FMO DATABASE

FMODB ID: 3K54L

Calculation Name: 2FP7-B-Xray547

Preferred Name: Genome polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: n-(4-amino-5-hydroxy-pentyl)-guanidine | benzoic acid | norleucine

Ligand 3-letter code: OAR | BEZ | NLE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FP7

Chain ID: B

ChEMBL ID: CHEMBL5419

UniProt ID: P06935

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1360083.546957
FMO2-HF: Nuclear repulsion	1302348.410182
FMO2-HF: Total energy	-57735.136775
FMO2-MP2: Total energy	-57902.272228

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:19:THR)

Summations of interaction energy for fragment #1(A:19:THR)

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.
-133.244	-124.75	15.437	-12.806	-11.124	-0.152

Interaction energy analysis for fragmet #1(A:19:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.892

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	21	GLY	0	0.036	0.025	2.807	-1.967	0.208	0.359	-1.099	-1.435	-0.009
4	A	22	VAL	0	0.003	0.007	5.290	0.215	0.237	-0.001	-0.003	-0.017	0.000
5	A	23	TYR	0	-0.057	-0.041	2.383	-6.800	-3.874	0.653	-1.513	-2.065	-0.016
23	A	41	MET	0	-0.038	0.011	2.535	1.532	2.523	0.271	-0.326	-0.937	-0.002
44	A	62	GLU	-1	-0.845	-0.913	1.822	-136.052	-133.672	14.155	-9.865	-6.670	-0.125
6	A	24	ARG	1	0.824	0.881	8.833	23.859	23.859	0.000	0.000	0.000	0.000
7	A	25	ILE	0	0.003	0.009	10.864	-2.045	-2.045	0.000	0.000	0.000	0.000
8	A	26	MET	0	-0.030	-0.007	12.850	2.078	2.078	0.000	0.000	0.000	0.000
9	A	27	THR	0	0.028	0.004	14.807	-0.094	-0.094	0.000	0.000	0.000	0.000
10	A	28	ARG	1	0.920	0.953	17.676	13.616	13.616	0.000	0.000	0.000	0.000
11	A	29	GLY	0	0.010	0.017	21.520	-0.125	-0.125	0.000	0.000	0.000	0.000
12	A	30	LEU	0	0.008	-0.003	23.913	0.461	0.461	0.000	0.000	0.000	0.000
13	A	31	LEU	0	0.029	0.032	19.605	0.155	0.155	0.000	0.000	0.000	0.000
14	A	32	GLY	0	0.018	0.004	20.237	-0.822	-0.822	0.000	0.000	0.000	0.000
15	A	33	SER	0	-0.065	-0.029	17.449	0.211	0.211	0.000	0.000	0.000	0.000
16	A	34	TYR	0	0.017	0.005	19.431	0.228	0.228	0.000	0.000	0.000	0.000
17	A	35	GLN	0	0.009	-0.025	15.605	-0.842	-0.842	0.000	0.000	0.000	0.000
18	A	36	ALA	0	-0.027	-0.015	17.251	0.852	0.852	0.000	0.000	0.000	0.000
19	A	37	GLY	0	0.041	0.019	16.514	0.761	0.761	0.000	0.000	0.000	0.000
20	A	38	ALA	0	-0.016	-0.003	12.985	-0.936	-0.936	0.000	0.000	0.000	0.000
21	A	39	GLY	0	0.059	0.042	11.281	1.059	1.059	0.000	0.000	0.000	0.000
22	A	40	VAL	0	-0.016	-0.009	8.674	-1.441	-1.441	0.000	0.000	0.000	0.000
24	A	42	VAL	0	0.043	-0.001	5.998	-1.430	-1.430	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.804	-0.893	7.683	-22.762	-22.762	0.000	0.000	0.000	0.000
26	A	44	GLY	0	-0.009	-0.003	5.012	2.419	2.419	0.000	0.000	0.000	0.000
27	A	45	VAL	0	-0.028	0.017	6.042	-0.320	-0.320	0.000	0.000	0.000	0.000
28	A	46	PHE	0	0.001	-0.001	6.637	-2.391	-2.391	0.000	0.000	0.000	0.000
29	A	47	HIS	0	0.011	0.009	8.035	5.450	5.450	0.000	0.000	0.000	0.000
30	A	48	THR	0	0.003	-0.028	11.510	-0.382	-0.382	0.000	0.000	0.000	0.000
31	A	49	LEU	0	0.013	0.020	14.280	0.720	0.720	0.000	0.000	0.000	0.000
32	A	50	TRP	0	-0.004	0.005	17.755	-0.559	-0.559	0.000	0.000	0.000	0.000
33	A	51	HIS	0	-0.081	-0.075	19.476	-0.177	-0.177	0.000	0.000	0.000	0.000
34	A	52	THR	0	-0.055	-0.027	16.613	0.095	0.095	0.000	0.000	0.000	0.000
35	A	53	THR	0	-0.017	-0.024	14.883	0.268	0.268	0.000	0.000	0.000	0.000
36	A	54	LYS	1	0.897	0.950	18.348	13.280	13.280	0.000	0.000	0.000	0.000
37	A	55	GLY	0	0.053	0.031	17.947	0.604	0.604	0.000	0.000	0.000	0.000
38	A	56	ALA	0	-0.042	-0.010	17.878	-0.346	-0.346	0.000	0.000	0.000	0.000
39	A	57	ALA	0	0.020	0.018	14.680	-1.084	-1.084	0.000	0.000	0.000	0.000
40	A	58	LEU	0	-0.008	0.008	10.740	0.612	0.612	0.000	0.000	0.000	0.000
41	A	59	MET	0	-0.025	-0.009	10.964	-0.497	-0.497	0.000	0.000	0.000	0.000
42	A	60	SER	0	-0.030	-0.026	5.416	-3.444	-3.444	0.000	0.000	0.000	0.000
43	A	61	GLY	0	0.023	0.005	5.802	3.921	3.921	0.000	0.000	0.000	0.000
45	A	63	GLY	0	0.037	0.031	5.976	4.192	4.192	0.000	0.000	0.000	0.000
46	A	64	ARG	1	0.784	0.853	9.169	18.278	18.278	0.000	0.000	0.000	0.000
47	A	65	LEU	0	0.010	0.014	6.094	-0.270	-0.270	0.000	0.000	0.000	0.000
48	A	66	ASP	-1	-0.769	-0.856	10.183	-18.960	-18.960	0.000	0.000	0.000	0.000
49	A	67	PRO	0	-0.031	-0.021	12.782	-1.446	-1.446	0.000	0.000	0.000	0.000
50	A	68	TYR	0	-0.035	-0.015	13.645	0.826	0.826	0.000	0.000	0.000	0.000
51	A	69	TRP	0	0.015	-0.007	15.530	0.917	0.917	0.000	0.000	0.000	0.000
52	A	70	GLY	0	0.037	0.011	16.804	-1.103	-1.103	0.000	0.000	0.000	0.000
53	A	71	SER	0	-0.066	-0.027	19.429	0.881	0.881	0.000	0.000	0.000	0.000
54	A	72	VAL	0	0.019	-0.006	22.729	-0.135	-0.135	0.000	0.000	0.000	0.000
55	A	73	LYS	1	0.946	0.976	24.707	10.446	10.446	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.770	-0.860	23.047	-13.362	-13.362	0.000	0.000	0.000	0.000
57	A	75	ASP	-1	-0.782	-0.869	22.174	-15.009	-15.009	0.000	0.000	0.000	0.000
58	A	76	ARG	1	0.853	0.943	18.359	14.914	14.914	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.025	-0.013	14.950	0.833	0.833	0.000	0.000	0.000	0.000
60	A	78	CYS	0	-0.045	-0.011	12.069	-0.637	-0.637	0.000	0.000	0.000	0.000
61	A	79	TYR	0	0.019	-0.006	9.846	1.584	1.584	0.000	0.000	0.000	0.000
62	A	80	GLY	0	0.010	0.001	9.205	-2.791	-2.791	0.000	0.000	0.000	0.000
63	A	81	GLY	0	0.006	-0.005	10.291	0.229	0.229	0.000	0.000	0.000	0.000
64	A	82	PRO	0	0.020	0.007	12.273	0.045	0.045	0.000	0.000	0.000	0.000
65	A	83	TRP	0	0.060	0.001	13.185	-2.213	-2.213	0.000	0.000	0.000	0.000
66	A	84	LYS	1	0.903	0.961	10.414	25.042	25.042	0.000	0.000	0.000	0.000
67	A	85	LEU	0	-0.075	-0.024	11.637	0.340	0.340	0.000	0.000	0.000	0.000
68	A	86	GLN	0	0.049	0.029	15.051	1.301	1.301	0.000	0.000	0.000	0.000
69	A	87	HIS	0	0.013	0.028	16.798	0.744	0.744	0.000	0.000	0.000	0.000
70	A	88	LYS	1	0.888	0.931	20.048	12.821	12.821	0.000	0.000	0.000	0.000
71	A	89	TRP	0	-0.004	-0.008	22.732	0.152	0.152	0.000	0.000	0.000	0.000
72	A	90	ASN	0	0.031	0.000	24.582	0.390	0.390	0.000	0.000	0.000	0.000
73	A	91	GLY	0	0.019	0.022	27.261	0.420	0.420	0.000	0.000	0.000	0.000
74	A	92	HIS	0	-0.091	-0.042	29.292	0.604	0.604	0.000	0.000	0.000	0.000
75	A	93	ASP	-1	-0.854	-0.916	26.118	-10.926	-10.926	0.000	0.000	0.000	0.000
76	A	94	GLU	-1	-0.923	-0.959	26.278	-10.757	-10.757	0.000	0.000	0.000	0.000
77	A	95	VAL	0	-0.016	-0.005	21.883	-0.356	-0.356	0.000	0.000	0.000	0.000
78	A	96	GLN	0	-0.017	-0.015	19.026	-0.289	-0.289	0.000	0.000	0.000	0.000
79	A	97	MET	0	-0.002	0.022	18.878	-0.482	-0.482	0.000	0.000	0.000	0.000
80	A	98	ILE	0	0.001	-0.001	12.883	0.291	0.291	0.000	0.000	0.000	0.000
81	A	99	VAL	0	-0.015	-0.015	16.088	-0.756	-0.756	0.000	0.000	0.000	0.000
82	A	100	VAL	0	0.020	0.006	13.569	-0.108	-0.108	0.000	0.000	0.000	0.000
83	A	101	GLU	-1	-0.778	-0.885	16.358	-13.207	-13.207	0.000	0.000	0.000	0.000
84	A	102	PRO	0	0.006	0.006	18.643	-0.587	-0.587	0.000	0.000	0.000	0.000
85	A	103	GLY	0	-0.031	-0.010	19.253	0.693	0.693	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.827	0.920	19.629	13.528	13.528	0.000	0.000	0.000	0.000
87	A	105	ASN	0	0.016	0.009	16.250	-1.579	-1.579	0.000	0.000	0.000	0.000
88	A	106	VAL	0	-0.002	0.005	12.807	0.588	0.588	0.000	0.000	0.000	0.000
89	A	107	LYS	1	0.942	0.981	15.920	13.588	13.588	0.000	0.000	0.000	0.000
90	A	108	ASN	0	0.011	0.001	15.876	-0.867	-0.867	0.000	0.000	0.000	0.000
91	A	109	VAL	0	-0.057	-0.024	18.889	0.744	0.744	0.000	0.000	0.000	0.000
92	A	110	GLN	0	-0.018	-0.007	22.091	-0.864	-0.864	0.000	0.000	0.000	0.000
93	A	111	THR	0	0.008	-0.002	24.145	0.503	0.503	0.000	0.000	0.000	0.000
94	A	112	LYS	1	0.947	0.987	26.345	9.700	9.700	0.000	0.000	0.000	0.000
95	A	113	PRO	0	-0.058	-0.014	26.080	0.203	0.203	0.000	0.000	0.000	0.000
96	A	114	GLY	0	0.025	0.027	28.867	0.373	0.373	0.000	0.000	0.000	0.000
97	A	115	VAL	0	-0.026	-0.022	30.594	-0.365	-0.365	0.000	0.000	0.000	0.000
98	A	116	PHE	0	-0.032	-0.006	28.709	0.318	0.318	0.000	0.000	0.000	0.000
99	A	117	LYS	1	0.962	0.975	32.632	8.160	8.160	0.000	0.000	0.000	0.000
100	A	118	THR	0	-0.027	-0.026	31.722	0.105	0.105	0.000	0.000	0.000	0.000
101	A	119	PRO	0	-0.002	-0.014	34.914	0.070	0.070	0.000	0.000	0.000	0.000
102	A	120	GLU	-1	-0.953	-0.969	30.962	-10.108	-10.108	0.000	0.000	0.000	0.000
103	A	121	GLY	0	0.018	0.021	32.396	-0.193	-0.193	0.000	0.000	0.000	0.000
104	A	122	GLU	-1	-0.959	-0.981	32.430	-9.211	-9.211	0.000	0.000	0.000	0.000
105	A	123	ILE	0	0.005	0.005	26.567	-0.329	-0.329	0.000	0.000	0.000	0.000
106	A	124	GLY	0	0.039	0.019	27.462	0.262	0.262	0.000	0.000	0.000	0.000
107	A	125	ALA	0	-0.023	-0.012	26.968	-0.450	-0.450	0.000	0.000	0.000	0.000
108	A	126	VAL	0	0.013	-0.007	24.177	0.275	0.275	0.000	0.000	0.000	0.000
109	A	127	THR	0	0.019	0.007	27.658	-0.068	-0.068	0.000	0.000	0.000	0.000
110	A	128	LEU	0	-0.021	-0.008	23.611	0.022	0.022	0.000	0.000	0.000	0.000
111	A	129	ASP	-1	-0.883	-0.928	27.081	-11.066	-11.066	0.000	0.000	0.000	0.000
112	A	130	TYR	0	0.045	0.010	23.179	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	131	PRO	0	0.031	0.017	23.080	0.014	0.014	0.000	0.000	0.000	0.000
114	A	132	THR	0	0.072	0.035	22.434	-0.529	-0.529	0.000	0.000	0.000	0.000
115	A	133	GLY	0	0.030	0.028	19.324	-0.456	-0.456	0.000	0.000	0.000	0.000
116	A	134	THR	0	-0.080	-0.039	17.645	-1.096	-1.096	0.000	0.000	0.000	0.000
117	A	135	SER	0	0.057	0.029	18.370	-0.390	-0.390	0.000	0.000	0.000	0.000
118	A	136	GLY	0	0.014	0.004	15.646	-0.870	-0.870	0.000	0.000	0.000	0.000
119	A	137	SER	0	-0.066	-0.050	14.664	-1.674	-1.674	0.000	0.000	0.000	0.000
120	A	138	PRO	0	-0.008	0.008	12.259	0.907	0.907	0.000	0.000	0.000	0.000
121	A	139	ILE	0	-0.010	-0.015	15.405	0.715	0.715	0.000	0.000	0.000	0.000
122	A	140	VAL	0	-0.006	-0.007	14.224	-0.589	-0.589	0.000	0.000	0.000	0.000
123	A	141	ASP	-1	-0.750	-0.883	17.509	-14.661	-14.661	0.000	0.000	0.000	0.000
124	A	142	LYS	1	0.938	0.952	18.791	11.371	11.371	0.000	0.000	0.000	0.000
125	A	143	ASN	0	-0.063	-0.033	18.226	0.545	0.545	0.000	0.000	0.000	0.000
126	A	144	GLY	0	-0.021	0.003	14.712	-0.638	-0.638	0.000	0.000	0.000	0.000
127	A	145	ASP	-1	-0.888	-0.936	13.785	-20.209	-20.209	0.000	0.000	0.000	0.000
128	A	146	VAL	0	-0.062	-0.050	12.277	0.686	0.686	0.000	0.000	0.000	0.000
129	A	147	ILE	0	-0.023	-0.006	15.471	0.251	0.251	0.000	0.000	0.000	0.000
130	A	148	GLY	0	0.004	-0.001	17.971	0.944	0.944	0.000	0.000	0.000	0.000
131	A	149	LEU	0	-0.064	-0.015	14.375	-1.079	-1.079	0.000	0.000	0.000	0.000
132	A	150	TYR	0	0.000	-0.033	18.291	0.963	0.963	0.000	0.000	0.000	0.000
133	A	151	GLY	0	0.041	0.003	19.712	-0.813	-0.813	0.000	0.000	0.000	0.000
134	A	152	ASN	0	-0.020	-0.008	22.353	0.638	0.638	0.000	0.000	0.000	0.000
135	A	153	GLY	0	-0.004	-0.002	24.858	-0.073	-0.073	0.000	0.000	0.000	0.000
136	A	154	VAL	0	-0.023	0.003	28.399	0.220	0.220	0.000	0.000	0.000	0.000
137	A	155	ILE	0	0.003	0.009	31.599	-0.180	-0.180	0.000	0.000	0.000	0.000
138	A	156	MET	0	-0.009	0.001	33.861	0.197	0.197	0.000	0.000	0.000	0.000
139	A	157	PRO	0	0.015	-0.014	37.033	0.033	0.033	0.000	0.000	0.000	0.000
140	A	158	ASN	0	-0.007	0.018	38.466	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	159	GLY	0	0.010	0.009	37.247	0.032	0.032	0.000	0.000	0.000	0.000
142	A	160	SER	0	-0.031	-0.024	34.552	-0.268	-0.268	0.000	0.000	0.000	0.000
143	A	161	TYR	0	0.020	0.008	25.973	-0.020	-0.020	0.000	0.000	0.000	0.000
144	A	162	ILE	0	-0.024	-0.015	29.634	0.019	0.019	0.000	0.000	0.000	0.000
145	A	163	SER	0	0.013	0.012	24.075	-0.154	-0.154	0.000	0.000	0.000	0.000
146	A	164	ALA	0	0.017	-0.005	25.451	0.265	0.265	0.000	0.000	0.000	0.000
147	A	165	ILE	0	-0.019	0.004	21.504	-0.534	-0.534	0.000	0.000	0.000	0.000
148	A	166	VAL	0	-0.046	-0.022	20.489	0.225	0.225	0.000	0.000	0.000	0.000
149	A	167	GLN	0	0.060	0.000	17.253	-1.293	-1.293	0.000	0.000	0.000	0.000
150	A	168	GLY	0	-0.057	-0.031	19.841	0.898	0.898	0.000	0.000	0.000	0.000
151	A	169	GLU	-1	-0.857	-0.921	20.115	-13.699	-13.699	0.000	0.000	0.000	0.000
152	A	170	ARG	0	-0.143	-0.090	13.730	3.362	3.362	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:THR)