FMO DATABASE

FMODB ID: N1MYQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-840802.072812
FMO2-HF: Nuclear repulsion	795166.444515
FMO2-HF: Total energy	-45635.628296
FMO2-MP2: Total energy	-45765.074707

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.
-168.432	-169.229	21.162	-10.216	-10.147	0.114

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 : -0.789 / q_NPA : -0.894

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	0.024	0.004	3.891	-4.691	-3.421	-0.007	-0.525	-0.737	0.002
4	B	85	ARG	1	0.912	0.949	1.786	-123.881	-126.626	21.168	-9.451	-8.972	0.111
5	B	86	ALA	0	0.048	0.040	3.706	-4.915	-4.342	0.002	-0.235	-0.340	0.001
6	B	87	LYS	1	0.820	0.894	5.329	-32.822	-32.717	-0.001	-0.005	-0.098	0.000
7	B	88	VAL	0	0.021	0.008	7.879	-2.830	-2.830	0.000	0.000	0.000	0.000
8	B	89	THR	0	-0.020	-0.024	7.212	-2.171	-2.171	0.000	0.000	0.000	0.000
9	B	90	SER	0	-0.001	-0.011	8.858	-3.097	-3.097	0.000	0.000	0.000	0.000
10	B	91	ALA	0	-0.010	0.010	11.119	-2.300	-2.300	0.000	0.000	0.000	0.000
11	B	92	MET	0	0.000	0.001	12.493	-1.625	-1.625	0.000	0.000	0.000	0.000
12	B	93	GLN	0	0.025	0.003	11.255	0.001	0.001	0.000	0.000	0.000	0.000
13	B	94	THR	0	-0.003	-0.008	14.952	-1.604	-1.604	0.000	0.000	0.000	0.000
14	B	95	MET	0	-0.032	0.004	17.114	-1.553	-1.553	0.000	0.000	0.000	0.000
15	B	96	LEU	0	0.033	0.013	16.964	-1.000	-1.000	0.000	0.000	0.000	0.000
16	B	97	PHE	0	0.047	0.008	17.087	-0.960	-0.960	0.000	0.000	0.000	0.000
17	B	98	THR	0	-0.061	-0.035	20.966	-1.027	-1.027	0.000	0.000	0.000	0.000
18	B	99	MET	0	-0.021	-0.021	22.526	-0.886	-0.886	0.000	0.000	0.000	0.000
19	B	100	LEU	0	-0.017	-0.011	21.401	-0.598	-0.598	0.000	0.000	0.000	0.000
20	B	101	ARG	1	0.967	0.978	24.088	-12.449	-12.449	0.000	0.000	0.000	0.000
21	B	102	LYS	1	0.910	0.964	26.776	-11.195	-11.195	0.000	0.000	0.000	0.000
22	B	103	LEU	0	-0.060	-0.036	26.518	-0.375	-0.375	0.000	0.000	0.000	0.000
23	B	104	ASP	-1	-0.898	-0.927	29.608	9.639	9.639	0.000	0.000	0.000	0.000
24	B	105	ASN	0	0.035	0.018	30.574	-0.135	-0.135	0.000	0.000	0.000	0.000
25	B	106	ASP	-1	-0.860	-0.930	31.127	9.291	9.291	0.000	0.000	0.000	0.000
26	B	107	ALA	0	-0.004	0.004	31.564	0.118	0.118	0.000	0.000	0.000	0.000
27	B	108	LEU	0	-0.013	-0.011	26.165	0.327	0.327	0.000	0.000	0.000	0.000
28	B	109	ASN	0	0.003	-0.014	27.423	0.739	0.739	0.000	0.000	0.000	0.000
29	B	110	ASN	0	-0.009	0.008	29.172	0.295	0.295	0.000	0.000	0.000	0.000
30	B	111	ILE	0	0.031	0.013	25.457	0.087	0.087	0.000	0.000	0.000	0.000
31	B	112	ILE	0	-0.019	-0.005	23.381	0.437	0.437	0.000	0.000	0.000	0.000
32	B	113	ASN	0	-0.036	-0.022	24.913	0.448	0.448	0.000	0.000	0.000	0.000
33	B	114	ASN	0	0.043	0.015	27.333	-0.082	-0.082	0.000	0.000	0.000	0.000
34	B	115	ALA	0	-0.017	-0.006	22.351	0.075	0.075	0.000	0.000	0.000	0.000
35	B	116	ARG	1	0.691	0.819	22.874	-11.365	-11.365	0.000	0.000	0.000	0.000
36	B	117	ASP	-1	-0.828	-0.887	24.116	11.185	11.185	0.000	0.000	0.000	0.000
37	B	118	GLY	0	0.038	0.020	24.997	-0.317	-0.317	0.000	0.000	0.000	0.000
38	B	119	CYS	0	-0.066	-0.011	26.050	-0.055	-0.055	0.000	0.000	0.000	0.000
39	B	120	VAL	0	0.025	0.009	21.903	0.075	0.075	0.000	0.000	0.000	0.000
40	B	121	PRO	0	-0.004	0.002	23.433	-0.381	-0.381	0.000	0.000	0.000	0.000
41	B	122	LEU	0	0.007	-0.007	23.694	0.568	0.568	0.000	0.000	0.000	0.000
42	B	123	ASN	0	-0.059	-0.033	24.574	0.093	0.093	0.000	0.000	0.000	0.000
43	B	124	ILE	0	0.000	-0.007	22.723	0.021	0.021	0.000	0.000	0.000	0.000
44	B	125	ILE	0	0.033	0.021	25.467	-0.431	-0.431	0.000	0.000	0.000	0.000
45	B	126	PRO	0	-0.009	0.024	28.427	0.046	0.046	0.000	0.000	0.000	0.000
46	B	127	LEU	0	0.030	-0.011	30.899	-0.158	-0.158	0.000	0.000	0.000	0.000
47	B	128	THR	0	-0.017	-0.006	33.820	-0.166	-0.166	0.000	0.000	0.000	0.000
48	B	129	THR	0	0.032	0.001	36.774	0.133	0.133	0.000	0.000	0.000	0.000
49	B	130	ALA	0	-0.007	-0.004	39.123	0.032	0.032	0.000	0.000	0.000	0.000
50	B	131	ALA	0	-0.011	0.009	34.009	0.091	0.091	0.000	0.000	0.000	0.000
51	B	132	LYS	1	0.927	0.960	32.180	-9.694	-9.694	0.000	0.000	0.000	0.000
52	B	133	LEU	0	-0.028	-0.005	28.909	0.378	0.378	0.000	0.000	0.000	0.000
53	B	134	MET	0	-0.006	0.000	29.057	-0.341	-0.341	0.000	0.000	0.000	0.000
54	B	135	VAL	0	0.014	0.008	28.005	0.472	0.472	0.000	0.000	0.000	0.000
55	B	136	VAL	0	0.010	0.014	25.431	-0.339	-0.339	0.000	0.000	0.000	0.000
56	B	137	VAL	0	0.002	-0.008	28.537	0.012	0.012	0.000	0.000	0.000	0.000
57	B	138	PRO	0	-0.018	-0.004	28.448	-0.189	-0.189	0.000	0.000	0.000	0.000
58	B	139	ASP	-1	-0.765	-0.875	30.417	9.177	9.177	0.000	0.000	0.000	0.000
59	B	140	TYR	0	0.045	0.015	33.979	-0.077	-0.077	0.000	0.000	0.000	0.000
60	B	141	GLY	0	-0.031	-0.013	36.599	-0.216	-0.216	0.000	0.000	0.000	0.000
61	B	142	THR	0	-0.006	-0.039	31.309	-0.032	-0.032	0.000	0.000	0.000	0.000
62	B	143	TYR	0	0.040	0.018	34.497	0.006	0.006	0.000	0.000	0.000	0.000
63	B	144	LYS	1	0.953	0.978	36.751	-7.737	-7.737	0.000	0.000	0.000	0.000
64	B	145	ASN	0	-0.061	-0.012	35.527	-0.313	-0.313	0.000	0.000	0.000	0.000
65	B	146	THR	0	-0.066	-0.048	33.609	0.089	0.089	0.000	0.000	0.000	0.000
66	B	147	CYS	0	-0.083	-0.033	36.760	0.081	0.081	0.000	0.000	0.000	0.000
67	B	148	ASP	-1	-0.856	-0.925	39.524	6.920	6.920	0.000	0.000	0.000	0.000
68	B	149	GLY	0	-0.003	0.004	43.367	0.000	0.000	0.000	0.000	0.000	0.000
69	B	150	ASN	0	0.001	-0.002	43.593	0.072	0.072	0.000	0.000	0.000	0.000
70	B	151	THR	0	-0.037	-0.010	41.319	0.137	0.137	0.000	0.000	0.000	0.000
71	B	152	PHE	0	0.036	0.002	31.974	0.052	0.052	0.000	0.000	0.000	0.000
72	B	153	THR	0	-0.031	-0.017	37.068	-0.100	-0.100	0.000	0.000	0.000	0.000
73	B	154	TYR	0	-0.004	-0.016	27.324	0.254	0.254	0.000	0.000	0.000	0.000
74	B	155	ALA	0	0.003	-0.001	30.290	-0.105	-0.105	0.000	0.000	0.000	0.000
75	B	156	SER	0	-0.045	-0.026	31.849	-0.029	-0.029	0.000	0.000	0.000	0.000
76	B	157	ALA	0	-0.026	0.000	35.284	-0.209	-0.209	0.000	0.000	0.000	0.000
77	B	158	LEU	0	0.040	0.020	36.926	0.057	0.057	0.000	0.000	0.000	0.000
78	B	159	TRP	0	-0.029	-0.042	32.413	0.140	0.140	0.000	0.000	0.000	0.000
79	B	160	GLU	-1	-0.863	-0.912	38.376	7.223	7.223	0.000	0.000	0.000	0.000
80	B	161	ILE	0	-0.007	-0.020	38.137	0.201	0.201	0.000	0.000	0.000	0.000
81	B	162	GLN	0	-0.111	-0.055	38.767	-0.253	-0.253	0.000	0.000	0.000	0.000
82	B	163	GLN	0	-0.035	-0.031	37.530	0.030	0.030	0.000	0.000	0.000	0.000
83	B	164	VAL	0	0.012	0.007	36.008	0.226	0.226	0.000	0.000	0.000	0.000
84	B	165	VAL	0	-0.011	0.005	33.287	-0.219	-0.219	0.000	0.000	0.000	0.000
85	B	166	ASP	-1	-0.772	-0.894	34.553	8.865	8.865	0.000	0.000	0.000	0.000
86	B	167	ALA	0	-0.003	-0.003	30.765	0.186	0.186	0.000	0.000	0.000	0.000
87	B	168	ASP	-1	-0.892	-0.929	31.579	8.995	8.995	0.000	0.000	0.000	0.000
88	B	169	SER	0	-0.092	-0.040	32.569	-0.079	-0.079	0.000	0.000	0.000	0.000
89	B	170	LYS	1	0.788	0.885	34.549	-8.660	-8.660	0.000	0.000	0.000	0.000
90	B	171	ILE	0	-0.019	-0.022	37.695	0.137	0.137	0.000	0.000	0.000	0.000
91	B	172	VAL	0	0.016	0.019	38.601	-0.109	-0.109	0.000	0.000	0.000	0.000
92	B	173	GLN	0	-0.023	-0.005	40.970	0.141	0.141	0.000	0.000	0.000	0.000
93	B	174	LEU	0	0.059	0.004	41.472	0.013	0.013	0.000	0.000	0.000	0.000
94	B	175	SER	0	-0.013	-0.008	43.792	0.003	0.003	0.000	0.000	0.000	0.000
95	B	176	GLU	-1	-0.877	-0.928	43.479	7.149	7.149	0.000	0.000	0.000	0.000
96	B	177	ILE	0	-0.031	0.011	39.028	0.070	0.070	0.000	0.000	0.000	0.000
97	B	178	ASN	0	-0.036	-0.023	42.468	-0.022	-0.022	0.000	0.000	0.000	0.000
98	B	179	MET	0	-0.006	-0.024	43.854	0.111	0.111	0.000	0.000	0.000	0.000
99	B	180	ASP	-1	-0.921	-0.960	44.593	6.624	6.624	0.000	0.000	0.000	0.000
100	B	181	ASN	0	-0.015	-0.024	44.026	-0.066	-0.066	0.000	0.000	0.000	0.000
101	B	182	SER	0	-0.003	0.020	40.248	0.226	0.226	0.000	0.000	0.000	0.000
102	B	183	PRO	0	-0.012	-0.014	40.012	0.232	0.232	0.000	0.000	0.000	0.000
103	B	184	ASN	0	-0.048	-0.026	40.701	0.039	0.039	0.000	0.000	0.000	0.000
104	B	185	LEU	0	0.001	0.017	38.309	0.015	0.015	0.000	0.000	0.000	0.000
105	B	186	ALA	0	0.013	0.009	34.933	0.123	0.123	0.000	0.000	0.000	0.000
106	B	187	TRP	0	-0.035	-0.007	33.123	0.275	0.275	0.000	0.000	0.000	0.000
107	B	188	PRO	0	-0.048	-0.026	27.978	0.133	0.133	0.000	0.000	0.000	0.000
108	B	189	LEU	0	0.025	0.017	31.252	-0.086	-0.086	0.000	0.000	0.000	0.000
109	B	190	ILE	0	-0.026	-0.020	28.590	0.424	0.424	0.000	0.000	0.000	0.000
110	B	191	VAL	0	0.023	0.024	31.967	-0.330	-0.330	0.000	0.000	0.000	0.000
111	B	192	THR	0	-0.020	-0.022	32.637	0.451	0.451	0.000	0.000	0.000	0.000
112	B	193	ALA	0	0.026	0.015	34.614	-0.319	-0.319	0.000	0.000	0.000	0.000
113	B	194	LEU	0	-0.031	-0.005	35.412	0.308	0.308	0.000	0.000	0.000	0.000
114	B	195	ARG	1	0.876	0.967	33.075	-9.455	-9.455	0.000	0.000	0.000	0.000
115	B	196	ALA	0	0.014	-0.001	37.573	-0.132	-0.132	0.000	0.000	0.000	0.000

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