FMO DATABASE

FMODB ID: Q1LRY

Calculation Name: 3UB0-C-Xray372

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UB0

Chain ID: C

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-515038.396683
FMO2-HF: Nuclear repulsion	481654.19181
FMO2-HF: Total energy	-33384.204873
FMO2-MP2: Total energy	-33477.939608

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(C:0:GLY)

Summations of interaction energy for fragment #1(C:0:GLY)

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.
-7.793	-4.282	1.924	-2.265	-3.169	0

Interaction energy analysis for fragmet #1(C:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.007

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	C	2	LYS	1	0.960	0.989	3.352	-6.602	-4.562	0.034	-1.028	-1.046	0.005
4	C	3	LEU	0	0.049	0.035	4.498	-0.369	-0.099	-0.001	-0.038	-0.230	0.000
5	C	4	THR	0	0.010	-0.014	5.049	0.423	0.513	-0.001	-0.005	-0.084	0.000
6	C	5	GLU	-1	-0.836	-0.913	7.256	1.117	1.117	0.000	0.000	0.000	0.000
7	C	6	MET	0	-0.022	0.012	3.151	-0.061	0.241	0.030	-0.094	-0.238	-0.001
8	C	7	LYS	1	0.878	0.946	7.933	0.885	0.885	0.000	0.000	0.000	0.000
9	C	8	CYS	0	-0.042	-0.027	10.373	0.041	0.041	0.000	0.000	0.000	0.000
10	C	9	THR	0	-0.012	-0.012	10.814	0.041	0.041	0.000	0.000	0.000	0.000
11	C	10	ASN	0	0.012	-0.007	12.050	0.038	0.038	0.000	0.000	0.000	0.000
12	C	11	VAL	0	-0.003	0.015	13.701	0.009	0.009	0.000	0.000	0.000	0.000
13	C	12	VAL	0	-0.007	0.002	16.133	0.007	0.007	0.000	0.000	0.000	0.000
14	C	13	LEU	0	0.002	0.010	14.293	0.002	0.002	0.000	0.000	0.000	0.000
15	C	14	LEU	0	-0.002	0.002	17.918	0.002	0.002	0.000	0.000	0.000	0.000
16	C	15	GLY	0	0.017	0.009	19.887	0.002	0.002	0.000	0.000	0.000	0.000
17	C	16	LEU	0	-0.014	-0.024	20.242	0.002	0.002	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.017	-0.012	19.770	-0.001	-0.001	0.000	0.000	0.000	0.000
19	C	18	SER	0	-0.021	0.003	23.542	0.000	0.000	0.000	0.000	0.000	0.000
20	C	19	LYS	1	0.875	0.941	25.873	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	20	MET	0	-0.041	-0.009	24.385	0.003	0.003	0.000	0.000	0.000	0.000
22	C	21	HIS	0	-0.025	-0.001	28.256	-0.003	-0.003	0.000	0.000	0.000	0.000
23	C	22	VAL	0	0.038	0.014	25.336	0.000	0.000	0.000	0.000	0.000	0.000
24	C	23	GLU	-1	-0.934	-0.974	28.394	-0.049	-0.049	0.000	0.000	0.000	0.000
25	C	24	SER	0	-0.041	-0.009	30.048	-0.002	-0.002	0.000	0.000	0.000	0.000
26	C	25	ASN	0	-0.028	-0.010	29.898	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	26	SER	0	0.071	0.022	29.452	-0.004	-0.004	0.000	0.000	0.000	0.000
28	C	27	LYS	1	0.914	0.958	28.689	0.042	0.042	0.000	0.000	0.000	0.000
29	C	28	GLU	-1	-0.853	-0.918	26.011	-0.030	-0.030	0.000	0.000	0.000	0.000
30	C	29	TRP	0	0.060	0.027	24.166	-0.006	-0.006	0.000	0.000	0.000	0.000
31	C	30	ASN	0	0.014	-0.014	24.333	-0.010	-0.010	0.000	0.000	0.000	0.000
32	C	31	TYR	0	-0.024	0.009	19.509	-0.012	-0.012	0.000	0.000	0.000	0.000
33	C	32	CYS	0	-0.009	-0.001	20.208	-0.012	-0.012	0.000	0.000	0.000	0.000
34	C	33	VAL	0	0.017	0.005	19.373	-0.017	-0.017	0.000	0.000	0.000	0.000
35	C	34	GLY	0	-0.007	0.005	19.828	-0.021	-0.021	0.000	0.000	0.000	0.000
36	C	35	LEU	0	0.023	0.009	15.478	-0.034	-0.034	0.000	0.000	0.000	0.000
37	C	36	HIS	0	0.011	0.007	15.137	-0.051	-0.051	0.000	0.000	0.000	0.000
38	C	37	ASN	0	-0.023	-0.027	15.310	-0.040	-0.040	0.000	0.000	0.000	0.000
39	C	38	GLU	-1	-0.881	-0.930	15.055	-0.297	-0.297	0.000	0.000	0.000	0.000
40	C	39	ILE	0	-0.038	-0.008	10.019	-0.087	-0.087	0.000	0.000	0.000	0.000
41	C	40	ASN	0	-0.010	-0.025	11.199	-0.153	-0.153	0.000	0.000	0.000	0.000
42	C	41	LEU	0	-0.046	-0.014	13.500	-0.021	-0.021	0.000	0.000	0.000	0.000
43	C	42	CYS	0	-0.048	0.004	9.396	0.023	0.023	0.000	0.000	0.000	0.000
44	C	43	ASP	-1	-0.878	-0.959	8.843	-1.069	-1.069	0.000	0.000	0.000	0.000
45	C	44	ASP	-1	-0.903	-0.950	6.998	-1.632	-1.632	0.000	0.000	0.000	0.000
46	C	45	PRO	0	-0.025	-0.039	2.271	-1.137	-0.504	1.863	-1.088	-1.407	-0.004
47	C	46	ASP	-1	-0.894	-0.932	4.349	-0.917	-0.741	-0.001	-0.012	-0.164	0.000
48	C	47	ALA	0	0.036	0.016	6.457	0.314	0.314	0.000	0.000	0.000	0.000
49	C	48	VAL	0	-0.049	-0.031	6.210	0.230	0.230	0.000	0.000	0.000	0.000
50	C	49	LEU	0	0.023	0.001	5.524	0.332	0.332	0.000	0.000	0.000	0.000
51	C	50	GLU	-1	-0.943	-0.971	7.517	-0.091	-0.091	0.000	0.000	0.000	0.000
52	C	51	LYS	1	0.865	0.925	10.866	0.457	0.457	0.000	0.000	0.000	0.000
53	C	52	LEU	0	0.009	0.000	8.583	0.073	0.073	0.000	0.000	0.000	0.000
54	C	53	LEU	0	-0.020	-0.014	10.382	0.082	0.082	0.000	0.000	0.000	0.000
55	C	54	ALA	0	-0.021	0.006	12.982	0.030	0.030	0.000	0.000	0.000	0.000
56	C	55	LEU	0	-0.011	-0.003	14.908	0.022	0.022	0.000	0.000	0.000	0.000
57	C	56	ILE	0	0.012	-0.002	12.413	0.019	0.019	0.000	0.000	0.000	0.000
58	C	57	ALA	0	0.022	0.023	16.414	0.010	0.010	0.000	0.000	0.000	0.000
59	C	58	PHE	0	0.004	-0.006	18.838	0.002	0.002	0.000	0.000	0.000	0.000
60	C	59	PHE	0	0.035	0.016	19.146	0.001	0.001	0.000	0.000	0.000	0.000
61	C	60	LEU	0	0.006	-0.006	18.684	0.004	0.004	0.000	0.000	0.000	0.000
62	C	61	SER	0	-0.092	-0.063	22.068	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	62	LYS	1	0.808	0.909	24.564	0.003	0.003	0.000	0.000	0.000	0.000
64	C	63	HIS	0	0.027	0.018	23.774	0.001	0.001	0.000	0.000	0.000	0.000
65	C	64	ASN	0	-0.004	0.015	27.453	0.003	0.003	0.000	0.000	0.000	0.000
66	C	65	THR	0	0.015	-0.024	28.159	0.004	0.004	0.000	0.000	0.000	0.000
67	C	66	CYS	0	-0.025	-0.016	28.672	0.008	0.008	0.000	0.000	0.000	0.000
68	C	67	ASP	-1	-0.845	-0.919	29.681	0.063	0.063	0.000	0.000	0.000	0.000
69	C	68	LEU	0	-0.039	-0.015	22.676	0.008	0.008	0.000	0.000	0.000	0.000
70	C	69	SER	0	-0.002	-0.006	25.153	0.015	0.015	0.000	0.000	0.000	0.000
71	C	70	ASP	-1	-0.905	-0.938	26.546	0.102	0.102	0.000	0.000	0.000	0.000
72	C	71	LEU	0	-0.053	-0.038	23.871	0.007	0.007	0.000	0.000	0.000	0.000
73	C	72	ILE	0	-0.039	-0.018	20.957	0.012	0.012	0.000	0.000	0.000	0.000
74	C	73	GLU	-1	-0.863	-0.937	22.804	0.184	0.184	0.000	0.000	0.000	0.000
75	C	74	SER	0	-0.061	-0.014	25.451	0.009	0.009	0.000	0.000	0.000	0.000
76	C	75	TYR	0	-0.056	-0.045	21.877	-0.001	-0.001	0.000	0.000	0.000	0.000
77	C	76	PHE	0	-0.079	-0.024	15.204	0.031	0.031	0.000	0.000	0.000	0.000
78	C	77	GLU	-1	-0.899	-0.965	20.017	0.284	0.284	0.000	0.000	0.000	0.000
79	C	78	ASN	0	-0.103	-0.040	22.200	0.010	0.010	0.000	0.000	0.000	0.000
80	C	79	THR	0	-0.017	0.007	19.059	-0.009	-0.009	0.000	0.000	0.000	0.000
81	C	80	THR	0	-0.029	-0.012	22.229	0.004	0.004	0.000	0.000	0.000	0.000
82	C	81	ILE	0	-0.053	-0.024	16.478	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:0:GLY)