FMO DATABASE

FMODB ID: 4J52N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1374648.534508
FMO2-HF: Nuclear repulsion	1318655.443293
FMO2-HF: Total energy	-55993.091215
FMO2-MP2: Total energy	-56158.722687

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.
-11.587	-5.691	7.07	-6.989	-5.974	-0.05

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 : 0.038 / 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	-0.877	-0.938	3.524	-1.878	0.316	-0.002	-1.101	-1.090	0.004
4	A	6	LYS	1	0.914	0.965	4.507	0.480	0.694	-0.001	-0.039	-0.173	0.000
5	A	7	TYR	0	-0.096	-0.082	5.422	0.302	0.302	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.035	-0.021	7.457	0.035	0.035	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.011	0.023	8.844	0.292	0.292	0.000	0.000	0.000	0.000
8	A	10	GLY	0	-0.006	-0.003	9.392	-0.114	-0.114	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.043	-0.013	10.583	-0.123	-0.123	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.918	-0.966	10.463	0.935	0.935	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.902	0.958	12.261	-0.382	-0.382	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.008	0.012	11.306	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.912	0.966	15.487	-0.197	-0.197	0.000	0.000	0.000	0.000
14	A	16	ARG	1	1.019	0.992	18.207	-0.202	-0.202	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.006	0.020	20.251	0.002	0.002	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.891	-0.953	23.955	0.098	0.098	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.065	-0.027	23.219	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.935	-0.984	18.221	0.286	0.286	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.042	-0.017	14.525	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.904	-0.956	12.780	0.604	0.604	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.033	0.014	7.409	-0.041	-0.041	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.978	0.976	8.432	-1.140	-1.140	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.087	-0.042	9.510	-0.118	-0.118	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.023	-0.021	8.126	-0.173	-0.173	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.002	0.006	7.195	-0.115	-0.115	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.003	0.001	7.316	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.847	0.947	8.622	-0.238	-0.238	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.014	0.016	7.868	-0.143	-0.143	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.013	-0.010	7.592	0.152	0.152	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.016	-0.010	9.746	-0.127	-0.127	0.000	0.000	0.000	0.000
31	A	33	PHE	0	0.020	0.005	7.990	0.089	0.089	0.000	0.000	0.000	0.000
32	A	34	TYR	0	-0.002	-0.033	13.396	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.034	0.022	14.145	0.026	0.026	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.030	-0.006	19.136	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.053	0.023	22.673	0.006	0.006	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.050	-0.065	25.579	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.025	-0.015	26.720	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.023	0.013	26.215	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	41	PRO	0	-0.009	-0.015	29.334	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.001	-0.010	28.511	0.002	0.002	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.063	0.021	25.983	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.934	0.984	27.472	0.007	0.007	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.030	0.017	30.353	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.020	0.000	21.641	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	47	THR	0	0.065	0.026	24.099	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.012	0.004	25.392	0.002	0.002	0.000	0.000	0.000	0.000
47	A	49	GLN	0	0.002	-0.003	26.664	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.014	0.008	19.141	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.000	-0.010	22.550	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.912	-0.945	24.413	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.027	-0.020	19.217	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.070	-0.072	17.043	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.907	-0.959	21.223	0.025	0.025	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.793	0.915	24.058	0.035	0.035	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.028	-0.023	20.645	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.870	0.951	17.421	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.922	-0.964	17.167	0.041	0.041	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.007	-0.009	18.537	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.880	0.944	17.707	0.071	0.071	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.012	0.007	12.498	0.015	0.015	0.000	0.000	0.000	0.000
61	A	63	PHE	0	-0.023	-0.010	12.632	-0.038	-0.038	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.831	-0.892	11.913	0.159	0.159	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.026	-0.014	13.105	-0.064	-0.064	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.033	0.009	11.285	0.050	0.050	0.000	0.000	0.000	0.000
65	A	67	PHE	0	-0.026	-0.024	14.407	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	68	CYS	0	-0.055	-0.024	14.620	0.028	0.028	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.036	0.007	17.310	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	70	TRP	0	0.008	-0.014	19.788	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.824	-0.871	23.323	0.011	0.011	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.916	-0.965	25.055	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.961	-0.968	27.431	0.028	0.028	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.934	-0.970	26.472	0.092	0.092	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.874	-0.941	28.036	0.053	0.053	0.000	0.000	0.000	0.000
74	A	76	GLY	0	-0.022	-0.005	29.834	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.009	-0.018	20.904	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	78	ALA	0	0.022	0.008	25.725	0.001	0.001	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.010	0.007	27.103	0.001	0.001	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.114	-0.075	24.363	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.037	-0.006	20.165	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.025	0.024	24.431	0.002	0.002	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.832	0.923	27.028	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.052	0.004	22.112	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	85	PRO	0	0.008	0.015	21.875	0.010	0.010	0.000	0.000	0.000	0.000
84	A	86	TRP	0	-0.035	-0.013	17.341	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.019	-0.017	13.337	0.022	0.022	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.001	0.006	17.033	-0.040	-0.040	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.000	0.008	13.535	0.053	0.053	0.000	0.000	0.000	0.000
88	A	90	PRO	0	-0.006	-0.005	16.116	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	91	PHE	0	0.051	0.038	19.118	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.039	0.026	21.256	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	93	GLN	0	-0.013	-0.010	15.955	0.002	0.002	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.050	0.000	17.278	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.933	-0.959	19.100	0.060	0.060	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.037	-0.020	13.578	-0.027	-0.027	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.047	0.030	14.696	-0.048	-0.048	0.000	0.000	0.000	0.000
96	A	98	GLN	0	0.021	0.016	16.417	-0.039	-0.039	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.930	0.955	15.313	-0.044	-0.044	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.014	0.026	10.566	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	101	SER	0	0.002	-0.012	14.003	-0.044	-0.044	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.951	0.987	17.194	0.094	0.094	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.073	-0.030	10.073	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.028	-0.027	9.760	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.030	-0.006	15.205	0.023	0.023	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.004	0.002	17.213	0.008	0.008	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.936	-0.964	19.933	-0.088	-0.088	0.000	0.000	0.000	0.000
106	A	108	SER	0	-0.066	-0.030	23.388	0.015	0.015	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.004	0.041	21.702	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	110	PRO	0	-0.065	-0.057	22.942	0.007	0.007	0.000	0.000	0.000	0.000
109	A	111	THR	0	-0.004	-0.019	17.862	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.054	-0.023	16.406	0.011	0.011	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.002	0.008	11.779	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	114	GLY	0	-0.008	0.011	11.500	0.015	0.015	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.001	-0.008	6.112	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.803	-0.883	5.910	-0.900	-0.900	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.029	-0.014	4.002	-1.384	-1.011	0.001	-0.159	-0.216	-0.001
116	A	118	ASP	-1	-0.841	-0.917	2.193	-2.269	-1.921	5.011	-3.283	-2.075	-0.028
117	A	119	SER	0	-0.062	-0.049	2.690	-4.244	-1.964	0.732	-1.507	-1.505	-0.017
118	A	120	GLY	0	0.015	0.006	2.895	-1.216	-0.454	1.228	-1.130	-0.860	-0.007
119	A	121	ASP	-1	-0.957	-0.951	3.440	-0.151	-0.426	0.101	0.230	-0.055	-0.001
120	A	122	VAL	0	-0.028	-0.026	6.957	0.025	0.025	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.009	0.006	9.394	0.076	0.076	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.059	-0.047	11.862	0.081	0.081	0.000	0.000	0.000	0.000
123	A	125	THR	0	0.000	-0.026	14.081	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.858	0.919	16.283	0.234	0.234	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.077	0.045	17.263	0.024	0.024	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.923	0.978	19.180	0.098	0.098	0.000	0.000	0.000	0.000
127	A	129	ALA	0	-0.045	-0.027	21.742	0.015	0.015	0.000	0.000	0.000	0.000
128	A	130	THR	0	-0.024	-0.025	20.931	0.007	0.007	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.030	0.029	20.570	0.008	0.008	0.000	0.000	0.000	0.000
130	A	132	VAL	0	-0.032	-0.021	23.315	0.009	0.009	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.883	0.938	26.422	0.080	0.080	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.767	-0.853	24.029	-0.095	-0.095	0.000	0.000	0.000	0.000
133	A	135	PRO	0	0.033	0.026	25.007	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.801	-0.917	26.077	-0.037	-0.037	0.000	0.000	0.000	0.000
135	A	137	GLY	0	-0.058	-0.024	22.765	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.963	-0.988	22.797	-0.074	-0.074	0.000	0.000	0.000	0.000
137	A	139	GLN	0	-0.064	-0.043	22.909	-0.016	-0.016	0.000	0.000	0.000	0.000
138	A	140	PHE	0	-0.001	0.038	15.184	-0.023	-0.023	0.000	0.000	0.000	0.000
139	A	141	PRO	0	-0.062	-0.038	14.597	0.004	0.004	0.000	0.000	0.000	0.000
140	A	142	TRP	0	-0.038	-0.066	16.485	-0.029	-0.029	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.962	0.991	15.310	0.235	0.235	0.000	0.000	0.000	0.000
142	A	144	ASP	-1	-0.746	-0.842	15.980	-0.259	-0.259	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.040	-0.012	17.788	-0.012	-0.012	0.000	0.000	0.000	0.000

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