FMO DATABASE

FMODB ID: KRY73

Calculation Name: 7C33-A-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7C33

Chain ID: A

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	168
LigandCharge	APR=-2
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1748323.986653
FMO2-HF: Nuclear repulsion	1682758.891481
FMO2-HF: Total energy	-65565.095172
FMO2-MP2: Total energy	-65755.160075

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.
-404.256	-379.670	147.077	-57.837	-113.826	-0.324

Interactive mode: IFIE and PIEDA for fragment #168(A:201:APR )

Summations of interaction energy for fragment #168(A: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.
-404.256	-379.67	147.077	-57.837	-113.826	0.324

Interaction energy analysis for fragmet #168(A:201:APR )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -2 / q_Mulliken : -1.677 / q_NPA : -1.793

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	A	5	SER	0	-0.026	-0.019	15.812	-0.293	-0.293	0.000	0.000	0.000	0.000
2	A	6	PHE	0	0.010	0.011	10.314	0.376	0.376	0.000	0.000	0.000	0.000
3	A	7	SER	0	0.028	0.007	13.054	-1.348	-1.348	0.000	0.000	0.000	0.000
4	A	8	GLY	0	0.024	0.005	12.350	1.600	1.600	0.000	0.000	0.000	0.000
5	A	9	TYR	0	-0.065	-0.046	8.119	1.497	1.497	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.024	0.000	12.187	-1.752	-1.752	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.850	0.906	13.706	-23.750	-23.750	0.000	0.000	0.000	0.000
8	A	12	LEU	0	-0.018	0.007	12.680	-0.552	-0.552	0.000	0.000	0.000	0.000
9	A	13	THR	0	0.037	0.006	16.502	-0.972	-0.972	0.000	0.000	0.000	0.000
10	A	14	ASP	-1	-0.880	-0.936	18.477	24.248	24.248	0.000	0.000	0.000	0.000
11	A	15	ASN	0	-0.039	-0.015	16.526	-1.424	-1.424	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.030	0.023	11.985	1.816	1.816	0.000	0.000	0.000	0.000
13	A	17	TYR	0	0.002	0.003	12.482	-2.043	-2.043	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.036	0.019	8.164	3.244	3.244	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.820	0.902	7.646	-38.376	-38.376	0.000	0.000	0.000	0.000
16	A	20	ASN	0	-0.051	-0.023	6.122	0.888	0.888	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.009	-0.014	4.618	-3.679	-3.488	-0.001	-0.023	-0.167	0.000
18	A	22	ASP	-1	-0.748	-0.871	1.735	43.798	41.095	14.311	-5.925	-5.683	-0.050
19	A	23	ILE	0	0.020	-0.004	1.990	-16.621	-18.562	12.089	-3.851	-6.297	0.029
20	A	24	VAL	0	-0.036	-0.022	3.153	-6.845	-5.728	0.043	-0.372	-0.789	0.003
21	A	25	GLU	-1	-0.854	-0.927	5.046	32.571	32.571	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.820	-0.891	6.302	33.707	33.707	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.020	0.013	7.775	-2.892	-2.892	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.869	0.935	9.495	-38.069	-38.069	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.791	0.890	8.989	-37.694	-37.694	0.000	0.000	0.000	0.000
26	A	30	VAL	0	-0.017	0.003	11.057	-1.541	-1.541	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.816	0.925	13.662	-32.356	-32.356	0.000	0.000	0.000	0.000
28	A	32	PRO	0	0.030	0.035	11.273	-1.206	-1.206	0.000	0.000	0.000	0.000
29	A	33	THR	0	0.033	0.000	14.514	-0.585	-0.585	0.000	0.000	0.000	0.000
30	A	34	VAL	0	0.040	0.008	13.656	-0.180	-0.180	0.000	0.000	0.000	0.000
31	A	35	VAL	0	-0.019	0.007	8.623	0.536	0.536	0.000	0.000	0.000	0.000
32	A	36	VAL	0	0.002	0.001	7.664	-0.967	-0.967	0.000	0.000	0.000	0.000
33	A	37	ASN	0	-0.027	-0.034	4.571	13.174	13.428	-0.001	-0.019	-0.235	0.000
34	A	38	ALA	0	-0.008	0.015	2.580	-9.463	-6.811	1.944	-1.870	-2.726	0.022
35	A	39	ALA	0	0.019	-0.004	2.379	-4.631	-0.448	3.549	-2.999	-4.732	-0.039
36	A	40	ASN	0	-0.017	-0.043	1.873	-13.517	-14.406	10.566	-4.173	-5.504	0.027
37	A	41	VAL	0	0.041	0.012	3.912	-2.834	-2.655	0.005	-0.025	-0.158	0.000
38	A	42	TYR	0	0.003	-0.001	6.596	-3.865	-3.865	0.000	0.000	0.000	0.000
39	A	43	LEU	0	-0.019	0.000	5.186	-1.453	-1.453	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.820	0.916	4.885	-39.397	-39.397	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.002	-0.021	2.757	8.598	11.301	0.883	-1.641	-1.945	-0.002
42	A	46	GLY	0	0.012	0.007	1.934	-10.162	-12.598	7.159	-1.934	-2.789	0.019
43	A	47	GLY	0	-0.008	-0.016	2.774	-1.351	-0.462	0.817	-0.278	-1.428	-0.007
44	A	48	GLY	0	0.027	0.026	2.290	-10.422	-8.356	5.463	-3.377	-4.151	0.028
45	A	49	VAL	0	0.005	-0.014	1.761	-37.959	-40.692	17.867	-4.065	-11.069	0.067
46	A	50	ALA	0	0.016	0.016	2.214	-26.766	-25.128	5.301	-2.565	-4.375	0.018
47	A	51	GLY	0	0.045	0.027	3.523	-15.188	-14.562	0.013	-0.189	-0.450	0.002
48	A	52	ALA	0	-0.061	-0.036	3.419	-12.155	-11.701	0.017	-0.086	-0.385	0.000
49	A	53	LEU	0	0.029	0.000	5.302	-8.619	-8.469	-0.001	-0.003	-0.146	0.000
50	A	54	ASN	0	0.050	0.015	7.444	-8.374	-8.374	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.958	0.980	6.967	-49.909	-49.909	0.000	0.000	0.000	0.000
52	A	56	ALA	0	-0.041	-0.010	8.257	-3.891	-3.891	0.000	0.000	0.000	0.000
53	A	57	THR	0	-0.046	-0.015	10.244	-2.981	-2.981	0.000	0.000	0.000	0.000
54	A	58	ASN	0	-0.053	-0.034	13.110	-1.831	-1.831	0.000	0.000	0.000	0.000
55	A	59	ASN	0	0.021	0.015	11.311	0.580	0.580	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.026	0.022	12.950	-0.236	-0.236	0.000	0.000	0.000	0.000
57	A	61	MET	0	0.025	0.021	8.703	1.295	1.295	0.000	0.000	0.000	0.000
58	A	62	GLN	0	0.010	0.007	6.953	3.779	3.779	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.012	0.002	9.925	-0.916	-0.916	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.760	-0.872	13.061	33.609	33.609	0.000	0.000	0.000	0.000
61	A	65	SER	0	-0.007	-0.010	8.714	0.669	0.669	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.808	-0.882	10.296	36.092	36.092	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.942	-0.962	12.147	25.374	25.374	0.000	0.000	0.000	0.000
64	A	68	TYR	0	0.069	0.011	11.961	-0.893	-0.893	0.000	0.000	0.000	0.000
65	A	69	ILE	0	-0.058	-0.028	9.803	-0.454	-0.454	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.061	-0.020	13.225	-0.892	-0.892	0.000	0.000	0.000	0.000
67	A	71	THR	0	-0.047	-0.014	16.390	-1.416	-1.416	0.000	0.000	0.000	0.000
68	A	72	ASN	0	-0.072	-0.047	15.846	-0.675	-0.675	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.002	0.021	15.183	-0.245	-0.245	0.000	0.000	0.000	0.000
70	A	74	PRO	0	-0.046	-0.036	11.389	0.992	0.992	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.014	-0.004	8.695	-1.078	-1.078	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.875	0.932	11.371	-36.830	-36.830	0.000	0.000	0.000	0.000
73	A	77	VAL	0	0.064	0.021	8.678	1.706	1.706	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.023	0.018	9.470	-3.844	-3.844	0.000	0.000	0.000	0.000
75	A	79	GLY	0	-0.049	-0.020	10.943	-2.510	-2.510	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.017	-0.036	10.230	3.653	3.653	0.000	0.000	0.000	0.000
77	A	81	CYS	0	-0.023	0.011	11.672	-1.678	-1.678	0.000	0.000	0.000	0.000
78	A	82	VAL	0	0.008	0.009	12.451	2.439	2.439	0.000	0.000	0.000	0.000
79	A	83	LEU	0	0.027	0.024	10.807	-1.727	-1.727	0.000	0.000	0.000	0.000
80	A	84	SER	0	0.006	-0.003	14.493	-0.063	-0.063	0.000	0.000	0.000	0.000
81	A	85	GLY	0	-0.008	0.000	13.786	2.442	2.442	0.000	0.000	0.000	0.000
82	A	86	HIS	0	-0.040	-0.038	13.685	-0.445	-0.445	0.000	0.000	0.000	0.000
83	A	87	ASN	0	-0.026	-0.027	13.174	0.068	0.068	0.000	0.000	0.000	0.000
84	A	88	LEU	0	-0.043	-0.037	8.747	-0.696	-0.696	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.004	0.002	12.259	-0.174	-0.174	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.912	0.985	14.508	-26.134	-26.134	0.000	0.000	0.000	0.000
87	A	91	HIS	0	0.004	-0.011	16.351	-1.787	-1.787	0.000	0.000	0.000	0.000
88	A	92	CYS	0	-0.004	-0.003	9.779	2.623	2.623	0.000	0.000	0.000	0.000
89	A	93	LEU	0	-0.032	0.003	11.927	-1.304	-1.304	0.000	0.000	0.000	0.000
90	A	94	HIS	0	0.052	0.009	7.698	8.619	8.619	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.023	0.013	7.629	-4.313	-4.313	0.000	0.000	0.000	0.000
92	A	96	VAL	0	-0.033	0.006	5.463	8.393	8.393	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.029	0.014	4.710	-7.351	-7.272	-0.001	-0.012	-0.066	0.000
94	A	98	PRO	0	-0.013	-0.003	5.629	1.120	1.176	-0.001	-0.007	-0.048	0.000
95	A	99	ASN	0	0.010	0.003	4.531	9.188	9.443	-0.001	-0.016	-0.238	0.000
96	A	100	VAL	0	0.030	0.012	7.001	-7.557	-7.557	0.000	0.000	0.000	0.000
97	A	101	ASN	0	-0.038	-0.010	6.726	-10.874	-10.874	0.000	0.000	0.000	0.000
98	A	102	LYS	1	0.862	0.935	6.544	-58.894	-58.894	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.001	0.004	10.483	-2.416	-2.416	0.000	0.000	0.000	0.000
100	A	104	GLU	-1	-0.889	-0.937	8.890	52.986	52.986	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.830	-0.919	11.978	37.611	37.611	0.000	0.000	0.000	0.000
102	A	106	ILE	0	0.047	0.013	9.271	2.134	2.134	0.000	0.000	0.000	0.000
103	A	107	GLN	0	0.002	0.005	11.479	2.185	2.185	0.000	0.000	0.000	0.000
104	A	108	LEU	0	-0.026	-0.019	10.877	-0.488	-0.488	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.008	-0.008	6.751	1.282	1.282	0.000	0.000	0.000	0.000
106	A	110	LYS	1	0.907	0.953	9.811	-32.810	-32.810	0.000	0.000	0.000	0.000
107	A	111	SER	0	-0.002	-0.011	12.717	-1.216	-1.216	0.000	0.000	0.000	0.000
108	A	112	ALA	0	-0.004	-0.008	7.969	-0.777	-0.777	0.000	0.000	0.000	0.000
109	A	113	TYR	0	0.046	0.005	6.542	0.749	0.749	0.000	0.000	0.000	0.000
110	A	114	GLU	-1	-0.837	-0.906	11.485	30.107	30.107	0.000	0.000	0.000	0.000
111	A	115	ASN	0	-0.085	-0.028	11.664	-3.481	-3.481	0.000	0.000	0.000	0.000
112	A	116	PHE	0	0.023	-0.015	8.168	-0.418	-0.418	0.000	0.000	0.000	0.000
113	A	117	ASN	0	0.012	-0.004	14.492	-0.892	-0.892	0.000	0.000	0.000	0.000
114	A	118	GLN	0	-0.072	-0.027	17.465	-1.273	-1.273	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.004	-0.006	16.401	-0.987	-0.987	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.917	-0.950	18.282	25.296	25.296	0.000	0.000	0.000	0.000
117	A	121	VAL	0	0.007	-0.021	14.849	0.124	0.124	0.000	0.000	0.000	0.000
118	A	122	LEU	0	-0.064	-0.013	12.670	0.675	0.675	0.000	0.000	0.000	0.000
119	A	123	LEU	0	-0.030	0.000	6.505	-0.820	-0.820	0.000	0.000	0.000	0.000
120	A	124	ALA	0	0.014	0.004	7.877	1.326	1.326	0.000	0.000	0.000	0.000
121	A	125	PRO	0	0.020	0.029	2.801	-4.524	-2.255	0.388	-0.702	-1.955	0.006
122	A	126	LEU	0	0.013	0.000	2.409	-8.760	-6.188	0.749	-0.846	-2.475	0.003
123	A	127	LEU	0	0.000	-0.006	2.474	5.373	8.792	2.184	-2.102	-3.501	-0.025
124	A	128	SER	0	0.048	-0.011	2.097	-24.250	-24.407	9.282	-4.664	-4.461	0.053
125	A	129	ALA	0	-0.028	-0.001	2.385	-3.062	-6.166	3.237	3.941	-4.074	0.000
126	A	130	GLY	0	0.004	-0.001	1.851	-30.019	-33.528	17.246	-7.131	-6.605	0.038
127	A	131	ILE	0	-0.044	-0.021	1.882	-37.679	-38.798	12.014	-0.942	-9.953	0.057
128	A	132	PHE	0	-0.096	-0.052	1.973	-50.162	-45.204	14.213	-6.296	-12.875	0.043
129	A	133	GLY	0	0.040	0.023	3.778	-17.908	-17.487	0.014	-0.018	-0.417	0.002
130	A	134	ALA	0	-0.010	-0.007	4.839	-12.135	-12.078	-0.001	-0.009	-0.047	0.000
131	A	135	ASP	-1	-0.786	-0.917	6.149	51.446	51.446	0.000	0.000	0.000	0.000
132	A	136	PRO	0	-0.012	-0.012	3.719	-1.306	-0.794	0.007	-0.143	-0.376	0.001
133	A	137	ILE	0	0.013	0.007	5.630	-0.584	-0.533	-0.001	-0.001	-0.050	0.000
134	A	138	HIS	0	0.024	0.017	9.039	-2.814	-2.814	0.000	0.000	0.000	0.000
135	A	139	SER	0	-0.008	-0.018	5.839	-3.980	-3.980	0.000	0.000	0.000	0.000
136	A	140	LEU	0	0.008	-0.005	7.989	-1.256	-1.256	0.000	0.000	0.000	0.000
137	A	141	ARG	1	0.938	0.962	8.948	-34.412	-34.412	0.000	0.000	0.000	0.000
138	A	142	VAL	0	0.018	0.008	11.014	-2.137	-2.137	0.000	0.000	0.000	0.000
139	A	143	CYS	0	-0.044	0.011	9.103	-2.236	-2.236	0.000	0.000	0.000	0.000
140	A	144	VAL	0	-0.010	-0.004	11.262	-2.233	-2.233	0.000	0.000	0.000	0.000
141	A	145	ASP	-1	-0.858	-0.942	14.019	30.127	30.127	0.000	0.000	0.000	0.000
142	A	146	THR	0	-0.142	-0.090	14.244	-2.237	-2.237	0.000	0.000	0.000	0.000
143	A	147	VAL	0	-0.023	0.016	12.375	-0.796	-0.796	0.000	0.000	0.000	0.000
144	A	148	ARG	1	0.823	0.900	15.663	-30.938	-30.938	0.000	0.000	0.000	0.000
145	A	149	THR	0	-0.014	0.017	17.262	-0.999	-0.999	0.000	0.000	0.000	0.000
146	A	150	ASN	0	-0.041	-0.011	16.547	0.611	0.611	0.000	0.000	0.000	0.000
147	A	151	VAL	0	0.037	0.016	10.783	1.146	1.146	0.000	0.000	0.000	0.000
148	A	152	TYR	0	-0.037	-0.023	10.029	-1.349	-1.349	0.000	0.000	0.000	0.000
149	A	153	LEU	0	0.005	-0.015	6.607	2.552	2.552	0.000	0.000	0.000	0.000
150	A	154	ALA	0	-0.019	-0.009	3.147	-4.294	-3.767	0.037	-0.123	-0.441	0.000
151	A	155	VAL	0	0.015	0.009	2.736	7.855	10.637	0.926	-1.337	-2.371	-0.010
152	A	156	PHE	0	0.023	0.011	2.614	-19.499	-12.907	6.473	-3.644	-9.421	0.037
153	A	157	ASP	-1	-0.830	-0.897	3.938	40.042	40.553	0.022	-0.066	-0.467	0.001
154	A	158	LYS	1	0.863	0.908	6.641	-33.093	-33.093	0.000	0.000	0.000	0.000
155	A	159	ASN	0	-0.005	-0.019	9.359	-3.944	-3.944	0.000	0.000	0.000	0.000
156	A	160	LEU	0	-0.024	-0.008	2.800	-2.360	-1.346	0.266	-0.324	-0.956	0.001
157	A	161	TYR	0	0.004	-0.002	6.910	-1.210	-1.210	0.000	0.000	0.000	0.000
158	A	162	ASP	-1	-0.771	-0.863	8.608	31.589	31.589	0.000	0.000	0.000	0.000
159	A	163	LYS	1	0.914	0.983	7.652	-46.521	-46.521	0.000	0.000	0.000	0.000
160	A	164	LEU	0	-0.040	-0.012	5.287	-0.691	-0.691	0.000	0.000	0.000	0.000
161	A	165	VAL	0	0.008	-0.003	9.711	-1.543	-1.543	0.000	0.000	0.000	0.000
162	A	166	SER	0	-0.037	-0.038	12.939	-1.953	-1.953	0.000	0.000	0.000	0.000
163	A	167	SER	0	-0.010	-0.032	12.042	-0.886	-0.886	0.000	0.000	0.000	0.000
164	A	168	PHE	0	-0.032	-0.015	13.304	-0.392	-0.392	0.000	0.000	0.000	0.000
165	A	169	LEU	0	-0.030	-0.028	14.901	-1.145	-1.145	0.000	0.000	0.000	0.000
166	A	170	GLU	-1	-1.027	-0.973	17.456	26.302	26.302	0.000	0.000	0.000	0.000
167	A	171	MET	-1	-0.984	-0.963	18.709	25.316	25.316	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #168(A:201:APR )