FMO DATABASE

FMODB ID: MMGKZ

Calculation Name: 3UB0-C-Xray308

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: 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	84
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-519882.898993
FMO2-HF: Nuclear repulsion	486327.762343
FMO2-HF: Total energy	-33555.13665
FMO2-MP2: Total energy	-33649.408383

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:-1:ACE )

Summations of interaction energy for fragment #1(C:-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.
0.277	2.737	0.587	-1.192	-1.852	-0.004

Interaction energy analysis for fragmet #1(C:-1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.008

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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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	1	SER	0	-0.007	0.000	3.785	0.955	1.748	-0.006	-0.341	-0.445	-0.001
4	C	2	LYS	1	0.955	0.986	3.473	-0.206	0.030	0.009	-0.055	-0.189	0.000
5	C	3	LEU	0	0.046	0.034	5.579	0.571	0.571	0.000	0.000	0.000	0.000
6	C	4	THR	0	0.013	-0.013	6.366	0.149	0.149	0.000	0.000	0.000	0.000
7	C	5	GLU	-1	-0.836	-0.912	7.484	0.340	0.340	0.000	0.000	0.000	0.000
8	C	6	MET	0	-0.026	0.010	2.704	0.283	0.649	0.302	-0.244	-0.424	-0.001
9	C	7	LYS	1	0.880	0.947	7.788	-0.186	-0.186	0.000	0.000	0.000	0.000
10	C	8	CYS	0	-0.043	-0.027	10.556	-0.069	-0.069	0.000	0.000	0.000	0.000
11	C	9	THR	0	-0.011	-0.012	10.204	-0.040	-0.040	0.000	0.000	0.000	0.000
12	C	10	ASN	0	0.012	-0.007	11.508	-0.048	-0.048	0.000	0.000	0.000	0.000
13	C	11	VAL	0	-0.004	0.015	13.106	-0.049	-0.049	0.000	0.000	0.000	0.000
14	C	12	VAL	0	-0.004	0.003	15.829	-0.032	-0.032	0.000	0.000	0.000	0.000
15	C	13	LEU	0	0.002	0.009	13.235	-0.025	-0.025	0.000	0.000	0.000	0.000
16	C	14	LEU	0	-0.003	0.002	17.119	-0.029	-0.029	0.000	0.000	0.000	0.000
17	C	15	GLY	0	0.015	0.009	19.125	-0.024	-0.024	0.000	0.000	0.000	0.000
18	C	16	LEU	0	-0.013	-0.024	19.019	-0.021	-0.021	0.000	0.000	0.000	0.000
19	C	17	LEU	0	0.015	-0.013	18.462	-0.018	-0.018	0.000	0.000	0.000	0.000
20	C	18	SER	0	-0.024	0.003	22.471	-0.017	-0.017	0.000	0.000	0.000	0.000
21	C	19	LYS	1	0.877	0.943	25.044	-0.119	-0.119	0.000	0.000	0.000	0.000
22	C	20	MET	0	-0.039	-0.008	22.889	-0.003	-0.003	0.000	0.000	0.000	0.000
23	C	21	HIS	0	-0.026	-0.001	27.118	-0.003	-0.003	0.000	0.000	0.000	0.000
24	C	22	VAL	0	0.038	0.013	23.998	-0.004	-0.004	0.000	0.000	0.000	0.000
25	C	23	GLU	-1	-0.935	-0.973	27.116	0.090	0.090	0.000	0.000	0.000	0.000
26	C	24	SER	0	-0.039	-0.008	28.939	-0.008	-0.008	0.000	0.000	0.000	0.000
27	C	25	ASN	0	-0.028	-0.011	28.417	-0.007	-0.007	0.000	0.000	0.000	0.000
28	C	26	SER	0	0.072	0.022	28.098	0.005	0.005	0.000	0.000	0.000	0.000
29	C	27	LYS	1	0.913	0.958	27.403	-0.084	-0.084	0.000	0.000	0.000	0.000
30	C	28	GLU	-1	-0.852	-0.918	24.447	0.131	0.131	0.000	0.000	0.000	0.000
31	C	29	TRP	0	0.061	0.027	23.154	0.018	0.018	0.000	0.000	0.000	0.000
32	C	30	ASN	0	0.013	-0.014	23.198	0.008	0.008	0.000	0.000	0.000	0.000
33	C	31	TYR	0	-0.022	0.010	17.642	0.008	0.008	0.000	0.000	0.000	0.000
34	C	32	CYS	0	-0.012	-0.003	18.893	0.021	0.021	0.000	0.000	0.000	0.000
35	C	33	VAL	0	0.020	0.006	18.294	0.019	0.019	0.000	0.000	0.000	0.000
36	C	34	GLY	0	-0.004	0.006	19.056	0.001	0.001	0.000	0.000	0.000	0.000
37	C	35	LEU	0	0.018	0.008	13.952	0.001	0.001	0.000	0.000	0.000	0.000
38	C	36	HIS	0	0.013	0.008	14.215	0.027	0.027	0.000	0.000	0.000	0.000
39	C	37	ASN	0	-0.021	-0.026	14.853	0.010	0.010	0.000	0.000	0.000	0.000
40	C	38	GLU	-1	-0.881	-0.930	14.247	0.142	0.142	0.000	0.000	0.000	0.000
41	C	39	ILE	0	-0.039	-0.009	9.619	-0.011	-0.011	0.000	0.000	0.000	0.000
42	C	40	ASN	0	-0.012	-0.025	11.151	0.003	0.003	0.000	0.000	0.000	0.000
43	C	41	LEU	0	-0.044	-0.013	13.635	-0.036	-0.036	0.000	0.000	0.000	0.000
44	C	42	CYS	0	-0.050	0.003	9.180	-0.048	-0.048	0.000	0.000	0.000	0.000
45	C	43	ASP	-1	-0.877	-0.959	9.674	-0.082	-0.082	0.000	0.000	0.000	0.000
46	C	44	ASP	-1	-0.901	-0.950	7.736	-0.567	-0.567	0.000	0.000	0.000	0.000
47	C	45	PRO	0	-0.023	-0.038	3.021	-0.122	0.135	0.210	-0.173	-0.293	-0.001
48	C	46	ASP	-1	-0.892	-0.931	3.707	-0.544	-0.087	0.010	-0.228	-0.240	-0.001
49	C	47	ALA	0	0.037	0.016	5.225	0.308	0.360	0.000	-0.002	-0.049	0.000
50	C	48	VAL	0	-0.052	-0.032	5.600	0.104	0.104	0.000	0.000	0.000	0.000
51	C	49	LEU	0	0.022	-0.001	3.146	-0.128	0.171	0.062	-0.149	-0.212	0.000
52	C	50	GLU	-1	-0.941	-0.969	5.595	0.066	0.066	0.000	0.000	0.000	0.000
53	C	51	LYS	1	0.864	0.925	8.847	-0.292	-0.292	0.000	0.000	0.000	0.000
54	C	52	LEU	0	0.006	-0.001	7.416	-0.069	-0.069	0.000	0.000	0.000	0.000
55	C	53	LEU	0	-0.018	-0.013	7.994	-0.106	-0.106	0.000	0.000	0.000	0.000
56	C	54	ALA	0	-0.018	0.007	10.950	-0.101	-0.101	0.000	0.000	0.000	0.000
57	C	55	LEU	0	-0.014	-0.005	13.196	-0.055	-0.055	0.000	0.000	0.000	0.000
58	C	56	ILE	0	0.012	-0.003	10.685	-0.050	-0.050	0.000	0.000	0.000	0.000
59	C	57	ALA	0	0.024	0.024	14.721	-0.054	-0.054	0.000	0.000	0.000	0.000
60	C	58	PHE	0	0.004	-0.006	16.878	-0.043	-0.043	0.000	0.000	0.000	0.000
61	C	59	PHE	0	0.035	0.015	17.553	-0.032	-0.032	0.000	0.000	0.000	0.000
62	C	60	LEU	0	0.007	-0.006	16.558	-0.023	-0.023	0.000	0.000	0.000	0.000
63	C	61	SER	0	-0.091	-0.062	20.118	-0.029	-0.029	0.000	0.000	0.000	0.000
64	C	62	LYS	1	0.806	0.908	22.855	-0.156	-0.156	0.000	0.000	0.000	0.000
65	C	63	HIS	0	0.023	0.017	22.113	-0.020	-0.020	0.000	0.000	0.000	0.000
66	C	64	ASN	0	0.000	0.015	25.547	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	65	THR	0	0.017	-0.023	25.845	0.007	0.007	0.000	0.000	0.000	0.000
68	C	66	CYS	0	-0.027	-0.016	26.302	0.003	0.003	0.000	0.000	0.000	0.000
69	C	67	ASP	-1	-0.845	-0.920	27.625	0.112	0.112	0.000	0.000	0.000	0.000
70	C	68	LEU	0	-0.041	-0.016	20.574	0.008	0.008	0.000	0.000	0.000	0.000
71	C	69	SER	0	0.001	-0.005	22.881	0.013	0.013	0.000	0.000	0.000	0.000
72	C	70	ASP	-1	-0.905	-0.938	24.149	0.112	0.112	0.000	0.000	0.000	0.000
73	C	71	LEU	0	-0.053	-0.038	21.976	0.002	0.002	0.000	0.000	0.000	0.000
74	C	72	ILE	0	-0.040	-0.018	18.620	0.012	0.012	0.000	0.000	0.000	0.000
75	C	73	GLU	-1	-0.863	-0.937	20.534	0.136	0.136	0.000	0.000	0.000	0.000
76	C	74	SER	0	-0.061	-0.013	23.135	-0.008	-0.008	0.000	0.000	0.000	0.000
77	C	75	TYR	0	-0.056	-0.044	20.143	-0.006	-0.006	0.000	0.000	0.000	0.000
78	C	76	PHE	0	-0.080	-0.026	12.857	0.032	0.032	0.000	0.000	0.000	0.000
79	C	77	GLU	-1	-0.899	-0.965	17.888	0.206	0.206	0.000	0.000	0.000	0.000
80	C	78	ASN	0	-0.105	-0.040	19.949	-0.020	-0.020	0.000	0.000	0.000	0.000
81	C	79	THR	0	-0.014	0.008	17.794	-0.012	-0.012	0.000	0.000	0.000	0.000
82	C	80	THR	0	-0.034	-0.015	20.472	-0.010	-0.010	0.000	0.000	0.000	0.000
83	C	81	ILE	0	-0.061	-0.038	15.240	-0.009	-0.009	0.000	0.000	0.000	0.000
84	C	82	NME	0	0.008	0.014	18.323	0.000	0.000	0.000	0.000	0.000	0.000

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