FMO DATABASE

FMODB ID: M3M4Z

Calculation Name: 5F22-B-Xray323

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5F22

Chain ID: B

ChEMBL ID: CHEMBL5118

UniProt ID: P0C6X7

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-844932.125526
FMO2-HF: Nuclear repulsion	799126.719294
FMO2-HF: Total energy	-45805.406232
FMO2-MP2: Total energy	-45935.526236

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:81:ACE )

Summations of interaction energy for fragment #1(B:81: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.
2.481	3.606	0.003	-0.524	-0.604	0

Interaction energy analysis for fragmet #1(B:81:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.016

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

Sort

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].
3	B	83	ASP	-1	-0.865	-0.937	3.621	0.550	1.675	0.003	-0.524	-0.604
4	B	84	LYN	0	0.000	0.007	5.296	0.123	0.123	0.000	0.000	0.000
5	B	85	ARG	1	1.032	1.009	6.472	1.186	1.186	0.000	0.000	0.000
6	B	86	ALA	0	0.056	0.037	7.588	0.209	0.209	0.000	0.000	0.000
7	B	87	LYS	1	0.920	0.967	8.815	0.118	0.118	0.000	0.000	0.000
8	B	88	VAL	0	-0.005	-0.001	11.072	0.062	0.062	0.000	0.000	0.000
9	B	89	THR	0	-0.007	0.001	11.717	0.062	0.062	0.000	0.000	0.000
10	B	90	SER	0	-0.005	-0.012	13.255	0.064	0.064	0.000	0.000	0.000
11	B	91	ALA	0	0.003	0.002	15.370	0.042	0.042	0.000	0.000	0.000
12	B	92	MET	0	-0.010	-0.001	16.532	0.029	0.029	0.000	0.000	0.000
13	B	93	GLN	0	0.016	0.000	16.899	-0.006	-0.006	0.000	0.000	0.000
14	B	94	THR	0	0.009	0.005	19.263	0.028	0.028	0.000	0.000	0.000
15	B	95	MET	0	-0.022	0.005	21.238	0.019	0.019	0.000	0.000	0.000
16	B	96	LEU	0	0.035	0.019	22.495	0.013	0.013	0.000	0.000	0.000
17	B	97	PHE	0	0.028	-0.003	22.847	0.014	0.014	0.000	0.000	0.000
18	B	98	THR	0	-0.056	-0.031	25.227	0.015	0.015	0.000	0.000	0.000
19	B	99	MET	0	-0.034	-0.025	26.945	0.012	0.012	0.000	0.000	0.000
20	B	100	LEU	0	-0.010	-0.004	27.078	0.007	0.007	0.000	0.000	0.000
21	B	101	ARG	1	0.961	0.978	29.296	0.076	0.076	0.000	0.000	0.000
22	B	102	LYS	1	0.931	0.967	31.600	0.065	0.065	0.000	0.000	0.000
23	B	103	LEU	0	-0.093	-0.048	32.322	0.004	0.004	0.000	0.000	0.000
24	B	104	ASP	-1	-0.918	-0.943	34.786	-0.050	-0.050	0.000	0.000	0.000
25	B	105	ASN	0	0.025	0.019	35.951	0.001	0.001	0.000	0.000	0.000
26	B	106	ASP	-1	-0.852	-0.930	36.957	-0.053	-0.053	0.000	0.000	0.000
27	B	107	ALA	0	0.000	0.006	37.879	-0.002	-0.002	0.000	0.000	0.000
28	B	108	LEU	0	-0.021	-0.029	32.332	-0.004	-0.004	0.000	0.000	0.000
29	B	109	ASN	0	0.025	0.012	33.283	-0.009	-0.009	0.000	0.000	0.000
30	B	110	ASN	0	-0.007	0.008	34.729	-0.003	-0.003	0.000	0.000	0.000
31	B	111	ILE	0	0.012	-0.001	31.974	-0.001	-0.001	0.000	0.000	0.000
32	B	112	ILE	0	-0.028	-0.012	28.943	-0.006	-0.006	0.000	0.000	0.000
33	B	113	ASN	0	-0.051	-0.037	30.797	-0.004	-0.004	0.000	0.000	0.000
34	B	114	ASN	0	0.042	0.020	33.088	0.003	0.003	0.000	0.000	0.000
35	B	115	ALA	0	0.005	0.016	28.541	-0.001	-0.001	0.000	0.000	0.000
36	B	116	ARG	1	0.837	0.916	28.031	0.072	0.072	0.000	0.000	0.000
37	B	117	ASP	-1	-0.917	-0.937	29.865	-0.062	-0.062	0.000	0.000	0.000
38	B	118	GLY	0	-0.011	-0.008	29.987	0.002	0.002	0.000	0.000	0.000
39	B	119	CYS	0	-0.090	-0.028	30.988	0.002	0.002	0.000	0.000	0.000
40	B	120	VAL	0	0.011	-0.007	28.159	-0.004	-0.004	0.000	0.000	0.000
41	B	121	PRO	0	-0.019	0.000	30.159	0.005	0.005	0.000	0.000	0.000
42	B	122	LEU	0	0.008	-0.015	30.477	-0.007	-0.007	0.000	0.000	0.000
43	B	123	ASN	0	-0.059	-0.049	30.966	-0.005	-0.005	0.000	0.000	0.000
44	B	124	ILE	0	0.000	-0.007	30.251	0.000	0.000	0.000	0.000	0.000
45	B	125	ILE	0	0.011	0.011	32.639	0.005	0.005	0.000	0.000	0.000
46	B	126	PRO	0	-0.012	0.021	35.454	-0.001	-0.001	0.000	0.000	0.000
47	B	127	LEU	0	0.017	-0.016	37.064	0.002	0.002	0.000	0.000	0.000
48	B	128	THR	0	-0.012	-0.004	40.611	0.002	0.002	0.000	0.000	0.000
49	B	129	THR	0	0.053	0.004	43.662	-0.002	-0.002	0.000	0.000	0.000
50	B	130	ALA	0	-0.023	-0.011	46.067	-0.001	-0.001	0.000	0.000	0.000
51	B	131	ALA	0	0.001	0.008	40.969	-0.001	-0.001	0.000	0.000	0.000
52	B	132	LYS	1	0.971	0.973	39.913	0.062	0.062	0.000	0.000	0.000
53	B	133	LEU	0	-0.033	0.026	35.984	-0.005	-0.005	0.000	0.000	0.000
54	B	134	MET	0	-0.022	-0.019	35.731	0.004	0.004	0.000	0.000	0.000
55	B	135	VAL	0	0.025	0.022	34.628	-0.007	-0.007	0.000	0.000	0.000
56	B	136	VAL	0	-0.002	0.009	31.792	0.005	0.005	0.000	0.000	0.000
57	B	137	VAL	0	0.014	-0.006	34.797	-0.001	-0.001	0.000	0.000	0.000
58	B	138	PRO	0	0.001	0.006	33.685	0.002	0.002	0.000	0.000	0.000
59	B	139	ASP	-1	-0.804	-0.922	35.656	-0.048	-0.048	0.000	0.000	0.000
60	B	140	TYR	0	0.062	0.014	38.979	0.000	0.000	0.000	0.000	0.000
61	B	141	GLY	0	-0.029	-0.004	41.333	0.001	0.001	0.000	0.000	0.000
62	B	142	THR	0	0.031	0.009	36.985	0.000	0.000	0.000	0.000	0.000
63	B	143	TYR	0	0.020	-0.007	39.859	0.001	0.001	0.000	0.000	0.000
64	B	144	LYS	1	0.929	0.967	42.221	0.033	0.033	0.000	0.000	0.000
65	B	145	ASN	0	-0.060	-0.016	40.545	0.003	0.003	0.000	0.000	0.000
66	B	146	THR	0	-0.045	-0.025	39.625	-0.001	-0.001	0.000	0.000	0.000
67	B	147	CYS	0	-0.072	-0.018	43.025	-0.001	-0.001	0.000	0.000	0.000
68	B	148	ASP	-1	-0.889	-0.937	45.800	-0.031	-0.031	0.000	0.000	0.000
69	B	149	GLY	0	0.032	0.020	49.566	0.000	0.000	0.000	0.000	0.000
70	B	150	ASN	0	-0.003	-0.018	49.604	-0.001	-0.001	0.000	0.000	0.000
71	B	151	THR	0	-0.026	0.006	47.834	-0.002	-0.002	0.000	0.000	0.000
72	B	152	PHE	0	0.013	0.003	38.659	0.000	0.000	0.000	0.000	0.000
73	B	153	THR	0	0.003	-0.007	43.667	0.000	0.000	0.000	0.000	0.000
74	B	154	TYR	0	0.022	-0.010	33.856	-0.002	-0.002	0.000	0.000	0.000
75	B	155	ALA	0	0.000	-0.001	37.098	0.000	0.000	0.000	0.000	0.000
76	B	156	SER	0	-0.043	-0.028	38.638	0.000	0.000	0.000	0.000	0.000
77	B	157	ALA	0	-0.024	-0.003	42.072	0.002	0.002	0.000	0.000	0.000
78	B	158	LEU	0	0.034	0.021	43.766	0.000	0.000	0.000	0.000	0.000
79	B	159	TRP	0	-0.001	-0.027	39.590	-0.002	-0.002	0.000	0.000	0.000
80	B	160	GLU	-1	-0.910	-0.946	45.249	-0.038	-0.038	0.000	0.000	0.000
81	B	161	ILE	0	-0.005	-0.043	44.817	-0.002	-0.002	0.000	0.000	0.000
82	B	162	GLN	0	-0.095	-0.038	45.071	0.003	0.003	0.000	0.000	0.000
83	B	163	GLN	0	-0.052	-0.041	43.884	0.001	0.001	0.000	0.000	0.000
84	B	164	VAL	0	0.020	0.010	42.344	-0.002	-0.002	0.000	0.000	0.000
85	B	165	VAL	0	-0.047	-0.020	39.238	0.002	0.002	0.000	0.000	0.000
86	B	166	ASP	-1	-0.737	-0.892	40.080	-0.047	-0.047	0.000	0.000	0.000
87	B	167	ALA	0	-0.016	-0.005	35.885	-0.003	-0.003	0.000	0.000	0.000
88	B	168	ASP	-1	-0.908	-0.937	37.015	-0.046	-0.046	0.000	0.000	0.000
89	B	169	SER	0	-0.145	-0.087	38.923	0.000	0.000	0.000	0.000	0.000
90	B	170	LYS	1	0.867	0.946	40.226	0.039	0.039	0.000	0.000	0.000
91	B	171	ILE	0	-0.004	0.002	43.651	-0.001	-0.001	0.000	0.000	0.000
92	B	172	VAL	0	0.052	0.032	44.453	0.001	0.001	0.000	0.000	0.000
93	B	173	GLN	0	-0.047	-0.003	46.913	-0.002	-0.002	0.000	0.000	0.000
94	B	174	LEU	0	0.061	0.001	47.385	0.000	0.000	0.000	0.000	0.000
95	B	175	SER	0	-0.042	-0.014	49.766	0.000	0.000	0.000	0.000	0.000
96	B	176	GLU	-1	-0.869	-0.938	49.073	-0.032	-0.032	0.000	0.000	0.000
97	B	177	ILE	0	-0.003	0.015	45.063	0.000	0.000	0.000	0.000	0.000
98	B	178	ASN	0	-0.013	-0.007	48.342	0.000	0.000	0.000	0.000	0.000
99	B	179	MET	0	-0.010	-0.017	48.716	0.000	0.000	0.000	0.000	0.000
100	B	180	ASP	-1	-0.926	-0.967	49.457	-0.024	-0.024	0.000	0.000	0.000
101	B	181	ASN	0	0.005	-0.018	49.748	0.001	0.001	0.000	0.000	0.000
102	B	182	SER	0	-0.026	0.007	44.870	-0.002	-0.002	0.000	0.000	0.000
103	B	183	PRO	0	-0.005	-0.018	44.341	-0.002	-0.002	0.000	0.000	0.000
104	B	184	ASN	0	-0.088	-0.036	44.829	0.000	0.000	0.000	0.000	0.000
105	B	185	LEU	0	-0.006	0.013	43.402	0.000	0.000	0.000	0.000	0.000
106	B	186	ALA	0	0.009	0.013	39.506	0.000	0.000	0.000	0.000	0.000
107	B	187	TRP	0	-0.039	0.011	37.846	-0.003	-0.003	0.000	0.000	0.000
108	B	188	PRO	0	-0.033	-0.033	33.340	0.000	0.000	0.000	0.000	0.000
109	B	189	LEU	0	0.022	0.018	36.615	0.001	0.001	0.000	0.000	0.000
110	B	190	ILE	0	-0.040	-0.023	34.560	-0.005	-0.005	0.000	0.000	0.000
111	B	191	VAL	0	0.030	0.028	38.271	0.004	0.004	0.000	0.000	0.000
112	B	192	THR	0	-0.017	-0.015	39.283	-0.005	-0.005	0.000	0.000	0.000
113	B	193	ALA	0	0.019	0.007	41.339	0.004	0.004	0.000	0.000	0.000
114	B	194	LEU	0	-0.056	0.007	42.389	-0.003	-0.003	0.000	0.000	0.000
115	B	195	ARG	1	0.896	0.979	40.202	0.060	0.060	0.000	0.000	0.000
116	B	196	ALA	0	0.063	0.023	44.885	0.002	0.002	0.000	0.000	0.000
117	B	197	NME	0	-0.027	-0.011	47.092	-0.002	-0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:81:ACE )