FMO DATABASE

FMODB ID: 82ZYY

Calculation Name: 5F22-B-Xray372

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: 2023-06-20

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	OptHSide
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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-839823.494978
FMO2-HF: Nuclear repulsion	794188.349302
FMO2-HF: Total energy	-45635.145676
FMO2-MP2: Total energy	-45764.643886

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:82:GLU)

Summations of interaction energy for fragment #1(B:82:GLU)

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.
-169.05	-165.123	15.164	-9.448	-9.642	0.105

Interaction energy analysis for fragmet #1(B:82:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.803 / q_NPA : -0.909

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	84	LYN	0	0.012	0.011	3.783	-6.417	-4.172	-0.035	-1.028	-1.182	0.000
4	B	85	ARG	1	0.934	0.950	1.848	-123.144	-121.946	15.198	-8.235	-8.161	0.105
5	B	86	ALA	0	0.037	0.040	3.790	-3.959	-3.475	0.001	-0.185	-0.299	0.000
6	B	87	LYS	1	0.832	0.898	5.425	-32.998	-32.998	0.000	0.000	0.000	0.000
7	B	88	VAL	0	0.000	-0.001	8.086	-2.854	-2.854	0.000	0.000	0.000	0.000
8	B	89	THR	0	-0.012	-0.016	6.933	-2.410	-2.410	0.000	0.000	0.000	0.000
9	B	90	SER	0	0.002	-0.005	8.964	-3.136	-3.136	0.000	0.000	0.000	0.000
10	B	91	ALA	0	-0.002	0.011	11.221	-2.339	-2.339	0.000	0.000	0.000	0.000
11	B	92	MET	0	-0.006	0.001	12.602	-1.721	-1.721	0.000	0.000	0.000	0.000
12	B	93	GLN	0	0.023	0.001	10.954	0.080	0.080	0.000	0.000	0.000	0.000
13	B	94	THR	0	-0.005	-0.011	14.855	-1.685	-1.685	0.000	0.000	0.000	0.000
14	B	95	MET	0	-0.028	0.000	17.085	-1.511	-1.511	0.000	0.000	0.000	0.000
15	B	96	LEU	0	0.033	0.015	16.939	-1.015	-1.015	0.000	0.000	0.000	0.000
16	B	97	PHE	0	0.035	0.002	17.049	-0.997	-0.997	0.000	0.000	0.000	0.000
17	B	98	THR	0	-0.066	-0.031	21.014	-1.019	-1.019	0.000	0.000	0.000	0.000
18	B	99	MET	0	-0.025	-0.022	22.633	-0.902	-0.902	0.000	0.000	0.000	0.000
19	B	100	LEU	0	-0.012	-0.004	21.322	-0.594	-0.594	0.000	0.000	0.000	0.000
20	B	101	ARG	1	0.965	0.979	24.413	-12.460	-12.460	0.000	0.000	0.000	0.000
21	B	102	LYS	1	0.929	0.968	27.027	-11.143	-11.143	0.000	0.000	0.000	0.000
22	B	103	LEU	0	-0.082	-0.044	26.547	-0.380	-0.380	0.000	0.000	0.000	0.000
23	B	104	ASP	-1	-0.905	-0.928	29.635	9.468	9.468	0.000	0.000	0.000	0.000
24	B	105	ASN	0	0.016	0.007	30.208	-0.206	-0.206	0.000	0.000	0.000	0.000
25	B	106	ASP	-1	-0.849	-0.930	31.133	9.188	9.188	0.000	0.000	0.000	0.000
26	B	107	ALA	0	0.002	0.007	31.552	0.143	0.143	0.000	0.000	0.000	0.000
27	B	108	LEU	0	-0.014	-0.020	26.106	0.300	0.300	0.000	0.000	0.000	0.000
28	B	109	ASN	0	0.022	0.004	27.213	0.797	0.797	0.000	0.000	0.000	0.000
29	B	110	ASN	0	-0.015	0.003	28.904	0.300	0.300	0.000	0.000	0.000	0.000
30	B	111	ILE	0	0.031	0.015	25.555	0.074	0.074	0.000	0.000	0.000	0.000
31	B	112	ILE	0	-0.020	-0.009	23.220	0.470	0.470	0.000	0.000	0.000	0.000
32	B	113	ASN	0	-0.053	-0.043	25.086	0.442	0.442	0.000	0.000	0.000	0.000
33	B	114	ASN	0	0.043	0.020	27.615	-0.113	-0.113	0.000	0.000	0.000	0.000
34	B	115	ALA	0	0.012	0.016	22.547	0.063	0.063	0.000	0.000	0.000	0.000
35	B	116	ARG	1	0.797	0.897	22.973	-11.695	-11.695	0.000	0.000	0.000	0.000
36	B	117	ASP	-1	-0.921	-0.938	24.639	10.907	10.907	0.000	0.000	0.000	0.000
37	B	118	GLY	0	-0.004	-0.004	24.472	-0.205	-0.205	0.000	0.000	0.000	0.000
38	B	119	CYS	0	-0.075	-0.021	25.533	-0.166	-0.166	0.000	0.000	0.000	0.000
39	B	120	VAL	0	-0.004	-0.012	22.139	0.232	0.232	0.000	0.000	0.000	0.000
40	B	121	PRO	0	-0.003	0.008	23.563	-0.375	-0.375	0.000	0.000	0.000	0.000
41	B	122	LEU	0	0.002	-0.018	23.722	0.568	0.568	0.000	0.000	0.000	0.000
42	B	123	ASN	0	-0.048	-0.037	24.063	0.292	0.292	0.000	0.000	0.000	0.000
43	B	124	ILE	0	-0.006	-0.008	23.044	0.011	0.011	0.000	0.000	0.000	0.000
44	B	125	ILE	0	0.027	0.018	25.609	-0.431	-0.431	0.000	0.000	0.000	0.000
45	B	126	PRO	0	-0.008	0.022	28.488	0.041	0.041	0.000	0.000	0.000	0.000
46	B	127	LEU	0	0.025	-0.006	30.701	-0.172	-0.172	0.000	0.000	0.000	0.000
47	B	128	THR	0	-0.007	-0.001	33.693	-0.176	-0.176	0.000	0.000	0.000	0.000
48	B	129	THR	0	0.041	0.000	36.676	0.170	0.170	0.000	0.000	0.000	0.000
49	B	130	ALA	0	-0.008	-0.002	39.029	0.042	0.042	0.000	0.000	0.000	0.000
50	B	131	ALA	0	-0.004	0.006	33.970	0.111	0.111	0.000	0.000	0.000	0.000
51	B	132	LYS	1	0.932	0.950	32.680	-9.585	-9.585	0.000	0.000	0.000	0.000
52	B	133	LEU	0	-0.029	0.019	29.198	0.415	0.415	0.000	0.000	0.000	0.000
53	B	134	MET	0	0.000	0.001	28.989	-0.357	-0.357	0.000	0.000	0.000	0.000
54	B	135	VAL	0	0.030	0.024	28.028	0.527	0.527	0.000	0.000	0.000	0.000
55	B	136	VAL	0	-0.014	0.002	25.582	-0.361	-0.361	0.000	0.000	0.000	0.000
56	B	137	VAL	0	0.014	-0.006	28.637	0.060	0.060	0.000	0.000	0.000	0.000
57	B	138	PRO	0	-0.006	-0.001	28.334	-0.203	-0.203	0.000	0.000	0.000	0.000
58	B	139	ASP	-1	-0.761	-0.871	30.307	9.341	9.341	0.000	0.000	0.000	0.000
59	B	140	TYR	0	0.061	0.015	33.853	-0.094	-0.094	0.000	0.000	0.000	0.000
60	B	141	GLY	0	-0.024	-0.009	36.318	-0.210	-0.210	0.000	0.000	0.000	0.000
61	B	142	THR	0	-0.005	-0.035	31.129	-0.080	-0.080	0.000	0.000	0.000	0.000
62	B	143	TYR	0	0.030	0.002	34.391	-0.051	-0.051	0.000	0.000	0.000	0.000
63	B	144	LYS	1	0.938	0.968	36.503	-7.710	-7.710	0.000	0.000	0.000	0.000
64	B	145	ASN	0	-0.069	-0.020	35.113	-0.345	-0.345	0.000	0.000	0.000	0.000
65	B	146	THR	0	-0.046	-0.028	33.484	0.006	0.006	0.000	0.000	0.000	0.000
66	B	147	CYS	0	-0.087	-0.027	36.967	0.050	0.050	0.000	0.000	0.000	0.000
67	B	148	ASP	-1	-0.887	-0.939	39.634	6.910	6.910	0.000	0.000	0.000	0.000
68	B	149	GLY	0	0.027	0.019	43.376	-0.056	-0.056	0.000	0.000	0.000	0.000
69	B	150	ASN	0	-0.006	-0.015	43.128	0.079	0.079	0.000	0.000	0.000	0.000
70	B	151	THR	0	-0.028	0.006	41.369	0.135	0.135	0.000	0.000	0.000	0.000
71	B	152	PHE	0	0.033	0.008	32.133	0.061	0.061	0.000	0.000	0.000	0.000
72	B	153	THR	0	-0.005	-0.006	37.283	-0.076	-0.076	0.000	0.000	0.000	0.000
73	B	154	TYR	0	0.025	-0.005	27.224	0.273	0.273	0.000	0.000	0.000	0.000
74	B	155	ALA	0	-0.005	-0.001	30.480	-0.088	-0.088	0.000	0.000	0.000	0.000
75	B	156	SER	0	-0.047	-0.029	32.097	0.001	0.001	0.000	0.000	0.000	0.000
76	B	157	ALA	0	-0.022	-0.004	35.437	-0.209	-0.209	0.000	0.000	0.000	0.000
77	B	158	LEU	0	0.038	0.025	37.103	0.074	0.074	0.000	0.000	0.000	0.000
78	B	159	TRP	0	-0.021	-0.041	32.580	0.149	0.149	0.000	0.000	0.000	0.000
79	B	160	GLU	-1	-0.891	-0.929	38.402	7.231	7.231	0.000	0.000	0.000	0.000
80	B	161	ILE	0	-0.010	-0.034	38.181	0.177	0.177	0.000	0.000	0.000	0.000
81	B	162	GLN	0	-0.124	-0.065	38.297	-0.233	-0.233	0.000	0.000	0.000	0.000
82	B	163	GLN	0	-0.052	-0.040	37.347	0.007	0.007	0.000	0.000	0.000	0.000
83	B	164	VAL	0	0.019	0.004	36.131	0.220	0.220	0.000	0.000	0.000	0.000
84	B	165	VAL	0	-0.029	-0.011	33.205	-0.200	-0.200	0.000	0.000	0.000	0.000
85	B	166	ASP	-1	-0.740	-0.874	34.190	8.926	8.926	0.000	0.000	0.000	0.000
86	B	167	ALA	0	-0.013	-0.011	30.846	0.181	0.181	0.000	0.000	0.000	0.000
87	B	168	ASP	-1	-0.947	-0.968	31.796	9.184	9.184	0.000	0.000	0.000	0.000
88	B	169	SER	0	-0.144	-0.075	33.075	-0.021	-0.021	0.000	0.000	0.000	0.000
89	B	170	LYS	1	0.897	0.956	34.539	-8.372	-8.372	0.000	0.000	0.000	0.000
90	B	171	ILE	0	-0.024	-0.016	37.936	0.067	0.067	0.000	0.000	0.000	0.000
91	B	172	VAL	0	0.037	0.029	38.498	-0.059	-0.059	0.000	0.000	0.000	0.000
92	B	173	GLN	0	-0.036	-0.003	41.050	0.126	0.126	0.000	0.000	0.000	0.000
93	B	174	LEU	0	0.068	0.003	41.170	0.041	0.041	0.000	0.000	0.000	0.000
94	B	175	SER	0	-0.007	-0.003	43.700	-0.013	-0.013	0.000	0.000	0.000	0.000
95	B	176	GLU	-1	-0.902	-0.937	43.589	7.158	7.158	0.000	0.000	0.000	0.000
96	B	177	ILE	0	-0.010	0.014	39.209	0.080	0.080	0.000	0.000	0.000	0.000
97	B	178	ASN	0	-0.035	-0.021	42.773	-0.067	-0.067	0.000	0.000	0.000	0.000
98	B	179	MET	0	-0.008	-0.016	43.855	0.071	0.071	0.000	0.000	0.000	0.000
99	B	180	ASP	-1	-0.915	-0.954	44.718	6.597	6.597	0.000	0.000	0.000	0.000
100	B	181	ASN	0	-0.014	-0.029	44.117	-0.029	-0.029	0.000	0.000	0.000	0.000
101	B	182	SER	0	-0.010	0.011	40.059	0.208	0.208	0.000	0.000	0.000	0.000
102	B	183	PRO	0	-0.004	-0.011	39.857	0.222	0.222	0.000	0.000	0.000	0.000
103	B	184	ASN	0	-0.073	-0.035	40.441	0.025	0.025	0.000	0.000	0.000	0.000
104	B	185	LEU	0	-0.010	0.011	38.308	0.007	0.007	0.000	0.000	0.000	0.000
105	B	186	ALA	0	0.014	0.013	34.760	0.109	0.109	0.000	0.000	0.000	0.000
106	B	187	TRP	0	-0.037	0.005	32.856	0.170	0.170	0.000	0.000	0.000	0.000
107	B	188	PRO	0	-0.024	-0.026	27.915	0.132	0.132	0.000	0.000	0.000	0.000
108	B	189	LEU	0	0.020	0.016	31.249	-0.073	-0.073	0.000	0.000	0.000	0.000
109	B	190	ILE	0	-0.046	-0.026	28.736	0.389	0.389	0.000	0.000	0.000	0.000
110	B	191	VAL	0	0.040	0.034	32.079	-0.330	-0.330	0.000	0.000	0.000	0.000
111	B	192	THR	0	-0.018	-0.019	32.652	0.435	0.435	0.000	0.000	0.000	0.000
112	B	193	ALA	0	0.019	0.011	34.539	-0.323	-0.323	0.000	0.000	0.000	0.000
113	B	194	LEU	0	-0.026	0.015	35.433	0.288	0.288	0.000	0.000	0.000	0.000
114	B	195	ARG	1	0.876	0.965	33.035	-9.400	-9.400	0.000	0.000	0.000	0.000
115	B	196	ALA	0	0.028	0.008	37.916	-0.113	-0.113	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:82:GLU)