FMO DATABASE

FMODB ID: Q8R7Y

Calculation Name: 7C33-B-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7C33

Chain ID: B

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	167
LigandCharge	APR=-2
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1729334.523489
FMO2-HF: Nuclear repulsion	1664490.826709
FMO2-HF: Total energy	-64843.696781
FMO2-MP2: Total energy	-65032.628872

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.
-402.957	-378.840	149.314	-58.975	-114.457	-0.330

Interactive mode: IFIE and PIEDA for fragment #167(B:201:APR )

Summations of interaction energy for fragment #167(B: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.
-402.957	-378.84	149.314	-58.975	-114.457	0.33

Interaction energy analysis for fragmet #167(B: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 : -1.790

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	B	5	SER	0	-0.026	-0.019	15.803	-0.298	-0.298	0.000	0.000	0.000	0.000
2	B	6	PHE	0	0.010	0.011	10.296	0.377	0.377	0.000	0.000	0.000	0.000
3	B	7	SER	0	0.028	0.007	13.027	-1.349	-1.349	0.000	0.000	0.000	0.000
4	B	8	GLY	0	0.024	0.005	12.312	1.611	1.611	0.000	0.000	0.000	0.000
5	B	9	TYR	0	-0.066	-0.046	8.083	1.490	1.490	0.000	0.000	0.000	0.000
6	B	10	LEU	0	-0.023	0.000	12.125	-1.780	-1.780	0.000	0.000	0.000	0.000
7	B	11	LYS	1	0.850	0.906	13.645	-23.790	-23.790	0.000	0.000	0.000	0.000
8	B	12	LEU	0	-0.018	0.008	12.528	-0.547	-0.547	0.000	0.000	0.000	0.000
9	B	13	THR	0	0.040	0.007	16.436	-0.988	-0.988	0.000	0.000	0.000	0.000
10	B	14	ASP	-1	-0.883	-0.938	18.427	24.289	24.289	0.000	0.000	0.000	0.000
11	B	15	ASN	0	-0.042	-0.018	16.518	-1.425	-1.425	0.000	0.000	0.000	0.000
12	B	16	VAL	0	0.030	0.024	11.968	1.814	1.814	0.000	0.000	0.000	0.000
13	B	17	TYR	0	-0.001	0.002	12.439	-2.043	-2.043	0.000	0.000	0.000	0.000
14	B	18	ILE	0	0.034	0.018	7.890	3.092	3.092	0.000	0.000	0.000	0.000
15	B	19	LYS	1	0.823	0.905	7.584	-38.486	-38.486	0.000	0.000	0.000	0.000
16	B	20	ASN	0	-0.055	-0.025	6.056	0.880	0.880	0.000	0.000	0.000	0.000
17	B	21	ALA	0	0.010	-0.013	4.559	-3.697	-3.498	-0.001	-0.025	-0.173	0.000
18	B	22	ASP	-1	-0.751	-0.875	1.736	44.449	41.771	14.175	-5.856	-5.640	-0.049
19	B	23	ILE	0	0.019	-0.004	2.008	-16.668	-18.168	11.402	-3.688	-6.214	0.030
20	B	24	VAL	0	-0.033	-0.020	3.204	-6.832	-5.782	0.039	-0.347	-0.742	0.003
21	B	25	GLU	-1	-0.861	-0.920	5.099	32.408	32.408	0.000	0.000	0.000	0.000
22	B	26	GLU	-1	-0.790	-0.875	6.274	33.803	33.803	0.000	0.000	0.000	0.000
23	B	27	ALA	0	0.020	0.013	7.807	-2.914	-2.914	0.000	0.000	0.000	0.000
24	B	28	LYS	1	0.869	0.935	9.543	-38.050	-38.050	0.000	0.000	0.000	0.000
25	B	29	LYS	1	0.769	0.871	9.044	-37.730	-37.730	0.000	0.000	0.000	0.000
26	B	30	VAL	0	-0.019	0.002	11.047	-1.551	-1.551	0.000	0.000	0.000	0.000
27	B	31	LYS	1	0.815	0.924	13.698	-32.368	-32.368	0.000	0.000	0.000	0.000
28	B	32	PRO	0	0.030	0.035	11.291	-1.207	-1.207	0.000	0.000	0.000	0.000
29	B	33	THR	0	0.033	0.000	14.529	-0.592	-0.592	0.000	0.000	0.000	0.000
30	B	34	VAL	0	0.040	0.008	13.770	-0.190	-0.190	0.000	0.000	0.000	0.000
31	B	35	VAL	0	-0.018	0.007	8.636	0.549	0.549	0.000	0.000	0.000	0.000
32	B	36	VAL	0	0.001	0.001	7.789	-0.995	-0.995	0.000	0.000	0.000	0.000
33	B	37	ASN	0	-0.026	-0.033	4.585	13.011	13.263	-0.001	-0.018	-0.233	0.000
34	B	38	ALA	0	-0.007	0.016	2.555	-9.206	-6.695	2.000	-1.832	-2.680	0.021
35	B	39	ALA	0	0.018	-0.005	2.393	-5.234	-1.016	3.499	-2.990	-4.728	-0.039
36	B	40	ASN	0	-0.018	-0.044	1.865	-13.689	-14.809	11.108	-4.330	-5.658	0.027
37	B	41	VAL	0	0.041	0.012	3.892	-2.813	-2.631	0.005	-0.025	-0.162	0.000
38	B	42	TYR	0	0.001	-0.002	6.560	-3.848	-3.848	0.000	0.000	0.000	0.000
39	B	43	LEU	0	-0.017	0.001	5.164	-1.438	-1.438	0.000	0.000	0.000	0.000
40	B	44	LYS	1	0.823	0.918	4.858	-39.235	-39.235	0.000	0.000	0.000	0.000
41	B	45	HIS	0	-0.001	-0.021	2.749	8.668	11.360	0.906	-1.641	-1.957	-0.002
42	B	46	GLY	0	0.011	0.007	1.942	-10.312	-12.544	6.912	-1.900	-2.779	0.019
43	B	47	GLY	0	-0.009	-0.017	2.748	-1.382	-0.509	0.817	-0.282	-1.408	-0.007
44	B	48	GLY	0	0.027	0.027	2.331	-10.191	-8.146	5.317	-3.287	-4.075	0.028
45	B	49	VAL	0	0.004	-0.014	1.749	-38.339	-41.493	18.380	-4.330	-10.897	0.071
46	B	50	ALA	0	0.012	0.015	2.224	-26.051	-24.236	4.784	-2.451	-4.148	0.017
47	B	51	GLY	0	0.046	0.028	3.532	-14.739	-14.131	0.011	-0.195	-0.424	0.002
48	B	52	ALA	0	-0.060	-0.035	3.468	-11.947	-11.526	0.013	-0.076	-0.358	0.000
49	B	53	LEU	0	0.030	0.001	5.366	-8.529	-8.385	-0.001	-0.003	-0.141	0.000
50	B	54	ASN	0	0.049	0.014	7.485	-8.303	-8.303	0.000	0.000	0.000	0.000
51	B	55	LYS	1	0.958	0.980	7.125	-49.883	-49.883	0.000	0.000	0.000	0.000
52	B	56	ALA	0	-0.040	-0.010	8.327	-3.872	-3.872	0.000	0.000	0.000	0.000
53	B	57	THR	0	-0.045	-0.014	10.311	-2.972	-2.972	0.000	0.000	0.000	0.000
54	B	58	ASN	0	-0.055	-0.035	13.188	-1.831	-1.831	0.000	0.000	0.000	0.000
55	B	59	ASN	0	0.021	0.015	11.321	0.569	0.569	0.000	0.000	0.000	0.000
56	B	60	ALA	0	0.026	0.022	12.964	-0.239	-0.239	0.000	0.000	0.000	0.000
57	B	61	MET	0	0.025	0.022	8.714	1.266	1.266	0.000	0.000	0.000	0.000
58	B	62	GLN	0	0.010	0.007	6.959	3.756	3.756	0.000	0.000	0.000	0.000
59	B	63	VAL	0	-0.012	0.002	9.932	-0.914	-0.914	0.000	0.000	0.000	0.000
60	B	64	GLU	-1	-0.760	-0.872	13.062	33.525	33.525	0.000	0.000	0.000	0.000
61	B	65	SER	0	-0.007	-0.010	8.704	0.652	0.652	0.000	0.000	0.000	0.000
62	B	66	ASP	-1	-0.811	-0.884	10.272	36.009	36.009	0.000	0.000	0.000	0.000
63	B	67	ASP	-1	-0.943	-0.963	12.134	25.315	25.315	0.000	0.000	0.000	0.000
64	B	68	TYR	0	0.069	0.011	11.941	-0.891	-0.891	0.000	0.000	0.000	0.000
65	B	69	ILE	0	-0.058	-0.028	9.776	-0.452	-0.452	0.000	0.000	0.000	0.000
66	B	70	ALA	0	-0.062	-0.020	13.201	-0.889	-0.889	0.000	0.000	0.000	0.000
67	B	71	THR	0	-0.047	-0.014	16.367	-1.410	-1.410	0.000	0.000	0.000	0.000
68	B	72	ASN	0	-0.072	-0.047	15.822	-0.670	-0.670	0.000	0.000	0.000	0.000
69	B	73	GLY	0	0.002	0.021	15.153	-0.244	-0.244	0.000	0.000	0.000	0.000
70	B	74	PRO	0	-0.046	-0.036	11.354	0.980	0.980	0.000	0.000	0.000	0.000
71	B	75	LEU	0	-0.013	-0.004	8.671	-1.069	-1.069	0.000	0.000	0.000	0.000
72	B	76	LYS	1	0.875	0.932	11.350	-36.731	-36.731	0.000	0.000	0.000	0.000
73	B	77	VAL	0	0.063	0.020	8.702	1.694	1.694	0.000	0.000	0.000	0.000
74	B	78	GLY	0	0.023	0.018	9.480	-3.820	-3.820	0.000	0.000	0.000	0.000
75	B	79	GLY	0	-0.049	-0.020	10.976	-2.484	-2.484	0.000	0.000	0.000	0.000
76	B	80	SER	0	-0.017	-0.036	10.226	3.640	3.640	0.000	0.000	0.000	0.000
77	B	81	CYS	0	-0.024	0.010	11.648	-1.672	-1.672	0.000	0.000	0.000	0.000
78	B	82	VAL	0	0.008	0.009	12.468	2.429	2.429	0.000	0.000	0.000	0.000
79	B	83	LEU	0	0.027	0.024	10.801	-1.725	-1.725	0.000	0.000	0.000	0.000
80	B	84	SER	0	0.006	-0.003	14.507	-0.052	-0.052	0.000	0.000	0.000	0.000
81	B	85	GLY	0	-0.007	0.000	13.797	2.431	2.431	0.000	0.000	0.000	0.000
82	B	86	HIS	0	-0.041	-0.039	13.694	-0.429	-0.429	0.000	0.000	0.000	0.000
83	B	87	ASN	0	-0.026	-0.027	13.238	0.067	0.067	0.000	0.000	0.000	0.000
84	B	88	LEU	0	-0.043	-0.037	8.791	-0.687	-0.687	0.000	0.000	0.000	0.000
85	B	89	ALA	0	-0.003	0.002	12.305	-0.164	-0.164	0.000	0.000	0.000	0.000
86	B	90	LYS	1	0.912	0.985	14.539	-26.126	-26.126	0.000	0.000	0.000	0.000
87	B	91	HIS	0	0.004	-0.011	16.367	-1.790	-1.790	0.000	0.000	0.000	0.000
88	B	92	CYS	0	-0.004	-0.003	9.796	2.625	2.625	0.000	0.000	0.000	0.000
89	B	93	LEU	0	-0.032	0.003	11.945	-1.320	-1.320	0.000	0.000	0.000	0.000
90	B	94	HIS	0	0.051	0.008	7.714	8.548	8.548	0.000	0.000	0.000	0.000
91	B	95	VAL	0	0.025	0.014	7.628	-4.263	-4.263	0.000	0.000	0.000	0.000
92	B	96	VAL	0	-0.034	0.005	5.464	8.300	8.300	0.000	0.000	0.000	0.000
93	B	97	GLY	0	0.029	0.014	4.746	-7.196	-7.118	-0.001	-0.011	-0.065	0.000
94	B	98	PRO	0	-0.013	-0.003	5.669	1.069	1.125	-0.001	-0.007	-0.047	0.000
95	B	99	ASN	0	0.009	0.003	4.498	9.112	9.366	-0.001	-0.017	-0.237	0.000
96	B	100	VAL	0	0.030	0.013	7.009	-7.494	-7.494	0.000	0.000	0.000	0.000
97	B	101	ASN	0	-0.037	-0.010	6.736	-10.850	-10.850	0.000	0.000	0.000	0.000
98	B	102	LYS	1	0.861	0.934	6.424	-59.084	-59.084	0.000	0.000	0.000	0.000
99	B	103	GLY	0	0.001	0.003	10.465	-2.418	-2.418	0.000	0.000	0.000	0.000
100	B	104	GLU	-1	-0.889	-0.936	8.927	52.781	52.781	0.000	0.000	0.000	0.000
101	B	105	ASP	-1	-0.831	-0.920	12.026	37.550	37.550	0.000	0.000	0.000	0.000
102	B	106	ILE	0	0.047	0.013	9.288	2.114	2.114	0.000	0.000	0.000	0.000
103	B	107	GLN	0	0.002	0.005	11.510	2.176	2.176	0.000	0.000	0.000	0.000
104	B	108	LEU	0	-0.027	-0.020	10.920	-0.483	-0.483	0.000	0.000	0.000	0.000
105	B	109	LEU	0	-0.008	-0.008	6.771	1.279	1.279	0.000	0.000	0.000	0.000
106	B	110	LYS	1	0.906	0.953	9.837	-32.810	-32.810	0.000	0.000	0.000	0.000
107	B	111	SER	0	-0.002	-0.010	12.750	-1.206	-1.206	0.000	0.000	0.000	0.000
108	B	112	ALA	0	-0.005	-0.008	7.989	-0.767	-0.767	0.000	0.000	0.000	0.000
109	B	113	TYR	0	0.046	0.005	6.494	0.779	0.779	0.000	0.000	0.000	0.000
110	B	114	GLU	-1	-0.837	-0.906	11.490	30.101	30.101	0.000	0.000	0.000	0.000
111	B	115	ASN	0	-0.086	-0.029	11.679	-3.485	-3.485	0.000	0.000	0.000	0.000
112	B	116	PHE	0	0.024	-0.014	8.254	-0.424	-0.424	0.000	0.000	0.000	0.000
113	B	117	ASN	0	0.012	-0.004	14.563	-0.891	-0.891	0.000	0.000	0.000	0.000
114	B	118	GLN	0	-0.073	-0.028	17.461	-1.275	-1.275	0.000	0.000	0.000	0.000
115	B	119	HIS	0	-0.005	-0.006	16.396	-0.987	-0.987	0.000	0.000	0.000	0.000
116	B	120	GLU	-1	-0.917	-0.950	18.375	25.297	25.297	0.000	0.000	0.000	0.000
117	B	121	VAL	0	0.006	-0.021	14.838	0.128	0.128	0.000	0.000	0.000	0.000
118	B	122	LEU	0	-0.064	-0.013	12.669	0.665	0.665	0.000	0.000	0.000	0.000
119	B	123	LEU	0	-0.030	0.001	6.492	-0.810	-0.810	0.000	0.000	0.000	0.000
120	B	124	ALA	0	0.013	0.003	7.928	1.287	1.287	0.000	0.000	0.000	0.000
121	B	125	PRO	0	0.016	0.028	2.878	-4.545	-2.276	0.331	-0.700	-1.901	0.006
122	B	126	LEU	0	0.011	0.001	2.354	-9.099	-6.407	0.842	-0.924	-2.610	0.004
123	B	127	LEU	0	0.002	-0.005	2.450	5.372	8.704	2.428	-2.153	-3.608	-0.026
124	B	128	SER	0	0.047	-0.011	2.089	-24.406	-24.408	9.011	-4.560	-4.449	0.053
125	B	129	ALA	0	-0.029	-0.001	2.291	-3.484	-6.208	3.606	3.425	-4.307	-0.001
126	B	130	GLY	0	0.005	-0.001	1.841	-29.596	-33.704	18.035	-7.226	-6.700	0.039
127	B	131	ILE	0	-0.045	-0.023	1.845	-38.481	-40.344	13.309	-1.310	-10.136	0.059
128	B	132	PHE	0	-0.097	-0.052	1.982	-50.370	-45.331	13.905	-6.205	-12.739	0.041
129	B	133	GLY	0	0.040	0.024	3.794	-17.873	-17.436	0.014	-0.039	-0.412	0.002
130	B	134	ALA	0	-0.010	-0.007	4.852	-12.138	-12.078	-0.001	-0.009	-0.050	0.000
131	B	135	ASP	-1	-0.785	-0.916	6.090	51.646	51.646	0.000	0.000	0.000	0.000
132	B	136	PRO	0	-0.011	-0.012	3.629	-1.411	-0.809	0.012	-0.184	-0.430	0.001
133	B	137	ILE	0	0.017	0.009	5.521	-0.603	-0.547	-0.001	-0.001	-0.054	0.000
134	B	138	HIS	0	0.023	0.015	8.915	-2.860	-2.860	0.000	0.000	0.000	0.000
135	B	139	SER	0	-0.012	-0.018	5.765	-3.967	-3.967	0.000	0.000	0.000	0.000
136	B	140	LEU	0	0.006	-0.005	7.897	-1.249	-1.249	0.000	0.000	0.000	0.000
137	B	141	ARG	1	0.888	0.941	8.869	-34.038	-34.038	0.000	0.000	0.000	0.000
138	B	142	VAL	0	0.018	0.013	10.943	-2.062	-2.062	0.000	0.000	0.000	0.000
139	B	143	CYS	0	-0.045	0.010	9.060	-2.236	-2.236	0.000	0.000	0.000	0.000
140	B	144	VAL	0	-0.002	-0.003	11.219	-2.168	-2.168	0.000	0.000	0.000	0.000
141	B	145	ASP	-1	-0.869	-0.938	13.970	30.013	30.013	0.000	0.000	0.000	0.000
142	B	146	THR	0	-0.152	-0.098	14.212	-2.232	-2.232	0.000	0.000	0.000	0.000
143	B	147	VAL	0	-0.025	0.014	12.370	-0.804	-0.804	0.000	0.000	0.000	0.000
144	B	148	ARG	1	0.826	0.904	15.650	-30.937	-30.937	0.000	0.000	0.000	0.000
145	B	149	THR	0	-0.015	0.016	17.348	-1.000	-1.000	0.000	0.000	0.000	0.000
146	B	150	ASN	0	-0.041	-0.012	16.518	0.615	0.615	0.000	0.000	0.000	0.000
147	B	151	VAL	0	0.037	0.016	10.803	1.139	1.139	0.000	0.000	0.000	0.000
148	B	152	TYR	0	-0.037	-0.023	10.000	-1.352	-1.352	0.000	0.000	0.000	0.000
149	B	153	LEU	0	0.008	-0.011	6.899	2.676	2.676	0.000	0.000	0.000	0.000
150	B	154	ALA	0	-0.015	-0.009	3.121	-4.329	-3.768	0.041	-0.135	-0.466	0.000
151	B	155	VAL	0	0.015	0.010	2.692	7.901	10.735	1.205	-1.417	-2.622	-0.010
152	B	156	PHE	0	0.022	0.011	2.594	-19.782	-13.206	6.753	-3.752	-9.577	0.038
153	B	157	ASP	-1	-0.831	-0.898	3.904	40.019	40.548	0.026	-0.064	-0.491	0.001
154	B	158	LYS	1	0.863	0.908	6.487	-33.207	-33.207	0.000	0.000	0.000	0.000
155	B	159	ASN	0	-0.005	-0.019	9.165	-3.950	-3.950	0.000	0.000	0.000	0.000
156	B	160	LEU	0	-0.025	-0.009	2.674	-2.526	-1.413	0.436	-0.410	-1.139	0.002
157	B	161	TYR	0	0.006	-0.002	6.791	-1.171	-1.171	0.000	0.000	0.000	0.000
158	B	162	ASP	-1	-0.774	-0.864	8.461	31.653	31.653	0.000	0.000	0.000	0.000
159	B	163	LYS	1	0.908	0.979	7.544	-46.572	-46.572	0.000	0.000	0.000	0.000
160	B	164	LEU	0	-0.042	-0.012	5.159	-0.669	-0.669	0.000	0.000	0.000	0.000
161	B	165	VAL	0	0.007	-0.004	9.550	-1.528	-1.528	0.000	0.000	0.000	0.000
162	B	166	SER	0	-0.038	-0.038	12.774	-1.945	-1.945	0.000	0.000	0.000	0.000
163	B	167	SER	0	-0.003	-0.028	11.908	-0.823	-0.823	0.000	0.000	0.000	0.000
164	B	168	PHE	0	-0.067	-0.038	13.161	-0.352	-0.352	0.000	0.000	0.000	0.000
165	B	169	LEU	0	-0.078	-0.040	14.769	-1.057	-1.057	0.000	0.000	0.000	0.000
166	B	170	GLU	-2	-1.845	-1.873	17.319	53.781	53.781	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #167(B:201:APR )