FMO DATABASE

FMODB ID: 67QQZ

Calculation Name: 1A30-A-Xray547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A30

Chain ID: A

ChEMBL ID: CHEMBL3638360

UniProt ID: P04585

Base Structure: X-ray

Registration Date: 2025-10-05

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-686169.791645
FMO2-HF: Nuclear repulsion	648440.978142
FMO2-HF: Total energy	-37728.813503
FMO2-MP2: Total energy	-37838.424912

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:1:PRO)

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

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.
-18.395	-15.368	0.075	-1.268	-1.835	-0.005

Interaction energy analysis for fragmet #1(A:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.884 / q_NPA : 0.918

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	3	ILE	0	0.012	0.005	3.260	-0.542	1.821	0.057	-0.975	-1.445	-0.003
4	A	4	THR	0	-0.003	0.000	5.247	3.823	3.842	-0.001	-0.004	-0.014	0.000
67	A	67	CYS	0	-0.005	-0.002	4.203	-2.065	-1.917	-0.001	-0.015	-0.133	0.000
69	A	69	HIS	0	-0.067	-0.026	3.412	-4.004	-3.507	0.020	-0.274	-0.243	-0.002
5	A	5	LEU	0	0.046	0.010	8.859	0.070	0.070	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.009	0.013	11.806	1.954	1.954	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.928	0.960	12.808	18.940	18.940	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.995	0.997	12.628	14.915	14.915	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.047	0.038	8.758	-0.220	-0.220	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.025	-0.019	9.969	0.142	0.142	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.022	-0.012	6.012	-3.169	-3.169	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.013	-0.009	8.885	1.702	1.702	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.043	-0.026	9.687	-2.143	-2.143	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.911	0.960	12.342	18.293	18.293	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.058	0.022	15.120	-0.287	-0.287	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.038	0.019	17.940	0.579	0.579	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.030	-0.011	20.114	0.574	0.574	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.003	-0.004	20.224	-0.324	-0.324	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.009	0.004	13.782	-0.589	-0.589	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.892	0.945	15.442	15.552	15.552	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.795	-0.873	12.207	-24.036	-24.036	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.027	-0.021	12.497	1.469	1.469	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.013	-0.005	11.607	-1.631	-1.631	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.017	-0.009	5.903	0.033	0.033	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.830	-0.929	10.612	-17.796	-17.796	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.005	-0.021	12.056	0.331	0.331	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.012	0.001	14.692	0.769	0.769	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.014	0.011	17.308	0.981	0.981	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.826	-0.898	17.681	-15.523	-15.523	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.865	-0.952	18.835	-14.001	-14.001	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.003	-0.005	16.143	-0.921	-0.921	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.041	-0.020	18.007	0.990	0.990	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.019	-0.010	16.768	-0.699	-0.699	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.812	-0.928	20.420	-13.643	-13.643	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.839	-0.910	22.926	-10.905	-10.905	0.000	0.000	0.000	0.000
36	A	36	MET	0	0.006	0.011	21.761	-0.224	-0.224	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.007	-0.009	26.001	0.088	0.088	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.017	0.006	22.073	-0.486	-0.486	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.003	0.003	24.815	0.497	0.497	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.041	0.021	27.328	-0.237	-0.237	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.855	0.934	29.647	9.485	9.485	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.049	0.024	29.070	-0.279	-0.279	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.894	0.950	29.002	11.189	11.189	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.015	-0.009	30.557	-0.324	-0.324	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.884	0.951	25.102	12.492	12.492	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.024	0.001	30.446	0.056	0.056	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.018	0.005	24.103	-0.144	-0.144	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.040	0.007	26.943	0.350	0.350	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.017	0.017	25.653	-0.493	-0.493	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.003	-0.003	25.177	0.496	0.496	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.009	0.009	27.376	-0.129	-0.129	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.014	0.009	29.924	0.361	0.361	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.002	-0.018	29.544	-0.373	-0.373	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.001	0.015	25.610	0.268	0.268	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.968	0.972	29.749	8.839	8.839	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.003	0.001	25.613	-0.107	-0.107	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.779	0.870	28.034	11.135	11.135	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.011	-0.031	25.677	-0.228	-0.228	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.028	0.015	24.268	0.588	0.588	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.786	-0.881	23.891	-12.413	-12.413	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.028	-0.022	21.772	0.286	0.286	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.037	0.034	19.268	0.076	0.076	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.017	-0.015	16.089	-0.688	-0.688	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.015	-0.009	13.001	0.719	0.719	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.941	-0.961	10.499	-23.892	-23.892	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.052	0.013	7.142	1.172	1.172	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.029	0.031	5.537	-4.640	-4.640	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.915	0.968	7.759	19.984	19.984	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.050	0.024	11.402	-0.141	-0.141	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.049	-0.055	13.080	1.103	1.103	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.039	0.023	16.827	-0.301	-0.301	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.064	-0.039	19.093	0.347	0.347	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.012	0.000	18.449	-0.806	-0.806	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.026	-0.002	21.103	0.892	0.892	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.037	-0.008	22.370	-0.475	-0.475	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.028	0.014	24.716	0.561	0.561	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.006	0.010	25.512	-0.389	-0.389	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.014	-0.021	21.111	0.297	0.297	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.033	-0.029	23.198	0.041	0.041	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.000	0.009	17.316	-0.128	-0.128	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.025	0.018	16.632	0.446	0.446	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.005	0.000	15.108	-1.012	-1.012	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.007	-0.010	11.369	0.683	0.683	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.095	0.051	13.409	-0.804	-0.804	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.885	0.907	14.212	15.140	15.140	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.035	-0.011	14.775	-1.423	-1.423	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.013	-0.006	12.817	0.245	0.245	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.015	-0.001	9.526	-2.096	-2.096	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.025	-0.014	9.629	-2.287	-2.287	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.071	-0.023	11.551	-0.311	-0.311	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.030	-0.011	6.034	0.174	0.174	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.004	0.009	6.485	-5.264	-5.264	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.084	-0.034	6.007	-4.843	-4.843	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.011	-0.018	6.915	4.085	4.085	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.037	-0.016	8.291	-1.981	-1.981	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.033	-0.024	8.946	-1.670	-1.670	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.898	-0.927	11.513	-20.521	-20.521	0.000	0.000	0.000	0.000

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