FMO DATABASE

FMODB ID: R1ZN8

Calculation Name: 7C33-C-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7C33

Chain ID: C

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	-1715892.460396
FMO2-HF: Nuclear repulsion	1651469.835096
FMO2-HF: Total energy	-64422.6253
FMO2-MP2: Total energy	-64610.280222

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.
-421.140	-397.436	149.085	-58.390	-114.405	-0.330

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

Summations of interaction energy for fragment #166(C: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.
-421.14	-397.436	149.085	-58.39	-114.405	0.33

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -2 / q_Mulliken : -1.670 / q_NPA : -1.791

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	C	4	ASN	0	-0.011	-0.007	15.421	1.049	1.049	0.000	0.000	0.000	0.000
2	C	5	SER	0	-0.005	0.000	16.146	-0.948	-0.948	0.000	0.000	0.000	0.000
3	C	6	PHE	0	-0.003	0.006	10.312	0.461	0.461	0.000	0.000	0.000	0.000
4	C	7	SER	0	0.018	0.005	13.043	-1.322	-1.322	0.000	0.000	0.000	0.000
5	C	8	GLY	0	0.018	0.001	12.329	1.667	1.667	0.000	0.000	0.000	0.000
6	C	9	TYR	0	-0.062	-0.048	8.091	1.476	1.476	0.000	0.000	0.000	0.000
7	C	10	LEU	0	-0.005	0.008	12.135	-1.859	-1.859	0.000	0.000	0.000	0.000
8	C	11	LYS	1	0.841	0.901	13.651	-23.777	-23.777	0.000	0.000	0.000	0.000
9	C	12	LEU	0	-0.017	0.010	12.261	-0.575	-0.575	0.000	0.000	0.000	0.000
10	C	13	THR	0	0.044	0.008	16.473	-0.999	-0.999	0.000	0.000	0.000	0.000
11	C	14	ASP	-1	-0.888	-0.939	18.427	24.255	24.255	0.000	0.000	0.000	0.000
12	C	15	ASN	0	-0.042	-0.020	16.540	-1.462	-1.462	0.000	0.000	0.000	0.000
13	C	16	VAL	0	0.029	0.024	11.994	1.851	1.851	0.000	0.000	0.000	0.000
14	C	17	TYR	0	-0.004	0.000	12.442	-2.056	-2.056	0.000	0.000	0.000	0.000
15	C	18	ILE	0	0.033	0.025	8.151	3.201	3.201	0.000	0.000	0.000	0.000
16	C	19	LYS	1	0.848	0.905	7.592	-38.570	-38.570	0.000	0.000	0.000	0.000
17	C	20	ASN	0	-0.054	-0.026	6.069	0.899	0.899	0.000	0.000	0.000	0.000
18	C	21	ALA	0	0.012	-0.012	4.577	-3.730	-3.532	-0.001	-0.024	-0.173	0.000
19	C	22	ASP	-1	-0.750	-0.874	1.734	44.595	41.827	14.391	-5.975	-5.649	-0.049
20	C	23	ILE	0	0.026	-0.001	2.008	-17.373	-18.928	11.335	-3.514	-6.267	0.029
21	C	24	VAL	0	-0.036	-0.021	3.187	-7.037	-5.970	0.041	-0.360	-0.748	0.003
22	C	25	GLU	-1	-0.852	-0.926	5.084	32.477	32.477	0.000	0.000	0.000	0.000
23	C	26	GLU	-1	-0.803	-0.879	6.301	33.832	33.832	0.000	0.000	0.000	0.000
24	C	27	ALA	0	0.014	0.010	7.793	-2.937	-2.937	0.000	0.000	0.000	0.000
25	C	28	LYS	1	0.870	0.936	9.528	-38.179	-38.179	0.000	0.000	0.000	0.000
26	C	29	LYS	1	0.784	0.885	9.017	-37.816	-37.816	0.000	0.000	0.000	0.000
27	C	30	VAL	0	-0.004	0.014	11.062	-1.581	-1.581	0.000	0.000	0.000	0.000
28	C	31	LYS	1	0.836	0.930	13.686	-32.466	-32.466	0.000	0.000	0.000	0.000
29	C	32	PRO	0	0.027	0.024	11.296	-1.271	-1.271	0.000	0.000	0.000	0.000
30	C	33	THR	0	0.012	-0.011	14.532	-0.645	-0.645	0.000	0.000	0.000	0.000
31	C	34	VAL	0	0.038	0.009	13.743	-0.172	-0.172	0.000	0.000	0.000	0.000
32	C	35	VAL	0	-0.013	0.009	8.632	0.572	0.572	0.000	0.000	0.000	0.000
33	C	36	VAL	0	-0.013	-0.005	7.767	-0.910	-0.910	0.000	0.000	0.000	0.000
34	C	37	ASN	0	-0.024	-0.032	4.579	13.181	13.426	-0.001	-0.017	-0.227	0.000
35	C	38	ALA	0	0.000	0.017	2.573	-9.057	-6.518	1.935	-1.835	-2.640	0.021
36	C	39	ALA	0	0.016	-0.005	2.385	-4.866	-0.650	3.469	-2.934	-4.751	-0.038
37	C	40	ASN	0	-0.015	-0.045	1.871	-13.133	-14.159	10.798	-4.247	-5.525	0.027
38	C	41	VAL	0	0.035	0.011	3.904	-2.764	-2.612	0.005	-0.024	-0.134	0.000
39	C	42	TYR	0	0.008	0.004	6.579	-3.851	-3.851	0.000	0.000	0.000	0.000
40	C	43	LEU	0	-0.020	-0.002	5.168	-1.441	-1.441	0.000	0.000	0.000	0.000
41	C	44	LYS	1	0.824	0.916	4.869	-39.183	-39.183	0.000	0.000	0.000	0.000
42	C	45	HIS	0	-0.007	-0.022	2.752	8.671	11.406	0.900	-1.615	-2.021	-0.002
43	C	46	GLY	0	0.012	0.006	1.938	-9.576	-11.977	7.163	-2.041	-2.721	0.019
44	C	47	GLY	0	-0.013	-0.017	2.761	-1.154	-0.234	0.823	-0.285	-1.458	-0.008
45	C	48	GLY	0	0.032	0.027	2.315	-9.602	-7.629	5.431	-3.340	-4.063	0.028
46	C	49	VAL	0	0.007	-0.014	1.753	-37.346	-40.391	18.168	-4.126	-10.997	0.068
47	C	50	ALA	0	0.010	0.016	2.220	-25.404	-23.738	5.078	-2.500	-4.245	0.018
48	C	51	GLY	0	0.049	0.029	3.526	-14.887	-14.267	0.012	-0.186	-0.447	0.002
49	C	52	ALA	0	-0.065	-0.035	3.465	-11.999	-11.569	0.013	-0.078	-0.364	0.000
50	C	53	LEU	0	0.022	-0.003	5.360	-8.480	-8.340	-0.001	-0.003	-0.137	0.000
51	C	54	ASN	0	0.051	0.015	7.483	-8.229	-8.229	0.000	0.000	0.000	0.000
52	C	55	LYS	1	0.958	0.979	7.147	-49.663	-49.663	0.000	0.000	0.000	0.000
53	C	56	ALA	0	-0.039	-0.010	8.316	-3.832	-3.832	0.000	0.000	0.000	0.000
54	C	57	THR	0	-0.043	-0.012	10.301	-2.891	-2.891	0.000	0.000	0.000	0.000
55	C	58	ASN	0	-0.056	-0.037	13.175	-1.826	-1.826	0.000	0.000	0.000	0.000
56	C	59	ASN	0	0.018	0.015	11.315	0.593	0.593	0.000	0.000	0.000	0.000
57	C	60	ALA	0	0.035	0.026	12.956	-0.243	-0.243	0.000	0.000	0.000	0.000
58	C	61	MET	0	0.024	0.019	8.710	1.313	1.313	0.000	0.000	0.000	0.000
59	C	62	GLN	0	0.009	0.005	6.949	3.706	3.706	0.000	0.000	0.000	0.000
60	C	63	VAL	0	-0.010	0.003	9.921	-0.934	-0.934	0.000	0.000	0.000	0.000
61	C	64	GLU	-1	-0.756	-0.871	13.052	33.552	33.552	0.000	0.000	0.000	0.000
62	C	65	SER	0	-0.008	-0.010	8.701	0.627	0.627	0.000	0.000	0.000	0.000
63	C	66	ASP	-1	-0.813	-0.882	10.272	35.983	35.983	0.000	0.000	0.000	0.000
64	C	67	ASP	-1	-0.936	-0.959	12.134	25.283	25.283	0.000	0.000	0.000	0.000
65	C	68	TYR	0	0.061	0.008	11.944	-0.908	-0.908	0.000	0.000	0.000	0.000
66	C	69	ILE	0	-0.059	-0.028	9.785	-0.439	-0.439	0.000	0.000	0.000	0.000
67	C	70	ALA	0	-0.057	-0.019	13.208	-0.886	-0.886	0.000	0.000	0.000	0.000
68	C	71	THR	0	-0.046	-0.013	16.374	-1.430	-1.430	0.000	0.000	0.000	0.000
69	C	72	ASN	0	-0.072	-0.049	15.829	-0.665	-0.665	0.000	0.000	0.000	0.000
70	C	73	GLY	0	0.005	0.020	15.165	-0.243	-0.243	0.000	0.000	0.000	0.000
71	C	74	PRO	0	-0.051	-0.036	11.372	0.982	0.982	0.000	0.000	0.000	0.000
72	C	75	LEU	0	-0.009	-0.003	8.693	-1.016	-1.016	0.000	0.000	0.000	0.000
73	C	76	LYS	1	0.872	0.931	11.364	-36.828	-36.828	0.000	0.000	0.000	0.000
74	C	77	VAL	0	0.069	0.025	8.692	1.749	1.749	0.000	0.000	0.000	0.000
75	C	78	GLY	0	0.021	0.018	9.481	-3.821	-3.821	0.000	0.000	0.000	0.000
76	C	79	GLY	0	-0.060	-0.025	10.968	-2.491	-2.491	0.000	0.000	0.000	0.000
77	C	80	SER	0	-0.010	-0.037	10.241	3.652	3.652	0.000	0.000	0.000	0.000
78	C	81	CYS	0	-0.029	0.012	11.672	-1.670	-1.670	0.000	0.000	0.000	0.000
79	C	82	VAL	0	0.012	0.008	12.457	2.525	2.525	0.000	0.000	0.000	0.000
80	C	83	LEU	0	0.022	0.024	10.795	-1.748	-1.748	0.000	0.000	0.000	0.000
81	C	84	SER	0	0.009	-0.001	14.500	-0.033	-0.033	0.000	0.000	0.000	0.000
82	C	85	GLY	0	-0.005	0.000	13.794	2.404	2.404	0.000	0.000	0.000	0.000
83	C	86	HIS	0	-0.041	-0.038	13.692	-0.378	-0.378	0.000	0.000	0.000	0.000
84	C	87	ASN	0	-0.030	-0.029	13.225	0.077	0.077	0.000	0.000	0.000	0.000
85	C	88	LEU	0	-0.048	-0.038	8.788	-0.714	-0.714	0.000	0.000	0.000	0.000
86	C	89	ALA	0	0.000	0.006	12.294	-0.233	-0.233	0.000	0.000	0.000	0.000
87	C	90	LYS	1	0.916	0.985	14.530	-26.182	-26.182	0.000	0.000	0.000	0.000
88	C	91	HIS	0	-0.001	-0.012	16.360	-1.773	-1.773	0.000	0.000	0.000	0.000
89	C	92	CYS	0	-0.007	-0.005	9.788	2.678	2.678	0.000	0.000	0.000	0.000
90	C	93	LEU	0	-0.045	-0.001	11.935	-1.339	-1.339	0.000	0.000	0.000	0.000
91	C	94	HIS	0	0.058	0.010	7.705	8.373	8.373	0.000	0.000	0.000	0.000
92	C	95	VAL	0	0.031	0.017	7.636	-4.313	-4.313	0.000	0.000	0.000	0.000
93	C	96	VAL	0	-0.034	0.003	5.474	8.361	8.361	0.000	0.000	0.000	0.000
94	C	97	GLY	0	0.032	0.015	4.734	-6.968	-6.891	-0.001	-0.011	-0.065	0.000
95	C	98	PRO	0	-0.012	-0.002	5.656	0.958	1.021	-0.001	-0.008	-0.055	0.000
96	C	99	ASN	0	0.007	0.004	4.496	9.054	9.299	-0.001	-0.016	-0.229	0.000
97	C	100	VAL	0	0.029	0.011	7.007	-7.411	-7.411	0.000	0.000	0.000	0.000
98	C	101	ASN	0	-0.037	-0.010	6.722	-10.805	-10.805	0.000	0.000	0.000	0.000
99	C	102	LYS	1	0.869	0.937	6.397	-59.391	-59.391	0.000	0.000	0.000	0.000
100	C	103	GLY	0	-0.002	0.004	10.477	-2.432	-2.432	0.000	0.000	0.000	0.000
101	C	104	GLU	-1	-0.894	-0.940	8.904	52.928	52.928	0.000	0.000	0.000	0.000
102	C	105	ASP	-1	-0.830	-0.920	12.000	37.641	37.641	0.000	0.000	0.000	0.000
103	C	106	ILE	0	0.043	0.012	9.277	2.209	2.209	0.000	0.000	0.000	0.000
104	C	107	GLN	0	0.007	0.007	11.499	2.216	2.216	0.000	0.000	0.000	0.000
105	C	108	LEU	0	-0.027	-0.020	10.904	-0.521	-0.521	0.000	0.000	0.000	0.000
106	C	109	LEU	0	-0.014	-0.011	6.768	1.431	1.431	0.000	0.000	0.000	0.000
107	C	110	LYS	1	0.909	0.956	9.832	-32.759	-32.759	0.000	0.000	0.000	0.000
108	C	111	SER	0	-0.004	-0.010	12.740	-1.229	-1.229	0.000	0.000	0.000	0.000
109	C	112	ALA	0	0.002	-0.005	7.988	-0.765	-0.765	0.000	0.000	0.000	0.000
110	C	113	TYR	0	0.038	0.002	6.518	0.801	0.801	0.000	0.000	0.000	0.000
111	C	114	GLU	-1	-0.838	-0.908	11.498	30.182	30.182	0.000	0.000	0.000	0.000
112	C	115	ASN	0	-0.077	-0.025	11.682	-3.475	-3.475	0.000	0.000	0.000	0.000
113	C	116	PHE	0	0.024	-0.013	8.225	-0.432	-0.432	0.000	0.000	0.000	0.000
114	C	117	ASN	0	0.005	-0.007	14.549	-0.944	-0.944	0.000	0.000	0.000	0.000
115	C	118	GLN	0	-0.069	-0.026	17.474	-1.301	-1.301	0.000	0.000	0.000	0.000
116	C	119	HIS	0	-0.002	-0.006	16.411	-0.966	-0.966	0.000	0.000	0.000	0.000
117	C	120	GLU	-1	-0.921	-0.952	18.351	25.306	25.306	0.000	0.000	0.000	0.000
118	C	121	VAL	0	0.001	-0.023	14.848	0.069	0.069	0.000	0.000	0.000	0.000
119	C	122	LEU	0	-0.060	-0.011	12.665	0.702	0.702	0.000	0.000	0.000	0.000
120	C	123	LEU	0	-0.027	0.003	6.488	-0.727	-0.727	0.000	0.000	0.000	0.000
121	C	124	ALA	0	0.031	0.010	7.926	1.281	1.281	0.000	0.000	0.000	0.000
122	C	125	PRO	0	0.007	0.023	2.878	-4.585	-2.340	0.327	-0.689	-1.884	0.006
123	C	126	LEU	0	0.005	-0.003	2.387	-8.872	-6.285	0.767	-0.846	-2.508	0.004
124	C	127	LEU	0	0.013	0.000	2.458	5.442	8.774	2.343	-2.120	-3.555	-0.025
125	C	128	SER	0	0.042	-0.014	2.102	-24.402	-24.322	8.936	-4.563	-4.454	0.052
126	C	129	ALA	0	-0.045	-0.007	2.309	-3.463	-6.239	3.478	3.526	-4.227	0.000
127	C	130	GLY	0	0.013	0.003	1.845	-29.451	-33.150	17.908	-7.258	-6.952	0.040
128	C	131	ILE	0	-0.041	-0.023	1.856	-36.587	-38.551	13.047	-1.056	-10.027	0.059
129	C	132	PHE	0	-0.089	-0.048	1.967	-49.698	-44.904	14.332	-6.307	-12.819	0.043
130	C	133	GLY	0	0.040	0.023	3.778	-17.745	-17.329	0.016	-0.030	-0.403	0.002
131	C	134	ALA	0	-0.013	-0.007	4.842	-12.252	-12.175	-0.001	-0.008	-0.068	0.000
132	C	135	ASP	-1	-0.791	-0.919	6.102	51.421	51.421	0.000	0.000	0.000	0.000
133	C	136	PRO	0	-0.007	-0.009	3.650	-1.482	-0.895	0.011	-0.175	-0.422	0.001
134	C	137	ILE	0	0.012	0.006	5.562	-0.928	-0.869	-0.001	-0.001	-0.057	0.000
135	C	138	HIS	0	0.014	0.009	8.966	-3.081	-3.081	0.000	0.000	0.000	0.000
136	C	139	SER	0	-0.015	-0.020	5.787	-4.085	-4.085	0.000	0.000	0.000	0.000
137	C	140	LEU	0	0.017	0.000	7.928	-1.138	-1.138	0.000	0.000	0.000	0.000
138	C	141	ARG	1	0.887	0.952	8.902	-35.578	-35.578	0.000	0.000	0.000	0.000
139	C	142	VAL	0	0.011	0.012	10.970	-2.162	-2.162	0.000	0.000	0.000	0.000
140	C	143	CYS	0	-0.050	0.009	9.086	-2.306	-2.306	0.000	0.000	0.000	0.000
141	C	144	VAL	0	0.012	0.003	11.244	-2.307	-2.307	0.000	0.000	0.000	0.000
142	C	145	ASP	-1	-0.874	-0.944	13.998	30.012	30.012	0.000	0.000	0.000	0.000
143	C	146	THR	0	-0.148	-0.095	14.229	-2.285	-2.285	0.000	0.000	0.000	0.000
144	C	147	VAL	0	-0.028	0.013	12.385	-0.805	-0.805	0.000	0.000	0.000	0.000
145	C	148	ARG	1	0.827	0.904	15.669	-30.965	-30.965	0.000	0.000	0.000	0.000
146	C	149	THR	0	-0.007	0.020	17.320	-1.006	-1.006	0.000	0.000	0.000	0.000
147	C	150	ASN	0	-0.039	-0.011	16.513	0.666	0.666	0.000	0.000	0.000	0.000
148	C	151	VAL	0	0.033	0.015	10.811	1.121	1.121	0.000	0.000	0.000	0.000
149	C	152	TYR	0	-0.036	-0.022	10.010	-1.264	-1.264	0.000	0.000	0.000	0.000
150	C	153	LEU	0	0.015	-0.009	6.998	2.859	2.859	0.000	0.000	0.000	0.000
151	C	154	ALA	0	-0.017	-0.010	3.130	-4.355	-3.777	0.040	-0.142	-0.475	0.000
152	C	155	VAL	0	0.016	0.009	2.685	7.745	10.509	1.169	-1.424	-2.508	-0.010
153	C	156	PHE	0	0.021	0.010	2.613	-19.230	-12.676	6.770	-3.714	-9.610	0.037
154	C	157	ASP	-1	-0.839	-0.901	3.914	39.943	40.435	0.025	-0.060	-0.456	0.001
155	C	158	LYS	1	0.872	0.911	6.559	-33.221	-33.221	0.000	0.000	0.000	0.000
156	C	159	ASN	0	0.002	-0.016	9.242	-3.982	-3.982	0.000	0.000	0.000	0.000
157	C	160	LEU	0	-0.030	-0.013	2.723	-2.468	-1.381	0.362	-0.384	-1.064	0.002
158	C	161	TYR	0	-0.001	0.002	6.837	-1.103	-1.103	0.000	0.000	0.000	0.000
159	C	162	ASP	-1	-0.785	-0.872	8.531	31.560	31.560	0.000	0.000	0.000	0.000
160	C	163	LYS	1	0.901	0.977	7.568	-46.657	-46.657	0.000	0.000	0.000	0.000
161	C	164	LEU	0	-0.052	-0.023	5.213	-0.718	-0.718	0.000	0.000	0.000	0.000
162	C	165	VAL	0	0.009	-0.006	9.621	-1.469	-1.469	0.000	0.000	0.000	0.000
163	C	166	SER	0	-0.053	-0.029	12.853	-1.922	-1.922	0.000	0.000	0.000	0.000
164	C	167	SER	0	-0.084	-0.053	11.950	-0.943	-0.943	0.000	0.000	0.000	0.000
165	C	168	PHE	-1	-0.906	-0.940	13.193	29.065	29.065	0.000	0.000	0.000	0.000

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