FMO DATABASE

FMODB ID: 7N2VK

Calculation Name: 3EW5-B-Xray547

Preferred Name: Replicase polyprotein 1ab

Target Type: SINGLE PROTEIN

Ligand Name: sn-glycerol-1-phosphate | sulfate ion | chloride ion

Ligand 3-letter code: 1GP | SO4 | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EW5

Chain ID: B

ChEMBL ID: CHEMBL4295624

UniProt ID: Q98VG9

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1649204.686788
FMO2-HF: Nuclear repulsion	1586367.503126
FMO2-HF: Total energy	-62837.183662
FMO2-MP2: Total energy	-63023.426353

3D Structure Molmil

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(A:36:ILE)

Summations of interaction energy for fragment #1(A:36:ILE)

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.
-44.894	-38.271	4.209	-3.239	-7.596	-0.033

Interaction energy analysis for fragmet #1(A:36:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.917

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	A	38	PRO	0	-0.009	0.010	3.854	-1.014	1.054	-0.021	-0.927	-1.121	0.000
13	A	48	TYR	0	0.033	0.001	3.591	-1.399	-1.068	0.005	-0.052	-0.285	0.000
15	A	50	GLY	0	0.014	0.011	4.876	-5.507	-5.379	-0.001	-0.006	-0.121	0.000
19	A	54	VAL	0	0.043	0.015	3.861	-1.491	-1.278	0.003	-0.033	-0.183	0.000
20	A	55	LEU	0	-0.042	-0.014	2.785	-4.220	-3.688	0.112	-0.112	-0.533	-0.001
21	A	56	ILE	0	-0.027	-0.020	4.930	-0.586	-0.564	-0.001	-0.001	-0.019	0.000
23	A	58	PHE	0	0.036	0.021	2.837	-9.269	-6.048	4.113	-2.101	-5.234	-0.032
24	A	59	LEU	0	-0.047	-0.029	4.722	0.471	0.579	-0.001	-0.007	-0.100	0.000
4	A	39	PHE	0	-0.001	-0.004	6.254	-0.159	-0.159	0.000	0.000	0.000	0.000
5	A	40	TYR	0	0.037	0.019	8.635	2.117	2.117	0.000	0.000	0.000	0.000
6	A	41	LYS	1	0.934	0.959	10.750	23.920	23.920	0.000	0.000	0.000	0.000
7	A	42	ALA	0	0.022	0.036	13.131	0.890	0.890	0.000	0.000	0.000	0.000
8	A	43	GLY	0	0.000	-0.004	16.687	0.621	0.621	0.000	0.000	0.000	0.000
9	A	44	LYS	1	0.861	0.930	16.063	14.388	14.388	0.000	0.000	0.000	0.000
10	A	45	VAL	0	0.017	0.019	14.285	-0.771	-0.771	0.000	0.000	0.000	0.000
11	A	46	SER	0	-0.023	-0.011	9.286	-0.777	-0.777	0.000	0.000	0.000	0.000
12	A	47	PHE	0	-0.006	-0.013	9.962	0.800	0.800	0.000	0.000	0.000	0.000
14	A	49	GLN	0	-0.028	-0.033	5.498	1.874	1.874	0.000	0.000	0.000	0.000
16	A	51	ASP	-1	-0.852	-0.944	6.386	-23.266	-23.266	0.000	0.000	0.000	0.000
17	A	52	LEU	0	-0.028	-0.022	6.928	-1.910	-1.910	0.000	0.000	0.000	0.000
18	A	53	ASP	-1	-0.884	-0.935	8.414	-24.034	-24.034	0.000	0.000	0.000	0.000
22	A	57	ASN	0	-0.076	-0.041	6.929	-0.545	-0.545	0.000	0.000	0.000	0.000
25	A	60	GLU	-1	-0.953	-0.963	6.865	-23.000	-23.000	0.000	0.000	0.000	0.000
26	A	61	PRO	0	-0.065	-0.031	9.621	0.816	0.816	0.000	0.000	0.000	0.000
27	A	62	ASP	-1	-0.769	-0.867	12.472	-16.456	-16.456	0.000	0.000	0.000	0.000
28	A	63	VAL	0	-0.026	-0.018	15.692	0.956	0.956	0.000	0.000	0.000	0.000
29	A	64	LEU	0	-0.002	0.002	12.637	-0.999	-0.999	0.000	0.000	0.000	0.000
30	A	65	VAL	0	-0.029	-0.020	15.042	1.119	1.119	0.000	0.000	0.000	0.000
31	A	66	ASN	0	-0.020	-0.032	16.029	-0.911	-0.911	0.000	0.000	0.000	0.000
32	A	67	ALA	0	-0.005	-0.002	18.306	0.545	0.545	0.000	0.000	0.000	0.000
33	A	68	ALA	0	0.003	0.012	20.080	0.095	0.095	0.000	0.000	0.000	0.000
34	A	69	ASN	0	0.007	-0.020	23.233	0.080	0.080	0.000	0.000	0.000	0.000
35	A	70	GLY	0	0.033	0.015	26.847	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	71	ASP	-1	-0.949	-0.972	29.992	-8.768	-8.768	0.000	0.000	0.000	0.000
37	A	72	LEU	0	-0.053	-0.027	25.590	0.011	0.011	0.000	0.000	0.000	0.000
38	A	73	ARG	1	0.893	0.942	27.005	9.240	9.240	0.000	0.000	0.000	0.000
39	A	74	HIS	0	0.059	0.021	21.752	-0.385	-0.385	0.000	0.000	0.000	0.000
40	A	75	VAL	0	-0.014	-0.019	22.789	-0.279	-0.279	0.000	0.000	0.000	0.000
41	A	76	GLY	0	0.024	0.000	21.545	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	77	GLY	0	-0.006	-0.006	17.937	-0.055	-0.055	0.000	0.000	0.000	0.000
43	A	78	VAL	0	0.060	0.023	14.064	-0.097	-0.097	0.000	0.000	0.000	0.000
44	A	79	ALA	0	0.053	0.041	16.077	-0.241	-0.241	0.000	0.000	0.000	0.000
45	A	80	ARG	1	0.883	0.965	19.054	12.398	12.398	0.000	0.000	0.000	0.000
46	A	81	ALA	0	0.039	0.019	13.704	0.065	0.065	0.000	0.000	0.000	0.000
47	A	82	ILE	0	0.040	0.026	14.857	-0.232	-0.232	0.000	0.000	0.000	0.000
48	A	83	ASP	-1	-0.843	-0.916	16.373	-11.752	-11.752	0.000	0.000	0.000	0.000
49	A	84	VAL	0	-0.039	-0.024	16.988	0.380	0.380	0.000	0.000	0.000	0.000
50	A	85	PHE	0	0.047	0.032	11.757	0.296	0.296	0.000	0.000	0.000	0.000
51	A	86	THR	0	-0.016	-0.006	16.013	0.384	0.384	0.000	0.000	0.000	0.000
52	A	87	GLY	0	0.030	0.014	19.013	0.619	0.619	0.000	0.000	0.000	0.000
53	A	88	GLY	0	-0.028	-0.013	21.447	0.649	0.649	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.888	0.940	22.275	12.233	12.233	0.000	0.000	0.000	0.000
55	A	90	LEU	0	0.058	0.038	19.924	0.445	0.445	0.000	0.000	0.000	0.000
56	A	91	THR	0	0.020	-0.011	23.061	0.520	0.520	0.000	0.000	0.000	0.000
57	A	92	LYS	1	0.853	0.930	25.857	10.897	10.897	0.000	0.000	0.000	0.000
58	A	93	ARG	1	0.892	0.918	25.260	10.439	10.439	0.000	0.000	0.000	0.000
59	A	94	SER	0	0.010	-0.005	25.676	0.168	0.168	0.000	0.000	0.000	0.000
60	A	95	LYS	0	-0.003	0.018	28.218	0.275	0.275	0.000	0.000	0.000	0.000
61	A	96	GLU	-1	-0.857	-0.899	30.803	-9.031	-9.031	0.000	0.000	0.000	0.000
62	A	97	TYR	0	0.030	0.008	30.023	0.182	0.182	0.000	0.000	0.000	0.000
63	A	98	LEU	0	0.010	-0.016	30.974	0.245	0.245	0.000	0.000	0.000	0.000
64	A	99	LYS	1	0.902	0.960	33.818	8.008	8.008	0.000	0.000	0.000	0.000
65	A	100	SER	0	-0.054	-0.018	35.219	0.194	0.194	0.000	0.000	0.000	0.000
66	A	101	SER	0	-0.009	0.015	33.573	0.104	0.104	0.000	0.000	0.000	0.000
67	A	102	LYS	1	0.948	0.976	34.130	8.227	8.227	0.000	0.000	0.000	0.000
68	A	103	ALA	0	0.077	0.036	33.088	-0.263	-0.263	0.000	0.000	0.000	0.000
69	A	104	ILE	0	-0.013	0.001	27.504	0.127	0.127	0.000	0.000	0.000	0.000
70	A	105	ALA	0	0.022	0.008	30.482	-0.097	-0.097	0.000	0.000	0.000	0.000
71	A	106	PRO	0	0.004	-0.014	29.331	-0.174	-0.174	0.000	0.000	0.000	0.000
72	A	107	GLY	0	-0.047	-0.023	28.506	0.299	0.299	0.000	0.000	0.000	0.000
73	A	108	ASN	0	-0.088	-0.036	28.855	0.083	0.083	0.000	0.000	0.000	0.000
74	A	109	ALA	0	0.020	-0.003	24.127	-0.282	-0.282	0.000	0.000	0.000	0.000
75	A	110	VAL	0	-0.027	-0.003	25.548	0.306	0.306	0.000	0.000	0.000	0.000
76	A	111	LEU	0	0.015	0.015	21.330	-0.375	-0.375	0.000	0.000	0.000	0.000
77	A	112	PHE	0	-0.078	-0.038	23.295	0.499	0.499	0.000	0.000	0.000	0.000
78	A	113	GLU	-1	-0.846	-0.943	22.522	-11.447	-11.447	0.000	0.000	0.000	0.000
79	A	114	ASN	0	-0.023	-0.003	21.691	-0.086	-0.086	0.000	0.000	0.000	0.000
80	A	115	VAL	0	-0.054	-0.016	20.371	0.384	0.384	0.000	0.000	0.000	0.000
81	A	116	LEU	0	-0.080	-0.052	16.798	0.311	0.311	0.000	0.000	0.000	0.000
82	A	117	GLU	-1	-0.841	-0.912	20.431	-12.180	-12.180	0.000	0.000	0.000	0.000
83	A	118	HIS	0	-0.029	-0.031	18.750	-0.696	-0.696	0.000	0.000	0.000	0.000
84	A	119	LEU	0	-0.021	0.023	14.110	-0.496	-0.496	0.000	0.000	0.000	0.000
85	A	120	SER	0	0.012	-0.002	17.968	0.943	0.943	0.000	0.000	0.000	0.000
86	A	121	VAL	0	-0.021	-0.016	17.656	-0.692	-0.692	0.000	0.000	0.000	0.000
87	A	122	LEU	0	0.014	0.010	19.081	0.735	0.735	0.000	0.000	0.000	0.000
88	A	123	ASN	0	0.014	0.012	20.452	-0.617	-0.617	0.000	0.000	0.000	0.000
89	A	124	ALA	0	0.030	0.005	21.343	0.517	0.517	0.000	0.000	0.000	0.000
90	A	125	VAL	0	-0.023	0.009	23.102	-0.245	-0.245	0.000	0.000	0.000	0.000
91	A	126	GLY	0	0.072	0.028	24.928	0.207	0.207	0.000	0.000	0.000	0.000
92	A	127	PRO	0	-0.075	-0.026	25.916	0.312	0.312	0.000	0.000	0.000	0.000
93	A	128	ARG	1	0.970	1.002	27.440	9.026	9.026	0.000	0.000	0.000	0.000
94	A	129	ASN	0	-0.007	-0.014	28.739	0.143	0.143	0.000	0.000	0.000	0.000
95	A	130	GLY	0	0.012	0.003	30.471	0.115	0.115	0.000	0.000	0.000	0.000
96	A	131	ASP	-1	-0.862	-0.913	32.148	-8.726	-8.726	0.000	0.000	0.000	0.000
97	A	132	SER	0	0.011	-0.003	34.507	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	133	ARG	1	0.947	0.947	34.489	7.864	7.864	0.000	0.000	0.000	0.000
99	A	134	VAL	0	0.050	0.032	28.711	-0.150	-0.150	0.000	0.000	0.000	0.000
100	A	135	GLU	-1	-0.825	-0.922	28.931	-9.933	-9.933	0.000	0.000	0.000	0.000
101	A	136	GLY	0	0.019	0.016	28.985	-0.225	-0.225	0.000	0.000	0.000	0.000
102	A	137	LYS	1	0.851	0.937	29.445	8.753	8.753	0.000	0.000	0.000	0.000
103	A	138	LEU	0	0.062	0.017	23.498	-0.173	-0.173	0.000	0.000	0.000	0.000
104	A	139	CYS	0	-0.012	0.001	25.116	-0.370	-0.370	0.000	0.000	0.000	0.000
105	A	140	ASN	0	-0.064	-0.040	26.666	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	141	VAL	0	0.017	0.019	22.353	-0.117	-0.117	0.000	0.000	0.000	0.000
107	A	142	TYR	0	0.058	0.003	18.642	-0.509	-0.509	0.000	0.000	0.000	0.000
108	A	143	LYS	1	0.922	0.972	22.782	10.145	10.145	0.000	0.000	0.000	0.000
109	A	144	ALA	0	-0.017	-0.016	24.866	-0.073	-0.073	0.000	0.000	0.000	0.000
110	A	145	ILE	0	0.017	0.003	18.260	-0.104	-0.104	0.000	0.000	0.000	0.000
111	A	146	ALA	0	0.009	0.001	20.717	-0.303	-0.303	0.000	0.000	0.000	0.000
112	A	147	LYS	1	0.870	0.933	21.934	10.228	10.228	0.000	0.000	0.000	0.000
113	A	148	CYS	0	-0.019	0.014	20.149	0.323	0.323	0.000	0.000	0.000	0.000
114	A	149	ASP	-1	-0.846	-0.908	21.237	-12.371	-12.371	0.000	0.000	0.000	0.000
115	A	150	GLY	0	0.016	0.012	18.275	-0.345	-0.345	0.000	0.000	0.000	0.000
116	A	151	LYS	1	0.846	0.921	9.285	25.171	25.171	0.000	0.000	0.000	0.000
117	A	152	ILE	0	0.006	0.008	14.452	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	153	LEU	0	0.008	0.005	7.873	-1.201	-1.201	0.000	0.000	0.000	0.000
119	A	154	THR	0	-0.004	-0.026	11.822	1.681	1.681	0.000	0.000	0.000	0.000
120	A	155	PRO	0	0.010	0.028	12.582	-1.092	-1.092	0.000	0.000	0.000	0.000
121	A	156	LEU	0	0.058	0.033	14.333	0.533	0.533	0.000	0.000	0.000	0.000
122	A	157	ILE	0	-0.001	0.000	17.206	0.376	0.376	0.000	0.000	0.000	0.000
123	A	158	SER	0	-0.026	-0.049	20.474	0.073	0.073	0.000	0.000	0.000	0.000
124	A	159	VAL	0	0.024	0.029	18.628	0.478	0.478	0.000	0.000	0.000	0.000
125	A	160	GLY	0	0.058	0.044	20.925	0.088	0.088	0.000	0.000	0.000	0.000
126	A	161	ILE	0	0.008	-0.010	21.534	0.457	0.457	0.000	0.000	0.000	0.000
127	A	162	PHE	0	-0.083	-0.034	24.547	0.474	0.474	0.000	0.000	0.000	0.000
128	A	163	LYS	1	0.958	0.980	25.070	10.681	10.681	0.000	0.000	0.000	0.000
129	A	164	VAL	0	0.010	0.010	24.973	0.398	0.398	0.000	0.000	0.000	0.000
130	A	165	LYS	1	0.927	0.971	24.250	10.580	10.580	0.000	0.000	0.000	0.000
131	A	166	LEU	0	0.060	0.041	17.395	0.123	0.123	0.000	0.000	0.000	0.000
132	A	167	GLU	-1	-0.774	-0.909	21.468	-12.575	-12.575	0.000	0.000	0.000	0.000
133	A	168	VAL	0	-0.034	-0.012	23.048	0.154	0.154	0.000	0.000	0.000	0.000
134	A	169	SER	0	-0.012	-0.021	21.230	0.009	0.009	0.000	0.000	0.000	0.000
135	A	170	LEU	0	0.015	0.017	17.421	-0.118	-0.118	0.000	0.000	0.000	0.000
136	A	171	GLN	0	0.052	0.025	20.739	-0.210	-0.210	0.000	0.000	0.000	0.000
137	A	172	CYS	0	-0.092	-0.040	24.032	0.296	0.296	0.000	0.000	0.000	0.000
138	A	173	LEU	0	-0.004	0.021	16.731	0.164	0.164	0.000	0.000	0.000	0.000
139	A	174	LEU	0	0.041	0.007	18.413	0.004	0.004	0.000	0.000	0.000	0.000
140	A	175	LYS	1	0.933	0.979	21.800	10.188	10.188	0.000	0.000	0.000	0.000
141	A	176	THR	0	-0.093	-0.066	23.931	0.596	0.596	0.000	0.000	0.000	0.000
142	A	177	VAL	0	-0.063	-0.037	18.649	0.278	0.278	0.000	0.000	0.000	0.000
143	A	178	THR	0	-0.017	-0.002	21.084	-0.440	-0.440	0.000	0.000	0.000	0.000
144	A	179	ASP	-1	-0.908	-0.952	21.904	-13.626	-13.626	0.000	0.000	0.000	0.000
145	A	180	ARG	1	0.766	0.864	17.428	15.474	15.474	0.000	0.000	0.000	0.000
146	A	181	ASP	-1	-0.870	-0.922	14.745	-18.099	-18.099	0.000	0.000	0.000	0.000
147	A	182	LEU	0	-0.023	-0.013	14.237	0.508	0.508	0.000	0.000	0.000	0.000
148	A	183	ASN	0	0.036	0.023	8.756	-0.889	-0.889	0.000	0.000	0.000	0.000
149	A	184	VAL	0	0.023	0.007	10.796	1.006	1.006	0.000	0.000	0.000	0.000
150	A	185	PHE	0	-0.040	-0.022	7.893	-2.026	-2.026	0.000	0.000	0.000	0.000
151	A	186	VAL	0	0.007	-0.007	9.416	2.109	2.109	0.000	0.000	0.000	0.000
152	A	187	TYR	0	-0.050	-0.009	9.719	-1.100	-1.100	0.000	0.000	0.000	0.000
153	A	188	THR	0	-0.037	-0.029	11.607	-0.672	-0.672	0.000	0.000	0.000	0.000
154	A	189	ASP	-1	-0.791	-0.893	12.772	-21.524	-21.524	0.000	0.000	0.000	0.000
155	A	190	GLN	0	-0.016	-0.009	14.391	0.085	0.085	0.000	0.000	0.000	0.000
156	A	191	GLU	-1	-0.831	-0.900	15.069	-16.760	-16.760	0.000	0.000	0.000	0.000
157	A	192	ARG	1	0.839	0.906	9.200	27.043	27.043	0.000	0.000	0.000	0.000
158	A	193	VAL	0	0.034	0.017	13.751	0.137	0.137	0.000	0.000	0.000	0.000
159	A	194	THR	0	-0.077	-0.050	16.604	0.850	0.850	0.000	0.000	0.000	0.000
160	A	195	ILE	0	-0.036	-0.023	13.843	0.537	0.537	0.000	0.000	0.000	0.000
161	A	196	GLU	-1	-0.863	-0.928	12.526	-22.489	-22.489	0.000	0.000	0.000	0.000
162	A	197	ASN	0	0.015	0.000	16.462	0.356	0.356	0.000	0.000	0.000	0.000
163	A	198	PHE	0	-0.035	-0.018	19.526	0.757	0.757	0.000	0.000	0.000	0.000
164	A	199	PHE	0	-0.068	-0.038	16.001	0.439	0.439	0.000	0.000	0.000	0.000
165	A	200	ASN	0	-0.068	-0.039	20.135	-0.710	-0.710	0.000	0.000	0.000	0.000
166	A	201	GLY	-1	-0.916	-0.932	22.974	-11.071	-11.071	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:36:ILE)