FMO DATABASE

FMODB ID: VRY31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-559324.316491
FMO2-HF: Nuclear repulsion	525651.516368
FMO2-HF: Total energy	-33672.800123
FMO2-MP2: Total energy	-33767.616426

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.
-233.837	-238.957	31.264	-14.741	-11.402	-0.17

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 : 0.843 / q_NPA : 0.899

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	-0.018	-0.017	1.764	-43.807	-44.849	12.056	-6.066	-4.948	-0.061
4	B	5	GLU	-1	-0.793	-0.878	1.887	-132.880	-137.367	19.208	-8.532	-6.188	-0.109
5	B	6	MET	0	-0.020	0.008	5.051	5.620	5.652	-0.001	-0.003	-0.029	0.000
6	B	7	LYS	1	0.835	0.917	8.872	23.769	23.769	0.000	0.000	0.000	0.000
7	B	8	CYS	0	-0.026	-0.017	10.627	1.419	1.419	0.000	0.000	0.000	0.000
8	B	9	THR	0	-0.002	-0.016	10.702	0.307	0.307	0.000	0.000	0.000	0.000
9	B	10	ASN	0	0.093	0.069	12.760	1.258	1.258	0.000	0.000	0.000	0.000
10	B	11	VAL	0	0.022	-0.009	14.876	-1.127	-1.127	0.000	0.000	0.000	0.000
11	B	12	VAL	0	0.045	0.032	16.490	-0.482	-0.482	0.000	0.000	0.000	0.000
12	B	13	LEU	0	0.004	0.008	13.209	-0.068	-0.068	0.000	0.000	0.000	0.000
13	B	14	LEU	0	-0.012	-0.010	10.500	-0.809	-0.809	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.014	0.007	13.426	-0.165	-0.165	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.016	-0.014	16.718	0.479	0.479	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.020	-0.018	10.494	0.241	0.241	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.014	-0.016	13.996	0.625	0.625	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.826	0.932	15.145	15.055	15.055	0.000	0.000	0.000	0.000
19	B	20	MET	0	-0.079	-0.033	16.987	1.141	1.141	0.000	0.000	0.000	0.000
20	B	21	HIS	0	-0.006	0.016	14.377	0.225	0.225	0.000	0.000	0.000	0.000
21	B	22	VAL	0	0.061	0.033	10.904	-0.537	-0.537	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.842	-0.918	8.676	-26.426	-26.426	0.000	0.000	0.000	0.000
23	B	24	SER	0	-0.077	-0.044	7.572	-1.647	-1.647	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.073	-0.048	8.307	-0.091	-0.091	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.043	0.014	3.768	0.694	0.918	0.002	-0.058	-0.169	0.000
26	B	27	LYS	1	0.927	0.968	5.663	18.819	18.819	0.000	0.000	0.000	0.000
27	B	28	GLU	-1	-0.785	-0.876	8.394	-18.798	-18.798	0.000	0.000	0.000	0.000
28	B	29	TRP	0	0.048	0.021	5.829	1.895	1.895	0.000	0.000	0.000	0.000
29	B	30	ASN	0	0.007	-0.004	4.163	-4.059	-3.906	-0.001	-0.082	-0.068	0.000
30	B	31	TYR	0	-0.023	0.003	8.193	0.921	0.921	0.000	0.000	0.000	0.000
31	B	32	CYS	0	-0.006	0.007	11.938	1.423	1.423	0.000	0.000	0.000	0.000
32	B	33	VAL	0	-0.009	-0.014	7.051	1.320	1.320	0.000	0.000	0.000	0.000
33	B	34	GLY	0	-0.027	-0.005	10.196	0.206	0.206	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.064	0.023	11.845	1.035	1.035	0.000	0.000	0.000	0.000
35	B	36	HIS	0	0.043	0.047	12.337	1.557	1.557	0.000	0.000	0.000	0.000
36	B	37	ASN	0	-0.009	-0.023	8.743	2.113	2.113	0.000	0.000	0.000	0.000
37	B	38	GLU	-1	-0.870	-0.913	13.223	-18.497	-18.497	0.000	0.000	0.000	0.000
38	B	39	ILE	0	0.043	0.031	16.523	1.107	1.107	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.063	-0.043	15.001	-0.422	-0.422	0.000	0.000	0.000	0.000
40	B	41	LEU	0	-0.093	-0.059	15.742	-0.288	-0.288	0.000	0.000	0.000	0.000
41	B	42	CYS	0	-0.039	0.001	19.210	0.445	0.445	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.922	-0.959	22.402	-12.901	-12.901	0.000	0.000	0.000	0.000
43	B	44	ASP	-1	-0.832	-0.925	25.459	-10.932	-10.932	0.000	0.000	0.000	0.000
44	B	45	PRO	0	0.004	-0.004	25.863	-0.519	-0.519	0.000	0.000	0.000	0.000
45	B	46	ASP	-1	-0.888	-0.935	26.839	-10.756	-10.756	0.000	0.000	0.000	0.000
46	B	47	ALA	0	-0.003	-0.012	24.148	-0.347	-0.347	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.032	-0.019	21.857	-0.809	-0.809	0.000	0.000	0.000	0.000
48	B	49	LEU	0	0.000	-0.003	22.809	-0.516	-0.516	0.000	0.000	0.000	0.000
49	B	50	GLU	-1	-0.948	-0.967	24.612	-12.261	-12.261	0.000	0.000	0.000	0.000
50	B	51	LYS	1	0.838	0.909	18.826	15.792	15.792	0.000	0.000	0.000	0.000
51	B	52	LEU	0	-0.001	0.002	20.089	-0.676	-0.676	0.000	0.000	0.000	0.000
52	B	53	LEU	0	0.012	0.008	21.766	-0.103	-0.103	0.000	0.000	0.000	0.000
53	B	54	ALA	0	-0.001	0.000	20.134	0.041	0.041	0.000	0.000	0.000	0.000
54	B	55	LEU	0	-0.021	-0.011	15.355	-0.524	-0.524	0.000	0.000	0.000	0.000
55	B	56	ILE	0	-0.002	-0.001	19.265	-0.055	-0.055	0.000	0.000	0.000	0.000
56	B	57	ALA	0	0.004	-0.003	22.582	0.211	0.211	0.000	0.000	0.000	0.000
57	B	58	PHE	0	-0.010	0.001	14.385	0.044	0.044	0.000	0.000	0.000	0.000
58	B	59	PHE	0	0.062	0.023	15.447	0.034	0.034	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.027	0.019	20.526	0.375	0.375	0.000	0.000	0.000	0.000
60	B	61	SER	0	-0.118	-0.073	19.767	0.360	0.360	0.000	0.000	0.000	0.000
61	B	62	LYS	1	0.811	0.906	16.004	16.984	16.984	0.000	0.000	0.000	0.000
62	B	63	HIS	0	0.041	0.006	20.853	-0.071	-0.071	0.000	0.000	0.000	0.000
63	B	64	ASN	0	-0.029	-0.027	24.026	0.375	0.375	0.000	0.000	0.000	0.000
64	B	65	THR	0	-0.021	-0.009	27.047	0.268	0.268	0.000	0.000	0.000	0.000
65	B	66	CYS	0	-0.096	-0.046	23.975	-0.024	-0.024	0.000	0.000	0.000	0.000
66	B	67	ASP	-1	-0.802	-0.876	26.469	-11.178	-11.178	0.000	0.000	0.000	0.000
67	B	68	LEU	0	-0.007	-0.013	21.846	-0.734	-0.734	0.000	0.000	0.000	0.000
68	B	69	SER	0	0.014	-0.003	24.835	-0.334	-0.334	0.000	0.000	0.000	0.000
69	B	70	ASP	-1	-0.843	-0.914	23.588	-12.878	-12.878	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.071	-0.017	18.287	-0.580	-0.580	0.000	0.000	0.000	0.000
71	B	72	ILE	0	0.002	-0.008	22.049	-0.334	-0.334	0.000	0.000	0.000	0.000
72	B	73	GLU	-1	-0.921	-0.962	24.750	-11.291	-11.291	0.000	0.000	0.000	0.000
73	B	74	SER	0	0.017	-0.013	20.804	-0.319	-0.319	0.000	0.000	0.000	0.000
74	B	75	TYR	0	-0.012	-0.045	15.901	-0.381	-0.381	0.000	0.000	0.000	0.000
75	B	76	PHE	0	-0.003	-0.003	22.093	0.047	0.047	0.000	0.000	0.000	0.000
76	B	77	GLU	-1	-0.940	-0.950	24.093	-12.230	-12.230	0.000	0.000	0.000	0.000
77	B	78	ASN	0	-0.129	-0.076	19.653	-0.781	-0.781	0.000	0.000	0.000	0.000
78	B	79	THR	0	-0.032	-0.008	20.703	-0.571	-0.571	0.000	0.000	0.000	0.000
79	B	80	THR	0	0.039	0.011	22.343	0.366	0.366	0.000	0.000	0.000	0.000
80	B	81	ILE	0	-0.013	0.009	24.041	0.584	0.584	0.000	0.000	0.000	0.000
81	B	82	LEU	0	-0.012	-0.004	24.379	0.382	0.382	0.000	0.000	0.000	0.000
82	B	83	GLN	0	-0.144	-0.061	25.677	0.834	0.834	0.000	0.000	0.000	0.000

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