FMO DATABASE

FMODB ID: 4K3NN

Calculation Name: 2YG2-B-Xray549

Preferred Name:

Target Type:

Ligand Name: citrate anion | (2s,3r,4e)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate

Ligand 3-letter code: FLC | S1P

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YG2

Chain ID: B

ChEMBL ID:

UniProt ID: O95445

Base Structure: X-ray

Registration Date: 2025-10-12

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1544997.932184
FMO2-HF: Nuclear repulsion	1481956.373116
FMO2-HF: Total energy	-63041.559068
FMO2-MP2: Total energy	-63220.397185

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(B:29:LEU)

Summations of interaction energy for fragment #1(B:29:LEU)

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.
-92.584	-84.657	8.684	-4.083	-12.527	-0.034

Interaction energy analysis for fragmet #1(B:29:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.927

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	B	31	THR	0	0.056	0.023	3.864	1.620	3.445	-0.013	-0.657	-1.156	-0.001
4	B	32	LEU	0	-0.025	-0.011	5.014	1.754	1.805	-0.001	-0.005	-0.044	0.000
96	B	124	PHE	0	0.013	-0.011	2.309	-9.362	-7.583	6.865	-2.132	-6.511	-0.027
97	B	125	SER	0	-0.031	-0.018	4.444	5.532	5.669	-0.001	-0.013	-0.123	0.000
98	B	126	SER	0	-0.052	-0.015	3.989	-5.391	-5.118	0.001	-0.049	-0.226	0.000
105	B	133	MET	0	0.003	0.011	2.761	-0.396	0.383	0.478	-0.179	-1.079	0.000
107	B	135	ASN	0	-0.038	-0.013	4.082	-0.975	-0.834	-0.001	-0.012	-0.128	0.000
116	B	144	PHE	0	0.027	0.023	2.768	-2.845	-2.032	0.371	-0.310	-0.873	-0.002
135	B	164	LEU	0	-0.020	-0.012	2.384	-4.303	-3.065	0.813	-0.498	-1.553	-0.002
139	B	168	LEU	0	-0.045	-0.009	2.870	-3.565	-2.674	0.172	-0.228	-0.834	-0.002
5	B	33	GLY	0	0.001	-0.006	8.293	1.050	1.050	0.000	0.000	0.000	0.000
6	B	34	VAL	0	-0.014	-0.009	10.783	1.024	1.024	0.000	0.000	0.000	0.000
7	B	35	ASP	-1	-0.746	-0.859	13.480	-16.105	-16.105	0.000	0.000	0.000	0.000
8	B	36	GLY	0	0.027	0.007	16.681	0.769	0.769	0.000	0.000	0.000	0.000
9	B	37	LYS	1	0.780	0.896	19.264	14.667	14.667	0.000	0.000	0.000	0.000
10	B	38	GLU	-1	-0.816	-0.909	18.854	-13.762	-13.762	0.000	0.000	0.000	0.000
11	B	39	PHE	0	-0.040	-0.036	11.746	-0.130	-0.130	0.000	0.000	0.000	0.000
12	B	40	PRO	0	-0.011	-0.022	16.798	-0.086	-0.086	0.000	0.000	0.000	0.000
13	B	41	GLU	-1	-0.895	-0.929	19.165	-11.704	-11.704	0.000	0.000	0.000	0.000
14	B	42	VAL	0	-0.025	-0.015	16.341	-0.018	-0.018	0.000	0.000	0.000	0.000
15	B	43	HIS	1	0.801	0.892	12.614	18.232	18.232	0.000	0.000	0.000	0.000
16	B	44	LEU	0	0.055	0.053	17.058	0.016	0.016	0.000	0.000	0.000	0.000
17	B	45	GLY	0	0.035	0.033	20.004	-0.279	-0.279	0.000	0.000	0.000	0.000
18	B	46	GLN	0	0.003	-0.014	19.957	-0.234	-0.234	0.000	0.000	0.000	0.000
19	B	47	TRP	0	-0.050	-0.017	13.042	-0.973	-0.973	0.000	0.000	0.000	0.000
20	B	48	TYR	0	0.024	0.017	16.314	0.756	0.756	0.000	0.000	0.000	0.000
21	B	49	PHE	0	-0.010	-0.002	12.330	-0.788	-0.788	0.000	0.000	0.000	0.000
22	B	50	ILE	0	-0.043	0.000	13.158	0.856	0.856	0.000	0.000	0.000	0.000
23	B	51	ALA	0	0.037	0.014	11.656	0.687	0.687	0.000	0.000	0.000	0.000
24	B	52	GLY	0	0.003	0.008	11.220	-1.057	-1.057	0.000	0.000	0.000	0.000
25	B	53	ALA	0	-0.011	-0.005	8.847	0.764	0.764	0.000	0.000	0.000	0.000
26	B	54	ALA	0	0.019	0.007	9.714	-1.318	-1.318	0.000	0.000	0.000	0.000
27	B	55	PRO	0	0.022	0.021	10.710	0.190	0.190	0.000	0.000	0.000	0.000
28	B	56	THR	0	-0.069	-0.048	13.187	1.099	1.099	0.000	0.000	0.000	0.000
29	B	57	LYS	1	0.906	0.917	15.863	11.889	11.889	0.000	0.000	0.000	0.000
30	B	58	GLU	-1	-0.812	-0.900	18.293	-13.026	-13.026	0.000	0.000	0.000	0.000
31	B	59	GLU	-1	-0.747	-0.852	14.088	-17.730	-17.730	0.000	0.000	0.000	0.000
32	B	60	LEU	0	-0.046	-0.016	12.745	-0.545	-0.545	0.000	0.000	0.000	0.000
33	B	61	ALA	0	0.058	0.039	16.693	0.272	0.272	0.000	0.000	0.000	0.000
34	B	62	THR	0	-0.096	-0.041	17.982	0.360	0.360	0.000	0.000	0.000	0.000
35	B	63	PHE	0	0.013	-0.008	14.733	0.313	0.313	0.000	0.000	0.000	0.000
36	B	64	ASP	-1	-0.827	-0.899	19.957	-12.733	-12.733	0.000	0.000	0.000	0.000
37	B	65	PRO	0	-0.059	-0.028	22.681	0.325	0.325	0.000	0.000	0.000	0.000
38	B	66	VAL	0	-0.012	-0.002	20.929	0.381	0.381	0.000	0.000	0.000	0.000
39	B	67	ASP	-1	-0.796	-0.898	23.052	-11.537	-11.537	0.000	0.000	0.000	0.000
40	B	68	ASN	0	-0.056	-0.063	20.895	-0.676	-0.676	0.000	0.000	0.000	0.000
41	B	69	ILE	0	0.025	0.007	17.904	0.315	0.315	0.000	0.000	0.000	0.000
42	B	70	VAL	0	0.019	0.034	19.351	-0.665	-0.665	0.000	0.000	0.000	0.000
43	B	71	PHE	0	0.041	-0.003	17.048	0.280	0.280	0.000	0.000	0.000	0.000
44	B	72	ASN	0	0.023	-0.006	19.745	-0.097	-0.097	0.000	0.000	0.000	0.000
45	B	73	MET	0	-0.049	0.006	17.310	0.298	0.298	0.000	0.000	0.000	0.000
46	B	74	ALA	0	0.012	0.004	20.271	0.291	0.291	0.000	0.000	0.000	0.000
47	B	75	ALA	0	0.046	0.011	20.995	-0.168	-0.168	0.000	0.000	0.000	0.000
48	B	76	GLY	0	0.027	0.011	23.125	0.397	0.397	0.000	0.000	0.000	0.000
49	B	77	SER	0	-0.020	-0.014	23.379	0.050	0.050	0.000	0.000	0.000	0.000
50	B	78	ALA	0	0.025	0.011	24.504	-0.061	-0.061	0.000	0.000	0.000	0.000
51	B	79	PRO	0	-0.018	-0.007	25.891	0.118	0.118	0.000	0.000	0.000	0.000
52	B	80	MET	0	-0.011	0.009	21.713	-0.185	-0.185	0.000	0.000	0.000	0.000
53	B	81	GLN	0	-0.059	-0.049	21.187	-0.995	-0.995	0.000	0.000	0.000	0.000
54	B	82	LEU	0	0.001	-0.002	16.580	0.011	0.011	0.000	0.000	0.000	0.000
55	B	83	HIS	0	-0.031	-0.012	20.550	0.055	0.055	0.000	0.000	0.000	0.000
56	B	84	LEU	0	-0.002	0.005	16.945	-0.157	-0.157	0.000	0.000	0.000	0.000
57	B	85	ARG	1	0.840	0.895	20.796	10.648	10.648	0.000	0.000	0.000	0.000
58	B	86	ALA	0	0.027	0.003	20.460	-0.589	-0.589	0.000	0.000	0.000	0.000
59	B	87	THR	0	-0.040	-0.034	22.499	0.417	0.417	0.000	0.000	0.000	0.000
60	B	88	ILE	0	-0.023	-0.008	21.780	-0.316	-0.316	0.000	0.000	0.000	0.000
61	B	89	ARG	1	0.892	0.949	24.049	10.282	10.282	0.000	0.000	0.000	0.000
62	B	90	MET	0	0.006	-0.002	25.016	-0.584	-0.584	0.000	0.000	0.000	0.000
63	B	91	LYS	1	0.874	0.917	23.523	11.924	11.924	0.000	0.000	0.000	0.000
64	B	92	ASP	-1	-0.895	-0.947	28.259	-9.139	-9.139	0.000	0.000	0.000	0.000
65	B	93	GLY	0	0.029	0.022	30.229	0.287	0.287	0.000	0.000	0.000	0.000
66	B	94	LEU	0	-0.045	-0.011	30.751	0.048	0.048	0.000	0.000	0.000	0.000
67	B	95	CYS	0	-0.041	-0.016	25.995	0.065	0.065	0.000	0.000	0.000	0.000
68	B	96	VAL	0	0.000	-0.005	26.712	0.283	0.283	0.000	0.000	0.000	0.000
69	B	97	PRO	0	0.019	0.011	26.251	-0.437	-0.437	0.000	0.000	0.000	0.000
70	B	98	ARG	1	0.872	0.942	21.915	11.862	11.862	0.000	0.000	0.000	0.000
71	B	99	LYS	1	0.964	0.970	24.018	9.759	9.759	0.000	0.000	0.000	0.000
72	B	100	TRP	0	-0.031	-0.014	19.332	0.067	0.067	0.000	0.000	0.000	0.000
73	B	101	ILE	0	-0.004	0.018	21.814	0.097	0.097	0.000	0.000	0.000	0.000
74	B	102	TYR	0	-0.018	-0.011	14.196	0.265	0.265	0.000	0.000	0.000	0.000
75	B	103	HIS	0	0.029	0.018	18.722	0.117	0.117	0.000	0.000	0.000	0.000
76	B	104	LEU	0	0.033	0.015	15.981	-0.799	-0.799	0.000	0.000	0.000	0.000
77	B	105	THR	0	-0.044	-0.036	17.895	0.682	0.682	0.000	0.000	0.000	0.000
78	B	106	GLU	-1	-0.814	-0.916	18.292	-14.175	-14.175	0.000	0.000	0.000	0.000
79	B	107	GLY	0	-0.017	-0.004	17.420	0.332	0.332	0.000	0.000	0.000	0.000
80	B	108	SER	0	-0.068	-0.023	14.716	-0.561	-0.561	0.000	0.000	0.000	0.000
81	B	109	THR	0	-0.003	-0.010	9.864	-0.070	-0.070	0.000	0.000	0.000	0.000
82	B	110	ASP	-1	-0.943	-0.962	11.146	-21.989	-21.989	0.000	0.000	0.000	0.000
83	B	111	LEU	0	0.006	-0.003	11.991	1.568	1.568	0.000	0.000	0.000	0.000
84	B	112	ARG	1	0.935	0.975	13.823	15.356	15.356	0.000	0.000	0.000	0.000
85	B	113	THR	0	0.036	-0.007	16.161	0.119	0.119	0.000	0.000	0.000	0.000
86	B	114	GLU	-1	-0.844	-0.925	18.484	-10.846	-10.846	0.000	0.000	0.000	0.000
87	B	115	GLY	0	-0.022	-0.019	22.316	0.036	0.036	0.000	0.000	0.000	0.000
88	B	116	ARG	1	0.859	0.924	18.572	13.251	13.251	0.000	0.000	0.000	0.000
89	B	117	PRO	0	0.019	0.011	19.237	-0.547	-0.547	0.000	0.000	0.000	0.000
90	B	118	ASP	-1	-0.854	-0.943	17.740	-15.117	-15.117	0.000	0.000	0.000	0.000
91	B	119	MET	0	-0.067	0.009	14.416	-0.140	-0.140	0.000	0.000	0.000	0.000
92	B	120	LYS	1	0.872	0.955	11.424	17.366	17.366	0.000	0.000	0.000	0.000
93	B	121	THR	0	0.008	-0.001	9.911	-0.528	-0.528	0.000	0.000	0.000	0.000
94	B	122	GLU	-1	-0.853	-0.907	5.809	-32.777	-32.777	0.000	0.000	0.000	0.000
95	B	123	LEU	0	0.010	0.000	6.953	-0.391	-0.391	0.000	0.000	0.000	0.000
99	B	127	SER	0	-0.016	-0.035	6.533	-1.561	-1.561	0.000	0.000	0.000	0.000
100	B	128	CYS	0	-0.030	0.011	7.849	1.017	1.017	0.000	0.000	0.000	0.000
101	B	129	PRO	0	0.060	0.009	10.948	-0.427	-0.427	0.000	0.000	0.000	0.000
102	B	130	GLY	0	0.026	0.013	13.614	0.405	0.405	0.000	0.000	0.000	0.000
103	B	131	GLY	0	0.016	0.008	10.604	0.827	0.827	0.000	0.000	0.000	0.000
104	B	132	ILE	0	-0.061	-0.037	8.062	-0.520	-0.520	0.000	0.000	0.000	0.000
106	B	134	LEU	0	0.012	0.003	5.729	-0.223	-0.223	0.000	0.000	0.000	0.000
108	B	136	GLU	-1	-0.816	-0.902	6.027	-16.418	-16.418	0.000	0.000	0.000	0.000
109	B	137	THR	0	-0.008	-0.008	9.212	0.082	0.082	0.000	0.000	0.000	0.000
110	B	138	GLY	0	0.022	0.002	11.857	0.631	0.631	0.000	0.000	0.000	0.000
111	B	139	GLN	0	-0.007	-0.006	15.609	-0.127	-0.127	0.000	0.000	0.000	0.000
112	B	140	GLY	0	-0.031	-0.012	18.130	0.336	0.336	0.000	0.000	0.000	0.000
113	B	141	TYR	0	-0.045	-0.021	13.088	0.019	0.019	0.000	0.000	0.000	0.000
114	B	142	GLN	0	-0.015	-0.020	6.895	0.821	0.821	0.000	0.000	0.000	0.000
115	B	143	ARG	1	0.760	0.860	9.678	17.581	17.581	0.000	0.000	0.000	0.000
117	B	145	LEU	0	-0.047	-0.022	7.297	2.395	2.395	0.000	0.000	0.000	0.000
118	B	146	LEU	0	-0.009	0.006	7.884	-1.851	-1.851	0.000	0.000	0.000	0.000
119	B	147	TYR	0	0.038	0.006	9.433	2.629	2.629	0.000	0.000	0.000	0.000
120	B	148	ASN	0	-0.020	-0.015	11.218	-0.392	-0.392	0.000	0.000	0.000	0.000
121	B	149	ARG	1	0.845	0.912	13.930	15.962	15.962	0.000	0.000	0.000	0.000
122	B	150	SER	0	-0.025	-0.003	17.070	1.021	1.021	0.000	0.000	0.000	0.000
123	B	151	PRO	0	0.044	0.027	17.635	-0.730	-0.730	0.000	0.000	0.000	0.000
124	B	152	HIS	0	0.019	-0.009	19.417	-0.415	-0.415	0.000	0.000	0.000	0.000
125	B	153	PRO	0	-0.032	-0.006	15.283	0.227	0.227	0.000	0.000	0.000	0.000
126	B	154	PRO	0	0.024	-0.006	16.585	0.188	0.188	0.000	0.000	0.000	0.000
127	B	155	GLU	-1	-0.860	-0.930	16.045	-16.434	-16.434	0.000	0.000	0.000	0.000
128	B	156	LYS	1	0.933	0.962	14.584	18.456	18.456	0.000	0.000	0.000	0.000
129	B	158	VAL	0	0.050	0.034	10.773	-1.862	-1.862	0.000	0.000	0.000	0.000
130	B	159	GLU	-1	-0.868	-0.955	11.541	-20.065	-20.065	0.000	0.000	0.000	0.000
131	B	160	GLU	-1	-0.902	-0.907	9.113	-26.731	-26.731	0.000	0.000	0.000	0.000
132	B	161	PHE	0	0.032	0.012	6.054	-3.293	-3.293	0.000	0.000	0.000	0.000
133	B	162	LYS	1	0.937	0.999	7.562	16.881	16.881	0.000	0.000	0.000	0.000
134	B	163	SER	0	-0.046	-0.032	10.095	0.696	0.696	0.000	0.000	0.000	0.000
136	B	165	THR	0	-0.022	-0.038	5.737	-1.032	-1.032	0.000	0.000	0.000	0.000
137	B	166	SER	0	0.004	0.010	7.227	1.246	1.246	0.000	0.000	0.000	0.000
138	B	167	CYS	0	-0.079	-0.054	7.608	2.433	2.433	0.000	0.000	0.000	0.000
140	B	169	ASP	-1	-0.876	-0.941	7.318	-22.064	-22.064	0.000	0.000	0.000	0.000
141	B	170	SER	0	-0.005	0.012	8.132	1.145	1.145	0.000	0.000	0.000	0.000
142	B	171	LYS	1	0.831	0.902	9.957	21.759	21.759	0.000	0.000	0.000	0.000
143	B	172	ALA	0	-0.041	0.015	13.043	1.051	1.051	0.000	0.000	0.000	0.000
144	B	173	PHE	0	0.032	-0.009	10.895	-0.980	-0.980	0.000	0.000	0.000	0.000
145	B	174	LEU	0	-0.012	0.001	14.288	1.145	1.145	0.000	0.000	0.000	0.000
146	B	175	LEU	0	0.001	0.002	14.710	-1.084	-1.084	0.000	0.000	0.000	0.000
147	B	176	THR	0	-0.015	-0.019	16.865	0.790	0.790	0.000	0.000	0.000	0.000
148	B	177	PRO	0	-0.054	-0.020	19.042	-0.168	-0.168	0.000	0.000	0.000	0.000
149	B	178	ARG	1	0.801	0.892	18.715	14.645	14.645	0.000	0.000	0.000	0.000
150	B	179	ASN	0	0.014	0.009	23.089	0.058	0.058	0.000	0.000	0.000	0.000
151	B	180	GLN	0	-0.049	-0.018	26.453	0.586	0.586	0.000	0.000	0.000	0.000
152	B	181	GLU	-1	-0.900	-0.944	26.472	-9.582	-9.582	0.000	0.000	0.000	0.000
153	B	182	ALA	0	0.002	0.013	24.633	-0.160	-0.160	0.000	0.000	0.000	0.000
154	B	184	GLU	-1	-0.869	-0.934	27.170	-9.495	-9.495	0.000	0.000	0.000	0.000
155	B	185	LEU	-1	-0.887	-0.906	22.897	-10.333	-10.333	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:29:LEU)