FMO DATABASE

FMODB ID: 7ZJLK

Calculation Name: 2VWA-F-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphatidylethanolamine

Ligand 3-letter code: PTY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VWA

Chain ID: F

ChEMBL ID:

UniProt ID: Q8IEU1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-803011.337951
FMO2-HF: Nuclear repulsion	761463.224905
FMO2-HF: Total energy	-41548.113046
FMO2-MP2: Total energy	-41669.521082

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(F:130:ASN)

Summations of interaction energy for fragment #1(F:130:ASN)

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.
-10.225	-9.924	16.359	-8.021	-8.641	-0.06

Interaction energy analysis for fragmet #1(F:130:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.821 / q_NPA : 0.891

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	F	132	ILE	0	0.048	0.030	3.847	-0.558	0.930	-0.016	-0.545	-0.928	0.001
66	F	195	ASN	0	-0.053	-0.024	1.895	-25.497	-28.149	16.245	-6.752	-6.842	-0.055
67	F	196	ARG	1	0.927	0.963	3.102	28.340	29.786	0.131	-0.722	-0.855	-0.006
68	F	197	ASN	0	-0.030	0.004	4.965	4.452	4.471	-0.001	-0.002	-0.016	0.000
4	F	133	ASN	0	0.004	-0.006	6.331	4.701	4.701	0.000	0.000	0.000	0.000
5	F	134	LEU	0	0.031	0.013	8.887	1.465	1.465	0.000	0.000	0.000	0.000
6	F	135	ASN	0	0.012	0.004	12.269	1.802	1.802	0.000	0.000	0.000	0.000
7	F	136	LYS	1	0.840	0.930	10.433	26.221	26.221	0.000	0.000	0.000	0.000
8	F	137	PRO	0	0.025	0.003	14.828	0.056	0.056	0.000	0.000	0.000	0.000
9	F	138	ILE	0	-0.014	0.008	17.022	-0.764	-0.764	0.000	0.000	0.000	0.000
10	F	139	ILE	0	-0.002	0.009	17.255	0.983	0.983	0.000	0.000	0.000	0.000
11	F	140	GLU	-1	-0.848	-0.925	18.954	-12.405	-12.405	0.000	0.000	0.000	0.000
12	F	141	ASN	0	-0.015	-0.023	16.365	0.786	0.786	0.000	0.000	0.000	0.000
13	F	142	LYS	1	0.864	0.923	19.480	12.922	12.922	0.000	0.000	0.000	0.000
14	F	143	ASN	0	0.038	0.024	17.226	0.811	0.811	0.000	0.000	0.000	0.000
15	F	144	ASN	0	-0.011	-0.012	20.841	-0.129	-0.129	0.000	0.000	0.000	0.000
16	F	145	VAL	0	-0.008	0.003	21.065	0.467	0.467	0.000	0.000	0.000	0.000
17	F	146	ASP	-1	-0.832	-0.888	19.806	-13.999	-13.999	0.000	0.000	0.000	0.000
18	F	147	VAL	0	-0.038	-0.016	14.615	0.068	0.068	0.000	0.000	0.000	0.000
19	F	148	SER	0	0.032	0.006	17.889	0.186	0.186	0.000	0.000	0.000	0.000
20	F	149	ILE	0	0.088	0.031	18.033	-0.795	-0.795	0.000	0.000	0.000	0.000
21	F	150	LYS	1	0.974	0.985	18.265	12.609	12.609	0.000	0.000	0.000	0.000
22	F	151	ARG	1	0.970	0.984	11.395	19.873	19.873	0.000	0.000	0.000	0.000
23	F	152	TYR	0	-0.009	0.005	13.665	-1.056	-1.056	0.000	0.000	0.000	0.000
24	F	153	ASN	0	0.040	0.007	14.993	-0.762	-0.762	0.000	0.000	0.000	0.000
25	F	154	ASN	0	0.012	0.013	11.438	-1.609	-1.609	0.000	0.000	0.000	0.000
26	F	155	PHE	0	-0.011	-0.008	8.337	-1.456	-1.456	0.000	0.000	0.000	0.000
27	F	156	VAL	0	0.031	0.012	11.254	-1.403	-1.403	0.000	0.000	0.000	0.000
28	F	157	ASP	-1	-0.885	-0.945	13.847	-17.839	-17.839	0.000	0.000	0.000	0.000
29	F	158	ILE	0	-0.029	-0.020	7.260	-1.089	-1.089	0.000	0.000	0.000	0.000
30	F	159	ALA	0	-0.016	0.003	9.777	-2.061	-2.061	0.000	0.000	0.000	0.000
31	F	160	ARG	1	0.803	0.868	10.886	16.190	16.190	0.000	0.000	0.000	0.000
32	F	161	LEU	0	0.047	0.026	11.471	0.006	0.006	0.000	0.000	0.000	0.000
33	F	162	SER	0	-0.091	-0.054	7.470	-2.450	-2.450	0.000	0.000	0.000	0.000
34	F	163	ILE	0	-0.024	-0.016	9.202	-0.547	-0.547	0.000	0.000	0.000	0.000
35	F	164	GLN	0	0.007	0.014	11.834	0.632	0.632	0.000	0.000	0.000	0.000
36	F	165	LYS	1	0.967	0.991	9.348	25.904	25.904	0.000	0.000	0.000	0.000
37	F	166	HIS	0	-0.052	-0.018	10.319	-0.152	-0.152	0.000	0.000	0.000	0.000
38	F	167	PHE	0	0.051	0.022	12.190	0.879	0.879	0.000	0.000	0.000	0.000
39	F	168	GLU	-1	-0.819	-0.917	15.587	-17.230	-17.230	0.000	0.000	0.000	0.000
40	F	169	HIS	0	-0.076	-0.033	14.019	0.188	0.188	0.000	0.000	0.000	0.000
41	F	170	LEU	0	-0.047	-0.008	15.002	0.149	0.149	0.000	0.000	0.000	0.000
42	F	171	SER	0	-0.018	-0.023	17.764	0.318	0.318	0.000	0.000	0.000	0.000
43	F	172	ASN	0	0.078	0.033	21.470	-0.660	-0.660	0.000	0.000	0.000	0.000
44	F	173	ASP	-1	-0.771	-0.857	24.317	-13.532	-13.532	0.000	0.000	0.000	0.000
45	F	174	GLN	0	-0.010	0.001	17.978	-0.437	-0.437	0.000	0.000	0.000	0.000
46	F	175	LYS	1	0.791	0.900	19.139	15.804	15.804	0.000	0.000	0.000	0.000
47	F	176	ASP	-1	-0.797	-0.871	21.488	-12.189	-12.189	0.000	0.000	0.000	0.000
48	F	177	SER	0	-0.069	-0.047	23.206	0.004	0.004	0.000	0.000	0.000	0.000
49	F	178	HIS	0	-0.063	-0.050	16.845	-0.042	-0.042	0.000	0.000	0.000	0.000
50	F	179	VAL	0	-0.015	0.014	20.091	-0.434	-0.434	0.000	0.000	0.000	0.000
51	F	180	ASN	0	-0.011	-0.012	21.681	-0.095	-0.095	0.000	0.000	0.000	0.000
52	F	181	ASN	0	-0.015	0.009	19.975	0.183	0.183	0.000	0.000	0.000	0.000
53	F	182	MET	0	0.054	0.008	19.388	-0.793	-0.793	0.000	0.000	0.000	0.000
54	F	183	GLU	-1	-0.814	-0.886	19.045	-16.138	-16.138	0.000	0.000	0.000	0.000
55	F	184	TYR	0	0.008	-0.016	13.515	-0.824	-0.824	0.000	0.000	0.000	0.000
56	F	185	MET	0	0.026	0.011	14.697	-1.423	-1.423	0.000	0.000	0.000	0.000
57	F	186	GLN	0	-0.005	-0.005	14.554	-0.776	-0.776	0.000	0.000	0.000	0.000
58	F	187	LYS	1	0.859	0.930	13.680	16.728	16.728	0.000	0.000	0.000	0.000
59	F	188	PHE	0	-0.014	-0.004	8.370	-2.864	-2.864	0.000	0.000	0.000	0.000
60	F	189	VAL	0	0.006	-0.006	9.889	-2.724	-2.724	0.000	0.000	0.000	0.000
61	F	190	GLN	0	-0.055	-0.046	11.029	-1.249	-1.249	0.000	0.000	0.000	0.000
62	F	191	GLY	0	0.045	0.024	9.199	-0.985	-0.985	0.000	0.000	0.000	0.000
63	F	192	LEU	0	-0.045	-0.025	5.117	-6.061	-6.061	0.000	0.000	0.000	0.000
64	F	193	GLN	0	-0.023	-0.032	6.324	-1.541	-1.541	0.000	0.000	0.000	0.000
65	F	194	GLU	-1	-0.857	-0.918	7.861	-30.630	-30.630	0.000	0.000	0.000	0.000
69	F	198	ILE	0	-0.068	-0.028	8.102	2.582	2.582	0.000	0.000	0.000	0.000
70	F	199	SER	0	0.026	0.017	10.533	-0.452	-0.452	0.000	0.000	0.000	0.000
71	F	200	LEU	0	-0.011	-0.010	12.711	0.803	0.803	0.000	0.000	0.000	0.000
72	F	201	SER	0	0.006	-0.012	15.719	0.149	0.149	0.000	0.000	0.000	0.000
73	F	202	LYS	1	0.984	0.989	18.815	11.833	11.833	0.000	0.000	0.000	0.000
74	F	203	TYR	0	-0.025	-0.006	20.785	-0.056	-0.056	0.000	0.000	0.000	0.000
75	F	204	GLN	0	0.025	0.003	17.491	-0.732	-0.732	0.000	0.000	0.000	0.000
76	F	205	GLU	-1	-0.791	-0.870	15.486	-18.597	-18.597	0.000	0.000	0.000	0.000
77	F	206	ASN	0	0.019	0.001	17.315	-0.661	-0.661	0.000	0.000	0.000	0.000
78	F	207	LYS	1	0.937	0.978	20.327	13.121	13.121	0.000	0.000	0.000	0.000
79	F	208	ALA	0	0.008	0.007	15.065	0.077	0.077	0.000	0.000	0.000	0.000
80	F	209	VAL	0	0.009	0.002	16.657	-0.390	-0.390	0.000	0.000	0.000	0.000
81	F	210	MET	0	-0.007	-0.009	18.033	0.144	0.144	0.000	0.000	0.000	0.000
82	F	211	ASP	-1	-0.840	-0.872	18.245	-15.617	-15.617	0.000	0.000	0.000	0.000
83	F	212	LEU	0	0.022	-0.007	12.753	0.043	0.043	0.000	0.000	0.000	0.000
84	F	213	LYS	1	0.933	0.987	17.371	12.559	12.559	0.000	0.000	0.000	0.000
85	F	214	TYR	0	0.003	0.006	20.455	0.262	0.262	0.000	0.000	0.000	0.000
86	F	215	HIS	0	-0.049	-0.037	16.320	0.929	0.929	0.000	0.000	0.000	0.000
87	F	216	LEU	0	0.026	0.005	15.864	0.050	0.050	0.000	0.000	0.000	0.000
88	F	217	GLN	0	-0.018	-0.021	19.697	0.465	0.465	0.000	0.000	0.000	0.000
89	F	218	LYS	1	0.896	0.962	22.682	13.416	13.416	0.000	0.000	0.000	0.000
90	F	219	VAL	0	-0.001	0.003	18.002	0.228	0.228	0.000	0.000	0.000	0.000
91	F	220	TYR	0	-0.039	-0.062	21.313	0.131	0.131	0.000	0.000	0.000	0.000
92	F	221	ALA	0	0.018	0.017	23.426	0.328	0.328	0.000	0.000	0.000	0.000
93	F	222	ASN	0	-0.063	-0.024	22.919	0.648	0.648	0.000	0.000	0.000	0.000
94	F	223	TYR	0	0.006	-0.024	22.750	0.080	0.080	0.000	0.000	0.000	0.000
95	F	224	LEU	0	0.033	0.014	24.817	0.184	0.184	0.000	0.000	0.000	0.000
96	F	225	SER	0	-0.027	-0.028	28.171	0.256	0.256	0.000	0.000	0.000	0.000
97	F	226	GLN	0	-0.064	-0.034	24.351	-0.199	-0.199	0.000	0.000	0.000	0.000
98	F	227	GLU	-1	-1.052	-1.016	28.223	-10.845	-10.845	0.000	0.000	0.000	0.000
99	F	228	GLU	-2	-1.941	-1.945	29.919	-18.493	-18.493	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:130:ASN)