FMO DATABASE

FMODB ID: 8GLZY

Calculation Name: 2B60-A-Xray547

Preferred Name:

Target Type:

Ligand Name: ritonavir

Ligand 3-letter code: RIT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B60

Chain ID: A

ChEMBL ID:

UniProt ID: Q7SMT3

Base Structure: X-ray

Registration Date: 2025-10-03

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	-687756.17105
FMO2-HF: Nuclear repulsion	649772.896275
FMO2-HF: Total energy	-37983.274775
FMO2-MP2: Total energy	-38093.561867

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.
-29.154	-25.84	0.147	-1.419	-2.038	-0.007

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 : 0.871 / q_NPA : 0.911

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	0.007	0.002	3.172	-2.697	-0.034	0.082	-1.198	-1.545	-0.005
4	A	4	THR	0	0.006	0.004	5.308	3.615	3.625	-0.001	-0.003	-0.005	0.000
67	A	67	CYS	0	0.026	0.006	4.024	-5.917	-5.523	0.057	-0.128	-0.323	-0.001
69	A	69	HIS	0	-0.050	-0.018	3.350	-1.247	-1.000	0.009	-0.090	-0.165	-0.001
5	A	5	LEU	0	0.044	0.006	9.005	-0.216	-0.216	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.016	0.021	12.086	1.871	1.871	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.047	-0.025	11.698	1.618	1.618	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.998	0.999	12.506	17.064	17.064	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.047	0.035	8.806	-0.769	-0.769	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.036	-0.017	9.619	0.352	0.352	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.007	-0.005	6.582	-3.791	-3.791	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.021	0.014	8.405	2.299	2.299	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.034	-0.017	9.570	-2.207	-2.207	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.920	0.963	12.253	18.547	18.547	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.035	0.018	15.261	-0.414	-0.414	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.063	0.036	17.883	0.629	0.629	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.054	-0.026	20.174	0.587	0.587	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.038	-0.015	20.357	0.197	0.197	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.023	0.011	15.220	-0.766	-0.766	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.869	0.920	15.425	15.408	15.408	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.892	-0.930	12.686	-21.749	-21.749	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.019	-0.019	12.164	1.628	1.628	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.011	-0.006	11.372	-1.790	-1.790	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.005	-0.010	5.950	0.202	0.202	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.849	-0.925	10.550	-18.154	-18.154	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.015	-0.028	12.162	0.556	0.556	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.002	0.006	14.806	0.749	0.749	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.018	0.010	17.070	1.057	1.057	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.819	-0.892	17.391	-15.776	-15.776	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.848	-0.933	18.515	-14.432	-14.432	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.008	-0.009	15.823	-0.774	-0.774	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.043	-0.023	17.696	1.003	1.003	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.003	-0.010	15.101	-0.836	-0.836	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.897	-0.949	20.329	-11.636	-11.636	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.939	-0.972	22.385	-11.207	-11.207	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.018	0.002	20.232	-0.368	-0.368	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.008	-0.006	23.907	0.516	0.516	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.010	0.011	21.668	-0.334	-0.334	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.002	0.002	25.249	0.486	0.486	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.012	0.001	27.945	-0.176	-0.176	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.933	0.955	30.500	8.904	8.904	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.021	0.022	28.763	-0.363	-0.363	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.898	0.952	28.759	11.190	11.190	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.016	-0.005	30.370	-0.346	-0.346	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.861	0.950	24.562	12.496	12.496	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.032	-0.020	30.241	0.227	0.227	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.021	0.019	24.292	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.021	0.016	27.619	0.312	0.312	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.031	-0.004	25.786	-0.578	-0.578	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.001	-0.006	25.222	0.427	0.427	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.016	0.017	27.299	0.324	0.324	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.002	0.014	29.845	0.379	0.379	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.011	-0.014	29.737	-0.346	-0.346	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.015	0.026	25.603	0.331	0.331	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.908	0.939	30.075	8.827	8.827	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.004	0.003	25.849	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.918	0.965	27.544	10.530	10.530	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.017	-0.033	25.303	-0.329	-0.329	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.015	0.004	24.071	0.587	0.587	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.779	-0.878	23.648	-12.517	-12.517	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.026	-0.017	21.834	0.554	0.554	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.060	0.031	19.544	0.202	0.202	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.033	-0.022	17.701	-0.825	-0.825	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.003	-0.009	13.208	0.529	0.529	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.877	-0.924	11.583	-20.516	-20.516	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.059	0.013	7.534	0.766	0.766	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.001	0.012	5.956	-3.373	-3.373	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.854	0.911	8.319	21.008	21.008	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.007	0.016	11.898	-0.309	-0.309	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.014	-0.007	13.666	0.838	0.838	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.025	0.012	17.289	-0.259	-0.259	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.064	-0.040	18.964	0.409	0.409	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.021	-0.003	18.198	-0.817	-0.817	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.037	-0.016	20.839	0.934	0.934	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.018	0.003	22.054	-0.496	-0.496	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.015	0.003	24.565	0.592	0.592	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.020	0.025	25.289	-0.388	-0.388	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.016	-0.019	21.011	0.305	0.305	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.030	0.013	23.084	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.005	-0.007	18.082	-0.336	-0.336	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.021	0.012	16.443	0.743	0.743	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.008	0.004	14.981	-0.924	-0.924	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.020	-0.012	10.877	0.599	0.599	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.100	0.050	13.189	-0.721	-0.721	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.885	0.894	14.116	15.316	15.316	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.040	-0.019	14.629	-1.419	-1.419	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.024	0.002	12.769	0.434	0.434	0.000	0.000	0.000	0.000
90	A	90	MET	0	-0.011	-0.007	9.765	-2.764	-2.764	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.003	0.005	9.850	-2.093	-2.093	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.008	-0.016	11.773	-1.199	-1.199	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.063	-0.017	5.949	0.163	0.163	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.001	0.011	6.709	-5.291	-5.291	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.078	-0.035	6.285	-3.958	-3.958	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.014	-0.017	7.154	4.072	4.072	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.030	-0.012	8.472	-2.177	-2.177	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.040	-0.026	8.901	-1.681	-1.681	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.902	-0.930	11.829	-20.004	-20.004	0.000	0.000	0.000	0.000

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