	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.035	0.037	29.650	-0.004	-0.004	0.000	0.000	0.000
48	A	52	ALA	0	0.053	0.009	27.624	-0.010	-0.010	0.000	0.000	0.000
49	A	53	ALA	0	-0.037	-0.010	27.167	-0.005	-0.005	0.000	0.000	0.000
50	A	54	ILE	0	0.025	0.005	27.656	-0.008	-0.008	0.000	0.000	0.000
51	A	55	LEU	0	0.020	0.018	23.002	-0.011	-0.011	0.000	0.000	0.000
52	A	56	LYS	1	0.769	0.869	23.134	0.080	0.080	0.000	0.000	0.000
53	A	57	LYS	1	0.781	0.906	22.888	0.097	0.097	0.000	0.000	0.000
54	A	58	VAL	0	0.058	0.016	21.609	-0.010	-0.010	0.000	0.000	0.000
55	A	59	ILE	0	0.055	0.042	17.734	-0.022	-0.022	0.000	0.000	0.000
56	A	60	GLN	0	-0.002	0.006	18.373	-0.022	-0.022	0.000	0.000	0.000
57	A	61	TRP	0	-0.015	-0.015	19.260	-0.014	-0.014	0.000	0.000	0.000
58	A	62	CYS	0	0.003	0.000	17.044	0.000	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.033	-0.024	13.839	-0.054	-0.054	0.000	0.000	0.000
60	A	64	HIS	1	0.784	0.893	14.703	0.162	0.162	0.000	0.000	0.000
61	A	65	HIS	1	0.762	0.841	16.818	0.246	0.246	0.000	0.000	0.000
62	A	66	LYS	1	0.811	0.910	7.647	1.167	1.167	0.000	0.000	0.000
63	A	67	ASP	-1	-0.857	-0.920	9.943	-0.784	-0.784	0.000	0.000	0.000
64	A	68	ASP	-1	-0.848	-0.900	12.960	-0.191	-0.191	0.000	0.000	0.000
65	A	69	PRO	0	-0.042	-0.031	16.570	-0.012	-0.012	0.000	0.000	0.000
66	A	70	GLY	0	-0.022	0.008	17.841	0.026	0.026	0.000	0.000	0.000
67	A	71	GLY	0	0.035	-0.003	19.462	-0.019	-0.019	0.000	0.000	0.000
68	A	72	SER	0	-0.070	-0.030	22.412	-0.001	-0.001	0.000	0.000	0.000
69	A	73	GLY	0	0.031	0.023	24.319	0.000	0.000	0.000	0.000	0.000
70	A	82	THR	0	-0.025	-0.020	25.686	0.007	0.007	0.000	0.000	0.000
71	A	83	ASP	-1	-0.828	-0.906	28.469	-0.093	-0.093	0.000	0.000	0.000
72	A	84	ASP	-1	-0.905	-0.928	30.396	-0.074	-0.074	0.000	0.000	0.000
73	A	85	ILE	0	0.006	0.011	28.117	-0.007	-0.007	0.000	0.000	0.000
74	A	86	PRO	0	0.046	0.027	24.083	0.009	0.009	0.000	0.000	0.000
75	A	87	VAL	0	0.059	0.015	26.542	-0.002	-0.002	0.000	0.000	0.000
76	A	88	TRP	0	0.009	0.006	21.311	-0.002	-0.002	0.000	0.000	0.000
77	A	89	ASP	-1	-0.755	-0.863	23.435	-0.160	-0.160	0.000	0.000	0.000
78	A	90	GLN	0	-0.041	-0.026	26.091	0.007	0.007	0.000	0.000	0.000
79	A	91	GLU	-1	-0.859	-0.916	27.620	-0.059	-0.059	0.000	0.000	0.000
80	A	92	PHE	0	-0.045	-0.011	24.551	0.002	0.002	0.000	0.000	0.000
81	A	93	LEU	0	0.023	0.015	27.220	-0.001	-0.001	0.000	0.000	0.000
82	A	94	LYS	1	0.788	0.888	30.505	0.071	0.071	0.000	0.000	0.000
83	A	95	VAL	0	-0.046	-0.017	30.826	0.002	0.002	0.000	0.000	0.000
84	A	96	ASP	-1	-0.792	-0.864	33.973	-0.063	-0.063	0.000	0.000	0.000
85	A	97	GLN	0	0.014	-0.034	35.922	-0.005	-0.005	0.000	0.000	0.000
86	A	98	GLY	0	0.007	0.021	37.449	-0.002	-0.002	0.000	0.000	0.000
87	A	99	THR	0	-0.004	-0.040	31.396	-0.006	-0.006	0.000	0.000	0.000
88	A	100	LEU	0	-0.018	-0.011	32.340	-0.008	-0.008	0.000	0.000	0.000
89	A	101	PHE	0	-0.002	-0.001	33.218	-0.006	-0.006	0.000	0.000	0.000
90	A	102	GLU	-1	-0.830	-0.936	32.490	-0.088	-0.088	0.000	0.000	0.000
91	A	103	LEU	0	-0.010	-0.007	27.105	-0.009	-0.009	0.000	0.000	0.000
92	A	104	ILE	0	-0.014	0.000	29.294	-0.010	-0.010	0.000	0.000	0.000
93	A	105	LEU	0	-0.018	-0.013	31.164	-0.005	-0.005	0.000	0.000	0.000
94	A	106	ALA	0	0.019	0.011	27.687	-0.004	-0.004	0.000	0.000	0.000
95	A	107	ALA	0	-0.003	-0.004	26.282	-0.011	-0.011	0.000	0.000	0.000
96	A	108	ASN	0	-0.025	-0.011	27.151	-0.007	-0.007	0.000	0.000	0.000
97	A	109	TYR	0	-0.020	-0.001	28.365	-0.001	-0.001	0.000	0.000	0.000
98	A	110	LEU	0	-0.004	0.000	23.669	-0.004	-0.004	0.000	0.000	0.000
99	A	111	ASP	-1	-0.868	-0.904	24.214	-0.200	-0.200	0.000	0.000	0.000
100	A	112	ILE	0	0.023	0.020	21.248	-0.020	-0.020	0.000	0.000	0.000
101	A	113	LYS	1	0.872	0.915	23.676	0.150	0.150	0.000	0.000	0.000
102	A	114	GLY	0	0.050	0.029	23.396	0.012	0.012	0.000	0.000	0.000
103	A	115	LEU	0	0.023	0.010	23.664	0.013	0.013	0.000	0.000	0.000
104	A	116	LEU	0	0.034	0.024	25.348	0.015	0.015	0.000	0.000	0.000
105	A	117	ASP	-1	-0.800	-0.880	27.533	-0.126	-0.126	0.000	0.000	0.000
106	A	118	VAL	0	-0.017	-0.002	25.982	0.012	0.012	0.000	0.000	0.000
107	A	119	THR	0	0.015	-0.001	28.536	0.011	0.011	0.000	0.000	0.000
108	A	120	CYS	0	-0.014	-0.010	30.863	0.010	0.010	0.000	0.000	0.000
109	A	121	LYS	1	0.760	0.851	32.043	0.093	0.093	0.000	0.000	0.000
110	A	122	THR	0	-0.025	-0.025	31.611	0.008	0.008	0.000	0.000	0.000
111	A	123	VAL	0	0.026	0.007	34.308	0.006	0.006	0.000	0.000	0.000
112	A	124	ALA	0	0.011	-0.001	36.839	0.005	0.005	0.000	0.000	0.000
113	A	125	ASN	0	-0.033	-0.022	34.835	0.006	0.006	0.000	0.000	0.000
114	A	126	MET	0	-0.007	0.009	38.120	0.003	0.003	0.000	0.000	0.000
115	A	127	ILE	0	0.016	0.024	40.532	0.004	0.004	0.000	0.000	0.000
116	A	128	LYS	1	0.873	0.932	37.679	0.068	0.068	0.000	0.000	0.000
117	A	129	GLY	0	-0.026	-0.007	43.505	0.001	0.001	0.000	0.000	0.000
118	A	130	LYS	1	0.850	0.933	43.354	0.048	0.048	0.000	0.000	0.000
119	A	131	THR	0	-0.013	-0.042	48.748	0.000	0.000	0.000	0.000	0.000
120	A	132	PRO	0	0.070	0.009	50.777	-0.001	-0.001	0.000	0.000	0.000
121	A	133	GLU	-1	-0.805	-0.868	51.618	-0.032	-0.032	0.000	0.000	0.000
122	A	134	GLU	-1	-0.814	-0.878	49.279	-0.034	-0.034	0.000	0.000	0.000
123	A	135	ILE	0	0.004	0.024	46.297	-0.002	-0.002	0.000	0.000	0.000
124	A	136	ARG	1	0.814	0.883	47.719	0.032	0.032	0.000	0.000	0.000
125	A	137	LYS	1	0.858	0.910	49.502	0.030	0.030	0.000	0.000	0.000
126	A	138	THR	0	-0.053	-0.028	43.475	0.000	0.000	0.000	0.000	0.000
127	A	139	PHE	0	-0.020	-0.010	40.594	-0.002	-0.002	0.000	0.000	0.000
128	A	140	ASN	0	-0.046	-0.014	45.538	0.001	0.001	0.000	0.000	0.000
129	A	141	ILE	0	-0.017	0.001	46.970	0.000	0.000	0.000	0.000	0.000
130	A	142	LYS	1	0.808	0.889	50.087	0.041	0.041	0.000	0.000	0.000
131	A	143	ASN	0	0.012	-0.010	53.577	-0.002	-0.002	0.000	0.000	0.000
132	A	144	ASP	-1	-0.828	-0.898	54.284	-0.036	-0.036	0.000	0.000	0.000
133	A	145	PHE	0	-0.070	-0.014	54.404	0.000	0.000	0.000	0.000	0.000
134	A	146	THR	0	0.019	-0.019	59.339	0.001	0.001	0.000	0.000	0.000
135	A	147	GLU	-1	-0.950	-0.993	62.344	-0.023	-0.023	0.000	0.000	0.000
136	A	148	GLU	-1	-0.950	-0.960	64.175	-0.025	-0.025	0.000	0.000	0.000
137	A	149	GLU	-1	-0.778	-0.877	59.947	-0.029	-0.029	0.000	0.000	0.000
138	A	150	GLU	-1	-0.812	-0.881	57.966	-0.032	-0.032	0.000	0.000	0.000
139	A	151	ALA	0	-0.014	-0.015	59.994	0.000	0.000	0.000	0.000	0.000
140	A	152	GLN	0	-0.046	-0.022	60.513	-0.001	-0.001	0.000	0.000	0.000
141	A	153	VAL	0	-0.024	-0.010	54.989	-0.001	-0.001	0.000	0.000	0.000
142	A	154	ARG	1	0.770	0.874	56.487	0.028	0.028	0.000	0.000	0.000
143	A	155	LYS	1	0.788	0.889	58.342	0.031	0.031	0.000	0.000	0.000
144	A	156	GLU	-1	-0.833	-0.893	54.714	-0.033	-0.033	0.000	0.000	0.000

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