FMO DATABASE

FMODB ID: M33MZ

Calculation Name: 7RBR-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

ligand 3-letter code: EDO

PDB ID: 7RBR

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-517748.120735
FMO2-HF: Nuclear repulsion	486901.534366
FMO2-HF: Total energy	-30846.586369
FMO2-MP2: Total energy	-30937.593493

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:MET )

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

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.
-205.586	-195.18	30.039	-16.381	-24.06	-0.19

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.723 / q_NPA : 0.864

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

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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	ILE	0	-0.024	-0.006	2.934	4.347	6.474	0.091	-0.710	-1.508	-0.001
4	B	4	PHE	0	0.009	0.003	5.492	0.021	0.021	0.000	0.000	0.000	0.000
5	B	5	VAL	0	0.015	0.007	9.083	0.451	0.451	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.931	0.975	11.432	15.914	15.914	0.000	0.000	0.000	0.000
7	B	7	THR	0	0.018	0.009	14.966	0.607	0.607	0.000	0.000	0.000	0.000
8	B	8	LEU	0	0.030	0.002	17.736	0.255	0.255	0.000	0.000	0.000	0.000
9	B	9	THR	0	-0.014	-0.005	21.117	0.320	0.320	0.000	0.000	0.000	0.000
10	B	10	GLY	0	0.004	0.011	19.842	0.439	0.439	0.000	0.000	0.000	0.000
11	B	11	LYS	1	0.813	0.898	17.966	16.963	16.963	0.000	0.000	0.000	0.000
12	B	12	THR	0	-0.009	-0.008	13.117	-0.288	-0.288	0.000	0.000	0.000	0.000
13	B	13	ILE	0	-0.015	0.005	11.866	0.389	0.389	0.000	0.000	0.000	0.000
14	B	14	THR	0	0.029	0.014	7.787	0.735	0.735	0.000	0.000	0.000	0.000
15	B	15	LEU	0	-0.003	0.008	7.015	3.008	3.008	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.786	-0.884	1.730	-123.244	-125.205	13.205	-6.655	-4.589	-0.086
17	B	17	VAL	0	-0.063	-0.055	2.289	14.717	16.081	1.898	-1.011	-2.250	-0.003
18	B	18	GLU	-1	-0.841	-0.934	1.886	-145.551	-140.256	8.190	-6.801	-6.683	-0.086
19	B	19	PRO	0	0.022	0.007	2.697	5.957	7.953	1.517	-0.615	-2.898	-0.003
20	B	20	SER	0	0.018	0.005	3.305	3.915	3.724	0.044	0.325	-0.179	0.000
21	B	21	ASP	-1	-0.832	-0.893	5.322	-41.256	-41.256	0.000	0.000	0.000	0.000
22	B	22	THR	0	-0.004	-0.040	7.018	0.124	0.124	0.000	0.000	0.000	0.000
23	B	23	ILE	0	0.003	-0.006	9.071	-2.148	-2.148	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.760	-0.871	10.904	-19.795	-19.795	0.000	0.000	0.000	0.000
25	B	25	ASN	0	-0.035	-0.003	9.378	-0.380	-0.380	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.024	0.012	6.935	-0.675	-0.675	0.000	0.000	0.000	0.000
27	B	27	LYS	1	0.798	0.883	9.690	17.814	17.814	0.000	0.000	0.000	0.000
28	B	28	ALA	0	0.009	0.016	13.380	1.000	1.000	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.849	0.925	6.359	44.131	44.131	0.000	0.000	0.000	0.000
30	B	30	ILE	0	-0.008	-0.002	11.269	0.391	0.391	0.000	0.000	0.000	0.000
31	B	31	GLN	0	-0.042	-0.028	14.042	1.801	1.801	0.000	0.000	0.000	0.000
32	B	32	ASP	-1	-0.977	-0.978	14.166	-20.509	-20.509	0.000	0.000	0.000	0.000
33	B	33	LYS	1	0.852	0.929	11.641	26.823	26.823	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.830	-0.916	15.927	-17.363	-17.363	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.027	0.027	18.800	0.995	0.995	0.000	0.000	0.000	0.000
36	B	36	ILE	0	-0.059	-0.032	18.317	0.936	0.936	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.051	0.018	19.209	-0.819	-0.819	0.000	0.000	0.000	0.000
38	B	38	PRO	0	0.042	0.016	17.233	0.168	0.168	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.758	-0.855	18.589	-12.598	-12.598	0.000	0.000	0.000	0.000
40	B	40	GLN	0	0.017	0.020	21.251	0.978	0.978	0.000	0.000	0.000	0.000
41	B	41	GLN	0	-0.035	-0.018	15.036	-0.479	-0.479	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.833	0.917	16.824	14.110	14.110	0.000	0.000	0.000	0.000
43	B	43	LEU	0	0.031	0.022	10.387	-0.032	-0.032	0.000	0.000	0.000	0.000
44	B	44	ILE	0	-0.004	0.009	13.535	0.609	0.609	0.000	0.000	0.000	0.000
45	B	45	PHE	0	0.028	0.012	8.674	-1.205	-1.205	0.000	0.000	0.000	0.000
46	B	46	ALA	0	-0.010	-0.006	11.980	0.822	0.822	0.000	0.000	0.000	0.000
47	B	47	GLY	0	0.033	0.020	14.666	0.659	0.659	0.000	0.000	0.000	0.000
48	B	48	LYS	1	0.919	0.975	12.802	17.128	17.128	0.000	0.000	0.000	0.000
49	B	49	GLN	0	-0.014	-0.014	14.479	-0.535	-0.535	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.044	-0.022	9.344	-0.082	-0.082	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.881	-0.948	13.446	-14.040	-14.040	0.000	0.000	0.000	0.000
52	B	52	ASP	-1	-0.850	-0.920	13.894	-18.155	-18.155	0.000	0.000	0.000	0.000
53	B	53	GLY	0	0.010	0.003	14.227	0.790	0.790	0.000	0.000	0.000	0.000
54	B	54	ARG	1	0.811	0.911	11.986	17.243	17.243	0.000	0.000	0.000	0.000
55	B	55	THR	0	-0.008	-0.034	7.525	-1.259	-1.259	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.018	-0.004	2.835	1.211	1.787	0.219	-0.128	-0.666	-0.001
57	B	57	SER	0	0.048	0.019	5.404	1.146	1.146	0.000	0.000	0.000	0.000
58	B	58	ASP	-1	-0.824	-0.854	6.154	-17.901	-17.901	0.000	0.000	0.000	0.000
59	B	59	TYR	0	-0.067	-0.035	8.026	2.035	2.035	0.000	0.000	0.000	0.000
60	B	60	ASN	0	-0.097	-0.047	6.767	0.687	0.687	0.000	0.000	0.000	0.000
61	B	61	ILE	0	-0.022	0.001	3.765	0.468	0.684	0.002	-0.039	-0.179	0.000
62	B	62	GLN	0	0.020	0.015	2.794	-7.003	-5.181	0.447	-1.034	-1.234	-0.011
63	B	63	LYS	1	1.030	1.007	2.201	31.935	32.379	4.280	-1.250	-3.474	0.000
64	B	64	GLU	-1	-0.894	-0.940	3.567	-33.473	-34.755	0.146	1.537	-0.400	0.001
65	B	65	SER	0	-0.027	-0.003	5.502	4.782	4.782	0.000	0.000	0.000	0.000
66	B	66	THR	0	-0.031	-0.031	7.239	-2.065	-2.065	0.000	0.000	0.000	0.000
67	B	67	LEU	0	-0.016	0.006	7.120	1.519	1.519	0.000	0.000	0.000	0.000
68	B	68	HIS	0	-0.042	-0.024	10.449	1.118	1.118	0.000	0.000	0.000	0.000
69	B	69	LEU	0	0.019	0.020	14.121	-0.130	-0.130	0.000	0.000	0.000	0.000
70	B	70	VAL	0	0.016	0.012	15.584	0.676	0.676	0.000	0.000	0.000	0.000
71	B	71	LEU	0	0.027	0.005	18.745	-0.483	-0.483	0.000	0.000	0.000	0.000
72	B	72	ARG	1	0.790	0.897	21.557	12.348	12.348	0.000	0.000	0.000	0.000
73	B	73	LEU	0	0.023	0.007	23.794	0.137	0.137	0.000	0.000	0.000	0.000
74	B	74	ARG	1	0.850	0.900	27.412	10.185	10.185	0.000	0.000	0.000	0.000
75	B	75	GLY	0	-0.009	0.009	30.409	0.165	0.165	0.000	0.000	0.000	0.000
76	B	76	GLY	-1	-0.897	-0.938	33.251	-7.998	-7.998	0.000	0.000	0.000	0.000
77	B	301	HOH	0	0.002	0.003	10.153	0.497	0.497	0.000	0.000	0.000	0.000
78	B	302	HOH	0	0.009	0.007	25.562	-0.020	-0.020	0.000	0.000	0.000	0.000
79	B	303	HOH	0	-0.029	-0.029	17.001	0.314	0.314	0.000	0.000	0.000	0.000
80	B	305	HOH	0	-0.024	-0.018	12.483	0.135	0.135	0.000	0.000	0.000	0.000
81	B	308	HOH	0	-0.006	-0.005	19.246	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	309	HOH	0	0.017	0.000	15.111	-0.093	-0.093	0.000	0.000	0.000	0.000
83	B	310	HOH	0	0.006	-0.015	11.969	0.347	0.347	0.000	0.000	0.000	0.000
84	B	312	HOH	0	-0.037	-0.028	23.017	-0.102	-0.102	0.000	0.000	0.000	0.000
85	B	313	HOH	0	-0.006	-0.010	26.040	0.057	0.057	0.000	0.000	0.000	0.000
86	B	314	HOH	0	-0.038	-0.030	26.132	0.068	0.068	0.000	0.000	0.000	0.000
87	B	315	HOH	0	0.008	-0.003	18.582	-0.240	-0.240	0.000	0.000	0.000	0.000
88	B	316	HOH	0	-0.004	-0.013	10.640	-0.089	-0.089	0.000	0.000	0.000	0.000
89	B	317	HOH	0	0.011	0.004	14.407	0.212	0.212	0.000	0.000	0.000	0.000
90	B	319	HOH	0	0.041	0.029	30.895	-0.077	-0.077	0.000	0.000	0.000	0.000
91	B	320	HOH	0	0.040	0.029	13.647	-0.140	-0.140	0.000	0.000	0.000	0.000
92	B	321	HOH	0	-0.021	-0.023	18.913	0.044	0.044	0.000	0.000	0.000	0.000

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