FMO DATABASE

FMODB ID: 5357Z

Calculation Name: 3UB0-B-Xray372

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UB0

Chain ID: B

ChEMBL ID: CHEMBL4295624

UniProt ID: Q98VG9

Base Structure: X-ray

Registration Date: 2023-03-14

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554139.77772
FMO2-HF: Nuclear repulsion	520467.846044
FMO2-HF: Total energy	-33671.931677
FMO2-MP2: Total energy	-33766.697025

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(B:2:LYS)

Summations of interaction energy for fragment #1(B:2:LYS)

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.
-117.451	-113.158	0.044	-2.149	-2.187	-0.015

Interaction energy analysis for fragmet #1(B:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.955

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].	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	B	4	THR	0	-0.026	-0.017	3.138	-15.356	-11.502	0.042	-2.056	-1.840	-0.015
4	B	5	GLU	-1	-0.907	-0.943	5.366	-43.033	-42.868	-0.001	-0.004	-0.160	0.000
5	B	6	MET	0	-0.016	0.005	7.544	2.940	2.940	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.949	0.979	11.294	21.659	21.659	0.000	0.000	0.000	0.000
7	B	8	CYS	0	0.003	0.001	13.802	0.253	0.253	0.000	0.000	0.000	0.000
8	B	9	THR	0	0.001	-0.017	12.485	0.176	0.176	0.000	0.000	0.000	0.000
9	B	10	ASN	0	0.098	0.070	14.878	0.927	0.927	0.000	0.000	0.000	0.000
10	B	11	VAL	0	0.017	-0.020	16.347	-0.846	-0.846	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.057	0.033	17.323	-0.691	-0.691	0.000	0.000	0.000	0.000
12	B	13	LEU	0	0.021	0.011	14.686	-0.178	-0.178	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.010	-0.018	10.775	-0.847	-0.847	0.000	0.000	0.000	0.000
14	B	15	GLY	0	-0.005	0.009	14.356	-0.594	-0.594	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.011	-0.007	17.313	0.335	0.335	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.011	-0.012	11.006	0.076	0.076	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.017	0.010	14.029	-0.195	-0.195	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.947	0.970	14.844	14.198	14.198	0.000	0.000	0.000	0.000
19	B	20	MET	0	-0.094	-0.043	17.252	0.885	0.885	0.000	0.000	0.000	0.000
20	B	21	HIS	0	0.004	0.017	14.350	0.399	0.399	0.000	0.000	0.000	0.000
21	B	22	VAL	0	0.034	0.013	11.284	-0.626	-0.626	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.913	-0.970	8.340	-25.691	-25.691	0.000	0.000	0.000	0.000
23	B	24	SER	0	-0.046	-0.015	7.844	-1.851	-1.851	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.029	-0.008	9.084	-0.288	-0.288	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.053	0.012	3.736	-0.289	-0.050	0.004	-0.066	-0.176	0.000
26	B	27	LYS	1	0.913	0.955	5.789	18.401	18.401	0.000	0.000	0.000	0.000
27	B	28	GLU	-1	-0.875	-0.938	7.967	-18.244	-18.244	0.000	0.000	0.000	0.000
28	B	29	TRP	0	0.030	0.011	6.804	0.947	0.947	0.000	0.000	0.000	0.000
29	B	30	ASN	0	0.016	-0.006	3.945	-2.294	-2.259	-0.001	-0.023	-0.011	0.000
30	B	31	TYR	0	-0.016	0.020	8.329	1.082	1.082	0.000	0.000	0.000	0.000
31	B	32	CYS	0	0.007	0.008	11.756	1.323	1.323	0.000	0.000	0.000	0.000
32	B	33	VAL	0	0.001	-0.006	8.907	1.202	1.202	0.000	0.000	0.000	0.000
33	B	34	GLY	0	-0.032	-0.009	11.752	0.657	0.657	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.031	0.011	13.093	1.029	1.029	0.000	0.000	0.000	0.000
35	B	36	HIS	0	0.026	0.032	14.209	1.279	1.279	0.000	0.000	0.000	0.000
36	B	37	ASN	0	-0.018	-0.031	11.069	1.226	1.226	0.000	0.000	0.000	0.000
37	B	38	GLU	-1	-0.926	-0.963	15.447	-16.661	-16.661	0.000	0.000	0.000	0.000
38	B	39	ILE	0	0.001	0.004	18.224	0.872	0.872	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.053	-0.041	17.796	-0.352	-0.352	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.063	-0.027	17.273	0.110	0.110	0.000	0.000	0.000	0.000
41	B	42	CYS	0	-0.072	-0.015	21.233	0.502	0.502	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.895	-0.940	24.146	-11.526	-11.526	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.905	-0.972	27.531	-9.856	-9.856	0.000	0.000	0.000	0.000
44	B	45	PRO	0	0.026	-0.001	27.978	-0.436	-0.436	0.000	0.000	0.000	0.000
45	B	46	ASP	-1	-0.911	-0.940	29.034	-9.790	-9.790	0.000	0.000	0.000	0.000
46	B	47	ALA	0	0.037	0.018	25.863	-0.262	-0.262	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.034	-0.024	24.125	-0.599	-0.599	0.000	0.000	0.000	0.000
48	B	49	LEU	0	0.010	-0.003	24.570	-0.486	-0.486	0.000	0.000	0.000	0.000
49	B	50	GLU	-1	-0.938	-0.962	25.066	-11.103	-11.103	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.845	0.928	19.799	14.190	14.190	0.000	0.000	0.000	0.000
51	B	52	LEU	0	0.027	0.011	21.073	-0.657	-0.657	0.000	0.000	0.000	0.000
52	B	53	LEU	0	-0.004	0.000	23.126	-0.153	-0.153	0.000	0.000	0.000	0.000
53	B	54	ALA	0	-0.007	0.003	19.934	0.033	0.033	0.000	0.000	0.000	0.000
54	B	55	LEU	0	-0.015	-0.006	16.876	-0.398	-0.398	0.000	0.000	0.000	0.000
55	B	56	ILE	0	-0.009	-0.004	19.813	-0.173	-0.173	0.000	0.000	0.000	0.000
56	B	57	ALA	0	0.005	0.000	21.991	0.088	0.088	0.000	0.000	0.000	0.000
57	B	58	PHE	0	-0.023	-0.004	14.233	0.034	0.034	0.000	0.000	0.000	0.000
58	B	59	PHE	0	0.070	0.029	16.341	-0.039	-0.039	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.025	0.018	20.633	0.247	0.247	0.000	0.000	0.000	0.000
60	B	61	SER	0	-0.108	-0.068	19.831	0.293	0.293	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.846	0.932	16.505	15.680	15.680	0.000	0.000	0.000	0.000
62	B	63	HIS	0	-0.003	-0.012	21.300	0.104	0.104	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.010	-0.018	24.614	0.438	0.438	0.000	0.000	0.000	0.000
64	B	65	THR	0	-0.013	-0.003	27.521	0.233	0.233	0.000	0.000	0.000	0.000
65	B	66	CYS	0	-0.065	-0.016	24.276	-0.075	-0.075	0.000	0.000	0.000	0.000
66	B	67	ASP	-1	-0.859	-0.888	26.948	-10.607	-10.607	0.000	0.000	0.000	0.000
67	B	68	LEU	0	-0.021	-0.038	22.632	-0.436	-0.436	0.000	0.000	0.000	0.000
68	B	69	SER	0	-0.015	-0.031	25.668	-0.276	-0.276	0.000	0.000	0.000	0.000
69	B	70	ASP	-1	-0.803	-0.901	24.972	-11.725	-11.725	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.067	-0.035	19.550	-0.376	-0.376	0.000	0.000	0.000	0.000
71	B	72	ILE	0	-0.014	-0.016	23.264	-0.192	-0.192	0.000	0.000	0.000	0.000
72	B	73	GLU	-1	-0.919	-0.946	26.223	-10.641	-10.641	0.000	0.000	0.000	0.000
73	B	74	SER	0	-0.008	-0.004	22.281	-0.265	-0.265	0.000	0.000	0.000	0.000
74	B	75	TYR	0	-0.046	-0.053	17.782	-0.319	-0.319	0.000	0.000	0.000	0.000
75	B	76	PHE	0	-0.020	-0.024	24.097	0.081	0.081	0.000	0.000	0.000	0.000
76	B	77	GLU	-1	-0.950	-0.964	26.404	-11.238	-11.238	0.000	0.000	0.000	0.000
77	B	78	ASN	0	-0.125	-0.063	22.009	-0.703	-0.703	0.000	0.000	0.000	0.000
78	B	79	THR	0	-0.044	-0.010	23.332	-0.202	-0.202	0.000	0.000	0.000	0.000
79	B	80	THR	0	0.049	0.011	25.042	0.268	0.268	0.000	0.000	0.000	0.000
80	B	81	ILE	0	-0.031	0.004	26.285	0.442	0.442	0.000	0.000	0.000	0.000
81	B	82	LEU	0	-0.019	-0.011	26.317	0.319	0.319	0.000	0.000	0.000	0.000
82	B	83	GLN	0	-0.059	-0.012	28.811	0.190	0.190	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:LYS)