FMO DATABASE

FMODB ID: YV452

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	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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1378331.319798
FMO2-HF: Nuclear repulsion	1322337.506448
FMO2-HF: Total energy	-55993.81335
FMO2-MP2: Total energy	-56159.563737

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.
-8.737	-3.618	8.382	-6.872	-6.631	-0.06

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 : 0.040 / q_NPA : 0.024

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	-0.868	-0.924	3.547	-1.581	0.149	0.002	-0.842	-0.890	0.003
4	A	6	LYS	1	0.871	0.939	4.244	0.899	1.206	-0.001	-0.096	-0.210	0.000
5	A	7	TYR	0	-0.066	-0.062	5.622	0.342	0.342	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.025	-0.014	7.550	0.121	0.121	0.000	0.000	0.000	0.000
7	A	9	PRO	0	0.021	0.026	8.353	0.235	0.235	0.000	0.000	0.000	0.000
8	A	10	GLY	0	-0.011	-0.010	8.897	-0.066	-0.066	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.068	-0.028	10.453	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.850	-0.938	10.956	0.919	0.919	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.818	0.916	12.439	-0.393	-0.393	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.021	0.022	11.446	-0.040	-0.040	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.839	0.907	15.715	-0.165	-0.165	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.945	0.955	18.280	-0.212	-0.212	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.052	0.039	20.414	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.888	-0.953	23.537	0.096	0.096	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.033	0.002	23.465	0.004	0.004	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.882	-0.939	18.346	0.248	0.248	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.024	-0.015	14.371	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.815	-0.908	12.810	0.580	0.580	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.024	0.018	7.311	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.874	0.929	8.828	-0.697	-0.697	0.000	0.000	0.000	0.000
23	A	25	SER	0	-0.099	-0.061	9.837	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.012	-0.011	8.119	-0.164	-0.164	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.023	0.018	7.208	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	28	GLY	0	-0.002	-0.005	7.459	-0.179	-0.179	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.756	0.885	8.668	-0.300	-0.300	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.006	0.003	8.017	-0.072	-0.072	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.013	-0.012	7.921	0.111	0.111	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.025	-0.016	9.883	-0.124	-0.124	0.000	0.000	0.000	0.000
31	A	33	PHE	0	0.042	0.019	7.772	0.075	0.075	0.000	0.000	0.000	0.000
32	A	34	TYR	0	0.009	-0.023	13.395	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.036	0.023	13.956	0.024	0.024	0.000	0.000	0.000	0.000
34	A	36	SER	0	0.022	-0.014	19.051	0.001	0.001	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.041	0.020	22.546	0.005	0.005	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.019	-0.038	25.615	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	39	TRP	0	-0.002	-0.006	26.829	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.023	0.014	26.732	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.020	-0.003	29.583	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.002	-0.012	28.701	0.002	0.002	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.056	0.022	26.016	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.868	0.944	27.369	0.008	0.008	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.010	0.016	30.194	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.016	-0.004	21.457	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	THR	0	0.062	0.017	24.033	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.014	0.006	25.523	0.004	0.004	0.000	0.000	0.000	0.000
47	A	49	GLN	0	0.007	0.002	26.705	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.016	0.004	19.222	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.002	-0.003	22.522	0.004	0.004	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.900	-0.937	24.573	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	53	PHE	0	-0.006	-0.011	19.329	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.029	-0.055	17.190	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.925	-0.960	21.380	0.052	0.052	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.732	0.862	24.158	0.015	0.015	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.009	-0.013	20.639	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.831	0.906	17.701	-0.073	-0.073	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.866	-0.915	17.092	0.102	0.102	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.005	-0.009	18.745	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.765	0.887	18.057	0.022	0.022	0.000	0.000	0.000	0.000
60	A	62	ASN	0	-0.021	-0.010	12.748	0.000	0.000	0.000	0.000	0.000	0.000
61	A	63	PHE	0	-0.027	-0.004	12.722	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.775	-0.856	11.962	0.198	0.198	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.017	-0.006	13.304	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.044	0.017	11.321	0.042	0.042	0.000	0.000	0.000	0.000
65	A	67	PHE	0	-0.013	0.000	14.506	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	68	CYS	0	-0.060	-0.031	14.642	0.015	0.015	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.016	0.003	17.326	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	70	TRP	0	0.011	-0.011	19.777	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.797	-0.862	23.349	0.002	0.002	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.932	-0.974	25.196	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.938	-0.967	27.226	0.014	0.014	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.921	-0.964	25.648	0.073	0.073	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.872	-0.941	27.920	0.041	0.041	0.000	0.000	0.000	0.000
74	A	76	GLY	0	-0.013	0.000	29.685	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.008	-0.017	20.797	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	ALA	0	0.029	0.016	25.529	0.003	0.003	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.026	0.015	26.983	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.084	-0.046	24.597	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.027	-0.010	20.191	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.001	0.003	24.532	0.005	0.005	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.777	0.887	26.787	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.033	0.004	22.093	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	85	PRO	0	-0.006	0.015	21.912	0.009	0.009	0.000	0.000	0.000	0.000
84	A	86	TRP	0	-0.015	-0.007	17.566	0.004	0.004	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.002	-0.004	13.345	0.014	0.014	0.000	0.000	0.000	0.000
86	A	88	ALA	0	-0.016	-0.006	17.055	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	89	VAL	0	0.008	0.005	13.769	0.043	0.043	0.000	0.000	0.000	0.000
88	A	90	PRO	0	0.006	0.002	16.337	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	91	PHE	0	0.040	0.045	19.308	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.029	0.022	21.285	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	93	GLN	0	-0.019	-0.015	16.010	0.016	0.016	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.034	-0.006	17.386	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.856	-0.915	18.996	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.029	-0.011	13.543	-0.027	-0.027	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.050	0.032	14.725	-0.050	-0.050	0.000	0.000	0.000	0.000
96	A	98	GLN	0	0.021	0.028	16.369	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.836	0.903	15.379	0.013	0.013	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.004	0.018	10.596	-0.044	-0.044	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.005	-0.033	13.847	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.932	0.974	17.053	0.128	0.128	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.034	-0.015	10.416	-0.082	-0.082	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.030	-0.024	9.703	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.073	-0.032	15.232	0.021	0.021	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.006	0.004	17.220	0.014	0.014	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.892	-0.941	19.998	-0.095	-0.095	0.000	0.000	0.000	0.000
106	A	108	SER	0	-0.039	-0.017	23.168	0.013	0.013	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.023	0.027	21.767	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	110	PRO	0	-0.077	-0.043	23.184	0.006	0.006	0.000	0.000	0.000	0.000
109	A	111	THR	0	-0.016	-0.037	18.222	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.045	-0.020	16.562	0.007	0.007	0.000	0.000	0.000	0.000
111	A	113	ILE	0	-0.008	0.007	12.326	0.002	0.002	0.000	0.000	0.000	0.000
112	A	114	GLY	0	-0.003	0.004	11.628	0.013	0.013	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.009	-0.011	6.436	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.784	-0.865	5.540	-0.475	-0.475	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.029	-0.004	4.177	-1.013	-0.788	0.000	-0.095	-0.130	0.000
116	A	118	ASP	-1	-0.826	-0.909	2.428	-0.255	1.115	2.285	-2.110	-1.545	-0.021
117	A	119	SER	0	-0.053	-0.066	2.318	-5.714	-3.749	2.092	-1.876	-2.182	-0.026
118	A	120	GLY	0	0.021	0.014	2.633	-1.459	-1.046	3.805	-2.583	-1.636	-0.015
119	A	121	ASP	-1	-0.935	-0.948	3.259	0.424	-0.467	0.199	0.730	-0.038	-0.001
120	A	122	VAL	0	-0.050	-0.034	6.747	0.024	0.024	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.014	-0.003	9.314	0.066	0.066	0.000	0.000	0.000	0.000
122	A	124	THR	0	-0.050	-0.044	11.919	0.064	0.064	0.000	0.000	0.000	0.000
123	A	125	THR	0	0.000	-0.031	14.145	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.841	0.898	16.508	0.188	0.188	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.054	0.040	17.138	0.021	0.021	0.000	0.000	0.000	0.000
126	A	128	ARG	1	0.899	0.957	19.171	0.083	0.083	0.000	0.000	0.000	0.000
127	A	129	ALA	0	-0.044	-0.020	21.707	0.013	0.013	0.000	0.000	0.000	0.000
128	A	130	THR	0	-0.018	-0.019	21.143	0.005	0.005	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.033	0.035	20.607	0.007	0.007	0.000	0.000	0.000	0.000
130	A	132	VAL	0	-0.025	-0.019	23.539	0.007	0.007	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.849	0.920	26.469	0.058	0.058	0.000	0.000	0.000	0.000
132	A	134	ASP	-1	-0.740	-0.839	24.044	-0.059	-0.059	0.000	0.000	0.000	0.000
133	A	135	PRO	0	0.042	0.026	24.948	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.776	-0.884	26.393	-0.009	-0.009	0.000	0.000	0.000	0.000
135	A	137	GLY	0	-0.018	-0.007	22.587	0.002	0.002	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.958	-0.985	22.773	-0.042	-0.042	0.000	0.000	0.000	0.000
137	A	139	GLN	0	-0.044	-0.030	23.038	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	140	PHE	0	0.023	0.040	15.683	-0.020	-0.020	0.000	0.000	0.000	0.000
139	A	141	PRO	0	-0.060	-0.037	14.205	0.002	0.002	0.000	0.000	0.000	0.000
140	A	142	TRP	0	-0.034	-0.058	16.546	-0.025	-0.025	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.974	1.003	15.977	0.131	0.131	0.000	0.000	0.000	0.000
142	A	144	ASP	-1	-0.753	-0.825	15.807	-0.217	-0.217	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.034	-0.006	17.699	-0.005	-0.005	0.000	0.000	0.000	0.000

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