FMO DATABASE

FMODB ID: 5J47Z

Calculation Name: 1O8X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O8X

Chain ID: A

ChEMBL ID:

UniProt ID: O96438

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:

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1375549.169236
FMO2-HF: Nuclear repulsion	1319555.48541
FMO2-HF: Total energy	-55993.683826
FMO2-MP2: Total energy	-56159.41923

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:3:GLY)

Summations of interaction energy for fragment #1(A:3: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.
-9.728	-4.071	7.126	-6.868	-5.916	-0.051

Interaction energy analysis for fragmet #1(A:3:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.025

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	5	ASP	-1	-0.889	-0.942	3.364	-1.980	0.097	-0.002	-1.023	-1.052	0.003
4	A	6	LYS	1	0.890	0.952	4.448	0.808	1.029	-0.001	-0.041	-0.179	0.000
5	A	7	TYR	0	-0.065	-0.059	5.469	0.375	0.375	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.035	-0.020	7.457	0.097	0.097	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.015	0.024	8.664	0.275	0.275	0.000	0.000	0.000	0.000
8	A	10	GLY	0	-0.007	-0.002	9.214	-0.070	-0.070	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.049	-0.016	10.407	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.841	-0.926	10.463	0.975	0.975	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.830	0.915	12.261	-0.418	-0.418	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.015	0.018	11.289	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.871	0.931	15.487	-0.183	-0.183	0.000	0.000	0.000	0.000
14	A	16	ARG	1	1.017	0.993	18.195	-0.216	-0.216	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.011	0.019	20.238	0.002	0.002	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.878	-0.944	23.943	0.096	0.096	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.068	-0.033	23.219	0.001	0.001	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.899	-0.947	18.200	0.263	0.263	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.039	-0.019	14.696	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.823	-0.912	12.757	0.641	0.641	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.027	0.018	7.372	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.880	0.925	8.496	-0.886	-0.886	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.095	-0.053	9.551	-0.092	-0.092	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.023	-0.018	8.058	-0.180	-0.180	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.001	0.007	7.334	-0.086	-0.086	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.000	-0.003	7.292	-0.161	-0.161	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.788	0.915	8.619	-0.322	-0.322	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.000	0.008	7.864	-0.112	-0.112	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.018	-0.009	7.699	0.139	0.139	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.016	-0.012	9.740	-0.134	-0.134	0.000	0.000	0.000	0.000
31	A	33	PHE	0	0.026	0.009	7.845	0.087	0.087	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.012	-0.019	13.390	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.034	0.020	14.101	0.025	0.025	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.022	-0.015	19.131	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.056	0.026	22.667	0.004	0.004	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.027	-0.040	25.572	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.015	-0.016	26.740	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.017	0.019	26.280	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.010	-0.008	29.328	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	PRO	0	-0.002	-0.010	28.435	0.002	0.002	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.061	0.020	26.059	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.881	0.963	27.466	0.009	0.009	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.035	0.021	30.347	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.018	-0.001	21.595	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	THR	0	0.062	0.017	24.041	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.020	0.006	25.385	0.003	0.003	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.001	-0.002	26.634	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.016	0.007	19.117	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.000	-0.011	22.545	0.003	0.003	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.890	-0.930	24.406	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.016	-0.012	19.269	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.038	-0.062	17.090	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.911	-0.946	21.216	0.044	0.044	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.741	0.875	24.051	0.024	0.024	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.022	-0.029	20.654	0.001	0.001	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.803	0.899	17.485	-0.066	-0.066	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.850	-0.918	17.161	0.083	0.083	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.023	-0.014	18.532	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.797	0.907	17.816	0.046	0.046	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.023	0.003	12.340	0.005	0.005	0.000	0.000	0.000	0.000
61	A	63	PHE	0	-0.012	-0.003	12.626	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.809	-0.883	11.947	0.197	0.197	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.008	0.000	13.098	-0.059	-0.059	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.032	0.009	11.260	0.048	0.048	0.000	0.000	0.000	0.000
65	A	67	PHE	0	-0.028	-0.020	14.398	-0.049	-0.049	0.000	0.000	0.000	0.000
66	A	68	CYS	0	-0.062	-0.030	14.612	0.022	0.022	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.049	0.017	17.310	-0.022	-0.022	0.000	0.000	0.000	0.000
68	A	70	TRP	0	-0.007	-0.022	19.791	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.823	-0.887	23.323	0.005	0.005	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.908	-0.963	25.055	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.961	-0.966	27.431	0.019	0.019	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.918	-0.968	26.009	0.080	0.080	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.873	-0.940	28.036	0.046	0.046	0.000	0.000	0.000	0.000
74	A	76	GLY	0	-0.026	-0.008	29.834	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.013	-0.019	20.937	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	78	ALA	0	0.024	0.013	25.714	0.003	0.003	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.020	0.008	27.103	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.116	-0.073	24.576	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.038	-0.002	20.129	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.020	0.022	24.421	0.004	0.004	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.828	0.923	27.017	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.066	-0.011	22.143	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	85	PRO	0	0.006	0.015	21.802	0.009	0.009	0.000	0.000	0.000	0.000
84	A	86	TRP	0	-0.024	-0.010	17.425	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.011	-0.008	13.334	0.018	0.018	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.002	0.002	17.007	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.004	0.006	13.548	0.051	0.051	0.000	0.000	0.000	0.000
88	A	90	PRO	0	-0.003	-0.002	16.116	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	91	PHE	0	0.048	0.040	19.118	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.036	0.029	21.264	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	93	GLN	0	-0.032	-0.018	16.078	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.060	0.002	17.278	-0.017	-0.017	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.859	-0.921	19.100	0.007	0.007	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.031	-0.016	13.582	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.057	0.034	14.696	-0.050	-0.050	0.000	0.000	0.000	0.000
96	A	98	GLN	0	0.005	0.015	16.417	-0.037	-0.037	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.844	0.914	15.483	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.020	0.027	10.568	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.010	-0.026	14.003	-0.036	-0.036	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.953	0.986	17.194	0.120	0.120	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.043	-0.017	10.561	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.043	-0.037	9.605	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.076	-0.026	15.207	0.020	0.020	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.009	-0.003	17.183	0.011	0.011	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.884	-0.937	19.935	-0.102	-0.102	0.000	0.000	0.000	0.000
106	A	108	SER	0	-0.033	-0.016	23.443	0.014	0.014	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.038	0.025	21.732	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	110	PRO	0	-0.062	-0.055	22.899	0.007	0.007	0.000	0.000	0.000	0.000
109	A	111	THR	0	-0.010	-0.019	17.825	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.056	-0.024	16.408	0.010	0.010	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.006	0.005	11.885	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	114	GLY	0	-0.012	0.013	11.498	0.014	0.014	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.005	-0.008	6.268	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.784	-0.859	5.784	-0.695	-0.695	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.041	-0.016	4.004	-1.363	-0.989	0.001	-0.160	-0.215	-0.001
116	A	118	ASP	-1	-0.822	-0.906	2.185	-1.307	-0.986	5.095	-3.329	-2.087	-0.029
117	A	119	SER	0	-0.055	-0.064	2.688	-4.277	-2.035	0.715	-1.455	-1.502	-0.017
118	A	120	GLY	0	0.002	-0.001	2.891	-1.170	-0.445	1.219	-1.096	-0.848	-0.006
119	A	121	ASP	-1	-0.947	-0.948	3.435	-0.061	-0.364	0.099	0.236	-0.033	-0.001
120	A	122	VAL	0	-0.039	-0.032	6.951	0.030	0.030	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.010	0.004	9.393	0.078	0.078	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.052	-0.047	11.867	0.073	0.073	0.000	0.000	0.000	0.000
123	A	125	THR	0	0.001	-0.034	14.083	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.844	0.904	16.285	0.219	0.219	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.070	0.043	17.214	0.023	0.023	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.913	0.966	19.180	0.092	0.092	0.000	0.000	0.000	0.000
127	A	129	ALA	0	-0.038	-0.017	21.741	0.015	0.015	0.000	0.000	0.000	0.000
128	A	130	THR	0	-0.017	-0.023	20.957	0.007	0.007	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.023	0.027	20.555	0.008	0.008	0.000	0.000	0.000	0.000
130	A	132	VAL	0	-0.030	-0.021	23.313	0.008	0.008	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.878	0.938	26.425	0.071	0.071	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.755	-0.845	23.986	-0.076	-0.076	0.000	0.000	0.000	0.000
133	A	135	PRO	0	0.040	0.028	25.006	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.776	-0.889	26.075	-0.021	-0.021	0.000	0.000	0.000	0.000
135	A	137	GLY	0	-0.028	-0.021	22.757	0.001	0.001	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.958	-0.986	22.798	-0.057	-0.057	0.000	0.000	0.000	0.000
137	A	139	GLN	0	-0.056	-0.038	22.911	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	140	PHE	0	0.006	0.037	15.357	-0.023	-0.023	0.000	0.000	0.000	0.000
139	A	141	PRO	0	-0.060	-0.035	14.512	0.005	0.005	0.000	0.000	0.000	0.000
140	A	142	TRP	0	-0.038	-0.063	16.487	-0.029	-0.029	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.980	1.003	15.573	0.185	0.185	0.000	0.000	0.000	0.000
142	A	144	ASP	-1	-0.755	-0.831	16.014	-0.248	-0.248	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.029	-0.006	17.795	-0.010	-0.010	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLY)