FMO DATABASE

FMODB ID: 43Y2N

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	OptAll
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	-518584.411382
FMO2-HF: Nuclear repulsion	485199.595658
FMO2-HF: Total energy	-33384.815724
FMO2-MP2: Total energy	-33478.626144

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.
-5.32	-2.345	2.062	-2.303	-2.731	0.003

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 : 0.054 / q_NPA : 0.013

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	0.857	0.913	3.177	-4.624	-2.454	0.066	-1.076	-1.159	0.005
4	C	3	LEU	0	0.031	0.030	4.510	-0.362	-0.141	-0.001	-0.032	-0.187	0.000
5	C	4	THR	0	0.031	0.006	5.603	0.456	0.456	0.000	0.000	0.000	0.000
6	C	5	GLU	-1	-0.771	-0.863	7.225	1.063	1.063	0.000	0.000	0.000	0.000
7	C	6	MET	0	-0.026	0.016	3.583	0.080	0.249	0.002	-0.037	-0.133	0.000
8	C	7	LYS	1	0.844	0.913	8.244	0.996	0.996	0.000	0.000	0.000	0.000
9	C	8	CYS	0	-0.057	-0.034	11.032	0.100	0.100	0.000	0.000	0.000	0.000
10	C	9	THR	0	-0.018	-0.027	10.806	0.072	0.072	0.000	0.000	0.000	0.000
11	C	10	ASN	0	0.004	-0.008	12.370	0.068	0.068	0.000	0.000	0.000	0.000
12	C	11	VAL	0	-0.011	0.006	14.095	0.039	0.039	0.000	0.000	0.000	0.000
13	C	12	VAL	0	-0.028	-0.010	16.356	0.028	0.028	0.000	0.000	0.000	0.000
14	C	13	LEU	0	0.007	0.010	14.519	0.019	0.019	0.000	0.000	0.000	0.000
15	C	14	LEU	0	0.012	0.011	18.215	0.017	0.017	0.000	0.000	0.000	0.000
16	C	15	GLY	0	0.019	0.008	20.300	0.015	0.015	0.000	0.000	0.000	0.000
17	C	16	LEU	0	-0.027	-0.019	20.975	0.014	0.014	0.000	0.000	0.000	0.000
18	C	17	LEU	0	0.016	-0.006	20.160	0.010	0.010	0.000	0.000	0.000	0.000
19	C	18	SER	0	-0.044	-0.032	23.826	0.009	0.009	0.000	0.000	0.000	0.000
20	C	19	LYS	1	0.828	0.900	26.025	0.061	0.061	0.000	0.000	0.000	0.000
21	C	20	MET	0	0.008	0.025	24.822	0.006	0.006	0.000	0.000	0.000	0.000
22	C	21	HIS	0	-0.004	0.004	28.266	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	22	VAL	0	0.058	0.033	25.458	0.002	0.002	0.000	0.000	0.000	0.000
24	C	23	GLU	-1	-0.850	-0.909	28.246	-0.098	-0.098	0.000	0.000	0.000	0.000
25	C	24	SER	0	-0.078	-0.040	30.104	0.002	0.002	0.000	0.000	0.000	0.000
26	C	25	ASN	0	-0.036	-0.018	30.242	0.001	0.001	0.000	0.000	0.000	0.000
27	C	26	SER	0	0.064	0.021	29.687	-0.006	-0.006	0.000	0.000	0.000	0.000
28	C	27	LYS	1	0.910	0.958	29.320	0.083	0.083	0.000	0.000	0.000	0.000
29	C	28	GLU	-1	-0.784	-0.877	26.215	-0.093	-0.093	0.000	0.000	0.000	0.000
30	C	29	TRP	0	0.021	0.014	23.573	-0.017	-0.017	0.000	0.000	0.000	0.000
31	C	30	ASN	0	-0.021	-0.026	24.642	-0.016	-0.016	0.000	0.000	0.000	0.000
32	C	31	TYR	0	-0.024	0.006	19.782	-0.018	-0.018	0.000	0.000	0.000	0.000
33	C	32	CYS	0	-0.016	-0.001	20.526	-0.019	-0.019	0.000	0.000	0.000	0.000
34	C	33	VAL	0	0.009	-0.001	19.806	-0.025	-0.025	0.000	0.000	0.000	0.000
35	C	34	GLY	0	-0.013	0.001	20.460	-0.019	-0.019	0.000	0.000	0.000	0.000
36	C	35	LEU	0	0.048	0.025	15.908	-0.032	-0.032	0.000	0.000	0.000	0.000
37	C	36	HIS	0	0.008	-0.003	15.671	-0.056	-0.056	0.000	0.000	0.000	0.000
38	C	37	ASN	0	-0.029	-0.021	16.065	-0.043	-0.043	0.000	0.000	0.000	0.000
39	C	38	GLU	-1	-0.882	-0.949	15.355	-0.368	-0.368	0.000	0.000	0.000	0.000
40	C	39	ILE	0	-0.039	-0.012	10.691	-0.078	-0.078	0.000	0.000	0.000	0.000
41	C	40	ASN	0	0.013	-0.009	11.925	-0.149	-0.149	0.000	0.000	0.000	0.000
42	C	41	LEU	0	-0.053	-0.015	13.995	-0.020	-0.020	0.000	0.000	0.000	0.000
43	C	42	CYS	0	-0.028	0.024	9.442	0.049	0.049	0.000	0.000	0.000	0.000
44	C	43	ASP	-1	-0.852	-0.939	8.738	-0.945	-0.945	0.000	0.000	0.000	0.000
45	C	44	ASP	-1	-0.841	-0.924	6.669	-1.490	-1.490	0.000	0.000	0.000	0.000
46	C	45	PRO	0	-0.030	-0.031	2.351	-0.700	-0.460	1.996	-1.137	-1.099	-0.002
47	C	46	ASP	-1	-0.887	-0.930	4.418	-1.160	-0.985	-0.001	-0.021	-0.153	0.000
48	C	47	ALA	0	0.002	-0.010	6.535	0.195	0.195	0.000	0.000	0.000	0.000
49	C	48	VAL	0	-0.029	-0.020	7.093	0.161	0.161	0.000	0.000	0.000	0.000
50	C	49	LEU	0	0.013	-0.003	5.444	0.246	0.246	0.000	0.000	0.000	0.000
51	C	50	GLU	-1	-0.934	-0.962	7.810	-0.210	-0.210	0.000	0.000	0.000	0.000
52	C	51	LYS	1	0.863	0.933	11.296	0.544	0.544	0.000	0.000	0.000	0.000
53	C	52	LEU	0	0.023	0.009	8.581	0.087	0.087	0.000	0.000	0.000	0.000
54	C	53	LEU	0	-0.007	-0.003	10.324	0.107	0.107	0.000	0.000	0.000	0.000
55	C	54	ALA	0	-0.012	0.004	12.968	0.061	0.061	0.000	0.000	0.000	0.000
56	C	55	LEU	0	-0.010	-0.003	15.151	0.043	0.043	0.000	0.000	0.000	0.000
57	C	56	ILE	0	0.006	-0.002	12.405	0.038	0.038	0.000	0.000	0.000	0.000
58	C	57	ALA	0	0.002	0.003	16.382	0.032	0.032	0.000	0.000	0.000	0.000
59	C	58	PHE	0	-0.016	-0.009	18.703	0.020	0.020	0.000	0.000	0.000	0.000
60	C	59	PHE	0	0.042	0.021	19.140	0.016	0.016	0.000	0.000	0.000	0.000
61	C	60	LEU	0	0.019	0.001	18.882	0.014	0.014	0.000	0.000	0.000	0.000
62	C	61	SER	0	-0.123	-0.071	22.035	0.010	0.010	0.000	0.000	0.000	0.000
63	C	62	LYS	1	0.786	0.879	24.657	0.080	0.080	0.000	0.000	0.000	0.000
64	C	63	HIS	0	0.016	0.018	22.891	0.010	0.010	0.000	0.000	0.000	0.000
65	C	64	ASN	0	-0.049	-0.025	27.458	0.000	0.000	0.000	0.000	0.000	0.000
66	C	65	THR	0	0.010	-0.016	27.451	0.001	0.001	0.000	0.000	0.000	0.000
67	C	66	CYS	0	-0.023	-0.004	28.414	0.006	0.006	0.000	0.000	0.000	0.000
68	C	67	ASP	-1	-0.796	-0.902	29.440	0.002	0.002	0.000	0.000	0.000	0.000
69	C	68	LEU	0	-0.020	-0.006	22.265	0.003	0.003	0.000	0.000	0.000	0.000
70	C	69	SER	0	0.003	0.006	24.686	0.007	0.007	0.000	0.000	0.000	0.000
71	C	70	ASP	-1	-0.904	-0.945	25.980	0.038	0.038	0.000	0.000	0.000	0.000
72	C	71	LEU	0	-0.049	-0.033	23.808	0.005	0.005	0.000	0.000	0.000	0.000
73	C	72	ILE	0	-0.027	-0.005	20.681	0.005	0.005	0.000	0.000	0.000	0.000
74	C	73	GLU	-1	-0.865	-0.939	22.397	0.098	0.098	0.000	0.000	0.000	0.000
75	C	74	SER	0	-0.033	-0.012	24.612	0.010	0.010	0.000	0.000	0.000	0.000
76	C	75	TYR	0	-0.094	-0.050	21.566	0.000	0.000	0.000	0.000	0.000	0.000
77	C	76	PHE	0	-0.102	-0.022	14.403	0.010	0.010	0.000	0.000	0.000	0.000
78	C	77	GLU	-1	-0.856	-0.942	19.319	0.167	0.167	0.000	0.000	0.000	0.000
79	C	78	ASN	0	-0.106	-0.047	21.596	0.016	0.016	0.000	0.000	0.000	0.000
80	C	79	THR	0	-0.055	-0.032	18.933	-0.004	-0.004	0.000	0.000	0.000	0.000
81	C	80	THR	0	-0.006	-0.003	21.622	0.013	0.013	0.000	0.000	0.000	0.000
82	C	81	ILE	0	-0.067	-0.029	16.608	-0.002	-0.002	0.000	0.000	0.000	0.000

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