FMO DATABASE

FMODB ID: YYY72

Calculation Name: 7PKU-A-Other89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7PKU

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: SolutionNMR

Registration Date: 2022-02-03

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 main protease 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	96
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-670089.575812
FMO2-HF: Nuclear repulsion	631233.300715
FMO2-HF: Total energy	-38856.275097
FMO2-MP2: Total energy	-38967.260184

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(A:16:GLN)

Summations of interaction energy for fragment #1(A:16:GLN)

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.
-12.16	-7.588	3.172	-3.594	-4.15	0.021

Interaction energy analysis for fragmet #1(A:16:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.000

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	A	18	TYR	0	0.007	-0.006	2.080	-12.519	-7.947	3.172	-3.594	-4.150	0.021
4	A	19	LYS	1	0.888	0.932	5.726	0.473	0.473	0.000	0.000	0.000	0.000
5	A	20	SER	0	0.010	0.002	9.268	0.193	0.193	0.000	0.000	0.000	0.000
6	A	21	VAL	0	-0.070	-0.024	11.923	-0.119	-0.119	0.000	0.000	0.000	0.000
7	A	22	ASN	0	-0.018	-0.013	15.609	0.102	0.102	0.000	0.000	0.000	0.000
8	A	23	ILE	0	-0.034	-0.012	19.115	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	24	THR	0	0.019	0.008	21.404	0.019	0.019	0.000	0.000	0.000	0.000
10	A	25	PHE	0	0.056	0.003	23.093	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	26	GLU	-1	-0.850	-0.929	26.554	0.077	0.077	0.000	0.000	0.000	0.000
12	A	27	LEU	0	-0.132	-0.057	26.410	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	28	ASP	-1	-0.873	-0.939	30.155	0.034	0.034	0.000	0.000	0.000	0.000
14	A	29	GLU	-1	-1.008	-0.997	32.882	0.034	0.034	0.000	0.000	0.000	0.000
15	A	30	ARG	1	0.906	0.948	33.947	-0.065	-0.065	0.000	0.000	0.000	0.000
16	A	31	ILE	0	-0.024	-0.021	30.350	0.005	0.005	0.000	0.000	0.000	0.000
17	A	32	ASP	-1	-0.741	-0.860	29.207	0.084	0.084	0.000	0.000	0.000	0.000
18	A	33	LYS	1	0.977	0.963	27.775	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	34	VAL	0	-0.055	-0.013	27.155	0.011	0.011	0.000	0.000	0.000	0.000
20	A	35	LEU	0	0.039	0.012	25.170	0.022	0.022	0.000	0.000	0.000	0.000
21	A	36	ASN	0	-0.058	-0.011	23.443	0.014	0.014	0.000	0.000	0.000	0.000
22	A	37	GLU	-1	-0.966	-0.979	22.374	0.103	0.103	0.000	0.000	0.000	0.000
23	A	38	LYS	1	0.856	0.936	21.995	-0.185	-0.185	0.000	0.000	0.000	0.000
24	A	39	CYS	0	-0.069	-0.042	20.055	0.046	0.046	0.000	0.000	0.000	0.000
25	A	40	SER	0	0.105	0.033	20.085	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	41	ALA	0	-0.009	0.015	15.540	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	42	TYR	0	-0.013	0.018	14.289	0.120	0.120	0.000	0.000	0.000	0.000
28	A	43	THR	0	-0.053	-0.024	8.777	0.005	0.005	0.000	0.000	0.000	0.000
29	A	44	VAL	0	0.039	0.005	10.497	0.082	0.082	0.000	0.000	0.000	0.000
30	A	45	GLU	-1	-0.849	-0.925	9.133	-0.948	-0.948	0.000	0.000	0.000	0.000
31	A	46	LEU	0	-0.085	-0.028	4.996	-0.174	-0.174	0.000	0.000	0.000	0.000
32	A	47	GLY	0	-0.006	-0.001	7.372	0.084	0.084	0.000	0.000	0.000	0.000
33	A	48	THR	0	-0.072	-0.025	10.590	0.069	0.069	0.000	0.000	0.000	0.000
34	A	49	GLU	-1	-0.913	-0.940	13.306	-0.052	-0.052	0.000	0.000	0.000	0.000
35	A	50	VAL	0	0.029	-0.007	16.788	0.026	0.026	0.000	0.000	0.000	0.000
36	A	51	ASN	0	0.022	0.013	19.931	0.005	0.005	0.000	0.000	0.000	0.000
37	A	52	GLU	-1	-0.833	-0.938	17.668	0.164	0.164	0.000	0.000	0.000	0.000
38	A	53	PHE	0	-0.048	-0.024	16.660	0.055	0.055	0.000	0.000	0.000	0.000
39	A	54	ALA	0	0.053	0.014	18.804	0.019	0.019	0.000	0.000	0.000	0.000
40	A	55	CYS	0	-0.003	-0.006	21.397	0.002	0.002	0.000	0.000	0.000	0.000
41	A	56	VAL	0	-0.023	0.004	16.122	0.027	0.027	0.000	0.000	0.000	0.000
42	A	57	VAL	0	-0.020	-0.018	19.513	0.025	0.025	0.000	0.000	0.000	0.000
43	A	58	ALA	0	0.032	0.023	21.282	0.000	0.000	0.000	0.000	0.000	0.000
44	A	59	ASP	-1	-0.909	-0.960	21.172	0.305	0.305	0.000	0.000	0.000	0.000
45	A	60	ALA	0	-0.056	-0.031	19.659	0.009	0.009	0.000	0.000	0.000	0.000
46	A	61	VAL	0	-0.004	-0.003	21.662	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	62	ILE	0	0.005	0.010	25.097	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	63	LYS	1	0.924	0.965	20.335	-0.420	-0.420	0.000	0.000	0.000	0.000
49	A	64	THR	0	-0.080	-0.049	23.689	0.004	0.004	0.000	0.000	0.000	0.000
50	A	65	LEU	0	-0.018	-0.011	25.699	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	66	GLN	0	0.073	0.040	28.828	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	67	PRO	0	-0.088	-0.045	28.426	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	68	VAL	0	0.002	0.022	31.610	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	69	SER	0	0.046	0.028	34.160	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	70	GLU	-1	-0.992	-1.016	36.500	0.109	0.109	0.000	0.000	0.000	0.000
56	A	71	LEU	0	-0.019	-0.024	36.663	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	72	LEU	0	-0.003	-0.012	32.686	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	73	THR	0	0.047	0.043	37.129	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	74	PRO	0	-0.065	-0.037	40.198	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	75	LEU	0	-0.066	-0.012	36.167	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	76	GLY	0	-0.038	-0.035	40.523	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	77	ILE	0	-0.072	-0.019	34.835	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	78	ASP	-1	-0.828	-0.911	38.131	0.076	0.076	0.000	0.000	0.000	0.000
64	A	79	LEU	0	-0.100	-0.058	31.976	0.005	0.005	0.000	0.000	0.000	0.000
65	A	80	ASP	-1	-0.873	-0.944	33.974	0.112	0.112	0.000	0.000	0.000	0.000
66	A	81	GLU	-1	-0.977	-0.991	35.210	0.073	0.073	0.000	0.000	0.000	0.000
67	A	82	TRP	0	-0.027	-0.016	28.971	0.003	0.003	0.000	0.000	0.000	0.000
68	A	83	SER	0	-0.023	-0.013	29.579	0.015	0.015	0.000	0.000	0.000	0.000
69	A	84	MET	0	-0.072	-0.032	30.550	0.005	0.005	0.000	0.000	0.000	0.000
70	A	85	ALA	0	0.028	0.028	32.650	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	86	THR	0	-0.014	0.003	27.617	0.009	0.009	0.000	0.000	0.000	0.000
72	A	87	TYR	0	0.020	0.005	27.155	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	88	TYR	0	-0.020	-0.018	26.495	0.007	0.007	0.000	0.000	0.000	0.000
74	A	89	LEU	0	-0.015	-0.010	20.472	0.000	0.000	0.000	0.000	0.000	0.000
75	A	90	PHE	0	-0.052	-0.016	24.418	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	91	ASP	-1	-0.819	-0.918	22.855	-0.074	-0.074	0.000	0.000	0.000	0.000
77	A	92	GLU	-1	-0.906	-0.960	24.871	-0.095	-0.095	0.000	0.000	0.000	0.000
78	A	93	SER	0	-0.051	-0.016	28.215	0.000	0.000	0.000	0.000	0.000	0.000
79	A	94	GLY	0	-0.010	-0.020	29.113	0.009	0.009	0.000	0.000	0.000	0.000
80	A	95	GLU	-1	-0.905	-0.927	25.799	-0.085	-0.085	0.000	0.000	0.000	0.000
81	A	96	PHE	0	0.015	0.003	21.576	0.006	0.006	0.000	0.000	0.000	0.000
82	A	97	LYS	1	0.749	0.863	20.157	0.075	0.075	0.000	0.000	0.000	0.000
83	A	98	LEU	0	-0.009	-0.012	13.837	0.019	0.019	0.000	0.000	0.000	0.000
84	A	99	ALA	0	0.010	-0.004	17.496	-0.051	-0.051	0.000	0.000	0.000	0.000
85	A	100	SER	0	-0.040	-0.044	17.360	0.014	0.014	0.000	0.000	0.000	0.000
86	A	101	HIS	0	0.010	0.005	18.408	0.014	0.014	0.000	0.000	0.000	0.000
87	A	102	MET	0	-0.010	0.030	18.863	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	103	TYR	0	0.022	0.007	22.069	0.020	0.020	0.000	0.000	0.000	0.000
89	A	104	CYS	0	-0.042	-0.006	23.620	0.005	0.005	0.000	0.000	0.000	0.000
90	A	105	SER	0	0.049	0.029	25.649	0.003	0.003	0.000	0.000	0.000	0.000
91	A	106	PHE	0	0.022	0.016	29.378	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	107	TYR	0	-0.045	-0.014	31.949	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	108	PRO	0	-0.058	-0.033	32.140	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	109	PRO	0	-0.034	-0.023	35.227	0.002	0.002	0.000	0.000	0.000	0.000
95	A	110	ASP	-1	-0.897	-0.938	37.116	0.051	0.051	0.000	0.000	0.000	0.000
96	A	111	GLU	-2	-1.980	-1.984	38.297	0.074	0.074	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLN)