FMO DATABASE

FMODB ID: 3NVZL

Calculation Name: 6W9Q-A-Xray102

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 6W9Q

Chain ID: A

ChEMBL ID:

UniProt ID: P0DTD1

Base Structure: X-ray

Registration Date: 2020-04-16

Reference: K. Kato, Y. Handa, Y. Kawashima, K. Fukuzawa et. Al., FMO Calculation for SARS Cov-2 related proteins. To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Selected crystal waters in PDB.
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	127
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-959551.079271
FMO2-HF: Nuclear repulsion	912004.605982
FMO2-HF: Total energy	-47546.473289
FMO2-MP2: Total energy	-47683.616367

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:-9:ALA )

Summations of interaction energy for fragment #1(A:-9: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.
2.669	4.013	0.011	-0.486	-0.869	0

Interaction energy analysis for fragmet #1(A:-9:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : ******

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].	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	A	-7	GLU	-1	-0.869	3.896	-59.082	-58.050	-0.001	-0.430	-0.601
4	A	-6	VAL	0	-0.013	6.411	4.087	4.087	0.000	0.000	0.000
5	A	-5	LEU	0	0.010	10.230	-0.582	-0.582	0.000	0.000	0.000
6	A	-4	PHE	0	-0.023	12.814	1.426	1.426	0.000	0.000	0.000
7	A	-3	GLN	0	0.011	14.959	0.765	0.765	0.000	0.000	0.000
8	A	-2	GLY	0	0.028	18.308	0.762	0.762	0.000	0.000	0.000
9	A	-1	PRO	0	-0.045	17.873	-0.886	-0.886	0.000	0.000	0.000
10	A	0	GLY	0	0.005	20.416	0.658	0.658	0.000	0.000	0.000
11	A	1	ASN	0	-0.028	22.707	0.047	0.047	0.000	0.000	0.000
12	A	2	ASN	0	-0.021	23.305	0.319	0.319	0.000	0.000	0.000
13	A	3	GLU	-1	-0.864	18.911	-15.187	-15.187	0.000	0.000	0.000
14	A	4	LEU	0	-0.029	15.898	-0.255	-0.255	0.000	0.000	0.000
15	A	5	SER	0	0.020	13.920	-0.076	-0.076	0.000	0.000	0.000
16	A	6	PRO	0	-0.027	8.939	-0.009	-0.009	0.000	0.000	0.000
17	A	7	VAL	0	-0.023	9.178	0.509	0.509	0.000	0.000	0.000
18	A	8	ALA	0	0.053	5.228	-1.307	-1.307	0.000	0.000	0.000
19	A	9	LEU	0	-0.049	6.075	6.134	6.134	0.000	0.000	0.000
20	A	10	ARG	1	0.929	5.834	27.239	27.239	0.000	0.000	0.000
21	A	11	GLN	0	0.029	3.380	6.275	6.538	0.013	-0.051	-0.225
22	A	12	MET	0	-0.070	7.867	-0.155	-0.155	0.000	0.000	0.000
23	A	13	SER	0	-0.013	11.147	0.084	0.084	0.000	0.000	0.000
24	A	14	CYS	0	-0.056	13.860	0.268	0.268	0.000	0.000	0.000
25	A	15	ALA	0	0.093	17.026	0.055	0.055	0.000	0.000	0.000
26	A	16	ALA	0	0.017	20.050	0.088	0.088	0.000	0.000	0.000
27	A	17	GLY	0	0.058	21.881	0.264	0.264	0.000	0.000	0.000
28	A	18	THR	0	0.039	25.193	-0.058	-0.058	0.000	0.000	0.000
29	A	19	THR	0	0.005	28.075	0.207	0.207	0.000	0.000	0.000
30	A	20	GLN	0	0.044	27.987	-0.092	-0.092	0.000	0.000	0.000
31	A	21	THR	0	-0.021	28.548	-0.140	-0.140	0.000	0.000	0.000
32	A	22	ALA	0	-0.037	28.099	-0.046	-0.046	0.000	0.000	0.000
33	A	23	CYS	0	-0.087	24.162	-0.337	-0.337	0.000	0.000	0.000
34	A	24	THR	0	0.042	25.614	-0.064	-0.064	0.000	0.000	0.000
35	A	25	ASP	-1	-0.885	22.826	-12.016	-12.016	0.000	0.000	0.000
36	A	26	ASP	-1	-0.865	17.512	-16.341	-16.341	0.000	0.000	0.000
37	A	27	ASN	0	-0.001	18.874	-0.483	-0.483	0.000	0.000	0.000
38	A	28	ALA	0	-0.011	16.044	0.124	0.124	0.000	0.000	0.000
39	A	29	LEU	0	-0.018	8.294	-0.486	-0.486	0.000	0.000	0.000
40	A	30	ALA	0	0.035	12.580	0.294	0.294	0.000	0.000	0.000
41	A	31	TYR	0	0.026	7.066	-0.936	-0.936	0.000	0.000	0.000
42	A	32	TYR	0	-0.030	10.114	2.406	2.406	0.000	0.000	0.000
43	A	33	ASN	0	0.046	10.596	-4.262	-4.262	0.000	0.000	0.000
44	A	34	THR	0	-0.018	12.546	0.749	0.749	0.000	0.000	0.000
45	A	35	THR	0	-0.045	14.492	0.076	0.076	0.000	0.000	0.000
46	A	36	LYS	1	1.006	17.761	13.878	13.878	0.000	0.000	0.000
47	A	37	GLY	0	0.023	21.015	0.596	0.596	0.000	0.000	0.000
48	A	38	GLY	0	0.052	19.251	0.425	0.425	0.000	0.000	0.000
49	A	39	ARG	1	0.907	13.718	19.590	19.590	0.000	0.000	0.000
50	A	40	PHE	0	0.008	15.940	0.954	0.954	0.000	0.000	0.000
51	A	41	VAL	0	0.027	14.783	-1.676	-1.676	0.000	0.000	0.000
52	A	42	LEU	0	-0.046	12.787	0.932	0.932	0.000	0.000	0.000
53	A	43	ALA	0	0.016	13.624	1.063	1.063	0.000	0.000	0.000
54	A	44	LEU	0	0.005	13.844	-1.028	-1.028	0.000	0.000	0.000
55	A	45	LEU	0	-0.027	10.651	0.505	0.505	0.000	0.000	0.000
56	A	46	SER	0	0.008	14.080	0.128	0.128	0.000	0.000	0.000
57	A	47	ASP	-1	-0.795	16.749	-16.484	-16.484	0.000	0.000	0.000
58	A	48	LEU	0	0.012	18.938	0.520	0.520	0.000	0.000	0.000
59	A	49	GLN	0	0.025	21.166	-0.565	-0.565	0.000	0.000	0.000
60	A	50	ASP	-1	-0.899	23.606	-11.394	-11.394	0.000	0.000	0.000
61	A	51	LEU	0	-0.050	20.189	0.299	0.299	0.000	0.000	0.000
62	A	52	LYS	1	0.939	24.164	10.070	10.070	0.000	0.000	0.000
63	A	53	TRP	0	-0.034	24.521	0.035	0.035	0.000	0.000	0.000
64	A	54	ALA	0	0.043	19.604	-0.203	-0.203	0.000	0.000	0.000
65	A	55	ARG	1	0.883	21.278	12.636	12.636	0.000	0.000	0.000
66	A	56	PHE	0	-0.001	16.620	-0.661	-0.661	0.000	0.000	0.000
67	A	57	PRO	0	0.017	20.117	0.610	0.610	0.000	0.000	0.000
68	A	58	LYS	1	0.909	21.155	10.590	10.590	0.000	0.000	0.000
69	A	59	SER	0	-0.013	19.921	-0.023	-0.023	0.000	0.000	0.000
70	A	60	ASP	-1	-0.924	21.492	-12.617	-12.617	0.000	0.000	0.000
71	A	61	GLY	0	0.054	25.079	0.221	0.221	0.000	0.000	0.000
72	A	62	THR	0	-0.047	26.346	0.337	0.337	0.000	0.000	0.000
73	A	63	GLY	0	0.037	27.515	0.361	0.361	0.000	0.000	0.000
74	A	64	THR	0	-0.054	25.109	-0.415	-0.415	0.000	0.000	0.000
75	A	65	ILE	0	-0.009	22.432	0.394	0.394	0.000	0.000	0.000
76	A	66	TYR	0	0.032	23.810	-0.485	-0.485	0.000	0.000	0.000
77	A	67	THR	0	-0.041	21.332	0.094	0.094	0.000	0.000	0.000
78	A	68	GLU	-1	-0.880	23.620	-10.863	-10.863	0.000	0.000	0.000
79	A	69	LEU	0	-0.026	19.833	-0.535	-0.535	0.000	0.000	0.000
80	A	70	GLU	-1	-0.783	22.338	-12.000	-12.000	0.000	0.000	0.000
81	A	71	PRO	0	-0.007	23.209	-0.246	-0.246	0.000	0.000	0.000
82	A	72	PRO	0	-0.013	21.008	-0.308	-0.308	0.000	0.000	0.000
83	A	73	CYS	0	-0.050	18.719	0.499	0.499	0.000	0.000	0.000
84	A	74	ARG	1	0.993	18.750	12.123	12.123	0.000	0.000	0.000
85	A	75	PHE	0	-0.013	12.142	0.156	0.156	0.000	0.000	0.000
86	A	76	VAL	0	-0.009	17.505	0.148	0.148	0.000	0.000	0.000
87	A	77	THR	0	-0.002	12.198	-0.829	-0.829	0.000	0.000	0.000
88	A	78	ASP	-1	-0.816	14.368	-14.930	-14.930	0.000	0.000	0.000
89	A	79	THR	0	-0.055	13.188	-1.160	-1.160	0.000	0.000	0.000
90	A	80	PRO	0	0.063	12.451	0.876	0.876	0.000	0.000	0.000
91	A	81	LYS	1	0.884	15.441	15.641	15.641	0.000	0.000	0.000
92	A	82	GLY	0	0.058	17.636	0.867	0.867	0.000	0.000	0.000
93	A	83	PRO	0	0.010	17.648	-0.745	-0.745	0.000	0.000	0.000
94	A	84	LYS	1	0.871	17.074	15.313	15.313	0.000	0.000	0.000
95	A	85	VAL	0	-0.035	17.483	-0.491	-0.491	0.000	0.000	0.000
96	A	86	LYS	1	0.862	13.201	18.159	18.159	0.000	0.000	0.000
97	A	87	TYR	0	0.000	16.726	0.438	0.438	0.000	0.000	0.000
98	A	88	LEU	0	-0.011	13.120	-0.806	-0.806	0.000	0.000	0.000
99	A	89	TYR	0	-0.018	16.484	0.930	0.930	0.000	0.000	0.000
100	A	90	PHE	0	0.025	15.537	-0.825	-0.825	0.000	0.000	0.000
101	A	91	ILE	0	0.011	17.927	0.773	0.773	0.000	0.000	0.000
102	A	92	LYS	1	0.964	20.493	11.135	11.135	0.000	0.000	0.000
103	A	93	GLY	0	-0.078	24.205	0.063	0.063	0.000	0.000	0.000
104	A	94	LEU	0	-0.062	17.466	-0.009	-0.009	0.000	0.000	0.000
105	A	95	ASN	0	0.054	21.410	-0.353	-0.353	0.000	0.000	0.000
106	A	96	ASN	0	0.085	21.149	-0.789	-0.789	0.000	0.000	0.000
107	A	97	LEU	0	0.009	19.006	-0.375	-0.375	0.000	0.000	0.000
108	A	98	ASN	0	0.033	17.141	-1.707	-1.707	0.000	0.000	0.000
109	A	99	ARG	1	0.805	16.167	12.770	12.770	0.000	0.000	0.000
110	A	100	GLY	0	0.018	16.492	-0.567	-0.567	0.000	0.000	0.000
111	A	101	MET	0	-0.015	13.601	-0.442	-0.442	0.000	0.000	0.000
112	A	102	VAL	0	0.002	11.616	-1.858	-1.858	0.000	0.000	0.000
113	A	103	LEU	0	-0.005	11.540	-1.285	-1.285	0.000	0.000	0.000
114	A	104	GLY	0	0.018	13.091	-0.065	-0.065	0.000	0.000	0.000
115	A	105	SER	0	-0.027	7.998	-2.248	-2.248	0.000	0.000	0.000
116	A	106	LEU	0	0.011	7.484	-3.851	-3.851	0.000	0.000	0.000
117	A	107	ALA	0	0.014	8.818	0.090	0.090	0.000	0.000	0.000
118	A	108	ALA	0	0.017	8.242	1.319	1.319	0.000	0.000	0.000
119	A	109	THR	0	-0.032	4.474	-1.133	-1.084	-0.001	-0.005	-0.043
120	A	110	VAL	0	-0.059	7.923	1.355	1.355	0.000	0.000	0.000
121	A	111	ARG	1	0.917	11.207	18.510	18.510	0.000	0.000	0.000
122	A	112	LEU	0	-0.059	8.727	1.065	1.065	0.000	0.000	0.000
123	A	113	GLN	-1	-0.939	11.883	-19.770	-19.770	0.000	0.000	0.000
124	A	301	HOH	0	-0.028	9.084	0.762	0.762	0.000	0.000	0.000
125	A	302	HOH	0	-0.019	6.240	-0.144	-0.144	0.000	0.000	0.000
126	A	303	HOH	0	0.011	6.509	-2.643	-2.643	0.000	0.000	0.000
127	A	304	HOH	0	-0.011	6.806	1.931	1.931	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-9:ALA )