FMO DATABASE

FMODB ID: G5ZV1

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-634303.10099
FMO2-HF: Nuclear repulsion	595043.163271
FMO2-HF: Total energy	-39259.937719
FMO2-MP2: Total energy	-39373.720709

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.
-0.395	1.963	0.563	-1.061	-1.86	-0.01

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 : 0.006 / 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	-0.017	0.001	2.709	-2.776	-0.532	0.564	-1.057	-1.751	-0.010
4	A	201	THR	0	0.068	0.020	4.644	0.719	0.833	-0.001	-0.004	-0.109	0.000
5	A	202	LEU	0	0.033	0.025	6.628	0.400	0.400	0.000	0.000	0.000	0.000
6	A	203	ASN	0	0.048	0.006	8.534	0.348	0.348	0.000	0.000	0.000	0.000
7	A	204	VAL	0	0.003	0.012	7.823	0.270	0.270	0.000	0.000	0.000	0.000
8	A	205	LEU	0	0.020	-0.002	10.289	0.206	0.206	0.000	0.000	0.000	0.000
9	A	206	ALA	0	0.002	0.005	12.502	0.137	0.137	0.000	0.000	0.000	0.000
10	A	207	TRP	0	-0.007	-0.003	13.427	0.101	0.101	0.000	0.000	0.000	0.000
11	A	208	LEU	0	0.031	0.018	13.879	0.080	0.080	0.000	0.000	0.000	0.000
12	A	209	TYR	0	0.024	0.007	16.419	0.085	0.085	0.000	0.000	0.000	0.000
13	A	210	ALA	0	-0.009	0.003	18.025	0.054	0.054	0.000	0.000	0.000	0.000
14	A	211	ALA	0	0.016	0.004	18.984	0.044	0.044	0.000	0.000	0.000	0.000
15	A	212	VAL	0	-0.024	0.005	20.601	0.038	0.038	0.000	0.000	0.000	0.000
16	A	213	ILE	0	-0.070	-0.025	22.434	0.033	0.033	0.000	0.000	0.000	0.000
17	A	214	ASN	0	-0.067	-0.038	22.611	0.037	0.037	0.000	0.000	0.000	0.000
18	A	215	GLY	0	-0.011	0.000	25.455	0.021	0.021	0.000	0.000	0.000	0.000
19	A	216	ASP	-1	-0.871	-0.925	21.940	-0.182	-0.182	0.000	0.000	0.000	0.000
20	A	217	ARG	1	0.805	0.862	24.369	0.186	0.186	0.000	0.000	0.000	0.000
21	A	218	TRP	0	0.095	0.038	19.718	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	219	PHE	0	-0.017	0.008	19.081	0.002	0.002	0.000	0.000	0.000	0.000
23	A	220	LEU	0	-0.057	-0.019	20.689	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	221	ASN	0	-0.084	-0.040	22.977	0.008	0.008	0.000	0.000	0.000	0.000
25	A	222	ARG	1	0.993	1.000	24.927	0.098	0.098	0.000	0.000	0.000	0.000
26	A	223	PHE	0	0.025	0.010	20.954	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	224	THR	0	0.016	0.016	27.033	0.008	0.008	0.000	0.000	0.000	0.000
28	A	225	THR	0	-0.010	-0.026	29.215	0.002	0.002	0.000	0.000	0.000	0.000
29	A	226	THR	0	-0.019	0.018	31.230	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	227	LEU	0	0.090	0.027	33.227	0.001	0.001	0.000	0.000	0.000	0.000
31	A	228	ASN	0	-0.043	-0.036	33.591	0.008	0.008	0.000	0.000	0.000	0.000
32	A	229	ASP	-1	-0.832	-0.927	28.925	0.015	0.015	0.000	0.000	0.000	0.000
33	A	230	PHE	0	-0.020	-0.007	29.822	0.003	0.003	0.000	0.000	0.000	0.000
34	A	231	ASN	0	0.070	0.030	31.512	0.000	0.000	0.000	0.000	0.000	0.000
35	A	232	LEU	0	-0.043	-0.003	29.026	0.006	0.006	0.000	0.000	0.000	0.000
36	A	233	VAL	0	-0.049	-0.029	26.416	0.008	0.008	0.000	0.000	0.000	0.000
37	A	234	ALA	0	0.033	0.014	28.725	0.002	0.002	0.000	0.000	0.000	0.000
38	A	235	MET	0	0.008	0.000	31.872	0.001	0.001	0.000	0.000	0.000	0.000
39	A	236	LYS	1	0.871	0.951	24.260	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	237	TYR	0	-0.036	-0.026	23.912	0.008	0.008	0.000	0.000	0.000	0.000
41	A	238	ASN	0	-0.040	-0.012	30.431	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	239	TYR	0	0.039	0.024	32.637	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	240	GLU	-1	-0.930	-0.965	35.457	0.005	0.005	0.000	0.000	0.000	0.000
44	A	241	PRO	0	-0.087	-0.048	36.950	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	242	LEU	0	0.049	0.027	37.375	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	243	THR	0	-0.010	-0.021	39.217	0.003	0.003	0.000	0.000	0.000	0.000
47	A	244	GLN	0	-0.056	-0.065	42.171	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	245	ASP	-1	-0.866	-0.932	43.541	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	246	HIS	0	0.064	0.037	42.173	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	247	VAL	0	-0.027	-0.019	39.801	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	248	ASP	-1	-0.847	-0.915	42.472	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	249	ILE	0	-0.050	-0.014	45.946	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	250	LEU	0	-0.023	-0.015	40.757	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	251	GLY	0	0.006	0.009	44.571	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	252	PRO	0	-0.012	-0.016	46.133	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	253	LEU	0	0.073	0.033	43.828	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	254	SER	0	-0.061	-0.014	41.557	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	255	ALA	0	-0.025	-0.023	43.222	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	256	GLN	0	-0.039	-0.013	46.089	0.000	0.000	0.000	0.000	0.000	0.000
60	A	257	THR	0	-0.047	-0.028	41.133	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	258	GLY	0	-0.003	0.013	41.627	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	259	ILE	0	-0.059	-0.026	35.459	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	260	ALA	0	0.016	0.009	37.451	0.005	0.005	0.000	0.000	0.000	0.000
64	A	261	VAL	0	0.104	0.043	37.538	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	262	LEU	0	0.010	-0.007	35.065	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	263	ASP	-1	-0.898	-0.951	33.164	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	264	MET	0	0.020	0.016	32.776	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	265	CYS	0	-0.051	-0.017	33.391	0.001	0.001	0.000	0.000	0.000	0.000
69	A	266	ALA	0	-0.012	0.006	29.077	0.002	0.002	0.000	0.000	0.000	0.000
70	A	267	ALA	0	-0.009	-0.002	28.690	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	268	LEU	0	0.031	0.007	29.184	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.905	0.955	25.818	0.028	0.028	0.000	0.000	0.000	0.000
73	A	270	GLU	-1	-0.852	-0.918	22.517	-0.127	-0.127	0.000	0.000	0.000	0.000
74	A	271	LEU	0	-0.041	-0.016	24.878	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	272	LEU	0	-0.038	-0.007	26.583	0.001	0.001	0.000	0.000	0.000	0.000
76	A	273	GLN	0	-0.078	-0.032	22.141	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	274	ASN	0	-0.071	-0.055	20.024	0.009	0.009	0.000	0.000	0.000	0.000
78	A	275	GLY	0	0.013	0.020	22.242	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	276	MET	0	0.007	-0.003	25.083	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	277	ASN	0	-0.089	-0.040	21.892	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	278	GLY	0	-0.006	0.003	25.070	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	279	ARG	1	0.927	0.960	24.132	0.180	0.180	0.000	0.000	0.000	0.000
83	A	280	THR	0	-0.004	0.002	29.898	0.005	0.005	0.000	0.000	0.000	0.000
84	A	281	ILE	0	0.002	-0.002	32.210	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	282	LEU	0	0.010	-0.004	35.500	0.004	0.004	0.000	0.000	0.000	0.000
86	A	283	GLY	0	-0.019	-0.003	37.815	0.004	0.004	0.000	0.000	0.000	0.000
87	A	284	SER	0	0.063	0.046	37.328	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	285	THR	0	-0.029	-0.036	32.786	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	286	ILE	0	-0.054	-0.018	32.382	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	287	LEU	0	-0.018	-0.031	30.973	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	288	GLU	-1	-0.934	-0.974	35.111	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	289	ASP	-1	-0.947	-0.969	38.830	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	290	GLU	-1	-0.911	-0.943	40.627	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.098	-0.036	43.022	0.000	0.000	0.000	0.000	0.000	0.000
95	A	292	THR	0	-0.004	-0.005	44.162	0.000	0.000	0.000	0.000	0.000	0.000
96	A	293	PRO	0	0.011	-0.018	44.670	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	294	PHE	0	-0.030	-0.041	46.601	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.841	-0.893	47.702	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	296	VAL	0	-0.073	-0.032	44.204	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	297	VAL	0	-0.063	-0.015	47.471	-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:198:THR)