FMO DATABASE

FMODB ID: Z25LN

Calculation Name: 6LVN-ABCD-Xray95

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6LVN

Chain ID: ABCD

ChEMBL ID:

UniProt ID: P0DTC2

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	158
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1044281.963538
FMO2-HF: Nuclear repulsion	990346.242468
FMO2-HF: Total energy	-53935.72107
FMO2-MP2: Total energy	-54095.707125

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:ILE )

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

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.
-13.398	-7.736	2.444	-2.645	-5.463	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / 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

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].	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	GLY	0	0.005	3.332	-5.087	-2.404	0.038	-1.272	-1.450	0.008
4	A	5	ILE	0	0.051	2.276	-2.954	-1.574	2.285	-0.808	-2.857	-0.001
5	A	6	ASN	0	0.042	2.831	-2.136	-0.592	0.121	-0.552	-1.113	-0.002
6	A	7	ALA	0	-0.018	5.634	0.192	0.192	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.016	7.392	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.038	6.992	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.008	9.387	0.071	0.071	0.000	0.000	0.000	0.000
10	A	11	ASN	0	-0.036	11.831	-0.044	-0.044	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.047	11.165	0.012	0.012	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.003	13.632	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.875	15.506	-0.143	-0.143	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.865	17.286	0.114	0.114	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.016	16.210	0.005	0.005	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.891	19.782	-0.102	-0.102	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.834	21.698	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.013	21.291	0.003	0.003	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.028	22.773	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.870	25.963	0.016	0.016	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.005	27.477	0.004	0.004	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.028	28.571	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.917	28.052	0.054	0.054	0.000	0.000	0.000	0.000
24	A	25	ASN	0	0.015	32.064	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.014	31.960	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.038	34.608	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.855	36.461	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.024	37.823	0.003	0.003	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.054	38.039	0.002	0.002	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.012	40.116	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.899	42.502	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.099	41.992	0.002	0.002	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.067	43.313	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.983	46.892	-0.009	-0.009	0.000	0.000	0.000	0.000
35	B	2	ILE	0	0.069	35.860	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	3	SER	0	0.029	37.686	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	4	GLY	0	0.076	36.035	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	5	ILE	0	0.046	32.755	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	6	ASN	0	0.020	34.994	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	7	ALA	0	-0.012	37.129	-0.003	-0.003	0.000	0.000	0.000	0.000
41	B	8	SER	0	-0.002	32.311	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	9	VAL	0	0.025	34.290	-0.005	-0.005	0.000	0.000	0.000	0.000
43	B	10	VAL	0	0.007	35.500	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	11	ASN	0	-0.080	35.671	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	12	ILE	0	0.038	30.447	-0.004	-0.004	0.000	0.000	0.000	0.000
46	B	13	GLN	0	0.034	34.279	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	14	LYS	1	0.844	37.094	0.047	0.047	0.000	0.000	0.000	0.000
48	B	15	GLU	-1	-0.749	34.316	-0.060	-0.060	0.000	0.000	0.000	0.000
49	B	16	ILE	0	0.010	33.256	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	17	ASP	-1	-0.847	35.985	-0.033	-0.033	0.000	0.000	0.000	0.000
51	B	18	ARG	1	0.785	37.710	0.055	0.055	0.000	0.000	0.000	0.000
52	B	19	LEU	0	-0.005	32.309	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	20	ASN	0	0.028	36.687	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	21	GLU	-1	-0.868	39.060	-0.039	-0.039	0.000	0.000	0.000	0.000
55	B	22	VAL	0	-0.035	36.809	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	23	ALA	0	0.026	37.415	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	24	LYS	1	0.839	39.080	0.038	0.038	0.000	0.000	0.000	0.000
58	B	25	ASN	0	0.050	42.531	0.002	0.002	0.000	0.000	0.000	0.000
59	B	26	LEU	0	-0.032	37.036	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	27	ASN	0	-0.004	41.266	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	28	GLU	-1	-0.928	42.852	-0.041	-0.041	0.000	0.000	0.000	0.000
62	B	29	SER	0	0.013	43.448	0.000	0.000	0.000	0.000	0.000	0.000
63	B	30	LEU	0	-0.044	40.710	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	31	ILE	0	0.005	43.953	0.000	0.000	0.000	0.000	0.000	0.000
65	B	32	ASP	-1	-0.878	47.298	-0.044	-0.044	0.000	0.000	0.000	0.000
66	B	33	LEU	0	-0.087	43.230	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	34	GLN	0	-0.081	43.536	0.002	0.002	0.000	0.000	0.000	0.000
68	B	35	GLU	-1	-1.016	47.794	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	36	LEU	-1	-1.046	50.212	-0.048	-0.048	0.000	0.000	0.000	0.000
70	C	3	SER	0	-0.003	51.340	0.000	0.000	0.000	0.000	0.000	0.000
71	C	4	GLY	0	0.023	49.078	0.000	0.000	0.000	0.000	0.000	0.000
72	C	5	ILE	0	0.065	46.746	0.001	0.001	0.000	0.000	0.000	0.000
73	C	6	ASN	0	0.054	45.797	0.001	0.001	0.000	0.000	0.000	0.000
74	C	7	ALA	0	0.033	45.324	-0.002	-0.002	0.000	0.000	0.000	0.000
75	C	8	SER	0	-0.010	42.721	0.001	0.001	0.000	0.000	0.000	0.000
76	C	9	VAL	0	0.011	41.266	0.000	0.000	0.000	0.000	0.000	0.000
77	C	10	VAL	0	0.004	40.623	-0.002	-0.002	0.000	0.000	0.000	0.000
78	C	11	ASN	0	-0.089	39.124	0.000	0.000	0.000	0.000	0.000	0.000
79	C	12	ILE	0	0.051	36.412	0.000	0.000	0.000	0.000	0.000	0.000
80	C	13	GLN	0	-0.009	35.407	0.000	0.000	0.000	0.000	0.000	0.000
81	C	14	LYS	1	0.877	35.132	-0.002	-0.002	0.000	0.000	0.000	0.000
82	C	15	GLU	-1	-0.796	32.639	0.000	0.000	0.000	0.000	0.000	0.000
83	C	16	ILE	0	0.014	31.116	-0.001	-0.001	0.000	0.000	0.000	0.000
84	C	17	ASP	-1	-0.863	30.360	-0.044	-0.044	0.000	0.000	0.000	0.000
85	C	18	ARG	1	0.848	28.213	-0.002	-0.002	0.000	0.000	0.000	0.000
86	C	19	LEU	0	-0.010	26.686	-0.002	-0.002	0.000	0.000	0.000	0.000
87	C	20	ASN	0	-0.029	25.418	-0.008	-0.008	0.000	0.000	0.000	0.000
88	C	21	GLU	-1	-0.803	24.913	-0.064	-0.064	0.000	0.000	0.000	0.000
89	C	22	VAL	0	-0.041	21.852	-0.009	-0.009	0.000	0.000	0.000	0.000
90	C	23	ALA	0	-0.006	20.919	-0.009	-0.009	0.000	0.000	0.000	0.000
91	C	24	LYS	1	0.815	19.938	0.102	0.102	0.000	0.000	0.000	0.000
92	C	25	ASN	0	0.020	19.501	-0.038	-0.038	0.000	0.000	0.000	0.000
93	C	26	LEU	0	-0.018	16.408	-0.018	-0.018	0.000	0.000	0.000	0.000
94	C	27	ASN	0	0.009	15.120	-0.014	-0.014	0.000	0.000	0.000	0.000
95	C	28	GLU	-1	-0.862	14.978	-0.239	-0.239	0.000	0.000	0.000	0.000
96	C	29	SER	0	0.026	13.095	-0.035	-0.035	0.000	0.000	0.000	0.000
97	C	30	LEU	0	-0.063	10.651	-0.083	-0.083	0.000	0.000	0.000	0.000
98	C	31	ILE	0	-0.051	10.091	-0.180	-0.180	0.000	0.000	0.000	0.000
99	C	32	ASP	-1	-0.920	10.399	-0.529	-0.529	0.000	0.000	0.000	0.000
100	C	33	LEU	0	-0.106	6.749	-0.100	-0.100	0.000	0.000	0.000	0.000
101	C	34	GLN	0	-0.094	5.533	-0.513	-0.513	0.000	0.000	0.000	0.000
102	C	35	GLU	-1	-0.961	5.305	-1.518	-1.518	0.000	0.000	0.000	0.000
103	D	2	ILE	0	0.071	47.620	-0.002	-0.002	0.000	0.000	0.000	0.000
104	D	3	SER	0	-0.002	42.855	-0.001	-0.001	0.000	0.000	0.000	0.000
105	D	4	GLY	0	0.033	41.594	-0.003	-0.003	0.000	0.000	0.000	0.000
106	D	5	ILE	0	0.075	41.792	-0.003	-0.003	0.000	0.000	0.000	0.000
107	D	6	ASN	0	0.033	41.849	0.001	0.001	0.000	0.000	0.000	0.000
108	D	7	ALA	0	-0.006	37.920	-0.001	-0.001	0.000	0.000	0.000	0.000
109	D	8	SER	0	-0.031	38.005	-0.005	-0.005	0.000	0.000	0.000	0.000
110	D	9	VAL	0	0.032	39.118	-0.001	-0.001	0.000	0.000	0.000	0.000
111	D	10	VAL	0	-0.009	35.599	-0.001	-0.001	0.000	0.000	0.000	0.000
112	D	11	ASN	0	-0.076	33.574	-0.007	-0.007	0.000	0.000	0.000	0.000
113	D	12	ILE	0	0.028	34.684	-0.004	-0.004	0.000	0.000	0.000	0.000
114	D	13	GLN	0	-0.002	36.674	0.003	0.003	0.000	0.000	0.000	0.000
115	D	14	LYS	1	0.950	29.250	0.119	0.119	0.000	0.000	0.000	0.000
116	D	15	GLU	-1	-0.811	30.332	-0.125	-0.125	0.000	0.000	0.000	0.000
117	D	16	ILE	0	0.009	33.062	0.000	0.000	0.000	0.000	0.000	0.000
118	D	17	ASP	-1	-0.870	32.649	-0.067	-0.067	0.000	0.000	0.000	0.000
119	D	18	ARG	1	0.814	26.275	0.133	0.133	0.000	0.000	0.000	0.000
120	D	19	LEU	0	-0.007	30.185	0.000	0.000	0.000	0.000	0.000	0.000
121	D	20	ASN	0	-0.003	32.577	0.005	0.005	0.000	0.000	0.000	0.000
122	D	21	GLU	-1	-0.833	25.585	-0.098	-0.098	0.000	0.000	0.000	0.000
123	D	22	VAL	0	-0.028	27.663	0.002	0.002	0.000	0.000	0.000	0.000
124	D	23	ALA	0	0.032	29.400	0.005	0.005	0.000	0.000	0.000	0.000
125	D	24	LYS	1	0.860	27.505	0.051	0.051	0.000	0.000	0.000	0.000
126	D	25	ASN	0	0.008	25.151	0.017	0.017	0.000	0.000	0.000	0.000
127	D	26	LEU	0	-0.001	28.073	0.005	0.005	0.000	0.000	0.000	0.000
128	D	27	ASN	0	-0.049	29.843	0.010	0.010	0.000	0.000	0.000	0.000
129	D	28	GLU	-1	-0.923	27.318	-0.010	-0.010	0.000	0.000	0.000	0.000
130	D	29	SER	0	-0.003	26.513	0.003	0.003	0.000	0.000	0.000	0.000
131	D	30	LEU	0	-0.041	28.289	0.005	0.005	0.000	0.000	0.000	0.000
132	D	31	ILE	0	-0.025	30.969	0.005	0.005	0.000	0.000	0.000	0.000
133	D	32	ASP	-1	-0.919	25.677	0.019	0.019	0.000	0.000	0.000	0.000
134	D	33	LEU	0	-0.100	28.804	0.004	0.004	0.000	0.000	0.000	0.000
135	D	34	GLN	0	-0.109	30.366	0.001	0.001	0.000	0.000	0.000	0.000
136	D	35	GLU	-1	-1.028	30.872	0.039	0.039	0.000	0.000	0.000	0.000
137	A	101	HOH	0	-0.059	50.286	0.001	0.001	0.000	0.000	0.000	0.000
138	A	102	HOH	0	-0.034	49.001	0.000	0.000	0.000	0.000	0.000	0.000
139	A	103	HOH	0	0.008	10.161	-0.043	-0.043	0.000	0.000	0.000	0.000
140	A	104	HOH	0	-0.034	30.888	0.001	0.001	0.000	0.000	0.000	0.000
141	A	105	HOH	0	-0.042	35.700	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	106	HOH	0	-0.039	17.228	0.004	0.004	0.000	0.000	0.000	0.000
143	B	101	HOH	0	-0.041	37.029	0.000	0.000	0.000	0.000	0.000	0.000
144	B	102	HOH	0	-0.058	48.790	0.001	0.001	0.000	0.000	0.000	0.000
145	B	103	HOH	0	-0.049	43.385	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	104	HOH	0	-0.016	39.689	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	105	HOH	0	-0.046	42.232	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	106	HOH	0	-0.018	40.157	0.000	0.000	0.000	0.000	0.000	0.000
149	B	107	HOH	0	-0.017	40.768	-0.001	-0.001	0.000	0.000	0.000	0.000
150	B	108	HOH	0	0.004	38.537	0.000	0.000	0.000	0.000	0.000	0.000
151	B	109	HOH	0	-0.009	42.070	-0.001	-0.001	0.000	0.000	0.000	0.000
152	C	101	HOH	0	-0.024	24.987	-0.001	-0.001	0.000	0.000	0.000	0.000
153	C	102	HOH	0	-0.054	3.740	0.241	0.296	0.000	-0.013	-0.043	0.000
154	C	103	HOH	0	-0.011	19.367	-0.006	-0.006	0.000	0.000	0.000	0.000
155	C	104	HOH	0	-0.010	29.121	-0.004	-0.004	0.000	0.000	0.000	0.000
156	C	105	HOH	0	-0.005	27.134	-0.005	-0.005	0.000	0.000	0.000	0.000
157	D	101	HOH	0	-0.011	36.984	-0.001	-0.001	0.000	0.000	0.000	0.000
158	D	102	HOH	0	-0.040	31.937	0.003	0.003	0.000	0.000	0.000	0.000

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