FMO DATABASE

FMODB ID: NNJLQ

Calculation Name: 3EBN-A-Xray372

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3EBN

Chain ID: A

ChEMBL ID: CHEMBL5118

UniProt ID: P0C6X7

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-636018.455495
FMO2-HF: Nuclear repulsion	596757.650727
FMO2-HF: Total energy	-39260.804768
FMO2-MP2: Total energy	-39374.419604

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:198:THR)

Summations of interaction energy for fragment #1(A:198:THR)

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.
-0.53	1.777	0.18	-1.012	-1.474	-0.005

Interaction energy analysis for fragmet #1(A:198:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.012

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	200	ILE	0	0.027	0.017	3.016	-2.715	-0.518	0.181	-1.008	-1.370	-0.005
4	A	201	THR	0	0.050	0.010	4.722	0.701	0.811	-0.001	-0.004	-0.104	0.000
5	A	202	LEU	0	0.031	0.024	6.797	0.340	0.340	0.000	0.000	0.000	0.000
6	A	203	ASN	0	0.030	0.004	8.539	0.172	0.172	0.000	0.000	0.000	0.000
7	A	204	VAL	0	0.014	0.015	7.991	0.221	0.221	0.000	0.000	0.000	0.000
8	A	205	LEU	0	0.025	0.011	10.650	0.154	0.154	0.000	0.000	0.000	0.000
9	A	206	ALA	0	-0.001	0.002	12.716	0.101	0.101	0.000	0.000	0.000	0.000
10	A	207	TRP	0	-0.010	-0.001	13.595	0.082	0.082	0.000	0.000	0.000	0.000
11	A	208	LEU	0	0.025	0.015	13.981	0.063	0.063	0.000	0.000	0.000	0.000
12	A	209	TYR	0	0.014	-0.002	16.471	0.059	0.059	0.000	0.000	0.000	0.000
13	A	210	ALA	0	0.001	0.003	18.148	0.037	0.037	0.000	0.000	0.000	0.000
14	A	211	ALA	0	0.032	0.025	19.212	0.036	0.036	0.000	0.000	0.000	0.000
15	A	212	VAL	0	-0.018	0.000	20.770	0.025	0.025	0.000	0.000	0.000	0.000
16	A	213	ILE	0	-0.055	-0.024	22.679	0.019	0.019	0.000	0.000	0.000	0.000
17	A	214	ASN	0	-0.077	-0.053	22.983	0.027	0.027	0.000	0.000	0.000	0.000
18	A	215	GLY	0	0.001	0.012	25.383	0.017	0.017	0.000	0.000	0.000	0.000
19	A	216	ASP	-1	-0.823	-0.913	22.485	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	217	ARG	1	0.818	0.876	24.634	0.092	0.092	0.000	0.000	0.000	0.000
21	A	218	TRP	0	0.037	0.024	19.439	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	219	PHE	0	-0.030	-0.007	19.435	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	220	LEU	0	-0.043	-0.011	20.953	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	221	ASN	0	-0.101	-0.054	23.455	0.006	0.006	0.000	0.000	0.000	0.000
25	A	222	ARG	1	0.911	0.949	25.493	0.028	0.028	0.000	0.000	0.000	0.000
26	A	223	PHE	0	0.005	0.001	21.281	0.004	0.004	0.000	0.000	0.000	0.000
27	A	224	THR	0	0.004	-0.020	27.167	0.008	0.008	0.000	0.000	0.000	0.000
28	A	225	THR	0	-0.001	-0.007	29.661	0.011	0.011	0.000	0.000	0.000	0.000
29	A	226	THR	0	-0.031	-0.022	31.657	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	227	LEU	0	0.057	0.023	33.660	0.003	0.003	0.000	0.000	0.000	0.000
31	A	228	ASN	0	-0.035	-0.010	34.070	0.008	0.008	0.000	0.000	0.000	0.000
32	A	229	ASP	-1	-0.767	-0.889	28.941	0.083	0.083	0.000	0.000	0.000	0.000
33	A	230	PHE	0	0.021	0.026	29.820	0.004	0.004	0.000	0.000	0.000	0.000
34	A	231	ASN	0	0.053	0.002	31.989	0.002	0.002	0.000	0.000	0.000	0.000
35	A	232	LEU	0	-0.062	-0.032	29.680	0.005	0.005	0.000	0.000	0.000	0.000
36	A	233	VAL	0	-0.049	-0.019	27.019	0.014	0.014	0.000	0.000	0.000	0.000
37	A	234	ALA	0	0.039	0.017	29.531	0.001	0.001	0.000	0.000	0.000	0.000
38	A	235	MET	0	0.023	0.005	32.848	0.000	0.000	0.000	0.000	0.000	0.000
39	A	236	LYS	1	0.865	0.949	24.273	-0.186	-0.186	0.000	0.000	0.000	0.000
40	A	237	TYR	0	-0.030	-0.020	24.768	0.015	0.015	0.000	0.000	0.000	0.000
41	A	238	ASN	0	-0.074	-0.037	31.125	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	239	TYR	0	0.061	0.036	33.166	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	240	GLU	-1	-0.881	-0.933	36.086	0.048	0.048	0.000	0.000	0.000	0.000
44	A	241	PRO	0	-0.067	-0.045	37.631	0.000	0.000	0.000	0.000	0.000	0.000
45	A	242	LEU	0	0.021	0.037	38.097	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	243	THR	0	0.003	-0.032	39.924	0.003	0.003	0.000	0.000	0.000	0.000
47	A	244	GLN	0	-0.050	-0.058	42.667	0.001	0.001	0.000	0.000	0.000	0.000
48	A	245	ASP	-1	-0.899	-0.936	44.089	0.027	0.027	0.000	0.000	0.000	0.000
49	A	246	HIS	0	0.056	0.038	42.951	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	247	VAL	0	-0.049	-0.027	40.532	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	248	ASP	-1	-0.846	-0.920	43.284	0.022	0.022	0.000	0.000	0.000	0.000
52	A	249	ILE	0	-0.029	-0.018	46.768	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	250	LEU	0	-0.001	0.000	41.113	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	251	GLY	0	0.005	0.009	44.915	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	252	PRO	0	-0.028	-0.023	46.305	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	253	LEU	0	0.068	0.040	44.320	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	254	SER	0	-0.068	-0.028	41.558	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	255	ALA	0	-0.020	-0.022	43.437	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	256	GLN	0	-0.048	-0.020	46.292	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	257	THR	0	-0.048	-0.044	41.330	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	258	GLY	0	-0.009	0.013	41.922	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	259	ILE	0	-0.058	-0.025	36.016	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	260	ALA	0	0.037	0.037	37.532	0.004	0.004	0.000	0.000	0.000	0.000
64	A	261	VAL	0	0.078	0.036	37.774	0.000	0.000	0.000	0.000	0.000	0.000
65	A	262	LEU	0	0.012	0.012	35.503	0.002	0.002	0.000	0.000	0.000	0.000
66	A	263	ASP	-1	-0.791	-0.875	33.363	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	264	MET	0	0.013	0.012	33.215	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	265	CYS	0	-0.040	-0.018	34.173	0.002	0.002	0.000	0.000	0.000	0.000
69	A	266	ALA	0	-0.019	-0.007	29.756	0.006	0.006	0.000	0.000	0.000	0.000
70	A	267	ALA	0	-0.016	-0.006	29.294	0.001	0.001	0.000	0.000	0.000	0.000
71	A	268	LEU	0	0.022	0.011	29.872	0.000	0.000	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.840	0.922	27.150	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	270	GLU	-1	-0.863	-0.912	23.028	0.010	0.010	0.000	0.000	0.000	0.000
74	A	271	LEU	0	-0.035	-0.029	25.446	0.000	0.000	0.000	0.000	0.000	0.000
75	A	272	LEU	0	-0.026	0.001	27.646	0.001	0.001	0.000	0.000	0.000	0.000
76	A	273	GLN	0	-0.072	-0.039	22.440	0.014	0.014	0.000	0.000	0.000	0.000
77	A	274	ASN	0	-0.067	-0.049	20.271	0.029	0.029	0.000	0.000	0.000	0.000
78	A	275	GLY	0	0.035	0.037	22.456	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	276	MET	0	-0.003	0.002	25.435	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	277	ASN	0	-0.103	-0.054	22.259	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	278	GLY	0	0.010	0.002	25.314	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	279	ARG	1	0.869	0.946	24.116	0.080	0.080	0.000	0.000	0.000	0.000
83	A	280	THR	0	0.006	0.000	30.459	0.005	0.005	0.000	0.000	0.000	0.000
84	A	281	ILE	0	0.008	0.000	32.501	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	282	LEU	0	-0.006	-0.009	36.051	0.003	0.003	0.000	0.000	0.000	0.000
86	A	283	GLY	0	-0.003	0.010	38.036	0.001	0.001	0.000	0.000	0.000	0.000
87	A	284	SER	0	-0.007	-0.025	37.636	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	285	THR	0	-0.022	-0.035	33.219	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	286	ILE	0	-0.035	-0.017	32.681	0.003	0.003	0.000	0.000	0.000	0.000
90	A	287	LEU	0	-0.013	-0.020	31.269	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	288	GLU	-1	-0.851	-0.904	35.299	0.009	0.009	0.000	0.000	0.000	0.000
92	A	289	ASP	-1	-0.936	-0.967	39.153	0.030	0.030	0.000	0.000	0.000	0.000
93	A	290	GLU	-1	-0.943	-0.957	40.975	0.023	0.023	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.093	-0.040	43.349	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	292	THR	0	-0.023	-0.038	44.591	0.002	0.002	0.000	0.000	0.000	0.000
96	A	293	PRO	0	0.026	-0.016	44.964	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	294	PHE	0	0.000	-0.007	46.931	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.832	-0.871	48.261	0.008	0.008	0.000	0.000	0.000	0.000
99	A	296	VAL	0	-0.056	-0.014	44.400	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	297	VAL	0	-0.111	-0.051	47.685	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:198:THR)