FMO DATABASE

FMODB ID: KK1Y3

Calculation Name: 2KOD-A-Other547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KOD

Chain ID: A

ChEMBL ID: CHEMBL3638360

UniProt ID: P04585

Base Structure: SolutionNMR

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-574996.430372
FMO2-HF: Nuclear repulsion	539620.473812
FMO2-HF: Total energy	-35375.95656
FMO2-MP2: Total energy	-35475.6705

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:144:MET)

Summations of interaction energy for fragment #1(A:144:MET)

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.
-12.668	-10.27	0.795	-0.881	-2.312	-0.005

Interaction energy analysis for fragmet #1(A:144:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.902

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

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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	146	SER	0	0.058	0.014	3.847	1.989	3.197	-0.010	-0.449	-0.749	-0.001
4	A	147	PRO	0	-0.035	-0.012	2.509	2.044	3.187	0.806	-0.428	-1.521	-0.004
5	A	148	THR	0	0.001	-0.029	5.152	3.781	3.828	-0.001	-0.004	-0.042	0.000
6	A	149	SER	0	0.004	-0.004	7.726	-0.804	-0.804	0.000	0.000	0.000	0.000
7	A	150	ILE	0	0.024	0.005	10.559	0.868	0.868	0.000	0.000	0.000	0.000
8	A	151	LEU	0	-0.036	-0.019	9.029	1.012	1.012	0.000	0.000	0.000	0.000
9	A	152	ASP	-1	-0.974	-0.973	11.823	-19.074	-19.074	0.000	0.000	0.000	0.000
10	A	153	ILE	0	-0.054	-0.011	13.537	1.367	1.367	0.000	0.000	0.000	0.000
11	A	154	ARG	1	0.962	0.972	16.390	15.895	15.895	0.000	0.000	0.000	0.000
12	A	155	GLN	0	-0.042	-0.071	19.527	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	156	GLY	0	0.026	0.006	23.284	-0.070	-0.070	0.000	0.000	0.000	0.000
14	A	157	PRO	0	-0.035	-0.042	24.775	0.264	0.264	0.000	0.000	0.000	0.000
15	A	158	LYS	1	0.976	0.991	27.767	9.287	9.287	0.000	0.000	0.000	0.000
16	A	159	GLU	-1	-0.792	-0.869	24.475	-11.741	-11.741	0.000	0.000	0.000	0.000
17	A	160	PRO	0	-0.010	0.012	28.712	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	161	PHE	0	0.126	0.020	25.223	-0.201	-0.201	0.000	0.000	0.000	0.000
19	A	162	ARG	1	0.921	0.959	26.961	8.737	8.737	0.000	0.000	0.000	0.000
20	A	163	ASP	-1	-0.870	-0.922	25.098	-11.866	-11.866	0.000	0.000	0.000	0.000
21	A	164	TYR	0	-0.018	0.000	19.950	-0.586	-0.586	0.000	0.000	0.000	0.000
22	A	165	VAL	0	0.015	0.006	22.444	-0.567	-0.567	0.000	0.000	0.000	0.000
23	A	166	ASP	-1	-0.921	-0.953	23.492	-11.776	-11.776	0.000	0.000	0.000	0.000
24	A	167	ARG	1	0.844	0.905	19.660	12.799	12.799	0.000	0.000	0.000	0.000
25	A	168	PHE	0	0.039	0.033	18.049	-0.757	-0.757	0.000	0.000	0.000	0.000
26	A	169	TYR	0	0.041	-0.010	18.957	-0.575	-0.575	0.000	0.000	0.000	0.000
27	A	170	LYS	1	0.907	0.958	20.231	12.583	12.583	0.000	0.000	0.000	0.000
28	A	171	THR	0	-0.033	-0.026	14.415	-0.435	-0.435	0.000	0.000	0.000	0.000
29	A	172	LEU	0	0.059	0.025	15.808	-0.635	-0.635	0.000	0.000	0.000	0.000
30	A	173	ARG	1	0.866	0.939	17.322	13.085	13.085	0.000	0.000	0.000	0.000
31	A	174	ALA	0	-0.065	-0.035	15.479	0.373	0.373	0.000	0.000	0.000	0.000
32	A	175	GLU	-1	-0.819	-0.876	11.880	-22.563	-22.563	0.000	0.000	0.000	0.000
33	A	176	GLN	0	-0.033	-0.015	11.218	0.026	0.026	0.000	0.000	0.000	0.000
34	A	177	ALA	0	0.008	0.006	12.817	-1.290	-1.290	0.000	0.000	0.000	0.000
35	A	178	SER	0	-0.003	0.000	14.942	1.231	1.231	0.000	0.000	0.000	0.000
36	A	179	GLN	0	0.051	0.003	18.333	0.030	0.030	0.000	0.000	0.000	0.000
37	A	180	GLU	-1	-0.863	-0.921	20.833	-12.535	-12.535	0.000	0.000	0.000	0.000
38	A	181	VAL	0	-0.029	-0.017	14.741	-0.065	-0.065	0.000	0.000	0.000	0.000
39	A	182	LYS	1	0.940	0.985	18.194	12.639	12.639	0.000	0.000	0.000	0.000
40	A	183	ASN	0	0.010	0.017	19.828	0.284	0.284	0.000	0.000	0.000	0.000
41	A	184	TRP	0	0.113	0.059	16.452	-0.270	-0.270	0.000	0.000	0.000	0.000
42	A	185	MET	0	-0.039	-0.007	13.613	0.298	0.298	0.000	0.000	0.000	0.000
43	A	186	THR	0	-0.084	-0.082	19.009	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	187	GLU	-1	-0.928	-0.948	21.640	-11.125	-11.125	0.000	0.000	0.000	0.000
45	A	188	THR	0	-0.067	-0.033	20.211	0.373	0.373	0.000	0.000	0.000	0.000
46	A	189	LEU	0	-0.013	-0.027	14.721	0.123	0.123	0.000	0.000	0.000	0.000
47	A	190	LEU	0	-0.046	0.010	19.212	0.073	0.073	0.000	0.000	0.000	0.000
48	A	191	VAL	0	0.082	0.024	21.676	0.241	0.241	0.000	0.000	0.000	0.000
49	A	192	GLN	0	-0.082	-0.035	18.333	-0.053	-0.053	0.000	0.000	0.000	0.000
50	A	193	ASN	0	-0.041	-0.031	15.830	0.466	0.466	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.040	0.032	20.387	0.089	0.089	0.000	0.000	0.000	0.000
52	A	195	ASN	0	-0.046	-0.069	23.955	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	196	PRO	0	-0.030	-0.050	26.070	0.100	0.100	0.000	0.000	0.000	0.000
54	A	197	ASP	-1	-0.853	-0.915	28.482	-9.546	-9.546	0.000	0.000	0.000	0.000
55	A	198	CYS	-1	-0.758	-0.751	28.215	-9.974	-9.974	0.000	0.000	0.000	0.000
56	A	199	LYS	1	0.853	0.949	24.385	12.086	12.086	0.000	0.000	0.000	0.000
57	A	200	THR	0	-0.065	-0.033	28.597	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	201	ILE	0	0.002	0.006	32.175	0.193	0.193	0.000	0.000	0.000	0.000
59	A	202	LEU	0	0.023	-0.007	28.213	0.161	0.161	0.000	0.000	0.000	0.000
60	A	203	LYS	1	0.906	0.959	28.362	10.482	10.482	0.000	0.000	0.000	0.000
61	A	204	ALA	0	-0.036	-0.010	32.621	0.136	0.136	0.000	0.000	0.000	0.000
62	A	205	LEU	0	-0.025	-0.002	33.373	0.227	0.227	0.000	0.000	0.000	0.000
63	A	206	GLY	0	0.038	0.037	34.916	0.158	0.158	0.000	0.000	0.000	0.000
64	A	207	PRO	0	-0.051	-0.044	31.327	-0.127	-0.127	0.000	0.000	0.000	0.000
65	A	208	ALA	0	-0.022	-0.019	31.772	-0.141	-0.141	0.000	0.000	0.000	0.000
66	A	209	ALA	0	-0.005	0.026	32.781	0.072	0.072	0.000	0.000	0.000	0.000
67	A	210	THR	0	0.033	-0.008	31.445	-0.415	-0.415	0.000	0.000	0.000	0.000
68	A	211	LEU	0	0.000	-0.010	26.209	0.021	0.021	0.000	0.000	0.000	0.000
69	A	212	GLU	-1	-0.924	-0.963	30.054	-8.727	-8.727	0.000	0.000	0.000	0.000
70	A	213	GLU	-1	-0.816	-0.881	33.314	-8.391	-8.391	0.000	0.000	0.000	0.000
71	A	214	MET	0	-0.031	-0.010	27.910	-0.050	-0.050	0.000	0.000	0.000	0.000
72	A	215	MET	0	-0.029	-0.018	29.355	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	216	THR	0	-0.084	-0.042	31.791	0.162	0.162	0.000	0.000	0.000	0.000
74	A	217	ALA	0	-0.004	-0.004	34.776	0.179	0.179	0.000	0.000	0.000	0.000
75	A	218	CYS	0	-0.027	-0.032	30.968	0.082	0.082	0.000	0.000	0.000	0.000
76	A	219	GLN	0	-0.067	-0.032	33.684	-0.169	-0.169	0.000	0.000	0.000	0.000
77	A	220	GLY	0	-0.026	-0.021	35.911	0.188	0.188	0.000	0.000	0.000	0.000
78	A	221	VAL	0	-0.008	0.018	32.733	0.124	0.124	0.000	0.000	0.000	0.000
79	A	222	GLY	0	0.013	0.011	31.919	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	223	GLY	0	-0.031	-0.020	32.691	0.287	0.287	0.000	0.000	0.000	0.000
81	A	224	PRO	0	-0.041	-0.047	33.536	-0.121	-0.121	0.000	0.000	0.000	0.000
82	A	225	GLY	0	0.058	0.034	30.755	-0.149	-0.149	0.000	0.000	0.000	0.000
83	A	226	HIS	0	0.013	0.015	30.525	-0.432	-0.432	0.000	0.000	0.000	0.000
84	A	227	LYS	1	0.962	0.963	33.022	7.780	7.780	0.000	0.000	0.000	0.000
85	A	228	ALA	0	-0.050	-0.019	33.874	-0.191	-0.191	0.000	0.000	0.000	0.000
86	A	229	ARG	1	0.924	0.965	28.755	9.659	9.659	0.000	0.000	0.000	0.000
87	A	230	VAL	0	-0.013	0.006	29.370	0.244	0.244	0.000	0.000	0.000	0.000
88	A	231	LEU	-1	-0.900	-0.948	30.418	-9.341	-9.341	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:144:MET)