FMO DATABASE

FMODB ID: 8KY5Y

Calculation Name: 1NH0-A-Xray549

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: 3-benzyloxycarbonylamino-2-hydroxy-4-phenyl-butyric acid | beta-mercaptoethanol | amino group

Ligand 3-letter code: KI2 | BME | NH2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NH0

Chain ID: A

ChEMBL ID: CHEMBL3638326

UniProt ID: P03367

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-682442.833453
FMO2-HF: Nuclear repulsion	644679.743117
FMO2-HF: Total energy	-37763.090336
FMO2-MP2: Total energy	-37872.715522

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.
-36.321	-32.558	1.928	-1.739	-3.951	-0.015

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 : 0.868 / q_NPA : 0.912

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	-0.001	0.000	2.524	0.543	2.902	0.886	-0.953	-2.292	-0.005
4	A	4	THR	0	0.019	0.009	4.663	3.924	3.962	-0.001	-0.014	-0.023	0.000
67	A	67	CYS	0	-0.010	-0.007	2.689	-6.588	-6.005	0.962	-0.460	-1.085	-0.007
68	A	68	GLY	0	0.014	0.016	4.689	-6.634	-6.493	-0.001	-0.005	-0.134	0.000
69	A	69	HIS	0	-0.024	-0.001	3.165	-1.934	-1.292	0.082	-0.307	-0.417	-0.003
5	A	5	LEU	0	0.027	-0.003	8.380	-0.342	-0.342	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.005	0.012	11.363	1.976	1.976	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.009	0.005	10.996	1.673	1.673	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.976	0.981	11.923	15.205	15.205	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.042	0.033	7.933	-0.342	-0.342	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.023	-0.011	9.054	-0.506	-0.506	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.011	-0.010	4.913	-3.201	-3.201	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.038	0.021	7.761	1.968	1.968	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.022	-0.015	8.657	-2.663	-2.663	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.942	0.978	11.385	19.182	19.182	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.049	0.015	14.356	-0.375	-0.375	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.012	0.008	17.602	0.514	0.514	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.054	-0.031	19.083	0.542	0.542	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.028	0.016	19.390	-0.089	-0.089	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.023	-0.010	12.959	-0.814	-0.814	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.828	0.903	14.462	15.346	15.346	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.899	-0.951	11.855	-21.287	-21.287	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.001	-0.011	11.283	1.704	1.704	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.006	0.003	10.581	-1.942	-1.942	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.018	-0.013	4.933	0.021	0.021	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.833	-0.927	9.561	-18.071	-18.071	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.005	-0.022	11.135	0.463	0.463	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.007	0.005	13.786	0.798	0.798	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.017	0.008	16.336	1.059	1.059	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.826	-0.893	16.668	-15.776	-15.776	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.871	-0.948	17.995	-14.311	-14.311	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.006	-0.005	15.369	-0.840	-0.840	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.039	-0.021	17.221	1.043	1.043	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.016	-0.002	15.793	-0.771	-0.771	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.722	-0.849	19.293	-13.859	-13.859	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.900	-0.958	22.146	-11.598	-11.598	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.012	-0.003	19.224	-0.460	-0.460	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.069	-0.037	22.797	0.061	0.061	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.012	0.004	21.405	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.016	0.012	24.979	0.473	0.473	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.011	0.005	27.508	-0.190	-0.190	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.831	0.920	30.171	9.463	9.463	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.077	0.041	28.486	-0.283	-0.283	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.907	0.950	28.210	11.335	11.335	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.027	-0.009	29.383	-0.358	-0.358	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.874	0.932	24.069	12.602	12.602	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.005	0.008	29.704	0.028	0.028	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.027	0.014	23.190	-0.160	-0.160	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.017	-0.012	25.958	0.445	0.445	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.027	0.029	24.573	-0.521	-0.521	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.011	0.004	23.537	0.527	0.527	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.008	0.011	26.409	-0.166	-0.166	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.016	0.008	28.866	0.365	0.365	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.009	-0.014	28.598	-0.351	-0.351	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.007	0.005	24.588	0.295	0.295	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.956	0.962	28.966	8.922	8.922	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.008	0.008	24.781	-0.154	-0.154	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.924	0.962	27.046	10.312	10.312	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.011	-0.016	24.435	-0.198	-0.198	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.042	0.016	23.488	0.609	0.609	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.798	-0.874	22.640	-13.092	-13.092	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.020	-0.021	21.229	0.166	0.166	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.015	0.021	18.161	0.065	0.065	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.003	-0.001	17.225	-0.902	-0.902	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.004	0.002	12.612	0.338	0.338	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.982	-0.993	9.914	-24.386	-24.386	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.070	0.026	7.264	1.470	1.470	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.885	0.934	7.165	22.792	22.792	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.039	0.025	10.917	-0.480	-0.480	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.015	-0.015	12.765	1.032	1.032	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.022	0.015	16.477	-0.256	-0.256	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.080	-0.051	18.280	0.369	0.369	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.004	0.005	17.591	-0.873	-0.873	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.050	-0.015	20.146	0.963	0.963	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.045	0.032	21.858	-0.395	-0.395	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.013	-0.009	24.068	0.604	0.604	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.033	0.004	24.752	-0.329	-0.329	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.003	-0.015	20.201	0.356	0.356	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.021	-0.018	22.354	0.018	0.018	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.008	-0.001	16.377	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.034	-0.006	15.675	0.820	0.820	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.001	0.001	14.222	-1.073	-1.073	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.003	-0.009	10.320	0.858	0.858	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.102	0.052	12.362	-0.913	-0.913	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.885	0.907	13.648	15.565	15.565	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.030	-0.012	14.595	-1.322	-1.322	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.018	-0.010	12.439	0.186	0.186	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.016	-0.005	8.405	-2.162	-2.162	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.012	-0.015	9.571	-2.230	-2.230	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.058	-0.019	11.541	-0.296	-0.296	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.042	-0.015	5.595	0.036	0.036	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.005	0.007	6.444	-5.143	-5.143	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.085	-0.036	6.117	-4.126	-4.126	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.010	-0.016	6.928	4.083	4.083	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.042	-0.019	8.208	-2.330	-2.330	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.032	-0.021	8.872	-1.417	-1.417	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.898	-0.929	11.358	-20.730	-20.730	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:1:PRO)