FMO DATABASE

FMODB ID: K29L3

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	OptH
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	-1200006.710377
FMO2-HF: Nuclear repulsion	1143243.572868
FMO2-HF: Total energy	-56763.137508
FMO2-MP2: Total energy	-56927.06108

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.
-1.659	-0.662	-0.014	-0.395	-0.588	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 : -0.006 / q_NPA : -0.014

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	-0.013	-0.001	3.805	-0.052	0.945	-0.014	-0.395	-0.588
4	A	2	PRO	0	0.007	0.005	6.368	0.408	0.408	0.000	0.000	0.000
5	A	3	SER	0	-0.027	-0.009	9.558	-0.105	-0.105	0.000	0.000	0.000
6	A	4	ILE	0	-0.005	0.011	12.834	0.036	0.036	0.000	0.000	0.000
7	A	5	LYS	1	0.922	0.951	16.307	0.089	0.089	0.000	0.000	0.000
8	A	6	LEU	0	-0.009	0.010	19.482	0.000	0.000	0.000	0.000	0.000
9	A	7	GLN	0	-0.044	-0.027	22.161	0.008	0.008	0.000	0.000	0.000
10	A	8	SER	0	-0.080	-0.088	25.772	-0.001	-0.001	0.000	0.000	0.000
11	A	9	SER	0	-0.001	-0.016	27.980	0.005	0.005	0.000	0.000	0.000
12	A	10	ASP	-1	-0.766	-0.835	30.245	-0.063	-0.063	0.000	0.000	0.000
13	A	11	GLY	0	-0.022	-0.003	30.257	0.006	0.006	0.000	0.000	0.000
14	A	12	GLU	-1	-0.941	-0.965	26.629	-0.060	-0.060	0.000	0.000	0.000
15	A	13	ILE	0	-0.007	-0.011	22.121	-0.008	-0.008	0.000	0.000	0.000
16	A	14	PHE	0	-0.043	-0.026	20.289	0.007	0.007	0.000	0.000	0.000
17	A	15	GLU	-1	-0.928	-0.962	15.346	-0.092	-0.092	0.000	0.000	0.000
18	A	16	VAL	0	-0.023	-0.022	14.667	-0.004	-0.004	0.000	0.000	0.000
19	A	17	ASP	-1	-0.840	-0.915	8.946	-0.850	-0.850	0.000	0.000	0.000
20	A	18	VAL	0	0.007	-0.012	10.071	0.043	0.043	0.000	0.000	0.000
21	A	19	GLU	-1	-0.936	-0.980	7.289	-1.256	-1.256	0.000	0.000	0.000
22	A	20	ILE	0	-0.033	-0.009	11.039	0.090	0.090	0.000	0.000	0.000
23	A	21	ALA	0	0.009	-0.005	13.262	0.069	0.069	0.000	0.000	0.000
24	A	22	LYS	1	0.856	0.942	14.012	0.421	0.421	0.000	0.000	0.000
25	A	23	GLN	0	-0.006	-0.007	14.252	0.059	0.059	0.000	0.000	0.000
26	A	24	SER	0	-0.082	-0.041	17.606	0.033	0.033	0.000	0.000	0.000
27	A	25	VAL	0	0.049	0.015	20.212	-0.015	-0.015	0.000	0.000	0.000
28	A	26	THR	0	-0.019	-0.040	22.064	0.000	0.000	0.000	0.000	0.000
29	A	27	ILE	0	0.034	0.005	19.241	0.007	0.007	0.000	0.000	0.000
30	A	28	LYS	1	0.850	0.925	16.899	0.260	0.260	0.000	0.000	0.000
31	A	29	THR	0	-0.047	-0.039	19.781	0.003	0.003	0.000	0.000	0.000
32	A	30	MET	0	-0.023	-0.020	23.011	0.010	0.010	0.000	0.000	0.000
33	A	31	LEU	0	-0.023	-0.007	17.101	0.002	0.002	0.000	0.000	0.000
34	A	32	GLU	-1	-0.916	-0.955	17.258	-0.269	-0.269	0.000	0.000	0.000
35	A	33	ASP	-1	-0.857	-0.904	20.736	-0.143	-0.143	0.000	0.000	0.000
36	A	34	LEU	0	-0.104	-0.046	24.477	0.014	0.014	0.000	0.000	0.000
37	A	35	GLY	0	-0.012	0.015	22.432	0.011	0.011	0.000	0.000	0.000
38	A	36	MET	0	-0.093	-0.053	23.508	0.013	0.013	0.000	0.000	0.000
39	A	37	ASP	-1	-0.786	-0.898	18.364	-0.187	-0.187	0.000	0.000	0.000
40	A	44	PRO	0	-0.042	-0.041	21.966	0.013	0.013	0.000	0.000	0.000
41	A	45	VAL	0	-0.009	-0.006	21.340	0.007	0.007	0.000	0.000	0.000
42	A	46	PRO	0	-0.029	0.004	24.047	0.002	0.002	0.000	0.000	0.000
43	A	47	LEU	0	0.021	-0.005	23.844	-0.005	-0.005	0.000	0.000	0.000
44	A	48	PRO	0	0.021	0.001	28.272	0.004	0.004	0.000	0.000	0.000
45	A	49	ASN	0	-0.036	-0.023	30.639	0.003	0.003	0.000	0.000	0.000
46	A	50	VAL	0	-0.003	0.010	26.792	-0.001	-0.001	0.000	0.000	0.000
47	A	51	ASN	0	0.034	0.040	29.539	-0.003	-0.003	0.000	0.000	0.000
48	A	52	ALA	0	0.098	0.024	27.568	-0.009	-0.009	0.000	0.000	0.000
49	A	53	ALA	0	-0.083	-0.036	26.944	-0.007	-0.007	0.000	0.000	0.000
50	A	54	ILE	0	0.058	0.025	27.394	-0.008	-0.008	0.000	0.000	0.000
51	A	55	LEU	0	0.035	0.022	22.808	-0.010	-0.010	0.000	0.000	0.000
52	A	56	LYS	1	0.914	0.961	23.000	0.060	0.060	0.000	0.000	0.000
53	A	57	LYS	1	0.820	0.913	22.617	0.083	0.083	0.000	0.000	0.000
54	A	58	VAL	0	0.052	0.018	21.529	-0.011	-0.011	0.000	0.000	0.000
55	A	59	ILE	0	0.045	0.034	17.611	-0.021	-0.021	0.000	0.000	0.000
56	A	60	GLN	0	-0.016	0.000	18.144	-0.022	-0.022	0.000	0.000	0.000
57	A	61	TRP	0	-0.008	-0.009	19.129	-0.016	-0.016	0.000	0.000	0.000
58	A	62	CYS	0	0.015	0.003	16.847	-0.004	-0.004	0.000	0.000	0.000
59	A	63	THR	0	-0.014	-0.013	13.836	-0.051	-0.051	0.000	0.000	0.000
60	A	64	HIS	1	0.827	0.921	14.565	0.149	0.149	0.000	0.000	0.000
61	A	65	HIS	1	0.738	0.869	16.733	0.206	0.206	0.000	0.000	0.000
62	A	66	LYS	1	0.896	0.959	8.444	0.785	0.785	0.000	0.000	0.000
63	A	67	ASP	-1	-0.904	-0.940	9.899	-0.696	-0.696	0.000	0.000	0.000
64	A	68	ASP	-1	-0.826	-0.917	12.799	-0.182	-0.182	0.000	0.000	0.000
65	A	69	PRO	0	-0.055	-0.029	16.280	-0.006	-0.006	0.000	0.000	0.000
66	A	70	GLY	0	-0.025	0.030	17.570	0.018	0.018	0.000	0.000	0.000
67	A	71	GLY	0	0.017	-0.011	19.206	-0.011	-0.011	0.000	0.000	0.000
68	A	72	SER	0	-0.042	-0.038	22.389	0.004	0.004	0.000	0.000	0.000
69	A	73	GLY	0	0.016	0.016	23.955	-0.002	-0.002	0.000	0.000	0.000
70	A	82	THR	0	-0.048	-0.016	25.807	0.004	0.004	0.000	0.000	0.000
71	A	83	ASP	-1	-0.872	-0.963	28.514	-0.090	-0.090	0.000	0.000	0.000
72	A	84	ASP	-1	-0.955	-0.965	30.552	-0.067	-0.067	0.000	0.000	0.000
73	A	85	ILE	0	-0.021	-0.014	28.272	-0.007	-0.007	0.000	0.000	0.000
74	A	86	PRO	0	0.053	0.044	24.251	0.008	0.008	0.000	0.000	0.000
75	A	87	VAL	0	0.081	0.020	26.420	-0.001	-0.001	0.000	0.000	0.000
76	A	88	TRP	0	0.004	0.001	21.412	-0.001	-0.001	0.000	0.000	0.000
77	A	89	ASP	-1	-0.757	-0.886	23.534	-0.144	-0.144	0.000	0.000	0.000
78	A	90	GLN	0	-0.096	-0.072	26.050	0.008	0.008	0.000	0.000	0.000
79	A	91	GLU	-1	-0.914	-0.973	27.662	-0.057	-0.057	0.000	0.000	0.000
80	A	92	PHE	0	-0.061	-0.014	24.148	0.002	0.002	0.000	0.000	0.000
81	A	93	LEU	0	0.010	0.004	27.330	0.001	0.001	0.000	0.000	0.000
82	A	94	LYS	1	0.883	0.977	30.316	0.062	0.062	0.000	0.000	0.000
83	A	95	VAL	0	-0.057	-0.024	30.956	0.002	0.002	0.000	0.000	0.000
84	A	96	ASP	-1	-0.839	-0.912	33.987	-0.053	-0.053	0.000	0.000	0.000
85	A	97	GLN	0	0.012	-0.040	35.823	-0.004	-0.004	0.000	0.000	0.000
86	A	98	GLY	0	0.013	0.022	37.112	-0.002	-0.002	0.000	0.000	0.000
87	A	99	THR	0	0.026	-0.003	31.326	-0.004	-0.004	0.000	0.000	0.000
88	A	100	LEU	0	0.004	0.001	31.808	-0.006	-0.006	0.000	0.000	0.000
89	A	101	PHE	0	-0.008	-0.004	33.058	-0.005	-0.005	0.000	0.000	0.000
90	A	102	GLU	-1	-0.873	-0.952	32.650	-0.069	-0.069	0.000	0.000	0.000
91	A	103	LEU	0	-0.015	-0.009	27.149	-0.007	-0.007	0.000	0.000	0.000
92	A	104	ILE	0	-0.017	-0.001	29.292	-0.008	-0.008	0.000	0.000	0.000
93	A	105	LEU	0	-0.028	-0.019	31.050	-0.004	-0.004	0.000	0.000	0.000
94	A	106	ALA	0	0.016	0.012	27.596	-0.003	-0.003	0.000	0.000	0.000
95	A	107	ALA	0	0.001	0.002	26.192	-0.009	-0.009	0.000	0.000	0.000
96	A	108	ASN	0	-0.015	-0.009	26.956	-0.008	-0.008	0.000	0.000	0.000
97	A	109	TYR	0	-0.017	0.006	28.035	-0.001	-0.001	0.000	0.000	0.000
98	A	110	LEU	0	-0.024	0.006	23.533	-0.003	-0.003	0.000	0.000	0.000
99	A	111	ASP	-1	-0.890	-0.913	24.015	-0.162	-0.162	0.000	0.000	0.000
100	A	112	ILE	0	0.034	0.012	20.979	-0.017	-0.017	0.000	0.000	0.000
101	A	113	LYS	1	0.925	0.952	23.510	0.136	0.136	0.000	0.000	0.000
102	A	114	GLY	0	0.045	0.022	23.214	0.010	0.010	0.000	0.000	0.000
103	A	115	LEU	0	0.041	0.023	23.524	0.012	0.012	0.000	0.000	0.000
104	A	116	LEU	0	0.046	0.037	25.185	0.013	0.013	0.000	0.000	0.000
105	A	117	ASP	-1	-0.831	-0.912	27.471	-0.107	-0.107	0.000	0.000	0.000
106	A	118	VAL	0	-0.042	-0.018	26.064	0.011	0.011	0.000	0.000	0.000
107	A	119	THR	0	0.006	-0.011	28.396	0.009	0.009	0.000	0.000	0.000
108	A	120	CYS	0	-0.009	-0.005	30.709	0.010	0.010	0.000	0.000	0.000
109	A	121	LYS	1	0.907	0.966	31.623	0.084	0.084	0.000	0.000	0.000
110	A	122	THR	0	-0.018	-0.027	31.471	0.006	0.006	0.000	0.000	0.000
111	A	123	VAL	0	0.034	0.007	34.148	0.006	0.006	0.000	0.000	0.000
112	A	124	ALA	0	0.014	0.004	36.756	0.005	0.005	0.000	0.000	0.000
113	A	125	ASN	0	-0.036	-0.031	34.820	0.005	0.005	0.000	0.000	0.000
114	A	126	MET	0	-0.046	-0.007	37.960	0.002	0.002	0.000	0.000	0.000
115	A	127	ILE	0	0.007	0.014	40.382	0.003	0.003	0.000	0.000	0.000
116	A	128	LYS	1	0.867	0.936	37.727	0.061	0.061	0.000	0.000	0.000
117	A	129	GLY	0	-0.022	-0.010	43.372	0.001	0.001	0.000	0.000	0.000
118	A	130	LYS	1	0.874	0.959	43.439	0.043	0.043	0.000	0.000	0.000
119	A	131	THR	0	-0.009	-0.012	48.348	0.000	0.000	0.000	0.000	0.000
120	A	132	PRO	0	0.082	0.014	50.709	-0.001	-0.001	0.000	0.000	0.000
121	A	133	GLU	-1	-0.847	-0.928	51.381	-0.029	-0.029	0.000	0.000	0.000
122	A	134	GLU	-1	-0.851	-0.912	49.121	-0.031	-0.031	0.000	0.000	0.000
123	A	135	ILE	0	-0.002	0.003	45.995	-0.001	-0.001	0.000	0.000	0.000
124	A	136	ARG	1	0.854	0.928	47.415	0.028	0.028	0.000	0.000	0.000
125	A	137	LYS	1	0.942	0.973	49.468	0.027	0.027	0.000	0.000	0.000
126	A	138	THR	0	-0.053	-0.015	43.285	0.000	0.000	0.000	0.000	0.000
127	A	139	PHE	0	-0.036	-0.019	40.490	-0.001	-0.001	0.000	0.000	0.000
128	A	140	ASN	0	-0.028	-0.002	45.345	0.001	0.001	0.000	0.000	0.000
129	A	141	ILE	0	-0.030	-0.005	47.032	0.000	0.000	0.000	0.000	0.000
130	A	142	LYS	1	0.939	0.966	49.995	0.034	0.034	0.000	0.000	0.000
131	A	143	ASN	0	0.008	-0.007	53.411	-0.001	-0.001	0.000	0.000	0.000
132	A	144	ASP	-1	-0.922	-0.954	55.231	-0.030	-0.030	0.000	0.000	0.000
133	A	145	PHE	0	-0.011	-0.003	54.507	0.000	0.000	0.000	0.000	0.000
134	A	146	THR	0	0.013	0.007	59.023	0.001	0.001	0.000	0.000	0.000
135	A	147	GLU	-1	-0.964	-1.001	62.085	-0.020	-0.020	0.000	0.000	0.000
136	A	148	GLU	-1	-0.957	-0.968	63.838	-0.022	-0.022	0.000	0.000	0.000
137	A	149	GLU	-1	-0.834	-0.936	59.829	-0.024	-0.024	0.000	0.000	0.000
138	A	150	GLU	-1	-0.894	-0.941	57.473	-0.029	-0.029	0.000	0.000	0.000
139	A	151	ALA	0	-0.050	-0.045	59.915	-0.001	-0.001	0.000	0.000	0.000
140	A	152	GLN	0	-0.051	-0.027	59.851	-0.001	-0.001	0.000	0.000	0.000
141	A	153	VAL	0	-0.011	0.008	54.905	-0.001	-0.001	0.000	0.000	0.000
142	A	154	ARG	1	0.841	0.930	56.719	0.025	0.025	0.000	0.000	0.000
143	A	155	LYS	1	0.906	0.968	57.712	0.025	0.025	0.000	0.000	0.000
144	A	156	GLU	-1	-0.958	-0.973	54.834	-0.031	-0.031	0.000	0.000	0.000

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