FMO DATABASE

FMODB ID: K3VY3

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	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	-516107.067076
FMO2-HF: Nuclear repulsion	482722.489007
FMO2-HF: Total energy	-33384.578069
FMO2-MP2: Total energy	-33478.359828

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.
-6	-2.644	2.057	-2.258	-3.154	0.001

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 : 0.046 / q_NPA : 0.009

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	0.951	0.985	3.358	-5.129	-3.152	0.029	-1.006	-1.000	0.005
4	C	3	LEU	0	0.042	0.032	4.483	-0.342	-0.077	-0.001	-0.038	-0.225	0.000
5	C	4	THR	0	0.038	0.003	5.067	0.345	0.434	-0.001	-0.005	-0.083	0.000
6	C	5	GLU	-1	-0.845	-0.920	7.224	1.284	1.284	0.000	0.000	0.000	0.000
7	C	6	MET	0	-0.023	0.007	3.157	0.002	0.294	0.027	-0.086	-0.233	-0.001
8	C	7	LYS	1	0.861	0.926	7.943	0.848	0.848	0.000	0.000	0.000	0.000
9	C	8	CYS	0	-0.047	-0.029	10.383	0.035	0.035	0.000	0.000	0.000	0.000
10	C	9	THR	0	-0.018	-0.019	10.811	0.038	0.038	0.000	0.000	0.000	0.000
11	C	10	ASN	0	-0.002	-0.011	12.061	0.027	0.027	0.000	0.000	0.000	0.000
12	C	11	VAL	0	0.005	0.016	13.706	0.007	0.007	0.000	0.000	0.000	0.000
13	C	12	VAL	0	-0.013	0.001	16.144	0.006	0.006	0.000	0.000	0.000	0.000
14	C	13	LEU	0	-0.007	0.004	14.262	0.001	0.001	0.000	0.000	0.000	0.000
15	C	14	LEU	0	0.002	0.005	17.923	0.001	0.001	0.000	0.000	0.000	0.000
16	C	15	GLY	0	0.019	0.009	19.890	0.001	0.001	0.000	0.000	0.000	0.000
17	C	16	LEU	0	-0.026	-0.024	20.888	0.002	0.002	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.015	-0.013	19.895	-0.001	-0.001	0.000	0.000	0.000	0.000
19	C	18	SER	0	-0.026	-0.002	23.543	0.001	0.001	0.000	0.000	0.000	0.000
20	C	19	LYS	1	0.821	0.921	25.876	-0.002	-0.002	0.000	0.000	0.000	0.000
21	C	20	MET	0	-0.002	-0.001	24.625	0.003	0.003	0.000	0.000	0.000	0.000
22	C	21	HIS	0	-0.023	0.000	28.257	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	22	VAL	0	0.056	0.022	25.277	0.000	0.000	0.000	0.000	0.000	0.000
24	C	23	GLU	-1	-0.874	-0.947	28.187	-0.047	-0.047	0.000	0.000	0.000	0.000
25	C	24	SER	0	-0.049	-0.015	30.045	-0.002	-0.002	0.000	0.000	0.000	0.000
26	C	25	ASN	0	-0.021	-0.002	30.034	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	26	SER	0	0.077	0.028	29.446	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	27	LYS	1	0.912	0.955	28.682	0.041	0.041	0.000	0.000	0.000	0.000
29	C	28	GLU	-1	-0.812	-0.897	25.999	-0.027	-0.027	0.000	0.000	0.000	0.000
30	C	29	TRP	0	0.039	0.022	23.458	-0.008	-0.008	0.000	0.000	0.000	0.000
31	C	30	ASN	0	0.002	-0.017	24.328	-0.010	-0.010	0.000	0.000	0.000	0.000
32	C	31	TYR	0	-0.031	0.005	19.624	-0.019	-0.019	0.000	0.000	0.000	0.000
33	C	32	CYS	0	-0.020	-0.004	20.211	-0.011	-0.011	0.000	0.000	0.000	0.000
34	C	33	VAL	0	0.021	0.004	19.369	-0.016	-0.016	0.000	0.000	0.000	0.000
35	C	34	GLY	0	-0.013	0.002	19.825	-0.019	-0.019	0.000	0.000	0.000	0.000
36	C	35	LEU	0	0.036	0.014	15.373	-0.031	-0.031	0.000	0.000	0.000	0.000
37	C	36	HIS	0	0.006	-0.003	15.132	-0.044	-0.044	0.000	0.000	0.000	0.000
38	C	37	ASN	0	-0.027	-0.026	15.310	-0.036	-0.036	0.000	0.000	0.000	0.000
39	C	38	GLU	-1	-0.870	-0.922	15.013	-0.291	-0.291	0.000	0.000	0.000	0.000
40	C	39	ILE	0	-0.036	-0.012	10.064	-0.082	-0.082	0.000	0.000	0.000	0.000
41	C	40	ASN	0	-0.005	-0.020	11.199	-0.144	-0.144	0.000	0.000	0.000	0.000
42	C	41	LEU	0	-0.039	-0.010	13.503	-0.018	-0.018	0.000	0.000	0.000	0.000
43	C	42	CYS	0	-0.050	0.007	9.218	0.019	0.019	0.000	0.000	0.000	0.000
44	C	43	ASP	-1	-0.865	-0.943	8.800	-0.989	-0.989	0.000	0.000	0.000	0.000
45	C	44	ASP	-1	-0.886	-0.940	7.006	-1.569	-1.569	0.000	0.000	0.000	0.000
46	C	45	PRO	0	-0.025	-0.039	2.229	-1.019	-0.475	2.004	-1.111	-1.437	-0.003
47	C	46	ASP	-1	-0.885	-0.930	4.334	-0.916	-0.727	-0.001	-0.012	-0.176	0.000
48	C	47	ALA	0	0.020	0.011	6.493	0.297	0.297	0.000	0.000	0.000	0.000
49	C	48	VAL	0	-0.036	-0.028	6.211	0.211	0.211	0.000	0.000	0.000	0.000
50	C	49	LEU	0	0.009	-0.002	5.341	0.328	0.328	0.000	0.000	0.000	0.000
51	C	50	GLU	-1	-0.970	-0.975	7.501	-0.093	-0.093	0.000	0.000	0.000	0.000
52	C	51	LYS	1	0.907	0.937	10.859	0.436	0.436	0.000	0.000	0.000	0.000
53	C	52	LEU	0	0.002	-0.001	8.552	0.073	0.073	0.000	0.000	0.000	0.000
54	C	53	LEU	0	-0.018	-0.012	10.266	0.080	0.080	0.000	0.000	0.000	0.000
55	C	54	ALA	0	-0.014	0.007	12.969	0.030	0.030	0.000	0.000	0.000	0.000
56	C	55	LEU	0	-0.022	-0.009	14.832	0.022	0.022	0.000	0.000	0.000	0.000
57	C	56	ILE	0	0.014	-0.003	12.443	0.018	0.018	0.000	0.000	0.000	0.000
58	C	57	ALA	0	0.020	0.024	16.408	0.010	0.010	0.000	0.000	0.000	0.000
59	C	58	PHE	0	-0.003	-0.009	18.828	0.002	0.002	0.000	0.000	0.000	0.000
60	C	59	PHE	0	0.034	0.017	19.145	0.003	0.003	0.000	0.000	0.000	0.000
61	C	60	LEU	0	0.002	-0.006	18.911	0.004	0.004	0.000	0.000	0.000	0.000
62	C	61	SER	0	-0.098	-0.059	22.062	-0.002	-0.002	0.000	0.000	0.000	0.000
63	C	62	LYS	1	0.770	0.880	24.558	0.004	0.004	0.000	0.000	0.000	0.000
64	C	63	HIS	0	0.019	0.010	23.181	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	64	ASN	0	-0.059	-0.019	27.449	0.000	0.000	0.000	0.000	0.000	0.000
66	C	65	THR	0	0.020	-0.021	28.043	0.004	0.004	0.000	0.000	0.000	0.000
67	C	66	CYS	0	-0.019	-0.009	28.668	0.008	0.008	0.000	0.000	0.000	0.000
68	C	67	ASP	-1	-0.808	-0.899	29.666	0.059	0.059	0.000	0.000	0.000	0.000
69	C	68	LEU	0	-0.022	-0.005	22.471	0.007	0.007	0.000	0.000	0.000	0.000
70	C	69	SER	0	0.002	-0.002	25.152	0.014	0.014	0.000	0.000	0.000	0.000
71	C	70	ASP	-1	-0.903	-0.939	26.546	0.098	0.098	0.000	0.000	0.000	0.000
72	C	71	LEU	0	-0.046	-0.033	24.183	0.007	0.007	0.000	0.000	0.000	0.000
73	C	72	ILE	0	-0.039	-0.019	21.001	0.012	0.012	0.000	0.000	0.000	0.000
74	C	73	GLU	-1	-0.869	-0.940	22.808	0.173	0.173	0.000	0.000	0.000	0.000
75	C	74	SER	0	-0.058	-0.007	25.457	0.009	0.009	0.000	0.000	0.000	0.000
76	C	75	TYR	0	-0.038	-0.035	21.901	-0.001	-0.001	0.000	0.000	0.000	0.000
77	C	76	PHE	0	-0.103	-0.016	15.085	0.033	0.033	0.000	0.000	0.000	0.000
78	C	77	GLU	-1	-0.870	-0.952	20.017	0.280	0.280	0.000	0.000	0.000	0.000
79	C	78	ASN	0	-0.108	-0.046	22.200	0.007	0.007	0.000	0.000	0.000	0.000
80	C	79	THR	0	-0.055	-0.033	19.306	-0.008	-0.008	0.000	0.000	0.000	0.000
81	C	80	THR	0	-0.015	-0.008	22.241	0.002	0.002	0.000	0.000	0.000	0.000
82	C	81	ILE	0	-0.051	-0.020	16.685	-0.005	-0.005	0.000	0.000	0.000	0.000

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