FMO DATABASE

FMODB ID: 5RV5Z

Calculation Name: 1RBP-A-Xray547

Preferred Name: Plasma retinol-binding protein

Target Type: SINGLE PROTEIN

Ligand Name: retinol

Ligand 3-letter code: RTL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RBP

Chain ID: A

ChEMBL ID: CHEMBL3100

UniProt ID: P02753

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	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1897626.920498
FMO2-HF: Nuclear repulsion	1825897.170416
FMO2-HF: Total energy	-71729.750082
FMO2-MP2: Total energy	-71934.280249

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:GLU)

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

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.
-12.214	-10.451	0.09	-0.625	-1.228	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.034

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	ASP	-1	-0.779	-0.863	3.529	-12.352	-10.589	0.090	-0.625	-1.228	0.003
4	A	4	CYS	0	-0.072	-0.024	6.527	-1.448	-1.448	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.867	0.917	8.752	-1.468	-1.468	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.058	0.035	11.926	0.835	0.835	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.034	-0.027	14.697	0.319	0.319	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.086	-0.051	9.262	0.562	0.562	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.002	0.008	9.988	1.174	1.174	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.870	0.931	11.319	-4.653	-4.653	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.017	-0.002	13.153	-0.429	-0.429	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.815	0.923	16.845	-1.598	-1.598	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.842	-0.919	17.652	2.708	2.708	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.051	-0.040	20.211	-0.142	-0.142	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.010	0.009	23.496	-0.086	-0.086	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.825	-0.906	25.022	0.817	0.817	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.852	0.888	28.650	-0.752	-0.752	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.002	0.017	30.742	-0.070	-0.070	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.793	0.872	28.273	-0.943	-0.943	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.009	-0.007	25.671	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.008	0.003	30.083	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.019	0.028	33.682	0.022	0.022	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.036	-0.055	34.043	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	TRP	0	-0.063	-0.022	27.040	0.035	0.035	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.041	0.025	31.133	-0.056	-0.056	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.007	0.005	27.220	0.030	0.030	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.010	0.012	24.969	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.036	-0.034	22.198	-0.097	-0.097	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.803	0.902	22.842	0.702	0.702	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.799	0.910	17.413	1.237	1.237	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.777	-0.894	20.805	-0.641	-0.641	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.010	0.019	22.126	-0.161	-0.161	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.941	-0.974	23.717	-1.084	-1.084	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.030	-0.012	25.417	0.106	0.106	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.069	-0.032	29.236	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.047	0.012	26.240	0.035	0.035	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.020	0.018	30.180	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.028	-0.022	29.580	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.833	-0.898	30.052	-0.376	-0.376	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.005	-0.023	32.376	0.050	0.050	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.010	0.013	28.946	0.028	0.028	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.003	0.000	31.446	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.015	-0.001	31.148	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.825	-0.891	33.094	0.269	0.269	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.013	-0.001	29.104	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.009	0.006	34.253	0.016	0.016	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.001	0.000	34.610	0.017	0.017	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.822	-0.884	36.689	0.385	0.385	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.949	-0.986	38.856	0.457	0.457	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.042	-0.033	39.874	0.018	0.018	0.000	0.000	0.000	0.000
51	A	51	GLY	0	-0.014	0.001	35.964	0.031	0.031	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.075	-0.032	34.651	0.011	0.011	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.011	0.007	28.649	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.016	-0.020	34.312	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.029	0.011	33.151	0.031	0.031	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.022	0.007	35.193	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.026	-0.021	32.785	0.018	0.018	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.922	0.979	34.659	0.020	0.020	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.057	0.025	34.323	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.774	0.860	34.666	0.378	0.378	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.012	-0.014	34.243	-0.031	-0.031	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.822	0.909	35.426	0.413	0.413	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.001	0.001	36.475	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.048	0.012	36.682	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.029	-0.012	39.744	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.018	-0.015	39.823	0.003	0.003	0.000	0.000	0.000	0.000
67	A	67	TRP	0	-0.002	0.009	41.934	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.758	-0.850	38.890	-0.374	-0.374	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.023	-0.004	39.225	0.026	0.026	0.000	0.000	0.000	0.000
70	A	174	CYS	-1	-0.856	-0.914	39.097	-0.099	-0.099	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.035	-0.022	36.630	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.874	-0.935	37.669	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.058	-0.030	34.775	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.002	-0.001	37.366	0.029	0.029	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.030	0.012	33.884	-0.031	-0.031	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.033	-0.022	34.890	0.018	0.018	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.003	-0.018	28.906	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.049	-0.022	30.921	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.807	-0.902	28.659	0.720	0.720	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.045	-0.025	24.726	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.906	-0.960	23.457	1.113	1.113	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.832	-0.904	19.406	1.999	1.999	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.020	0.002	22.630	-0.109	-0.109	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.002	0.006	20.665	-0.105	-0.105	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.791	0.901	16.985	-1.905	-1.905	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.042	0.028	23.168	-0.026	-0.026	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.839	0.911	25.773	-0.405	-0.405	0.000	0.000	0.000	0.000
88	A	88	MET	0	0.009	0.007	28.664	0.044	0.044	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.935	0.988	30.546	-0.187	-0.187	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.000	-0.014	30.435	0.022	0.022	0.000	0.000	0.000	0.000
91	A	91	TRP	0	-0.023	-0.020	34.823	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.070	0.026	37.737	0.010	0.010	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.014	-0.009	39.621	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.017	0.022	42.742	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.008	-0.025	42.587	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	PHE	0	-0.012	-0.013	41.492	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.031	0.010	38.370	-0.031	-0.031	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.001	0.010	31.687	0.029	0.029	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.954	0.970	36.102	0.126	0.126	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.017	0.008	32.654	-0.045	-0.045	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.067	-0.050	31.497	0.072	0.072	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.741	-0.808	26.440	-0.200	-0.200	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.788	-0.864	22.850	0.459	0.459	0.000	0.000	0.000	0.000
104	A	104	HIS	0	-0.001	-0.006	24.527	-0.166	-0.166	0.000	0.000	0.000	0.000
105	A	105	TRP	0	-0.020	-0.032	16.063	0.169	0.169	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.004	0.007	21.741	-0.141	-0.141	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.006	-0.004	15.519	0.220	0.220	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.763	-0.871	17.029	2.388	2.388	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.022	-0.035	19.103	-0.295	-0.295	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.793	-0.864	22.398	1.059	1.059	0.000	0.000	0.000	0.000
111	A	111	TYR	0	-0.016	-0.009	24.302	-0.022	-0.022	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.811	-0.878	27.419	0.693	0.693	0.000	0.000	0.000	0.000
113	A	113	THR	0	-0.062	-0.048	25.851	-0.110	-0.110	0.000	0.000	0.000	0.000
114	A	114	TYR	0	-0.056	-0.070	19.075	-0.163	-0.163	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.023	0.029	22.849	0.131	0.131	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.049	-0.013	17.232	-0.176	-0.176	0.000	0.000	0.000	0.000
117	A	117	GLN	0	0.044	0.028	20.632	0.110	0.110	0.000	0.000	0.000	0.000
118	A	118	TYR	0	0.015	0.009	15.859	-0.100	-0.100	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.000	0.003	20.083	0.115	0.115	0.000	0.000	0.000	0.000
120	A	120	CYS	0	-0.076	-0.034	13.631	0.183	0.183	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.830	0.906	20.499	0.522	0.522	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.027	0.014	21.619	0.072	0.072	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.026	0.009	18.249	-0.119	-0.119	0.000	0.000	0.000	0.000
124	A	124	ASN	0	-0.019	-0.008	14.988	0.187	0.187	0.000	0.000	0.000	0.000
125	A	125	LEU	0	0.002	-0.019	17.931	0.162	0.162	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.845	-0.892	13.107	-2.598	-2.598	0.000	0.000	0.000	0.000
127	A	127	GLY	0	-0.007	-0.004	13.909	0.124	0.124	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.044	-0.028	10.882	0.284	0.284	0.000	0.000	0.000	0.000
129	A	130	ALA	0	-0.028	-0.002	15.974	-0.341	-0.341	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.793	-0.899	18.610	-0.968	-0.968	0.000	0.000	0.000	0.000
131	A	132	SER	0	0.023	-0.008	17.943	0.099	0.099	0.000	0.000	0.000	0.000
132	A	133	TYR	0	-0.072	-0.051	20.289	-0.104	-0.104	0.000	0.000	0.000	0.000
133	A	134	SER	0	-0.032	-0.023	18.596	0.075	0.075	0.000	0.000	0.000	0.000
134	A	135	PHE	0	0.024	0.020	20.619	-0.158	-0.158	0.000	0.000	0.000	0.000
135	A	136	VAL	0	-0.011	-0.002	19.967	0.120	0.120	0.000	0.000	0.000	0.000
136	A	137	PHE	0	-0.005	-0.014	22.628	-0.099	-0.099	0.000	0.000	0.000	0.000
137	A	138	SER	0	-0.003	-0.024	25.474	0.112	0.112	0.000	0.000	0.000	0.000
138	A	139	ARG	1	0.835	0.897	28.115	-0.523	-0.523	0.000	0.000	0.000	0.000
139	A	140	ASP	-1	-0.850	-0.910	30.891	0.149	0.149	0.000	0.000	0.000	0.000
140	A	141	PRO	0	-0.002	0.005	31.394	-0.024	-0.024	0.000	0.000	0.000	0.000
141	A	142	ASN	0	-0.092	-0.048	32.730	-0.083	-0.083	0.000	0.000	0.000	0.000
142	A	143	GLY	0	-0.043	-0.019	28.600	-0.044	-0.044	0.000	0.000	0.000	0.000
143	A	144	LEU	0	-0.017	-0.018	23.091	0.055	0.055	0.000	0.000	0.000	0.000
144	A	145	PRO	0	0.033	0.030	25.932	-0.069	-0.069	0.000	0.000	0.000	0.000
145	A	146	PRO	0	0.042	0.003	23.935	0.036	0.036	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.913	-0.966	21.925	0.582	0.582	0.000	0.000	0.000	0.000
147	A	148	ALA	0	0.054	0.027	20.638	0.154	0.154	0.000	0.000	0.000	0.000
148	A	149	GLN	0	-0.020	-0.009	20.425	0.005	0.005	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.937	0.970	17.411	-1.102	-1.102	0.000	0.000	0.000	0.000
150	A	151	ILE	0	0.024	0.019	16.063	0.047	0.047	0.000	0.000	0.000	0.000
151	A	152	VAL	0	0.033	0.021	15.876	0.124	0.124	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.835	0.915	11.674	2.123	2.123	0.000	0.000	0.000	0.000
153	A	154	GLN	0	-0.039	-0.017	10.879	-1.002	-1.002	0.000	0.000	0.000	0.000
154	A	155	ARG	1	0.823	0.874	11.575	-2.983	-2.983	0.000	0.000	0.000	0.000
155	A	156	GLN	0	0.010	0.005	12.937	-0.302	-0.302	0.000	0.000	0.000	0.000
156	A	157	GLU	-1	-0.816	-0.904	7.588	-5.786	-5.786	0.000	0.000	0.000	0.000
157	A	158	GLU	-1	-0.881	-0.932	8.239	3.542	3.542	0.000	0.000	0.000	0.000
158	A	159	LEU	0	0.005	0.014	9.542	0.230	0.230	0.000	0.000	0.000	0.000
159	A	161	LEU	0	0.052	0.031	9.779	-0.246	-0.246	0.000	0.000	0.000	0.000
160	A	162	ALA	0	-0.025	-0.002	10.878	0.275	0.275	0.000	0.000	0.000	0.000
161	A	163	ARG	1	0.776	0.853	9.403	4.581	4.581	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.012	0.021	13.366	0.446	0.446	0.000	0.000	0.000	0.000
163	A	165	TYR	0	-0.014	-0.016	15.498	0.136	0.136	0.000	0.000	0.000	0.000
164	A	166	ARG	1	0.923	0.958	19.757	0.997	0.997	0.000	0.000	0.000	0.000
165	A	167	LEU	0	0.022	0.005	23.346	0.069	0.069	0.000	0.000	0.000	0.000
166	A	168	ILE	0	-0.032	-0.004	25.825	-0.055	-0.055	0.000	0.000	0.000	0.000
167	A	169	VAL	0	-0.012	0.000	28.796	0.035	0.035	0.000	0.000	0.000	0.000
168	A	170	HIS	0	0.011	-0.009	30.618	0.019	0.019	0.000	0.000	0.000	0.000
169	A	171	ASN	0	-0.026	-0.028	34.970	0.015	0.015	0.000	0.000	0.000	0.000
170	A	172	GLY	0	0.037	0.028	38.402	0.004	0.004	0.000	0.000	0.000	0.000
171	A	173	TYR	0	-0.086	-0.059	39.446	0.001	0.001	0.000	0.000	0.000	0.000

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