FMO DATABASE

FMODB ID: Z2JRN

Calculation Name: 7C33-D-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7C33

Chain ID: D

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-03-24

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandCharge	APR=-2
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1715935.548883
FMO2-HF: Nuclear repulsion	1651512.921026
FMO2-HF: Total energy	-64422.627856
FMO2-MP2: Total energy	-64610.281234

3D Structure

Snapshot

Ligand structure

APR

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.
-420.226	-396.670	149.778	-58.751	-114.586	-0.333

Interactive mode: IFIE and PIEDA for fragment #166(D:201:APR )

Summations of interaction energy for fragment #166(D:201:APR )

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.
-420.226	-396.67	149.778	-58.751	-114.586	0.333

Interaction energy analysis for fragmet #166(D:201:APR )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -2 / q_Mulliken : -1.667 / q_NPA : -1.789

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].
1	D	4	ASN	0	-0.011	-0.007	15.409	1.047	1.047	0.000	0.000	0.000	0.000
2	D	5	SER	0	-0.005	0.000	16.130	-0.947	-0.947	0.000	0.000	0.000	0.000
3	D	6	PHE	0	-0.003	0.005	10.302	0.462	0.462	0.000	0.000	0.000	0.000
4	D	7	SER	0	0.018	0.004	13.020	-1.323	-1.323	0.000	0.000	0.000	0.000
5	D	8	GLY	0	0.018	0.002	12.303	1.673	1.673	0.000	0.000	0.000	0.000
6	D	9	TYR	0	-0.063	-0.049	8.080	1.477	1.477	0.000	0.000	0.000	0.000
7	D	10	LEU	0	-0.005	0.008	12.116	-1.860	-1.860	0.000	0.000	0.000	0.000
8	D	11	LYS	1	0.840	0.900	13.637	-23.794	-23.794	0.000	0.000	0.000	0.000
9	D	12	LEU	0	-0.013	0.011	12.196	-0.577	-0.577	0.000	0.000	0.000	0.000
10	D	13	THR	0	0.041	0.007	16.471	-0.996	-0.996	0.000	0.000	0.000	0.000
11	D	14	ASP	-1	-0.889	-0.939	18.418	24.293	24.293	0.000	0.000	0.000	0.000
12	D	15	ASN	0	-0.041	-0.020	16.524	-1.462	-1.462	0.000	0.000	0.000	0.000
13	D	16	VAL	0	0.029	0.024	11.976	1.850	1.850	0.000	0.000	0.000	0.000
14	D	17	TYR	0	-0.004	0.000	12.426	-2.064	-2.064	0.000	0.000	0.000	0.000
15	D	18	ILE	0	0.033	0.025	8.138	3.207	3.207	0.000	0.000	0.000	0.000
16	D	19	LYS	1	0.849	0.905	7.576	-38.639	-38.639	0.000	0.000	0.000	0.000
17	D	20	ASN	0	-0.055	-0.026	6.047	0.910	0.910	0.000	0.000	0.000	0.000
18	D	21	ALA	0	0.012	-0.011	4.552	-3.736	-3.534	-0.001	-0.025	-0.176	0.000
19	D	22	ASP	-1	-0.751	-0.877	1.737	44.788	42.156	14.253	-5.944	-5.677	-0.049
20	D	23	ILE	0	0.027	-0.001	2.003	-17.437	-19.124	11.508	-3.533	-6.288	0.029
21	D	24	VAL	0	-0.036	-0.021	3.200	-7.083	-6.021	0.041	-0.359	-0.744	0.003
22	D	25	GLU	-1	-0.859	-0.920	5.093	32.428	32.428	0.000	0.000	0.000	0.000
23	D	26	GLU	-1	-0.781	-0.869	6.279	33.877	33.877	0.000	0.000	0.000	0.000
24	D	27	ALA	0	0.014	0.010	7.800	-2.953	-2.953	0.000	0.000	0.000	0.000
25	D	28	LYS	1	0.869	0.936	9.538	-38.185	-38.185	0.000	0.000	0.000	0.000
26	D	29	LYS	1	0.769	0.872	9.034	-37.838	-37.838	0.000	0.000	0.000	0.000
27	D	30	VAL	0	-0.005	0.013	11.045	-1.590	-1.590	0.000	0.000	0.000	0.000
28	D	31	LYS	1	0.836	0.930	13.695	-32.494	-32.494	0.000	0.000	0.000	0.000
29	D	32	PRO	0	0.028	0.025	11.288	-1.274	-1.274	0.000	0.000	0.000	0.000
30	D	33	THR	0	0.012	-0.011	14.524	-0.647	-0.647	0.000	0.000	0.000	0.000
31	D	34	VAL	0	0.038	0.009	13.775	-0.179	-0.179	0.000	0.000	0.000	0.000
32	D	35	VAL	0	-0.013	0.009	8.639	0.573	0.573	0.000	0.000	0.000	0.000
33	D	36	VAL	0	-0.013	-0.004	7.800	-0.946	-0.946	0.000	0.000	0.000	0.000
34	D	37	ASN	0	-0.025	-0.033	4.588	13.099	13.343	-0.001	-0.017	-0.226	0.000
35	D	38	ALA	0	0.001	0.018	2.562	-8.975	-6.493	1.961	-1.820	-2.624	0.021
36	D	39	ALA	0	0.015	-0.006	2.392	-5.083	-0.848	3.431	-2.923	-4.744	-0.038
37	D	40	ASN	0	-0.013	-0.044	1.867	-13.285	-14.450	11.076	-4.315	-5.596	0.027
38	D	41	VAL	0	0.035	0.011	3.894	-2.744	-2.590	0.006	-0.024	-0.136	0.000
39	D	42	TYR	0	0.008	0.004	6.559	-3.852	-3.852	0.000	0.000	0.000	0.000
40	D	43	LEU	0	-0.021	-0.002	5.165	-1.437	-1.437	0.000	0.000	0.000	0.000
41	D	44	LYS	1	0.825	0.917	4.857	-39.153	-39.153	0.000	0.000	0.000	0.000
42	D	45	HIS	0	-0.008	-0.022	2.752	8.804	11.530	0.907	-1.611	-2.023	-0.002
43	D	46	GLY	0	0.012	0.006	1.946	-9.772	-11.999	6.937	-1.997	-2.712	0.019
44	D	47	GLY	0	-0.013	-0.016	2.743	-1.126	-0.217	0.819	-0.283	-1.444	-0.008
45	D	48	GLY	0	0.033	0.028	2.324	-9.548	-7.656	5.477	-3.321	-4.048	0.029
46	D	49	VAL	0	0.006	-0.015	1.748	-37.488	-40.808	18.449	-4.191	-10.937	0.070
47	D	50	ALA	0	0.009	0.015	2.228	-25.060	-23.258	4.747	-2.432	-4.118	0.017
48	D	51	GLY	0	0.049	0.029	3.530	-14.717	-14.103	0.011	-0.192	-0.432	0.002
49	D	52	ALA	0	-0.065	-0.035	3.476	-11.936	-11.514	0.012	-0.076	-0.358	0.000
50	D	53	LEU	0	0.022	-0.003	5.375	-8.448	-8.309	-0.001	-0.003	-0.135	0.000
51	D	54	ASN	0	0.052	0.016	7.491	-8.215	-8.215	0.000	0.000	0.000	0.000
52	D	55	LYS	1	0.958	0.979	7.213	-49.614	-49.614	0.000	0.000	0.000	0.000
53	D	56	ALA	0	-0.038	-0.010	8.329	-3.825	-3.825	0.000	0.000	0.000	0.000
54	D	57	THR	0	-0.043	-0.013	10.315	-2.892	-2.892	0.000	0.000	0.000	0.000
55	D	58	ASN	0	-0.056	-0.037	13.194	-1.821	-1.821	0.000	0.000	0.000	0.000
56	D	59	ASN	0	0.019	0.015	11.318	0.592	0.592	0.000	0.000	0.000	0.000
57	D	60	ALA	0	0.035	0.025	12.961	-0.247	-0.247	0.000	0.000	0.000	0.000
58	D	61	MET	0	0.025	0.019	8.724	1.305	1.305	0.000	0.000	0.000	0.000
59	D	62	GLN	0	0.009	0.005	6.961	3.709	3.709	0.000	0.000	0.000	0.000
60	D	63	VAL	0	-0.010	0.003	9.935	-0.935	-0.935	0.000	0.000	0.000	0.000
61	D	64	GLU	-1	-0.757	-0.871	13.064	33.542	33.542	0.000	0.000	0.000	0.000
62	D	65	SER	0	-0.008	-0.011	8.704	0.623	0.623	0.000	0.000	0.000	0.000
63	D	66	ASP	-1	-0.813	-0.882	10.272	35.974	35.974	0.000	0.000	0.000	0.000
64	D	67	ASP	-1	-0.936	-0.958	12.135	25.266	25.266	0.000	0.000	0.000	0.000
65	D	68	TYR	0	0.061	0.008	11.940	-0.911	-0.911	0.000	0.000	0.000	0.000
66	D	69	ILE	0	-0.060	-0.029	9.775	-0.443	-0.443	0.000	0.000	0.000	0.000
67	D	70	ALA	0	-0.057	-0.019	13.201	-0.889	-0.889	0.000	0.000	0.000	0.000
68	D	71	THR	0	-0.046	-0.012	16.368	-1.429	-1.429	0.000	0.000	0.000	0.000
69	D	72	ASN	0	-0.072	-0.048	15.822	-0.660	-0.660	0.000	0.000	0.000	0.000
70	D	73	GLY	0	0.004	0.020	15.153	-0.243	-0.243	0.000	0.000	0.000	0.000
71	D	74	PRO	0	-0.051	-0.036	11.355	0.978	0.978	0.000	0.000	0.000	0.000
72	D	75	LEU	0	-0.009	-0.003	8.679	-1.016	-1.016	0.000	0.000	0.000	0.000
73	D	76	LYS	1	0.872	0.931	11.351	-36.777	-36.777	0.000	0.000	0.000	0.000
74	D	77	VAL	0	0.070	0.025	8.706	1.739	1.739	0.000	0.000	0.000	0.000
75	D	78	GLY	0	0.021	0.018	9.490	-3.797	-3.797	0.000	0.000	0.000	0.000
76	D	79	GLY	0	-0.060	-0.024	10.987	-2.475	-2.475	0.000	0.000	0.000	0.000
77	D	80	SER	0	-0.010	-0.037	10.239	3.644	3.644	0.000	0.000	0.000	0.000
78	D	81	CYS	0	-0.028	0.012	11.658	-1.671	-1.671	0.000	0.000	0.000	0.000
79	D	82	VAL	0	0.011	0.008	12.472	2.528	2.528	0.000	0.000	0.000	0.000
80	D	83	LEU	0	0.022	0.024	10.800	-1.748	-1.748	0.000	0.000	0.000	0.000
81	D	84	SER	0	0.009	-0.001	14.514	-0.032	-0.032	0.000	0.000	0.000	0.000
82	D	85	GLY	0	-0.005	0.000	13.805	2.404	2.404	0.000	0.000	0.000	0.000
83	D	86	HIS	0	-0.041	-0.038	13.700	-0.366	-0.366	0.000	0.000	0.000	0.000
84	D	87	ASN	0	-0.030	-0.029	13.242	0.082	0.082	0.000	0.000	0.000	0.000
85	D	88	LEU	0	-0.047	-0.038	8.796	-0.719	-0.719	0.000	0.000	0.000	0.000
86	D	89	ALA	0	-0.001	0.006	12.304	-0.229	-0.229	0.000	0.000	0.000	0.000
87	D	90	LYS	1	0.916	0.985	14.539	-26.187	-26.187	0.000	0.000	0.000	0.000
88	D	91	HIS	0	-0.002	-0.012	16.372	-1.776	-1.776	0.000	0.000	0.000	0.000
89	D	92	CYS	0	-0.006	-0.005	9.801	2.674	2.674	0.000	0.000	0.000	0.000
90	D	93	LEU	0	-0.045	-0.001	11.949	-1.336	-1.336	0.000	0.000	0.000	0.000
91	D	94	HIS	0	0.057	0.010	7.719	8.352	8.352	0.000	0.000	0.000	0.000
92	D	95	VAL	0	0.031	0.018	7.639	-4.307	-4.307	0.000	0.000	0.000	0.000
93	D	96	VAL	0	-0.035	0.004	5.467	8.320	8.320	0.000	0.000	0.000	0.000
94	D	97	GLY	0	0.032	0.015	4.754	-6.906	-6.830	-0.001	-0.011	-0.064	0.000
95	D	98	PRO	0	-0.013	-0.002	5.676	0.923	0.987	-0.001	-0.008	-0.055	0.000
96	D	99	ASN	0	0.008	0.005	4.523	9.157	9.400	-0.001	-0.015	-0.226	0.000
97	D	100	VAL	0	0.029	0.011	7.011	-7.379	-7.379	0.000	0.000	0.000	0.000
98	D	101	ASN	0	-0.036	-0.009	6.725	-10.779	-10.779	0.000	0.000	0.000	0.000
99	D	102	LYS	1	0.870	0.937	6.531	-58.425	-58.425	0.000	0.000	0.000	0.000
100	D	103	GLY	0	-0.001	0.005	10.461	-2.425	-2.425	0.000	0.000	0.000	0.000
101	D	104	GLU	-1	-0.894	-0.940	8.926	52.728	52.728	0.000	0.000	0.000	0.000
102	D	105	ASP	-1	-0.829	-0.920	12.024	37.609	37.609	0.000	0.000	0.000	0.000
103	D	106	ILE	0	0.043	0.013	9.301	2.195	2.195	0.000	0.000	0.000	0.000
104	D	107	GLN	0	0.006	0.006	11.517	2.171	2.171	0.000	0.000	0.000	0.000
105	D	108	LEU	0	-0.026	-0.019	10.926	-0.517	-0.517	0.000	0.000	0.000	0.000
106	D	109	LEU	0	-0.013	-0.011	6.778	1.393	1.393	0.000	0.000	0.000	0.000
107	D	110	LYS	1	0.909	0.956	9.846	-32.718	-32.718	0.000	0.000	0.000	0.000
108	D	111	SER	0	-0.004	-0.011	12.759	-1.228	-1.228	0.000	0.000	0.000	0.000
109	D	112	ALA	0	0.003	-0.005	8.000	-0.771	-0.771	0.000	0.000	0.000	0.000
110	D	113	TYR	0	0.038	0.002	6.492	0.790	0.790	0.000	0.000	0.000	0.000
111	D	114	GLU	-1	-0.837	-0.908	11.503	30.181	30.181	0.000	0.000	0.000	0.000
112	D	115	ASN	0	-0.077	-0.025	11.695	-3.469	-3.469	0.000	0.000	0.000	0.000
113	D	116	PHE	0	0.025	-0.013	8.252	-0.445	-0.445	0.000	0.000	0.000	0.000
114	D	117	ASN	0	0.004	-0.007	14.576	-0.941	-0.941	0.000	0.000	0.000	0.000
115	D	118	GLN	0	-0.070	-0.026	17.474	-1.303	-1.303	0.000	0.000	0.000	0.000
116	D	119	HIS	0	-0.002	-0.006	16.413	-0.961	-0.961	0.000	0.000	0.000	0.000
117	D	120	GLU	-1	-0.923	-0.953	18.379	25.315	25.315	0.000	0.000	0.000	0.000
118	D	121	VAL	0	0.001	-0.023	14.842	0.070	0.070	0.000	0.000	0.000	0.000
119	D	122	LEU	0	-0.060	-0.011	12.668	0.694	0.694	0.000	0.000	0.000	0.000
120	D	123	LEU	0	-0.027	0.004	6.478	-0.724	-0.724	0.000	0.000	0.000	0.000
121	D	124	ALA	0	0.030	0.009	7.924	1.270	1.270	0.000	0.000	0.000	0.000
122	D	125	PRO	0	0.008	0.023	2.890	-4.647	-2.378	0.331	-0.701	-1.899	0.006
123	D	126	LEU	0	0.004	-0.003	2.363	-9.092	-6.424	0.835	-0.898	-2.605	0.005
124	D	127	LEU	0	0.013	0.000	2.444	5.431	8.679	2.470	-2.125	-3.593	-0.026
125	D	128	SER	0	0.042	-0.014	2.100	-24.542	-24.339	8.738	-4.505	-4.435	0.052
126	D	129	ALA	0	-0.046	-0.007	2.287	-3.597	-6.213	3.568	3.331	-4.283	0.000
127	D	130	GLY	0	0.015	0.003	1.840	-29.162	-33.139	18.200	-7.295	-6.929	0.041
128	D	131	ILE	0	-0.042	-0.023	1.850	-36.957	-39.015	13.328	-1.175	-10.095	0.060
129	D	132	PHE	0	-0.089	-0.049	1.972	-49.701	-44.805	14.031	-6.245	-12.683	0.042
130	D	133	GLY	0	0.040	0.024	3.787	-17.679	-17.264	0.015	-0.033	-0.398	0.002
131	D	134	ALA	0	-0.014	-0.008	4.851	-12.232	-12.155	-0.001	-0.008	-0.069	0.000
132	D	135	ASP	-1	-0.789	-0.918	6.093	51.517	51.517	0.000	0.000	0.000	0.000
133	D	136	PRO	0	-0.008	-0.010	3.634	-1.471	-0.860	0.012	-0.186	-0.438	0.001
134	D	137	ILE	0	0.017	0.009	5.522	-0.843	-0.782	-0.001	-0.001	-0.059	0.000
135	D	138	HIS	0	0.013	0.008	8.915	-3.152	-3.152	0.000	0.000	0.000	0.000
136	D	139	SER	0	-0.017	-0.021	5.760	-4.084	-4.084	0.000	0.000	0.000	0.000
137	D	140	LEU	0	0.019	0.002	7.895	-1.130	-1.130	0.000	0.000	0.000	0.000
138	D	141	ARG	1	0.908	0.973	8.870	-35.107	-35.107	0.000	0.000	0.000	0.000
139	D	142	VAL	0	0.012	0.010	10.943	-2.183	-2.183	0.000	0.000	0.000	0.000
140	D	143	CYS	0	-0.048	0.009	9.061	-2.318	-2.318	0.000	0.000	0.000	0.000
141	D	144	VAL	0	0.003	0.000	11.218	-2.353	-2.353	0.000	0.000	0.000	0.000
142	D	145	ASP	-1	-0.876	-0.947	13.971	29.983	29.983	0.000	0.000	0.000	0.000
143	D	146	THR	0	-0.145	-0.091	14.200	-2.306	-2.306	0.000	0.000	0.000	0.000
144	D	147	VAL	0	-0.027	0.014	12.369	-0.808	-0.808	0.000	0.000	0.000	0.000
145	D	148	ARG	1	0.827	0.905	15.650	-30.966	-30.966	0.000	0.000	0.000	0.000
146	D	149	THR	0	-0.006	0.021	17.347	-1.005	-1.005	0.000	0.000	0.000	0.000
147	D	150	ASN	0	-0.037	-0.010	16.494	0.691	0.691	0.000	0.000	0.000	0.000
148	D	151	VAL	0	0.033	0.015	10.800	1.118	1.118	0.000	0.000	0.000	0.000
149	D	152	TYR	0	-0.035	-0.022	9.995	-1.274	-1.274	0.000	0.000	0.000	0.000
150	D	153	LEU	0	0.014	-0.009	6.988	2.860	2.860	0.000	0.000	0.000	0.000
151	D	154	ALA	0	-0.017	-0.009	3.111	-4.390	-3.803	0.043	-0.146	-0.484	0.000
152	D	155	VAL	0	0.016	0.009	2.687	7.868	10.656	1.242	-1.438	-2.591	-0.010
153	D	156	PHE	0	0.021	0.010	2.591	-19.274	-12.755	6.870	-3.740	-9.650	0.037
154	D	157	ASP	-1	-0.840	-0.901	3.902	39.908	40.409	0.026	-0.060	-0.467	0.001
155	D	158	LYS	1	0.871	0.910	6.477	-33.255	-33.255	0.000	0.000	0.000	0.000
156	D	159	ASN	0	0.002	-0.016	9.151	-3.982	-3.982	0.000	0.000	0.000	0.000
157	D	160	LEU	0	-0.030	-0.012	2.668	-2.532	-1.403	0.442	-0.426	-1.145	0.002
158	D	161	TYR	0	-0.002	0.002	6.789	-1.094	-1.094	0.000	0.000	0.000	0.000
159	D	162	ASP	-1	-0.786	-0.873	8.453	31.600	31.600	0.000	0.000	0.000	0.000
160	D	163	LYS	1	0.901	0.977	7.544	-46.644	-46.644	0.000	0.000	0.000	0.000
161	D	164	LEU	0	-0.053	-0.023	5.142	-0.681	-0.681	0.000	0.000	0.000	0.000
162	D	165	VAL	0	0.007	-0.007	9.545	-1.468	-1.468	0.000	0.000	0.000	0.000
163	D	166	SER	0	-0.056	-0.031	12.767	-1.922	-1.922	0.000	0.000	0.000	0.000
164	D	167	SER	0	-0.091	-0.060	11.894	-0.936	-0.936	0.000	0.000	0.000	0.000
165	D	168	PHE	-1	-0.914	-0.950	13.126	29.068	29.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #166(D:201:APR )