FMO DATABASE

FMODB ID: 3K4ML

Calculation Name: 1HN4-A-Xray547

Preferred Name: Phospholipase A2 group 1B

Target Type: SINGLE PROTEIN

Ligand Name: 1-hexadecyl-3-trifluoroethyl-sn-glycero-2-phosphate methane

Ligand 3-letter code: MJI

Ligand of Interest (LOI):

PDB ID: 1HN4

Chain ID: A

ChEMBL ID: CHEMBL4715

UniProt ID: P00592

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1105905.070519
FMO2-HF: Nuclear repulsion	1051230.905868
FMO2-HF: Total energy	-54674.164651
FMO2-MP2: Total energy	-54820.559621

3D Structure

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:-5:GLY)

Summations of interaction energy for fragment #1(A:-5:GLY)

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.
5.203	7.521	5.185	-4.15	-3.35	-0.022

Interaction energy analysis for fragmet #1(A:-5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.901 / q_NPA : 0.943

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

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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	SER	0	0.049	0.021	3.854	0.570	1.289	-0.011	-0.332	-0.376	0.000
56	A	52	TYR	0	-0.001	-0.042	4.037	0.264	0.655	-0.001	-0.189	-0.200	0.000
60	A	56	LYS	1	0.877	0.935	3.025	67.321	67.785	0.063	-0.163	-0.363	-0.001
68	A	64	LEU	0	-0.075	-0.042	3.880	-2.534	-2.441	0.000	-0.027	-0.066	0.000
69	A	65	VAL	0	-0.063	-0.021	3.208	-16.357	-15.020	0.078	-0.635	-0.780	-0.005
70	A	66	ASP	-1	-0.881	-0.938	4.902	-37.343	-37.227	-0.001	-0.015	-0.100	0.000
72	A	68	PRO	0	0.021	0.008	2.096	-0.651	-1.453	5.058	-2.762	-1.494	-0.016
73	A	69	TYR	0	-0.006	-0.003	4.544	1.776	1.776	-0.001	-0.027	0.029	0.000
4	A	-2	SER	0	0.058	0.011	6.701	1.062	1.062	0.000	0.000	0.000	0.000
5	A	-1	ARG	1	0.854	0.931	10.003	25.869	25.869	0.000	0.000	0.000	0.000
6	A	1	ALA	0	0.048	0.029	8.196	1.997	1.997	0.000	0.000	0.000	0.000
7	A	2	LEU	0	0.015	0.007	8.188	2.245	2.245	0.000	0.000	0.000	0.000
8	A	3	TRP	0	0.010	-0.006	11.397	2.153	2.153	0.000	0.000	0.000	0.000
9	A	4	GLN	0	0.009	0.011	13.726	2.480	2.480	0.000	0.000	0.000	0.000
10	A	5	PHE	0	0.061	0.037	12.974	1.168	1.168	0.000	0.000	0.000	0.000
11	A	6	ARG	1	0.935	0.970	14.917	17.811	17.811	0.000	0.000	0.000	0.000
12	A	7	SER	0	-0.008	0.004	17.195	1.504	1.504	0.000	0.000	0.000	0.000
13	A	8	MET	0	0.011	0.018	17.043	0.985	0.985	0.000	0.000	0.000	0.000
14	A	9	ILE	0	0.014	0.006	16.800	0.935	0.935	0.000	0.000	0.000	0.000
15	A	10	LYS	1	0.801	0.902	20.780	13.869	13.869	0.000	0.000	0.000	0.000
16	A	11	CYS	0	-0.081	0.004	22.708	0.858	0.858	0.000	0.000	0.000	0.000
17	A	12	ALA	0	0.064	0.017	23.363	0.575	0.575	0.000	0.000	0.000	0.000
18	A	13	ILE	0	-0.010	0.003	23.247	0.465	0.465	0.000	0.000	0.000	0.000
19	A	14	PRO	0	0.054	0.033	25.988	-0.245	-0.245	0.000	0.000	0.000	0.000
20	A	15	GLY	0	-0.032	-0.015	28.457	0.146	0.146	0.000	0.000	0.000	0.000
21	A	16	SER	0	-0.010	0.002	23.878	-0.210	-0.210	0.000	0.000	0.000	0.000
22	A	17	HIS	0	0.002	-0.018	23.094	-0.454	-0.454	0.000	0.000	0.000	0.000
23	A	18	PRO	0	0.018	0.000	18.315	-0.323	-0.323	0.000	0.000	0.000	0.000
24	A	19	LEU	0	-0.011	0.006	15.501	-0.520	-0.520	0.000	0.000	0.000	0.000
25	A	20	MET	0	-0.011	-0.007	18.308	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	21	ASP	-1	-0.888	-0.946	21.593	-13.096	-13.096	0.000	0.000	0.000	0.000
27	A	22	PHE	0	0.080	0.007	18.041	0.315	0.315	0.000	0.000	0.000	0.000
28	A	23	ASN	0	-0.023	-0.004	13.458	-1.972	-1.972	0.000	0.000	0.000	0.000
29	A	24	ASN	0	-0.002	-0.014	15.566	-0.781	-0.781	0.000	0.000	0.000	0.000
30	A	25	TYR	0	-0.029	-0.027	17.998	1.391	1.391	0.000	0.000	0.000	0.000
31	A	26	GLY	0	-0.001	0.004	18.460	-0.707	-0.707	0.000	0.000	0.000	0.000
32	A	124	CYS	-1	-0.906	-0.893	18.096	-15.730	-15.730	0.000	0.000	0.000	0.000
33	A	28	TYR	0	-0.015	-0.033	13.174	-1.616	-1.616	0.000	0.000	0.000	0.000
34	A	29	CYS	0	-0.126	-0.010	13.939	-1.846	-1.846	0.000	0.000	0.000	0.000
35	A	30	GLY	0	0.051	0.014	13.545	1.330	1.330	0.000	0.000	0.000	0.000
36	A	31	LEU	0	-0.078	-0.032	7.762	-2.073	-2.073	0.000	0.000	0.000	0.000
37	A	32	GLY	0	0.000	0.003	9.092	-0.874	-0.874	0.000	0.000	0.000	0.000
38	A	33	GLY	0	0.027	0.001	9.555	1.808	1.808	0.000	0.000	0.000	0.000
39	A	34	SER	0	-0.098	-0.070	12.822	-1.258	-1.258	0.000	0.000	0.000	0.000
40	A	35	GLY	0	0.081	0.049	15.650	0.609	0.609	0.000	0.000	0.000	0.000
41	A	36	THR	0	-0.024	-0.012	18.543	-0.397	-0.397	0.000	0.000	0.000	0.000
42	A	37	PRO	0	-0.009	0.005	18.797	0.334	0.334	0.000	0.000	0.000	0.000
43	A	38	VAL	0	-0.004	-0.012	20.489	0.761	0.761	0.000	0.000	0.000	0.000
44	A	39	ASP	-1	-0.824	-0.883	23.022	-12.534	-12.534	0.000	0.000	0.000	0.000
45	A	40	GLU	-1	-0.908	-0.961	23.064	-12.252	-12.252	0.000	0.000	0.000	0.000
46	A	41	LEU	0	0.064	0.034	20.837	-0.549	-0.549	0.000	0.000	0.000	0.000
47	A	42	ASP	-1	-0.694	-0.871	18.571	-17.475	-17.475	0.000	0.000	0.000	0.000
48	A	43	ARG	1	0.962	0.986	18.187	12.075	12.075	0.000	0.000	0.000	0.000
49	A	44	CYS	0	-0.062	0.022	18.749	0.339	0.339	0.000	0.000	0.000	0.000
50	A	46	GLU	-1	-0.842	-0.910	14.030	-19.347	-19.347	0.000	0.000	0.000	0.000
51	A	47	THR	0	0.024	-0.004	14.346	-0.939	-0.939	0.000	0.000	0.000	0.000
52	A	48	HIS	1	0.763	0.872	11.328	24.946	24.946	0.000	0.000	0.000	0.000
53	A	49	ASP	-1	-0.887	-0.951	10.169	-29.971	-29.971	0.000	0.000	0.000	0.000
54	A	50	ASN	0	-0.054	-0.036	10.125	-3.625	-3.625	0.000	0.000	0.000	0.000
55	A	51	CYS	0	0.017	0.026	12.382	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	53	ARG	1	0.836	0.925	7.859	22.278	22.278	0.000	0.000	0.000	0.000
58	A	54	ASP	-1	-0.869	-0.935	9.477	-21.870	-21.870	0.000	0.000	0.000	0.000
59	A	55	ALA	0	-0.019	-0.019	8.900	0.358	0.358	0.000	0.000	0.000	0.000
61	A	57	ASN	0	-0.020	0.007	7.672	-0.710	-0.710	0.000	0.000	0.000	0.000
62	A	58	LEU	0	-0.008	0.011	11.017	2.244	2.244	0.000	0.000	0.000	0.000
63	A	59	ASP	-1	-0.825	-0.908	11.457	-20.356	-20.356	0.000	0.000	0.000	0.000
64	A	60	SER	0	-0.043	-0.026	13.214	-0.690	-0.690	0.000	0.000	0.000	0.000
65	A	61	CYS	0	-0.072	0.003	8.164	-0.912	-0.912	0.000	0.000	0.000	0.000
66	A	62	LYS	1	0.923	0.945	7.892	18.099	18.099	0.000	0.000	0.000	0.000
67	A	63	PHE	0	0.060	0.024	8.238	-1.983	-1.983	0.000	0.000	0.000	0.000
71	A	67	ASN	0	-0.021	0.001	6.333	0.383	0.383	0.000	0.000	0.000	0.000
74	A	70	THR	0	-0.050	-0.027	7.727	4.047	4.047	0.000	0.000	0.000	0.000
75	A	71	GLU	-1	-0.803	-0.886	8.914	-21.571	-21.571	0.000	0.000	0.000	0.000
76	A	72	SER	0	-0.110	-0.074	10.123	-1.282	-1.282	0.000	0.000	0.000	0.000
77	A	73	TYR	0	-0.010	-0.005	12.476	2.201	2.201	0.000	0.000	0.000	0.000
78	A	74	SER	0	-0.005	0.003	15.031	0.526	0.526	0.000	0.000	0.000	0.000
79	A	75	TYR	0	0.002	-0.036	18.649	0.026	0.026	0.000	0.000	0.000	0.000
80	A	76	SER	0	-0.051	-0.018	20.716	0.442	0.442	0.000	0.000	0.000	0.000
81	A	78	SER	0	-0.011	-0.011	25.561	0.439	0.439	0.000	0.000	0.000	0.000
82	A	79	ASN	0	0.000	-0.005	29.299	0.174	0.174	0.000	0.000	0.000	0.000
83	A	80	THR	0	-0.017	-0.013	27.707	0.181	0.181	0.000	0.000	0.000	0.000
84	A	81	GLU	-1	-0.888	-0.926	26.789	-11.638	-11.638	0.000	0.000	0.000	0.000
85	A	82	ILE	0	-0.016	-0.016	20.872	-0.238	-0.238	0.000	0.000	0.000	0.000
86	A	83	THR	0	0.004	0.009	24.126	0.238	0.238	0.000	0.000	0.000	0.000
87	A	84	CYS	0	-0.048	-0.015	12.282	0.292	0.292	0.000	0.000	0.000	0.000
88	A	85	ASN	0	-0.007	-0.009	20.640	1.000	1.000	0.000	0.000	0.000	0.000
89	A	86	SER	0	0.024	0.007	21.153	-0.594	-0.594	0.000	0.000	0.000	0.000
90	A	87	LYS	1	0.930	0.957	22.406	12.074	12.074	0.000	0.000	0.000	0.000
91	A	88	ASN	0	-0.025	0.007	17.173	-0.393	-0.393	0.000	0.000	0.000	0.000
92	A	89	ASN	0	0.063	0.027	13.569	0.259	0.259	0.000	0.000	0.000	0.000
93	A	90	ALA	0	0.030	-0.007	16.269	-0.450	-0.450	0.000	0.000	0.000	0.000
94	A	92	GLU	-1	-0.844	-0.933	12.621	-20.559	-20.559	0.000	0.000	0.000	0.000
95	A	93	ALA	0	0.002	-0.016	13.619	0.018	0.018	0.000	0.000	0.000	0.000
96	A	94	PHE	0	0.003	0.016	12.575	0.592	0.592	0.000	0.000	0.000	0.000
97	A	95	ILE	0	0.034	0.002	8.627	-0.381	-0.381	0.000	0.000	0.000	0.000
98	A	97	ASN	0	0.036	0.007	15.558	1.338	1.338	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.786	-0.858	12.701	-24.985	-24.985	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.936	0.947	15.409	14.475	14.475	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.025	-0.013	18.514	1.387	1.387	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.008	0.013	16.124	0.587	0.587	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.002	0.002	18.133	0.620	0.620	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.006	-0.004	20.187	0.795	0.795	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.024	-0.023	16.237	0.339	0.339	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.099	-0.053	22.318	0.550	0.550	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.906	0.956	25.469	12.098	12.098	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.047	0.044	24.224	0.369	0.369	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.032	-0.008	26.307	0.018	0.018	0.000	0.000	0.000	0.000
110	A	111	TYR	0	-0.030	-0.020	23.255	-0.217	-0.217	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.024	-0.029	26.326	0.857	0.857	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.942	0.965	26.204	11.531	11.531	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.866	-0.934	27.497	-10.502	-10.502	0.000	0.000	0.000	0.000
114	A	115	HIS	1	0.813	0.891	23.781	12.132	12.132	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.812	0.919	20.924	14.126	14.126	0.000	0.000	0.000	0.000
116	A	117	ASN	0	-0.057	-0.026	21.821	-0.115	-0.115	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.030	0.037	21.917	0.601	0.601	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.804	-0.915	22.061	-13.215	-13.215	0.000	0.000	0.000	0.000
119	A	120	THR	0	0.045	-0.006	17.922	0.119	0.119	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.824	0.911	17.718	16.103	16.103	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.913	0.974	22.620	11.120	11.120	0.000	0.000	0.000	0.000
122	A	123	TYR	0	-0.052	-0.042	23.646	0.574	0.574	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:GLY)