FMO DATABASE

FMODB ID: 7KM7K

Calculation Name: 2CTF-A-Other547

Preferred Name: Vigilin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2CTF

Chain ID: A

ChEMBL ID: CHEMBL4295796

UniProt ID: Q00341

Base Structure: SolutionNMR

Registration Date: 2025-10-05

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-611148.253547
FMO2-HF: Nuclear repulsion	573129.258712
FMO2-HF: Total energy	-38018.994835
FMO2-MP2: Total energy	-38130.041326

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-57.28	-56.387	-0.015	-0.348	-0.53	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.916

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].
3	A	3	SER	0	0.018	0.007	3.836	-0.870	0.023	-0.015	-0.348	-0.530
4	A	4	GLY	0	0.010	0.022	5.629	1.515	1.515	0.000	0.000	0.000
5	A	5	SER	0	0.002	0.000	6.372	4.143	4.143	0.000	0.000	0.000
6	A	6	SER	0	-0.023	-0.029	9.286	-1.838	-1.838	0.000	0.000	0.000
7	A	7	GLY	0	0.017	0.000	11.707	0.761	0.761	0.000	0.000	0.000
8	A	8	GLU	-1	-0.958	-0.958	15.495	-15.609	-15.609	0.000	0.000	0.000
9	A	9	PRO	0	-0.027	-0.004	18.420	-0.112	-0.112	0.000	0.000	0.000
10	A	10	GLU	-1	-0.869	-0.930	19.726	-12.538	-12.538	0.000	0.000	0.000
11	A	11	LYS	1	0.869	0.936	22.849	11.052	11.052	0.000	0.000	0.000
12	A	12	LEU	0	0.029	0.011	26.242	0.245	0.245	0.000	0.000	0.000
13	A	13	GLY	0	0.006	0.000	29.967	0.001	0.001	0.000	0.000	0.000
14	A	14	GLN	0	-0.029	-0.035	32.190	-0.360	-0.360	0.000	0.000	0.000
15	A	15	ALA	0	-0.019	-0.014	35.483	0.105	0.105	0.000	0.000	0.000
16	A	16	LEU	0	0.005	0.028	35.634	0.146	0.146	0.000	0.000	0.000
17	A	17	THR	0	0.021	-0.008	39.433	0.104	0.104	0.000	0.000	0.000
18	A	18	GLU	-1	-0.898	-0.935	42.102	-7.629	-7.629	0.000	0.000	0.000
19	A	19	VAL	0	-0.049	-0.012	44.337	0.228	0.228	0.000	0.000	0.000
20	A	20	TYR	0	-0.005	-0.007	46.454	-0.055	-0.055	0.000	0.000	0.000
21	A	21	ALA	0	0.038	0.020	49.131	0.087	0.087	0.000	0.000	0.000
22	A	22	LYS	1	0.886	0.918	51.425	6.105	6.105	0.000	0.000	0.000
23	A	23	ALA	0	0.054	0.031	54.320	0.104	0.104	0.000	0.000	0.000
24	A	24	ASN	0	-0.016	0.004	54.603	-0.136	-0.136	0.000	0.000	0.000
25	A	25	SER	0	-0.032	-0.031	53.627	0.092	0.092	0.000	0.000	0.000
26	A	26	PHE	0	-0.005	0.009	50.153	-0.041	-0.041	0.000	0.000	0.000
27	A	27	THR	0	-0.030	-0.014	45.912	-0.018	-0.018	0.000	0.000	0.000
28	A	28	VAL	0	0.030	0.013	44.298	0.003	0.003	0.000	0.000	0.000
29	A	29	SER	0	-0.019	0.003	40.662	-0.068	-0.068	0.000	0.000	0.000
30	A	30	SER	0	-0.016	-0.015	37.655	0.085	0.085	0.000	0.000	0.000
31	A	31	VAL	0	0.001	0.018	33.681	-0.099	-0.099	0.000	0.000	0.000
32	A	32	ALA	0	0.010	0.007	30.611	0.035	0.035	0.000	0.000	0.000
33	A	33	ALA	0	-0.020	-0.024	30.989	-0.222	-0.222	0.000	0.000	0.000
34	A	34	PRO	0	-0.012	0.000	27.467	0.117	0.117	0.000	0.000	0.000
35	A	35	SER	0	0.071	0.017	29.842	0.063	0.063	0.000	0.000	0.000
36	A	36	TRP	0	-0.029	-0.018	24.900	0.200	0.200	0.000	0.000	0.000
37	A	37	LEU	0	-0.010	0.000	27.969	-0.003	-0.003	0.000	0.000	0.000
38	A	38	HIS	0	0.081	0.043	30.739	0.198	0.198	0.000	0.000	0.000
39	A	39	ARG	1	0.888	0.941	33.497	8.801	8.801	0.000	0.000	0.000
40	A	40	PHE	0	-0.094	-0.064	29.907	0.225	0.225	0.000	0.000	0.000
41	A	41	ILE	0	0.024	0.034	33.135	0.169	0.169	0.000	0.000	0.000
42	A	42	ILE	0	0.045	0.042	35.263	0.274	0.274	0.000	0.000	0.000
43	A	43	GLY	0	0.069	0.039	37.243	0.228	0.228	0.000	0.000	0.000
44	A	44	LYS	1	0.887	0.911	35.034	9.158	9.158	0.000	0.000	0.000
45	A	45	LYS	1	0.909	0.945	39.294	7.494	7.494	0.000	0.000	0.000
46	A	46	GLY	0	0.059	0.051	41.788	0.161	0.161	0.000	0.000	0.000
47	A	47	GLN	0	-0.022	-0.012	41.651	0.204	0.204	0.000	0.000	0.000
48	A	48	ASN	0	0.010	0.003	37.289	0.166	0.166	0.000	0.000	0.000
49	A	49	LEU	0	0.115	0.054	40.736	0.064	0.064	0.000	0.000	0.000
50	A	50	ALA	0	0.004	0.038	42.822	0.139	0.139	0.000	0.000	0.000
51	A	51	LYS	1	0.903	0.937	43.227	7.183	7.183	0.000	0.000	0.000
52	A	52	ILE	0	0.035	0.024	39.790	0.117	0.117	0.000	0.000	0.000
53	A	53	THR	0	0.024	-0.010	44.477	0.166	0.166	0.000	0.000	0.000
54	A	54	GLN	0	-0.043	-0.017	47.342	0.152	0.152	0.000	0.000	0.000
55	A	55	GLN	0	-0.051	-0.025	47.290	0.231	0.231	0.000	0.000	0.000
56	A	56	MET	0	-0.027	0.001	43.475	0.092	0.092	0.000	0.000	0.000
57	A	57	PRO	0	0.004	0.008	48.472	-0.055	-0.055	0.000	0.000	0.000
58	A	58	LYS	1	0.873	0.927	50.981	6.025	6.025	0.000	0.000	0.000
59	A	59	VAL	0	-0.040	0.000	44.520	0.011	0.011	0.000	0.000	0.000
60	A	60	HIS	0	-0.063	-0.019	47.138	0.003	0.003	0.000	0.000	0.000
61	A	61	ILE	0	-0.012	-0.029	41.012	-0.136	-0.136	0.000	0.000	0.000
62	A	62	GLU	-1	-0.894	-0.934	42.542	-7.304	-7.304	0.000	0.000	0.000
63	A	63	PHE	0	0.002	-0.027	35.643	-0.256	-0.256	0.000	0.000	0.000
64	A	64	THR	0	-0.055	-0.038	36.929	0.079	0.079	0.000	0.000	0.000
65	A	65	GLU	-1	-0.918	-0.968	34.406	-9.467	-9.467	0.000	0.000	0.000
66	A	66	GLY	0	0.011	0.000	34.015	-0.245	-0.245	0.000	0.000	0.000
67	A	67	GLU	-1	-0.922	-0.970	33.906	-8.695	-8.695	0.000	0.000	0.000
68	A	68	ASP	-1	-0.877	-0.904	30.545	-10.505	-10.505	0.000	0.000	0.000
69	A	69	LYS	1	0.905	0.953	32.368	8.289	8.289	0.000	0.000	0.000
70	A	70	ILE	0	-0.016	0.019	35.051	0.188	0.188	0.000	0.000	0.000
71	A	71	THR	0	-0.018	-0.021	37.751	-0.053	-0.053	0.000	0.000	0.000
72	A	72	LEU	0	-0.017	0.001	39.275	0.085	0.085	0.000	0.000	0.000
73	A	73	GLU	-1	-0.876	-0.941	43.223	-6.760	-6.760	0.000	0.000	0.000
74	A	74	GLY	0	0.073	0.023	46.954	0.065	0.065	0.000	0.000	0.000
75	A	75	PRO	0	-0.048	-0.019	49.365	0.045	0.045	0.000	0.000	0.000
76	A	76	THR	0	0.030	0.000	47.060	-0.134	-0.134	0.000	0.000	0.000
77	A	77	GLU	-1	-0.964	-0.980	46.374	-6.401	-6.401	0.000	0.000	0.000
78	A	78	ASP	-1	-0.849	-0.939	46.812	-6.854	-6.854	0.000	0.000	0.000
79	A	79	VAL	0	-0.015	-0.009	43.480	-0.154	-0.154	0.000	0.000	0.000
80	A	80	SER	0	0.004	0.018	42.264	-0.284	-0.284	0.000	0.000	0.000
81	A	81	VAL	0	0.058	0.025	41.253	-0.206	-0.206	0.000	0.000	0.000
82	A	82	ALA	0	-0.006	-0.015	41.300	-0.190	-0.190	0.000	0.000	0.000
83	A	83	GLN	0	-0.017	-0.015	37.388	0.011	0.011	0.000	0.000	0.000
84	A	84	GLU	-1	-0.916	-0.943	37.009	-8.505	-8.505	0.000	0.000	0.000
85	A	85	GLN	0	-0.020	-0.026	36.291	-0.129	-0.129	0.000	0.000	0.000
86	A	86	ILE	0	-0.026	-0.010	35.230	-0.225	-0.225	0.000	0.000	0.000
87	A	87	GLU	-1	-0.862	-0.943	32.802	-9.673	-9.673	0.000	0.000	0.000
88	A	88	GLY	0	-0.010	-0.003	31.596	-0.407	-0.407	0.000	0.000	0.000
89	A	89	MET	0	-0.089	-0.045	31.672	-0.239	-0.239	0.000	0.000	0.000
90	A	90	VAL	0	0.009	0.000	29.055	-0.277	-0.277	0.000	0.000	0.000
91	A	91	LYS	1	0.947	0.985	24.769	11.666	11.666	0.000	0.000	0.000
92	A	92	ASP	-1	-0.941	-0.966	26.716	-11.497	-11.497	0.000	0.000	0.000
93	A	93	LEU	0	-0.018	-0.026	26.926	-0.418	-0.418	0.000	0.000	0.000
94	A	94	ILE	0	0.000	0.003	22.886	-0.391	-0.391	0.000	0.000	0.000
95	A	95	ASN	0	-0.001	-0.005	22.675	-0.882	-0.882	0.000	0.000	0.000
96	A	96	ARG	1	0.873	0.947	22.411	10.988	10.988	0.000	0.000	0.000
97	A	97	SER	0	-0.064	-0.019	22.177	-0.352	-0.352	0.000	0.000	0.000
98	A	98	GLY	0	0.025	0.020	17.860	-0.328	-0.328	0.000	0.000	0.000
99	A	99	PRO	0	-0.019	-0.017	17.804	-0.333	-0.333	0.000	0.000	0.000
100	A	100	SER	0	0.011	0.002	14.991	-1.214	-1.214	0.000	0.000	0.000
101	A	101	SER	0	-0.072	-0.048	13.573	0.862	0.862	0.000	0.000	0.000
102	A	102	GLY	-1	-0.940	-0.944	12.608	-23.843	-23.843	0.000	0.000	0.000

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