FMO DATABASE

FMODB ID: QM84Y

Calculation Name: 2RKF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n-{1-benzyl-4-[2-(2,6-dimethyl-phenoxy)-acetylamino]-3-hydroxy-5-phenyl-pentyl}-3-methyl-2-(2-oxo-tetrahydro-pyrimidin-1-yl)-butyramide | glycerol

Ligand 3-letter code: AB1 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q90JJ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-681335.086583
FMO2-HF: Nuclear repulsion	643293.117736
FMO2-HF: Total energy	-38041.968847
FMO2-MP2: Total energy	-38151.280515

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.
-51.651	-48.921	0.09	-1.194	-1.626	-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 : 0.861 / q_NPA : 0.907

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	0.006	0.003	3.182	-2.429	-0.128	0.076	-1.059	-1.318	-0.004
4	A	4	THR	0	0.005	0.004	5.124	3.934	3.937	-0.001	-0.003	0.002	0.000
67	A	67	CYS	0	-0.034	-0.026	4.355	-5.380	-5.105	0.013	-0.091	-0.198	-0.001
69	A	69	HIS	0	-0.006	-0.003	3.640	4.553	4.704	0.002	-0.041	-0.112	0.000
5	A	5	LEU	0	0.034	0.004	8.919	-0.153	-0.153	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.004	0.007	11.738	2.009	2.009	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.020	-0.006	11.260	0.075	0.075	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.977	0.987	12.140	16.030	16.030	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.048	0.031	8.625	-0.335	-0.335	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.003	-0.005	9.630	0.269	0.269	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.001	0.001	5.343	-3.687	-3.687	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.034	0.020	8.318	2.175	2.175	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.030	-0.019	9.394	-2.344	-2.344	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.923	0.973	12.038	18.643	18.643	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.027	0.012	14.972	-0.451	-0.451	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.028	0.015	18.017	0.629	0.629	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.033	-0.014	20.255	0.548	0.548	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.043	-0.019	20.115	0.056	0.056	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.002	-0.011	15.088	-0.853	-0.853	0.000	0.000	0.000	0.000
20	A	20	MET	0	0.014	0.014	15.233	0.899	0.899	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.925	-0.959	12.139	-22.855	-22.855	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.013	-0.020	11.979	1.514	1.514	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.035	-0.016	11.027	-1.952	-1.952	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.011	-0.013	5.526	0.155	0.155	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.843	-0.928	10.214	-18.108	-18.108	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.023	-0.031	11.844	0.463	0.463	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.006	0.002	14.429	0.757	0.757	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.011	0.016	16.785	1.065	1.065	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.828	-0.896	17.174	-15.624	-15.624	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.875	-0.946	18.477	-14.213	-14.213	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.013	-0.014	15.782	-0.795	-0.795	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.040	-0.022	17.641	1.047	1.047	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.009	-0.006	16.250	-0.789	-0.789	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.843	-0.941	20.085	-13.567	-13.567	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.898	-0.937	22.690	-10.948	-10.948	0.000	0.000	0.000	0.000
36	A	36	MET	0	0.034	0.030	21.183	-0.208	-0.208	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.002	-0.005	25.259	0.356	0.356	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.024	0.019	21.774	-0.376	-0.376	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.016	-0.009	25.379	0.478	0.478	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.026	0.007	27.804	-0.228	-0.228	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.883	0.942	30.398	9.730	9.730	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.038	0.031	28.946	-0.284	-0.284	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.004	-0.018	29.706	0.555	0.555	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.017	-0.002	30.206	-0.314	-0.314	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.915	0.967	25.172	12.284	12.284	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.032	-0.019	30.056	0.086	0.086	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.017	0.006	24.591	-0.147	-0.147	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.021	0.014	27.333	0.317	0.317	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.031	0.005	25.557	-0.550	-0.550	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.002	-0.019	24.768	0.381	0.381	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.019	0.017	27.503	0.275	0.275	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.022	0.001	30.170	0.371	0.371	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.014	-0.008	29.831	-0.346	-0.346	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.010	0.018	24.311	0.283	0.283	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.929	0.956	29.464	8.591	8.591	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.010	0.005	25.259	-0.121	-0.121	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.831	0.910	27.624	11.061	11.061	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.024	-0.031	25.372	-0.373	-0.373	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.017	0.000	24.106	0.552	0.552	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.811	-0.890	23.716	-12.600	-12.600	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.044	-0.032	21.947	0.533	0.533	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.021	0.026	19.307	0.077	0.077	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.017	-0.006	15.979	-0.643	-0.643	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.006	-0.010	13.451	0.473	0.473	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.862	-0.931	12.037	-20.572	-20.572	0.000	0.000	0.000	0.000
66	A	66	ILE	0	0.034	0.011	7.597	0.450	0.450	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.013	0.020	6.487	-2.534	-2.534	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.840	0.914	8.595	20.967	20.967	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.014	0.015	10.700	-0.324	-0.324	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.010	-0.008	13.554	0.940	0.940	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.011	0.014	17.258	-0.115	-0.115	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.061	-0.036	19.211	0.274	0.274	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.011	-0.002	18.353	-0.823	-0.823	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.040	-0.012	20.868	0.882	0.882	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.010	0.014	22.182	-0.435	-0.435	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.028	0.008	24.404	0.620	0.620	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.026	0.000	25.216	-0.352	-0.352	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.004	-0.017	20.919	0.353	0.353	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.021	-0.011	22.747	0.038	0.038	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.013	0.000	17.923	-0.264	-0.264	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.012	0.029	16.340	0.473	0.473	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.008	-0.002	14.902	-1.008	-1.008	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.011	-0.009	10.692	0.668	0.668	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.102	0.052	13.031	-0.761	-0.761	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.866	0.895	14.158	15.355	15.355	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.015	0.003	15.030	-1.403	-1.403	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.007	0.000	12.905	0.169	0.169	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.018	-0.010	9.062	-2.214	-2.214	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.024	-0.027	9.908	-2.358	-2.358	0.000	0.000	0.000	0.000
92	A	92	GLN	0	-0.046	-0.027	11.733	-0.759	-0.759	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.038	-0.015	6.124	-0.168	-0.168	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.021	0.004	6.356	-5.543	-5.543	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.077	-0.033	6.399	-4.194	-4.194	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.016	-0.015	7.093	3.441	3.441	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.024	-0.009	8.495	-1.938	-1.938	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.042	-0.028	9.081	-1.377	-1.377	0.000	0.000	0.000	0.000
99	A	99	PHE	-1	-0.906	-0.933	11.830	-19.690	-19.690	0.000	0.000	0.000	0.000

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