FMO DATABASE

FMODB ID: LQRV9

Calculation Name: 1EPB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (9cis)-retinoic acid

Ligand 3-letter code: 9CR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EPB

Chain ID: A

ChEMBL ID:

UniProt ID: P06911

Base Structure: X-ray

Registration Date: 2025-09-02

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1572738.093783
FMO2-HF: Nuclear repulsion	1509945.809095
FMO2-HF: Total energy	-62792.284688
FMO2-MP2: Total energy	-62974.566399

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:3:VAL)

Summations of interaction energy for fragment #1(A:3:VAL)

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.
-186.021	-170.991	14.308	-11.682	-17.658	-0.126

Interaction energy analysis for fragmet #1(A:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / 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	5	ASP	-1	-0.840	-0.918	3.334	-35.849	-34.093	0.074	-0.673	-1.158	-0.002
4	A	6	PHE	0	-0.005	-0.006	2.277	-8.545	-6.487	2.636	-1.468	-3.227	-0.013
5	A	7	ASP	-1	-0.752	-0.849	3.736	-20.101	-20.012	0.016	-0.016	-0.089	0.000
71	A	73	PRO	0	-0.012	0.011	4.486	-1.675	-1.493	-0.001	-0.030	-0.151	0.000
72	A	74	ALA	0	-0.009	-0.012	2.532	0.061	1.005	0.973	-0.654	-1.264	-0.004
73	A	75	LYS	1	0.884	0.965	4.405	31.648	31.838	-0.001	-0.032	-0.157	0.000
86	A	88	VAL	0	0.020	0.008	4.174	-1.268	-1.214	-0.001	-0.007	-0.046	0.000
87	A	89	VAL	0	0.017	0.012	2.559	2.347	3.309	0.808	-0.390	-1.380	-0.002
88	A	90	GLU	-1	-0.876	-0.925	2.267	-85.649	-82.494	4.405	-3.927	-3.633	-0.048
89	A	91	ALA	0	-0.022	-0.022	2.406	-26.153	-21.642	1.575	-3.139	-2.947	-0.041
90	A	92	THR	0	-0.008	-0.030	2.249	3.668	3.759	1.432	-0.229	-1.294	-0.002
91	A	93	ASP	-1	-0.753	-0.833	4.646	-27.064	-26.994	-0.001	-0.003	-0.066	0.000
92	A	94	TYR	0	-0.116	-0.078	2.552	-1.349	-0.381	2.393	-1.114	-2.246	-0.014
6	A	8	ILE	0	0.043	0.015	7.351	0.109	0.109	0.000	0.000	0.000	0.000
7	A	9	SER	0	-0.016	-0.027	8.913	1.426	1.426	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.824	0.903	7.807	24.495	24.495	0.000	0.000	0.000	0.000
9	A	11	PHE	0	-0.021	-0.016	4.991	-0.131	-0.131	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.025	0.038	10.172	0.696	0.696	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.029	0.027	13.801	0.126	0.126	0.000	0.000	0.000	0.000
12	A	14	PHE	0	0.001	-0.007	15.695	-0.619	-0.619	0.000	0.000	0.000	0.000
13	A	15	TRP	0	-0.040	-0.006	9.089	-1.039	-1.039	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.015	0.000	15.253	0.792	0.792	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.829	-0.903	15.281	-18.550	-18.550	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.023	-0.011	15.466	1.116	1.116	0.000	0.000	0.000	0.000
17	A	19	ALA	0	0.005	-0.012	15.624	1.012	1.012	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.018	0.007	15.083	-1.357	-1.357	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.005	0.013	15.244	0.820	0.820	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.006	-0.022	16.865	-0.783	-0.783	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.867	0.918	19.647	14.468	14.468	0.000	0.000	0.000	0.000
22	A	24	MET	0	-0.007	-0.017	21.707	0.336	0.336	0.000	0.000	0.000	0.000
23	A	25	GLY	0	-0.010	0.019	23.109	0.494	0.494	0.000	0.000	0.000	0.000
24	A	26	THR	0	-0.011	-0.001	22.918	-0.611	-0.611	0.000	0.000	0.000	0.000
25	A	27	PRO	0	0.017	0.007	24.600	0.402	0.402	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.034	0.018	26.357	0.388	0.388	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.017	0.002	26.342	0.231	0.231	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.004	0.018	28.409	0.279	0.279	0.000	0.000	0.000	0.000
29	A	31	HIS	0	-0.068	-0.041	26.837	0.633	0.633	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.838	0.914	32.330	8.970	8.970	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.872	-0.937	31.045	-9.580	-9.580	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.801	-0.896	24.704	-12.288	-12.288	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.786	0.874	25.865	10.397	10.397	0.000	0.000	0.000	0.000
34	A	36	MET	0	-0.067	-0.009	20.194	-0.386	-0.386	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.052	0.027	20.039	0.354	0.354	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.053	-0.030	18.066	-0.192	-0.192	0.000	0.000	0.000	0.000
37	A	39	MET	0	-0.025	-0.016	13.171	-0.215	-0.215	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.022	0.020	17.024	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.024	-0.003	11.966	-0.114	-0.114	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.908	-0.961	15.242	-13.618	-13.618	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.012	-0.008	14.381	-0.815	-0.815	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.951	0.968	17.132	13.407	13.407	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.891	-0.949	20.195	-12.612	-12.612	0.000	0.000	0.000	0.000
44	A	46	ASN	0	-0.069	-0.044	17.823	-0.127	-0.127	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.006	0.026	16.489	-1.018	-1.018	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.017	0.011	11.068	0.181	0.181	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.019	-0.010	15.269	0.280	0.280	0.000	0.000	0.000	0.000
48	A	50	LEU	0	-0.004	-0.008	13.844	-0.730	-0.730	0.000	0.000	0.000	0.000
49	A	51	THR	0	0.027	0.018	17.682	0.874	0.874	0.000	0.000	0.000	0.000
50	A	52	THR	0	-0.031	-0.018	17.111	-0.535	-0.535	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.013	-0.011	19.905	0.842	0.842	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.018	-0.033	20.948	-0.503	-0.503	0.000	0.000	0.000	0.000
53	A	55	TYR	0	-0.039	-0.035	23.042	0.607	0.607	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.024	-0.048	25.718	-0.502	-0.502	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.854	-0.905	28.204	-9.892	-9.892	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.839	-0.893	31.873	-8.566	-8.566	0.000	0.000	0.000	0.000
57	A	59	HIS	1	0.844	0.928	30.129	10.223	10.223	0.000	0.000	0.000	0.000
58	A	60	CYS	0	0.007	-0.004	24.909	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.030	-0.005	25.008	0.365	0.365	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.028	0.020	24.595	-0.306	-0.306	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.866	-0.920	21.559	-14.501	-14.501	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.988	1.009	21.577	11.000	11.000	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.066	-0.051	18.727	0.380	0.380	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.036	-0.026	18.277	0.309	0.309	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.040	-0.015	13.857	0.150	0.150	0.000	0.000	0.000	0.000
66	A	68	THR	0	0.026	0.023	15.316	0.673	0.673	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.886	-0.945	10.925	-22.352	-22.352	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.057	-0.038	10.774	2.169	2.169	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.941	-0.991	9.995	-30.946	-30.946	0.000	0.000	0.000	0.000
70	A	72	GLY	0	0.042	0.021	9.701	-1.244	-1.244	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.048	0.024	6.453	3.227	3.227	0.000	0.000	0.000	0.000
75	A	77	GLN	0	0.020	-0.002	10.452	1.675	1.675	0.000	0.000	0.000	0.000
76	A	78	VAL	0	0.018	0.010	13.783	1.209	1.209	0.000	0.000	0.000	0.000
77	A	79	THR	0	-0.028	-0.021	16.719	-0.094	-0.094	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.947	0.978	20.051	14.493	14.493	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.015	-0.013	22.983	-0.028	-0.028	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.001	0.008	24.598	0.206	0.206	0.000	0.000	0.000	0.000
81	A	83	GLY	0	0.020	0.029	22.953	0.120	0.120	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.858	0.945	16.485	18.043	18.043	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.925	0.951	15.729	16.617	16.617	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.840	-0.897	10.464	-26.984	-26.984	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.029	-0.023	9.684	0.446	0.446	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.045	-0.010	7.146	2.143	2.143	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.041	-0.052	10.412	1.336	1.336	0.000	0.000	0.000	0.000
95	A	97	TYR	0	0.016	-0.002	7.390	-0.188	-0.188	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.019	0.017	6.110	-3.269	-3.269	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.021	0.002	6.081	3.421	3.421	0.000	0.000	0.000	0.000
98	A	100	ILE	0	-0.046	-0.026	5.585	-6.794	-6.794	0.000	0.000	0.000	0.000
99	A	101	ASP	-1	-0.813	-0.917	7.946	-25.017	-25.017	0.000	0.000	0.000	0.000
100	A	102	ILE	0	0.007	0.000	9.602	-0.888	-0.888	0.000	0.000	0.000	0.000
101	A	103	THR	0	0.008	0.014	12.409	2.059	2.059	0.000	0.000	0.000	0.000
102	A	104	SER	0	-0.017	-0.019	14.608	-0.043	-0.043	0.000	0.000	0.000	0.000
103	A	105	LEU	0	-0.040	-0.008	17.796	0.464	0.464	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.013	-0.005	21.103	0.103	0.103	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.014	-0.002	23.919	0.366	0.366	0.000	0.000	0.000	0.000
106	A	108	GLY	0	0.026	0.016	25.448	0.415	0.415	0.000	0.000	0.000	0.000
107	A	109	ALA	0	-0.011	0.002	25.346	-0.154	-0.154	0.000	0.000	0.000	0.000
108	A	110	VAL	0	0.006	0.004	19.482	-0.453	-0.453	0.000	0.000	0.000	0.000
109	A	111	HIS	0	-0.012	-0.012	19.696	0.026	0.026	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.929	0.956	16.084	15.468	15.468	0.000	0.000	0.000	0.000
111	A	113	THR	0	-0.018	0.003	15.085	1.291	1.291	0.000	0.000	0.000	0.000
112	A	114	MET	0	-0.016	0.019	9.507	-0.714	-0.714	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.843	0.897	11.141	20.452	20.452	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.004	0.020	10.361	-2.745	-2.745	0.000	0.000	0.000	0.000
115	A	117	TYR	0	-0.007	-0.014	10.612	1.871	1.871	0.000	0.000	0.000	0.000
116	A	118	SER	0	0.024	-0.019	10.813	-1.672	-1.672	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.828	0.896	11.909	20.767	20.767	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.037	0.020	14.705	1.199	1.199	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.031	0.020	17.441	-0.480	-0.480	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.937	-0.973	19.978	-12.538	-12.538	0.000	0.000	0.000	0.000
121	A	123	ASP	-1	-0.940	-0.977	18.631	-15.116	-15.116	0.000	0.000	0.000	0.000
122	A	124	ASN	0	0.006	0.024	15.532	-1.559	-1.559	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.021	0.011	16.094	-0.706	-0.706	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.874	-0.939	13.040	-19.111	-19.111	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.024	0.007	11.655	-1.078	-1.078	0.000	0.000	0.000	0.000
126	A	128	LEU	0	0.008	-0.008	12.536	-0.968	-0.968	0.000	0.000	0.000	0.000
127	A	129	TYR	0	-0.023	-0.002	15.309	-0.092	-0.092	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.021	-0.005	10.213	0.267	0.267	0.000	0.000	0.000	0.000
129	A	131	PHE	0	0.014	0.009	10.869	-1.088	-1.088	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.943	0.989	12.331	15.088	15.088	0.000	0.000	0.000	0.000
131	A	133	LYS	1	0.916	0.987	13.305	21.211	21.211	0.000	0.000	0.000	0.000
132	A	134	ILE	0	0.085	0.055	7.400	0.216	0.216	0.000	0.000	0.000	0.000
133	A	135	THR	0	-0.031	-0.055	11.226	0.267	0.267	0.000	0.000	0.000	0.000
134	A	136	SER	0	-0.072	-0.034	13.623	0.865	0.865	0.000	0.000	0.000	0.000
135	A	137	ASP	-1	-0.907	-0.958	11.835	-22.624	-22.624	0.000	0.000	0.000	0.000
136	A	138	HIS	1	0.739	0.858	8.168	31.776	31.776	0.000	0.000	0.000	0.000
137	A	139	GLY	0	-0.018	0.001	13.512	0.674	0.674	0.000	0.000	0.000	0.000
138	A	140	PHE	0	-0.081	-0.037	14.210	1.239	1.239	0.000	0.000	0.000	0.000
139	A	141	SER	0	-0.048	-0.053	18.132	0.263	0.263	0.000	0.000	0.000	0.000
140	A	142	GLU	-1	-0.902	-0.970	20.736	-13.464	-13.464	0.000	0.000	0.000	0.000
141	A	143	THR	0	-0.016	-0.016	22.006	0.005	0.005	0.000	0.000	0.000	0.000
142	A	144	ASP	-1	-0.760	-0.836	20.081	-13.968	-13.968	0.000	0.000	0.000	0.000
143	A	145	LEU	0	-0.020	-0.008	16.835	-0.759	-0.759	0.000	0.000	0.000	0.000
144	A	146	TYR	0	0.004	0.006	19.391	1.109	1.109	0.000	0.000	0.000	0.000
145	A	147	ILE	0	0.004	-0.005	19.293	-0.784	-0.784	0.000	0.000	0.000	0.000
146	A	148	LEU	0	-0.016	0.003	18.704	0.751	0.751	0.000	0.000	0.000	0.000
147	A	149	LYS	1	0.890	0.939	22.030	10.511	10.511	0.000	0.000	0.000	0.000
148	A	150	HIS	1	0.835	0.911	21.436	12.992	12.992	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.772	-0.845	25.480	-9.912	-9.912	0.000	0.000	0.000	0.000
150	A	152	LEU	0	0.035	-0.011	24.667	-0.367	-0.367	0.000	0.000	0.000	0.000
151	A	153	THR	0	-0.047	-0.035	26.756	0.071	0.071	0.000	0.000	0.000	0.000
152	A	155	VAL	0	0.028	0.022	21.998	-0.112	-0.112	0.000	0.000	0.000	0.000
153	A	156	LYS	1	0.941	0.958	24.180	9.984	9.984	0.000	0.000	0.000	0.000
154	A	157	VAL	0	0.005	0.020	27.399	0.186	0.186	0.000	0.000	0.000	0.000
155	A	158	LEU	0	0.037	0.040	20.181	0.070	0.070	0.000	0.000	0.000	0.000
156	A	159	GLN	0	-0.059	-0.038	23.523	-0.441	-0.441	0.000	0.000	0.000	0.000
157	A	160	SER	0	-0.124	-0.061	25.201	0.287	0.287	0.000	0.000	0.000	0.000
158	A	161	ALA	0	-0.026	-0.026	27.346	0.331	0.331	0.000	0.000	0.000	0.000
159	A	162	ALA	-1	-0.864	-0.924	24.943	-12.270	-12.270	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL)