FMO DATABASE

FMODB ID: 2KVZR

Calculation Name: 6WC1-A-Xray89

Preferred Name:

Target Type:

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 6WC1

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	117
LigandCharge
Software	MIZUHO/ABINIT-MP 4.0(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-837989.929484
FMO2-HF: Nuclear repulsion	794213.39721
FMO2-HF: Total energy	-43776.532274
FMO2-MP2: Total energy	-43902.487259

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:2:ASN )

Summations of interaction energy for fragment #1(A:2:ASN )

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.
1.718	2.668	-0.003	-0.446	-0.501	0.001

Interaction energy analysis for fragmet #1(A:2:ASN )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.044

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	A	4	LEU	0	-0.012	0.004	3.861	-0.426	0.524	-0.003	-0.446	-0.501	0.001
4	A	5	SER	0	-0.026	-0.022	5.791	0.808	0.808	0.000	0.000	0.000	0.000
5	A	6	PRO	0	-0.025	0.003	8.986	0.113	0.113	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.011	-0.022	11.869	0.112	0.112	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.002	0.008	15.280	0.005	0.005	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.032	0.012	18.663	0.016	0.016	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.910	0.968	21.111	0.291	0.291	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.053	0.024	24.301	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	12	MET	0	-0.034	-0.002	27.718	0.001	0.001	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.022	-0.004	30.835	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.039	-0.014	33.015	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.055	0.043	35.108	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.008	-0.014	36.160	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.075	0.031	37.995	0.008	0.008	0.000	0.000	0.000	0.000
17	A	18	THR	0	0.049	0.037	39.667	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.002	-0.012	41.857	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.036	0.007	38.130	0.002	0.002	0.000	0.000	0.000	0.000
20	A	21	THR	0	0.017	0.000	41.557	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.039	0.005	43.767	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	CYS	0	-0.091	-0.024	39.612	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.033	-0.029	41.710	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.839	-0.912	42.337	-0.099	-0.099	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.843	-0.924	37.793	-0.140	-0.140	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.043	-0.020	39.096	0.004	0.004	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.031	-0.006	34.237	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.003	0.007	30.006	0.003	0.003	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.029	0.001	28.941	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	31	TYR	0	0.014	0.005	24.142	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.025	-0.036	23.889	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	ASN	0	0.058	0.027	17.739	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.033	-0.018	20.415	0.029	0.029	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.008	0.014	17.626	-0.039	-0.039	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.980	0.985	18.104	0.282	0.282	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.044	0.014	19.787	0.028	0.028	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.003	0.016	23.031	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.885	0.925	23.448	0.193	0.193	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.019	0.014	20.144	0.013	0.013	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.028	0.002	23.061	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.052	-0.018	19.270	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.025	-0.005	23.898	0.007	0.007	0.000	0.000	0.000	0.000
43	A	44	LEU	0	-0.012	-0.006	26.861	0.002	0.002	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.013	0.010	29.787	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	SER	0	0.006	-0.019	31.965	0.008	0.008	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.790	-0.882	35.751	-0.132	-0.132	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.035	0.027	38.805	0.005	0.005	0.000	0.000	0.000	0.000
48	A	49	GLN	0	0.007	0.023	38.100	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.899	-0.953	39.431	-0.114	-0.114	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.043	-0.016	36.584	0.002	0.002	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.890	0.950	36.769	0.127	0.127	0.000	0.000	0.000	0.000
52	A	53	TRP	0	-0.016	-0.014	35.283	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.042	0.022	32.801	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.880	0.944	34.921	0.118	0.118	0.000	0.000	0.000	0.000
55	A	56	PHE	0	-0.013	-0.017	30.895	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	57	PRO	0	0.022	0.010	34.545	0.000	0.000	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.809	0.901	32.828	0.139	0.139	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.043	0.013	31.100	0.002	0.002	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.846	-0.899	33.074	-0.137	-0.137	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.026	0.014	34.871	0.007	0.007	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.062	-0.043	35.920	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.077	0.028	37.458	0.005	0.005	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.058	-0.016	36.880	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.022	-0.011	30.799	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	TYR	0	0.034	0.014	34.662	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	THR	0	-0.024	-0.009	29.480	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.840	-0.926	32.379	-0.148	-0.148	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.040	-0.018	31.307	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.808	-0.868	28.000	-0.224	-0.224	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.002	-0.015	31.747	0.005	0.005	0.000	0.000	0.000	0.000
71	A	72	PRO	0	-0.014	0.010	32.413	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.009	-0.005	30.481	0.004	0.004	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.949	0.983	32.497	0.118	0.118	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.010	-0.008	31.040	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	76	VAL	0	0.017	0.009	34.259	0.005	0.005	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.008	0.010	32.651	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.818	-0.903	35.158	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	79	THR	0	-0.059	-0.050	36.146	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.054	0.017	38.544	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.940	0.966	41.360	0.099	0.099	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.028	0.028	42.004	0.004	0.004	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.036	0.025	39.649	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.837	0.921	38.297	0.109	0.109	0.000	0.000	0.000	0.000
84	A	85	VAL	0	0.003	0.003	37.658	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.816	0.904	34.148	0.142	0.142	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.035	0.010	34.456	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.006	-0.006	26.532	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.003	-0.024	30.748	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.049	0.018	24.143	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.026	0.010	26.056	0.018	0.018	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.858	0.910	26.936	0.159	0.159	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.015	-0.006	26.365	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.086	-0.016	21.511	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	95	ASN	0	0.068	0.032	17.281	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.079	0.008	18.801	0.007	0.007	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.027	0.033	11.981	0.010	0.010	0.000	0.000	0.000	0.000
97	A	98	ASN	0	0.022	-0.002	16.201	0.005	0.005	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.825	0.889	18.345	0.290	0.290	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.029	0.017	18.346	0.023	0.023	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.012	0.000	14.214	0.017	0.017	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.017	0.002	18.270	0.018	0.018	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.020	-0.012	21.979	0.022	0.022	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.002	0.003	19.662	0.019	0.019	0.000	0.000	0.000	0.000
104	A	105	SER	0	0.021	0.012	20.751	0.008	0.008	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.019	-0.003	21.942	0.024	0.024	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.013	0.003	24.154	0.017	0.017	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.026	0.005	21.962	0.013	0.013	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.096	-0.062	24.028	0.015	0.015	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.043	-0.014	26.582	0.020	0.020	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.934	0.975	29.279	0.134	0.134	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.025	-0.018	28.756	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	GLN	-1	-0.965	-0.978	32.677	-0.128	-0.128	0.000	0.000	0.000	0.000
113	A	301	HOH	0	-0.047	-0.039	40.096	0.003	0.003	0.000	0.000	0.000	0.000
114	A	302	HOH	0	0.000	-0.007	19.481	0.011	0.011	0.000	0.000	0.000	0.000
115	A	303	HOH	0	-0.021	-0.020	20.954	-0.016	-0.016	0.000	0.000	0.000	0.000
116	A	304	HOH	0	0.036	0.023	40.963	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	305	HOH	0	0.010	0.008	41.443	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN )