FMO DATABASE

FMODB ID: YYR52

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

Total energy (hartree)

FMO2-HF: Electronic energy	-555141.398406
FMO2-HF: Nuclear repulsion	521468.922787
FMO2-HF: Total energy	-33672.475619
FMO2-MP2: Total energy	-33767.261314

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.
-217.428	-218.834	23.773	-12.938	-9.429	-0.155

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 : 0.868 / q_NPA : 0.921

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	-0.002	-0.005	1.745	-43.026	-43.915	12.037	-6.382	-4.767	-0.066
4	B	5	GLU	-1	-0.837	-0.905	1.741	-118.382	-119.262	11.724	-6.417	-4.426	-0.089
5	B	6	MET	0	-0.023	0.001	5.610	4.699	4.699	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.943	0.977	9.442	24.212	24.212	0.000	0.000	0.000	0.000
7	B	8	CYS	0	0.002	0.006	11.388	0.557	0.557	0.000	0.000	0.000	0.000
8	B	9	THR	0	0.005	-0.017	11.179	-0.047	-0.047	0.000	0.000	0.000	0.000
9	B	10	ASN	0	0.076	0.061	13.166	1.339	1.339	0.000	0.000	0.000	0.000
10	B	11	VAL	0	0.023	-0.021	15.158	-0.965	-0.965	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.063	0.038	16.485	-0.669	-0.669	0.000	0.000	0.000	0.000
12	B	13	LEU	0	0.013	0.007	13.422	-0.119	-0.119	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.011	-0.019	10.617	-0.817	-0.817	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.015	0.016	13.631	-0.383	-0.383	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.015	-0.007	16.856	0.513	0.513	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.011	-0.014	10.422	0.189	0.189	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.027	0.008	14.011	0.291	0.291	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.936	0.966	14.971	14.754	14.754	0.000	0.000	0.000	0.000
19	B	20	MET	0	-0.087	-0.040	16.794	0.869	0.869	0.000	0.000	0.000	0.000
20	B	21	HIS	0	-0.014	0.013	14.109	0.457	0.457	0.000	0.000	0.000	0.000
21	B	22	VAL	0	0.037	0.011	10.620	-0.525	-0.525	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.908	-0.974	8.328	-25.808	-25.808	0.000	0.000	0.000	0.000
23	B	24	SER	0	-0.033	-0.003	7.388	-1.397	-1.397	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.051	-0.023	8.157	-0.629	-0.629	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.043	0.008	3.448	-0.177	0.113	0.014	-0.092	-0.212	0.000
26	B	27	LYS	1	0.928	0.963	5.260	18.431	18.425	-0.001	-0.004	0.011	0.000
27	B	28	GLU	-1	-0.801	-0.890	8.033	-18.540	-18.540	0.000	0.000	0.000	0.000
28	B	29	TRP	0	0.051	0.022	5.790	1.976	1.976	0.000	0.000	0.000	0.000
29	B	30	ASN	0	0.010	-0.005	4.067	-3.587	-3.508	-0.001	-0.043	-0.035	0.000
30	B	31	TYR	0	-0.007	0.022	8.547	0.949	0.949	0.000	0.000	0.000	0.000
31	B	32	CYS	0	-0.007	0.001	11.974	1.461	1.461	0.000	0.000	0.000	0.000
32	B	33	VAL	0	0.003	-0.007	7.441	1.376	1.376	0.000	0.000	0.000	0.000
33	B	34	GLY	0	-0.032	-0.011	10.536	0.578	0.578	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.038	0.013	12.405	1.120	1.120	0.000	0.000	0.000	0.000
35	B	36	HIS	0	0.024	0.033	12.532	1.609	1.609	0.000	0.000	0.000	0.000
36	B	37	ASN	0	-0.019	-0.029	9.530	1.593	1.593	0.000	0.000	0.000	0.000
37	B	38	GLU	-1	-0.897	-0.927	14.022	-17.692	-17.692	0.000	0.000	0.000	0.000
38	B	39	ILE	0	0.014	0.013	17.156	1.052	1.052	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.057	-0.041	15.916	-0.284	-0.284	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.068	-0.032	16.223	0.042	0.042	0.000	0.000	0.000	0.000
41	B	42	CYS	0	-0.071	-0.019	19.845	0.582	0.582	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.911	-0.945	22.895	-12.610	-12.610	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.860	-0.951	26.267	-10.634	-10.634	0.000	0.000	0.000	0.000
44	B	45	PRO	0	0.005	-0.005	26.696	-0.479	-0.479	0.000	0.000	0.000	0.000
45	B	46	ASP	-1	-0.909	-0.943	27.705	-10.413	-10.413	0.000	0.000	0.000	0.000
46	B	47	ALA	0	0.006	0.002	24.956	-0.290	-0.290	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.031	-0.020	22.575	-0.667	-0.667	0.000	0.000	0.000	0.000
48	B	49	LEU	0	-0.003	-0.009	23.309	-0.551	-0.551	0.000	0.000	0.000	0.000
49	B	50	GLU	-1	-0.941	-0.958	25.226	-11.935	-11.935	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.827	0.896	19.402	15.461	15.461	0.000	0.000	0.000	0.000
51	B	52	LEU	0	0.011	0.007	20.447	-0.721	-0.721	0.000	0.000	0.000	0.000
52	B	53	LEU	0	0.002	0.002	22.140	-0.129	-0.129	0.000	0.000	0.000	0.000
53	B	54	ALA	0	0.000	0.007	20.186	0.087	0.087	0.000	0.000	0.000	0.000
54	B	55	LEU	0	-0.022	-0.010	15.668	-0.408	-0.408	0.000	0.000	0.000	0.000
55	B	56	ILE	0	-0.006	-0.005	19.505	-0.113	-0.113	0.000	0.000	0.000	0.000
56	B	57	ALA	0	0.004	-0.001	22.150	0.150	0.150	0.000	0.000	0.000	0.000
57	B	58	PHE	0	-0.018	-0.004	14.040	0.056	0.056	0.000	0.000	0.000	0.000
58	B	59	PHE	0	0.060	0.019	15.775	0.024	0.024	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.026	0.019	20.261	0.327	0.327	0.000	0.000	0.000	0.000
60	B	61	SER	0	-0.121	-0.067	19.452	0.411	0.411	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.821	0.912	15.702	16.808	16.808	0.000	0.000	0.000	0.000
62	B	63	HIS	0	-0.009	-0.014	20.693	0.050	0.050	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.006	-0.019	23.975	0.336	0.336	0.000	0.000	0.000	0.000
64	B	65	THR	0	-0.017	-0.009	27.004	0.200	0.200	0.000	0.000	0.000	0.000
65	B	66	CYS	0	-0.064	-0.015	24.017	-0.062	-0.062	0.000	0.000	0.000	0.000
66	B	67	ASP	-1	-0.854	-0.894	26.447	-10.979	-10.979	0.000	0.000	0.000	0.000
67	B	68	LEU	0	-0.023	-0.035	21.841	-0.489	-0.489	0.000	0.000	0.000	0.000
68	B	69	SER	0	0.005	-0.018	24.715	-0.415	-0.415	0.000	0.000	0.000	0.000
69	B	70	ASP	-1	-0.823	-0.905	23.891	-12.540	-12.540	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.084	-0.035	18.363	-0.448	-0.448	0.000	0.000	0.000	0.000
71	B	72	ILE	0	0.001	-0.007	22.170	-0.271	-0.271	0.000	0.000	0.000	0.000
72	B	73	GLU	-1	-0.919	-0.951	24.968	-11.145	-11.145	0.000	0.000	0.000	0.000
73	B	74	SER	0	-0.003	-0.005	21.078	-0.342	-0.342	0.000	0.000	0.000	0.000
74	B	75	TYR	0	-0.017	-0.053	16.355	-0.335	-0.335	0.000	0.000	0.000	0.000
75	B	76	PHE	0	-0.008	-0.014	22.562	0.042	0.042	0.000	0.000	0.000	0.000
76	B	77	GLU	-1	-0.929	-0.949	24.748	-12.042	-12.042	0.000	0.000	0.000	0.000
77	B	78	ASN	0	-0.127	-0.070	20.384	-0.758	-0.758	0.000	0.000	0.000	0.000
78	B	79	THR	0	-0.026	-0.006	21.462	-0.268	-0.268	0.000	0.000	0.000	0.000
79	B	80	THR	0	0.036	0.011	23.186	0.345	0.345	0.000	0.000	0.000	0.000
80	B	81	ILE	0	0.007	0.013	24.925	0.536	0.536	0.000	0.000	0.000	0.000
81	B	82	LEU	0	-0.026	-0.013	24.782	0.378	0.378	0.000	0.000	0.000	0.000
82	B	83	GLN	0	-0.121	-0.039	26.488	0.803	0.803	0.000	0.000	0.000	0.000

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