FMO DATABASE

FMODB ID: 894QY

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	OptHSide
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	-634006.296255
FMO2-HF: Nuclear repulsion	594745.717138
FMO2-HF: Total energy	-39260.579116
FMO2-MP2: Total energy	-39374.263157

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.
-0.41	2.128	0.34	-1.117	-1.762	-0.007

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 : -0.001 / 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	-0.003	0.000	2.830	-2.495	-0.066	0.341	-1.114	-1.657	-0.007
4	A	201	THR	0	0.070	0.021	4.767	0.548	0.657	-0.001	-0.003	-0.105	0.000
5	A	202	LEU	0	0.034	0.027	6.725	0.271	0.271	0.000	0.000	0.000	0.000
6	A	203	ASN	0	0.036	0.001	8.697	0.225	0.225	0.000	0.000	0.000	0.000
7	A	204	VAL	0	0.017	0.017	7.936	0.207	0.207	0.000	0.000	0.000	0.000
8	A	205	LEU	0	0.016	-0.001	10.411	0.158	0.158	0.000	0.000	0.000	0.000
9	A	206	ALA	0	0.002	0.002	12.629	0.097	0.097	0.000	0.000	0.000	0.000
10	A	207	TRP	0	-0.008	-0.002	13.562	0.076	0.076	0.000	0.000	0.000	0.000
11	A	208	LEU	0	0.034	0.020	13.870	0.060	0.060	0.000	0.000	0.000	0.000
12	A	209	TYR	0	0.031	0.012	16.572	0.061	0.061	0.000	0.000	0.000	0.000
13	A	210	ALA	0	-0.007	0.006	18.155	0.037	0.037	0.000	0.000	0.000	0.000
14	A	211	ALA	0	0.033	0.018	19.107	0.035	0.035	0.000	0.000	0.000	0.000
15	A	212	VAL	0	-0.013	0.008	20.717	0.028	0.028	0.000	0.000	0.000	0.000
16	A	213	ILE	0	-0.060	-0.024	22.556	0.023	0.023	0.000	0.000	0.000	0.000
17	A	214	ASN	0	-0.095	-0.060	22.971	0.025	0.025	0.000	0.000	0.000	0.000
18	A	215	GLY	0	-0.010	0.000	25.581	0.014	0.014	0.000	0.000	0.000	0.000
19	A	216	ASP	-1	-0.841	-0.926	21.995	-0.098	-0.098	0.000	0.000	0.000	0.000
20	A	217	ARG	1	0.822	0.880	24.463	0.114	0.114	0.000	0.000	0.000	0.000
21	A	218	TRP	0	0.060	0.026	19.399	0.004	0.004	0.000	0.000	0.000	0.000
22	A	219	PHE	0	-0.041	0.000	19.058	0.003	0.003	0.000	0.000	0.000	0.000
23	A	220	LEU	0	-0.066	-0.023	20.728	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	221	ASN	0	-0.090	-0.045	23.022	0.005	0.005	0.000	0.000	0.000	0.000
25	A	222	ARG	1	0.923	0.951	24.949	0.024	0.024	0.000	0.000	0.000	0.000
26	A	223	PHE	0	0.029	0.013	20.911	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	224	THR	0	-0.014	-0.025	27.040	0.008	0.008	0.000	0.000	0.000	0.000
28	A	225	THR	0	-0.009	-0.018	29.211	0.007	0.007	0.000	0.000	0.000	0.000
29	A	226	THR	0	-0.042	-0.012	31.280	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	227	LEU	0	0.057	0.018	33.389	0.004	0.004	0.000	0.000	0.000	0.000
31	A	228	ASN	0	-0.032	-0.023	33.915	0.008	0.008	0.000	0.000	0.000	0.000
32	A	229	ASP	-1	-0.764	-0.892	28.952	0.055	0.055	0.000	0.000	0.000	0.000
33	A	230	PHE	0	-0.029	-0.005	29.962	0.007	0.007	0.000	0.000	0.000	0.000
34	A	231	ASN	0	0.067	0.020	31.632	0.004	0.004	0.000	0.000	0.000	0.000
35	A	232	LEU	0	-0.054	-0.009	29.250	0.006	0.006	0.000	0.000	0.000	0.000
36	A	233	VAL	0	-0.034	-0.022	26.404	0.010	0.010	0.000	0.000	0.000	0.000
37	A	234	ALA	0	0.027	0.013	28.832	0.006	0.006	0.000	0.000	0.000	0.000
38	A	235	MET	0	0.011	0.001	31.963	0.001	0.001	0.000	0.000	0.000	0.000
39	A	236	LYS	1	0.876	0.953	23.995	-0.156	-0.156	0.000	0.000	0.000	0.000
40	A	237	TYR	0	-0.037	-0.025	23.976	0.012	0.012	0.000	0.000	0.000	0.000
41	A	238	ASN	0	-0.055	-0.020	30.477	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	239	TYR	0	0.057	0.033	32.521	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	240	GLU	-1	-0.913	-0.942	35.521	0.046	0.046	0.000	0.000	0.000	0.000
44	A	241	PRO	0	-0.052	-0.034	37.056	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	242	LEU	0	0.010	0.009	37.426	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	243	THR	0	0.013	-0.031	39.335	0.001	0.001	0.000	0.000	0.000	0.000
47	A	244	GLN	0	-0.051	-0.059	42.302	0.000	0.000	0.000	0.000	0.000	0.000
48	A	245	ASP	-1	-0.891	-0.938	43.691	0.024	0.024	0.000	0.000	0.000	0.000
49	A	246	HIS	0	0.060	0.050	42.301	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	247	VAL	0	-0.046	-0.032	39.905	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	248	ASP	-1	-0.855	-0.922	42.616	0.017	0.017	0.000	0.000	0.000	0.000
52	A	249	ILE	0	-0.038	-0.013	46.075	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	250	LEU	0	-0.025	-0.014	40.922	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	251	GLY	0	0.007	0.010	44.565	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	252	PRO	0	-0.015	-0.019	46.111	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	253	LEU	0	0.071	0.034	43.808	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	254	SER	0	-0.058	-0.020	41.164	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	255	ALA	0	-0.034	-0.024	43.205	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	256	GLN	0	-0.045	-0.015	46.081	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	257	THR	0	-0.046	-0.037	41.026	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	258	GLY	0	-0.010	0.012	41.622	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	259	ILE	0	-0.052	-0.026	35.343	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	260	ALA	0	0.038	0.029	37.484	0.003	0.003	0.000	0.000	0.000	0.000
64	A	261	VAL	0	0.105	0.046	37.524	0.001	0.001	0.000	0.000	0.000	0.000
65	A	262	LEU	0	0.020	0.004	35.074	0.002	0.002	0.000	0.000	0.000	0.000
66	A	263	ASP	-1	-0.797	-0.868	33.077	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	264	MET	0	0.015	0.015	32.757	0.000	0.000	0.000	0.000	0.000	0.000
68	A	265	CYS	0	-0.060	-0.025	33.428	0.004	0.004	0.000	0.000	0.000	0.000
69	A	266	ALA	0	-0.013	0.004	29.123	0.006	0.006	0.000	0.000	0.000	0.000
70	A	267	ALA	0	-0.010	-0.002	28.741	0.003	0.003	0.000	0.000	0.000	0.000
71	A	268	LEU	0	0.028	0.009	29.244	0.003	0.003	0.000	0.000	0.000	0.000
72	A	269	LYS	1	0.884	0.940	26.278	-0.045	-0.045	0.000	0.000	0.000	0.000
73	A	270	GLU	-1	-0.869	-0.922	22.586	0.038	0.038	0.000	0.000	0.000	0.000
74	A	271	LEU	0	-0.026	-0.010	24.965	0.006	0.006	0.000	0.000	0.000	0.000
75	A	272	LEU	0	-0.029	0.000	26.638	0.008	0.008	0.000	0.000	0.000	0.000
76	A	273	GLN	0	-0.078	-0.038	21.738	0.004	0.004	0.000	0.000	0.000	0.000
77	A	274	ASN	0	-0.067	-0.057	19.983	0.033	0.033	0.000	0.000	0.000	0.000
78	A	275	GLY	0	0.017	0.026	22.301	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	276	MET	0	0.015	0.001	25.115	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	277	ASN	0	-0.095	-0.048	21.962	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	278	GLY	0	-0.004	0.000	25.070	-0.008	-0.008	0.000	0.000	0.000	0.000
82	A	279	ARG	1	0.902	0.954	23.700	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	280	THR	0	0.001	0.003	29.839	0.005	0.005	0.000	0.000	0.000	0.000
84	A	281	ILE	0	0.007	0.000	32.117	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	282	LEU	0	0.004	-0.006	35.488	0.002	0.002	0.000	0.000	0.000	0.000
86	A	283	GLY	0	-0.025	-0.007	37.761	0.001	0.001	0.000	0.000	0.000	0.000
87	A	284	SER	0	0.016	-0.006	37.336	0.002	0.002	0.000	0.000	0.000	0.000
88	A	285	THR	0	-0.036	-0.038	32.848	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	286	ILE	0	-0.049	-0.022	32.379	0.006	0.006	0.000	0.000	0.000	0.000
90	A	287	LEU	0	-0.020	-0.020	31.088	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	288	GLU	-1	-0.860	-0.906	35.146	0.036	0.036	0.000	0.000	0.000	0.000
92	A	289	ASP	-1	-0.952	-0.974	38.842	0.046	0.046	0.000	0.000	0.000	0.000
93	A	290	GLU	-1	-0.918	-0.951	40.674	0.039	0.039	0.000	0.000	0.000	0.000
94	A	291	PHE	0	-0.107	-0.040	43.081	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	292	THR	0	-0.009	-0.036	44.229	0.000	0.000	0.000	0.000	0.000	0.000
96	A	293	PRO	0	0.021	-0.014	44.757	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	294	PHE	0	-0.019	-0.027	46.695	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	295	ASP	-1	-0.835	-0.874	47.897	0.021	0.021	0.000	0.000	0.000	0.000
99	A	296	VAL	0	-0.065	-0.025	44.227	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	297	VAL	0	-0.082	-0.021	47.535	-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)