FMO DATABASE

FMODB ID: 3QQNL

Calculation Name: 7RBS-B-Xray89

Preferred Name:

Target Type:

Ligand Name: zinc ion

ligand 3-letter code: ZN

PDB ID: 7RBS

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

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	160
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-1362341.748132
FMO2-HF: Nuclear repulsion	1302522.190928
FMO2-HF: Total energy	-59819.557205
FMO2-MP2: Total energy	-59995.043497

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(B:1:ALA )

Summations of interaction energy for fragment #1(B:1:ALA )

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.
-10.223	-8.084	0.02	-0.995	-1.165	-0.003

Interaction energy analysis for fragmet #1(B:1:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.915

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	B	3	TRP	0	-0.043	-0.026	3.354	-4.215	-2.243	0.021	-0.975	-1.019	-0.003
4	B	4	ASP	-1	-0.831	-0.896	5.923	-27.428	-27.428	0.000	0.000	0.000	0.000
5	B	5	LEU	0	-0.033	-0.010	9.725	0.208	0.208	0.000	0.000	0.000	0.000
6	B	6	THR	0	0.009	-0.005	12.609	0.454	0.454	0.000	0.000	0.000	0.000
7	B	7	VAL	0	0.009	-0.002	16.234	0.132	0.132	0.000	0.000	0.000	0.000
8	B	8	LYS	1	0.896	0.945	19.145	12.787	12.787	0.000	0.000	0.000	0.000
9	B	9	MET	0	0.006	0.022	22.473	-0.037	-0.037	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.022	-0.007	25.579	0.114	0.114	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.033	-0.002	29.025	0.343	0.343	0.000	0.000	0.000	0.000
12	B	12	GLY	0	0.006	0.013	28.362	0.274	0.274	0.000	0.000	0.000	0.000
13	B	13	ASN	0	-0.042	-0.027	25.551	0.002	0.002	0.000	0.000	0.000	0.000
14	B	14	GLU	-1	-0.844	-0.924	20.884	-13.480	-13.480	0.000	0.000	0.000	0.000
15	B	15	PHE	0	-0.017	-0.016	18.905	0.259	0.259	0.000	0.000	0.000	0.000
16	B	16	GLN	0	0.073	0.051	13.226	0.370	0.370	0.000	0.000	0.000	0.000
17	B	17	VAL	0	-0.016	-0.004	13.565	0.785	0.785	0.000	0.000	0.000	0.000
18	B	18	SER	0	-0.006	-0.012	9.686	-0.246	-0.246	0.000	0.000	0.000	0.000
19	B	19	LEU	0	-0.022	-0.014	8.982	1.822	1.822	0.000	0.000	0.000	0.000
20	B	20	SER	0	0.019	-0.016	5.496	-5.349	-5.349	0.000	0.000	0.000	0.000
21	B	21	SER	0	0.046	0.013	4.263	1.312	1.479	-0.001	-0.020	-0.146	0.000
22	B	22	SER	0	-0.020	-0.018	6.113	3.064	3.064	0.000	0.000	0.000	0.000
23	B	23	MET	0	-0.035	0.030	8.953	2.687	2.687	0.000	0.000	0.000	0.000
24	B	24	SER	0	0.042	0.005	11.210	-0.095	-0.095	0.000	0.000	0.000	0.000
25	B	25	VAL	0	0.038	0.008	14.446	-0.375	-0.375	0.000	0.000	0.000	0.000
26	B	26	SER	0	0.015	0.008	17.534	0.588	0.588	0.000	0.000	0.000	0.000
27	B	27	GLU	-1	-0.786	-0.885	13.739	-20.055	-20.055	0.000	0.000	0.000	0.000
28	B	28	LEU	0	0.023	0.028	14.870	-0.090	-0.090	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.950	0.992	16.267	14.868	14.868	0.000	0.000	0.000	0.000
30	B	30	ALA	0	0.021	0.033	18.053	0.746	0.746	0.000	0.000	0.000	0.000
31	B	31	GLN	0	0.008	-0.006	13.786	1.037	1.037	0.000	0.000	0.000	0.000
32	B	32	ILE	0	-0.026	-0.021	17.442	0.400	0.400	0.000	0.000	0.000	0.000
33	B	33	THR	0	-0.078	-0.055	20.159	0.784	0.784	0.000	0.000	0.000	0.000
34	B	34	GLN	0	-0.024	-0.003	18.951	0.779	0.779	0.000	0.000	0.000	0.000
35	B	35	LYS	1	0.863	0.926	16.217	18.856	18.856	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.031	-0.011	21.876	0.478	0.478	0.000	0.000	0.000	0.000
37	B	37	GLY	0	0.010	0.025	24.754	0.563	0.563	0.000	0.000	0.000	0.000
38	B	38	VAL	0	-0.087	-0.050	25.667	0.651	0.651	0.000	0.000	0.000	0.000
39	B	39	HIS	0	0.074	0.030	25.612	-0.831	-0.831	0.000	0.000	0.000	0.000
40	B	40	ALA	0	0.067	0.027	23.322	0.076	0.076	0.000	0.000	0.000	0.000
41	B	41	PHE	0	0.026	0.019	24.860	-0.053	-0.053	0.000	0.000	0.000	0.000
42	B	42	GLN	0	-0.027	0.004	27.681	0.135	0.135	0.000	0.000	0.000	0.000
43	B	43	GLN	0	-0.031	-0.018	22.450	-0.270	-0.270	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.784	0.868	25.582	10.676	10.676	0.000	0.000	0.000	0.000
45	B	45	LEU	0	0.022	0.003	19.359	-0.066	-0.066	0.000	0.000	0.000	0.000
46	B	46	ALA	0	-0.002	0.000	22.120	0.173	0.173	0.000	0.000	0.000	0.000
47	B	47	VAL	0	0.022	0.015	18.274	-0.330	-0.330	0.000	0.000	0.000	0.000
48	B	48	HIS	0	-0.005	0.032	19.751	1.297	1.297	0.000	0.000	0.000	0.000
49	B	49	PRO	0	-0.012	-0.027	20.163	-0.623	-0.623	0.000	0.000	0.000	0.000
50	B	50	SER	0	-0.008	-0.023	21.632	0.376	0.376	0.000	0.000	0.000	0.000
51	B	51	GLY	0	0.050	0.034	23.543	0.465	0.465	0.000	0.000	0.000	0.000
52	B	52	VAL	0	-0.038	-0.009	21.467	0.436	0.436	0.000	0.000	0.000	0.000
53	B	53	ALA	0	0.017	-0.003	22.449	-0.491	-0.491	0.000	0.000	0.000	0.000
54	B	54	LEU	0	-0.003	0.002	17.461	-0.279	-0.279	0.000	0.000	0.000	0.000
55	B	55	GLN	0	-0.048	-0.027	18.516	0.573	0.573	0.000	0.000	0.000	0.000
56	B	56	ASP	-1	-0.855	-0.948	18.579	-14.982	-14.982	0.000	0.000	0.000	0.000
57	B	57	ARG	1	0.949	0.970	18.589	14.930	14.930	0.000	0.000	0.000	0.000
58	B	58	VAL	0	-0.011	0.014	15.385	-0.824	-0.824	0.000	0.000	0.000	0.000
59	B	59	PRO	0	0.044	0.018	10.981	0.402	0.402	0.000	0.000	0.000	0.000
60	B	60	LEU	0	-0.012	-0.011	11.356	1.067	1.067	0.000	0.000	0.000	0.000
61	B	61	ALA	0	0.010	0.004	7.633	0.539	0.539	0.000	0.000	0.000	0.000
62	B	62	SER	0	-0.036	-0.014	9.509	0.349	0.349	0.000	0.000	0.000	0.000
63	B	63	GLN	0	-0.045	-0.004	12.302	2.195	2.195	0.000	0.000	0.000	0.000
64	B	64	GLY	0	0.029	0.012	13.406	-0.614	-0.614	0.000	0.000	0.000	0.000
65	B	65	LEU	0	-0.039	-0.010	12.811	-0.418	-0.418	0.000	0.000	0.000	0.000
66	B	66	GLY	0	0.106	0.055	9.081	-1.648	-1.648	0.000	0.000	0.000	0.000
67	B	67	PRO	0	-0.032	-0.023	6.325	1.176	1.176	0.000	0.000	0.000	0.000
68	B	68	GLY	0	0.015	0.017	8.878	1.058	1.058	0.000	0.000	0.000	0.000
69	B	69	SER	0	-0.058	-0.023	12.242	1.770	1.770	0.000	0.000	0.000	0.000
70	B	70	THR	0	0.025	-0.003	14.333	-0.293	-0.293	0.000	0.000	0.000	0.000
71	B	71	VAL	0	-0.032	-0.015	17.118	0.228	0.228	0.000	0.000	0.000	0.000
72	B	72	LEU	0	-0.009	-0.007	18.910	0.169	0.169	0.000	0.000	0.000	0.000
73	B	73	LEU	0	-0.001	-0.003	22.219	-0.143	-0.143	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.002	-0.008	23.887	0.365	0.365	0.000	0.000	0.000	0.000
75	B	75	VAL	0	-0.016	-0.018	27.215	-0.242	-0.242	0.000	0.000	0.000	0.000
76	B	76	ASP	-1	-0.844	-0.903	29.401	-9.166	-9.166	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.942	0.956	31.312	10.099	10.099	0.000	0.000	0.000	0.000
78	B	78	CYS	0	-0.025	0.010	34.232	0.265	0.265	0.000	0.000	0.000	0.000
79	B	79	ASP	-1	-0.786	-0.897	36.111	-8.886	-8.886	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.905	-0.944	38.373	-7.264	-7.264	0.000	0.000	0.000	0.000
81	B	81	PRO	0	-0.061	-0.012	40.658	-0.181	-0.181	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.002	-0.005	38.460	0.072	0.072	0.000	0.000	0.000	0.000
83	B	83	SER	0	0.016	0.006	42.875	0.074	0.074	0.000	0.000	0.000	0.000
84	B	84	ILE	0	0.016	0.020	39.082	-0.114	-0.114	0.000	0.000	0.000	0.000
85	B	85	LEU	0	-0.020	-0.013	42.294	0.219	0.219	0.000	0.000	0.000	0.000
86	B	86	VAL	0	0.028	0.013	41.101	-0.230	-0.230	0.000	0.000	0.000	0.000
87	B	87	ARG	1	0.881	0.971	42.809	7.419	7.419	0.000	0.000	0.000	0.000
88	B	88	ASN	0	0.027	-0.013	43.417	-0.149	-0.149	0.000	0.000	0.000	0.000
89	B	89	ASN	0	0.035	-0.007	45.625	-0.026	-0.026	0.000	0.000	0.000	0.000
90	B	90	LYS	1	0.856	0.940	46.502	6.574	6.574	0.000	0.000	0.000	0.000
91	B	91	GLY	0	0.078	0.034	47.521	0.039	0.039	0.000	0.000	0.000	0.000
92	B	92	ARG	1	0.837	0.923	48.571	6.269	6.269	0.000	0.000	0.000	0.000
93	B	93	SER	0	0.002	-0.013	45.854	-0.093	-0.093	0.000	0.000	0.000	0.000
94	B	94	SER	0	0.005	0.019	47.052	0.228	0.228	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.003	-0.019	46.395	-0.130	-0.130	0.000	0.000	0.000	0.000
96	B	96	TYR	0	0.012	0.010	43.801	0.152	0.152	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.934	-0.959	44.410	-7.051	-7.051	0.000	0.000	0.000	0.000
98	B	98	VAL	0	-0.030	-0.013	39.636	-0.050	-0.050	0.000	0.000	0.000	0.000
99	B	99	ARG	1	0.935	0.950	39.262	7.855	7.855	0.000	0.000	0.000	0.000
100	B	100	LEU	0	0.023	0.018	33.957	-0.127	-0.127	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.022	-0.040	33.820	-0.333	-0.333	0.000	0.000	0.000	0.000
102	B	102	GLN	0	0.006	0.026	34.826	-0.108	-0.108	0.000	0.000	0.000	0.000
103	B	103	THR	0	0.030	0.002	33.139	-0.036	-0.036	0.000	0.000	0.000	0.000
104	B	104	VAL	0	0.031	0.013	32.336	0.353	0.353	0.000	0.000	0.000	0.000
105	B	105	ALA	0	0.011	0.006	35.284	0.275	0.275	0.000	0.000	0.000	0.000
106	B	106	HIS	0	-0.050	-0.031	37.141	0.379	0.379	0.000	0.000	0.000	0.000
107	B	107	LEU	0	0.008	0.017	37.824	0.244	0.244	0.000	0.000	0.000	0.000
108	B	108	LYS	1	0.821	0.909	36.992	8.845	8.845	0.000	0.000	0.000	0.000
109	B	109	GLN	0	-0.018	0.000	40.800	0.368	0.368	0.000	0.000	0.000	0.000
110	B	110	GLN	0	-0.020	-0.008	42.225	0.295	0.295	0.000	0.000	0.000	0.000
111	B	111	VAL	0	0.002	-0.007	42.067	0.179	0.179	0.000	0.000	0.000	0.000
112	B	112	SER	0	-0.103	-0.067	44.364	0.156	0.156	0.000	0.000	0.000	0.000
113	B	113	GLY	0	0.023	0.010	46.039	0.145	0.145	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.060	-0.020	48.499	0.164	0.164	0.000	0.000	0.000	0.000
115	B	115	GLU	-1	-0.843	-0.919	46.798	-6.484	-6.484	0.000	0.000	0.000	0.000
116	B	116	GLY	0	-0.003	0.022	49.502	0.063	0.063	0.000	0.000	0.000	0.000
117	B	117	VAL	0	-0.061	-0.030	45.749	0.069	0.069	0.000	0.000	0.000	0.000
118	B	118	GLN	0	0.069	0.047	45.375	-0.155	-0.155	0.000	0.000	0.000	0.000
119	B	119	ASP	-1	-0.825	-0.926	40.254	-8.074	-8.074	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.794	-0.894	39.686	-7.954	-7.954	0.000	0.000	0.000	0.000
121	B	121	LEU	0	-0.019	-0.007	40.746	-0.099	-0.099	0.000	0.000	0.000	0.000
122	B	122	PHE	0	-0.050	-0.021	40.478	0.041	0.041	0.000	0.000	0.000	0.000
123	B	123	TRP	0	-0.015	-0.010	33.040	-0.232	-0.232	0.000	0.000	0.000	0.000
124	B	124	LEU	0	0.037	0.021	35.985	0.197	0.197	0.000	0.000	0.000	0.000
125	B	125	THR	0	0.003	-0.003	33.112	-0.304	-0.304	0.000	0.000	0.000	0.000
126	B	126	PHE	0	0.011	-0.005	32.295	0.450	0.450	0.000	0.000	0.000	0.000
127	B	127	GLU	-1	-0.913	-0.956	31.785	-10.159	-10.159	0.000	0.000	0.000	0.000
128	B	128	GLY	0	-0.019	-0.007	31.148	-0.306	-0.306	0.000	0.000	0.000	0.000
129	B	129	LYS	1	0.881	0.966	25.068	12.141	12.141	0.000	0.000	0.000	0.000
130	B	130	PRO	0	-0.009	-0.013	28.351	0.332	0.332	0.000	0.000	0.000	0.000
131	B	131	LEU	0	-0.008	-0.015	29.481	-0.362	-0.362	0.000	0.000	0.000	0.000
132	B	132	GLU	-1	-0.865	-0.922	25.870	-12.139	-12.139	0.000	0.000	0.000	0.000
133	B	133	ASP	-1	-0.777	-0.880	30.450	-9.149	-9.149	0.000	0.000	0.000	0.000
134	B	134	GLN	0	0.036	0.009	26.995	0.556	0.556	0.000	0.000	0.000	0.000
135	B	135	LEU	0	-0.011	0.005	25.436	-0.084	-0.084	0.000	0.000	0.000	0.000
136	B	136	PRO	0	-0.026	-0.007	28.744	0.395	0.395	0.000	0.000	0.000	0.000
137	B	137	LEU	0	0.035	0.009	30.951	-0.279	-0.279	0.000	0.000	0.000	0.000
138	B	138	GLY	0	0.002	-0.009	31.716	-0.039	-0.039	0.000	0.000	0.000	0.000
139	B	139	GLU	-1	-0.933	-0.966	24.371	-13.068	-13.068	0.000	0.000	0.000	0.000
140	B	140	TYR	0	-0.079	-0.059	27.524	-0.310	-0.310	0.000	0.000	0.000	0.000
141	B	141	GLY	0	-0.004	0.007	29.917	0.172	0.172	0.000	0.000	0.000	0.000
142	B	142	LEU	0	-0.034	-0.017	31.327	0.206	0.206	0.000	0.000	0.000	0.000
143	B	143	LYS	1	0.930	0.963	32.213	9.723	9.723	0.000	0.000	0.000	0.000
144	B	144	PRO	0	0.045	0.010	37.567	0.063	0.063	0.000	0.000	0.000	0.000
145	B	145	LEU	0	-0.029	-0.025	41.315	0.031	0.031	0.000	0.000	0.000	0.000
146	B	146	SER	0	-0.011	0.014	37.270	0.018	0.018	0.000	0.000	0.000	0.000
147	B	147	THR	0	-0.042	-0.027	39.303	0.216	0.216	0.000	0.000	0.000	0.000
148	B	148	VAL	0	0.005	0.007	36.861	-0.195	-0.195	0.000	0.000	0.000	0.000
149	B	149	PHE	0	-0.013	-0.007	38.090	0.357	0.357	0.000	0.000	0.000	0.000
150	B	150	MET	0	0.026	0.021	38.664	-0.162	-0.162	0.000	0.000	0.000	0.000
151	B	151	ASN	0	-0.040	-0.016	37.625	0.018	0.018	0.000	0.000	0.000	0.000
152	B	152	LEU	0	0.030	0.005	40.432	-0.060	-0.060	0.000	0.000	0.000	0.000
153	B	153	ARG	1	0.832	0.924	35.765	8.508	8.508	0.000	0.000	0.000	0.000
154	B	154	LEU	0	0.022	0.009	40.667	0.183	0.183	0.000	0.000	0.000	0.000
155	B	155	ARG	1	0.812	0.881	39.408	7.658	7.658	0.000	0.000	0.000	0.000
156	B	156	GLY	0	-0.021	0.003	40.464	0.184	0.184	0.000	0.000	0.000	0.000
157	B	157	GLY	-1	-0.911	-0.942	39.723	-7.919	-7.919	0.000	0.000	0.000	0.000
158	B	201	HOH	0	-0.032	-0.025	14.841	-0.328	-0.328	0.000	0.000	0.000	0.000
159	B	202	HOH	0	-0.015	-0.031	32.431	-0.080	-0.080	0.000	0.000	0.000	0.000
160	B	203	HOH	0	-0.056	-0.039	12.511	0.072	0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ALA )