FMO DATABASE

FMODB ID: 3Z6YL

Calculation Name: 6SPD-X-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPD

Chain ID: X

ChEMBL ID:

UniProt ID: A0A2V3

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-454955.611882
FMO2-HF: Nuclear repulsion	423968.139429
FMO2-HF: Total energy	-30987.472452
FMO2-MP2: Total energy	-31078.687538

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
219.408	222.421	1.444	-1.589	-2.868	0.005

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.947 / q_NPA : 0.966

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	4	VAL	0	0.065	0.029	2.590	2.555	5.149	1.447	-1.457	-2.584	0.005
4	A	5	CYS	0	-0.074	-0.026	4.914	1.220	1.257	-0.001	-0.015	-0.021	0.000
11	A	12	PRO	0	-0.100	-0.045	4.194	3.381	3.495	-0.001	-0.021	-0.092	0.000
49	A	50	ARG	1	0.865	0.947	3.628	52.030	52.298	-0.001	-0.096	-0.171	0.000
5	A	6	GLN	0	0.056	0.020	7.099	2.417	2.417	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.087	0.061	9.783	1.337	1.337	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.026	-0.035	12.307	-0.534	-0.534	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.072	0.053	8.660	0.779	0.779	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.927	0.966	8.848	21.326	21.326	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.078	0.029	5.529	-4.313	-4.313	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.062	0.041	6.957	-0.420	-0.420	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.041	-0.033	10.152	0.223	0.223	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.048	0.021	12.911	0.544	0.544	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.003	-0.005	16.608	-0.405	-0.405	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.041	-0.028	19.693	-0.169	-0.169	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.013	0.000	21.457	0.196	0.196	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.037	0.029	24.966	0.090	0.090	0.000	0.000	0.000	0.000
19	A	20	HIS	0	0.053	0.012	27.930	0.100	0.100	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.035	0.035	31.403	0.235	0.235	0.000	0.000	0.000	0.000
21	A	22	HIS	0	0.006	-0.005	29.166	-0.292	-0.292	0.000	0.000	0.000	0.000
22	A	23	ASN	0	0.017	0.004	28.128	-0.123	-0.123	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.919	0.970	23.830	10.691	10.691	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.083	0.046	21.356	-0.214	-0.214	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.934	0.962	15.907	16.333	16.333	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.945	0.977	15.142	17.077	17.077	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.967	0.970	5.921	31.934	31.934	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.028	0.030	11.317	1.197	1.197	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.012	-0.013	7.056	-3.115	-3.115	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.005	0.003	7.291	2.319	2.319	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.054	0.030	9.952	-2.159	-2.159	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.054	-0.038	6.890	-0.605	-0.605	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.030	0.012	11.570	-0.700	-0.700	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.004	-0.008	9.650	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	36	HIS	0	0.007	0.015	13.211	1.424	1.424	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.955	0.973	15.953	13.402	13.402	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.023	0.002	16.034	0.333	0.333	0.000	0.000	0.000	0.000
38	A	39	TRP	0	0.016	0.003	20.734	-0.549	-0.549	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.014	-0.002	22.177	-0.060	-0.060	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.792	-0.893	24.981	-10.218	-10.218	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.007	-0.011	27.011	0.077	0.077	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.813	-0.895	22.838	-13.817	-13.817	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.928	0.978	26.536	10.213	10.213	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.885	0.932	19.730	14.686	14.686	0.000	0.000	0.000	0.000
45	A	46	PHE	0	-0.011	-0.012	20.781	-0.330	-0.330	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.034	0.033	17.313	-0.336	-0.336	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.903	0.931	13.087	21.173	21.173	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.059	0.046	12.009	-1.286	-1.286	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.032	0.006	10.019	-2.358	-2.358	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.040	0.001	12.152	0.775	0.775	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.071	0.037	13.577	0.844	0.844	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.909	0.941	15.731	16.830	16.830	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.009	0.000	15.334	0.480	0.480	0.000	0.000	0.000	0.000
55	A	56	MET	0	0.057	0.031	16.220	0.165	0.165	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.999	0.998	19.201	13.831	13.831	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.086	-0.037	17.208	0.500	0.500	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.002	0.003	17.798	0.247	0.247	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.861	-0.933	21.258	-12.914	-12.914	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.832	0.927	23.368	12.567	12.567	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.866	0.925	19.974	14.997	14.997	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.073	0.060	24.572	0.338	0.338	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.037	-0.028	19.310	-0.547	-0.547	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.802	-0.905	21.152	-12.949	-12.949	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.004	-0.003	22.461	-0.349	-0.349	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.082	-0.043	17.016	-0.335	-0.335	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.025	-0.005	17.019	-1.086	-1.086	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.019	0.012	18.612	-0.439	-0.439	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.837	-0.929	18.375	-16.484	-16.484	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.069	-0.025	11.953	-1.178	-1.178	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.827	0.883	15.346	14.638	14.638	0.000	0.000	0.000	0.000
72	A	73	ALA	0	-0.005	0.007	17.635	-0.078	-0.078	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.843	0.942	11.240	23.651	23.651	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.023	0.023	14.182	-1.036	-1.036	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.947	-0.964	9.955	-31.173	-31.173	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.850	0.890	8.706	30.640	30.640	0.000	0.000	0.000	0.000
77	A	78	PHE	-1	-0.827	-0.885	10.965	-17.792	-17.792	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)