FMO DATABASE

FMODB ID: 7JL8K

Calculation Name: 3UB0-B-Xray308

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-557294.647543
FMO2-HF: Nuclear repulsion	523471.783563
FMO2-HF: Total energy	-33822.86398
FMO2-MP2: Total energy	-33918.057484

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:1:ACE )

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

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.
-1	0.099	0.023	-0.486	-0.635	-0.001

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.005

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	3	LEU	0	-0.015	0.003	3.822	0.870	1.708	-0.006	-0.376	-0.455	-0.001
4	B	4	THR	0	-0.029	-0.017	7.025	0.009	0.009	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.907	-0.943	9.883	-0.406	-0.406	0.000	0.000	0.000	0.000
6	B	6	MET	0	-0.010	0.007	13.461	0.046	0.046	0.000	0.000	0.000	0.000
7	B	7	LYS	1	0.943	0.978	16.642	0.126	0.126	0.000	0.000	0.000	0.000
8	B	8	CYS	0	0.006	0.003	19.179	-0.003	-0.003	0.000	0.000	0.000	0.000
9	B	9	THR	0	-0.002	-0.019	18.782	0.007	0.007	0.000	0.000	0.000	0.000
10	B	10	ASN	0	0.107	0.074	20.556	0.009	0.009	0.000	0.000	0.000	0.000
11	B	11	VAL	0	0.011	-0.023	21.090	-0.006	-0.006	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.062	0.036	21.990	-0.006	-0.006	0.000	0.000	0.000	0.000
13	B	13	LEU	0	0.023	0.012	17.440	0.004	0.004	0.000	0.000	0.000	0.000
14	B	14	LEU	0	-0.014	-0.020	15.940	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	15	GLY	0	-0.004	0.009	18.149	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.010	-0.007	19.984	0.007	0.007	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.016	-0.013	13.726	0.014	0.014	0.000	0.000	0.000	0.000
18	B	18	SER	0	-0.014	0.011	15.567	0.007	0.007	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.946	0.970	17.355	0.030	0.030	0.000	0.000	0.000	0.000
20	B	20	MET	0	-0.094	-0.043	17.609	0.016	0.016	0.000	0.000	0.000	0.000
21	B	21	HIS	0	0.002	0.015	14.703	0.037	0.037	0.000	0.000	0.000	0.000
22	B	22	VAL	0	0.033	0.013	11.698	0.022	0.022	0.000	0.000	0.000	0.000
23	B	23	GLU	-1	-0.909	-0.968	9.553	-0.106	-0.106	0.000	0.000	0.000	0.000
24	B	24	SER	0	-0.049	-0.015	8.113	-0.064	-0.064	0.000	0.000	0.000	0.000
25	B	25	ASN	0	-0.029	-0.009	7.882	0.244	0.244	0.000	0.000	0.000	0.000
26	B	26	SER	0	0.044	0.007	2.947	-0.427	-0.166	0.029	-0.110	-0.180	0.000
27	B	27	LYS	1	0.912	0.955	5.750	-0.972	-0.972	0.000	0.000	0.000	0.000
28	B	28	GLU	-1	-0.874	-0.937	8.098	0.078	0.078	0.000	0.000	0.000	0.000
29	B	29	TRP	0	0.034	0.012	8.461	-0.054	-0.054	0.000	0.000	0.000	0.000
30	B	30	ASN	0	0.012	-0.007	5.828	-0.218	-0.218	0.000	0.000	0.000	0.000
31	B	31	TYR	0	-0.015	0.021	10.064	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	32	CYS	0	0.004	0.007	13.103	-0.021	-0.021	0.000	0.000	0.000	0.000
33	B	33	VAL	0	-0.005	-0.008	12.391	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	34	GLY	0	-0.024	-0.006	13.711	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	35	LEU	0	0.028	0.010	14.977	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	36	HIS	0	0.028	0.033	17.697	0.007	0.007	0.000	0.000	0.000	0.000
37	B	37	ASN	0	-0.016	-0.030	15.164	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.928	-0.965	17.467	0.017	0.017	0.000	0.000	0.000	0.000
39	B	39	ILE	0	0.003	0.006	20.720	0.004	0.004	0.000	0.000	0.000	0.000
40	B	40	ASN	0	-0.058	-0.040	22.109	-0.010	-0.010	0.000	0.000	0.000	0.000
41	B	41	LEU	0	-0.059	-0.026	20.679	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	42	CYS	0	-0.073	-0.016	24.587	0.008	0.008	0.000	0.000	0.000	0.000
43	B	43	ASP	-1	-0.898	-0.941	26.908	-0.026	-0.026	0.000	0.000	0.000	0.000
44	B	44	ASP	-1	-0.908	-0.974	30.099	0.000	0.000	0.000	0.000	0.000	0.000
45	B	45	PRO	0	0.046	0.010	30.360	0.000	0.000	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.917	-0.943	31.230	0.002	0.002	0.000	0.000	0.000	0.000
47	B	47	ALA	0	0.030	0.014	27.501	0.003	0.003	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.029	-0.021	26.534	0.001	0.001	0.000	0.000	0.000	0.000
49	B	49	LEU	0	0.015	0.000	26.601	0.000	0.000	0.000	0.000	0.000	0.000
50	B	50	GLU	-1	-0.943	-0.965	26.549	0.024	0.024	0.000	0.000	0.000	0.000
51	B	51	LYS	1	0.842	0.926	21.331	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	52	LEU	0	0.030	0.013	22.640	0.001	0.001	0.000	0.000	0.000	0.000
53	B	53	LEU	0	-0.004	0.001	24.468	0.003	0.003	0.000	0.000	0.000	0.000
54	B	54	ALA	0	-0.010	0.001	21.097	0.007	0.007	0.000	0.000	0.000	0.000
55	B	55	LEU	0	-0.017	-0.008	18.404	0.010	0.010	0.000	0.000	0.000	0.000
56	B	56	ILE	0	-0.003	-0.002	21.004	0.003	0.003	0.000	0.000	0.000	0.000
57	B	57	ALA	0	0.003	0.000	22.713	0.004	0.004	0.000	0.000	0.000	0.000
58	B	58	PHE	0	-0.025	-0.005	14.336	0.013	0.013	0.000	0.000	0.000	0.000
59	B	59	PHE	0	0.072	0.029	17.571	0.009	0.009	0.000	0.000	0.000	0.000
60	B	60	LEU	0	0.023	0.018	21.042	0.002	0.002	0.000	0.000	0.000	0.000
61	B	61	SER	0	-0.107	-0.068	19.814	0.011	0.011	0.000	0.000	0.000	0.000
62	B	62	LYS	1	0.844	0.931	15.972	-0.111	-0.111	0.000	0.000	0.000	0.000
63	B	63	HIS	0	-0.006	-0.014	20.972	-0.005	-0.005	0.000	0.000	0.000	0.000
64	B	64	ASN	0	-0.011	-0.018	24.413	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	65	THR	0	-0.013	-0.003	27.404	0.000	0.000	0.000	0.000	0.000	0.000
66	B	66	CYS	0	-0.065	-0.017	25.006	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	67	ASP	-1	-0.860	-0.888	27.288	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	68	LEU	0	-0.024	-0.040	23.605	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	69	SER	0	-0.014	-0.031	27.448	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	70	ASP	-1	-0.803	-0.901	28.087	-0.032	-0.032	0.000	0.000	0.000	0.000
71	B	71	LEU	0	-0.070	-0.037	22.293	-0.005	-0.005	0.000	0.000	0.000	0.000
72	B	72	ILE	0	-0.015	-0.016	26.193	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	73	GLU	-1	-0.917	-0.945	28.941	-0.029	-0.029	0.000	0.000	0.000	0.000
74	B	74	SER	0	-0.012	-0.006	26.216	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	75	TYR	0	-0.055	-0.058	21.242	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	76	PHE	0	-0.013	-0.019	27.835	0.000	0.000	0.000	0.000	0.000	0.000
77	B	77	GLU	-1	-0.944	-0.959	31.035	-0.043	-0.043	0.000	0.000	0.000	0.000
78	B	78	ASN	0	-0.136	-0.070	27.043	-0.008	-0.008	0.000	0.000	0.000	0.000
79	B	79	THR	0	-0.058	-0.020	27.230	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	80	THR	0	0.048	0.011	29.394	0.003	0.003	0.000	0.000	0.000	0.000
81	B	81	ILE	0	-0.042	-0.001	29.543	0.003	0.003	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.055	-0.034	29.504	0.004	0.004	0.000	0.000	0.000	0.000
83	B	83	GLN	-1	-0.969	-0.965	33.210	-0.025	-0.025	0.000	0.000	0.000	0.000

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