FMO DATABASE

FMODB ID: 24R9R

Calculation Name: 6SPC-n-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPC

Chain ID: n

ChEMBL ID:

UniProt ID: E2RXU3

Base Structure: ElectronMicroscopy

Registration Date: 2025-09-02

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-591136.696254
FMO2-HF: Nuclear repulsion	552103.785948
FMO2-HF: Total energy	-39032.910305
FMO2-MP2: Total energy	-39146.628636

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(n:3:LYS)

Summations of interaction energy for fragment #1(n:3:LYS)

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.
552.683	556.176	2.872	-2.029	-4.337	-0.011

Interaction energy analysis for fragmet #1(n:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.849 / q_NPA : 1.901

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	n	5	SER	0	0.059	0.023	3.576	1.406	3.265	0.001	-0.811	-1.050	-0.003
4	n	6	MET	0	-0.068	-0.039	2.464	-3.424	-2.024	2.866	-1.195	-3.071	-0.008
5	n	7	LYS	1	0.920	0.942	4.086	72.979	73.213	0.005	-0.023	-0.216	0.000
6	n	8	ASN	0	0.040	0.024	6.642	9.024	9.024	0.000	0.000	0.000	0.000
7	n	9	ARG	1	0.909	0.964	5.027	82.051	82.051	0.000	0.000	0.000	0.000
8	n	10	GLU	-1	-0.918	-0.961	7.874	-61.490	-61.490	0.000	0.000	0.000	0.000
9	n	11	LEU	0	0.031	0.014	10.365	3.892	3.892	0.000	0.000	0.000	0.000
10	n	12	LYS	1	0.995	0.998	12.373	41.379	41.379	0.000	0.000	0.000	0.000
11	n	13	ARG	1	0.921	0.961	13.365	41.835	41.835	0.000	0.000	0.000	0.000
12	n	14	GLN	0	-0.015	0.003	16.478	0.406	0.406	0.000	0.000	0.000	0.000
13	n	15	LEU	0	0.043	0.024	18.700	1.392	1.392	0.000	0.000	0.000	0.000
14	n	16	THR	0	-0.047	-0.026	17.653	0.227	0.227	0.000	0.000	0.000	0.000
15	n	17	VAL	0	-0.006	0.001	19.014	0.929	0.929	0.000	0.000	0.000	0.000
16	n	18	ALA	0	-0.035	-0.022	21.713	1.229	1.229	0.000	0.000	0.000	0.000
17	n	19	LYS	1	0.986	1.006	22.692	26.254	26.254	0.000	0.000	0.000	0.000
18	n	20	TYR	0	0.004	-0.006	25.002	0.830	0.830	0.000	0.000	0.000	0.000
19	n	21	ALA	0	0.012	0.004	27.519	0.681	0.681	0.000	0.000	0.000	0.000
20	n	22	LYS	1	0.933	0.976	29.149	19.265	19.265	0.000	0.000	0.000	0.000
21	n	23	LYS	1	1.091	1.046	31.869	19.155	19.155	0.000	0.000	0.000	0.000
22	n	24	ARG	1	0.848	0.920	25.590	23.921	23.921	0.000	0.000	0.000	0.000
23	n	25	ALA	0	-0.030	-0.012	31.268	-0.213	-0.213	0.000	0.000	0.000	0.000
24	n	26	GLU	-1	-0.869	-0.932	33.315	-16.611	-16.611	0.000	0.000	0.000	0.000
25	n	27	LEU	0	0.010	-0.009	34.544	0.224	0.224	0.000	0.000	0.000	0.000
26	n	28	LYS	1	0.861	0.918	29.079	19.773	19.773	0.000	0.000	0.000	0.000
27	n	29	ALA	0	0.007	0.024	34.508	-0.068	-0.068	0.000	0.000	0.000	0.000
28	n	30	ILE	0	0.052	0.019	37.675	0.173	0.173	0.000	0.000	0.000	0.000
29	n	31	ILE	0	-0.017	-0.014	34.212	0.179	0.179	0.000	0.000	0.000	0.000
30	n	32	ALA	0	-0.038	-0.007	38.223	0.035	0.035	0.000	0.000	0.000	0.000
31	n	33	ASN	0	-0.017	0.003	39.642	0.452	0.452	0.000	0.000	0.000	0.000
32	n	34	PRO	0	0.002	-0.003	43.251	-0.051	-0.051	0.000	0.000	0.000	0.000
33	n	35	ASN	0	-0.019	-0.012	45.033	0.061	0.061	0.000	0.000	0.000	0.000
34	n	36	SER	0	-0.069	-0.038	43.910	0.063	0.063	0.000	0.000	0.000	0.000
35	n	37	SER	0	0.071	0.032	45.954	0.042	0.042	0.000	0.000	0.000	0.000
36	n	38	ALA	0	-0.028	-0.034	45.761	-0.341	-0.341	0.000	0.000	0.000	0.000
37	n	39	GLU	-1	-0.900	-0.952	45.825	-12.747	-12.747	0.000	0.000	0.000	0.000
38	n	40	GLU	-1	-0.840	-0.906	43.903	-13.855	-13.855	0.000	0.000	0.000	0.000
39	n	41	ARG	1	0.910	0.965	41.352	13.507	13.507	0.000	0.000	0.000	0.000
40	n	42	TRP	0	0.014	0.022	38.579	-0.349	-0.349	0.000	0.000	0.000	0.000
41	n	43	ASN	0	0.035	0.008	39.055	-0.609	-0.609	0.000	0.000	0.000	0.000
42	n	44	ALA	0	0.029	0.016	38.363	-0.445	-0.445	0.000	0.000	0.000	0.000
43	n	45	GLN	0	-0.087	-0.046	35.243	-0.720	-0.720	0.000	0.000	0.000	0.000
44	n	46	VAL	0	-0.016	-0.001	35.002	-0.420	-0.420	0.000	0.000	0.000	0.000
45	n	47	ALA	0	-0.028	0.005	33.582	-0.277	-0.277	0.000	0.000	0.000	0.000
46	n	48	LEU	0	-0.019	-0.037	29.354	-0.376	-0.376	0.000	0.000	0.000	0.000
47	n	49	GLN	0	-0.036	-0.017	27.207	-0.794	-0.794	0.000	0.000	0.000	0.000
48	n	50	LYS	1	0.996	0.992	26.362	17.829	17.829	0.000	0.000	0.000	0.000
49	n	51	GLN	0	0.030	0.028	28.343	-0.224	-0.224	0.000	0.000	0.000	0.000
50	n	52	PRO	0	0.023	0.021	23.750	-0.411	-0.411	0.000	0.000	0.000	0.000
51	n	53	ARG	1	1.019	1.001	19.858	26.736	26.736	0.000	0.000	0.000	0.000
52	n	54	ASP	-1	-0.957	-0.984	19.981	-28.885	-28.885	0.000	0.000	0.000	0.000
53	n	55	ALA	0	0.097	0.053	21.451	0.188	0.188	0.000	0.000	0.000	0.000
54	n	56	SER	0	-0.043	-0.032	20.562	0.501	0.501	0.000	0.000	0.000	0.000
55	n	57	ALA	0	0.035	0.002	20.961	-1.266	-1.266	0.000	0.000	0.000	0.000
56	n	58	SER	0	0.003	0.010	20.519	-0.695	-0.695	0.000	0.000	0.000	0.000
57	n	59	ARG	1	0.936	0.969	14.605	33.889	33.889	0.000	0.000	0.000	0.000
58	n	60	LEU	0	0.014	0.008	15.033	-2.022	-2.022	0.000	0.000	0.000	0.000
59	n	61	ARG	1	0.959	0.982	12.057	41.793	41.793	0.000	0.000	0.000	0.000
60	n	62	ASN	0	0.022	0.026	14.139	-2.118	-2.118	0.000	0.000	0.000	0.000
61	n	63	ARG	1	0.840	0.907	6.437	64.374	64.374	0.000	0.000	0.000	0.000
62	n	64	CYS	-1	-0.862	-0.830	12.818	-37.329	-37.329	0.000	0.000	0.000	0.000
63	n	65	ARG	1	0.961	0.972	12.572	33.626	33.626	0.000	0.000	0.000	0.000
64	n	66	LEU	0	0.047	0.030	12.815	-0.873	-0.873	0.000	0.000	0.000	0.000
65	n	67	THR	0	0.030	-0.050	10.598	-3.961	-3.961	0.000	0.000	0.000	0.000
66	n	68	GLY	0	-0.006	-0.008	8.638	-6.561	-6.561	0.000	0.000	0.000	0.000
67	n	69	ARG	1	0.971	0.973	9.036	42.944	42.944	0.000	0.000	0.000	0.000
68	n	70	PRO	0	0.018	0.000	11.237	2.246	2.246	0.000	0.000	0.000	0.000
69	n	71	HIS	0	0.061	0.026	14.174	2.150	2.150	0.000	0.000	0.000	0.000
70	n	72	GLY	0	0.001	-0.002	16.798	-0.648	-0.648	0.000	0.000	0.000	0.000
71	n	73	PHE	0	0.015	0.028	17.721	0.399	0.399	0.000	0.000	0.000	0.000
72	n	74	TYR	0	0.040	0.011	19.586	0.608	0.608	0.000	0.000	0.000	0.000
73	n	75	ARG	1	0.975	0.977	23.141	21.033	21.033	0.000	0.000	0.000	0.000
74	n	76	LYS	1	0.945	0.966	24.736	21.055	21.055	0.000	0.000	0.000	0.000
75	n	77	PHE	0	0.052	0.047	21.458	0.018	0.018	0.000	0.000	0.000	0.000
76	n	78	GLY	0	0.042	0.029	19.316	-0.216	-0.216	0.000	0.000	0.000	0.000
77	n	79	LEU	0	0.025	-0.009	17.157	-2.158	-2.158	0.000	0.000	0.000	0.000
78	n	80	SER	0	-0.014	-0.013	15.451	0.577	0.577	0.000	0.000	0.000	0.000
79	n	81	ARG	1	1.027	1.003	17.392	30.013	30.013	0.000	0.000	0.000	0.000
80	n	82	ASN	0	-0.030	-0.021	13.197	1.527	1.527	0.000	0.000	0.000	0.000
81	n	83	LYS	1	0.935	0.981	16.651	29.544	29.544	0.000	0.000	0.000	0.000
82	n	84	LEU	0	0.002	-0.008	18.282	1.071	1.071	0.000	0.000	0.000	0.000
83	n	85	ARG	1	0.962	0.978	21.472	25.529	25.529	0.000	0.000	0.000	0.000
84	n	86	GLU	-1	-0.935	-0.972	18.807	-29.327	-29.327	0.000	0.000	0.000	0.000
85	n	87	ALA	0	-0.056	-0.017	21.500	0.378	0.378	0.000	0.000	0.000	0.000
86	n	88	ALA	0	0.031	0.005	23.178	0.636	0.636	0.000	0.000	0.000	0.000
87	n	89	MET	0	-0.023	-0.007	26.002	0.893	0.893	0.000	0.000	0.000	0.000
88	n	90	ARG	1	0.945	0.973	23.338	23.983	23.983	0.000	0.000	0.000	0.000
89	n	91	GLY	0	0.069	0.048	27.058	0.461	0.461	0.000	0.000	0.000	0.000
90	n	92	ASP	-1	-0.906	-0.941	22.219	-25.352	-25.352	0.000	0.000	0.000	0.000
91	n	93	VAL	0	-0.086	-0.050	24.622	-0.552	-0.552	0.000	0.000	0.000	0.000
92	n	94	PRO	0	0.052	0.030	27.028	0.511	0.511	0.000	0.000	0.000	0.000
93	n	95	GLY	0	0.031	0.002	30.629	-0.232	-0.232	0.000	0.000	0.000	0.000
94	n	96	LEU	0	-0.073	-0.022	27.351	0.166	0.166	0.000	0.000	0.000	0.000
95	n	97	VAL	0	0.045	0.019	31.309	-0.265	-0.265	0.000	0.000	0.000	0.000
96	n	98	LYS	1	0.878	0.927	31.788	18.249	18.249	0.000	0.000	0.000	0.000
97	n	99	ALA	0	0.011	0.005	35.298	0.345	0.345	0.000	0.000	0.000	0.000
98	n	100	SER	-1	-0.913	-0.937	37.814	-16.068	-16.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(n:3:LYS)