FMO DATABASE

FMODB ID: GNK31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-840407.668007
FMO2-HF: Nuclear repulsion	794773.146024
FMO2-HF: Total energy	-45634.521983
FMO2-MP2: Total energy	-45764.110186

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.
-114.258	-109.257	0.133	-2.203	-2.93	0.009

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 : -0.896 / q_NPA : -0.962

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	-0.001	0.002	3.783	-7.036	-4.868	-0.037	-1.001	-1.130	0.001
4	B	85	ARG	1	1.024	1.005	2.889	-70.744	-68.489	0.170	-1.009	-1.415	0.008
5	B	86	ALA	0	0.053	0.037	3.762	-3.483	-2.996	0.001	-0.190	-0.298	0.000
6	B	87	LYS	1	0.918	0.966	5.362	-32.530	-32.439	-0.001	-0.003	-0.087	0.000
7	B	88	VAL	0	-0.002	0.000	8.105	-2.643	-2.643	0.000	0.000	0.000	0.000
8	B	89	THR	0	-0.011	-0.001	7.170	-2.411	-2.411	0.000	0.000	0.000	0.000
9	B	90	SER	0	-0.003	-0.012	8.938	-2.756	-2.756	0.000	0.000	0.000	0.000
10	B	91	ALA	0	0.003	0.002	11.158	-2.173	-2.173	0.000	0.000	0.000	0.000
11	B	92	MET	0	-0.010	-0.001	12.506	-1.769	-1.769	0.000	0.000	0.000	0.000
12	B	93	GLN	0	0.017	0.001	11.116	0.146	0.146	0.000	0.000	0.000	0.000
13	B	94	THR	0	0.007	0.005	14.916	-1.610	-1.610	0.000	0.000	0.000	0.000
14	B	95	MET	0	-0.020	0.006	17.023	-1.362	-1.362	0.000	0.000	0.000	0.000
15	B	96	LEU	0	0.030	0.017	17.163	-0.951	-0.951	0.000	0.000	0.000	0.000
16	B	97	PHE	0	0.031	-0.002	17.152	-0.946	-0.946	0.000	0.000	0.000	0.000
17	B	98	THR	0	-0.057	-0.031	20.932	-0.946	-0.946	0.000	0.000	0.000	0.000
18	B	99	MET	0	-0.031	-0.024	22.693	-0.839	-0.839	0.000	0.000	0.000	0.000
19	B	100	LEU	0	-0.011	-0.004	21.485	-0.577	-0.577	0.000	0.000	0.000	0.000
20	B	101	ARG	1	0.960	0.977	24.435	-12.286	-12.286	0.000	0.000	0.000	0.000
21	B	102	LYS	1	0.933	0.968	27.032	-10.970	-10.970	0.000	0.000	0.000	0.000
22	B	103	LEU	0	-0.093	-0.048	27.021	-0.377	-0.377	0.000	0.000	0.000	0.000
23	B	104	ASP	-1	-0.921	-0.944	29.771	9.233	9.233	0.000	0.000	0.000	0.000
24	B	105	ASN	0	0.027	0.021	30.323	-0.154	-0.154	0.000	0.000	0.000	0.000
25	B	106	ASP	-1	-0.850	-0.929	31.254	9.104	9.104	0.000	0.000	0.000	0.000
26	B	107	ALA	0	-0.004	0.004	31.697	0.143	0.143	0.000	0.000	0.000	0.000
27	B	108	LEU	0	-0.021	-0.029	26.228	0.308	0.308	0.000	0.000	0.000	0.000
28	B	109	ASN	0	0.029	0.012	27.313	0.775	0.775	0.000	0.000	0.000	0.000
29	B	110	ASN	0	-0.008	0.008	28.968	0.296	0.296	0.000	0.000	0.000	0.000
30	B	111	ILE	0	0.012	-0.001	25.692	0.091	0.091	0.000	0.000	0.000	0.000
31	B	112	ILE	0	-0.028	-0.012	23.283	0.481	0.481	0.000	0.000	0.000	0.000
32	B	113	ASN	0	-0.054	-0.038	25.113	0.545	0.545	0.000	0.000	0.000	0.000
33	B	114	ASN	0	0.045	0.022	27.612	-0.084	-0.084	0.000	0.000	0.000	0.000
34	B	115	ALA	0	0.003	0.015	22.538	0.083	0.083	0.000	0.000	0.000	0.000
35	B	116	ARG	1	0.839	0.916	22.933	-11.905	-11.905	0.000	0.000	0.000	0.000
36	B	117	ASP	-1	-0.917	-0.937	24.609	10.876	10.876	0.000	0.000	0.000	0.000
37	B	118	GLY	0	-0.010	-0.008	24.426	-0.193	-0.193	0.000	0.000	0.000	0.000
38	B	119	CYS	0	-0.091	-0.028	25.483	-0.228	-0.228	0.000	0.000	0.000	0.000
39	B	120	VAL	0	0.014	-0.005	22.021	0.217	0.217	0.000	0.000	0.000	0.000
40	B	121	PRO	0	-0.018	0.000	23.589	-0.391	-0.391	0.000	0.000	0.000	0.000
41	B	122	LEU	0	0.006	-0.015	23.781	0.557	0.557	0.000	0.000	0.000	0.000
42	B	123	ASN	0	-0.060	-0.049	24.145	0.387	0.387	0.000	0.000	0.000	0.000
43	B	124	ILE	0	0.002	-0.005	23.441	0.024	0.024	0.000	0.000	0.000	0.000
44	B	125	ILE	0	0.009	0.010	25.762	-0.407	-0.407	0.000	0.000	0.000	0.000
45	B	126	PRO	0	-0.007	0.022	28.635	0.030	0.030	0.000	0.000	0.000	0.000
46	B	127	LEU	0	0.014	-0.018	30.490	-0.171	-0.171	0.000	0.000	0.000	0.000
47	B	128	THR	0	-0.014	-0.005	33.882	-0.179	-0.179	0.000	0.000	0.000	0.000
48	B	129	THR	0	0.053	0.004	36.846	0.168	0.168	0.000	0.000	0.000	0.000
49	B	130	ALA	0	-0.023	-0.009	39.198	0.042	0.042	0.000	0.000	0.000	0.000
50	B	131	ALA	0	0.001	0.006	34.088	0.110	0.110	0.000	0.000	0.000	0.000
51	B	132	LYS	1	0.970	0.973	33.084	-9.460	-9.460	0.000	0.000	0.000	0.000
52	B	133	LEU	0	-0.036	0.024	29.199	0.413	0.413	0.000	0.000	0.000	0.000
53	B	134	MET	0	-0.023	-0.019	28.991	-0.337	-0.337	0.000	0.000	0.000	0.000
54	B	135	VAL	0	0.030	0.024	28.070	0.511	0.511	0.000	0.000	0.000	0.000
55	B	136	VAL	0	-0.004	0.008	25.683	-0.360	-0.360	0.000	0.000	0.000	0.000
56	B	137	VAL	0	0.011	-0.007	28.628	0.059	0.059	0.000	0.000	0.000	0.000
57	B	138	PRO	0	0.004	0.006	28.308	-0.194	-0.194	0.000	0.000	0.000	0.000
58	B	139	ASP	-1	-0.806	-0.921	30.237	9.535	9.535	0.000	0.000	0.000	0.000
59	B	140	TYR	0	0.064	0.015	33.772	-0.112	-0.112	0.000	0.000	0.000	0.000
60	B	141	GLY	0	-0.027	-0.003	36.246	-0.199	-0.199	0.000	0.000	0.000	0.000
61	B	142	THR	0	0.027	0.008	31.277	-0.041	-0.041	0.000	0.000	0.000	0.000
62	B	143	TYR	0	0.020	-0.007	34.353	-0.132	-0.132	0.000	0.000	0.000	0.000
63	B	144	LYS	1	0.929	0.966	36.476	-7.660	-7.660	0.000	0.000	0.000	0.000
64	B	145	ASN	0	-0.058	-0.016	34.943	-0.355	-0.355	0.000	0.000	0.000	0.000
65	B	146	THR	0	-0.044	-0.025	33.583	0.002	0.002	0.000	0.000	0.000	0.000
66	B	147	CYS	0	-0.075	-0.019	36.964	0.039	0.039	0.000	0.000	0.000	0.000
67	B	148	ASP	-1	-0.887	-0.936	39.651	6.898	6.898	0.000	0.000	0.000	0.000
68	B	149	GLY	0	0.031	0.020	43.398	-0.062	-0.062	0.000	0.000	0.000	0.000
69	B	150	ASN	0	-0.003	-0.018	43.147	0.088	0.088	0.000	0.000	0.000	0.000
70	B	151	THR	0	-0.028	0.005	41.308	0.113	0.113	0.000	0.000	0.000	0.000
71	B	152	PHE	0	0.020	0.006	32.237	0.056	0.056	0.000	0.000	0.000	0.000
72	B	153	THR	0	-0.002	-0.010	37.346	-0.093	-0.093	0.000	0.000	0.000	0.000
73	B	154	TYR	0	0.022	-0.009	27.239	0.270	0.270	0.000	0.000	0.000	0.000
74	B	155	ALA	0	0.001	-0.001	30.567	-0.094	-0.094	0.000	0.000	0.000	0.000
75	B	156	SER	0	-0.041	-0.027	32.207	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	157	ALA	0	-0.029	-0.005	35.591	-0.208	-0.208	0.000	0.000	0.000	0.000
77	B	158	LEU	0	0.035	0.022	37.204	0.079	0.079	0.000	0.000	0.000	0.000
78	B	159	TRP	0	-0.005	-0.028	32.789	0.135	0.135	0.000	0.000	0.000	0.000
79	B	160	GLU	-1	-0.909	-0.945	38.501	7.213	7.213	0.000	0.000	0.000	0.000
80	B	161	ILE	0	-0.003	-0.042	38.264	0.179	0.179	0.000	0.000	0.000	0.000
81	B	162	GLN	0	-0.096	-0.038	38.316	-0.246	-0.246	0.000	0.000	0.000	0.000
82	B	163	GLN	0	-0.051	-0.040	37.366	-0.017	-0.017	0.000	0.000	0.000	0.000
83	B	164	VAL	0	0.020	0.010	36.250	0.212	0.212	0.000	0.000	0.000	0.000
84	B	165	VAL	0	-0.046	-0.019	33.201	-0.201	-0.201	0.000	0.000	0.000	0.000
85	B	166	ASP	-1	-0.737	-0.892	34.154	9.002	9.002	0.000	0.000	0.000	0.000
86	B	167	ALA	0	-0.019	-0.007	30.686	0.186	0.186	0.000	0.000	0.000	0.000
87	B	168	ASP	-1	-0.908	-0.936	31.710	9.216	9.216	0.000	0.000	0.000	0.000
88	B	169	SER	0	-0.145	-0.087	33.332	0.006	0.006	0.000	0.000	0.000	0.000
89	B	170	LYS	1	0.869	0.946	34.494	-8.207	-8.207	0.000	0.000	0.000	0.000
90	B	171	ILE	0	-0.005	0.001	37.890	0.061	0.061	0.000	0.000	0.000	0.000
91	B	172	VAL	0	0.052	0.032	38.712	-0.059	-0.059	0.000	0.000	0.000	0.000
92	B	173	GLN	0	-0.047	-0.002	41.016	0.097	0.097	0.000	0.000	0.000	0.000
93	B	174	LEU	0	0.060	0.000	41.066	0.051	0.051	0.000	0.000	0.000	0.000
94	B	175	SER	0	-0.043	-0.015	43.688	0.022	0.022	0.000	0.000	0.000	0.000
95	B	176	GLU	-1	-0.867	-0.938	43.406	7.230	7.230	0.000	0.000	0.000	0.000
96	B	177	ILE	0	-0.001	0.014	39.178	0.092	0.092	0.000	0.000	0.000	0.000
97	B	178	ASN	0	-0.013	-0.006	42.720	-0.029	-0.029	0.000	0.000	0.000	0.000
98	B	179	MET	0	-0.011	-0.018	43.752	0.081	0.081	0.000	0.000	0.000	0.000
99	B	180	ASP	-1	-0.924	-0.966	44.614	6.609	6.609	0.000	0.000	0.000	0.000
100	B	181	ASN	0	0.005	-0.018	44.464	0.008	0.008	0.000	0.000	0.000	0.000
101	B	182	SER	0	-0.026	0.006	39.848	0.218	0.218	0.000	0.000	0.000	0.000
102	B	183	PRO	0	-0.007	-0.019	39.730	0.219	0.219	0.000	0.000	0.000	0.000
103	B	184	ASN	0	-0.087	-0.036	40.303	-0.016	-0.016	0.000	0.000	0.000	0.000
104	B	185	LEU	0	-0.006	0.013	38.127	0.015	0.015	0.000	0.000	0.000	0.000
105	B	186	ALA	0	0.008	0.013	34.586	0.109	0.109	0.000	0.000	0.000	0.000
106	B	187	TRP	0	-0.039	0.011	32.685	0.165	0.165	0.000	0.000	0.000	0.000
107	B	188	PRO	0	-0.031	-0.032	27.850	0.137	0.137	0.000	0.000	0.000	0.000
108	B	189	LEU	0	0.023	0.018	31.171	-0.074	-0.074	0.000	0.000	0.000	0.000
109	B	190	ILE	0	-0.041	-0.024	28.471	0.387	0.387	0.000	0.000	0.000	0.000
110	B	191	VAL	0	0.028	0.027	32.072	-0.333	-0.333	0.000	0.000	0.000	0.000
111	B	192	THR	0	-0.014	-0.014	32.695	0.431	0.431	0.000	0.000	0.000	0.000
112	B	193	ALA	0	0.017	0.006	34.613	-0.319	-0.319	0.000	0.000	0.000	0.000
113	B	194	LEU	0	-0.053	0.009	35.535	0.265	0.265	0.000	0.000	0.000	0.000
114	B	195	ARG	1	0.901	0.983	33.527	-9.236	-9.236	0.000	0.000	0.000	0.000
115	B	196	ALA	0	0.032	0.008	38.050	-0.115	-0.115	0.000	0.000	0.000	0.000

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