FMO DATABASE

FMODB ID: PKRJ3

Calculation Name: 2COV-D-Xray13

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2COV

Chain ID: D

ChEMBL ID:

UniProt ID: Q8RS40

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20181228
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-691728.253312
FMO2-HF: Nuclear repulsion	653659.076763
FMO2-HF: Total energy	-38069.176549
FMO2-MP2: Total energy	-38178.949155

3D Structure Molmil

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(D:377:ACE)

Summations of interaction energy for fragment #1(D:377:ACE)

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.
0.257	0.966	-0.002	-0.258	-0.449	0

Interaction energy analysis for fragmet #1(D:377:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.013

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].
3	D	379	PRO	0	0.041	0.020	3.864	0.699	1.408	-0.002	-0.258	-0.449
4	D	380	GLU	-1	-0.885	-0.947	6.029	-0.163	-0.163	0.000	0.000	0.000
5	D	381	ASN	0	-0.031	-0.027	9.096	-0.027	-0.027	0.000	0.000	0.000
6	D	468	CYS	0	-0.071	-0.026	8.062	-0.008	-0.008	0.000	0.000	0.000
7	D	383	GLN	0	-0.075	-0.031	6.259	0.292	0.292	0.000	0.000	0.000
8	D	384	ASP	-1	-0.930	-0.948	10.072	-0.271	-0.271	0.000	0.000	0.000
9	D	385	ASP	-1	-0.814	-0.923	13.815	-0.295	-0.295	0.000	0.000	0.000
10	D	386	PHE	0	-0.055	-0.007	15.867	0.021	0.021	0.000	0.000	0.000
11	D	387	ASN	0	-0.013	-0.025	13.139	0.022	0.022	0.000	0.000	0.000
12	D	388	PHE	0	0.013	0.004	16.161	0.047	0.047	0.000	0.000	0.000
13	D	389	ASN	0	-0.022	-0.011	14.312	-0.151	-0.151	0.000	0.000	0.000
14	D	390	TYR	0	-0.068	-0.063	16.314	0.052	0.052	0.000	0.000	0.000
15	D	391	VAL	0	-0.048	-0.007	17.778	-0.018	-0.018	0.000	0.000	0.000
16	D	392	SER	0	0.025	-0.003	20.521	0.008	0.008	0.000	0.000	0.000
17	D	393	ASP	-1	-0.821	-0.894	22.743	-0.176	-0.176	0.000	0.000	0.000
18	D	394	GLN	0	-0.091	-0.049	24.364	-0.001	-0.001	0.000	0.000	0.000
19	D	395	GLU	-1	-0.913	-0.954	24.535	-0.131	-0.131	0.000	0.000	0.000
20	D	396	ILE	0	-0.017	0.001	20.508	-0.019	-0.019	0.000	0.000	0.000
21	D	397	GLU	-1	-0.837	-0.917	18.492	-0.234	-0.234	0.000	0.000	0.000
22	D	398	VAL	0	0.007	0.002	19.518	-0.035	-0.035	0.000	0.000	0.000
23	D	399	TYR	0	0.022	-0.023	13.143	0.014	0.014	0.000	0.000	0.000
24	D	400	HIS	0	0.008	-0.009	19.146	-0.015	-0.015	0.000	0.000	0.000
25	D	401	VAL	0	-0.035	-0.012	14.598	0.022	0.022	0.000	0.000	0.000
26	D	402	ASP	-1	-0.848	-0.924	17.973	-0.086	-0.086	0.000	0.000	0.000
27	D	403	LYS	1	0.817	0.903	17.532	0.163	0.163	0.000	0.000	0.000
28	D	404	GLY	0	-0.004	0.003	21.809	0.011	0.011	0.000	0.000	0.000
29	D	405	TRP	0	-0.038	-0.008	22.346	0.005	0.005	0.000	0.000	0.000
30	D	406	SER	0	-0.057	-0.043	27.680	0.000	0.000	0.000	0.000	0.000
31	D	407	ALA	0	-0.016	-0.005	27.822	0.000	0.000	0.000	0.000	0.000
32	D	408	GLY	0	-0.028	-0.015	29.877	0.000	0.000	0.000	0.000	0.000
33	D	409	TRP	0	-0.032	-0.014	32.101	-0.001	-0.001	0.000	0.000	0.000
34	D	410	ASN	0	-0.005	-0.023	27.131	-0.011	-0.011	0.000	0.000	0.000
35	D	411	TYR	0	-0.038	-0.026	29.232	0.004	0.004	0.000	0.000	0.000
36	D	412	VAL	0	0.037	0.030	24.171	-0.005	-0.005	0.000	0.000	0.000
37	D	418	CYS	0	-0.080	-0.058	26.794	0.004	0.004	0.000	0.000	0.000
38	D	414	LEU	0	0.062	0.045	24.882	-0.013	-0.013	0.000	0.000	0.000
39	D	415	ASN	0	0.036	0.003	27.824	0.004	0.004	0.000	0.000	0.000
40	D	416	ASP	-1	-0.885	-0.925	30.382	-0.095	-0.095	0.000	0.000	0.000
41	D	417	TYR	0	-0.022	0.009	31.094	0.010	0.010	0.000	0.000	0.000
42	D	419	LEU	0	0.012	0.000	29.319	0.008	0.008	0.000	0.000	0.000
43	D	420	PRO	0	0.031	0.018	29.737	-0.006	-0.006	0.000	0.000	0.000
44	D	421	GLY	0	0.011	0.010	26.441	-0.004	-0.004	0.000	0.000	0.000
45	D	422	ASN	0	-0.063	-0.030	25.269	0.007	0.007	0.000	0.000	0.000
46	D	423	LYS	1	0.922	0.961	22.687	0.083	0.083	0.000	0.000	0.000
47	D	424	SER	0	-0.020	-0.011	21.529	0.013	0.013	0.000	0.000	0.000
48	D	425	ASN	0	0.013	-0.018	16.786	-0.010	-0.010	0.000	0.000	0.000
49	D	426	GLY	0	0.037	0.025	16.819	-0.023	-0.023	0.000	0.000	0.000
50	D	427	ALA	0	0.020	0.032	17.253	-0.008	-0.008	0.000	0.000	0.000
51	D	428	PHE	0	-0.027	-0.010	19.334	0.019	0.019	0.000	0.000	0.000
52	D	429	ARG	1	0.826	0.907	16.013	0.239	0.239	0.000	0.000	0.000
53	D	430	LYS	1	0.893	0.949	22.403	0.133	0.133	0.000	0.000	0.000
54	D	431	THR	0	0.045	0.031	23.496	-0.019	-0.019	0.000	0.000	0.000
55	D	432	PHE	0	-0.079	-0.022	25.084	0.019	0.019	0.000	0.000	0.000
56	D	433	ASN	0	0.050	0.025	26.315	-0.010	-0.010	0.000	0.000	0.000
57	D	434	ALA	0	-0.046	-0.026	25.008	-0.001	-0.001	0.000	0.000	0.000
58	D	435	VAL	0	0.004	-0.002	26.967	0.005	0.005	0.000	0.000	0.000
59	D	436	LEU	0	0.014	0.004	20.901	-0.008	-0.008	0.000	0.000	0.000
60	D	437	GLY	0	-0.027	-0.012	23.283	0.014	0.014	0.000	0.000	0.000
61	D	438	GLN	0	-0.053	-0.015	24.665	0.011	0.011	0.000	0.000	0.000
62	D	439	ASP	-1	-0.842	-0.906	24.850	-0.177	-0.177	0.000	0.000	0.000
63	D	440	TYR	0	-0.046	-0.030	24.573	0.013	0.013	0.000	0.000	0.000
64	D	441	LYS	1	0.869	0.931	25.185	0.098	0.098	0.000	0.000	0.000
65	D	442	LEU	0	-0.023	-0.006	20.391	0.005	0.005	0.000	0.000	0.000
66	D	443	THR	0	-0.032	-0.039	24.912	0.006	0.006	0.000	0.000	0.000
67	D	444	PHE	0	-0.018	0.000	24.049	-0.004	-0.004	0.000	0.000	0.000
68	D	445	LYS	1	0.931	0.963	26.173	0.098	0.098	0.000	0.000	0.000
69	D	446	VAL	0	0.000	0.007	26.733	-0.001	-0.001	0.000	0.000	0.000
70	D	447	GLU	-1	-0.777	-0.851	29.494	-0.054	-0.054	0.000	0.000	0.000
71	D	448	ASP	-1	-0.753	-0.908	30.054	-0.072	-0.072	0.000	0.000	0.000
72	D	449	ARG	1	0.891	0.945	31.612	0.056	0.056	0.000	0.000	0.000
73	D	450	TYR	0	0.000	-0.011	31.274	0.004	0.004	0.000	0.000	0.000
74	D	451	GLY	0	0.012	0.008	35.941	0.004	0.004	0.000	0.000	0.000
75	D	452	GLN	0	-0.078	-0.042	37.323	0.001	0.001	0.000	0.000	0.000
76	D	453	GLY	0	-0.017	-0.011	35.590	0.001	0.001	0.000	0.000	0.000
77	D	454	GLN	0	-0.022	-0.003	32.633	-0.002	-0.002	0.000	0.000	0.000
78	D	455	GLN	0	-0.062	-0.025	27.183	-0.004	-0.004	0.000	0.000	0.000
79	D	456	ILE	0	-0.009	-0.015	29.166	-0.002	-0.002	0.000	0.000	0.000
80	D	457	LEU	0	0.006	0.018	23.025	0.002	0.002	0.000	0.000	0.000
81	D	458	ASP	-1	-0.837	-0.925	26.266	-0.119	-0.119	0.000	0.000	0.000
82	D	459	ARG	1	0.890	0.937	16.409	0.319	0.319	0.000	0.000	0.000
83	D	460	ASN	0	0.002	0.009	23.937	0.001	0.001	0.000	0.000	0.000
84	D	461	ILE	0	-0.066	-0.023	19.428	-0.016	-0.016	0.000	0.000	0.000
85	D	462	THR	0	0.050	0.010	20.758	0.020	0.020	0.000	0.000	0.000
86	D	463	PHE	0	-0.033	-0.008	20.027	-0.035	-0.035	0.000	0.000	0.000
87	D	464	THR	0	0.029	0.008	16.449	0.010	0.010	0.000	0.000	0.000
88	D	465	THR	0	0.051	0.002	16.475	-0.014	-0.014	0.000	0.000	0.000
89	D	466	GLN	0	-0.043	0.006	12.397	-0.060	-0.060	0.000	0.000	0.000
90	D	467	VAL	0	0.031	0.004	12.009	0.075	0.075	0.000	0.000	0.000
91	D	469	ASN	0	-0.019	0.001	9.914	-0.057	-0.057	0.000	0.000	0.000
92	D	470	NME	0	0.072	0.044	12.483	0.076	0.076	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:377:ACE)